WO2011101472A2

WO2011101472A2 - Complexes of an3-interacting proteins and their use for plant growth promotion

Info

Publication number: WO2011101472A2
Application number: PCT/EP2011/052525
Authority: WO
Inventors: Geert De Jaeger; Dirk Gustaaf INZÉ; Aurine Verkest
Original assignee: Universiteit Gent; Vlaams Instituut voor Biotechnologie VIB
Current assignee: Universiteit Gent; Vlaams Instituut voor Biotechnologie VIB
Priority date: 2010-02-22
Filing date: 2011-02-21
Publication date: 2011-08-25
Anticipated expiration: 2012-08-22
Also published as: AU2011217175A1; CN102892889A; DE112011100622T5; CA2789849A1; BR112012020956A2; PH12012501656A1; IN2012CN07164A; WO2011101472A3; MX2012009692A; US20120324602A1; EP2539455A2

Abstract

The present invention relates to protein complexes based on AN3-interactors, more specifically interactors that are plant variants subunits of the SWI/SNF complex, and proteins that interact with those subunits, preferably in an AN3 free protein complex. It relates further to the use of the complexes to promote plant growth, and to a method for stimulating the complex formation, by overexpressing at least one, preferably at least two members of a complex.

Description

COMPLEXES OF AN3-INTERACTING PROTEINS AND THEIR USE FOR PLANT GROWTH PROMOTION

The demand for more plant derived products has spectacularly increased. In the near future the challenge for agriculture will be to fulfill the growing demands for feed and food in a sustainable manner. Moreover plants start to play an important role as energy sources. To cope with these major challenges, a profound increase in plant yield will have to be achieved. Biomass production is a multi-factorial system in which a plethora of processes are fed into the activity of meristems that give rise to new cells, tissues, and organs. Although a considerable amount of research on yield performance is being performed little is known about the molecular networks underpinning yield (Van Camp, 2005). Many genes have been described in Arabidopsis thaliana that, when mutated or ectopically expressed, result in the formation of larger structures, such as leaves or roots. These so-called "intrinsic yield genes" are involved in many different processes whose interrelationship is mostly unknown.

One of these "intrinsic yield genes", AN3 (also known as GIF1), was identified in search of GRF (growth regulating factor) interactors (Kim and Kende, 2004) and by analysis of narrow- leaf Arabidopsis mutants (Horiguchi et al., 2005). AN3 is a homolog of the human SYT (synovial sarcoma translocation) protein and is encoded by a small gene family in the Arabidopsis genome. SYT is a transcription co-activator whose biological function, despite the implication of its chromosomal translocation in tumorigenesis, is still unclear (Clark et al., 1994; de Bru ijn et al . , 1 996). Using the yeast GAL4 system , AN3 was shown to possess transactivation activity (Kim and Kende, 2004). This together with yeast two-hybrid and in vitro binding assays demonstrating interaction of AN3 with several GRFs (Kim and Kende, 2004; Horiguchi et al., 2005), suggests a role of AN3 as transcription co-activator of GRFs. GRF (growth regulating factor) genes occur in the genomes of all seed plants thus far examined and encode putative transcription factors that play a regulatory role in growth and development of leaves (Kim et al., 2003). In support of a GRF and AN3 transcription activator and co-activator complex, grf and an3 mutants display similar phenotypes, and combinations of grf and an3 mutations showed a cooperative effect (Kim and Kende, 2004). The an3 mutant narrow-leaf phenotype is shown to result of a reduction in cell numbers. Moreover, ectopic expression of AN3 resulted in transgenic plants with larger leaves consisting of more cells, indicating that AN3 controls both cell number and organ size (Horiguchi et al., 2005). Although the function of AN3 in plant growth regulation is not known, these results show that AN3 fulfills the requirements of an "intrinsic yield gene".

al., 2006) but so far none of the identified genes have been associated with stimulation of plant growth.

