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Comparative genomic analysis of wide and narrow host range strains of Xanthomonas citri subsp. citri, showing differences in the genetic content of their pathogenicity and virulence factors

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Abstract

The causal agent of Asiatic citrus bacterial canker, Xanthomonas citri subsp. citri (Xcc), has three pathotypes: A, A* and Aw. A*-type strains have a restricted host range to Mexican lime and are classified into four subgroups, among which strains isolated from the Sistan-Baluchistan province in Iran have not been defined and reported anywhere else in the world. For comparative analysis, we determined the genome sequence of strain NIGEB-386 from this new A* subgroup. We also select complete genome sequences of XccA306 (type A strain), Xcaw12879 (type Aw strain) and draft genome sequences of two A* strains, XccA* LG115 (isolated from India) and XccA* JS581 (Iranian strain from other subgroups), from GenBank sequence databases. Approximately 98% of coding DNA sequences (CDSs) are shared by the three pathotype genomes and there are about 2% unique CDSs for each pathotype. XccA* NIGEB-386 and XccA* JS581 contain 28 putative Type III secretion system effectors; Xcaw12879 and XccA* LG115 contain 29; and XccA306 contains 27. Despite previous data on the presence of the AvrGf1 effector and its contribution to the host range limitation in Xcaw12879, the only effector gene is in XccA* LG115 and was not detected in two narrow host range Iranian strains. Additionally, the Lipopolysaccharide gene cluster of XccA* NIGEB-386 showed a high similarity to other host-limited strains, and significant differences with the broad host range strain, XccA306. Generally, Iranian A* strains show a close relationship together, while XccA* LG115 shares a close relationship with Xcaw12879.

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References

  • Alizadeh A, Rahimian H (1990) Citrus canker in Kerman province. Iran J Plant Pathol 26:42

    Google Scholar 

  • Al-Saadi A, Reddy JD, Duan YP, Brunings AM, Yuan Q, Gabriel DW (2007) All five host-range variants of Xanthomonas citri carry one pthA homolog with 17.5 repeats that determines pathogenicity on citrus, but none determine host-range variation. Mol Plant-Microbe Interact 20:934–943

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Alvarez-Martinez CE, Christie PJ (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73:775–808

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Astua-Monge G, Minsavage GV, Stall RE, Davis MJ, Bonas U, Jones JB (2000) Resistance of tomato and pepper to T3 strains of Xanthomonas campestris pv. vesicatoria is specified by a plant-inducible avirulence gene. Mol Plant-Microbe Interact 13:911–921

    Article  CAS  PubMed  Google Scholar 

  • Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712. doi:10.1126/science.1138140

    Article  CAS  PubMed  Google Scholar 

  • Boch J, Bonas U (2010) Xanthomonas AvrBs3 type family-type III effectors: discovery and function. Phytopathology 48:419–436

    Article  CAS  Google Scholar 

  • Buttner D, Bonas U (2010) Regulation and secretion of Xanthomonas virulence factors. FEMS Microbiol Rev 34:107–133

    Article  PubMed  Google Scholar 

  • Conrath U, Thulke O, Katz V, Schwindling S, Kohler A (2001) Priming as a mechanism in induced systemic resistance of plants. Eur J Plant Pathol 107:113–119

    Article  CAS  Google Scholar 

  • Cornelis GR, Van Gijsegem F (2000) Assembly and function of type III secretory systems. Annu Rev Microbiol 54:735–774

    Article  CAS  PubMed  Google Scholar 

  • Cubero J, Graham JH (2002) Genetic relationship among worldwide strains of Xanthomonas causing canker in citrus species and design of new primers for their identification by PCR. Appl Environ Microbiol 68:1257–1264

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Darling AE, Mau B, Perna NT (2010) Progressive mauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5(6):e11147. doi:10.1371/journal.pone.0011147

    Article  PubMed  PubMed Central  Google Scholar 

  • Donlan RM (2002) Biofilms: microbial life on surfaces. Emerging Infect Dis 8:881–890

