WO2020200414A1 - Production de protéines dans de la levure mut-méthylotrophe - Google Patents

Production de protéines dans de la levure mut-méthylotrophe Download PDF

Info

Publication number
WO2020200414A1
WO2020200414A1 PCT/EP2019/058190 EP2019058190W WO2020200414A1 WO 2020200414 A1 WO2020200414 A1 WO 2020200414A1 EP 2019058190 W EP2019058190 W EP 2019058190W WO 2020200414 A1 WO2020200414 A1 WO 2020200414A1
Authority
WO
WIPO (PCT)
Prior art keywords
host cell
methanol
protein
mut
poi
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
PCT/EP2019/058190
Other languages
English (en)
Inventor
Domen ZAVEC
Brigitte Gasser
Diethard Mattanovich
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Lonza AG
Original Assignee
Lonza AG
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Lonza AG filed Critical Lonza AG
Priority to PCT/EP2019/058190 priority Critical patent/WO2020200414A1/fr
Priority to CN202080040100.0A priority patent/CN114026239B/zh
Priority to BR112021019477A priority patent/BR112021019477A2/pt
Priority to PCT/EP2020/059284 priority patent/WO2020201369A1/fr
Priority to SG11202110695PA priority patent/SG11202110695PA/en
Priority to KR1020217035698A priority patent/KR102874359B1/ko
Priority to ES20714242T priority patent/ES2964319T3/es
Priority to HUE20714242A priority patent/HUE064229T2/hu
Priority to CA3135444A priority patent/CA3135444C/fr
Priority to AU2020252241A priority patent/AU2020252241B2/en
Priority to EP20714242.3A priority patent/EP3947695B1/fr
Priority to US17/601,045 priority patent/US12270034B2/en
Priority to JP2021558927A priority patent/JP7570346B2/ja
Publication of WO2020200414A1 publication Critical patent/WO2020200414A1/fr
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/80—Vectors or expression systems specially adapted for eukaryotic hosts for fungi
    • C12N15/81—Vectors or expression systems specially adapted for eukaryotic hosts for fungi for yeasts
    • C12N15/815—Vectors or expression systems specially adapted for eukaryotic hosts for fungi for yeasts for yeasts other than Saccharomyces