I n ou r a m bition to d eci pher the molecu la r network u n derpi n n i n g yield en ha ncement mechanism a genome-wide protein centered approach was undertaken to study AN3 interacting proteins in Arabidopsis thaliana cell suspension cultures. The tandem affinity purification (TAP) technology combined with mass spectrometry (MS) based protein identification resulted in the isolation and identification of 25 AN3 interacting proteins that may function in the regulation of plant growth (Table 1 ). We isolated several proteins belonging to multiprotein complexes. Moreover, many interactors are completely uncharacterized. Reports on few of the AN3 interactors show that they are implicated in several developmental processes (Wagner & Meyerowitz, 2002; Meagher et al., 2005; Sarnowski et al., 2005; Hurtado et al., 2006; Kwon et al., 2006) but so far none of the identified genes have been associated with stimulation of plant growth.

Table 1 : Interactors of AN3 identified by TAP analysis on cell suspension cultures. TAP total gives the total number of time that an interactor was co-purified; C-GS and N-GS refers to whether a C or N terminal GS-tag was used in the experiment.

Several of the AN3p interactors were homologues of subunits of the SWI/SNF type chromatin remodeling complex (Thaete et al., 1999; Ishida et al., 2004). Recently, it was shown in mammalian cells that the SWI/SNF ATP-dependent chromatin remodeling complex plays an important role in cell differentiation and proliferation in mammalian cells (Riesman et al., 2009) Surprisingly we found that plant variants of subunits of the SWI/SNF complex, and their interactors play an important role in plant growth, and can be used to increase plant yield. A first aspect of the invention is an isolated protein complex, preferably an AN3p-free protein complex, comprising at least a plant variant of a SWI/SN F3 subunit, said subunit capable of interacting with AN3p, and one of more proteins interacting with said variant SWI/SNF3 subunit.

An AN3p-free protein complex, as used here, means that AN3p is not present in the complex as isolated; however, one or more subunits of the complex may be capable of interacting with AN3, and AN3 may be capable of interacting with the complex as a whole. I n a preferred embodiment, the complex according to the invention is not longer capable of interacting with AN3, whereby the protein interacting with the plant variant of the SWI/SNF3 subunit directly or indirectly inhibits binding of AN3p to said variant. Direct inhibition of AN3p binding may be caused by, as a non-limiting example, by binding to the same domain; indirect inhibition of AN3p binding may be caused, as a non-limiting example, by conformational changes in said variant upon binding with its interactor. Plant variants of SWI/SNF chromatin remodeling complex subunits are known to the person skilled in the art, and have been described, amongst others, by Jerzmanowski (2007), hereby incorporated by reference. Variants, as used here, are including, but not limited to homologues, orthologues and paralogues of said cell cycle related proteins. "Homologues" of a protein encompass peptides, oligopeptides, polypeptides, proteins and enzymes having amino acid substitutions, deletions and/or insertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived. Orthologues and paralogues encompass evolutionary concepts used to describe the ancestral relationships of genes. Paralogues are genes within the same species that have originated through duplication of an ancestral gene; orthologues are genes from different organisms that have originated through speciation, and are also derived from a common ancestral gene. . Preferably, said homologue, orthologue or paralogue has a sequence identity at protein level of at least 30%, preferably at least 40%, preferably 50%, 51 %, 52%, 53%, 54% or 55%, 56%, 57%, 58%, 59%, preferably 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, more preferably 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, even more preferably 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89% most preferably 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more as measured in a BLASTp (Altschul et al., 1997; Altschul et al., 2005). A plant as used here can be any plant. In one preferred embodiment, said plant is Arabidopsis thaliana. In another preferred embodiment, said plant is a crop plant, preferably a monocot or a cereal, even more preferably it is a cereal selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum and oats.

Preferably, said plant variant of the SWI/SNF chromatin remodelling complex is selected from the group consisting of proteins encoded by AT1 G18450 (ARP4), AT3G60830 (ARP7), AT5G14170 (Swp73B) and AT1 G21700 (SWI3C), or a variant thereof.