    Article  PubMed  PubMed Central  Google Scholar 

  • Escalon A, Javegny S, Vernière C, Noël LD, Vital K, Poussier S, Hajri A, Boureau T, Pruvost O, Arlat M, Gagnevin L (2013) Variations in type III effector repertoires, pathological phenotypes and host range of Xanthomonas citri pv. citri pathotypes. Mol Plant Pathol 14(5):483–496. doi:10.1111/mpp.12019

    Article  CAS  PubMed  Google Scholar 

  • Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer ELL, Tate J, Punta M (2014) The Pfam protein families database. Nucleic Acids Res Database Issue 42:D222–D230

    Article  CAS  Google Scholar 

  • Flemming HC, Wingender J (2001) Relevance of microbial extracellular polymeric substances (EPSs) part I: structural and ecological aspects. Water Sci Technol 43:1–8

    CAS  PubMed  Google Scholar 

  • Frank AC, Lobry JR (2000) Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes. Bioinformatics 16:560–561

    Article  CAS  PubMed  Google Scholar 

  • Furutani A, Takaoka M, Sanada H, Noguchi Y, Oku T, Tsuno K, Ochiai H, Tsuge S (2009) Identification of novel type III secretion effectors in Xanthomonas oryzae pv. oryzae. Mol Plant-Microbe Interact 22:96–106

    Article  CAS  PubMed  Google Scholar 

  • Gao F, Zhang CT (2006) GC-profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Res 34:W686–W691

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O (2015) Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges. BMC Genomics 16:1098. doi:10.1186/s12864-015-2310-x

  • Gottwald TR, Graham JH, Schubert TS (2002) Citrus canker: the pathogen and its impact. Plant Health Progress. doi:10.1094/PHP-2002-0812-01-RV

    Google Scholar 

  • Graham JH, Hartung JS, Stall RE, Chase AR (1990) Pathological, restriction-fragment length polymorphism, and fatty acid profile relationships between Xanthomonas campestris from citrus and noncitrus hosts. Phytopathology 80:829–836

    Article  CAS  Google Scholar 

  • Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucl Acids Res 35:W52–W57. doi:10.1093/nar/gkm360

    Article  PubMed  PubMed Central  Google Scholar 

  • Guidot A, Prior P, Schoenfeld J, Carrère S, Genin S, Boucher C (2007) Genomic structure and phylogeny of the plant pathogen Ralstonia solanacearum inferred from gene distribution analysis. J Bacteriol 189:377–387

    Article  CAS  PubMed  Google Scholar 

  • He SY, Nomura K, Whittam TS (2004) Type III protein secretion mechanism in mammalian and plant pathogens. Biochim Biophys Acta 1694(1–3):181–206

    Article  CAS  PubMed  Google Scholar 

  • Jacob TR, de Laia ML, Moreira LM, Gonçalves JF, de Carvalho FMS, Ferro MIT, Ferro JA (2014) Type IV secretion system is not involved in infection process in citrus. Int J Microbiol. doi:10.1155/2014/763575

    PubMed  PubMed Central  Google Scholar 

  • Jalan N, Aritua V, Kumar D, Yu F, Jones JB, Graham JH, Setubal JC, Wang N (2011) Comparative genomic analysis of Xanthomonas axonopodis pv. Citrumelo F1, which causes citrus bacterial spot disease and related strains provides insights into virulence and host specificity. J Bacteriol 193:6342–6357

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jalan N, Kumar D, Andrade MO, Yu F, Jones JB, Graham JH, White FF, Setubal JC, Wang N (2013) Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range. BMC Genomics 14:551

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang Y (2007) The rice XA21-binding protein 25 is an ankyrin repeat-containing protein and required for XA21-mediated disease resistance. University of Florida: Department of Plant Pathology. PhD thesis

  • Kearney B, Staskawicz BJ (1990) Widespread distribution and fitness contribution of Xanthomonas campestris avirulence gene avrBs2. Nature 346:385–386

    Article  CAS  PubMed  Google Scholar 

  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Mentjies P, Drummond A (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647–1649

