A predicted protein interactome for rice

Rice - 2012
Chai Ling Ho1, Yingzhou Wu2, Hong‐Bin Shen3, Nicholas J. Provart2, Matt Geisler4
1Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM-Serdang, Selangor, Malaysia
2Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
3Department of Automation, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai, 200240, China
4Department of Plant Biology, Southern Illinois University Carbondale, 1125 Lincoln Ave., Life Science II, Carbondale, IL, 62901-6509, USA

Tóm tắt

Abstract Background Protein-protein interactions (PPIs) create the steps in signaling and regulatory networks central to most fundamental biological processes. It is possible to predict these interactions by making use of experimentally determined orthologous interactions in other species. Results In this study, prediction of PPIs in rice was carried out by the interolog method of mapping deduced orthologous genes to protein interactions supported by experimental evidence from reference organisms. We predicted 37112 interactions for 4567 rice proteins, including 1671 predicted self interactions (homo-interactions) and 35441 predicted interactions between different proteins (hetero-interactions). These matched 168 of 675 experimentally-determined interactions in rice. Interacting proteins were significantly more co-expressed than expected by chance, which is typical of experimentally-determined interactomes. The rice interacting proteins were divided topologically into 981 free ends (proteins with single interactions), 499 pipes (proteins with two interactions) and 3087 hubs of different sizes ranging from three to more than 100 interactions. Conclusions This predicted rice interactome extends known pathways and improves functional annotation of unknown rice proteins and networks in rice, and is easily explored with software tools presented here.

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Tài liệu tham khảo

Alon U: Network motifs: theory and experimental approaches. Nat Rev Genet 2007, 8: 450–461. 10.1038/nrg2102

Arabidopsis Interactome Mapping Consortium: Evidence for network evolution in an Arabidopsis interactome map. Science 2011, 333: 601–607.

Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H: The IntAct molecular interaction database in 2010. Nucleic Acids Res 2010, 38: D525-D531. 10.1093/nar/gkp878

Arora R, Agarwal P, Ray S, Singh A, Singh V, Tyagi A, Kapoor S: MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics 2007, 8: 242. 10.1186/1471-2164-8-242

Bader GD, Donaldson I, Wolting C, Ouellette BFF, Pawson T, Hogue CWV: BIND - The biomolecular interaction network database. Nucleic Acids Res 2001, 29: 242–245. 10.1093/nar/29.1.242

Arabidopsis Interactome Mapping C: Evidence for network evolution in an Arabidopsis interactome map. Science 2011, 333: 601–607.

Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bahler J, Wood V, Dolinski K, Tyers M: The BioGRID interaction database: 2008 update. Nucleic Acids Res 2008, 36: D637-D640.

Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G: MINT, the molecular interaction database. Nucleic Acids Res 2009, 38: D532-D539.

Chou KC, Shen HB: Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS One 2010, 5: e9931. 10.1371

Cler E, Papai G, Schultz P, Davidson I: Recent advances in understanding the structure and function of general transcription factor TFIID. Cell Mol Life Sci 2009, 66: 2123–2134. 10.1007/s00018-009-0009-3

Cooper B, Clarke JD, Budworth P, Kreps J, Hutchison D, Park S, Guimil S, Dunn M, Luginbuhl P, Ellero C, Goff SA, Glazebrook J: A network of rice genes associated with stress response and seed development. Proc Natl Acad Sci USA 2003, 100: 4945–4950. 10.1073/pnas.0737574100

Cooper B, Hutchison D, Park S, Guimil S, Luginbuhl P, Ellero C, Goff SA, Glazebrook J: Identification of rice (Oryza sativa) proteins linked to the cyclin-mediated regulation of the cell cycle. Plant Mol Biol 2003, 53: 273–279.

de Folter S, Immink RGH, Kieffer M, Parenicova L, Henz SR, Weigel D, Busscher M, Kooiker M, Colombo L, Kater MM, Davies B, Angenent GC: Comprehensive interaction map of the Arabidopsis MADS box transcription factors. Plant Cell 2005, 17: 1424–1433. 10.1105/tpc.105.031831

