Skip to main content

Prediction of protein–protein interactions between Ralstonia solanacearum and Arabidopsis thaliana

Amino Acids volume 42, pages 2363–2371 (2012)Cite this article

Abstract

Ralstonia solanacearum is a devastating bacterial pathogen that has an unusually wide host range. R. solanacearum, together with Arabidopsis thaliana, has become a model system for studying the molecular basis of plant–pathogen interactions. Protein–protein interactions (PPIs) play a critical role in the infection process, and some PPIs can initiate a plant defense response. However, experimental investigations have rarely addressed such PPIs. Using two computational methods, the interolog and the domain-based methods, we predicted 3,074 potential PPIs between 119 R. solanacearum and 1,442 A. thaliana proteins. Interestingly, we found that the potential pathogen-targeted proteins are more important in the A. thaliana PPI network. To facilitate further studies, all predicted PPI data were compiled into a database server called PPIRA (http://protein.cau.edu.cn/ppira/). We hope that our work will provide new insights for future research addressing the pathogenesis of R. solanacearum.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

43,34 €

Price includes VAT (Finland)
Tax calculation will be finalised during checkout.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  • Adamcsek B, Palla G, Farkas IJ, Derenyi I, Vicsek T (2006) Cfinder: locating cliques and overlapping modules in biological networks. Bioinformatics 22(8):1021–1023

    PubMed  Article  CAS  Google Scholar 

  • Assenov Y, Ramirez F, Schelhorn SE, Lengauer T, Albrecht M (2008) Computing topological parameters of biological networks. Bioinformatics 24(2):282–284

    PubMed  Article  CAS  Google Scholar 

  • Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL (2000) The pfam protein families database. Nucleic Acids Res 28(1):263–266

    PubMed  Article  CAS  Google Scholar 

  • Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: Signalp 3.0. J Mol Biol 340(4):783–795

    PubMed  Article  Google Scholar 

  • Bishop JG, Dean AM, Mitchell-Olds T (2000) Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. Proc Natl Acad Sci USA 97(10):5322–5327

    PubMed  Article  CAS  Google Scholar 

  • Bogdanove AJ (2002) Protein-protein interactions in pathogen recognition by plants. Plant Mol Biol 50(6):981–989

    PubMed  Article  CAS  Google Scholar 

  • Boudsocq M, Willmann MR, McCormack M, Lee H, Shan L, He P, Bush J, Cheng SH, Sheen J (2010) Differential innate immune signalling via ca(2+) sensor protein kinases. Nature 464(7287):418–422

    PubMed  Article  CAS  Google Scholar 

  • Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Shi T (2008) Atpid: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology. Nucleic Acids Res 36(Database issue):D999–D1008

    PubMed  CAS  Google Scholar 

  • Derenyi I, Palla G, Vicsek T (2005) Clique percolation in random networks. Phys Rev Lett 94(16):160202

    PubMed  Article  Google Scholar 

  • Du L, Ali GS, Simons KA, Hou J, Yang T, Reddy AS, Poovaiah BW (2009) Ca(2+)/calmodulin regulates salicylic-acid-mediated plant immunity. Nature 457(7233):1154–1158

    PubMed  Article  CAS  Google Scholar 

  • Florez AF, Park D, Bhak J, Kim BC, Kuchinsky A, Morris JH, Espinosa J, Muskus C (2010) Protein network prediction and topological analysis in leishmania major as a tool for drug target selection. BMC Bioinform 11:484

    Article  Google Scholar 

  • Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the blast2go suite. Nucleic Acids Res 36(10):3420–3435

    PubMed  Article  CAS  Google Scholar 

  • Hayward AC (1991) Biology and epidemiology of bacterial wilt caused by Pseudomonas solanacearum. Annu Rev Phytopathol 29:65–87

    PubMed  Article  CAS  Google Scholar 

  • He F, Zhang Y, Chen H, Zhang Z, Peng YL (2008) The prediction of protein–protein interaction networks in rice blast fungus. BMC Genomics 9:519

    PubMed  Article  Google Scholar 

  • Iwakawa H, Shinmyo A, Sekine M (2006) Arabidopsis cdka;1, a cdc2 homologue, controls proliferation of generative cells in male gametogenesis. Plant J 45(5):819–831

    PubMed  Article  CAS  Google Scholar 

  • Jonsson PF, Bates PA (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22(18):2291–2297

    PubMed  Article  CAS  Google Scholar 

  • Jonsson PF, Cavanna T, Zicha D, Bates PA (2006) Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. BMC Bioinform 7:2

    Article  Google Scholar 

  • Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H (2007) Intact—open source resource for molecular interaction data. Nucleic Acids Res 35(Database issue):D561–D565

    PubMed  Article  CAS  Google Scholar 

  • Kim JG, Park D, Kim BC, Cho SW, Kim YT, Park YJ, Cho HJ, Park H, Kim KB, Yoon KO, Park SJ, Lee BM, Bhak J (2008) Predicting the interactome of Xanthomonas oryzae pathovar oryzae for target selection and db service. BMC Bioinform 9:41

    Article  Google Scholar 

  • Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J Mol Biol 305(3):567–580

    PubMed  Article  CAS  Google Scholar 

  • Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M (2001) Identification of potential interaction networks using sequence-based searches for conserved protein–protein interactions or “interologs”. Genome Res 11(12):2120–2126

    PubMed  Article  CAS  Google Scholar 

  • Moller S, Croning MD, Apweiler R (2001) Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17(7):646–653

    PubMed  Article  CAS  Google Scholar 

  • Ng SK, Zhang Z, Tan SH (2003) Integrative approach for computationally inferring protein domain interactions. Bioinformatics 19(8):923–929