Definitions

  • the invention refers to production of a protein of interest (POI) in a recombinant methylotrophic yeast which is deficient in alcohol oxidase 1 (AOX1 ) and alcohol oxidase 2 (AOX2).
  • POI protein of interest
  • Proteins produced in recombinant host cell culture have become increasingly important as diagnostic and therapeutic agents.
  • cells are engineered and/or selected to produce unusually high levels of a recombinant or heterologous protein of interest. Optimization of cell culture conditions is important for successful commercial production of recombinant or heterologous proteins.
  • Eukaryotic host cells in particular mammalian host cells, yeasts or filamentous fungi, or bacteria are commonly used as production hosts for biopharmaceutical proteins as well as for bulk chemicals.
  • the most prominent examples are methylotrophic yeasts like such as Pichia pastoris, which is well conceived for efficient secretion of heterologous proteins.
  • P. pastoris has been reclassified into a new genus, Komagataella, and split into three species, K. pastoris, K. phaffii, and K. pseudopastoris.
  • Strains commonly used for biotechnological applications belong to two proposed species, K. pastoris and K.
  • the strains GS115, X-33, CBS2612, and CBS7435 are K. phaffii, while the strain DSMZ70382 is classified into the type species, K. pastoris, which is the reference strain for all the available P. pastoris strains (Kurtzman 2009, J Ind Microbiol Biotechnol. 36(11 ):1435- 8). Mattanovich et al. (Microbial Cell Factories 2009, 8:29 doi:10.1186/1475-2859-8- 29) describe the genome sequencing of the type strain DSMZ 70382 of K. pastoris, and analyzed its secretome and sugar transporters.
  • P. pastoris strains have been used which are deficient in both AOX genes, AOX1 and AOX2 (referred to as Mut-), or deficient in only AOX2 (referred to as Mut s ), or not deficient in any of the AOX genes (referred to as Mut + ).
  • Promoters used for protein production in recombinant host cells are either regulated ( e.g ., induced upon addition of methanol to the medium, methanol- controlled), or constantly active (constitutive).
  • the methanol inducible promoter pAOX1 has been described to control protein expression in Mut-, Mut + or Mut s strains.
  • the invention provides for a method of producing a protein of interest (POI) comprising culturing a recombinant methanol utilization pathway deficient methylotrophic yeast (Mut-) host cell using methanol as a carbon source to produce the POI, which Mut- host cell comprises a heterologous gene of interest expression cassette (GOIEC) comprising an expression cassette promoter (ECP) operably linked to a gene of interest (GO!) encoding a protein of interest (POI),
  • GOIEC heterologous gene of interest expression cassette
  • ECP expression cassette promoter
  • Mut- host cell is engineered by one or more genetic modifications to reduce expression of a first and a second endogenous gene compared to the host cell prior to said one or more genetic modifications, wherein
  • the first endogenous gene encodes alcohol oxidase 1 (AOX1 ) comprising the amino acid sequence identified as SEQ ID NO:1 or a homologue thereof, and
  • the second endogenous gene encodes alcohol oxidase 2 (AOX2) comprising the amino acid sequence identified as SEQ ID NO:3 or a homologue thereof.
  • AOX2 alcohol oxidase 2
  • the invention provides for a method of producing a protein of interest (POI) comprising culturing a Mut- host cell described herein using methanol as a carbon source to produce the POI, in particular such methanol amounts for use as a source of energy, not (only) for methanol-induction of an ECP.
  • POI protein of interest
  • AOX1 shall refer to either a native alcohol oxidase 1 , such as P. pastoris alcohol oxidase 1 comprising or consisting of the amino acid sequence identified as SEQ ID NO:1 (UniProtKB - F2QY27), or a sequence which has a certain homology (or sequence identity) to SEQ ID NO:1 , which may be a homologue of the P. pastoris alcohol oxidase 1 that is endogenous to a methylotrophic yeast species, in particular which is endogenous to the methylotrophic yeast herein used as a host cell, prior to said one or more genetic modifications to reduce expression of said endogenous alcohol oxidase 1.
  • the AOX1 protein is an ortholog that is endogenous to the species of the host cell species.
  • the gene encoding the P. pastoris alcohol oxidase 1 herein referred to as AOX1 gene, comprises or consists of the nucleotide sequence identified as SEQ ID NO:2.
  • the homologous sequences are also referred to as AOX1 homologue or AOX1 homologue.
  • the AOX1 protein or AOX1 homologue is an alcohol oxidase enzyme classified as EC 1.1.3.13.
  • the AOX1 homologue has at least any one of 60%, 70%, 80%, 85%, 90%, or 95% sequence identity to SEQ ID NO:1
  • An AOX1 homologue is herein understood to encode an AOX1 homologue.
  • sequence identity is determined as further disclosed herein, for example when comparing the full-length sequence.
  • the term “A0X2” shall refer to either a native alcohol oxidase 2, such as P. pastoris alcohol oxidase 2 comprising or consisting of the amino acid sequence identified as SEQ ID NO:3 (UniProtKB - F2R038), or a sequence which has a certain homology (or sequence identity) to SEQ ID NO:3, which may be a homologue of the P.
  • the AOX2 protein is an ortholog that is endogenous to the species of the host cell species.
  • the gene encoding the P. pastoris alcohol oxidase 2, herein referred to as AOX2 gene comprises or consists of the nucleotide sequence identified as SEQ ID NO:4.
  • the homologous sequences are also referred to as AOX2 homologue or AOX2 homologue.
  • the AOX2 protein or AOX2 homologue is an alcohol oxidase enzyme classified as EC 1.1.3.13.
  • the AOX2 homologue has at least any one of 60%, 70%, 80%, 85%, 90%, or 95% sequence identity to SEQ ID NO:3.
  • An AOX2 homologue is herein understood to encode an AOX2 homologue.
  • sequence identity is determined as further disclosed herein, for example when comparing the full-length sequence.
  • the AOX1 and/or AOX2 proteins are of P. pastoris origin, in particular K. pastoris or K. phaffii origin, if the host cell is P. pastoris, in particular K. pastoris and K. phaffii, respectively.
  • each of the AOX1 and AOX2 proteins comprises a homologous (or orthologous) sequence of the respective protein of in P. pastoris, in particular K. pastoris or K. phaffii, origin, which homologous (orthologous) sequence is endogenous to a wild -type host cell, if of another origin or species.
  • an endogenous AOX1 or AOX2 protein comprises or consists of the amino acid sequence identified as SEQ ID NO:1 and SEQ ID NO:3, respectively.
  • the endogenous AOX1 protein comprises or consists of the amino acid sequence identified as SEQ ID NO:9 (Komagataella pastoris, ATCC 28485), which is 99.85% identical to SEQ ID NO:1.
  • the endogenous AOX2 protein comprises or consists of the amino acid sequence identified as SEQ ID NO:11 , which is 99.40% identical to SEQ ID NO:3.
  • SEQ ID NO:9 AOX1 amino acid sequence of Komagataella pastoris
  • ATCC 28485 SEQ ID NQ:10 AOX1 nucleotide sequence of Komagataella pastoris
  • ATCC 28485 SEQ ID NO:11 AOX2 amino acid sequence of Komagataella pastoris
  • ATCC 28485 SEQ ID NO:12 AOX2 nucleotide sequence of Komagataella pastoris
  • ATCC 28485 SEQ ID NO:13 MODI amino acid sequence of Ogataea methanolica JCM 10240 SEQ ID NO:14: MODI nucleotide sequence of Ogataea methanolica JCM 10240 SEQ ID NO:15: MOD2 amino acid sequence of Ogataea methanolica JCM 10240 SEQ ID NO:16: MOD2 nucleotide sequence of Ogataea methanolica JCM 10240 SEQ ID NO:17: pMOD1 promoter sequence of Ogataea methanolica
  • the AOX1 or AOX2 protein sequence which is endogenous to the host cell is a homologue to SEQ ID NO:1 and SEQ ID NO:3, respectively, and expression of such homologue in the host cell (the orthologous sequence of SEQ ID NO:1 and SEQ ID NO:3, respectively) is reduced for the purpose described herein.
  • any or each of the homologous sequences is characterized by the same qualitative function of the respective AOX1 and AOX2 protein in a wild -type host cell such as in P. pastoris, in particular K. pastoris or K. phaffii e.g., as alcohol oxidase (EC 1.1.3.13).
  • the respective homologous sequences of SEQ ID NO:1 and SEQ ID NO:3 are of a species other than P. pastoris, in particular K. pastoris or K. phaffii e.g., another yeast of the Komagataella or Pichia genus, and expression of the respective endogenous coding sequences reduced or abolished (knocked out) as described herein.
  • both, the AOX1 and AOX2 proteins are endogenous to the host cell, and the expression of the genes encoding AOX1 and AOX2, respectively, is reduced or deleted.
  • both, the AOX1 and AOX2 proteins are of the same origin, originating from or endogenous to the same host cell (or host cell species) prior to its engineering for reducing expression of said first and second endogenous genes.
  • both, the AOX1 and AOX2 proteins are of P. pastoris origin, in particular proteins encoded by a respective gene that is endogenous to the host cell, wherein the host cell is P. pastoris.
  • both, the AOX1 and AOX2 proteins are of Komagataella phaffii origin, in particular proteins encoded by a respective gene that is endogenous to the host cell, wherein the host cell is Komagataella phaffii.
  • both, the AOX1 and AOX2 proteins are of Komagataella pastoris origin, in particular proteins encoded by a respective gene that is endogenous to the host cell, wherein the host cell is Komagataella pastoris.
  • the host cell is genetically modified by one or more genetic modifications comprising genomic mutation(s) that reduce the transcription and/or translation of one or more polynucleotides, in particular the respective coding polynucleotides encoding said AOX1 and AOX2 proteins, respectively, and/or otherwise reduce expression of said coding polynucleotides, thereby reducing production of said AOX1 and AOX2 proteins, respectively, to obtain the Mut- host cell.
  • genomic mutation(s) that reduce the transcription and/or translation of one or more polynucleotides, in particular the respective coding polynucleotides encoding said AOX1 and AOX2 proteins, respectively, and/or otherwise reduce expression of said coding polynucleotides, thereby reducing production of said AOX1 and AOX2 proteins, respectively, to obtain the Mut- host cell.
  • said one or more genetic modifications comprises a disruption, substitution, deletion, knockin or knockout of (i) one or more polynucleotides, or a part thereof; or (ii) an expression control sequence.
  • said one or more genetic modifications are of one or more endogenous polynucleotides of the host cell described herein, such as coding polynucleotides, including e.g., said polynucleotide (or gene) encoding the respective AOX1 or AOX2 protein, in particular the wild-type (unmodified or native) protein, which is naturally-occurring in the host cell species, type or strain, or a nucleotide sequence controlling expression of said polynucleotide (or gene).
  • coding polynucleotides including e.g., said polynucleotide (or gene) encoding the respective AOX1 or AOX2 protein, in particular the wild-type (unmodified or native) protein, which is naturally-occurring in the host cell species, type or strain, or a nucleotide sequence controlling expression of said polynucleotide (or gene).
  • said one or more genetic modifications are of an expression control sequence, including e.g., a promoter, ribosomal binding site, transcriptional or translational start and stop sequences, or of an enhancer or activator sequence.
  • a variety of methods of engineering a host cell can be employed to reduce expression of an endogenous polynucleotide, such as a gene encoding the respective AOX1 or AOX2 protein, including e.g., disrupting the polynucleotide encoding the respective AOX1 or AOX2 protein, disrupting the promoter which is operably linked to such polynucleotide, replacing such promoter with another promoter which has lower promoter activity, modifying or modulating (e.g ., activating, up-regulating, inactivating, inhibiting, or down-regulating) regulatory sequences which modulate the expression of such polynucleotide, such as using respective transcription regulators targeted to the relevant sequences by an RNA guided ribonuclease used in a CRISPR based method of modifying a host cell, e.g., regulatory sequences selected from the group consisting of promoter, ribosomal binding sites, transcriptional start or stop sequences, translational start or stop sequences,
  • said one or more genetic modifications include one or more genomic mutations including deletion or inactivation of a gene or genomic sequence which reduces expression of a gene or part of a gene by at least 50%, 60%, 70%, 80%, 90%, or 95%, or even completely abolishes its expression, e.g., by a knockout of the gene, as compared to the respective host without (or prior to) such genetic modification.
  • the one or more genetic modifications comprise genomic mutations which constitutively impair or otherwise reduce the expression of one or more endogenous polynucleotides.
  • the one or more genetic modifications comprise genomic mutations introducing one or more inducible or repressible regulatory sequences which conditionally impair or otherwise reduce the expression of one or more endogenous polynucleotides.
  • conditionally active modifications are particularly targeting those regulatory elements and genes which are active and/or expressed dependent on cell culture conditions.
  • the expression of said one or more endogenous polynucleotides is reduced thereby reducing expression of the polynucleotide encoding the respective AOX1 or AOX2 protein when producing the POI.
  • expression of both, the AOX1 and AOX2 proteins is reduced under conditions of the host cell culture during which the POI is produced.
  • the host cell is genetically modified to reduce the amount (e.g., the level, activity or concentration) of both, the AOX1 and AOX2 proteins, by at least any one of 50%, 60%, 70%, 80%, 90%, or 95%, (activity%, or mol/mol) compared to the host cell without said modification, or even by 100%, e.g. to a non-detectable amount, thereby completely abolishing production of both, the AOX1 and AOX2 proteins, e.g., by a knockout of the respective AOX1 and AOX2 genes.
  • the amount e.g., the level, activity or concentration
  • the host cell is genetically modified to comprise one or more deletions of (one or more) genomic sequences, in particular genomic sequences encoding the respective AOX1 and/or AOX2 protein.
  • Such host cell is typically provided as a deletion or knockout strain.
  • said first and/or second endogenous gene is knocked out by said one or more genetic modifications.
  • the Mut- host cell is a AAOX1/AAOX2 knockout strain.
  • the total amount of the respective AOX1 and/or AOX2 protein in the host cell or host cell culture is reduced by at least any one of 50%, 60%, 70%, 80%, 90%, or 95%, (activity%, or mol/mol), or even by 100%, e.g. to a non-detectable amount, compared to a reference amount expressed or produced by the host cell prior to or without such genetic modification, or compared to a reference amount produced in a respective host cell culture, or compared to the host cell prior to or without said modification.
  • comparing the host cell described herein for the effect of said genetic modification to reduce production of the respective AOX1 or AOX2 protein it is typically compared to the comparable host cell prior to or without such genetic modification. Comparison is typically made with the same host cell species or type without such genetic modification, which is engineered to produce the recombinant or heterologous POI, in particular when cultured under conditions to produce said POL However, a comparison can also be made with the same host cell species or type which is not further engineered to produce the recombinant or heterologous POI.
  • the reduction of the respective AOX1 or AOX2 protein is determined by the reduction of the amount (e.g., the level, activity or concentration) of said protein in the cell.
  • the amount of said protein is determined by a suitable method, such as employing a Western Blot, immunofluorescence imaging, flow cytometry or mass spectrometry, in particular wherein mass spectrometry is liquid chromatography-mass spectrometry (LC-MS), or liquid chromatography tandem-mass spectrometry (LC-MS/MS) e.g., as described by Doneanu et al. (MAbs. 2012; 4(1 ): 24-44).
  • LC-MS liquid chromatography-mass spectrometry
  • LC-MS/MS liquid chromatography tandem-mass spectrometry
  • alcohol oxidase activity can be measured calorimetrically with the 2,2'-azino-bis-(3- ethylbenzothiazoline-6-sulfonic acid that reacts with hydrogen peroxide as described by Verduyn et al. (Journal of Microbiological Methods. 1984 (2)1 : 15-25), or by measuring the amount of formaldehyde formed as described by Couder and Baratti (Agric. Bioi. Chern. 1980; 44(10):2279-2289). A detailed assay is described herein in the examples section.
  • the Mut- host cell is cultured using methanol as a sole carbon source or in a mixture with other carbon sources (or carbohydrates), in particular as a source of energy, such as for growth and/or POI production (synthesis).
  • non-methanol carbon source is a carbohydrate.
  • non-methanol carbon source is selected from saccharides, polyols, alcohols, or mixtures of any one or more of the foregoing.
  • the saccharides may be any one or more of monosaccharides, such as a hexose, e.g. glucose, fructose, galactose or mannose, or a disaccharides, such as saccharose; or an alcohol or polyol e.g., ethanol, or any diol, or triol, e.g., glycerol, or a mixture of any of the foregoing.
  • any such non-methanol carbon source may be additionally used in the cell culture in an amount to produce said POI.
  • the Mut- host cell is a recombinant host cell comprising at least one heterologous GOIEC, wherein at least one component or combination of components comprised in the GOIEC is heterologous to the host cell.
  • an artificial expression cassette is used, in particular wherein the promoter and GOI are heterologous to each other, not occurring in such combination in nature e.g., wherein either one (or only one) of the promoter and GOI is artificial or heterologous to the other and/or to the host cell described herein; the promoter is an endogenous promoter and the GOI is a heterologous GOI; or the promoter is an artificial or heterologous promoter and the GOI is an endogenous GOI; wherein both, the promoter and GOI, are artificial, heterologous or from different origin, such as from a different species or type (strain) of cells compared to the host cell described herein.
  • the ECP is not naturally associated with and/or
  • the GOIEC comprises a constitutive, inducible or repressible promoter.
  • constitutive promoter include e.g., the pGAP and functional variants thereof, any of the constitutive promoter such as pCS1 , published in WO2014139608.
  • inducible or repressible promoter examples include e.g., the native pAOX1 or pAOX2 and functional variants thereof, any of the regulatory promoter, such as pG1 -pG8, and fragments thereof, published in WO2013050551 ; any of the regulatory promoter, such as pG1 and pG1 -x, published in WO2017021541 A1 .
  • Suitable promoter sequences for use with yeast host cells are described in Mattanovich et al. (Methods Mol. Biol. (2012) 824:329-58) and include glycolytic enzymes like triosephosphate isomerase (TPI), phosphoglycerate kinase (PGK), glyceraldehyde-3- phosphate dehydrogenase (GAPDH or GAP) and variants thereof, lactase (LAC) and galactosidase (GAL), P.
  • TPI triosephosphate isomerase
  • PGK phosphoglycerate kinase
  • GAP glyceraldehyde-3- phosphate dehydrogenase
  • LAC lactase
  • GAL galactosidase
  • PPGI glucose-6-phosphate isomerase promoter
  • PPGK 3- phosphoglycerate kinase promoter
  • pGAP glycerol aldehyde phosphate dehydrogenase promoter
  • PTEF translation elongation factor promoter
  • PEN01 triose phosphate isomerase
  • PTPI triose phosphate isomerase
  • PRPS2, PRPS7, PRPS31 , PRPL1 alcohol oxidase promoter
  • PAOX1 alcohol oxidase promoter
  • PAOX2 alcohol oxidase promoter
  • PFLD formaldehyde dehydrogenase promoter
  • PICL isocitrate lyase promoter
  • PTHI alpha-ketoisocaproate decarboxylase promoter
  • PSSA1 formaldehyde dehydrogenase promoter
  • PICL isocitrate lyase promoter
  • PTHI alpha-ketoisocaproate decarboxylase promoter
  • PSSA1 heat shock protein family members
  • PGND1 6- Phosphogluconate dehydrogenase
  • PGPM1 phosphoglycerate mutase
  • PKI phosphatidyl inosito
  • suitable promoters include Saccharomyces cerevisiae enolase (ENO-1 ), Saccharomyces cerevisiae galactokinase (GAL1 ), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH1 , ADH2/GAP), Saccharomyces cerevisiae triose phosphate isomerase (TPI), Saccharomyces cerevisiae metallothionein (CUP1 ), and Saccharomyces cerevisiae 3- phosphoglycerate kinase (PGK), and the maltase gene promoter (MAL).
  • ENO-1 Saccharomyces cerevisiae enolase
  • GAL1 Saccharomyces cerevisiae galactokinase
  • ADH1 alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase
  • the GAP promoter (pGAP), AOX1 (pAOX1 ) or AOX2 (pAOX2) promoter or a promoter which is a functional variant thereof and derived from any one of pGAP or pAOX1 or pAOX2 is particularly preferred.
  • pAOX promoters can be induced by methanol and are repressed by glucose.
  • the functional variant has at least at least any one of 80%, 85%, 90%, 95%, or 100% sequence identity to the promoter from which it is derived, and has about the same promoter activity (e.g. +/- any one of 50%, 40%, 30%, 20%, or 10%; although the promoter activity may be improved) as compared to the promoter from which it is derived.
  • the ECP is methanol-inducible.
  • the ECP is methanol-controlled.
  • the ECP can be fully induced in the methanol containing cell culture.
  • the methanol may be used not only as a source of energy supplied to the cell culture, but also to induce the PCI expression upon inducing the ECP.
  • the ECP is methanol-inducible by the amount of methanol present in the cell culture used as a carbon source to produce the POL
  • the GOI expression by the heterologous expression cassette is inducible by the methanol-inducible ECP.
  • the ECP is methanol-inducible, and e.g., repressed in the absence of a methanol amount which is less than any one of 0.1 %, 0.05%, or 0.01 % (v/v) in the cell culture medium or supernatant (herein referred to as a promoter-repressing amount).
  • the ECP is methanol-inducible, and e.g., induced in the presence of a methanol amount which is higher than the promoter-repressing amount e.g., by at least any one of 0.5%, 1 %, 1.5%, 2.0%, 2.5%, or 3% (v/v) in the cell culture medium or supernatant (herein referred to as a promoter-inducing amount).
  • the ECP is fully induced by the methanol amount as used in the cell culture method described herein.
  • the ECP promoter is considered to be fully induced, if the culture conditions provide for about maximum induction.
  • Such amounts in the cell culture medium or supernatant are particularly understood as the amount which upon feeding of the host cell and consumption by the host cell may be detectable.
  • the cell culture is fed by adding a supplemental carbon source, yet in an amount that is immediately consumed by the cells during PCI production, thus, leaving no or only a low remaining amount in the cell culture medium or supernatant, e.g. an amount up to 1.0 g/L.
  • the ECP is endogenous or heterologous to the host cell.
  • the ECP is any one of the following:
  • a pAOX1 promoter comprising or consisting of at least any one of 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% sequence identity to SEQ ID NO:5; or
  • a pAOX2 promoter comprising or consisting of at least any one of 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% sequence identity to SEQ ID NO:6; or
  • a promoter comprising or consisting of a nucleotide sequence selected from the group consisting of SEQ ID NO:36-49.
  • any of the methanol-inducible promoters may be used which are listed in Table 17, in particular those comprising or consisting of a nucleotide sequence selected from the group consisting of SEQ ID NO:36-49.
  • Functional pAOX1 and pAOX2 promoter variants characterized by a sequence identity of at least 60% are exemplified by the exemplary methanol-inducible promoters further described herein.
  • SEQ ID NO:17 (pMOD1 promoter sequence of Ogataea methanolica JCM 10240) has a sequence identity of 54.0% compared to SEQ ID NO:5; and SEQ ID NO:18 (pMOD2 promoter sequence of Ogataea methanolica JCM 10240) has a sequence identity of 53.7% compared to SEQ ID NO:6.
  • Sequence identity of the pMOD1 and pMOD2 promoter compared to the respective pAOX1 and pAOX2 promoter has been determined by alignment using LALIGN version 36.3.8g Dec, 2017; results refer to sequences aligned with the same sequence orientation and highest overlap (Parameters: Matrix: +5/-4; GAP OPEN: -5; Gap Extend: -4; E() Threshold 10.0; Output format: MARKX 0; Graphics: Yes).
  • methanol inducible promoter are listed in Table 17, or pSHB17, pALD4, pFDFH , pDAS1 , pDAS2, pPMP20, pFBA1 -2 pPMP47, pFLD, pFGFH , pTAL.1 -2, pDAS2, pCAM1 , pPP7435_Chr1 -0336 as described by Gasser et al. (Gasser, Steiger, & Mattanovich, 2015; Microb Cell Fact. 14: 196).
  • the term “pAOX1” shall refer to both, a promoter comprising the sequence identified as SEQ ID NO:5, or a sequence which has a certain homology (or sequence identity) to SEQ ID NO:5.
  • the homologous sequence is also referred to as pAOX1 homologue.
  • the pAOX1 homologue may be a native, naturally-occurring sequence or a mutant thereof e.g., produced by any suitable method of mutagenesis.
  • the term “pA0X2” shall refer to both, a promoter comprising the sequence identified as SEQ ID NO:6, or a sequence which has a certain homology (or sequence identity) to SEQ ID NO:6.
  • the homologous sequence is also referred to as pAOX2 homologue.
  • the pAOX2 homologue may be a native, naturally-occurring sequence or a mutant thereof e.g., produced by any suitable method of mutagenesis.
  • a pAOX1 or pAOX2 mutant described herein is specifically characterized by a promoter strength which is about 0.5-fold to at least any one of 1.1 -fold, 1.2-fold, 1.3- fold, 1 4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1 -fold, 2.2-fold, 2.3- fold, 2.4-fold, 2.5-fold, 2.6-fold, 2.7-fold, 2.8-fold, 2.9-fold, 3-fold, 3.3-fold, 3.5-fold, 3.8- fold, 4-fold, 4.5-fold, 5-fold, 5.5-fold, or at least 6-fold increased compared to the respective native pAOX1 or pAOX2 promoter when in the induced state, as determined in a comparable expression system or production host cell line.
  • the promoter strength is determined by the expression level of a POI, such as a model protein (e.g., Green Fluorescence Protein, GFP, including e.g., enhanced GFP, eGFP, Gene Bank Accession no. U57607), and/or the transcription strength, as compared to the reference promoter.
  • a POI such as a model protein (e.g., Green Fluorescence Protein, GFP, including e.g., enhanced GFP, eGFP, Gene Bank Accession no. U57607)
  • GFP Green Fluorescence Protein
  • the transcription analysis is quantitative or semi-quantitative, preferably employing qRT-PCR, DNA microarrays, RNA sequencing and transcriptome analysis.
  • the recombinant host cell described herein comprises only one or multiple heterologous GOIEC, e.g. multiple copies of said expression cassettes, such as at least 2, 3, 4, or 5 copies (gene copy number, GCN).
  • the recombinant host cell comprises up to 2, 3, 4, or five copies.
  • Each of the copies may comprise or consist of the same or different sequences, yet includes the ECP operably linked to the GOI.
  • the heterologous expression cassette is comprised in an autonomously replicating vector or plasmid, or integrated within a chromosome of said host cell.