On preferred embodiment is an isolated protein complex, preferably an isolated AN3-protein free protein complex, comprising at least ARP4p or a variant thereof and a protein selected from the group encoded by AT5G45600, AT1 G76380, AT3G01890, AT5G26360, AT5G14240, AT1 G47128, AT2G27100, AT5G55040, AT3G03460 and AT1 G54390, or a variant thereof. Another preferred embodiment is an isolated protein complex, preferably an isolated AN3- protein free protein complex, comprising at least ARP7p or a variant thereof and a protein selected from the group encoded by AT3G20050, AT5G14240, AT4G22320, AT5G26360, AT3G02530, AT3G18190, AT3G03960, AT3G08580, AT4G14880 and AT1 G07820, or a variant thereof.

Another preferred embodiment is an isolated protein complex, preferably an isolated AN3- protein free protein complex, comprising at least Swp73Bp or a variant thereof and a protein selected from the group encoded by AT2G47620, AT2G33610, AT3G17590, AT4G34430, AT1 G32730, AT3G22990, AT1 G06500, AT1 G47128, AT3G18380, AT3G06010, AT1 G58025, AT5G03290, AT5G55040, AT3G50000, AT4G28520, AT5G44120 and AT4G22320, or a variant thereof. Still another preferred embodiment is an isolated protein complex, preferably an isolated AN3- protein free protein complex, comprising at least SWI3Cp and a protein selected from the group encoded by AT3G01890, AT1 G76380, AT3G03460, AT4G22320, AT1 G1 1840, AT4G 14880 and AT4G04740, or a variant thereof.

Another aspect of the invention is the use of a protein complex according to the invention to modulate plant growth and/or plant yield. Preferably, said modulation is an increase of plant growth and/or yield. Preferably, increase of growth is measured as an increase of biomass production. "Yield" refers to a situation where only a part of the plant, preferably an economical important part of the plant, such as the leaves, roots or seeds, is increased in biomass. The term "increase" as used here means least a 5%, 6%, 7%, 8%, 9% or 10%, preferably at least 15% or 20%, more preferably 25%, 30%, 35% or 40% more yield and/or growth in comparison to control plants as defined herein. Increase of plant growth, as used here, is preferably measured as increase of any one or more of total plant biomass, leaf biomass, root biomass and seed biomass. In one preferred embodiment, said increase is an increase in total plant biomass. In a preferred embodiment, said plant is a crop plant, preferably a monocot or a cereal, even more preferably it is a cereal selected from the group consisting of rice, maize, wheat, barley, millet, rye, sorghum and oats.

Still another aspect of the invention is a method to promote the formation of a protein complex according to the inventions, comprising the overexpression of at least one protein, preferably at least two proteins of said complex. Overexpression of a target gene can be obtained by transfer of a genetic construct, intended for said overexpression into a plant. The transfer of foreign genes into the genome of a plant is called transformation. Transformation of plant species is a fairly routine technique known to the person skilled in the art. Advantageously, any of several transformation methods may be used to introduce the gene of interest into a suitable ancestor cell. The methods described for the transformation and regeneration of plants from plant tissues or plant cells may be utilized for transient or for stable transformation. Transformation methods include, but are not limited to agrobacterium mediated transformation, the use of liposomes, electroporation, chemicals that increase free DNA uptake, injection of the DNA directly into the plant, particle gun bombardment, transformation using viruses or pollen and microprojection. Preferably, said overexpression results in an increase of plant growth and/or yield. Increase of plant growth and/or yield is measured by comparing the test plant, comprising a gene used according to the invention, with the parental, non-transformed plant, grown under the same conditions as control.

Still another aspect of the invention is a method to inhibit the formation of a protein complex according to the inventions, comprising the repression of the expression of at least one protein, preferably at least two proteins of said complex. I nhibition of complex formation can be desirable in cases where the complex exerts a growth limiting effect. Repression of expression of a target gene can be obtained by transfer of a genetic construct, intended for said repression of expression into a plant. Methods for repressing the expression in plants are known to the person skilled in the art and include, but are not limited to the use of RNAi, anti- sense RNA and gene silencing.