    PubMed  Article  CAS  Google Scholar 

  • Niebel A, de Almeida Engler J, Hemerly A, Ferreira P, Inze D, Van Montagu M, Gheysen G (1996) Induction of cdc2a and cyc1at expression in Arabidopsis thaliana during early phases of nematode-induced feeding cell formation. Plant J 10(6):1037–1043

    PubMed  Article  CAS  Google Scholar 

  • Ogmen U, Keskin O, Aytuna AS, Nussinov R, Gursoy A (2005) Prism: protein interactions by structural matching. Nucleic Acids Res 33(Web Server issue):W331–W336

    PubMed  Article  CAS  Google Scholar 

  • Palla G, Derenyi I, Farkas I, Vicsek T (2005) Uncovering the overlapping community structure of complex networks in nature and society. Nature 435(7043):814–818

    PubMed  Article  CAS  Google Scholar 

  • Pinzon A, Rodriguez RL, Gonzalez A, Bernal A, Restrepo S (2011) Targeted metabolic reconstruction: a novel approach for the characterization of plant-pathogen interactions. Brief Bioinform 12(2):151–162

    Google Scholar 

  • Rhodes DR, Tomlins SA, Varambally S, Mahavisno V, Barrette T, Kalyana-Sundaram S, Ghosh D, Pandey A, Chinnaiyan AM (2005) Probabilistic model of the human protein–protein interaction network. Nat Biotechnol 23(8):951–959

    PubMed  Article  CAS  Google Scholar 

  • Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, Billault A, Brottier P, Camus JC, Cattolico L, Chandler M, Choisne N, Claudel-Renard C, Cunnac S, Demange N, Gaspin C, Lavie M, Moisan A, Robert C, Saurin W, Schiex T, Siguier P, Thebault P, Whalen M, Wincker P, Levy M, Weissenbach J, Boucher CA (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415(6871):497–502

    PubMed  Article  CAS  Google Scholar 

  • Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res 32(Database issue):D449–D451

    PubMed  Article  CAS  Google Scholar 

  • Shoemaker BA, Panchenko AR (2007) Deciphering protein–protein interactions. Part ii. Computational methods to predict protein and domain interaction partners. PLoS Comput Biol 3(4):e43

    PubMed  Article  Google Scholar 

  • Sonnhammer EL, von Heijne G, Krogh A (1998) A hidden markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6:175–182

    PubMed  CAS  Google Scholar 

  • Spok A, Stubenrauch G, Schorgendorfer K, Schwab H (1991) Molecular cloning and sequencing of a pectinesterase gene from Pseudomonas solanacearum. J Gen Microbiol 137(1):131–140

    PubMed  CAS  Google Scholar 

  • Stahl EA, Bishop JG (2000) Plant–pathogen arms races at the molecular level. Curr Opin Plant Biol 3(4):299–304

    PubMed  Article  CAS  Google Scholar 

  • Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) Biogrid: a general repository for interaction datasets. Nucleic Acids Res 34(Database issue):D535–D539

    PubMed  Article  CAS  Google Scholar 

  • Stéphane G, Christian B (2002) Ralstonia solanacearum: secrets of a major pathogen unveiled by analysis of its genome. Mol Plant Pathol 3(3):111–118

    Article  Google Scholar 

  • Storey JD (2002) A direct approach to false discovery rates. J Royal Stat Soc: Series B (Stat Methodol) 64(3):479–498

    Article  Google Scholar 

  • 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 (2008) The arabidopsis information resource (tair): gene structure and function annotation. Nucleic Acids Res 36(Database issue):D1009–D1014

    PubMed  CAS  Google Scholar 

  • Wu X, Zhu L, Guo J, Zhang DY, Lin K (2006) Prediction of yeast protein–protein interaction network: insights from the gene ontology and annotations. Nucleic Acids Res 34(7):2137–2150

    PubMed  Article  CAS  Google Scholar 

  • Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M (2004) Annotation transfer between genomes: protein–protein interologs and protein-DNA regulogs. Genome Res 14(6):1107–1118

    PubMed  Article  CAS  Google Scholar 

  • Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M (2007) The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3(4):e59

    PubMed  Article  Google Scholar 

Download references

Acknowledgments

We thank Ting-You Wang and Yuan Zhou at the bioinformatics center of China Agricultural University for helpful discussions. This research was supported by grants from the National Natural Science Foundation (30830058, 31070259 and J0730639) and the State Key Laboratory of Agrobiotechnology (2010SKLAB05-11).

Author information

Affiliations

  1. State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China

    Zhi-Gang Li, Fei He, Ziding Zhang & You-Liang Peng

  2. Department of Plant Pathology, China Agricultural University, Beijing, 100193, China

    Zhi-Gang Li & You-Liang Peng

  3. Bioinformatics Center, College of Biological Sciences, China Agricultural University, Beijing, 100193, China

    Fei He & Ziding Zhang

Authors
  1. Zhi-Gang Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fei He
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ziding Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. You-Liang Peng
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ziding Zhang.

Additional information

Z.-G. Li and F. He contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplemental File 1. This file contains two tables showing GO enrichment of the R. solanacearum and A. thaliana proteins in the predicted PPIs.

Supplemental File 2. This file contains 22 pathogen-targeted clusters in the A. thaliana PPI network.

Supplementary material 1 (DOC 142 kb)

Supplementary material 2 (DOC 229 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Li, ZG., He, F., Zhang, Z. et al. Prediction of protein–protein interactions between Ralstonia solanacearum and Arabidopsis thaliana . Amino Acids 42, 2363–2371 (2012). https://doi.org/10.1007/s00726-011-0978-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00726-011-0978-z

Keywords

  • Bioinformatics
  • Pathogenicity
  • Plant–pathogen interactions
  • Prediction
  • Protein–protein interaction