  • the expression cassette may be introduced into the host cell and integrated into the host cell genome (or any of its chromosomes) as intrachromosomal element e.g., at a specific site of integration or randomly integrated, whereupon a high producer host cell line is selected.
  • the expression cassette may be integrated within an extrachromosomal genetic element, such as a plasmid or an artificial chromosome e.g., a yeast artificial chromosome (YAC).
  • the expression cassette is introduced into the host cell by a vector, in particular an expression vector, which is introduced into the host cell by a suitable transformation technique.
  • the GO! may be ligated into an expression vector.
  • a preferred yeast expression vector (which is preferably used for expression in yeast) is selected from the group consisting of plasmids derived from pPICZ, pGAPZ, pPIC9, pPICZalfa, pGAPZalfa, pPIC9K, pGAPHis, pPUZZLE or Golden P/CS.
  • transfecting or transforming host cells for introducing a vector or plasmid are well known in the art. These can include electroporation, spheroplasting, lipid vesicle mediated uptake, heat shock mediated uptake, calcium phosphate mediated transfection (calcium phosphate/DNA co-precipitation), viral infection, and particularly using modified viruses such as, for example, modified adenoviruses, microinjection and electroporation.
  • Transformants as described herein can be obtained by introducing the expression cassette, vector or plasmid DNA into a host and selecting transformants which express the relevant protein or selection marker.
  • Host cells can be treated to introduce heterologous or foreign DNA by methods conventionally used for transformation of host cells, such as the electric pulse method, the protoplast method, the lithium acetate method, and modified methods thereof.
  • P. pastoris is preferably transformed by electroporation.
  • Preferred methods of transformation for the uptake of the recombinant DNA fragment by the microorganism include chemical transformation, electroporation or transformation by protoplastation.
  • the heterologous GOIEC described herein comprises or consists of an artificial fusion of polynucleotides, including the ECP operably linked to the GOI, and optionally further sequences, such as a signal, leader, or a terminator sequence.
  • the expression cassette comprises the ECP operably linked to the GOI, and optionally further comprises signal and leader sequences, as necessary to express and produce the POI as a secreted protein.
  • the GOIEC comprises a nucleotide sequence encoding a signal peptide enabling the secretion of the POI.
  • nucleotide sequence encoding the signal peptide is fused adjacent to the 5’-end of the GOI.
  • the signal peptide is selected from the group consisting of signal sequences from S. cerevisiae alpha-mating factor prepro peptide, the signal peptides from the P. pastoris acid phosphatase gene (PH01 ) and the extracellular protein X (EPX1 ) (Heiss, S., V. Puxbaum, C. Gruber, F. Altmann, D. Mattanovich & B. Gasser, Microbiology 2015;161 (7):1356-68).
  • any of the signal and/or leader sequences as described in WO2014067926 A1 can be used, in particular SEQ ID NO:22 or SEQ ID NO:23.
  • signal sequences as described in WO2012152823 A1 can be used, in particular the signal sequence of native alpha mating factor of S. cerevisiae identified as SEQ ID NO:24, or mutants thereof.
  • the host cell described herein may undergo one or more further genetic modifications e.g., for improving protein production.
  • the host cell is further engineered to modify one or more genes influencing proteolytic activity used to generate protease deficient strains, in particular a strain deficient in carboxypeptidase Y activity.
  • protease deficient strains in particular a strain deficient in carboxypeptidase Y activity.
  • a protease deficient Pichia strain with a functional deficiency in a vacuolar protease such as proteinase A or proteinase B
  • Pichia strains which have an ade2 deletion, and/or deletions of one or both of the protease genes, PEP4 and PRB1 are provided by e.g., ThermoFisher Scientific.
  • the host cell is engineered to modify at least one nucleic acid sequence encoding a functional gene product, in particular a protease, selected from the group consisting of PEP4, PRB1 , YPS1 , YPS2, YMP1 , YMP2, YMP1 , DAP2, GRHI, PRD1 , YSP3, and PRB3, as disclosed in WO2010099195A1.
  • a functional gene product in particular a protease, selected from the group consisting of PEP4, PRB1 , YPS1 , YPS2, YMP1 , YMP2, YMP1 , DAP2, GRHI, PRD1 , YSP3, and PRB3, as disclosed in WO2010099195A1.
  • Overexpression or underexpression of genes encoding helper factors is specifically applied to enhance expression of a GOI, e.g. as described in WO2015158800A1.
  • the POI can be any one of eukaryotic, prokaryotic or synthetic peptides, polypeptides, proteins, or metabolites of a host cell.
  • the POI is heterologous to the Mut- host cell or the ECP.
  • the POI is heterologous to the host cell species.
  • the POI is a secreted peptide, polypeptide, or protein, i.e. secreted from the host cell into the cell culture supernatant.
  • the POI is a eukaryotic protein, preferably a mammalian derived or related protein such as a human protein or a protein comprising a human protein sequence, or a bacterial protein or bacterial derived protein
  • the POI is a therapeutic protein functioning in mammals.
  • the POI is a multimeric protein, specifically a dimer or tetramer.
  • the POI is a peptide or protein selected from the group consisting of an antigen-binding protein, a therapeutic protein, an enzyme, a peptide, a protein antibiotic, a toxin fusion protein, a carbohydrate - protein conjugate, a structural protein, a regulatory protein, a vaccine antigen, a growth factor, a hormone, a cytokine, a process enzyme.
  • the antigen-binding protein is selected from the group consisting of a) antibodies or antibody fragments, such as any of chimeric antibodies, humanized antibodies, bi-specific antibodies, Fab, Fd, scFv, diabodies, triabodies, Fv tetramers, minibodies, single-domain antibodies like VH, VHH, IgNARs, or V-NAR; b) antibody mimetics, such as Adnectins, Affibodies, Affilins, Affimers, Affitins, Alphabodies, Anticalins, Avimers, DARPins, Fynomers, Kunitz domain peptides, Monobodies, or NanoCLAMPS; or
  • fusion proteins comprising one or more immunoglobulin-fold domains, antibody domains or antibody mimetics.
  • a specific POI is an antigen-binding molecule such as an antibody, or a fragment thereof, in particular an antibody fragment comprising an antigen-binding domain.
  • specific POIs are antibodies such as monoclonal antibodies (mAbs), immunoglobulin (Ig) or immunoglobulin class G (IgG), heavy-chain antibodies (HcAb’s), or fragments thereof such as fragment-antigen binding (Fab), Fd, single chain variable fragment (scFv), or engineered variants thereof such as for example Fv dimers (diabodies), Fv trimers (triabodies), Fv tetramers, or minibodies and single domain antibodies like VH, VHH, IgNARs, or V-NAR, or any protein comprising an immunoglobulin-fold domain.
  • mAbs monoclonal antibodies
  • Ig immunoglobulin
  • IgG immunoglobulin class G
  • HcAb’s heavy-chain antibodies
  • fragments thereof such as fragment-antigen binding (Fab), Fd,
  • antigen-binding molecules may be selected from antibody mimetics, or (alternative) scaffold proteins such as e.g., engineered Kunitz domains, Adnectins, Affibodies, Affiline, Anticalins, or DARPins.
  • scaffold proteins such as e.g., engineered Kunitz domains, Adnectins, Affibodies, Affiline, Anticalins, or DARPins.
  • the POI is e.g., BOTOX, Myobloc, Neurobloc, Dysport (or other serotypes of botulinum neurotoxins), alglucosidase alpha, daptomycin, YH-16, choriogonadotropin alpha, filgrastim, cetrorelix, interleukin-2, aldesleukin, teceleulin, denileukin diftitox, interferon alpha-n3 (injection), interferon alpha-nl, DL-8234, interferon, Suntory (gamma-1 a), interferon gamma, thymosin alpha 1 , tasonermin, DigiFab, ViperaTAb, EchiTAb, CroFab, nesiritide, abatacept, alefacept, Rebif, eptoterminalfa, teriparatide (osteoporosis), calcitonin injectable (bone disease),
  • BOTOX al
  • B/gastrin-receptor binding peptides 1111n-hEGF, AE-37, trasnizumab-DM1 , Antagonist G, IL-12 (recombinant), PM-02734, IMP-321 , rhlGF-BP3, BLX-883, CUV- 1647 (topical), L-19 based radioimmunotherapeutics (cancer), Re-188-P-2045, AMG- 386, DC/1540/KLH vaccine (cancer), VX-001 , AVE-9633, AC-9301 , NY-ESO-1 vaccine (peptides), NA17.A2 peptides, melanoma vaccine (pulsed antigen therapeutic), prostate cancer vaccine, CBP-501 , recombinant human lactoferrin (dry eye), FX-06, AP-214, WAP-8294A (injectable), ACP-HIP, SUN-11031 , peptide YY [3-36] (obesity, in
  • a fermentation product is isolated from the cell culture, which fermentation product comprises the PCI or a host cell metabolite obtained from the Mut- host cell.
  • the Mut- host cell is a yeast cell of the genus Pichia, Komagataella, Hansenula, Ogataea or Candida.
  • the Mut- host cell is originating from a strain which is of a yeast selected from the group consisting of a Pichia species, such as Pichia pastoris, Pichia methanolica, Pichia kluyveri, and Pichia angusta; Komagataella species, such as Komagataella pastoris, Komagataella pseudopastoris or Komagataella phaffii, Hansenula species, such as Hansenula polymorpha, Ogataea species, such as Ogataea polymorpha, or Ogataea parapolymorpha, and Candida species, such as Candida utilis, Candida cacaoi, and Candida boidinii.
  • a Pichia species such as Pichia pastoris, Pichia methanolica, Pichia kluyveri, and Pichia angusta
  • Komagataella species such as Komagataella pastoris, Komagataella pseudopastoris or Komagataella phaffii
  • the host cell is a Pichia pastoris strain selected from the group consisting of CBS 704, CBS 2612, CBS 7435, CBS 9173-9189, DSMZ 70877, X-33, GS115, KM71 , KM71 H and SMD1168.
  • a cell line of the Mut- host cell is cultured.
  • the cell line is cultured under batch, fed -batch or continuous culture conditions.
  • the culture may be performed in microtiter plates, shake-flasks, or a bioreactor, and optionally starting with a batch phase as the first step, followed by a fed-batch phase or a continuous culture phase as the second step.
  • the method described herein comprises a growing phase and a production phase.
  • the method comprises the steps:
  • the second step b) follows the first step a).
  • the host cell is cultured in the first step under growing conditions in a cell culture medium comprising the first carbon source, e.g. in an amount sufficient to enable growth of the host cell in cell culture, optionally until the amount of the carbon source is consumed, and further culturing can be under growth-limiting conditions.
  • the second carbon source is methanol and optionally one or more further carbon sources (other than methanol), said second carbon source being referred to as supplemental carbon source.
  • said basal carbon source and/or supplemental carbon source in addition to methanol can be selected from saccharides, polyols, alcohols, or mixtures of any one or more of the foregoing.
  • the basal carbon source is different from the supplemental carbon source, e.g. quantitatively and/or qualitatively different.
  • the quantitative difference typically provides for the different conditions to repress or induce the ECP promoter activity.
  • the basal and the supplemental carbon sources comprise the same type of molecules or carbohydrates, preferably in different concentrations.
  • the carbon source is a mixture of two or more different carbon sources.
  • the carbon source is a hexose, such as glucose, fructose, galactose or mannose, a disaccharide, such as saccharose, an alcohol, such as glycerol or ethanol, or a mixture thereof.
  • the basal carbon source is selected from the group consisting of glucose, glycerol, ethanol, or mixtures thereof. According to a preferred embodiment, the basal carbon source is glycerol.
  • the supplemental carbon source comprises (in addition to methanol) a hexose such as glucose, fructose, galactose and mannose, a disaccharide, such as saccharose, an alcohol, such as glycerol or ethanol, or a mixture thereof.
  • the supplemental carbon source comprises glucose in addition to methanol.
  • Both of said culturing steps specifically comprise cultivating the cell line in the presence of said carbon sources.
  • said growth phase (step a)) culturing is performed in a batch phase; and said production phase (step b)) culturing is performed in fed -batch or a continuous cultivation phase.
  • the host cells are grown in a carbon source rich medium comprising a basal carbon source during the phase of high growth rate (under growing conditions), step a) (e.g. at least 50%, or at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99%, or up to the maximum growth rate) and producing the POI during a phase of low growth rate (under growth-limiting conditions), step b) (e.g.
  • less than 90% preferably less than 80%, less than 70%, less than 60%, less than 50%, or less than 40%, less than 30%, less than 20%, less than 10%, less than 5%, less than 3%, less than 2%, less than 1 %, less than 0.5%, less than 0.4%, less than 0.3%, or less than 0.2% of the maximum growth rate
  • a defined minimal medium comprising only the amount of carbon source which is completely consumed when maintaining the cell culture in the production phase.
  • an average methanol concentration of at least any one of 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, or 1.0% (v/v) e.g., up to any one of 3%, 2.5%, 2%, 1.5%, or 1 % (v/v) is used in the host cell culture, specifically in the cell culture medium or supernatant, in particular during a production phase.
  • the average methanol concentration is maintained during a production phase of at least 24 hours, preferably, at least any one of 0.5%, 1 %, 1.5%, 2%, 2.5% or 3% (v/v).
  • the average methanol concentration is 0.5- 2% (v/v), during the production phase of at least 24 hours.
  • the average amount or concentration can be calculated as the sum of methanol concentrations as measured in the cell culture, in particular in the cell culture medium or supernatant, at least at the start and at the end of an observation period, and during the observation period e.g., at least every 24h, or per continuous measurement, divided by the number of measurements.
  • the methanol concentration in the cell culture can be measured using a suitable standard assay like HPLC, e.g. determined as a residual concentration in the culture medium upon consumption by the cell culture.
  • the methanol feed is at an average feed rate of at least any one of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14 or 15 mg methanol/(g dry biomass * h) during a production phase.
  • Methanol may be added to the cell culture in one or more instalments e.g., by one or more injections, or may be continuously added during a certain period of time while producing the POI.
  • the average amount can be calculated as the sum of all methanol additions during an observation period divided by the average total dry biomass divided by the duration of the observation period.
  • the average total dry biomass is calculated by measuring the dry biomass concentration at least at the start and at the end of an observation period, and optional during the observation period. The dry biomass concentration is then interpolated between start and the end of the observation period. The interpolated dry biomass concentration is multiplied by the reactor volume at each interval, the calculated values for all intervals are summed and divided by the number of intervals. An interval duration is less than or equal to 1 h.
  • the average feed rate is maintained during a production phase of at least 24 hours, preferably, at least any one of 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 , 12, 13, 14 or 15mg methanol/(g dry biomass*h).
  • the observation period is herein understood as a certain period of time during which the cell culture is producing the POI, and particularly understood as a production phase, in particular the production phase of a fed -batch or continuous cell cultivation method. Though the actual POI production process or production phase may be longer than the observation period, the average amount is calculated during a defined observation period.
  • the duration of the POI production process is 10 to 500h.
  • a batch phase is performed for around 10 to 36h.
  • the term“around” with respect to cultivation time shall mean +1-5% or +/-10%.
  • the specific batch performance time of around 10 to 36h may be 18 to 39.6h, specifically 19 to 37.8h.
  • a batch phase is performed using 10 to 50 g/L glycerol, specifically 20 to 40 g/L glycerol as a basal carbon source in batch media, and cultivation is performed at 25°C for around 27 to 30h, or at 30°C for around 23 to 36h, or at any temperature between 25°C and 30°C during a cultivation time of 23 to 36h.
  • Lowering the glycerol concentration in the batch medium would decrease the length of the batch phase, while increasing the glycerol in the batch medium would even prolong the batch phase.
  • glucose can be used, e.g. in about the same amounts.
  • the cultivation in the fed -batch phase is performed for any one of around 15 to 100h, around 15 to 80h, around 15 to 70h, around 15 to 60h, around 15 to 50h, around 15 to 45h, around 15 to 40h, around 15 to 35h, around 15 to 30h, around 15 to 35h, around 15 to 25h, or around 15 to 20h; preferably around 20 to 40h.
  • the cultivation in the fed -batch phase is performed for any one of around 100h, around 80h, around 70h, around 60h, around 55h, around 50h, around 45h, around 40h, around 35h, around 33h, around 30h, around 25h, around 20h, or around 15h.
  • volume specific product formation rate is the amount of product (mg) formed per Unit Volume (L) and Unit time (h) (mg (L h) 1 ). Volume specific product formation rate is also called space time yield (STY) or volumetric productivity.
  • a fed -batch cultivation of the method described herein is performed such that a space time yield of around 30 mg (L h) 1 (meaning 30 mg (L h) 1 +1-5% or +/-10%).
  • a space time yield of around 30 mg (L h) 1 is achieved within around 30h fed batch, specifically at least any of 27, 28, 29, 30, 31 , 32, or 33 mg (L h) 1 within less than any one of 33h, 32h, 31 h, 30h, 29h, 28h, 27h, 26h, or 25h fed batch time can be achieved.
  • the POI is expressed in the production phase under growth-limiting conditions, e.g. by cultivating the cell line at a growth rate of less than the maximal growth rate, typically less than 90%, preferably less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, less than 10%, less than 5%, less than 3%, less than 2%, less than 1 %, less than 0.5%, less than 0.4%, less than 0.3%, or less than 0.2% of the maximum growth rate of the cells.
  • the maximum growth rate is individually determined for each type of host cell.
  • the Mut- host cell is cultured during a production phase under conditions limiting the host cell growth to less than any one of 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1 % (w/w biomass).
  • the production phase employs a feed medium that provides for a supplemental carbon source in a growth limiting amount to keep the specific growth rate within the range of 0.0001 h 1 to 0.2 h 1 , preferably 0.005 h 1 to 0.15 h 1 .
  • the invention further provides for the use of a recombinant methanol utilization pathway deficient methylotrophic yeast (Mut-) host cell in a method of producing a fermentation product which method comprises culturing said Mut- host cell under conditions that permit the Mut- host cell to produce the fermentation product using methanol as a carbon source.
  • a recombinant methanol utilization pathway deficient methylotrophic yeast (Mut-) host cell comprises culturing said Mut- host cell under conditions that permit the Mut- host cell to produce the fermentation product using methanol as a carbon source.
  • said Mut- host cell is deficient of alcohol oxidase 1 (AOX1 ) and alcohol oxidase 2 (AOX2).
  • the genes encoding alcohol oxidase 1 (AOX1 ) and alcohol oxidase 2 (AOX2) are knocked out or deleted.
  • said Mut- host cell is engineered by one or more genetic modifications to reduce expression of a first and a second endogenous gene compared to the host cell prior to said one or more genetic modifications, wherein a) the first endogenous gene encodes alcohol oxidase 1 (AOX1 ) comprising the amino acid sequence identified as SEQ ID NO:1 or a homologue thereof, and
  • AOX1 alcohol oxidase 1
  • the second endogenous gene encodes alcohol oxidase 2 (AOX2) comprising the amino acid sequence identified as SEQ ID NO:3 or a homologue thereof.
  • AOX2 alcohol oxidase 2
  • the invention provides for a method for producing a protein of interest (POI) in a host cell, comprising the steps:
  • GOI gene of interest
  • ECP expression cassette promoter
  • step a) of the method described herein is carried out before, or after, or concomitantly with step b).
  • the host cell is first genetically modified to reduce expression of said first and second genes encoding the AOX1 and AOX2, respectively, before being engineered for producing the POI.
  • a wild-type host cell is genetically modified according to step a) of the method described herein. Specifically, the host cell is provided upon introducing said one or more genetic modifications into a wild-type host cell strain for reduction of said first and second genes encoding the AOX1 and AOX2, respectively.
  • the host cell is first engineered for producing the heterologous or recombinant POI, before being further genetically modified to reduce said first and second genes encoding the AOX1 and AOX2, respectively.
  • a wild-type host cell may first be engineered to comprise the expression cassette for POI production. Such engineered host cell may then be further modified to reduce said first and second genes encoding the AOX1 and AOX2, respectively.
  • the host cell is undergoing both, the engineering for POI production and genetically modifying for reduction of said first and second genes encoding the AOX1 and AOX2, respectively, concomitantly i.e. in one method step, e.g., employing the respective expression cassette, reagents and tools in one or more reaction mixtures.
  • the method employs method steps to produce the recombinant Mut- host cell as further described herein.
  • heterologous expression cassette comprises the ECP as further described herein.
  • the POI can be produced by culturing the Mut- host cell in an appropriate medium, producing the POI during a culturing step using a cell culture production medium comprising methanol, and isolating the expressed POI from the cell culture, in particular from the cell culture supernatant or medium upon separating the cells, and optionally purifying it by a method appropriate for the expressed product. Thereby, a purified POI preparation can be produced.
  • the growth of the Mut- host cells was advantageously limited during the production phase, which reduced the necessity of oxygen supply and cooling.
  • a methanol-inducible ECP has been advantageously used in a GOIEC.
  • the methanol amounts as used in the cell culture as a carbon source were sufficient to induce expression of the GO!.
  • carbon source as used herein shall mean a fermentable carbon substrate, typically a source carbohydrate, suitable as an energy source for microorganisms, such as those capable of being metabolized by host organisms or production cell lines, in particular sources selected from the group consisting of monosaccharides, oligosaccharides, polysaccharides, alcohols including glycerol, in the purified form, in minimal media or provided in raw materials, such as a complex nutrient material.
  • the carbon source may be used as described herein as a single carbon source or as a mixture of different carbon sources.
  • methanol is used as a carbon source, e.g., as a sole carbon source during a production phase, or in a mixture with a non-methanol carbon source. Specifically, methanol is co-fed to the cell culture with any non-methanol carbon source.
  • a non-methanol carbon source is herein understood as a carbon source which is any other than methanol, in particular a methanol-free carbon source.
  • A“basal carbon source” such as described herein typically is a carbon source suitable for cell growth, such as a nutrient for host cells, in particular for eukaryotic cells.
  • the basal carbon source may be provided in a medium, such as a basal medium or complex medium, but also in a chemically defined medium containing a purified carbon source.
  • the basal carbon source typically is provided in an amount to provide for cell growth, in particular during the growth phase in a cultivation process, for example to obtain cell densities of at least 5 g/L cell dry mass, preferably at least 10 g/L cell dry mass, or at least 15 g/L cell dry mass, e.g. exhibiting viabilities of more than 90% during standard sub-culture steps, preferably more than 95%.
  • the basal carbon source is typically used in an excess or surplus amount, which is understood as an excess providing energy to increase the biomass, e.g. during the cultivation of a cell line with a high specific growth rate, such as during the growth phase of a cell line in a batch or fed-batch cultivation process.
  • This surplus amount is particularly in excess of the limited amount of a supplemental carbon source (as used under growth -limited conditions) to achieve a residual concentration in the fermentation broth that is measurable and typically at least 10 fold higher, preferably at least 50 fold or at least 100 fold higher than during feeding the limited amount of the supplemental carbon source.
  • a “supplemental carbon source” such as described herein typically is a supplemental substrate facilitating the production of fermentation products by production cell lines, in particular in the production phase of a cultivation process.
  • the production phase specifically follows a growth phase, e.g. in batch, fed -batch and continuous cultivation process.
  • the supplemental carbon source specifically may be contained in the feed of a fed -batch process.
  • the supplemental carbon source is typically employed in a cell culture under carbon substrate limited conditions, i.e. using the carbon source in a limited amount.
  • methanol is used as a supplemental carbon source.
  • A“limited amount” of a carbon source or a“limited carbon source” is herein understood to specifically refer to the type and amount of a carbon substrate facilitating the production of fermentation products by production cell lines, in particular in a cultivation process with controlled growth rates of less than the maximum growth rate.
  • the production phase specifically follows a growth phase, e.g. in batch, fed -batch and continuous cultivation process.
  • Cell culture processes may employ batch culture, continuous culture, and fed -batch culture.
  • Batch culture is a culture process by which a small amount of a seed culture solution is added to a medium and cells are grown without adding an additional medium or discharging a culture solution during culture.
  • Continuous culture is a culture process by which a medium is continuously added and discharged during culture.
  • the continuous culture also includes perfusion culture.
  • Fed-batch culture which is an intermediate between the batch culture and the continuous culture and also referred to as semi-batch culture, is a culture process by which a medium is continuously or sequentially added during culture but, unlike the continuous culture, a culture solution is not continuously discharged.
  • a fed -batch process which is based on feeding of a growth limiting nutrient substrate to a culture.
  • the fed -batch strategy including single fed-batch or repeated fed-batch fermentation, is typically used in bio-industrial processes to reach a high cell density in the bioreactor.