BRIEF DESCRIPTION OF THE FIGURES

Figure 1 : leaf phenotype of 2 SWIRM overexpressing lines. A) total rosette area. B) area of individual leaves. Plants were grown in vitro for 21 days. SWIRM is an alternative name for SWI3C.

EXAMPLES

Materials and methods to the examples

Vector construction forAN3 interactors

Construction of N- and C-terminal GS-tagged GFP and AN3 under the control of the 35S (CaMV) promoter was obtained by Multisite Gateway LR reactions. The coding regions, without (-) and with (+) stopcodon, were amplified by polymerase chain reaction (PCR) and cloned into the Gateway pDONR221 vector (Invitrogen) resulting in pEntryLI L2-GFP(-), pEntryLI L2-GFP(+), pEntryLI L2-AN3(-) and pEntryLI L2-AN3(+). The Pro_35S:GFP-GS- and P/O_35S.'/W3-GS-containing plant transformation vectors were obtained by Multisite Gateway LR reaction between pEntryL4R1 -Pro₃₅s, pEntryl_1 L2-GFP(-) or pEntryLI L2-AN3(-), and pEntryR2L3-GS and the destination vector pKCTAP, respectively (Van Leene et al., 2007). To obtain the Pro35S.GS-GFP and Pro35S.GS-/A/V3 vectors Multisite LR recombination between pEntryL4L3-Pro₃₅s and pEntryL1 L2-GFP(+) or pEntryL1 L2-AN3(+) with pKNGSTAP occurred. All entry and destination vectors were checked by sequence analysis. Expression vectors were transformed to Agrobacterium tumefaciens strain C58C1 Rif^R (pMP90) by electroporation. Transformed bacteria were selected on yeast extract broth plates containing 100 μg mL rifampicin, 40 μg mL gentamicin, and 100 μg mL spectinomycin.

Vector construction for ARP4, ARP7, Swp73B and SW13C interactors

Construction of N- and C-terminal GS-tagged ARP4, ARP7, Swp73B and SWI3C under the control of the 35S (CaMV) promoter was obtained by Multisite Gateway LR reactions. The coding regions, without (-) and with (+) stopcodon, were amplified by polymerase chain reaction (PCR) and cloned into the Gateway pDONR221 vector (Invitrogen) resulting in pEntryLI L2-ARP4(-), pEntryLI L2-ARP4(+), pEntryLI L2-ARP7(-), pEntryLI L2-ARP7(+), pEntryLI L2-Swp73B(-), pEntryLI L2-Swp73B(+), pEntryLI L2-SWI3C(-) a n d pEntryLI L2-SWI3C(+) . The Pro₃₅s:ARP4-GS-, Pro₃₅s:ARP7-GS-, Pro₃₅s:Swp73B-GS- and Prosss.'SI l/iSC-GS-containing plant transformation vectors were obtained by Multisite Gateway L R reacti on betwee n p E ntryL4 R 1 -Pro₃₅s, pEntryLI L2-ARP4(-), pEntryLI L2-ARP7(-), pEntryLI L2-Swp73B(-) or pEntryLI L2-SWI3C(-), and pEntryR2L3-GS and the destination vector pKCTAP, respectively (Van Leene et al., 2007). To obtain the Pro35S:GS-ARP4, Pro35S.GS- ARP7, Pro35S:GS-Swp73B and Pro35S:GS-SI l73C vectors Multisite LR recombination between pEntryL4L3-Pro₃₅s and pEntryLI L2-ARP4(+), pEntryLI L2-ARP7(+), pEntryLI L2-Swp73B(+) or pEntryLI L2-SWI3C(+) with pKNGSTAP occurred.

All entry and destination vectors were checked by sequence analysis. Expression vectors were transformed to Agrobacterium tumefaciens strain C58C1 Rif^R (pMP90) by electroporation. Transformed bacteria were selected on yeast extract broth plates containing 100 μg/mL rifampicin, 40 μg mL gentamicin, and 100 μg mL spectinomycin.

