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Genome of Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses


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.


Vyšlo v časopise: Genome of Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses. PLoS Genet 7(5): e32767. doi:10.1371/journal.pgen.1002064
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002064

Souhrn

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.


Zdroje

1. PedrosaFOElmerichC 2007 Regulation of nitrogen fixation and ammonium assimilation in associative and endophytic nitrogen fixing bacteria. ElmerichCNewtonWE Associative and endophytic nitrogen fixing bacteria and cyanobacterial associations 47 71 Kluwer: The Netherlands

2. PimentelJPOlivaresFLPitardRMUrquiagaSAkibaF 1991 Dinitrogen fixation and infection of grass leaves by Pseudomonas rubrisubalbicans and Herbaspirillum seropedicae. Plant Soil 137 61 65

3. BaldaniVLDBaldaniJIOlivaresFLDöbereinerJ 1992 Identification and ecology of Herbaspirillum seropedicae and closely related Pseudomonas rubrisubalbicans. Symbiosis 13 65 73

4. GyaneshwarPJamesEKReddyPMLadhaJK 2002 Herbaspirillum colonization increases growth and nitrogen accumulation in aluminum-tolerant rice varieties. New Phytol 154 131 145

5. BaldaniJIPotBKirchhofGFalsenEBaldaniVLD 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. OlivaresFLJamesEKBaldaniJIDöbereinerJ 1997 Infection of mottled stripe disease-susceptible and resistant sugar cane varieties by the endophytic diazotroph Herbaspirillum. New Phytol 135 723 737

7. JamesEKOlivaresFLBaldaniJIDöbereinerJ 1997 Herbaspirillum, an endophytic diazotroph colonizing vascular tissue of Sorghum bicolor L. Moench. J Exp Bot 48 785 798

8. OlivaresFLBaldaniVLDReisVMBaldaniJIDöbereinerJ 1996 Occurrence of endophytic diazotrophs Herbaspirillum spp. in roots, stems and leaves predominantly of Gramineae. Biol Fertil Soils 21 197 200

9. JamesEKGyaneshwarPMathanNBarraquioWLReddyPM 2002 Infection and colonization of rice seedlings by the plant growth-promoting bacterium Herbaspirillum seropedicae Z67. Mol Plant Microbe In 15 894 906

10. ElbeltagyANishiokaKSatoTSuzukiHYeB 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-MaccariLDBRamosHJOPedrosaFOAlquiniYChubatsuLS 2003 Endophytic Herbaspirillum seropedicae expresses nif genes in gramineous plants. FEMS Microbiol Ecol 45 39 47

12. BoddeyRMDe OliveiraOCUrquiagaSReisVMOlivaresFL 1995 Biological Nitrogen-Fixation Associated with Sugar-Cane and Rice - Contributions and Prospects for Improvement. Plant Soil 174 195 209

13. DöbereinerJPedrosaFO 1987 Nitrogen-fixing Bacteria in Nonleguminous Crop Plants Madison Science Tech 155

14. PedrosaFOBenelliEMYatesMGWassenRMonteiroRA 2001 Recent developments in the structural organization and regulation of nitrogen fixation genes in Herbaspirillum seropedicae. J Biotechnol 91 189 195

15. BaldaniJIBaldaniVLDSeldinLDöbereinerJ 1986 Characterization of Herbaspirillum seropedicae gen. nov., sp. nov., a new root-associated nitrogen-fixing bacterium. Int J Syst Bacteriol 36 86 93

16. IbbaMSöllD 2000 Aminoacyl-tRNA Synthesis. Ann Rev of Biochem 69 617 650

17. FrancinoMPOchmanH 1997 Strand asymmetries in DNA evolution. Trends Genet 13 240 245

18. LehnherrHMaguinEJafriSYarmolinskyMB 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. ButsLLahJDao-ThiMWynsLLorisR 2005 Toxin–antitoxin modules as bacterial metabolic stress managers. Trends Biochem Sci 30 672 679

20. Van MelderenLSaavedra De BastM 2009 Bacterial Toxin–Antitoxin Systems: More Than Selfish Entities? PLoS Genet 5 e1000437 doi:10.1371/journal.pgen.1000437

21. BertalanMAlbanoRPáduaVRouwsLRojasC 2009 Complete genome sequence of the sugarcane nitrogen-fixing endophyte Gluconacetobacter diazotrophicus Pal5. BMC Genomics 10 450

22. KrauseARamakumarABartelsDBattistoniFBekelT 2008 Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol 24 1385 1391

23. MathiasALRigoLUFunayamaSPedrosaFO 1989 L-arabinose metabolism in Herbaspirillum seropedicae. J Bacteriol 171 5206 5209

24. FischerHM 1994 Genetic regulation of nitrogen fixation in rhizobia. Microbiol Rev 58 352 386

25. CatalánALFerreiraFGillPRBatistaS 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. KlassenGPedrosaFOSouzaEMFunayamaSRigoLU 1997 Effect of nitrogen compounds on nitrogenase activity in Herbaspirillum seropedicae strain SMR1. Can J Microbiol 43 841 846

27. GussoCLSouzaEMRigoLUPedrosaFOYatesMG 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. SchwabSRamosHJSouzaEMPedrosaFOYatesMG 2007 Identification of NH4+-regulated genes of Herbaspirillum seropedicae by random insertional mutagenesis. Arch Microbiol 187 379 86