  • the controlled addition of the carbon substrate directly affects the growth rate of the culture and helps to avoid overflow metabolism or the formation of unwanted metabolic byproducts.
  • the carbon source specifically may be contained in the feed of a fed-batch process. Thereby, the carbon substrate is provided in a limited amount.
  • the growth rate can be tightly controlled.
  • the limited amount of a carbon source is herein particularly understood as the amount of a carbon source necessary to keep a production cell line under growth- limited conditions, e.g. in a production phase or production mode. Such a limited amount may be employed in a fed -batch process, where the carbon source is contained in a feed medium and supplied to the culture at low feed rates for sustained energy delivery, e.g. to produce a POI, while keeping the biomass at low specific growth rates.
  • a feed medium is typically added to a fermentation broth during the production phase of a cell culture.
  • the limited amount of a carbon source may, for example, be determined by the residual amount of the carbon source in the cell culture broth, which is below a predetermined threshold or even below the detection limit as measured in a standard (carbohydrate) assay.
  • the residual amount typically would be determined in the fermentation broth upon harvesting a fermentation product.
  • the limited amount of a carbon source may as well be determined by defining the average feed rate of the carbon source to the fermenter, e.g. as determined by the amount added over the full cultivation process, e.g. the fed -batch phase, per cultivation time, to determine a calculated average amount per time.
  • This average feed rate is kept low to ensure complete usage of the supplemental carbon source by the cell culture, e.g. between 0.6 g L "1 h 1 (g carbon source per L initial fermentation volume and h time) and 25 g L "1 h 1 , preferably between 1.6 g L 1 h 1 and 20 g L "1 h 1 .
  • the limited amount of a carbon source may also be determined by measuring the specific growth rate, which specific growth rate is kept low, e.g. lower than the maximum specific growth rate, during the production phase, e.g. within a predetermined range, such as in the range of 0.001 h '1 to 0.20 h 1 , or 0.005 h 1 to 0.20 h 1 , preferably between 0.01 h 1 and 0.15 h 1 .
  • a feed medium which is chemically defined and comprising methanol.
  • cell culture medium such as a minimal medium or feed medium in a fed-batch process
  • a cultivation medium suitable for the in vitro cell culture of a production cell line in which all of the chemical components and (poly)peptides are known.
  • a chemically defined medium is entirely free of animal-derived components and represents a pure and consistent cell culture environment.
  • the term“cell” or“host cell” as used herein shall refer to a single cell, a single cell clone, or a cell line of a host cell.
  • the term“host cell” shall particularly apply to a cell of methylotrophic yeast, which is suitably used for recombination purposes to produce a POI or a host cell metabolite. It is well understood that the term“host cell” does not include human beings.
  • host cells as described herein are artificial organisms and derivatives of native (wild-type) host cells.
  • host cells, methods and uses described herein e.g., specifically referring to those comprising one or more genetic modifications, said heterologous expression cassettes or constructs, said transfected or transformed host cells and recombinant proteins, are non-naturally-occurring,“man-made” or synthetic, and are therefore not considered as a result of“law of nature”.
  • cell line refers to an established clone of a particular cell type that has acquired the ability to proliferate over a prolonged period of time.
  • a cell line is typically used for expressing an endogenous or recombinant gene, or products of a metabolic pathway to produce polypeptides or cell metabolites mediated by such polypeptides.
  • the host cell producing the POI as described herein is also referred to as “production host cell”, and a respective cell line a“production cell line”.
  • A“production cell line” is commonly understood to be a cell line ready-to-use for cell culture in a bioreactor to obtain the product of a production process, such as a POI.
  • Specific embodiments described herein refer to a production cell line which is engineered to underexpress endogenous genes encoding the AOX1 and AOX2 proteins, and/or has a reduced expression of such genes, and is characterized by a high yield of POI production under the control of an ECP described herein, using methanol as a carbon source.
  • cell culture or“culturing” or“cultivation” as used herein with respect to a host cell refers to the maintenance of cells in an artificial, e.g., an in vitro environment, under conditions favoring growth, differentiation or continued viability, in an active or quiescent state, of the cells, specifically in a controlled bioreactor according to methods known in the industry.
  • the cells When culturing a cell culture using appropriate culture media, the cells are brought into contact with the media in a culture vessel or with substrate under conditions suitable to support culturing the cells in the cell culture.
  • a culture medium is provided that can be used for the growth of host cells e.g., methylotrophic yeast. Standard cell culture techniques are well-known in the art.
  • the cell cultures as described herein particularly employ techniques which provide for the production of a secreted POI, such as to obtain the POI in the cell culture medium, which is separable from the cellular biomass, herein referred to as “cell culture supernatant”, and may be purified to obtain the POI at a higher degree of purity.
  • a protein such as e.g., a POI
  • a protein such as e.g., a POI
  • a cell culture supernatant can be obtained by separating the cell culture supernatant from the host cell biomass, and optionally further purifying the protein to produce a purified protein preparation.
  • Cell culture media provide the nutrients necessary to maintain and grow cells in a controlled, artificial and in vitro environment. Characteristics and compositions of the cell culture media vary depending on the particular cellular requirements. Important parameters include osmolality, pH, and nutrient formulations. Feeding of nutrients may be done in a continuous or discontinuous mode according to methods known in the art.
  • a batch process is a cell culture mode in which all the nutrients necessary for culturing the cells are contained in the initial culture medium, without additional supply of further nutrients during fermentation
  • a feeding phase takes place in which one or more nutrients are supplied to the culture by feeding.
  • the mode of feeding is critical and important, the host cell and methods described herein are not restricted with regard to a certain mode of cell culture.
  • a recombinant POI can be produced using the host cell and the respective cell line described herein, by culturing in an appropriate medium, isolating the expressed product or metabolite from the culture, and optionally purifying it by a suitable method.
  • a POI may be expressed, processed and optionally secreted by transfecting or transforming a host cell with an expression vector harboring recombinant DNA encoding the relevant protein, preparing a culture of the transfected or transformed cell, growing the culture, inducing transcription and POI production, and recovering the POI.
  • the cell culture process is a fed -batch process. Specifically, a host cell transformed with a nucleic acid construct encoding a desired recombinant POI, is cultured in a growth phase and transitioned to a production phase in order to produce a desired recombinant POI.
  • host cells described herein are cultured in a continuous mode, e.g., employing a chemostat.
  • a continuous fermentation process is characterized by a defined, constant and continuous rate of feeding of fresh culture medium into a bioreactor, whereby culture broth is at the same time removed from the bioreactor at the same defined, constant and continuous removal rate. By keeping culture medium, feeding rate and removal rate at the same constant level, the cell culture parameters and conditions in the bio reactor remain constant.
  • a stable cell culture as described herein is specifically understood to refer to a cell culture maintaining the genetic properties, specifically keeping the POI production level high, e.g. at least at a pg level, even after about 20 generations of cultivation, preferably at least 30 generations, more preferably at least 40 generations, most preferred of at least 50 generations.
  • a stable recombinant host cell line is provided which is considered a great advantage when used for industrial scale production.
  • the cell culture described herein is particularly advantageous for methods on an industrial manufacturing scale, e.g. with respect to both the volume and the technical system, in combination with a cultivation mode that is based on feeding of nutrients, in particular a fed-batch or batch process, or a continuous or semi-continuous process ⁇ e.g. chemostat).
  • the host cell described herein is typically tested for its capacity to express the GOI for POI production, tested for the POI yield by any of the following tests: ELISA, activity assay, HPLC, or other suitable tests, such as SDS-PAGE and Western Blotting techniques, or mass spectrometry.
  • the host cell line may be cultured in microtiter plates, shake flask, or bioreactor using fed-batch or chemostat fermentations in comparison with strains without such genetic modification(s) in the respective cell.
  • the production method described herein specifically allows for the fermentation on a pilot or industrial scale.
  • the industrial process scale would preferably employ volumes of at least 10 L, specifically at least 50 L, preferably at least 1 m 3 , preferably at least 10 m 3 , most preferably at least 100 m 3 .
  • Production conditions in industrial scale are preferred, which refer to e.g., fed batch culture in reactor volumes of 100 L to 10 m 3 or larger, employing typical process times of several days, or continuous processes in fermenter volumes of approximately 50 - 1000 L or larger, with dilution rates of approximately 0.02 - 0.15 h 1 .
  • the devices, facilities and methods used for the purpose described herein are specifically suitable for use in and with culturing any desired cell line including prokaryotic and/or eukaryotic cell lines. Further, in embodiments, the devices, facilities and methods are suitable for culturing any cell type including suspension cells or anchorage-dependent (adherent) cells and are suitable for production operations configured for production of pharmaceutical and biopharmaceutical products—such as polypeptide products (POI), nucleic acid products (for example DNA or RNA), or cells and/or viruses such as those used in cellular and/or viral therapies.
  • POI polypeptide products
  • nucleic acid products for example DNA or RNA
  • viruses such as those used in cellular and/or viral therapies.
  • the cells express or produce a product, such as a recombinant therapeutic or diagnostic product.
  • a product such as a recombinant therapeutic or diagnostic product.
  • products produced by cells include, but are not limited to, POIs such as exemplified herein including antibody molecules (e.g., monoclonal antibodies, bispecific antibodies), antibody mimetics (polypeptide molecules that bind specifically to antigens but that are not structurally related to antibodies such as e.g.
  • DARPins affibodies, adnectins, or IgNARs
  • fusion proteins e.g., Fc fusion proteins, chimeric cytokines
  • other recombinant proteins e.g., glycosylated proteins, enzymes, hormones
  • viral therapeutics e.g., anti-cancer oncolytic viruses, viral vectors for gene therapy and viral immunotherapy
  • cell therapeutics e.g., pluripotent stem cells, mesenchymal stem cells and adult stem cells
  • vaccines or lipid-encapsulated particles e.g., exosomes, virus-like particles
  • RNA such as e.g. siRNA
  • DNA such as e.g. plasmid DNA
  • antibiotics or amino acids antibiotics or amino acids.
  • the devices, facilities and methods can be used for producing biosimilars.
  • devices, facilities and methods allow for the production of eukaryotic cells, such as for example yeast cells, e.g., POIs including proteins, peptides, or antibiotics, amino acids, nucleic acids (such as DNA or RNA), synthesized by said cells in a large-scale manner.
  • yeast cells e.g., POIs including proteins, peptides, or antibiotics, amino acids, nucleic acids (such as DNA or RNA), synthesized by said cells in a large-scale manner.
  • the devices, facilities, and methods can include any desired volume or production capacity including but not limited to bench-scale, pilot-scale, and full production scale capacities.
  • the devices, facilities, and methods can include any suitable reactor(s) including but not limited to stirred tank, airlift, fiber, microfiber, hollow fiber, ceramic matrix, fluidized bed, fixed bed, and/or spouted bed bioreactors.
  • reactor can include a fermentor or fermentation unit, or any other reaction vessel and the term “reactor” is used interchangeably with “fermentor.”
  • an example bioreactor unit can perform one or more, or all, of the following: feeding of nutrients and/or carbon sources, injection of suitable gas (e.g ., oxygen), inlet and outlet flow of fermentation or cell culture medium, separation of gas and liquid phases, maintenance of temperature, maintenance of oxygen and CO2 levels, maintenance of pH level, agitation (e.g., stirring), and/or cleaning/sterilizing.
  • Example reactor units such as a fermentation unit, may contain multiple reactors within the unit, for example the unit can have 1 , 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, or 100, or more bioreactors in each unit and/or a facility may contain multiple units having a single or multiple reactors within the facility.
  • the bioreactor can be suitable for batch, semi fed -batch, fed-batch, perfusion, and/or a continuous fermentation processes. Any suitable reactor diameter can be used.
  • the bioreactor can have a volume between about 100 mL and about 50,000 L.
  • Non limiting examples include a volume of 100 mL, 250 mL, 500 mL, 750 mL, 1 liter, 2 liters, 3 liters, 4 liters, 5 liters, 6 liters, 7 liters, 8 liters, 9 liters, 10 liters, 15 liters, 20 liters, 25 liters, 30 liters, 40 liters, 50 liters, 60 liters, 70 liters, 80 liters, 90 liters, 100 liters, 150 liters, 200 liters, 250 liters, 300 liters, 350 liters, 400 liters, 450 liters, 500 liters, 550 liters, 600 liters, 650 liters, 700 liters, 750 liters, 800 liters, 850 liters, 900 liters, 950 liters, 1000 liters, 1500 liters, 2000 liters, 2500 liters, 3000 liters, 3
  • suitable reactors can be multi-use, single-use, disposable, or non-disposable and can be formed of any suitable material including metal alloys such as stainless steel (e.g., 316L or any other suitable stainless steel) and Inconel, plastics, and/or glass.
  • metal alloys such as stainless steel (e.g., 316L or any other suitable stainless steel) and Inconel, plastics, and/or glass.
  • the devices, facilities, and methods described herein can also include any suitable unit operation and/or equipment not otherwise mentioned, such as operations and/or equipment for separation, purification, and isolation of such products.
  • Any suitable facility and environment can be used, such as traditional stick-built facilities, modular, mobile and temporary facilities, or any other suitable construction, facility, and/or layout.
  • modular clean-rooms can be used.
  • the devices, systems, and methods described herein can be housed and/or performed in a single location or facility or alternatively be housed and/or performed at separate or multiple locations and/or facilities.
  • Suitable techniques may encompass culturing in a bioreactor starting with a batch phase, followed by a short exponential fed batch phase at high specific growth rate, further followed by a fed batch phase at a low specific growth rate.
  • Another suitable culture technique may encompass a batch phase followed by a fed -batch phase at any suitable specific growth rate or combinations of specific growth rate such as going from high to low growth rate over POI production time, or from low to high growth rate over POI production time.
  • Another suitable culture technique may encompass a batch phase followed by a continuous culturing phase at a low dilution rate.
  • a preferred embodiment includes a batch culture to provide biomass followed by a fed-batch culture for high yields POI production.
  • a host cell as described herein in a bioreactor under growth conditions to obtain a cell density of at least 1 g/L cell dry weight, more preferably at least 10 g/L cell dry weight, preferably at least 20 g/L cell dry weight, preferably at least any one of 30, 40, 50, 60, 70, or 80 g/L cell dry weight. It is advantageous to provide for such yields of biomass production on a pilot or industrial scale.
  • a growth medium allowing the accumulation of biomass typically comprises a carbon source, a nitrogen source, a source for sulphur and a source for phosphate.
  • a basal growth medium typically comprises furthermore trace elements and vitamins, and may further comprise amino acids, peptone or yeast extract.
  • Preferred nitrogen sources include NH4H2PO4, or NF or (NFU ⁇ SC ⁇
  • Preferred sulphur sources include MgS04, or(NH 4 ) 2 SC>4 or K2SO4;
  • Preferred phosphate sources include NH 4 H 2 P0 4, or H 3 P0 4 , or NaH 2 P0 4 , KH2PO4, Na 2 HP0 4 or K 2 HP0 4;
  • KCI KCI
  • CaC CaC
  • Trace elements such as: Fe, Co, Cu, Ni, Zn, Mo, Mn, I, B;
  • a typical growth medium for P. pastoris comprises glycerol, sorbitol or glucose, NH 4 H 2 PO 4 , MgSC>4, KCI, CaCh, biotin, and trace elements.
  • a production medium is specifically used with only a limited amount of a supplemental carbon source.
  • the host cell line is cultured in a mineral medium with a suitable carbon source, thereby further simplifying the isolation process significantly.
  • a preferred mineral medium is one containing an utilizable carbon source (in particular methanol as described herein optionally in combination with e.g., glucose, glycerol, or sorbitol), salts containing the macro elements (potassium, magnesium, calcium, ammonium, chloride, sulphate, phosphate) and trace elements (copper, iodide, manganese, molybdate, cobalt, zinc, and iron salts, and boric acid), and optionally vitamins or amino acids, e.g., to complement auxotrophies.
  • an utilizable carbon source in particular methanol as described herein optionally in combination with e.g., glucose, glycerol, or sorbitol
  • salts containing the macro elements potassium, magnesium, calcium, ammonium, chloride, sulphate, phosphate
  • trace elements copper,
  • the cells are cultured under conditions suitable to effect expression of the desired POI, which can be purified from the cells or culture medium, depending on the nature of the expression system and the expressed protein, e.g., whether the protein is fused to a signal peptide and whether the protein is soluble or membrane- bound.
  • culture conditions will vary according to factors that include the type of host cell and particular expression vector employed.
  • a typical production medium comprises a supplemental carbon source, and further NH 4 H 2 PO 4 , MgSC>4, KCI, CaCh, biotin, and trace elements.
  • the feed of the supplemental carbon source added to the fermen tation may comprise a carbon source with up to 50 wt % utilizable sugars.
  • the fermentation preferably is carried out at a pH ranging from 3 to 8.
  • Typical fermentation times are about 24 to 120 hours with temperatures in the range of 20 °C to 35°C, preferably 22-30°C.
  • the POI is preferably expressed employing conditions to produce titers of at least 1 mg/L, preferably at least 10 mg/L, preferably at least 100 mg/L, most preferred at least 1 g/L.
  • expression or“expression cassette” as used herein refers to nucleic acid molecules containing a desired coding sequence and control sequences in operable linkage, so that hosts transformed or transfected with these sequences are capable of producing the encoded proteins or host cell metabolites.
  • the expression system may be included in a vector; however, the re- levant DNA may also be integrated into a host cell chromosome.
  • Expression may refer to secreted or non-secreted expression products, including polypeptides or metabolites.
  • Expression cassettes are conveniently provided as expression constructs e.g., in the form of “vectors” or“plasmids”, which are typically DNA sequences that are required for the transcription of cloned recombinant nucleotide sequences, i.e. of recombinant genes and the translation of their mRNA in a suitable host organism.
  • vectors or“plasmids”
  • plasmids typically DNA sequences that are required for the transcription of cloned recombinant nucleotide sequences, i.e. of recombinant genes and the translation of their mRNA in a suitable host organism.
  • Expression vectors or plasmids usually comprise an origin for autonomous replication or a locus for genome integration in the host cells, selectable markers (e.g., an amino acid synthesis gene or a gene conferring resistance to antibiotics such as zeocin, kanamycin, G418 or hygromycin, nourseothricin), a number of restriction enzyme cleavage sites, a suitable promoter sequence and a transcription terminator, which components are operably linked together.
  • selectable markers e.g., an amino acid synthesis gene or a gene conferring resistance to antibiotics such as zeocin, kanamycin, G418 or hygromycin, nourseothricin
  • a number of restriction enzyme cleavage sites e.g., kanamycin, G418 or hygromycin, nourseothricin
  • a suitable promoter sequence e.g., a promoter sequence
  • transcription terminator e.g., a transcription terminator
  • Expression vectors may include but are not limited to cloning vectors, modified cloning vectors and specifically designed plasmids.
  • Preferred expression vectors described herein are expression vectors suitable for expressing of a recombinant gene in a eukaryotic host cell and are selected depending on the host organism.
  • Appropriate expression vectors typically comprise regulatory sequences suitable for expressing DNA encoding a POI in a eukaryotic host cell. Examples of regulatory sequences include promoter, operators, enhancers, ribosomal binding sites, and sequences that control transcription and translation initiation and termination. The regulatory sequences are typically operably linked to the DNA sequence to be expressed.
  • Specific expression constructs described herein comprise a promoter operably linked to a nucleotide sequence encoding a POI under the transcriptional control of said promoter.
  • the promoter is not natively associated with the coding sequence of the POI.
  • the expression cassette or vector described herein as GOIEC comprises an ECP, typically a promoter nucleotide sequence which is adjacent to the 5’ end of the coding sequence, e.g., upstream from and adjacent to a gene of interest (GOI), or if a signal or leader sequence is used, upstream from and adjacent to said signal and leader sequence, respectively, to facilitate expression and secretion of the POI.
  • the promoter sequence is typically regulating and initiating transcription of the downstream nucleotide sequence, with which it is operably linked, including in particular the GOI.
  • Specific expression constructs described herein comprise a polynucleotide encoding the POI linked with a leader sequence which causes secretion of the POI from the host cell.
  • a secretion leader sequence in the expression vector is typically required when the POI intended for recombinant expression and secretion is a protein which is not naturally secreted and therefore lacks a natural secretion leader sequence, or its nucleotide sequence has been cloned without its natural secretion leader sequence.
  • any secretion leader sequence effective to cause secretion of the POI from the host cell may be used.
  • the secretion leader sequence may originate from yeast source, e.g. from yeast a-factor such as MFa of Saccharomyces cerevisiae, or yeast phosphatase, from mammalian or plant source, or others.
  • multicloning vectors may be used, which are vectors having a multicloning site.
  • a desired heterologous gene can be integrated or incorporated at a multicloning site to prepare an expression vector.
  • a promoter is typically placed upstream of the multicloning site.
  • gene expression or“expressing a polynucleotide” as used herein, is meant to encompass at least one step selected from the group consisting of DNA transcription into mRNA, mRNA processing, mRNA maturation, mRNA export, translation, protein folding and/or protein transport.
  • reduce expression herein also referred to as "underexpression” refers to any amount or level (e.g., the activity or concentration) less than an expressed amount or level (e.g., the activity or concentration)exhibited by a reference standard, which may be the host cell prior to the genetic alteration to reduce expression of a certain polynucleotide, or which is otherwise expressed in a host cell of the same type or species which is not engineered to lower expression of said polynucleotide.
  • Reduction of expression as described herein specifically refers to a polynucleotide or gene encoding a defined AOX1 protein or AOX2 protein, in particular a gene that is endogenous to the host cell prior to engineering.
  • the respective gene product is the defined AOX1 protein or AOX2 protein as described herein.
  • the expression of said gene product or polypeptide is at a level which is less than the expression of the same gene product or polypeptide prior to a genetic modification of the host cell or in a comparable host which has not been genetically modified.“Less than” includes, e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80, 90% or more. No expression of the gene product or a polypeptide is also encompassed by the term“reduction of expression” or“underexpression.”
  • the host cell is engineered to knock-down or knockout (for inactivation or deletion of a gene or a part thereof) the endogenous host cell gene encoding the AOX1 protein or AOX2 protein (as defined herein, including e.g. homologues or orthologues of the sequences naturally-occurring in wild-type P. pastoris), or other (coding or non-coding) nucleotide sequences which confer the host cell’s ability to express or produce said AOX1 protein or AOX2 protein.
  • the endogenous host cell gene encoding the AOX1 protein or AOX2 protein (as defined herein, including e.g. homologues or orthologues of the sequences naturally-occurring in wild-type P. pastoris), or other (coding or non-coding) nucleotide sequences which confer the host cell’s ability to express or produce said AOX1 protein or AOX2 protein.
  • a deletion strain wherein a nucleotide sequence is disrupted.
  • disrupt refers to the significant reduction to complete removal of the expression or activity of one or more endogenous proteins in a host cell, such as by knock-down or knockout. This may be measured as presence of this one or more endogenous proteins in a cell culture or culture medium of the host cell, such as by mass spectrometry wherein the total content of a endogenous protein may be less than a threshold or non-detectable. Alternatively it may be measured as the enzymatic activity of the endogenous protein.
  • disrupted specifically refers to a result of genetic engineering by at least one step selected from the group consisting of gene silencing, gene knock-down, gene knockout, delivery of a dominant negative construct, conditional gene knockout, and/or by gene alteration with respect to a specific gene.