Cell suspension cultivation

Wild-type and transgenic Arabidopsis thaliana cell suspension PSB-D cultures were maintained in 50 mL MSMO medium (4.43 g/L MSMO, Sigma-Aldrich), 30 g/L sucrose, 0.5 mg/L NAA, 0.05 mg/L kinetin, pH 5.7 adjusted with 1 M KOH) at 25°C in the dark, by gentle agitation (130rpm). Every 7 days the cells were subcultured in fresh medium at a 1/10 dilution.

Cell culture transformation

The Arabidopsis culture was transformed by Agrobacterium co-cultivation as described previously (Van Leene et al., 2007). The Agrobacterium culture exponentially growing in YEB (OD₆oo between 1 .0 and 1 .5) was washed three times by centrifugation (10 min at 5000rpm) with an equal volume MSMO medium and resuspended in cell suspension growing medium until an OD₆oo of 1 .0. Two days after subcultivation, 3 mL suspension culture was incubated with 200 μ\- washed Agrobacteria and 200 μΜ acetoseringone, for 48 h in the dark at 25°C with gentle agitation (130rpm). Two days after co-cultivation, 7 mL MSMO containing a mix of three antibiotics (25 μg/mL kanamycin, 500 μg/mL carbenicellin, and 500 μg/mL vancomycin) was added to the cell cultures and grown further in suspension under standard conditions (25°C, 130rpm and continuous darkness). The stable transgenic cultures were selected by sequentional dilution in a 1 :5 and 1 : 10 ratio in 50 mL fresh MSMO medium containing the antibiotics mix, respectively at 1 1 , and 18 days post co-cultivation. After counter selecting the bacteria, the transgenic plant cells were further subcultured weekly in a 1 :5 ratio in 50 mL MSMO medium containing 25 μg/mL kanamycin for two more weeks. Thereafter the cells were weekly subcultured in fresh medium at a 1/10 dilution.

Expression analysis of cell suspension cultures

Transgene expression was analyzed in a total protein extract derived from exponentially growing cells, harvested two days after subculturing. Equal amounts of total protein were separated on 12% SDS-PAGE gels and blotted onto Immobilon-P membranes (Millipore, Bedford, MA). Protein gel blots were blocked in 3% skim milk in 20 mM Tris-HCI, pH 7.4, 150 mM NaCI, and 0.1 % Triton X-100. For detection of GS-tagged proteins, blots were incubated with human blood plasma followed by incubation with anti-human IgG coupled to horseradish peroxidase (HRP; GE-Healthcare). Protein gel blots were developed by Chemiluminiscent detection (Perkin Elmer, Norwalk, CT).

Protein extract preparation

Cell material (15 g) was grinded to homogeneity in liquid nitrogen. Crude protein extract were prepared in an equal volume (w/v) of extraction buffer (25 mM Tris-HCI, pH 7.6, 15 mM MgCI₂, 5 mM EGTA, 150 mM NaCI, 15 mM p-nitrophenylphosphate, 60 m M β-glycerophosphate, 0.1 % (v/v) Nonidet P-40 (NP-40), 0.1 mM sodium vanadate, 1 mM NaF, 1 mM DTT, 1 mM PMSF, 10 μg/mL leupeptin , 1 0 μg/mL aprotinin , 5 μg/mL antipain , 5 μg/mL chymostatin, 5 μg/mL pepstati n , 1 0 μg/m L soybean trypsi n i n h i bitor, 0. 1 m M benza m id i ne , 1 μΜ irans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane (E64), 5% (v/v) ethylene glycol) using an Ultra-Turrax T25 mixer (IKA Works, Wilmington, NC) at 4°C. The soluble protein fraction was obtained by a two-step centrifugation at 36900g for 20 min and at 178000g for 45 min, at 4°C. The extract was passed through a 0.45 μηη filter (Alltech, Deerfield, IL) and the protein content was determined with the Protein Assay kit (Bio-Rad, Hercules, CA). Tandem affinity purification

