US20110162110A1 - THE AN3 Protein Complex and its Use for Plant Growth Promotion - Google Patents

THE AN3 Protein Complex and its Use for Plant Growth Promotion Download PDF

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US20110162110A1
US20110162110A1 US13/060,911 US200913060911A US2011162110A1 US 20110162110 A1 US20110162110 A1 US 20110162110A1 US 200913060911 A US200913060911 A US 200913060911A US 2011162110 A1 US2011162110 A1 US 2011162110A1
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protein
proteins
complex
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protein complex
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Geert De Jaeger
Aurine Verkest
Dirk Inzé
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BASF Plant Science Co GmbH
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    • 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
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • 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
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • the present invention relates to an AN3-based protein complex. It relates further to the use of the complex to promote plant growth, and to a method for stimulating the complex formation, by overexpressing at least two members of the complex.
  • AN3 also known as GIF1
  • GRF growth regulating factor
  • 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 Bruijn et al., 1996).
  • 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
  • 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.
  • 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”.
  • a first aspect of the invention is an isolated AN3-based protein complex, comprising at least the proteins AN3p and one or more of the proteins selected from the group encoded by AT4G16143, AT1G09270, AT3G06720, AT5G53480, AT3G60830, AT1G18450, AT2G46020, AT2G28290, AT1G21700, AT5G14170, AT4G17330, AT4G27550, AT1G65980, AT5G55210, AT3G15000, AT4G35550, AT1G20670, AT1G08730, AT5G13030, AT2G 18876, AT5G17510, AT1G05370, AT4G21540, AT1G23900 and AT5G23690 (genes listed in Table II).
  • said AN3-based protein complex comprises at least the proteins AN3p and one or more proteins selected from the group consisting of ARP4 (AT1G18450), ARP7 (AT3G60830), SNF2 (AT2G46020), SYD (AT2G28290), SWI3C (AT1G21700) and SWP73B (AT5G14170).
  • said AN3-based protein complex comprises at least AN3p, an actin related protein selected from the group consisting of ARP4 and ARP7, an ATPase selected from the group consisting of SNF2 (BRM) and SYD and a SWIRM domain containing protein.
  • said SWIRM domain containing protein is SWI3C.
  • An AN3-based protein complex as used here means that AN3p is interacting, directly or indirectly, with the other proteins of the complex.
  • a direct interaction is an interaction where at least one domain of AN3p interacts with one or more domains or the interaction partner.
  • An indirect interaction is an interaction where AN3p itself is not interacting with the interacting protein by one of its domains, but where said interacting protein is interacting with a protein that is directly or indirectly interacting with AN3p.
  • a further aspect of the invention is the use of a protein complex according to the invention to promote plant growth.
  • said use is an overexpression of the protein complex, by overexpressing at least two members of the protein complex.
  • Promotion of plant growth is an increase in plant biomass in plants where the protein complex is used, compared with the same plant where the complex is not used, grown under the same conditions, except for the conditions needed for the use of the complex, if any.
  • Such conditions may be, as a non limited example, the addition of one or more compounds to induce one or more promoters of one or more genes encoding a protein of the complex.
  • the same plant is an untransformed parental plant, grown under the same conditions as the transformed plant, wherein the complex is used.
  • promotion of plant growth results in an increased yield. This yield can be a total increase in plant biomass, or a partial increase of yield, such as, but not limited to seed yield, leave yield or root yield.
  • Still another aspect of the invention is a method to promote AN3-based protein complex formation, by simultaneous overexpression of at least two proteins of the complex.
  • Proteins of the complex, beside AN3p itself, are listed in table II.
  • said overexpression is an overexpression of AN3p and one or more proteins selected from the group consisting of ARP4 (AT1G18450), ARP7 (AT3G60830), SNF2 (AT2G46020), SYD (AT2G28290), SWI3C (AT1G21700) and SWP73B (AT5G14170).