  • knock-down refers to experimental approaches leading to reduced expression of a given gene compared to expression in a control cell. Knock-down of a gene can be achieved by various experimental means such as introducing nucleic acid molecules into the cell which hybridize with parts of the gene's mRNA leading to its degradation (e.g., shRNAs, RNAi, miRNAs) or altering the sequence of the gene in a way that leads to reduced transcription, reduced mRNA stability, diminished mRNA translation, or reduced activity of the encoded protein.
  • shRNAs e.g., shRNAs, RNAi, miRNAs
  • Knockout of a gene means that no functional transcripts are synthesized from said gene leading to a loss of function normally provided by this gene. Gene knockout is achieved by altering the DNA sequence leading to disruption or deletion of the gene or its regulatory sequences, or part of such gene or regulatory sequences. Knockout technologies include the use of homologous recombination techniques to replace, interrupt or delete crucial parts or the entire gene sequence or the use of DNA- modifying enzymes such as zinc-finger or mega-nucleases to introduce double strand breaks into DNA of the target gene e.g., described by Gaj et al. (Trends Biotechnol. 2013;31 (7):397-405).
  • Specific embodiments employ one or more knockout plasmids or cassettes which are transformed or transfected into the host cells. By homologous recombination the target gene in the host cells can be disrupted. This procedure is typically repeated until all alleles of the target gene are stably removed.
  • CRISPR-Cas9 methods as described in e.g., Weninger et al. (J. Biotechnol. 2016, 235:139-49).
  • Another method includes the split marker approach as described by e.g. Heiss et al. 2013 (Appl Microbiol Biotechnol. 97(3):1241 -9.)
  • Another embodiment refers to target mRNA degradation by using small interfering RNA (siRNA) to transfect the host cell and targeting a mRNA encoding the target protein expressed endogenously by said host cell.
  • siRNA small interfering RNA
  • Expression of a gene may be inhibited or reduced by methods which directly interfere with gene expression, encompassing, but not restricted to, inhibition or reduction of DNA transcription, e.g., by use of specific promoter-related repressors, by site specific mutagenesis of a given promoter, by promoter exchange, or inhibition or reduction of translation, e.g., by RNAi or non-coding RNA induced post-transcriptional gene silencing.
  • the expression of a dysfunctional, or inactive gene product with reduced activity can, for example, be achieved by site specific or random mutagenesis, insertions or deletions within the coding gene.
  • the inhibition or reduction of the activity of gene product can, for example, be achieved by administration of, or incubation with, an inhibitor to the respective enzyme, prior to or simultaneously with protein expression.
  • inhibitors include, but are not limited to, an inhibitory peptide, an antibody, an aptamer, a fusion protein or an antibody mimetic against said enzyme, or a ligand or receptor thereof, or an inhibitory peptide or nucleic acid, or a small molecule with similar binding activity.
  • Gene silencing, gene knock-down and gene knockout refers to techniques by which the expression of a gene is reduced, either through genetic modification or by treatment with an oligonucleotide with a sequence complementary to either an mRNA transcript or a gene.
  • the result is a knock-down or knockout organism. If the change in gene expression is caused by an oligonucleotide binding to an mRNA or temporarily binding to a gene, this results in a temporary change in gene expression without modification of the chromosomal DNA and is referred to as a transient knock-down.
  • the binding of this oligonucleotide to the active gene or its transcripts causes decreased expression through blocking of transcription (in the case of gene-binding), degradation of the mRNA transcript (e.g ., by small interfering RNA (siRNA) or antisense RNA) or blocking mRNA translation.
  • siRNA small interfering RNA
  • antisense RNA blocking mRNA translation.
  • Gene knockout refers to techniques by which the expression of a gene is fully blocked, i.e. the respective gene is inoperative, or even removed. Methodological approaches to achieve this goal are manifold and known to the skilled person. Examples are the production of a mutant which is dominantly negative for the given gene. Such mutant can be produced by site directed mutagenesis (e.g., deletion, partial deletion, insertion or nucleic acid substitution), by use of suitable transposons, or by other approaches which are known to the skilled person from the respective literature, the application of which in the context of the present invention is thus considered as routine.
  • site directed mutagenesis e.g., deletion, partial deletion, insertion or nucleic acid substitution
  • TALENs Transcription activator-like effector nucleases
  • the delivery of a dominant negative construct involves the introduction of a sequence coding for a dysfunctional gene expression product, e.g., by transfection.
  • Said coding sequence is functionally coupled to a strong promoter, in such way that the gene expression of the dysfunctional enzyme overrules the natural expression of the gene expression product, which, in turn, leads to an effective physiological defect of the respective activity of said gene expression product.
  • a conditional gene knockout allows blocking gene expression in a tissue- or time-specific manner. This is done, for example, by introducing short sequences called loxP sites around the gene of interest. Again, other approaches are known to the skilled person from the respective literature, and their application in the context of the present invention is considered as routine.
  • gene alteration which may lead to a dysfunctional gene product or to a gene product with reduced activity.
  • This approach involves the introduction of frame shift mutations, nonsense mutations (i.e ., introduction of a premature stop codon) or mutations which lead to an amino acid substitution which renders the whole gene product dysfunctional, or causing a reduced activity.
  • Such gene alteration can for example be produced by mutagenesis (e.g., deletion, partial deletion, insertion or nucleic acid substitution), either unspecific (random) mutagenesis or site directed mutagenesis.
  • Protocols describing the practical application of gene silencing, gene knock-down, gene knockout, delivery of a dominant negative construct, conditional gene knockout, and/or gene alteration are commonly available to the skilled artisan, and are within his routine.
  • the technical teaching provided herein is thus entirely enabled with respect to all conceivable methods leading to an inhibition or reduction of gene expression of a gene product, or to the expression of a dysfunctional, or inactive gene product, or with reduced activity.
  • endogenous as used herein is meant to include those molecules and sequences, in particular endogenous genes or proteins, which are present in the wild- type (native) host cell, prior to its modification to reduce expression of the respective endogenous genes and/or reduce the production of the endogenous proteins.
  • an endogenous nucleic acid molecule e.g., a gene
  • protein that does occur in (and can be obtained from) a particular host cell as it is found in nature
  • a cell“endogenously expressing” a nucleic acid or protein expresses that nucleic acid or protein as does a host of the same particular type as it is found in nature.
  • a host cell“endogenously producing” or that“endogenously produces” a nucleic acid, protein, or other compound produces that nucleic acid, protein, or compound as does a host cell of the same particular type as it is found in nature.
  • an endogenous protein is no more produced by a host cell, such as in a knockout mutant of the host cell, where the protein encoding gene is inactivated or deleted, the protein is herein still referred to as“endogenous”.
  • heterologous refers to a compound which is either foreign to a given host cell, i.e.“exogenous”, such as not found in nature in said host cell; or that is naturally found in a given host cell, e.g., is “endogenous”, however, in the context of a heterologous construct or integrated in such heterologous construct, e.g., employing a heterologous nucleic acid fused or in conjunction with an endogenous nucleic acid, thereby rendering the construct heterologous.
  • heterologous nucleotide sequence as found endogenously may also be produced in an unnatural, e.g., greater than expected or greater than naturally found, amount in the cell.
  • the heterologous nucleotide sequence, or a nucleic acid comprising the heterologous nucleotide sequence possibly differs in sequence from the endogenous nucleotide sequence but encodes the same protein as found endogenously.
  • heterologous nucleotide sequences are those not found in the same relationship to a host cell in nature. Any recombinant or artificial nucleotide sequence is understood to be heterologous.
  • heterologous polynucleotide is a nucleotide sequence not natively associated with a promoter, e.g., to obtain a hybrid promoter, or operably linked to a coding sequence, as described herein. As a result, a hybrid or chimeric polynucleotide may be obtained.
  • a further example of a heterologous compound is a POI encoding polynucleotide operably linked to a transcriptional control element, e.g., a promoter, to which an endogenous, naturally-occurring POI coding sequence is not normally operably linked.
  • operably linked refers to the association of nucleotide sequences on a single nucleic acid molecule, e.g., a vector, or an expression cassette, in a way such that the function of one or more nucleotide sequences is affected by at least one other nucleotide sequence present on said nucleic acid molecule.
  • a nucleic acid sequence is placed into a functional relationship with another nucleic acid sequence on the same nucleic acid molecule.
  • a promoter is operably linked with a coding sequence of a recombinant gene, when it is capable of effecting the expression of that coding sequence.
  • a nucleic acid encoding a signal peptide is operably linked to a nucleic acid sequence encoding a POI, when it is capable of expressing a protein in the secreted form, such as a preform of a mature protein or the mature protein.
  • nucleic acids operably linked to each other may be immediately linked, i.e. without further elements or nucleic acid sequences in between the nucleic acid encoding the signal peptide and the nucleic acid sequence encoding a POI.
  • methylotrophic yeast refers to of yeast genera and species which share a common metabolic pathway that enables them to use methanol as a sole carbon source for their growth. In a transcriptionally regulated response to methanol induction, several of the enzymes are rapidly synthesized at high levels. Since the promoters controlling the expression of these genes are among the strongest and most strictly regulated yeast promoters, methylotrophic yeast are attractive as hosts for the large scale production of recombinant proteins.
  • the methylotrophic yeast as described herein is mutated by one or more genetic modifications to render it deficient in the methanol utilization pathway, in particular by underexpressing one or both of the genes encoding the endogenous AOX1 and AOX2 proteins, respectively.
  • a methylotrophic yeast which is underexpressing or otherwise deficient in expressing both, the gene encoding the AOX1 protein and the gene encoding the AOX2 protein is herein understood as“Mut-“.
  • Mut- yeast is still referred to as“methylotrophic yeast”, because comprising a functional methanol utilization pathway prior to such genetic modification(s).
  • A“promoter” sequence is typically understood to be operably linked to a coding sequence, if the promoter controls the transcription of the coding sequence. If a promoter sequence is not natively associated with the coding sequence, its transcription is either not controlled by the promoter in native (wild -type) cells or the sequences are recombined with different contiguous sequences.
  • the promoter which is used for the purpose described herein, is herein referred to as“ECP”.
  • the ECP may be a constitutive, inducible or repressible promoter.
  • the ECP is a promoter which is inducible by methanol and a methanol carbon source, respectively.
  • the ECP as described herein in particular initiates, regulates, or otherwise mediates or controls the expression of a POI coding DNA.
  • Promoter DNA and coding DNA may be from the same gene or from different genes, and may be from the same or different organisms.
  • an inducible ECP as described herein is specifically understood as being a regulatable promoter, which has different promoter strength in the repressed and induced state.
  • the term “regulatable” with respect to an inducible or repressible regulatory element, such as a promoter described herein shall refer to an element that is repressed in a host cell in the presence of an excess amount of a substance (such as a nutrient in the cell culture medium) e.g., in the growth phase of a batch culture, and de-repressed to induce strong activity e.g., in the production phase (such as upon upon feeding of a supplemental substrate, or adding methanol for methanol-induction), according to a fed-batch strategy.
  • a regulatory element can as well be designed to be regulatable, such that the element is inactive without addition of a cell culture additive, and active in the presence of such additive. Thus, expression of a POI under the control of such regulatory element can be induced upon addition of such additive.
  • the strength of the ECP specifically refers to its transcription strength, represented by the efficiency of initiation of transcription occurring at that promoter with high or low frequency. The higher transcription strength, the more frequently transcription will occur at that promoter. Promoter strength is a typical feature of a promoter, because it determines how often a given mRNA sequence is transcribed, effectively giving higher priority for transcription to some genes over others, leading to a higher concentration of the transcript. A gene that codes for a protein that is required in large quantities, for example, typically has a relatively strong promoter. The RNA polymerase can only perform one transcription task at a time and so must prioritize its work to be efficient. Differences in promoter strength are selected to allow for this prioritization.
  • a strong ECP is herein preferred, in particular an ECP which is relatively strong in the fully induced state, which is typically understood as the state of about maximal activity.
  • the relative strength is commonly determined with respect to a comparable promoter, herein referred to as a reference promoter, which can be a standard promoter, such as the respective pGAP promoter of the cell as used as the host cell.
  • the frequency of transcription is commonly understood as the transcription rate, e.g. as determined by the amount of a transcript in a suitable assay, e.g. RT-PCR or Northern blotting.
  • the transcription strength of a promoter according to the invention is determined in the host cell which is P. pastoris and compared to the native pGAP promoter of P. pastoris.
  • the strength of a promoter to express a gene of interest is commonly understood as the expression strength or the capability of support a high expression level/rate.
  • the expression and/or transcription strength of a promoter of the invention is determined in the host cell which is P. pastoris and compared to the native pGAP promoter of P. pastoris.
  • the comparative transcription strength compared to a reference promoter may be determined by standard methods, such as by measuring the quantity of transcripts, e.g. employing a microarray, or else in a cell culture, such as by measuring the quantity of respective gene expression products in recombinant cells.
  • the transcription rate may be determined by the transcription strength on a microarray, Northern blot or with quantitative real time PCR (qRT-PCR) or with RNA sequencing (RNA-seq) where the data show the difference of expression level between conditions with high growth rate and conditions with low growth rate, or conditions employing different media composition, and a high signal intensity as compared to the reference promoter.
  • the expression rate may, for example, be determined by the amount of expression of a reporter gene, such as eGFP.
  • ECP as described herein exerts a relatively high transcription strength, e.g., reflected by a transcription rate or transcription strength of at least 15% as compared to the native pGAP promoter in the host cell, also called “homologous pGAP promoter”.
  • the transcription rate or strength is at least any one of 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100%, or even higher, such as at least any one of 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, or 200%, or even higher, as compared to the native pGAP promoter, such as determined in the (e.g. eukaryotic) host cell selected as a host cell for recombination purpose to produce the POL
  • the native pGAP promoter typically initiates expression of the gap gene encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which is a constitutive promoter present in most living organisms.
  • GAPDH EC 1 .2.1.12
  • the native pGAP promoter specifically is active in a recombinant eukaryotic cell in a similar way as in a native eukaryotic cell of the same species or strain, including the unmodified (non-recombinant) or recombinant eukaryotic cell.
  • Such native pGAP promoter is commonly understood to be an endogenous promoter, thus, homologous to the host cell, and may serve as a standard or reference promoter for comparison purposes.
  • the relative expression or transcription strength of a promoter as described herein is usually compared to the native pGAP promoter of a cell of the same species or strain that is used as a host for producing a POI.
  • mutagenesis shall refer to a method of providing mutants of a nucleotide sequence, e.g. through insertion, deletion and/or substitution of one or more nucleotides, so to obtain variants thereof with at least one change in the non-coding or coding region. Mutagenesis may be through random, semi-random or site directed mutation. Variants can be produced by a suitable mutagenesis method using a parent sequence as a reference. Certain mutagenesis methods encompass those methods of engineering the nucleic acid or c/e novo synthesizing a nucleotide sequence using the respective parent sequence information as a template. Specific mutagenesis methods apply rational engineering of a mutant.
  • nucleotide sequence or“nucleic acid sequence” used herein refers to either DNA or RNA.
  • Nucleic acid sequence or “polynucleotide sequence” or simply “polynucleotide” refers to a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5' to the 3' end. It includes expression cassettes, self-replicating plasmids, infectious polymers of DNA or RNA, and non-functional DNA or RNA.
  • protein of interest refers to a polypeptide or a protein that is produced by means of recombinant technology in a host cell. More specifically, the protein may either be a polypeptide not naturally-occurring in the host cell, i.e. a heterologous protein, or else may be native to the host cell, i.e.
  • a homologous protein to the host cell is produced, for example, by transformation with a self-replicating vector containing the nucleic acid sequence encoding the POI, or upon integration by recombinant techniques of one or more copies of the nucleic acid sequence encoding the POI into the genome of the host cell, or by recombinant modification of one or more regulatory sequences controlling the expression of the gene encoding the POI, e.g., of a promoter sequence.
  • the term POI as used herein also refers to any metabolite product by the host cell as mediated by the recombinantly expressed protein.
  • sequence identity of a variant, homologue or orthologue as compared to a parent nucleotide or amino acid sequence indicates the degree of identity of two or more sequences.
  • Two or more amino acid sequences may have the same or conserved amino acid residues at a corresponding position, to a certain degree, up to 100%.
  • Two or more nucleotide sequences may have the same or conserved base pairs at a corresponding position, to a certain degree, up to 100%.
  • Sequence similarity searching is an effective and reliable strategy for identifying homologs with excess (e.g ., at least 50%) sequence identity. Sequence similarity search tools frequently used are e.g., BLAST, FASTA, and HMMER.
  • Sequence similarity searches can identify such homologous proteins or genes by detecting excess similarity, and statistically significant similarity that reflects common ancestry.
  • Homologues may encompass orthologues, which are herein understood as the same protein in different organisms, e.g., variants of such protein in different different organisms or species.
  • orthologous sequence of the same protein in different organisms or species is typically homologous to the protein sequence, specifically of orthologs originating from the same genus.
  • orthologs typically have at least about any one of 25%, 30%, 35%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, or 95% identity, up to 100% sequence identity.
  • orthologs of a protein can be determined upon replacement of said protein or the gene encoding said protein by the orthologous sequences in a knock-out host cell, which host cell has been modified to knockout the respective gene or protein prior to such replacement.
  • a putative AOX1 or AOX2 protein is functional in a P. pastoris host cell replacing the respective endogenous protein in a P. pastoris host cell in which the gene encoding such endogenous protein has been knocked out, such putative AOX1 or AOX2 protein can be considered a respective homologue for the purpose described herein.
  • the AOX1 protein comprising or consisting of the amino acid sequence identified as SEQ ID NO:1 is of K. phaffii origin it is well understood that there are homologous sequences present in other methylotrophic yeast host cells.
  • yeast of Pichia pastoris comprise the respective homologous sequences.
  • Pichia pastoris has been reclassified into a new genus, Komagataella, and split into three species, K. pastoris, K. phaffii, and K. pseudopastoris.
  • SEQ ID NO:1 Specific homologous sequences of SEQ ID NO:1 are e.g., found in K. pastoris (e.g., SEQ ID NO:9, such as encoded by the nucleotide sequence comprising or consisting of SEQ ID NQ:10), Ogataea polymorpha (e.g., SEQ ID NO:19, such as encoded by the nucleotide sequence comprising or consisting of SEQ ID NO:20), o rOgataea methanolica (e.g., SEQ ID NO:13 such as encoded by the nucleotide sequence comprising or consisting of SEQ ID NO:14),
  • the AOX2 protein comprising or consisting of the amino acid sequence identified as SEQ ID NO:3 is of K. phaffii origin. It is well understood that there are homologous sequences present in other methylotrophic yeast host cells. For example, yeast of Pichia pastoris comprise the respective homologous sequences. Pichia pastoris has been reclassified into a new genus, Komagataella, and split into three species, K. pastoris, K. phaffii, and K. pseudopastoris.
  • SEQ ID NO:3 Specific homologous sequences of SEQ ID NO:3 are e.g., found in K. pastoris (e.g., SEQ ID NO:11 , such as encoded by the nucleotide sequence comprising or consisting of SEQ ID NO:12), Ogataea polymorpha (e.g., SEQ ID NO:19, such as encoded by the nucleotide sequence comprising or consisting of SEQ ID NO:20), or Ogataea methanolica (e.g., SEQ ID NO:15, such as encoded by the nucleotide sequence comprising or consisting of SEQ ID NO:16).
  • SEQ ID NO:11 such as encoded by the nucleotide sequence comprising or consisting of SEQ ID NO:12
  • Ogataea polymorpha e.g., SEQ ID NO:19, such as encoded by the nucleotide sequence comprising or consisting of SEQ ID NO:20
  • Ogataea polymorpha has only one alcohol oxidase, herein exemplified by SEQ ID NO:19. Thus, reducing expression of AOX1 and AOX2 in Ogataea polymorpha as described herein is effectively carried out by reducing expression of the endogenous alcohol oxidase of Ogataea polymorpha.
  • Percent (%) amino acid sequence identity with respect to an amino acid sequence, homologs and orthologues described herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific polypeptide sequence, after aligning the sequence and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
  • Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
  • sequence identity between two amino acid sequences is determined using the NCBI BLAST program version BLASTP 2.8.1 with the following exemplary parameters: Program: blastp, Word size: 6, Expect value: 10, Hitlist size: 100, Gapcosts: 11.1 , Matrix: BLOSUM62, Filter string: F, Compositional adjustment: Conditional compositional score matrix adjustment.
  • Percent (%) identity with respect to a nucleotide sequence e.g., of a promoter or a gene, is defined as the percentage of nucleotides in a candidate DNA sequence that is identical with the nucleotides in the DNA sequence, after aligning the sequence and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent nucleotide sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
  • sequence identity between two DNA sequences is determined using the NCBI BLAST program version BLASTN 2.8.1 with the following exemplary parameters: Program: blastn, Word size: 11 , Expect threshold: 10, Hitlist size: 100, Gap Costs: 5.2, Match/Mismatch Scores: 2,-3, Filter string: Low complexity regions, Mark for lookup table only.
  • the term“isolated” or“isolation” as used herein with respect to a PCI shall refer to such compound that has been sufficiently separated from the environment with which it would naturally be associated, in particular a cell culture supernatant, so as to exist in “purified” or“substantially pure” form.
  • isolated does not necessarily mean the exclusion of artificial or synthetic mixtures with other compounds or materials, or the presence of impurities that do not interfere with the fundamental activity, and that may be present, for example, due to incomplete purification.
  • Isolated compounds can be further formulated to produce preparations thereof, and still for practical purposes be isolated - for example, a PCI can be mixed with pharmaceutically acceptable carriers or excipients when used in diagnosis or therapy.
  • purified shall refer to a preparation comprising at least 50% (mol/mol), preferably at least 60%, 70%, 80%, 90% or 95% of a compound (e.g., a POI).
  • Purity is measured by methods appropriate for the compound (e.g chromatographic methods, polyacrylamide gel electrophoresis, HPLC analysis, and the like).
  • An isolated, purified POI as described herein may be obtained by purifying the cell culture supernatants to reduce impurities.
  • methods such as methods utilizing difference in solubility, such as salting out and solvent precipitation, methods utilizing difference in molecular weight, such as ultrafiltration and gel electrophoresis, methods utilizing difference in electric charge, such as ion-exchange chromatography, methods utilizing specific affinity, such as affinity chromatography, methods utilizing difference in hydrophobicity, such as reverse phase high performance liquid chromatography, and methods utilizing difference in isoelectric point, such as isoelectric focusing may be used.
  • cell separation and wash by Microfiltration or Tangential Flow Filter (TFF) or centrifugation POI purification by precipitation or heat treatment