Ding XD, Richter T, Chen M, Fujii H, Seo YS, Xie MT, Zheng XW, Kanrar S, Stevenson RA, Dardick C, Li Y, Jiang H, Zhang Y, Yu FH, Bartley LE, Chern M, Bart R, Chen XH, Zhu LH, Farmerie WG, Gribskov M, Zhu JK, Fromm ME, Ronald PC, Song WY: A Rice kinase-protein interaction map. Plant Physiol 2009, 149: 1478–1492. 10.1104/pp.108.128298

Donoso I, Munoz-Centeno MC, Sanchez-Duran MA, Flores A, Daga RR, Guevara CM, Bejarano ER: Mpg1, a fission yeast protein required for proper septum structure, is involved in cell cycle progression through cell-size checkpoint. Mol Genet Genomics 2005, 274: 155–167. 10.1007/s00438-005-0005-8

Dortay H, Gruhn N, Pfeifer A, Schwerdtner M, Schmuälling T, Heyl A: Toward an Interaction Map of the two-component signaling pathway of Arabidopsis thaliana. J Proteome Res 2008, 7: 3649–3660. 10.1021/pr0703831

Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Graf S, Haider S, Hammond M, Howe K, Jenkinson A, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Koscielny G, Kulesha E, Lawson D, Longden I, Massingham T, McLaren W, Megy K, Overduin B, Pritchard B, Rios D, Ruffier M, Schuster M, Slater G, Smedley D, Spudich G, Tang YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJP, Parker A, Proctor G, Smith J, Searle SMJ: Ensembl's 10th year. Nucleic Acids Res 2010, 38: D557-D562. 10.1093/nar/gkp972

Gandhi TKB, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen BY, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A: Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 2006, 38: 285–293. 10.1038/ng1747

Geisler-Lee J, O'Toole N, Ammar R, Provart NJ, Millar AH, Geisler M: A predicted interactome for Arabidopsis. Plant Physiol 2007, 145: 317–329. 10.1104/pp.107.103465

Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM: A protein interaction map of Drosophila melanogaster. Science 2003, 302: 1727–1736. 10.1126/science.1090289

Goldberg AL, Rock KL: Proteolysis, proteasomes and antigen presentation. Nature 1992, 357: 375–379. 10.1038/357375a0

Gorynia S, Matias PM, Goncalves S, Coelho R, Lopes G, Thomaz M, Huber M, Haendler B, Donner P, Carrondo MA: Expression, purification, crystallization and preliminary X-ray analysis of the human RuvB-like protein RuvBL1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006, 62: 61–66. 10.1107/S1744309105041400

Gregis V, Sessa A, Colombo L, Kater MM: AGL24, SHORT VEGETATIVE PHASE, and APETALA1 redundantly control AGAMOUS during early stages of flower development in Arabidopsis. Plant Cell 2006, 18: 1373–1382. 10.1105/tpc.106.041798

Gu Y, Deng Z, Paredez AR, DeBolt S, Wang ZH, Somerville C: Prefoldin 6 is required for normal microtubule dynamics and organization in Arabidopsis. PNAS 2008,105(46):18064–18069. 10.1073/pnas.0808652105

Gu H, Zhu P, Jiao Y, Meng Y, Chen M: PRIN: a predicted rice interactome network. BMC Bioinformatics 2011, 12: 161. 10.1186/1471-2105-12-161

Hilt W, Wolf DH: Proteasomes: destruction as a programme. Trends Biochem Sci 1996, 21: 96–102.

Klopffleisch K, Phan N, Augustin K, Bayne RS, Booker KS, Botella JR, Carpita NC, Carr T, Chen J-G, Cooke TR, Frick-Cheng A, Friedman EJ, Fulk B, Hahn MG, Jiang K, Jorda L, Kruppe L, Liu C, Lorek J, McCann MC, Molina A, Moriyama EN, Mukhtar MS, Mudgil Y, Pattathil S, Schwarz J, Seta S, Tan M, Temp U, Trusov Y, Urano D, Welter B, Yang J, Panstruga R, Uhrig JF, Jones AM: Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Mol Syst Biol 2011,7(Article number):532.