29. BeckersGBendtAKKrämerRBurkovskiA 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. SohaskeyDC 2008 Nitrate Enhances the Survival of Mycobacterium tuberculosis during Inhibition of Respiration. J Bacteriol 190 2981 2986

31. WojtaszekP 2000 Nitric oxide in plants: To NO or not to NO. Phytochem 54 1 4

32. HuangXKieferEvon RadUErnstDFoissnerI 2002 Nitric oxide burst and nitric oxide-dependent gene induction in plants. Plant Physiol Biochem 40 625 631

33. YamasakiH 2005 The NO world for plants: achieving balance in an open system. Plant, Cell Environ 28 78 84

34. Besson-BardACourtoisCGauthierADahanJDobrowolskaG 2008 Nitric Oxide in Plants: Production and Cross-talk with Ca2+ Signaling. Mol Plant 1 218 228

35. MonteiroRASchmidtMABauraVABalsanelliEWassemR 2008 Early colonization pattern of maize (Zea mays L. Poales, Poaceae) roots by Herbaspirillum seropedicae (Burkholderiales, Oxalobacteraceae). Genet Mol Biol 31 932 937

36. SchmidtMASouzaEMBauraVAWassemRYatesMG 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. ValverdeAVelázquezEGutierrezCCervantesEVentosaA 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. DeakinWJBroughtonWJ 2009 Symbiotic use of pathogenic strategies: rhizobial protein secretion. Nat Rev Microbiol 7 312 320

39. MarieCDeakinWJVipreyVKopciñskaJGolinowski 2003 Characterization of Nops, nodulation outer proteins, secreted via the type III secretion system of NGR234. Mol Plant Microbe In 16 743 751

40. VipreyVDel GrecoAGolinowskiWBroughtonWJPerretX 1998 Symbiotic implications of type III protein secretion machinery in Rhizobium. Mol Microbiol 28 1381 1389

41. FrederickRDMajerczakDRCoplinDL 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. WeiZMBeerSV 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. XiaoYHutchesonSW 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. GeninSGoughCLZischekCBoucherCA 1992 Evidence that the hrpB gene encodes a positive regulator of pathogenicity genes from Pseudomonas solanacearum. Mol Microbiol 6 3065 3076

45. KamdarHVKamounSKadoCI 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. WengelnikKBonasU 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. BritoBMarendaMBarberisPBoucherCGeninS 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'TooleGAKolterR 1998 Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol Microbiol 30 295 304

49. HagerAJBoltonDLPelletierMRBrittnacherMJGallagherLA 2006 Type IV pili-mediated secretion modulates Francisella virulence. Mol Microbiol 62 227 237

50. HanXKennanRMParkerDDaviesJKRoodJI 2007 Type IV fimbrial biogenesis is required for protease secretion and natural transformation in Dichelobacter nodosus. J Bacteriol 189 5022 5033

51. ChavesDFSouzaEMMonteiroRAPedrosaFO 2009 A two-dimensional electrophoretic profile of the proteins secreted by Herbaspirillum seropedicae strain Z78. J Proteomics 73 50 56

52. SeufferheldMJAlvarezHMFariasME 2008 Role of Polyphosphates in Microbial Adaptation to Extreme Environments. Appl Environ Microb 74 5867 5874

53. HaunbergLSchmidtFScharfCDörrJVölkerUReinhold-HurekB 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. BastiánFCohenAPiccoliPLunaVBaraldiR 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. WangKLiHEckerJR 2002 Ethylene Biosynthesis and Signaling Networks. Plant Cell 14 s131 151

56. GlickBRTodorovicBCzarnyJChengZDuanJMcConkeyB 2007 Promotion of plant growth by bacterial ACC deaminase. Crit Rev Plant Sci 26 227 242

57. SunYChengZGlickBR 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. JiménezJICanalesAJiménez-BarberoJGinalskiKRychlewskiL 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 SluysMAMonteiro-VitorelloCBCamargoLEAMenckCFMda SilvaACR 2002 Comparative genomic analysis of plant-associated bacteria. Ann Rev Phytopathol 40 169 189

60. GottigNGaravagliaBSGarofaloCGOrellanoEGOttadoJ 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. SambrookJFritschEFManiatisT 1989 Molecular cloning: a laboratory manual. 2ed New York Cold Spring Harbor Laboratory Press

62. HeidelbergJFEisenJANelsonWCClaytonRAGwinnML 2000 DNA sequence of both chromosomes of the cholera pathogen Vibrio cholera. Nature 406 477 484

63. SalzbergSDelcherAKasifSWhiteO 1998 Microbial gene identification using interpolated Markov models. Nucleic Acids Res 26 544 548

64. DelcherALHarmonDKasifSWhiteOSalzbergSL 1999 Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27 4636 4641

65. AltschulSFMaddenTLSchäfferAAZhangJZhangZ 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 3389 402

66. TatusovRLFedorovaNDJacksonJDJacobsARKiryutinB 2003 The COG database: an updated version includes eukaryotes. BMC Bioinformatics 11 41

67. KanehisaMGotoSHattoriMAoki-KinoshitaKFItohM 2006 From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34 D354 357

68. FinnRDMistryJTateJCoggillPHegerA 2009 The Pfam protein families database. Nucleic Acids Res 38 D211 D222

69. CarverTBerrimanMTiveyAPatelCBöhmeU 2008 Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24 2672 2676

70. LoweTMEddySR 1997 tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25 955 964

71. VernikosGSParkhillJ 2006 Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22 2196 2203

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