  • POI activation by enzymatic digest POI purification by chromatography, such as ion exchange (I EX), hydrophobic interaction chromatography (HIC), Affinity chromatography, size exclusion (SEC) or HPLC Chromatography, POI precipitation of concentration and washing by ultrafiltration steps.
  • chromatography such as ion exchange (I EX), hydrophobic interaction chromatography (HIC), Affinity chromatography, size exclusion (SEC) or HPLC Chromatography
  • I EX ion exchange
  • HIC hydrophobic interaction chromatography
  • SEC size exclusion
  • HPLC Chromatography HPLC Chromatography
  • a highly purified product is essentially free from contaminating proteins, and preferably has a purity of at least 90%, more preferred at least 95%, or even at least 98%, up to 100%.
  • the purified products may be obtained by purification of the cell culture supernatant or else from cellular debris.
  • An isolated and purified POI can be identified by conventional methods such as Western blot, HPLC, activity assay, or ELISA.
  • recombinant shall mean“being prepared by or the result of genetic engineering.
  • a recombinant host may be engineered to delete and/or inactivate one or more nucleotides or nucleotide sequences, and may specifically comprise an expression vector or cloning vector containing a recombinant nucleic acid sequence, in particular employing nucleotide sequence foreign to the host.
  • a recombinant protein is produced by expressing a respective recombinant nucleic acid in a host.
  • recombinant with respect to a POI as used herein, includes a POI that is prepared, expressed, created or isolated by recombinant means, such as a POI isolated from a host cell transformed to express the POL
  • recombinant means such as a POI isolated from a host cell transformed to express the POL
  • conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art may be employed. Such techniques are explained fully in the literature. See, e.g., Maniatis, Fritsch & Sambrook, "Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, (1982).
  • Certain recombinant host cells are“engineered” host cells which are understood as host cells which have been manipulated using genetic engineering, i.e. by human intervention. When a host cell is engineered to reduce expression or to underexpress a given gene or the respective protein, the host cell is manipulated such that the host cell has no longer the capability to express such gene and protein, respectively, compared to the host cell under the same condition prior to manipulation, or compared to the host cells which are not engineered such that said gene or protein is underexpressed.
  • Example 1 Generation of Methanol utilization negative strains of Pichia pastoris.
  • the P. pastoris strain (CBS2612, CBS-KNAW Fungal Biodiversity Centre, Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands) was made electrocompetent.
  • the strain was inoculated into 100 mL YPD media (main culture) for 16-20 hours (25°C; 180 rpm) and harvested at an optical density (OD 6 oo) from 1.8 - 3 by centrifugation (5min; 1500g; 4°C) in two 50 mL falcon tubes.
  • the cell pellet was resuspended in 10 mL YPD + 20mM HEPES + 25mM DTT and incubated (30 min; 25°C; 180 rpm).
  • the falcon tubes were filled with 40 mL ice cold sterile distilled water and centrifuged (5min; 1500g; 4°C) (Eppendorf AG, Germany).
  • the cell pellet was resuspended in ice cold sterile 1 mM HEPES buffer, pH 8 and centrifuged (5min; 1500g; 4°C).
  • the cell pellet was resuspended in 45 mL ice cold 1 M sorbitol and centrifuged (5min; 1500g; 4°C).
  • the pellet was resuspended in 500 pl_ ice cold 1 M sorbitol and 80 pL aliquoted into ice cold 1.5 mL Eppendorf tubes.
  • the aliquoted electro competent cells were kept at -80°C till used.
  • YPD media (10 g/L yeast extract, 20 g/L peptone, 20 g/L glucose) or YPD agar plates (10 g/L yeast extract, 20 g/L peptone, 20 g/L glucose, 20 g/L agar-agar) containing 500 pg/mL Geneticin or 200 pg/mL Hygromycin when necessary for selection.
  • deletions were done by adding 0.5 pg AOX1 split marker cassette 1 and 0.5 pg AOX1 split marker cassette 2 to the aliquoted electro competent cells and incubated for 5 min on ice.
  • the electroporation was performed at 2 kV for 4 milliseconds (Gene Pulser, Bio-Rad Laboratories, Inc, USA). After transformation the electroporated cells were suspended in 1 mL YPD media and regenerated for 1.5 h to 3 h on 30°C shaking at 700 rpm on a thermoshaker (Eppendorf AG, Germany).
  • a liquid culture was incubated from a single positive colony and made electrocompetent as explained in Example 1 a), except for the addition of 500 pg/mL Geneticin to the liquid medium for generating the main culture.
  • the strains were electroporated with 500 pg pTAC_Cre_Hph_Mx4 plasmid carrying a Cre recombinase needed for deletion of the Geneticin antibiotic resistance cassette between the LoxP regions and a Hygromycin resistance cassette for selection (Marx, Mattanovich, & Sauer, 2008).
  • the electroporation was done as described and selected for loss of Geneticin resistance by restreaking the transformants in parallel on YPD with 500 pg/mL Geneticin and 200 pg/mL Hygromycin and YPD plates with only 200 pg/mL Hygromycin. Clones were selected which were unable to grow on YPD plates with 500 pg/mL Geneticin and 200 pg/mL Hygromycin, but could grow on YPD plates with only 200 pg/mL Hygromycin.
  • the successful deletion of the AOX1 coding region and antibiotic marker was verified by PCR amplification with the primers AOX1_ctrl_Fwd and AOX1_ctrl_Rev (Table 2) and sequencing of the PCR amplicon (Microsynth AG, Swiss).
  • the generated strain is called P. pastoris CBS2612 Aaoxl and has a Mut s phenotype. It was selected for further genetic manipulation.
  • the P. pastoris CBS2612 Aaoxl was used to generate electro competent cells with the protocol described in a) and was electroporated with 0.5 pg AOX2 split marker cassette 1 and 0.5 pg AOX2 split marker cassette 2 (Table 1 ) with the procedure described in d).
  • the antibiotic marker was removed with the same procedure as described in d).
  • the successful deletion of the AOX2 coding region and antibiotic marker was verified by PCR amplification with the primers AOX2_ctrl_fwd & AOX2_ctrl_rev (Table 2) and sequencing of the PCR amplicon (Microsynth AG, Swiss).
  • the generated strain is called P. pastoris CBS2612 Aaoxl Aaox2 and has a methanol utilization negative (Muf) phenotype.
  • Genomic DMA for PCR amplifications was isolated with the Wizard® Genomic DNA Purification Kit (Promega Corporation, USA) as per the manufacturer ' s recommendation. The PCR amplification reactions were done with the Q5 polymerase (New England Biolabs, Inc., USA) as per the manufacturer ' s recommendations.
  • Table 1 Split marker cassette DNA sequence used for generating the AOX1 and AOX2 deletion strains.
  • Example 2 Production of intracellular eGFP with P. pastoris Aaoxl and P. pastoris AaoxlAaox2 under the methanol inducible AOX1 promoter.
  • the P. pastoris Aaoxl Aaox2 and P. pastoris Aaoxl strains were transformed with an expression constructs for enhanced green fluorescent protein (eGFP) (Table 4).
  • the eGFP coding sequence was under the expression control of the P AOX T PP7435_chr4 (237941 ...238898).
  • BB3aN_14 * The plasmids and sequences are available in the Golden PiCS kit # 1000000133 (Addgene, Inc., USA). Before electroporation the plasmids were linearized with the restriction enzyme Ascl (New England Biolabs, Inc., USA) as per the manufacturer ' s protocol and purified with the Hi Yield® Gel/PCR DNA Fragment Extraction Kits (Siid-Labor room GmbH, Germany). 500 ng of the linearized plasmid was transformed into electrocompetent P. pastoris Aaoxl Aaox2 and P. pastoris Aaox1 as previously described in Example 1a) and id). Positive transformants were selected on YPD with 100 pg/L Nourseothricin and used for later screening experiments.
  • eGFP measurements were done 4 and 20 hours after induction using a Gallios flow cytometer (Beckman Coulter , Inc., USA). For this purpose the cells were diluted to an ODeoo of 0.5 in phosphate buffered saline containing 0.24 g/L KH 2 PO 4 , 1.8 g/L Na 2 HP0 4 * 2H 2 0, 0.2 g/L KCI, 8 g/L NaCI. 20,000 events were measured. FX values were calculated with the software FACS Express version 3 (De Novo Software, USA) using the equation: 8000
  • FL 1 Fluorescence measured with a 505— 545 nm filter
  • Minimal media ASMv6 6.3 g/L (NH 4 ) 2 HP0 4 , 0.8 g/L (NH 4 ) 2 S0 4 , 0.49 g/L MgS0 4 * 7H 2 0, 2.64 g/L KCI, 0.054 g/L CaCI 2 * 2H 2 0, 22 g/L citric acid monohydrate, 1.47 mL/L PTM0 trace metals, 0.8 mg/L biotin 20 mL/L NH 4 OH (25%); pH set to 6.5 with KOH. d) The results are displayed in Table 3.
  • BB3aN_pAOX1_GFP_ScCYCtt strain is better at 1 % than at 0.2% methanol after 20 h, no difference between methanol concentrations is observed in the P. pastoris Aaoxl strain.
  • Table 3 Results (FX values) with standard deviation from experiment described in Example 2b)
  • Example 3 Generation of P. pastoris Aaoxl and P. pastoris Aaox1Aaox2 strains producing secreted HSA and VHH under the methanol inducible AOX1 promoter.
  • pPM2pN21 _pAOX1 _HSAopt_CycTT and pPM2pZ30_pAOX1_aMF- vHH_CycTT expression constructs used for HSA and VHH production are derivatives of the pPuzzle ZeoR vector described in W02008128701 A2, consisting of the E.coli pUC19 ori and the Zeocin antibiotic resistance cassette.
  • p P M 2 p N 21 _p AOX 1 _H S Ao pt_Cy cTT the Zeocin resistance is exchanged for Nourseothricin resistance via restriction and ligation.
  • the vectors are carrying an integration sequence that is homologous to the PGI locus PP7435_Chr3 (1366329...1367193) for efficient integration.
  • the expression vector is described in more details elsewhere (Gasser et a!., 2013; Stadlmayr et al., 2010).
  • Expression of the gene of interest (GOI) was mediated by the PAOXI PP7435_chr4 (237941 ...238898) and the Saccharomyces cerevisiae CYC1 transcription terminator.
  • the gene for human serum albumin (HSA) (GenBank NP_000468) was codon optimized for P. pastoris and synthesized. It has a native secretion leader and is therefore secreted into the supernatant.
  • VHH The gene for VHH is codon optimized for P. pastoris and synthetized (Table 4), it has an N-terminal S. cerevisiae a-mating type leader for secretion into the supernatant.
  • the circular vectors were linearized by restriction in the PGM homologous sequence with Xmnl (New England Biolabs, Inc., USA) and purified with the Hi Yield® Gel/PCR DNA Fragment Extraction Kits (Sud- Labor site GmbH, Germany).
  • Example 4 Small scale screening of the HSA and VHH producing P. pastoris Aaox1Aaox2 and P. pastoris Aaoxl.
  • the transformants were inoculated in 2 mL YPD with 100 pg/mL Nourseothricin or 25 pg/mL Zeocin based on the antibiotic resistance used for selection. For each expression construct twelve transformants were picked for screening. Pre-culture and screening cultures were cultivated in 24 well plates sealed with an air permeable membrane and incubated on 25°C on 280 rpm. The screening culture was inoculated with a start optical density (OD 6 OO) of 8 into 2 mL of minimal media (ASMv6) with a slow glucose release system based on 6 mm feedbeads (Kuhner Shaker GmbH, Germany) to keep the cultures in glucose limit.
  • OD 6 OO start optical density
  • ASMv6 minimal media
  • Table 6 Average secreted product yield with standard deviation in pg product / g WCW of the tested strains in different screening conditions.
  • bioreactor cultivations were performed. The cultivations were performed as follows.
  • DASGIP bioreactors were used with a working volume of 0.7 L (Eppendorf AG, Germany).
  • One Bio reactor system consists of four reactors that are arranged in one bio-block for controlling the temperature. Each reactor was connected to 4 peristaltic pumps that were software controlled. Additionally each reactor had 2 balances available that were connected to the DASGIP control software (Eppendorf AG, Germany) for adjusting the pump speed gravimetrically.
  • Each reactor was connected with a controllable gas supply (pressured air, N 2 , 0 2 could be mixed in any desired amount) and a gas analyzer for 0 2 and C0 2 concentration measurement in the reactor off gas.
  • the reactors had a pH probe and Dissolved Oxygen (DO) probe connected to the DASGIP control software.
  • DO Dissolved Oxygen
  • the bioreactor cultivation media consisted of BSM medium (Mellitzer et a!., 2014): 11.48 g/L H 3 P0 4 , 0.5 g/L CaCI 2 * 2H 2 0, 7.5 g/L MgS0 4 * 7H 2 0, 9 g/L K 2 S0 4 , 2 g/L KOH, 40g/L Glycerol, 0.25 g/L NaCI, 4.35 mL/L PTM0, 0.87 mg/L Biotin, 0.1 mL/L Glanapon 2000, pH set to 5.5 with 25% NH 3 .
  • BSM medium Cellitzer et a!., 2014
  • PTM0 consisted of: 6.0 g CuS0 4 * 5H 2 0, 0.08 g Nal, 3.36 g MnS0 4 * H 2 0, 0.2 g Na 2 Mo0 4 * 2H 2 0, 0.02 g H 3 B0 3 , 0.82 g CoCI 2 , 20.0 g ZnCI 2 , 65.0 g FeS0 4 * 7H 2 0, 5 mL/L H 2 S0 4 (95 %-98 %).
  • the Glucose feed media consisted of: 50% (w/w) glucose, 2.08 mg/kg Biotin, 10.4 mL/kg PTM0.
  • the methanol feed media was: 50% (v/v) or 100% (v/v) methanol.
  • the glycerol feed media consisted of: 60% (w/w) glycerol, 2.08 mg/kg Biotin, 10.4 mL/kg PTM0.
  • the Dissolved Oxygen (DO) set point was 20%. In certain cases the DO control was deactivated and the agitation and aeration were manually set to a constant 750 rpm and 9.5 sL/h. The pH was set to 5.0 or 5.5 with either 12.5% or 25% NH 3 controlled by the DASGIP control software. Acid control was achieved with 10% H 3 P0 4 by manual addition when necessary. The temperature was set at 25°C. The start ODeoo was 2 and the start volume was 300 mL plus 15 mL of inoculation culture. f) Sampling was done on a daily basis (approximately every 24 hours).
  • Cell viability was measured by staining the cell suspension with propidium iodide.
  • the cell suspension from the reactor sample was diluted with phosphate buffered saline to on OD 6 oo of 0.5 and mixed with a stock solution of propidium iodide to a final concentration of 10 mM prior to measurement with the Gallios flow cytometer (Beckman coulter , Inc., USA) with a filter of 590 - 650 nm. 50,000 events were measured per sample.
  • Example 6 Determining the evaporation rate of methanol from the Bioreactors without cells.
  • Aminex HPX-87H (Bio-Rad Laboratories, Inc, USA) run at 60°C with a 4 mM H 2 SO 4 mobile phase at 0.6 mL/min.
  • the detector was a refraction index detector RID-10 A (Shimadzu, Corp., Japan) and the calculations were done with the LabSolutions v5.85 software (Shimadzu, Corp., Japan).
  • Table 7 Reactor parameters and methanol pulse volume.
  • Table 8 Methanol concentration at the sampling timepoints and the calculated evaporation rate. * are too low and are considered as outliers.
  • Example 7 Determining the methanol uptake rate of P. pastoris Aaox1Aaox2
  • the P. pastoris Aaoxl Aaox2 p P M 2 p N 21 _p AOX 1 _H S Ao pt_CycTT strain was cultivated in a bioreactor. The culture was grown till a certain biomass concentration. Then a methanol pulse was applied and samples were taken immediately after the pulse and approximately 20 hours later. The goal was to determine the methanol uptake rate of the Mut strain and compare it to the methanol evaporation rate measured in Example 6.
  • Pre-culture 24 hours prior to reactor inoculation 50 ml_ YPD containing 100 pg/L Nourseothricin were inoculated with P. pastoris Aaoxl Aaox2 pPM2pN21 _pAOX1 _HSAopt_CycTT. 3 hours prior to inoculation of the reactors the pre-culture was diluted by another 50 mL YPD containing 100 pg/L Nourseothricin. Before inoculation the appropriate amount of culture was centrifuged (1500g, 5 min, 20°C) and resuspended in 15 mL of BSM media with an OD 6 OO of 42.
  • Table 9 Data overview specific methanol uptake rate (qmethanoi) and apparent methanol loss (dc/dt).
  • Example 8 Cultivation strategy 1 - Applying a constant glucose/methanol co-feed to the P. pastoris Aaox1Aaox2
  • the P. pastoris Aaoxl Aaox2 p P M 2 p N 21 _pAOX 1 _H S Ao pt_CycTT strain was cultivated in a recombinant protein production scenario. The strain was fed with a constant limited glucose feed and induced with methanol for protein production.
  • Example 7a) The inoculation was done as described in Example 7a) b). The cultivation was separated into two phases.
  • Phase two A fed -batch phase with a 50% (w/w) glucose feed was started after phase one at a feed rate of 2.4 mL/h for 97 hours. At the same time a 50% (v/v) methanol pulse was added with the aim to increase the methanol concertation to 1.5% (v/v).
  • a HPLC sample was taken as described in Example 6d) to measure the exact concentration and an additional pulse was added if necessary.
  • a methanol feed calculated based on the predicted biomass concentration and the specific methanol uptake rate of 5 mg g 1 h 1 as measured in Example 7d) was applied. The methanol concentration was measured daily at line by HPLC.
  • methanoi specific methanol uptake rate (mg g 1 h -1 )
  • Fmethanol target target methanol concentration (mg /mL)
  • V reactor reactor volumen (mL)
  • V s ample volume of sample if applicable in the interval, else it is 0 d) Because of the predicted specific methanol uptake rate based on example 7d) it was possible to keep the methanol concentration at excess during the bioreactor cultivation from 1.19% to 1.5% (v/v) of methanol with only once per day at line methanol concentration measurements and feed adjustment.
  • Cmethanoi-end methanol concentration at feedend ( g/L )
  • Vreactor-en d reactor volume at feedend ( )
  • Example 9 Cultivation strategy 2 - A feed strategy with a separated glucose feed phase and a methanol only feed phase.
  • the P. pastoris Aaoxl Aaox2 p P M 2 p N 21 _pAOX 1 _H S Ao pt_CycTT strain was tested in a recombinant protein production scenario where first a limited glucose feed was applied to increase the biomass followed by a separated phase with a methanol pulse and feed to induce protein production
  • Phase one consisted of the batch phase on BSM media with a start ODeoo of 2. The inoculation was done as described in Example 7a) b). The batch phase lasted for 19.68 and 19.50 hours for reactor R3 and R4, respectively.
  • Phase two was a 50% (w/w) glucose feed at 4.8 mL/h for 25 hours to increase the biomass concentration.
  • Phase three was started with a 50% (v/v) methanol pulse to reach a target concentration of 1.5% (v/v) and a methanol feed profile calculated based on the predicted cell dry weigh and specific methanol uptake rate as described in Example 8c) for 72.7 hours.
  • Methanol concentration was measured at line with HPLC every day as described in Example 6d) to measure the exact concentration and an additional compensation pules was added if necessary.
  • the reactor stirrer speed was set to a constant 760 rpm and gassing to 9.5 sL/h.
  • ⁇ consumed methanol total ⁇ Co s me methanol ⁇ ⁇ T phase 3 (n ⁇ Cj ⁇ )
  • phase 3 duration of phase 3 ( h )
  • CDW cell dry weight
  • Table 11 Bioreactor cultivation process data and productivity (qp) for Example 9. The total biomass was corrected for 12 mL sampling as in Example 9 b). * Represents a control sample after the methanol pulse.
  • Example 10 Cultivation strategy 3 - A feed strategy with a glucose/methanol co-feed phase and a separated methanol only feed phase.
  • the P. pastoris Aaox1Aaox2 p P M 2 p N 21 _pAOX 1 _H S Ao pt_CycTT strain was tested in a recombinant protein production scenario where after the batch phase a limited glucose feed and an additional methanol pulse and feed was applied to achieve a biomass increase and recombinant protein production simultaneously. After the desired biomass was reached the glucose feed was stopped but the methanol feed continued for the rest of the cultivation. a) This bioreactor cultivation was separated into three phases. (1 ) Phase one was the batch phase. For this the reactors were inoculated with the production strain P.
  • Phase two was started. Phase two consisted of a 50% (w/w) glucose feed at 4.8 mL/h for 25 hours.
  • Phase two a 50% (v/v) methanol pulse was applied to increase methanol concentration to the target of 1.5% (v/v) and a subsequent methanol feed was started to counteract methanol consumption, evaporation and dilution by the glucose feed.
  • Phase three consisted of a methanol only feed for 72.9 hours. In this phase the reactor stirrer speed was set to a constant 760 rpm and gassing to 9.5 sL/h. Methanol concentration was measured at line with HPLC every day as described in Example 6d). An additional compensation pulse was added if necessary.
  • phase three the q methanoi for reactor R1 was 4.61 mg g 1 h "1 and for reactor R2 it was 4.54 mg g '1 h 1 .
  • Overall the biomass decreased by 5.7% and 5.5% for reactor R1 and R2 in phase three. Again, this shows that with the P. pastoris Aaoxl Aaox2 strain production at no apparent growth is possible.
  • the average total amount of recombinant protein produced in phase three with methanol as the only carbon source is 106 mg which is similar to the 105 mg of recombinant protein produced in Example 9, phase three. This is also illustrated by the similar specific productivity in phase three from Example 9 at 32.9 pg g 1 h 1 and at 34.0 pg g "1 h "1 in this example.
  • phase three did not depend whether the cultures were induced in phase two (glucose feed phase) or not.
  • recombinant protein production is independent of growth the methanol only feed strategy has several advantages when used with the P. pastoris Aaoxl Aaox2 strain.
  • the process is constrained by the maximal reactor volume and the yeast dry mass concentration. After a certain time this constraints stop the cultivation process either by reaching the maximal volume or maximal desired biomass concentration.
  • Example 9 the cultivation time is no longer limited by the biomass concentration or volume as the biomass is not increasing and the volume increase is negligible.
  • cultures at high biomass concentrations can be kept in the bioreactor for longer periods of time without reaching these constraints and allow for longer production phases that increase the concentration of the protein of interest.
  • a methanol only feed phase is also applied when using the methanol utilization slow P. pastoris Aaoxl strain as shown in the following Example 12 but these advantages are not present there because P. pastoris Aaoxl is continuously growing on a methanol only feed and therefore exhibits the same constraints as discussed. Restricting the P. pastoris Aaoxl to the same methanol feed rate as the P. pastoris Aaoxl Aaox2 results in productivity loss. Further process related improvements of the P. pastoris Aaoxl Aaox2 strain are discussed in Example 12.
  • Table 12 Bioreactor cultivation process data and specific productivity (q P ) for Example 10. The total biomass was corrected for 12 ml_ sampling as in Example 9 b). * Represents a control sample after the methanol pulse.
  • Example 11 Cultivation strategy 3 - A feed strategy with a glucose/methanol co-feed phase and a separated methanol only feed phase applied to P. pastoris Aaox1Aaox2 secreting VHH.
  • Example 10a To check secreted recombinant protein production with another secreted protein the bioreactor cultivation described in Example 10a) was repeated with the strain P. pastoris Aaoxl Aaox2 p P M 2 pZ30_pAOX 1 _a M F -v H H_Cy cTT .
  • Phase one was the batch phase.
  • the reactors were inoculated with the production strain P. pastoris Aaoxl Aaox2 p P M 2 pZ30_p AOX 1 _a M F - vHH_CycTT with a start OD 6 oo of 2 as described in Example 7a) b).
  • the batch phase lasted for 18.79 and 19.33 hours for reactor R1 and R2, respectively.
  • the end of the batch phase was indicated by a dissolved oxygen peak.
  • Phase two was started. Phase two consisted of a 50% (w/w) glucose feed at 4.8 mL/h for 33.9 hours to increase the biomass even higher than in Example 10.
  • Phase two a 50% (v/v) methanol pulse was added to increase the methanol concentration to the target value of 1.5% (v/v) and a subsequent methanol feed was started to counteract methanol consumption, evaporation and dilution by the glucose feed.
  • Phase three consisted of a methanol only feed for 63.9 hours. The stirrer speed was set to a constant 760 rpm and gassing to 9.5 sL/h. Methanol concentration was measured at line with HPLC every day as described in Example 6d). An additional compensation pulse was added if necessary.
  • the process and productivity data can be found in Table 13.
  • the maximal and minimal methanol concentration throughout the cultivation of the two repeats ranged from 8.7 g/L (R1 ) to 11.3 g/L (R1 ).
  • the overall average specific productivity was 118.0 pg g 1 h 1 and in phase three 88.2 pg g 1 h 1 .
  • the methanol concentration at the end of the cultivation was 10.5 and 10.8 g/L for reactor R1 and R2.
  • the amount of consumed methanol by reactor R1 and R2 was 26.6 g and 26.0 g. This was calculated by the following equation as shown in Example 8e).
  • Example 10 This amount is higher as in Example 10 due to the higher biomass concentration, but still significantly (5-times) lower than in a Mut s strain (as described in Example 12). Because the biomass was constant in phase three the methanol uptake rate (q m ethanoi) was calculated for phase three as shown in Example 9b). In phase three the q m ethanoi for reactor R1 was 4.75 mg g 1 h 1 and for reactor R2 it was 4.68 mg g 1 IT 1
  • Table 13 Bioreactor cultivation process data and productivity (qP) for Example 11. The total biomass was corrected for 12 ml_ sampling as in Example 9 b). * Represents a control sample after the methanol pulse.
  • Example 12 Process parameters obtained with P. pastoris Aaox1Aaox2 (Mut ) strains compared to a methanol utilization slow P. pastoris Aaoxl (Mut s ) cultivated with an established bioreactor cultivation protocol.
  • Phase one was the batch phase.
  • the batch phase lasted for 20.17 and 20.30 hours for reactors R1 and R2, respectively.
  • the end of the batch phase was indicated by a dissolved oxygen peak.
  • the total run time was 119.25 hours.
  • Phase four in this example corresponds to phase three in Examples 9, 10 and 11. Based on the average biomass in phase four the methanol uptake rate (qmethanoi) as shown in Example 9b) was calculated.
  • the q m ethanoi in phase four for reactor R1 is 37.1 mg g "1 h ”1 and 37.6 mg g 1 h 1 for reactor R2.
  • Overall the biomass increased by 53.2 % and 52.4 % for reactor R1 and R2 in phase four.
  • the lower specific methanol uptake rate reduces the amount of methanol needed in a cultivation. Methanol is toxic and flammable.
  • Use of the Mut strains represents a technical and safety improvement as it reduces the quantities of methanol that need to be handled and stored in a production facility.
  • Another advantage is the lower sensitivity of the P. pastoris Aaoxl Aaox2 to high methanol concentrations. This is confirmed by cell viability data of the strain P. pastoris Aaoxl Aaox2 in Example 10 and P. pastoris Aaoxl in this example.
  • Example 10 the viability of the Mut cells in reactors R1 and R2 at the end of the process was 99.8% and 99.7%.
  • the cell viability of the Mut s cells in reactors R1 and R2 in this example was
  • Table 15 Comparison of key bioreactor cultivation parameters overall and on the methanol only feed phases of P. pastoris Aaox1Aaox2 p P M 2 p N 21 _p AOX 1 _H S Ao pt_CycTT in Example 10 and P. pastoris Aaoxl pPM2pN21_pAOX1 _HSAopt_CycTT in Example 12.
  • Table 16 Specific methanol uptake rates and methanol feed rates based on average cell dry weight in the methanol only feed phase. * As Example 12 has a limited methanol feed the qme th anoi and feed rate are considered equal.
  • Table 17 Methanol inducible promoters and their respective chromosomal positions in the strain P. pastoris CBS7435 (Gasser, Steiger, & Mattanovich, 2015)
  • Pichia pastoris protein production host and model organism for biomedical research. Future Microbiology, 8(2), 191-208. https://doi.org/10.2217/fmb.12.133
  • GoldenPiCS a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris. BMC Systems Biology, 11 (1 ). https://doi.Org/10.1186/s12918-017-0492-3