Purifications were performed as described by Burckstummer et al. (2006), with some modifications. Briefly, 200 mg total protein extract was incubated for 1 h at 4°C under gentle rotation with 100 μΙ_ IgG Sepharose 6 Fast Flow Flow beads (GE-Healthcare, Little Chalfont, UK), pre-equilibrated with 3 mL extraction buffer. The IgG Sepharose beads were transferred to a 1 mL Mobicol column (MoBiTec, Goettingen, Germany) and washed with 10 mL IgG wash buffer (10 mM Tris-HCI, pH 8.0, 150 mM NaCI, 0.1 % NP-40, 5% ethylene glycol) and 5 mL Tobacco {Nicotiana tabacum L.) Etch Virus (TEV) buffer (10 mM Tris-HCI, pH 8.0, 150 mM NaCI, 0.1 % (v/v) NP-40, 0.5 mM EDTA, 1 mM PMSF, 1 μΜ E64, 5% (v/v) ethylene glycol). Bound complexes were eluted via AcTEV digest (2x 100U, Invitrogen) for 1 h at 16°C. The IgG eluted fraction was incubated for 1 h at 4°C under gentle rotation with 100 μί Streptavidin resin (Stratagene, La Jolla, CA), pre-equilibrated with 3 mL TEV buffer. The Streptavidin beads were packed in a Mobicol column, and washed with 10 mL TEV buffer. Bound complexes were eluted with 1 mL streptavidin elution buffer (10 mM Tris-HCI, pH 8.0, 150 mM NaCI, 0.1 % (v/v) NP-40, 0.5 mM EDTA, 1 mM PMSF, 1 μΜ E64, 5% (v/v) ethylene glycol, 20mM Desthiobiotin), and precipitated using TCA (25%v/v). The protein pellet was washed twice with ice-cold aceton containing 50 mM HCI, redissolved in sample buffer and separated on 4-12% gradient NuPAGE gels (Invitrogen). Proteins were visualized with colloidal Coomassie brilliant blue staining.

Proteolysis and peptide isolation

After destaining, gel slabs were washed for 1 hour in H₂0, polypeptide disulfide bridges were reduced for 40 min in 25 mL of 6,66 mM DTT in 50 mM NH₄HC0₃ and sequentially the thiol groups were alkylated for 30 min in 25 mL 55 mM IAM in 50 mM NH₄HC0₃. After washing the gel slabs 3 times with water, complete lanes from the protein gels were cut into slices, collected in microtiter plates and treated essentially as described before with minor modifications (Van Leene et al., 2007). Per microtiterplate well, dehydrated gel particles were rehydrated in 20 μΙ_ digest buffer containing 250 ng trypsin (MS Gold; Promega, Madison, Wl), 50 mM NH₄HC0₃ and 10% CH₃CIM (v/v) for 30 min at 4°C. After adding 10 μΙ_ of a buffer containing 50 mM NH₄HC0₃ and 10% CH₃CN (v/v), proteins were digested at 37°C for 3 hours. The resulting peptides were concentrated and desalted with microcolumn solid phase tips (PerfectPureTM C18 tip, 200 nl_ bed volume; Eppendorf, Hamburg, Germany) and eluted directly onto a MALDI target plate (Opti- TOF™384 Well Insert; Applied Biosystems, Foster City, CA) using 1.2 μΙ_ of 50% CH₃CN: 0.1 % CF₃COOH solution saturated with a-cyano-4-hydroxycinnamic acid and spiked with 20 frmole/μΙ-. Glu1 -Fibrinopeptide B (Sigma-Aldrich), 20 ίη"ΐοΙβ/μΙ_ des-Pro2-Bradykinin (Sigma-Aldrich), and 20 fmole/μΙ- Adrenocorticotropic Hormone Fragment 18-39 human (Sigma-Aldrich).

