Insights into the 1.59-Mbp largest plasmid of azospirillum brasilense CBG497

Archives of Microbiology

Volumn 194, Issue 9, 2012, Pages 725-736

  Acosta Cruz, Erika ^a   Wisniewski Dyé, Florence ^b   Rouy, Zoé ^c   Barbe, Valérie ^c   Valdés, María ^a   Mavingui, Patrick ^b  

^a INSTITUTO POLITÉCNICO NACIONAL   (Mexico)

^b UNIVERSITÉ LYON 1   (France)

^c DIF   (France)

Author keywords

Azospirillum; Essential genes; Phylogenetic analysis; Plasmid; Proteobacteria

Indexed keywords

BACTERIAL RNA; TRANSFER RNA;

ALKALINITY; ARTICLE; AZOSPIRILLUM BRASILENSE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIAL SURVIVAL; BACTERIUM DETECTION; BACTERIUM ISOLATION; CONTROLLED STUDY; DNA BASE COMPOSITION; EVOLUTIONARY ADAPTATION; GENE SEQUENCE; GENETIC CODE; GENETIC TRAIT; MOLECULAR PHYLOGENY; NONHUMAN; OPERON; PH MEASUREMENT; PLASMID; PRIORITY JOURNAL; REPLICON; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; AZOSPIRILLUM; AZOSPIRILLUM BRASILENSE; BASE SEQUENCE; GENE TRANSFER, HORIZONTAL; HYDROGEN-ION CONCENTRATION; MEXICO; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASMIDS; SEQUENCE ANALYSIS;

AZOSPIRILLUM; AZOSPIRILLUM BRASILENSE; BACTERIA (MICROORGANISMS); PROTEOBACTERIA; TRITICUM AESTIVUM; ZEA MAYS;

EID: 84865955876     PISSN: 03028933     EISSN: 1432072X     Source Type: Journal    
DOI: 10.1007/s00203-012-0805-2     Document Type: Article

References (48)