Li SM, Armstrong CM, Bertin N, Ge H, Milstein S, Boxem M, Vidalain PO, Han JDJ, Chesneau A, Hao T, Goldberg DS, Li N, Martinez M, Rual JF, Lamesch P, Xu L, Tewari M, Wong SL, Zhang LV, Berriz GF, Jacotot L, Vaglio P, Reboul J, Hirozane-Kishikawa T, Li QR, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu HY, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, van den Heuvel S, Piano F, Vandenhaute J, Sardet C, Gerstein M, Doucette-Stamm L, Gunsalus KC, Harper JW, Cusick ME, Roth FP, Hill DE, Vidal M: A map of the interactome network of the metazoan C-elegans. Science 2004, 303: 540–543. 10.1126/science.1091403

Liu JX, Howell SH: bZIP28 and NF-Y Transcription factors are activated by ER stress and assemble into a transcriptional complex to regulate stress response genes in Arabidopsis. Plant Cell 2010, 22: 782–796. 10.1105/tpc.109.072173

Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD: Cytoscape Web: an interactive web-based network browser. Bioinformatics 2010,26(18):2347–2348. 10.1093/bioinformatics/btq430

Miller JP, Lo RS, Ben-Hur A, Desmarais C, Stagljar I, Noble WS, Fields S: Large-scale identification of yeast integral membrane protein interactions. Proc Natl Acad Sci USA 2005, 102: 12123–12128. 10.1073/pnas.0505482102

Narayanan M, Vetta A, Schadt EE, Zhu J: Simultaneous clustering of multiple gene expression and physical interaction datasets. PLoS Comput Biol 2010, 6: 4.

O'Brien KP, Remm M, Sonnhammer ELL: Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 2005, 33: D476-D480.

Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW, Ruepp A, Frishman D: The MIPS mammalian protein-protein interaction database. Bioinformatics 2005, 21: 832–834. 10.1093/bioinformatics/bti115

Pelaz S, Ditta GS, Baumann E, Wisman E, Yanofsky MF: B and C floral organ identity functions require SEPALLATA MADS-box genes. Nature 2000, 405: 200–203. 10.1038/35012103

Rivett AJ: Proteasomes - Multicatalytic Proteinase Complexes. Biochem J 1993, 291: 1–10.

Rounsley SD, Ditta GS, Yanofsky MF: Diverse roles for mads box genes in Arabidopsis development. Plant Cell 1995, 7: 1259–1269.

Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li SM, Albala JS, Lim JH, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M: Towards a proteome-scale map of the human protein-protein interaction network. Nature 2005, 437: 1173–1178. 10.1038/nature04209

Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D: The database of interacting proteins: 2004 update. Nucleic Acids Res 2004, 32: D449-D451. 10.1093/nar/gkh086

Springer PS, Holding DR, Groover A, Yordan C, Martienssen RA: The essential Mcm7 protein PROLIFERA is localized to the nucleus of dividing cells during the G(1) phase and is required maternally for early Arabidopsis development. Development 2000, 127: 1815–1822.

Sridhar VV, Surendrarao A, Liu ZC: APETALA1 and SEPALLATA3 interact with SEUSS to mediate transcription repression during flower development (vol 133, pg 3159, 2001). Development 2006, 133: 3496.

Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E: The Arabidopsis information resource (TAIR): gene structure and function annotation. Nucleic Acids Res 2008, 36: D1009-D1014.

Theissen G, Melzer R: Molecular mechanisms underlying origin and diversification of the angiosperm flower. Ann Bot 2007, 100: 603–619. 10.1093/aob/mcm143

Toufighi K, Brady SM, Austin R, Ly E, Provart NJ: The botany array resource: e-Northerns, expression angling, and promoter analyses. Plant J 2005, 43: 153–163. 10.1111/j.1365-313X.2005.02437.x

Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang MJ, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000, 403: 623–627. 10.1038/35001009

Wiles AM, Doderer M, Ruan JH, Gu TT, Ravi D, Blackman B, Bishop AJR: Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst Biol 2010, 4: 36. 10.1186/1752-0509-4-36

Wilk S: Proteasomes - multicatalytic proteinase complexes. Enzyme protein 1993, 47: 187–188.

Yung MH, Schaffer R, Putterill J: Identification of genes expressed during early Arabidopsis carpel development by mRNA differential display: characterisation of ATCEL2, a novel endo-1,4-beta-D-glucanase gene. Plant J 1999, 17: 203–208. 10.1046/j.1365-313X.1999.00359.x

Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G: MINT: a molecular interaction database. FEBS Lett 2002, 513: 135–140. 10.1016/S0014-5793(01)03293-8

Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U: Just-in-time transcription program in metabolic pathways. Nat Genet 2004, 36: 486–491. 10.1038/ng1348

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