The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species.
References
[1]
Pedrosa FO, Elmerich C (2007) Regulation of nitrogen fixation and ammonium assimilation in associative and endophytic nitrogen fixing bacteria. In: Elmerich C, Newton WE, editors. Associative and endophytic nitrogen fixing bacteria and cyanobacterial associations. pp. 47–71. Kluwer: The Netherlands.
[2]
Pimentel JP, Olivares FL, Pitard RM, Urquiaga S, Akiba F, et al. (1991) Dinitrogen fixation and infection of grass leaves by Pseudomonas rubrisubalbicans and Herbaspirillum seropedicae. Plant Soil 137: 61–65.
[3]
Baldani VLD, Baldani JI, Olivares FL, D？bereiner J (1992) Identification and ecology of Herbaspirillum seropedicae and closely related Pseudomonas rubrisubalbicans. Symbiosis 13: 65–73.
[4]
Gyaneshwar P, James EK, Reddy PM, Ladha JK (2002) Herbaspirillum colonization increases growth and nitrogen accumulation in aluminum-tolerant rice varieties. New Phytol 154: 131–145.
[5]
Baldani JI, Pot B, Kirchhof G, Falsen E, Baldani VLD, et al. (1996) Emended description of Herbaspirillum; inclusion of (Pseudomonas) rubrisubalbicans, a mild pathogen, as Herbaspirillum rubrisubalbicans comb. nov., and classification of a group of clinical isolates (EFgroup 1) as Herbaspirillum species 3. Int J Syst Bacteriol 46: 802–810.
[6]
Olivares FL, James EK, Baldani JI, D？bereiner J (1997) Infection of mottled stripe disease-susceptible and resistant sugar cane varieties by the endophytic diazotroph Herbaspirillum. New Phytol 135: 723–737.
[7]
James EK, Olivares FL, Baldani JI, D？bereiner J (1997) Herbaspirillum, an endophytic diazotroph colonizing vascular tissue of Sorghum bicolor L. Moench. J Exp Bot 48: 785–798.
[8]
Olivares FL, Baldani VLD, Reis VM, Baldani JI, D？bereiner J (1996) Occurrence of endophytic diazotrophs Herbaspirillum spp. in roots, stems and leaves predominantly of Gramineae. Biol Fertil Soils 21: 197–200.
[9]
James EK, Gyaneshwar P, Mathan N, Barraquio WL, Reddy PM, et al. (2002) Infection and colonization of rice seedlings by the plant growth-promoting bacterium Herbaspirillum seropedicae Z67. Mol Plant Microbe In 15: 894–906.
[10]
Elbeltagy A, Nishioka K, Sato T, Suzuki H, Ye B, et al. (2001) Endophytic colonization and in planta nitrogen fixation by a Herbaspirillum sp. isolated from wild rice species. Appl Environ Microb 67: 5285–93.
[11]
Roncato-Maccari LDB, Ramos HJO, Pedrosa FO, Alquini Y, Chubatsu LS, et al. (2003) Endophytic Herbaspirillum seropedicae expresses nif genes in gramineous plants. FEMS Microbiol Ecol 45: 39–47.
[12]
Boddey RM, De Oliveira OC, Urquiaga S, Reis VM, Olivares FL, et al. (1995) Biological Nitrogen-Fixation Associated with Sugar-Cane and Rice - Contributions and Prospects for Improvement. Plant Soil 174: 195–209.
[13]
D？bereiner J, Pedrosa FO (1987) Nitrogen-fixing Bacteria in Nonleguminous Crop Plants. Madison: Science Tech. 155 p.
[14]
Pedrosa FO, Benelli EM, Yates MG, Wassen R, Monteiro RA, et al. (2001) Recent developments in the structural organization and regulation of nitrogen fixation genes in Herbaspirillum seropedicae. J Biotechnol 91: 189–195.
[15]
Baldani JI, Baldani VLD, Seldin L, D？bereiner J (1986) Characterization of Herbaspirillum seropedicae gen. nov., sp. nov., a new root-associated nitrogen-fixing bacterium. Int J Syst Bacteriol 36: 86–93.
[16]
Ibba M, S？ll D (2000) Aminoacyl-tRNA Synthesis. Ann Rev of Biochem 69: 617–650.
[17]
Francino MP, Ochman H (1997) Strand asymmetries in DNA evolution. Trends Genet 13: 240–245.
[18]
Lehnherr H, Maguin E, Jafri S, Yarmolinsky MB (1993) Plasmid addiction genes of bacteriophage P1: doc, which causes cell death on curing of prophage, and phd, which prevents host death when prophage is retained. J Mol Biol 233: 414–428.
[19]
Buts L, Lah J, Dao-Thi M, Wyns L, Loris R (2005) Toxin–antitoxin modules as bacterial metabolic stress managers. Trends Biochem Sci 30: 672–679.
[20]
Van Melderen L, Saavedra De Bast M (2009) Bacterial Toxin–Antitoxin Systems: More Than Selfish Entities? PLoS Genet 5: e1000437. doi:10.1371/journal.pgen.1000437.