Acquisition of mass spectra

A MALDI-tandem MS instrument (4800 Proteomics Analyzer; Applied Biosystems) was used to acquire peptide mass fingerprints and subsequent 1 kV CID fragmentation spectra of selected peptides. Peptide mass spectra and peptide sequence spectra were obtained using the settings essentially as presented in Van Leene et al. (2007). Each MALDI plate was calibrated according to the manufacturers' specifications. All peptide mass fingerprinting (PMF) spectra were internally calibrated with three internal standards at m/z 963.516 (des-Pro2-Bradykinin), m/z 1570.677 (Glu1 -Fibrinopeptide B), and m/z 2465,198 (Adrenocorticotropic Hormone Fragment 18-39) resulting in an average mass accuracy of 5 ppm ± 10 ppm for each analyzed peptide spot on the analyzed MALDI targets. Using the individual PMF spectra, up to sixteen peptides, exceeding a signal-to-noise ratio of 20 that passed through a mass exclusion filter were submitted to fragmentation analysis.

MS-based protein homology identification

PMF spectra and the peptide sequence spectra of each sample were processed using the accompanied software suite (GPS Explorer 3.6, Applied Biosystems) with parameter settings essentially as described in Van Leene et al. (2007). Data search files were generated and submitted for protein homology identification by using a local database search engine (Mascot 2.1 , Matrix Science). An in-house nonredundant Arabidopsis protein database called SNAPS Arabidopsis thaliana version 0.4 (SNAPS = Simple Nonredundant Assembly of Protein Sequences, 77488 sequence entries, 30468560 residues; available at http://www.ptools.ua.ac.be/snaps) was compiled from nine public databases. Protein homology identifications of the top hit (first rank) with a relative score exceeding 95% probability were retained. Additional positive identifications (second rank and more) were retained when the score exceeded the 98% probability threshold.

Example 1: Identification of AN3 interactors

In order to identify the interaction partners of AN3 in vivo, we performed tandem affinity (TAP) purifications on N- and C-terminal GS-fusions of AN3 ectopically expressed under control of the constitutive 35SCaMV promoter in transgenic Arabidopsis suspension cultures. Two independent TAP purifications were performed on extracts from AN3-GS and GS-AN3 lines, harvested two days after sub-culturing into fresh medium. The affinity purified proteins were separated on a 4-12% NuPAGE gel and stained with Coomassie Brilliant Blue. Protein bands were cut, in-gel digested with trypsin and subjected to MALDI-TOF/TOF mass spectrometry for protein identification. After subtracting background proteins, identified by the control purifications (Van Leene et al., 2007), from the obtained hit list we identified 25 AN3 interacting proteins, other than AN3 itself (Table 1 ). 9 proteins were identified only in one out of 8 TAP experiments.

Example 2: Identification of ARP4 interactors

ARP4 interactors were identified according to the methods described above. The results are summarized in Table 2. Apart from proteins, already identified in the AN3 complex (Table 1 ), several novel interactors were identified.

Table 2: Interactors of ARP4, identified by TAP analysis on cell suspension cultures. TAP total gives the total number of time that an interactor was co-purified; C-GS and N-GS refers to whether a C or N terminal GS-tag was used in the experiment.

Example 3: Identification of ARP7 interactors

ARP7 interactors were identified according to the methods described above. The results are summarized in Table 3. ARP4 and At5g55210 were also identified as AN3 interactors (Table 1 ). It is interesting to note that the ARP4 - ARP7 interaction is also identified using the ARP4 screening, confirming the reliability of the Tap-tag method. At5g55210 was also identified as AN3 as well as ARP4 interactor (Table 1 & 2).

Table 3: Interactors of ARP7, identified by TAP analysis on cell suspension cultures. TAP total gives the total number of time that an interactor was co-purified; C-GS and N-GS refers to whether a C or N terminal GS-tag was used in the experiment.