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biomedical Technology (AREA)
  • Organic Chemistry (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Mycology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Plant Pathology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)

Abstract

L'invention concerne un procédé de production d'une protéine d'intérêt (POI) comprenant la culture d'une cellule hôte de levure méthylotrophe à voie d'utilisation de méthanol déficiente recombimée (Mut-) à l'aide de méthanol en tant que source de carbone pour produire la POI, ladite cellule Mut-hôte comprenant un gène hétérologue d'une cassette d'expression d'intérêt (GOIEC) qui comprend un promoteur de cassette d'expression (ECP) fonctionnellement lié à un gène d'intérêt (GOI) codant pour une protéine d'intérêt (POI), la cellule Mut-hôte étant modifiée par une ou plusieurs modifications génétiques pour réduire l'expression d'un premier et d'un second gène endogène par rapport à la cellule hôte avant ladite ou lesdites modifications génétiques, dans ledit procédé a) le premier gène endogène codant pour l'alcool oxydase 1 (AOX1) comprenant la séquence d'acides aminés identifiée par la SEQ ID NO : 1 ou un de ses homologues, et b) le second gène endogène codant pour l'alcool oxydase 2 (AOX2) comprenant la séquence d'acides aminés identifiée par la SEQ ID NO : 3 ou un de ses homologues.
PCT/EP2019/058190 2019-04-01 2019-04-01 Production de protéines dans de la levure mut-méthylotrophe Ceased WO2020200414A1 (fr)