[21]
Bertalan M, Albano R, Pádua V, Rouws L, Rojas C, et al. (2009) Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics 10: 450.
[22]
Krause A, Ramakumar A, Bartels D, Battistoni F, Bekel T, et al. (2008) Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol 24: 1385–1391.
Fischer HM (1994) Genetic regulation of nitrogen fixation in rhizobia. Microbiol Rev 58: 352–386.
[25]
Catalán AL, Ferreira F, Gill PR, Batista S (2007) Production of polyhydroxyalkanoates by Herbaspirillum seropedicae grown with different sole carbon sources and on lactose when engineered to express the lacZlacY genes. Enzyme Microb Tech 40: 1352–1357.
[26]
Klassen G, Pedrosa FO, Souza EM, Funayama S, Rigo LU (1997) Effect of nitrogen compounds on nitrogenase activity in Herbaspirillum seropedicae strain SMR1. Can J Microbiol 43: 841–846.
[27]
Gusso CL, Souza EM, Rigo LU, Pedrosa FO, Yates MG, et al. (2008) Effect of an ntrC mutation on amino acid or urea utilization and on nitrogenase switch-off in Herbaspirillum seropedicae. Can J Microbiol 54: 235–239.
[28]
Schwab S, Ramos HJ, Souza EM, Pedrosa FO, Yates MG, et al. (2007) Identification of NH4+-regulated genes of Herbaspirillum seropedicae by random insertional mutagenesis. Arch Microbiol 187: 379–86.
[29]
Beckers G, Bendt AK, Kr？mer R, Burkovski A (2004) Molecular Identification of the Urea Uptake System and Transcriptional Analysis of Urea Transporter- and Urease-Encoding Genes in Corynebacterium glutamicum. J Bacteriol 186: 7645–7652.
[30]
Sohaskey DC (2008) Nitrate Enhances the Survival of Mycobacterium tuberculosis during Inhibition of Respiration. J Bacteriol 190: 2981–2986.
[31]
Wojtaszek P (2000) Nitric oxide in plants: To NO or not to NO. Phytochem 54: 1–4.
[32]
Huang X, Kiefer E, von Rad U, Ernst D, Foissner I, et al. (2002) Nitric oxide burst and nitric oxide-dependent gene induction in plants. Plant Physiol Biochem 40: 625–631.
[33]
Yamasaki H (2005) The NO world for plants: achieving balance in an open system. Plant, Cell Environ 28: 78–84.
[34]
Besson-Bard A, Courtois C, Gauthier A, Dahan J, Dobrowolska G, et al. (2008) Nitric Oxide in Plants: Production and Cross-talk with Ca2+ Signaling. Mol Plant 1: 218–228.
[35]
Monteiro RA, Schmidt MA, Baura VA, Balsanelli E, Wassem R, et al. (2008) Early colonization pattern of maize (Zea mays L. Poales, Poaceae) roots by Herbaspirillum seropedicae (Burkholderiales, Oxalobacteraceae). Genet Mol Biol 31: 932–937.
[36]
Schmidt MA, Souza EM, Baura VA, Wassem R, Yates MG, et al. (2011) Evidence for the endophytic colonization of Phaseolus vulgaris (common bean) roots by the diazotroph Herbaspirillum seropedicae. Braz J Med Biol Res 44: 182–185.
[37]
Valverde A, Velázquez E, Gutierrez C, Cervantes E, Ventosa A, et al. (2003) Herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of Phaseolus vulgaris. Int J Syst Evol Micr 53: 1979–1983.
[38]
Deakin WJ, Broughton WJ (2009) Symbiotic use of pathogenic strategies: rhizobial protein secretion. Nat Rev Microbiol 7: 312–320.
[39]
Marie C, Deakin WJ, Viprey V, Kopci？ska J, Golinowski , et al. (2003) Characterization of Nops, nodulation outer proteins, secreted via the type III secretion system of NGR234. Mol Plant Microbe In 16: 743–751.
[40]
Viprey V, Del Greco A, Golinowski W, Broughton WJ, Perret X (1998) Symbiotic implications of type III protein secretion machinery in Rhizobium. Mol Microbiol 28: 1381–1389.
[41]
Frederick RD, Majerczak DR, Coplin DL (1993) Erwinia stewartii WtsA, a positive regulator of pathogenicity gene expression, is similar to Pseudomonas syringae pv. phaseolicola HrpS. Mol Microbiol 9: 477–485.
[42]
Wei ZM, Beer SV (1995) hrpL activates Erwinia amylovora hrp gene transcription and is a member of the ECF subfamily of sigma factors. J Bacteriol 177: 6201–6210.
[43]
Xiao Y, Hutcheson SW (1994) A single promoter sequence recognized by a newly identified alternate sigma factor directs expression of pathogenicity and host range determinants in Pseudomonas syringae. J Bacteriol 176: 3089–3091.
[44]
Genin S, Gough CL, Zischek C, Boucher CA (1992) Evidence that the hrpB gene encodes a positive regulator of pathogenicity genes from Pseudomonas solanacearum. Mol Microbiol 6: 3065–3076.