Example 4: identification of Swp73B interactors

Swp73B interactors were identified according to the methods described above. The results are summarized in Table 4. Except for SYD, all AN3 interacting proteins of the SWI/SNF complex are interacting with Swp73B. Apart from those proteins, most of the other proteins show only interaction with Swp73B and not with the other proteins of the SWI/SNF complex used in the tap tag experiments (ARP4, ARP7 and SWI3C)

Table 4: Interactors of Swp73B, identified by TAP analysis on cell suspension cultures. TAP total gives the total number of time that an interactor was co-purified; C-GS and N-GS refers to whether a C or N terminal GS-tag was used in the experiment.

Example 5: Identification of SWI3C interactors

SWI3C interactors were identified according to the methods described above. The results are summarized in Table 5. There is a strong similarity in interactors identified with ARP4 and with SWI3C; all AN3 interacting proteins that do interact with ARP4 are also interacting with SWI3C. The interaction between ARP4 and SWI3C is confirmed in both experiments.

Table 5: Interactors of SWI3C, identified by TAP analysis on cell suspension cultures. TAP total gives the total number of time that an interactor was copurified; C-GS and N-GS refers to whether a C or N terminal GS-tag was used in the experiment.

Example 6: overexpression studies of SWI3C

Several SWI3C overexpressing lines of Arabidopsis thaliana (Ecotype Columbia) were isolated and analyzed for growth characteristics. Amongst the 13 SWI3C overexpressing lines that were analyzed, 8 showed clearly development of bigger leaves; the bigger leaves are correlated with a higher expression of SWI3C. The detailed analysis of two SWI3C overexpressing lines is shown in figure 1 , demonstrating that in the overexpressing lines both the individual leaves as well as the total rosette area is larger than for the control.

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Claims

1 . An isolated AN3-protein free protein complex, comprising at least a plant variant of a SWI/SNF3 subunit, said variant capable of interacting with AN3p, and one or more of the proteins interacting with said variant SWI/SNF3 subunit.

2. The isolated AN3-protein free protein complex of claim 1 , whereby said SWI/SNF3 subunit is selected from the group consisting of proteins encoded by AT1 G18450 (ARP4), AT3G60830 (ARP7), AT5G14170 (Swp73B) and AT1 G21700 (SWI3C), or a variant thereof.

3. An isolated AN3-protein free protein complex, according to claim 2, comprising at least ARP4p and a protein selected from the group encoded by AT5G45600, AT1 G76380, AT3G01890, AT5G26360, AT5G14240, AT1 G47128, AT2G27100, AT5G55040, AT3G03460 and AT1 G54390, or a variant thereof.

4. An isolated AN3-protein free protein complex, according to claim 2, comprising at least ARP7p and a protein selected from the group encoded by AT3G20050, AT5G14240, AT4G22320, AT5G26360, AT3G02530, AT3G18190, AT3G03960, AT3G08580, AT4G14880 and AT1 G07820, or a variant thereof.

5. An isolated AN3-protein free protein complex, according to claim 2, comprising at least Swp73Bp and a protein selected from the group encoded by AT2G47620, AT2G33610, AT3G17590, AT4G34430, AT1 G32730, AT3G22990, AT1 G06500, AT1 G47128, AT3G18380, AT3G06010, AT1 G58025, AT5G03290, AT5G55040, AT3G50000, AT4G28520, AT5G44120 and AT4G22320, or a variant thereof.

6. An isolated AN3-protein free protein complex, according to claim 2, comprising at least SWI3Cp and a protein selected from the group encoded by AT3G01890, AT1 G76380, AT3G03460, AT4G22320, AT1 G1 1840, AT4G14880 and AT4G04740, or a variant thereof.

7. The use of a protein complex according to any of the preceding claims to modulate plant growth and/or plant yield.

8. The use of a protein complex according to claim 7, whereby said modulation of plant growth and/or plant yield, is an increase of plant growth and/or plant yield.

9. A method to promote the complex formation of a protein complex according to any of the claims 1 -6, said method comprising overexpression of at least one protein of the complex.

10. A method to inhibit complex formation of a protein complex according to any of the claims 1 -6, said method comprising downregulation of the expression of at least one protein of the complex.