  • said overexpression is an overexpression of at least AN3p, an actin related protein selected from the group consisting of ARP4 and ARP7, an ATPase selected from the group consisting of SNF2 (BRM) and SYD and a SWIRM domain containing protein.
  • said SWIRM domain containing protein is SWI3C.
  • Methods for obtaining overexpression are known to the person skilled in the art, and comprise, but are not limited to placing the gene encoding the protein to be overexpressed after a strong promoter such as the Cauliflower Mosaic Virus 35S promoter.
  • Simultaneous overexpression as used here means that there is an overlap in timeframe for all the proteins to be overexpressed, whereby the level of said proteins is increased when compared to a non-overexpressed control. It does not necessarily mean that all genes should be induced at the same moment. Depending upon the turnover of the messenger RNA and/or the protein, one gene may be induced before or after another, as long as there is an overlap in time where both proteins are present in a concentration that is higher than the normal (non-overexpressed) concentration.
  • FIG. 1 Expression analysis of GS-tagged GFP and AN3 in transgenic cell suspension cultures.
  • the total protein extract of 2-day-old wild-type and N- and C-terminal GS-tagged GFP and AN3 overexpressing cultures (60 ⁇ g) was separated by 12% SDS-PAGE and immunoblotted.
  • blots were incubated with human blood plasma followed by incubation with anti-human IgG coupled to horseradish peroxidase.
  • Protein gel blots were developed by Chemiluminiscent detection.
  • the expected recombinant molecular masses for GS-tagged GFP and AN3 are 52.8 kDa and 43.5 kDa, respectively (indicated with a black dot).
  • FIG. 2 Analysis of the TAP protein eluates.
  • GS-tagged protein complexes were purified from transgenic plant cell suspension cultures, precipitated with TCA (25%, v/v), separated on 4-12% NuPAGE gels, and visualized with colloidal Coomassie G-250 staining. Bait proteins are indicated with a dot.
  • the Pro 35S :GFP-GS- and Pro 35S :AN3-GS-containing plant transformation vectors were obtained by Multisite Gateway LR reaction between pEntryL4R1-Pro 35S , pEntryL1L2-GFP( ⁇ ) or pEntryL1L2-AN3( ⁇ ), and pEntryR2L3-GS and the destination vector pKCTAP, respectively (Van Leene et al., 2007).
  • 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 ⁇ g/mL rifampicin, 40 ⁇ g/mL gentamicin, and 100 ⁇ g/mL spectinomycin.
  • 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 1M KOH) at 25° C. in the dark, by gentle agitation (130 rpm). Every 7 days the cells were subcultured in fresh medium at a 1/10 dilution.
  • the Arabidopsis culture was transformed by Agrobacterium co-cultivation as described previously (Van Leene et al., 2007).
  • the Agrobacterium culture exponentially growing in YEB (OD 600 between 1.0 and 1.5) was washed three times by centrifugation (10 min at 5000 rpm) with an equal volume MSMO medium and resuspended in cell suspension growing medium until an OD 600 of 1.0.
  • Two days after subcultivation, 3 mL suspension culture was incubated with 200 ⁇ L washed Agrobacteria and 200 ⁇ M acetoseringone, for 48 h in the dark at 25° C. with gentle agitation (130 rpm).
  • the transgenic plant cells were further subcultured weekly in a 1:5 ratio in 50 mL MSMO medium containing 25 ⁇ g/mL kanamycin for two more weeks. Thereafter the cells were weekly subcultured in fresh medium at a 1/10 dilution.
  • 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, Mass.). Protein gel blots were blocked in 3% skim milk in 20 mM Tris-HCl, pH 7.4, 150 mM NaCl, 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, Conn.).
  • the soluble protein fraction was obtained by a two-step centrifugation at 36900 g for 20 min and at 178000 g for 45 min, at 4° C.