Priority Applications (13)

Application Number Priority Date Filing Date Title
PCT/EP2019/058190 WO2020200414A1 (fr) 2019-04-01 2019-04-01 Production de protéines dans de la levure mut-méthylotrophe
CN202080040100.0A CN114026239B (zh) 2019-04-01 2020-04-01 Mut-甲醇营养型酵母
BR112021019477A BR112021019477A2 (pt) 2019-04-01 2020-04-01 Uma célula hospedeira de levedura metilotrófica deficiente de via de utilização de metanol recombinante, um método de produção de uma proteína de interesse, e uso de uma célula hospedeira em um método de produção de um produto de fermentação
PCT/EP2020/059284 WO2020201369A1 (fr) 2019-04-01 2020-04-01 Levure mut-méthylotrophe
SG11202110695PA SG11202110695PA (en) 2019-04-01 2020-04-01 Mut- methylotrophic yeast
KR1020217035698A KR102874359B1 (ko) 2019-04-01 2020-04-01 Mut- 메틸영양성 효모
ES20714242T ES2964319T3 (es) 2019-04-01 2020-04-01 Levadura metilotrófica Mut-
HUE20714242A HUE064229T2 (hu) 2019-04-01 2020-04-01 Mut-metilotróf élesztõ
CA3135444A CA3135444C (fr) 2019-04-01 2020-04-01 Levure mut-methylotrophe
AU2020252241A AU2020252241B2 (en) 2019-04-01 2020-04-01 Mut- methylotrophic yeast
EP20714242.3A EP3947695B1 (fr) 2019-04-01 2020-04-01 Levure mut-méthylotrophe
US17/601,045 US12270034B2 (en) 2019-04-01 2020-04-01 Mut- methylotrophic yeast
JP2021558927A JP7570346B2 (ja) 2019-04-01 2020-04-01 Ｍｕｔ－メチロトローフ酵母

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/EP2019/058190 WO2020200414A1 (fr) 2019-04-01 2019-04-01 Production de protéines dans de la levure mut-méthylotrophe

Publications (1)

Publication Number Publication Date
WO2020200414A1 true WO2020200414A1 (fr) 2020-10-08

Family

ID=66001233

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2019/058190 Ceased WO2020200414A1 (fr) 2019-04-01 2019-04-01 Production de protéines dans de la levure mut-méthylotrophe

Country Status (1)

Country Link
WO (1) WO2020200414A1 (fr)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN115927696A (zh) * 2022-07-07 2023-04-07 怡道生物科技(苏州)有限公司 重组毕赤酵母高产表达株的筛选方法及其应用
RU2851229C1 (ru) * 2024-11-02 2025-11-21 Общество с ограниченной ответственностью "Эй Пи Интернэйшнл" Способ производства биомассы дрожжей для получения кормового белка

Citations (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1992017595A1 (fr) 1991-04-01 1992-10-15 The Salk Institute Biotechnology/Industrial Associates, Inc. Genes influançant l'activite proteolytique de pichia, et leurs utilisations
US6153424A (en) 1995-11-09 2000-11-28 Zymogenetics, Inc. Protease-deficient strains of Pichia methanolica
EP1905836A1 (fr) * 2006-09-28 2008-04-02 Institut Pasteur Souches récombinantes de pichia pastoris et procédure de fabrication d'alpha interferon humain rècombinée
WO2008128701A2 (fr) 2007-04-20 2008-10-30 Polymun Scientific Immunbiologische Forschung Gmbh Système d'expression
WO2010099195A1 (fr) 2009-02-26 2010-09-02 Glaxosmithkline Llc. Cellules hôtes et procédés d'utilisation
WO2012152823A1 (fr) 2011-05-09 2012-11-15 Ablynx Nv Procédé pour la production de domaines variables uniques d'immunoglobuline
WO2013050551A1 (fr) 2011-10-07 2013-04-11 Lonza Ltd Promoteur régulable
WO2014067926A1 (fr) 2012-10-29 2014-05-08 Lonza Ltd Séquences d'expression
WO2014139608A1 (fr) 2013-03-15 2014-09-18 Lonza Ltd Promoteur constitutif
WO2015158800A1 (fr) 2014-04-17 2015-10-22 Boehringer Ingelheim Rcv Gmbh & Co Kg Cellule hôte recombinante pour l'expression de protéines d'intérêt
WO2017021541A1 (fr) 2015-08-05 2017-02-09 Lonza Ltd Variants de promoteur

Patent Citations (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1992017595A1 (fr) 1991-04-01 1992-10-15 The Salk Institute Biotechnology/Industrial Associates, Inc. Genes influançant l'activite proteolytique de pichia, et leurs utilisations
US6153424A (en) 1995-11-09 2000-11-28 Zymogenetics, Inc. Protease-deficient strains of Pichia methanolica
EP1905836A1 (fr) * 2006-09-28 2008-04-02 Institut Pasteur Souches récombinantes de pichia pastoris et procédure de fabrication d'alpha interferon humain rècombinée
WO2008128701A2 (fr) 2007-04-20 2008-10-30 Polymun Scientific Immunbiologische Forschung Gmbh Système d'expression
WO2010099195A1 (fr) 2009-02-26 2010-09-02 Glaxosmithkline Llc. Cellules hôtes et procédés d'utilisation
WO2012152823A1 (fr) 2011-05-09 2012-11-15 Ablynx Nv Procédé pour la production de domaines variables uniques d'immunoglobuline
WO2013050551A1 (fr) 2011-10-07 2013-04-11 Lonza Ltd Promoteur régulable
WO2014067926A1 (fr) 2012-10-29 2014-05-08 Lonza Ltd Séquences d'expression
WO2014139608A1 (fr) 2013-03-15 2014-09-18 Lonza Ltd Promoteur constitutif
WO2015158800A1 (fr) 2014-04-17 2015-10-22 Boehringer Ingelheim Rcv Gmbh & Co Kg Cellule hôte recombinante pour l'expression de protéines d'intérêt
WO2017021541A1 (fr) 2015-08-05 2017-02-09 Lonza Ltd Variants de promoteur

Non-Patent Citations (36)

* Cited by examiner, † Cited by third party
Title
ANAMIKA SINGH ET AL: "Abstract", BIORXIV, 10 March 2019 (2019-03-10), XP055589047, Retrieved from the Internet <URL:https://www.biorxiv.org/content/early/2019/03/11/573519.full.pdf> DOI: 10.1101/573519 *
ATA, O.; PRIELHOFER, R.; GASSER, B.; MATTANOVICH, D.; QALIK, P.: "Transcriptional engineering of the glyceraldehyde-3-phosphate dehydrogenase promoter for improved heterologous protein production in Pichia pastoris: Transcriptional Engineering of the P GAP for Gene Overexpression in P. pastoris", BIOTECHNOLOGY AND BIOENGINEERING, vol. 114, no. 10, 2017, pages 2319 - 2327, Retrieved from the Internet <URL:https://doi.org/10.1002/bit.26363>
AW, R.; POLIZZI, K. M.: "Can too many copies spoil the broth?", MICROBIAL CELL FACTORIES, vol. 12, 2013, pages 128, XP021171256, Retrieved from the Internet <URL:https://doi.org/10.1186/1475-2859-12-128> DOI: doi:10.1186/1475-2859-12-128
BLUMHOFF, M.; STEIGER, M. G.; MARX, H.; MATTANOVICH, D.; SAUER, M.: "Six novel constitutive promoters for metabolic engineering of Aspergillus niger", APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, vol. 97, no. 1, 2013, pages 259 - 267, Retrieved from the Internet <URL:https://doi.org/10.1007/s00253-012-4207-9>
CHAUHAN ET AL., PROCESS BIOCHEMISTRY, vol. 34, 1999, pages 139 - 145
CHING-HSIANG CHANG ET AL: "Enhancing the efficiency of the Pichia pastoris AOX1 promoter via the synthetic positive feedback circuit of transcription factor Mxr1", BMC BIOTECHNOLOGY, vol. 18, no. 1, 27 December 2018 (2018-12-27), XP055589028, DOI: 10.1186/s12896-018-0492-4 *
CHIRUVOLU ET AL., ENZYME MICROB. TECHNOL., vol. 21, 1997, pages 277 - 283
COUDER; BARATTI, AGRIC. BIOI. CHERN., vol. 44, no. 10, 1980, pages 2279 - 2289
DONEANU ET AL., MABS, vol. 4, no. 1, 2012, pages 24 - 44
GAJ ET AL., TRENDS BIOTECHNOL., vol. 31, no. 7, 2013, pages 397 - 405
GASSER, B.; PRIELHOFER, R.; MARX, H.; MAURER, M.; NOCON, J.; STEIGER, M.; MATTANOVICH, D.: "Pichia pastoris: protein production host and model organism for biomedical research", FUTURE MICROBIOLOGY, vol. 8, no. 2, 2013, pages 191 - 208, XP009179190, Retrieved from the Internet <URL:https://doi.org/10.2217/fmb.12.133> DOI: doi:10.2217/fmb.12.133
GASSER, B.; STEIGER, M. G.; MATTANOVICH, D.: "Methanol regulated yeast promoters: production vehicles and toolbox for synthetic biology", MICROBIAL CELL FACTORIES, vol. 14, no. 1, 2015, Retrieved from the Internet <URL:https://doi.org/10.1186/s12934-015-0387-1>
GASSER; STEIGER; MATTANOVICH, MICROB CELL FACT., vol. 14, 2015, pages 196
HANNES RUSSMAYER ET AL: "Systems-level organization of yeast methylotrophic lifestyle", BMC BIOLOGY, vol. 13, no. 1, 23 September 2015 (2015-09-23), XP055589013, DOI: 10.1186/s12915-015-0186-5 *
HEISS ET AL., APPL MICROBIOL BIOTECHNOL., vol. 97, no. 3, 2013, pages 1241 - 9
HEISS, S.; V. PUXBAUM; C. GRUBER; F. ALTMANN; D. MATTANOVICH; B. GASSER, MICROBIOLOGY, vol. 161, no. 7, 2015, pages 1356 - 68
HOHENBLUM, H.; BORTH, N.; MATTANOVICH, D.: "Assessing viability and cell-associated product of recombinant protein producing Pichia pastoris with flow cytometry", JOURNAL OF BIOTECHNOLOGY, vol. 102, no. 3, 2003, pages 281 - 290, Retrieved from the Internet <URL:https://doi.org/10.1016/S0168-1656(03)00049-X>
IA PLA ET AL: "Evaluation of Mut+ and MutS Pichia pastoris phenotypes for high level extracellular scFv expression under feedback control of the methanol concentration.", BIOTECHNOL PROG, 1 June 2006 (2006-06-01), pages 881 - 888, XP055589113 *
J. SAMBROOK ET AL.: "Molecular Cloning: A Laboratory Manual", 2001, COLD SPRING HARBOR LABORATORY PRESS
JOSEF W. MOSER ET AL: "Implications of evolutionary engineering for growth and recombinant protein production in methanol-based growth media in the yeast Pichia pastoris", MICROBIAL CELL FACTORIES, vol. 16, no. 1, 17 March 2017 (2017-03-17), XP055589021, DOI: 10.1186/s12934-017-0661-5 *
KURTZMAN, J IND MICROBIOL BIOTECHNOL., vol. 36, no. 11, 2009, pages 1435 - 8
LOOSER, V.; BRUHLMANN, B.; BUMBAK, F.; STENGER, C.; COSTA, M.; CAMATTARI, A.; KOVAR, K.: "Cultivation strategies to enhance productivity of Pichia pastoris: A review", BIOTECHNOLOGY ADVANCES, vol. 33, no. 6, 2015, pages 1177 - 1193, Retrieved from the Internet <URL:https://doi.org/10.1016/j.biotechadv.2015.05.008>
MANIATIS; FRITSCH; SAMBROOK: "Molecular Cloning: A Laboratory Manual", 1982, COLD SPRING HARBOR
MÀRIUS TOMÀS-GAMISANS ET AL: "Fine-tuning the P. pastoris iMT1026 genome-scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources", MICROBIAL BIOTECHNOLOGY, vol. 11, no. 1, 1 January 2018 (2018-01-01), GB, pages 224 - 237, XP055589017, ISSN: 1751-7915, DOI: 10.1111/1751-7915.12871 *
MARX, H.; MATTANOVICH, D.; SAUER, M.: "Overexpression of the riboflavin biosynthetic pathway in Pichia pastoris", MICROBIAL CELL FACTORIES, vol. 7, no. 1, 2008, pages 23, XP021036435, Retrieved from the Internet <URL:https://doi.org/10.1186/1475-2859-7-23>
MATTANOVICH ET AL., CELL FACTORIES, vol. 8, 2009, pages 29
MATTANOVICH ET AL., METHODS MOL. BIOL., vol. 824, 2012, pages 329 - 58
MELLITZER, A.; RUTH, C.; GUSTAFSSON, C.; WELCH, M.; BIRNER-GRUNBERGER, R.; WEIS, R.; GLIEDER, A.: "Synergistic modular promoter and gene optimization to push cellulase secretion by Pichia pastoris beyond existing benchmarks", JOURNAL OF BIOTECHNOLOGY, vol. 191, 2014, pages 187 - 195, Retrieved from the Internet <URL:https://doi.org/10.1016/j.jbiotec.2014.08.035>
POTVIN, G.; AHMAD, A.; ZHANG, Z.: "Bioprocess engineering aspects of heterologous protein production in Pichia pastoris: A review", BIOCHEMICAL ENGINEERING JOURNAL, vol. 64, 2012, pages 91 - 105, XP055312900, Retrieved from the Internet <URL:https://doi.org/10.1016/j.bej.2010.07.017> DOI: doi:10.1016/j.bej.2010.07.017
PRIELHOFER, R.; BARRERO, J. J.; STEUER, S.; GASSIER, T.; ZAHRL, R.; BAUMANN, K.; MARX, H.: "GoldenPiCS: a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris", BMC SYSTEMS BIOLOGY, vol. 11, no. 1, 2017, XP055527656, Retrieved from the Internet <URL:https://doi.org/1 0.1186/s12918-017-0492-3> DOI: doi:10.1186/s12918-017-0492-3
PRIELHOFER, R.; MAURER, M.; KLEIN, J.; WENGER, J.; KIZIAK, C.; GASSER, B.; MATTANOVICH, D.: "Induction without methanol: novel regulated promoters enable high-level expression in Pichia pastoris", MICROBIAL CELL FACTORIES, vol. 12, no. 1, 2013, pages 5, XP055301811, Retrieved from the Internet <URL:https://doi.org/1 0.1186/1475-2859-12-5> DOI: doi:10.1186/1475-2859-12-5
SCHWARZHANS, J.-P.; WIBBERG, D.; WINKLER, A.; LUTTERMANN, T.; KALINOWSKI, J.; FRIEHS, K.: "Integration event induced changes in recombinant protein productivity in Pichia pastoris discovered by whole genome sequencing and derived vector optimization", MICROBIAL CELL FACTORIES, vol. 15, 2016, pages 84, Retrieved from the Internet <URL:https://doi.org/10.1186/s12934-016-0486-7>
STADLMAYR, G.; MECKLENBRAUKER, A; ROTHMULLER, M.; MAURER, M.; SAUER, M.; MATTANOVICH, D.; GASSER, B.: "Identification and characterisation of novel Pichia pastoris promoters for heterologous protein production", JOURNAL OF BIOTECHNOLOGY, vol. 150, no. 4, 2010, pages 519 - 529, XP027516642, Retrieved from the Internet <URL:https://doi.org/10.1016/j.jbiotec.2010.09.957> DOI: doi:10.1016/j.jbiotec.2010.09.957
VERDUYN ET AL., JOURNAL OF MICROBIOLOGICAL METHODS, vol. 1, no. 2, 1984, pages 15 - 25
WEI SHEN ET AL: "A novel methanol-free Pichia pastoris system for recombinant protein expression", MICROBIAL CELL FACTORIES, vol. 15, no. 1, 21 December 2016 (2016-12-21), XP055589024, DOI: 10.1186/s12934-016-0578-4 *
WENINGER ET AL., J. BIOTECHNOL., vol. 235, 2016, pages 139 - 49

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN115927696A (zh) * 2022-07-07 2023-04-07 怡道生物科技(苏州)有限公司 重组毕赤酵母高产表达株的筛选方法及其应用
RU2851229C1 (ru) * 2024-11-02 2025-11-21 Общество с ограниченной ответственностью "Эй Пи Интернэйшнл" Способ производства биомассы дрожжей для получения кормового белка

Similar Documents

Publication Publication Date Title
US20240018563A1 (en) Carbon-source regulated protein production in a recombinant host cell
EP4127185B1 (fr) Facteurs d&#39;aide pour l&#39;expression de protéines dans la levure
JP2023156329A (ja) 目的タンパク質を産生するための宿主細胞
EP4638756A1 (fr) Cellules hôtes à inactivation de pat1 permettant une productivité accrue de protéine spécifique
WO2020200414A1 (fr) Production de protéines dans de la levure mut-méthylotrophe
EP3947695B1 (fr) Levure mut-méthylotrophe
CA3135444C (fr) Levure mut-methylotrophe
WO2020200415A1 (fr) Levure mut-méthylotrophe
HK40062436A (en) Mut- methylotrophic yeast

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 19715081

Country of ref document: EP

Kind code of ref document: A1

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 19715081

Country of ref document: EP

Kind code of ref document: A1