    Article  PubMed  PubMed Central  Google Scholar 

  • Khodakaramian G, Swings J (2011) Genetic diversity and pathogenicity of Xanthomonas axonopodis strains inducing citrus canker disease in Iran and South Korea. Indian J Microbiol 51:194–199. doi:10.1007/s12088-011-0103-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khodakaramian G, Rahimian H, Mohamadi M, Allameh A (1999) Phenotypic characteristics, host range and distribution of the strains of Xanthomonas axonopodis inducing citrus canker in southern Iran. Iran J Plant Pathol 35:40–43

    Google Scholar 

  • Kim JG, Li X, Roden JA, Taylor KW, Aakre CD, Su B, Lalonde S, Kirik A, Chen Y, Baranage G, McLanr H, Martin GB, Mudgett MB (2009) Xanthomonas T3S effector XopN suppresses PAMP-triggered immunity and interacts with a tomato atypical receptor-like kinase and TFT1. Plant Cell 21:1305–1323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kingsley M, Gabriel D, Marlow G, Roberts P (1993) The opsX locus of Xanthomonas campestris affects host range and biosynthesis of lipopolysaccharide and extracellular polysaccharide. J Bacteriol 175:5839–5850

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li J, Wang N (2011) Genome-wide mutagenesis of Xanthomonas axonopodis pv. citri reveals novel genetic determinants and regulation mechanisms of biofilm formation. PLoS One 6(7):e21804. doi:10.1371/journal.pone.0021804

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lorenz C, Kirchner O, Egler M, Stuttmann J, Bonas U, Buttner D (2008) HpaA from Xanthomonas is a regulator of type III secretion. Mol Microbiol 69:344–360

    Article  CAS  PubMed  Google Scholar 

  • Metz M, Dahlbeck D, Morales CQ, Al Sady B, Clark ET, Staskawicz BJ (2005) The conserved Xanthomonas campestris pv. vesicatoria effector protein XopX is a virulence factor and suppresses host defense in Nicotiana benthamiana. Plant J 41:801–814

    Article  CAS  PubMed  Google Scholar 

  • Mohammadi M, Mirzaee MR, Rahimian H (2001) Physiological and biochemical characteristics of Iranian strains of Xanthomonas axonopodis pv. citri, the causal agent of citrus bacterial canker disease. J Phytopath 149:65–75. doi:10.1046/j.1439-0434.2001.00570.x

    Article  CAS  Google Scholar 

  • Moreira LM, Almeida NF, Potnis N, Digiampietri LA, Adi SS, Bortolossi JC, da Silva AC, da Silva AM, de Moraes FE, de Oliveira JC, de Souza RF, Facincani AP, Ferraz AL, Ferro MI, Furlan LR, Gimenez DF, Jones JB, Kitajima EW, Laia ML, Leite RP Jr, Nishiyama MY, Rodrigues Neto J, Nociti LA, Norman DJ, Ostroski EH, Pereira HA Jr, Staskawicz BJ, Tezza RI, Ferro JA, Vinatzer BA, Setubal JC (2010) Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii. BMC Genomics 11:238. doi:10.1186/1471-2164-11-238

    Article  PubMed  PubMed Central  Google Scholar 

  • Mukaihara T, Tamura N, Iwabuchi M (2010) Genome-wide identification of large repertoire of Ralstonia solanacearum type III effector proteins by a new functional screen. Mol Plant-Microbe Interact 23:251–262

    Article  CAS  PubMed  Google Scholar 

  • Nimchuk ZL, Fisher EJ, Desveaux D, Chang JH, Dangl JL (2007) The HopX (AvrPphE) family of Pseudomonas syringae type III effectors require a catalytic triad and a novel N-terminal domain for function. Mol Plant-Microbe Interact 20:346–357

    Article  CAS  PubMed  Google Scholar 

  • Nivaskumar M, Francetic O (2014) Type II secretion system: a magic beanstalk or a protein escalator. Biochim Biophys Acta 1843:1568–1577