  • the extract was passed through a 0.45 ⁇ m filter (Alltech, Deerfield, Ill.) and the protein content was determined with the Protein Assay kit (Bio-Rad, Hercules, Calif.).
  • 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-HCl, pH 8.0, 150 mM NaCl, 0.1% NP-40, 5% ethylene glycol) and 5 mL Tobacco ( Nicotiana tabacum L.) Etch Virus (TEV) buffer (10 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% (v/v) NP-40, 0.5 mM EDTA, 1 mM PMSF, 1 ⁇ M E64, 5% (v/v) ethylene glycol).
  • IgG wash buffer 10 mM Tris-HCl, pH 8.0, 150 mM NaCl, 0.1% NP-40, 5% ethylene glycol
  • TMV Etch Virus
  • Bound complexes were eluted via AcTEV digest (2 ⁇ 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 ⁇ L Streptavidin resin (Stratagene, La Jolla, Calif.), 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-HCl, pH 8.0, 150 mM NaCl, 0.1% (v/v) NP-40, 0.5 mM EDTA, 1 mM PMSF, 1 ⁇ M E64, 5% (v/v) ethylene glycol, 20 mM Desthiobiotin), and precipitated using TCA (25% v/v).
  • the protein pellet was washed twice with ice-cold aceton containing 50 mM HCl, redissolved in sample buffer and separated on 4-12% gradient NuPAGE gels (Invitrogen). Proteins were visualized with colloidal Coomassie brilliant blue staining.
  • dehydrated gel particles were rehydrated in 20 ⁇ L digest buffer containing 250 ng trypsin (MS Gold; Promega, Madison, Wis.), 50 mM NH 4 HCO 3 and 10% CH 3 CN (v/v) for 30 min at 4° C. After adding 10 ⁇ L of a buffer containing 50 mM NH 4 HCO 3 and 10% CH 3 CN (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-TOFTM 384 Well Insert; Applied Biosystems, Foster City, Calif.) using 1.2 ⁇ L of 50% CH 3 CN: 0.1% CF 3 COOH solution saturated with ⁇ -cyano-4-hydroxycinnamic acid and spiked with 20 fmole/ ⁇ L Glu1-Fibrinopeptide B (Sigma-Aldrich), 20 fmole/ ⁇ L des-Pro2-Bradykinin (Sigma-Aldrich), and 20 fmole/ ⁇ L Adrenocorticotropic Hormone Fragment 18-39 human (Sigma-Aldrich).
  • 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.
  • PMF peptide mass fingerprinting
  • TAP tandem affinity
  • Protein bands were cut, in-gel digested with trypsin and subjected to MALDI-TOF/TOF mass spectrometry for protein identification. After substracting background proteins, identified by the control purifications described in example 2 and in other analyses (GUS and cytosolic GFP, Van Leene et al., 2007), from the obtained hit list we identified 25 AN3 interacting proteins (Table 2). These can be divided into two groups: 14 proteins were confirmed experimentally and 11 proteins were identified only in one out of four TAP experiments.
  • AN3 interactors six proteins act as subunits of macromolecular machines that remodel chromatin structure.
  • a database survey (ChromDB, Gendler et al., 2008) illustrates that all of them belong to the SWI/SNF ATPase family.
  • SWI/SNF chromatin remodeling ATPases are conserved in the animal and the plant kingdom and regulate transcriptional programs in response to endogenous and exogenous cues. This suggests that the transcriptional activity of AN3 is regulated through chromatin remodeling.
  • Mutants of the accessory components ARP4 and ARP7 display pleiotropic defects with less resemblance to the syd, brm and swi3c phenotypes (Meagher et al., 2005). Down-regulation of ARP4 resulted in phenotypes including altered organization of plant organs, early flowering, delayed flower senescence and partial sterility (Kandasamy et al., 2005a). ARP7 knockdown results in dwarfed plants with small rosette leaves, highly retarded root growth, altered flower development and reduced fertility (Kandasamy et al., 2005b). Finally, RNAi-mediated silencing of the accessory SWI/SNF complex component SWP73B (At5g14170) resulted in dwarfed plants with shorter roots (Crane & Gelvin, 2007).