[45]
Kamdar HV, Kamoun S, Kado CI (1993) Restoration of pathogenicity of avirulent Xanthomonas oryzae pv. oryzae and X. campestris pathovars by reciprocal complementation with the hrpXo and hrpXc genes and identification of HrpX function by sequence analyses. J Bacteriol 175: 2017–2025.
[46]
Wengelnik K, Bonas U (1996) HrpXv, an AraC-type regulator, activates expression of five of the six loci in the hrp cluster of Xanthomonas campestris pv. vesicatoria. J Bacteriol 178: 3462–3469.
[47]
Brito B, Marenda M, Barberis P, Boucher C, Genin S (1999) prhJ and hrpG, two new components of the plant signal-dependent regulatory cascade controlled by PrhA in Ralstonia solanacearum. Mol Microbiol 31: 237–251.
[48]
O'Toole GA, Kolter R (1998) Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol Microbiol 30: 295–304.
[49]
Hager AJ, Bolton DL, Pelletier MR, Brittnacher MJ, Gallagher LA, et al. (2006) Type IV pili-mediated secretion modulates Francisella virulence. Mol Microbiol 62: 227–237.
[50]
Han X, Kennan RM, Parker D, Davies JK, Rood JI (2007) Type IV fimbrial biogenesis is required for protease secretion and natural transformation in Dichelobacter nodosus. J Bacteriol 189: 5022–5033.
[51]
Chaves DF, Souza EM, Monteiro RA, Pedrosa FO (2009) A two-dimensional electrophoretic profile of the proteins secreted by Herbaspirillum seropedicae strain Z78. J Proteomics 73: 50–56.
[52]
Seufferheld MJ, Alvarez HM, Farias ME (2008) Role of Polyphosphates in Microbial Adaptation to Extreme Environments. Appl Environ Microb 74: 5867–5874.
[53]
Haunberg L, Schmidt F, Scharf C, D？rr J, V？lker U, Reinhold-Hurek B (2010) Proteomic characterization of a pilR regulatory mutant of Azoarcus sp. strain BH72 with the aid of gel-based and gel-free approaches. Proteomics 10: 458–469.
[54]
Bastián F, Cohen A, Piccoli P, Luna V, Baraldi R, et al. (1998) Production of indole-3-acetic acid and gibberellins A1 and A3 by Acetobacter diazotrophicus and Herbaspirillum seropedicae in chemically-defined culture media. Plant Growth Regul 24: 7–11.
[55]
Wang K, Li H, Ecker JR (2002) Ethylene Biosynthesis and Signaling Networks. Plant Cell 14: s131–151.
[56]
Glick BR, Todorovic B, Czarny J, Cheng Z, Duan J, McConkey B (2007) Promotion of plant growth by bacterial ACC deaminase. Crit Rev Plant Sci 26: 227–242.
[57]
Sun Y, Cheng Z, Glick BR (2009) The presence of a 1-aminocyclopropane-1-carboxylate (ACC) deaminase deletion mutation alters the physiology of the endophytic plant growth-promoting bacterium Burkholderia phytofirmans PsJN. FEMS Microbiol Lett 296: 131–136.
[58]
Jiménez JI, Canales A, Jiménez-Barbero J, Ginalski K, Rychlewski L, et al. (2008) Deciphering the genetic determinants for aerobic nicotinic acid degradation: The nic cluster from Pseudomonas putida KT2440. Proc Natl Acad Sci 105: 11329–11334.
[59]
Van Sluys MA, Monteiro-Vitorello CB, Camargo LEA, Menck CFM, da Silva ACR, et al. (2002) Comparative genomic analysis of plant-associated bacteria. Ann Rev Phytopathol 40: 169–189.
[60]
Gottig N, Garavaglia BS, Garofalo CG, Orellano EG, Ottado J (2009) A Filamentous Hemagglutinin-Like Protein of Xanthomonas axonopodis pv.citri, the Phytopathogen Responsible for Citrus Canker, Is Involved in Bacterial Virulence. PLoS ONE 4: e4358. doi:10.1371/journal.pone.0004358.
[61]
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. 2ed. New York: Cold Spring Harbor Laboratory Press.
[62]
Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, et al. (2000) DNA sequence of both chromosomes of the cholera pathogen Vibrio cholera. Nature 406: 477–484.
[63]
Salzberg S, Delcher A, Kasif S, White O (1998) Microbial gene identification using interpolated Markov models. Nucleic Acids Res 26: 544–548.
[64]
Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636–4641.
[65]
Altschul SF, Madden TL, Sch？ffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–402.
[66]
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 11: 41.
[67]
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, et al. (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34: D354–357.
[68]
Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2009) The Pfam protein families database. Nucleic Acids Res 38: D211–D222.
[69]
Carver T, Berriman M, Tivey A, Patel C, B？hme U, et al. (2008) Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24: 2672–2676.
[70]
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955–964.
[71]
Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22: 2196–2203.