    Article  CAS  PubMed  Google Scholar 

  • Noël L, Thieme F, Nennstiel D, Bonas U (2002) Two novel type III-secreted proteins of Xanthomonas campestris pv. vesicatoria are encoded within the hrp pathogenicity island. J Bacteriol 184:1340–1348

    Article  PubMed  PubMed Central  Google Scholar 

  • Park DS, Hyun JW, Park YJ, Kim JS, Kang HW, Hahn JH, Go SJ (2006) Sensitive and specific detection of Xanthomonas axonopodis pv. citri by PCR using pathovar specific primers based on hrpW gene sequences. Microbiol Res 161:145–149

    Article  CAS  PubMed  Google Scholar 

  • Petnicki-Ocwieja T, Schneider DJ, Tam VC, Chancey ST, Shan L, Jamir Y, Schechter LM, Janes MD, Buell CR, Tang X, Collmer A, Alfano JR (2002) Genome wide identification of proteins secreted by the hrp type III protein secretion system of Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci U S A 99:7652–7657

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petrocelli S, Tondo ML, Daurelio LD, Orellano EG (2012) Modifications of Xanthomonas axonopodis pv. citri lipopolysaccharide affect the basal response and the virulence process during citrus canker. PLoS One 7(7):e40051. doi:10.1371/journal.pone.0040051

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P (2014) eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res 42(D1):D231–D239. doi:10.1093/nar/gkt1253

    Article  CAS  PubMed  Google Scholar 

  • Pruvost O, Goodarzi T, Boyer K, Soltaninejad H, Escalon A, Alavi SM, Javegny S, Boyer C, Cottyn B, Gagnevin L, Vernière C (2015) Genetic structure analysis of strains causing citrus canker in Iran reveals the presence of two different lineages of Xanthomonas citri pv. citri pathotype a*. Plant Pathol 64(4):776–784. doi:10.1111/ppa.12324

    Article  Google Scholar 

  • Ramey BE, Koutsoudis M, von Bodman SB, Fuqua C (2004) Biofilm formation in plant-microbe associations. Curr Opin Microbiol 7(6):602–609

    Article  CAS  PubMed  Google Scholar 

  • Roden JA, Belt B, Ross JB, Tachibana T, Vargas J, Mudgett MB (2004) A genetic screen to isolate type III effectors translocated into pepper cells during Xanthomonas infection. Proc Natl Acad Sci U S A 101:16624–16629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rybak MA, Minsavage GV, Stall RE, Jones JB (2009) Identification of Xanthomonas citri ssp. citri host specificity genes in a heterologous expression host. Mol Plant Pathol 10:249–262

    Article  CAS  PubMed  Google Scholar 

  • Schaad NW, Ostnikova EP, Lacy G, Sechler A, Agarkova I, Stromberg PE, Stromberg VK, Vidaver AK (2006) Emended classification of xanthomonad pathogens on citrus. Syst Appl Microbiol 29:690–695

    Article  PubMed  Google Scholar 

  • Schröter K, Flaschel E, Pühler A, Becker A (2001) Xanthomonas campestris pv. campestris secretes the endoglucanases ENGXCA and ENGXCB: construction of an endoglucanase-deficient mutant for industrial xanthan production. Appl Microbiol Biotechnol 55(6):727–733

    Article  PubMed  Google Scholar 

  • Siciliano F, Torres P, Sendín L, Bermejo C, Filippone P, Vellice G, Ramallo J, Castagnaro A, Vojnov A, Marano MR (2006) Analysis of the molecular basis of Xanthomonas axonopodis pv. citri pathogenesis in Citrus limon. Electron. J Biotechnol 9:5. doi:10.2225/vol9-issue3-fulltext-20

    Google Scholar 

  • Stall RE, Civerolo EL (1991) Research relating to the recent outbreak of citrus canker in Florida. Annu Rev Phytopathol 29:399–420