  • At4g16143, At1g09270, At3g06720 and At5g53480 are involved in nucleocytoplasmic trafficking which identifies AN3 as one of the targets of plant nuclear transporters. Indeed a precise cellular localization is essential for protein function and nuclear localization is a key to the function of transcription factors.
  • nucleocytoplasmic trafficking plays a critical role in various biological processes (Meier, 2007; Xu & Meier, 2008) and nuclear transporters have been shown to be involved in regulating different signal transduction pathways during plant development (Bollman et al., 2003) and in plant responses to biotic (Palma et al., 2005) and abiotic stresses (Verslues et al., 2006).
  • TPS4 trehalose phosphatase/synthase 4
  • the other identified interactors indicate links of AN3 function in multiple processes.
  • sphingosine kinases in plant cell signaling (Coursol et al., 2003; Coursol et al., 2005; Worral et al., 2008), whereas reports on myosin homologues (Peremyslov et al., 2008; Jiang et al., 2007) implicate roles of protein and organelle trafficking in plant development.
  • the connections between these genes, the other identified interactors and AN3 will be interesting to study in the future.

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CN102257142A (zh) 2008-08-29 2011-11-23 巴斯夫植物科学有限公司 具有增强的产量相关性状的植物及其制备方法
MA33933B1 (fr) 2010-01-22 2013-01-02 Bayer Ip Gmbh Combinaisons de principes actifs acaricides et/ou insecticides
WO2011104155A2 (fr) * 2010-02-24 2011-09-01 Basf Plant Science Company Gmbh Plantes présentant des traits relatifs au rendement améliorés et leur procédé de fabrication
WO2011104128A2 (fr) * 2010-02-24 2011-09-01 Basf Plant Science Company Gmbh Plantes présentant des traits relatifs au rendement améliorés et leur procédé de fabrication
WO2012153267A1 (fr) * 2011-05-09 2012-11-15 Basf Plant Science Company Gmbh Plantes ayant des caractères améliorés liés au rendement et leur procédé de fabrication
KR20140053973A (ko) 2011-06-23 2014-05-08 방글라데시 주트 리서치 인스티튜트 황마에서 질환 저항성을 부여하는 효소들을 인코딩하는 핵산 분자들
AU2012293636B2 (en) 2011-08-10 2015-12-03 Bayer Intellectual Property Gmbh Active compound combinations comprising specific tetramic acid derivatives
US9650646B2 (en) 2013-01-11 2017-05-16 University Of Florida Research Foundation, Inc. Materials and methods to increase plant growth and yield
WO2014110431A1 (fr) * 2013-01-11 2014-07-17 University Of Florida Research Foundation, Inc. Matériel et méthodes pour améliorer la croissance et le rendement de plante
CN109089579B (zh) * 2018-07-06 2021-04-06 中国农业大学 一种用于砧穗互作研究的黄瓜下胚轴嫁接方法

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US8575421B2 (en) 2007-12-20 2013-11-05 Basf Plant Science Gmbh Plants having enhanced yield-related traits and a method for making the same
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CA2734964A1 (fr) 2010-03-04
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EP2321416A2 (fr) 2011-05-18
BRPI0917114A2 (pt) 2015-07-28
EP2321415A2 (fr) 2011-05-18
CN102257142A (zh) 2011-11-23
CN102137934A (zh) 2011-07-27
WO2010023310A2 (fr) 2010-03-04
CA2734812A1 (fr) 2010-03-04
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WO2010023310A3 (fr) 2010-05-06
WO2010023320A3 (fr) 2010-05-20
AU2009286617A1 (en) 2010-03-04
MX2011002022A (es) 2011-05-23
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US8946512B2 (en) 2015-02-03
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