    Article  CAS  PubMed  Google Scholar 

  • Stanley SA, Raghavan S, Hwang WW, Cox JS (2003) Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system. Proc Natl Acad Sci U S A 100:13001–13006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sun X, Stall RE, Jones JB, Cubero J, Gottwald TR, Graham JH, Dixon WD, Schubert TS, Chaloux PH, Stromberg VK, Lacy GH, Sutton BD (2004) Detection and characterization of a new strain of citrus canker bacteria from key/Mexican lime and alemow in South Florida. Plant Dis 88:1179–1188. doi:10.1094/PDIS.2004.88.11.1179

    Article  CAS  Google Scholar 

  • Swarup S, Yang Y, Kingsley MT, Gabriel DW (1992) A Xanthomonas citri pathogenicity gene, pthA, pleiotropically encodes gratuitous avirulence on nonhosts. Mol Plant-Microbe Interact 5:204–213

    Article  CAS  PubMed  Google Scholar 

  • Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. doi:10.1093/nar/gkw569

    PubMed Central  Google Scholar 

  • Thieme F, Szczesny R, Urban A, Kirchner O, Hause G, Bonas U (2007) New type III effectors from Xanthomonas campestris pv. vesicatoria trigger plant reactions dependent on a conserved N-myristoylation motif. Mol Plant-Microbe Interact 20:1250–1261

    Article  CAS  PubMed  Google Scholar 

  • Vernière C, Hartung JS, Pruvost O, Civerolo EL, Alvarez AM, Maestri P, Luisetti J (1998) Characterization of phenotypically distinct strains of Xanthomonas axonopodis pv. citri from Southwest Asia. Eur J Plant Pathol 104:447–487

    Article  Google Scholar 

  • Welch RA (1991) Pore-forming cytolysins of gram-negative bacteria. Mol Microbiol 5:521–528

    Article  CAS  PubMed  Google Scholar 

  • White FF, Potnis N, Jones JB, Koebnik R (2009) The type III effectors of Xanthomonas. Mol Plant Pathol 10:749–766

    Article  CAS  PubMed  Google Scholar 

  • Yan Q, Wang N (2011) The ColR/ColS two-component system plays multiple roles in the pathogenicity of the citrus canker pathogen Xanthomonas citri subsp. citri. J Bacteriol 193:1590–1599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yan Q, Wang W (2012) High-throughput screening and analysis of genes of Xanthomonas citri subsp. citri involved in citrus canker symptom development. Mol Plant-Microbe Interact 25(1):69–84. doi:10.1094/MPMI-05-11-0121

    Article  CAS  PubMed  Google Scholar 

  • Yang TC, Leu YW, Chang HC, Hu RM (2009) Flagellar biogenesis of Xanthomonas campestris requires the alternative sigma factors RpoN2 and FliA and is temporally regulated by FlhA, FlhB, and FlgM. J Bacteriol 191(7):2266–2275. doi:10.1128/JB.01152-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zeidler D, Zahringer U, Gerber I, Dubery I, Hartung T, Bors W, Hutzler P, Durner J (2004) Innate immunity in Arabidopsis thaliana: lipopolysaccharides activate nitric oxide synthase (NOS) and induce defense genes. Proc Natl Acad Sci U S A 101:15811–15816

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This study was supported by National Institute of Genetic Engineering and Biotechnology, Grant Project M-406.

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  1. Institute of Agriculture Biotechnology, National Institute for Genetic Engineering and Biotechnology (NIGEB), Pajoohesh Blvd. Tehran -Karaj Highway, 17th Km, P.O. Box 14155-6343, Tehran, Iran

    Amir Jalali & Seyed Mehdi Alavi

  2. Deptartment of Biology, Faculty of Sciences, University of Sistan and Baluchestan, Zahedan, Iran

    Amir Jalali & Mohammad Hossein Sangtarash

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  1. Amir Jalali
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Jalali, A., Alavi, S.M. & Sangtarash, M.H. Comparative genomic analysis of wide and narrow host range strains of Xanthomonas citri subsp. citri, showing differences in the genetic content of their pathogenicity and virulence factors. Australasian Plant Pathol. 46, 49–61 (2017). https://doi.org/10.1007/s13313-016-0462-z

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