1. Alexeyev MF (1999) The pKnock series of broad-host-range mobilizable suicide vectors for gene knockout and targeted DNA insertion into the chromosome of gram-negative bacteria. Biotechniques 26:824-828
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
3. Baldani VLD, Baldani JI, Döbereiner J (1983) Effects of Azospirillum inoculation on root infection and nitrogen incorporation in wheat. Can J Microbiol 29:924-929
4. Bashan Y, Holguin G, de-Bashan LE (2004) Azospirillum-plant relationships: physiological, molecular, agricultural, and environmental advances (1997-2003). Can J Microbiol 50:521-577
5. Bi C, Benham CJ (2004) WebSIDD: server for predicting of the stress-induced duplex destabilized (SIDD) sites in superhelical DNA. Bioinformatics 20:1477-1479
6. Bocs S, Cruveiller S, Vallenet D, Nuel G, Médigue C (2003) AMIGene: annotation of MIcrobial genes. Nucleic Acids Res 31:3723-3726
7. Bozouklian H, Fogher C, Elmerich C (1986) Cloning and characterization of the glnA gene of Azospirillum brasilense Sp7. Ann Inst Pasteur Microbiol 137B:3-18
8. Caballero-Mellado J, López-Reyes L, Bustillos-Cristales R (1999) Presence of 16S rRNA genes in multiple replicons in Azospirillum brasilense. FEMS Microbiol Lett 178:283-288
9. Chilton MD, Currier T, Farrand S, Bendich A, Gordon M, Nester E (1974) Agrobacterium tumefaciens DNA and PS8 bacteriophague DNA not detected in crown gall tumors. Proc Natl Acad Sci USA 71:3672-3676
10. Creus CM, Graziano M, Casanovas EM, Pereyra MA, Simontacchi M, Puntarulo S, Barassi CA, Lamattina L (2005) Nitric oxide is involved in the Azospirillum brasilense-induced lateral root formation in tomato. Planta 221:297-303
11. -MDa plasmid. Plasmid 26:83-93
12. DelVecchio VG, Kapatral V, Redkar RJ, Patra G, Mujer C, Los T, Ivanova N, Anderson I, Bhattacharyya A, Lykidis A, Reznik G, Jablonski L, Larsen N, D'Souza M, Bernal A, Mazur M, Goltsman E, Selkov E, Elzer PH, Hagius S, O'Callaghan D, Letesson JJ, Haselkorn R, Kyrpides N, Overbeek R (2002) The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc Natl Acad Sci USA 99:443-448
13. Egan ES, Fogel MA, Waldor MK (2005) Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol Microbiol 56:1129-1138
14. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
15. García-Olivares J, Moreno-Medina V, Rodríguez-Luna I, Mendoza-Herrera A, Mayek-Pérez N (2007) Efecto de cepas de Azospirillum brasilense en el crecimiento y rendimiento de grano del maíz. Rev Fitotec Mex 30:305-310
16. Gil R, Silva FJ, Peretó J, Moya A (2004) Determination of the core of a minimal bacterial gene set. Microbiol Mol Biol Rev 68:518-537
17. Gonzalez V, Bustos P, Ramirez-Romero MA, Medrano-Soto A, Salgado H, Hernandez-Gonzalez I, Hernandez-Celis JC, Quintero V, Moreno-Hagelsieb G, Girard L, Rodri'guez O, Flores M, Cevallos MA, Collado-Vides J, Romero D, Da'vila G (2003) The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biol 4:R36
18. Harrison PW, Lower RP, Kim NK, Young JP (2010) Introducing the bacterial 'chromid': not a chromosome, not a plasmid. Trends Microbiol 18(4):141-148
19. Hauwaerts D, Alexandre G, Das SK, Vanderleyden J, Zhulin IB (2002) A major chemotaxis gene cluster in Azospirillum brasilense and relationships between chemotaxis operons in a-proteobacteria. FEMS Microbiol Lett 208:61-67
20. Hynes MF, McGregor NF (1990) Two plasmids other than the nodulation plasmid are necessary for the formation of nitrogenfixing nodules in Rhizobium leguminosarum. Mol Microbiol 4:567-574
21. Kadouri D, Jurkevitch E, Okon Y, Castro-Sowinski S (2005) Ecological and agricultural significance of bacterial polyhydroxyalkanoates. Crtical Rev Microbiol 31:55-67
22. Kaneko T, Minamisawa K, Isawa T, Nakatsukasa H, Mitsui H, Kawaharada Y, Nakamura Y, Watanabe A, Kawashima K, Ono A, Shimizu Y, Takahashi C, Minami C, Fujishiro T, Kohara M, Katoh M, Nakazaki N, Nakayama S, Yamada M, Tabata S, Sato S (2010) Complete genomic structure of the cultivated rice endophyte Azospirillum sp. B510. DNA Res 17:37-50
23. Lerner A, Okon Y, Burdman S (2009) The wzm gene located in the pRhico plasmid of Azospirillum brasilense Sp7 is involved in lipopolysaccharide synthesis. Microbiology 155:791-804
24. Martin-Didonet CCG, Chubatsu LS, Souza EM, Kleina M, Rego FGM, Rigo LU, Yates MG, Pedrosa FO (2000) Genome structure of the genus Azospirillum. J Bacteriol 182:4113-4116
25. Mavingui P, Flores M, Romero D, Martínez-Romero E, Palacios R (1997) Generation of Rhizobium strains with improved symbiotic properties by random DNA amplification (RDA). Nat Biotechnol 15:564-569
26. Mavingui P, Flores M, Guo X, Davila G, Perret X, Broughton WJ, Palacios R (2002) Dynamics of genome architecture in Rhizobium sp. strain NGR234. J Bacteriol 184:171-176
27. Michiels K, De Troch P, Onyeocha I, Van Gool A, Elmerich C, Vanderleyden J (1989) Plasmid localization and mapping of two Azospirillum brasilense loci that affect exopolysaccharide synthesis. Plasmid 21:142-146
28. Nelson LM, Knowles R (1978) Effect of oxygen and nitrate on nitrogen fixation and denitrification by Azospirillum brasilense grown in continuous culture. Can J Microbiol 24:1395-1403
29. Onyeocha I, Vieille C, Zimmer W, Baca BE, Flores M, Palacios R, Elmerich C (1990) Physical map and properties of a 90-MDa plasmid of Azospirillum brasilense Sp7. Plasmid 23:169-182
30. Paddan E, Bibi E, Ito M, Krulwich TA (2005) Alkaline pH homeostasis in bacteria: new insights. Biochim Biophys Acta 30:67-88
31. Pedrosa FO, Yates MG (1984) Regulation of nitrogen fixation (nif) genes of Azospirillum brasilense by nifA and ntr (gln) type gene products. FEMS Microbiol Lett 23:95-101
32. Pothier JF, Prigent-Combaret C, Haurat J, Moënne-Loccoz Y, Wisniewski-Dyé F (2008) Duplication of plasmid-borne nitrite reductase gene nirK in the wheat-associated plant growthpromoting rhizobacterium Azospirillum brasilense Sp245. Mol Plant Microbe Interact 21:831-842
33. Putnoky P, Kereszt A, Nakamura T, Endre G, Grosskopf E, Kiss P, Kondorosi A (1998) The pha gene cluster of Rhizobium meliloti involved in pH adaptation and symbiosis encodes a novel type of K? efflux system. Mol Microbiol 28:1091-1101
34. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
35. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor
36. Sant'Anna FH, Almeida LGP, Cecagno R, Reolon LA, Siqueira FM, Machado MRS, Vasconcelos ATR, Schrank IS (2011) Genomic insights into the versatility of the plant growth-promoting bacterium Azospirillum amazonense. BMC Genomics 12:409-422
37. Simon R, Priefer U, Pülher A (1983) A broad host range mobilization system for in vivo genetic engineering transposon mutagenesis in gramnegative bacteria. Bio/Technology 1:784-791
38. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739
39. Tarrand JJ, Krieg NR, Döbereiner J (1978) A taxonomic study of the Spirillum lipoferum group, with descriptions of a new genus, Azospirillum gen. nov. and two species, Azospirillum lipoferum (Beijerinck) comb. nov. and Azospirillum brasilense sp. nov. Can J Microbiol 24:967-980
40. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673- 4680
41. Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S, Lajus A, Pascal G, Scarpelli C, Médigue C (2006) MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34:53-65
42. Van Dommelen A, Van Bastelaere E, Keijers V, Vanderleyden J (1997) Genetics of Azospirillum brasilense with respect to ammonium transport, sugar uptake and chemotaxis. Plant Soil 194:155-160
43. Vanbleu E, Marchal K, Lambrecht M, Mathys J, Vanderleyden J (2004) Annotation of the pRhico plasmid of Azospirillum brasilense reveals its role in determining the outer surface composition. FEMS Microbiol Lett 232:165-172
44. Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22:2196-2203
45. Vial L, Lavire C, Mavingui P, Blaha D, Haurat J, Möenne-Loccoz Y, Bally R, Wisniewsky-Dyé F (2006) Phase variation and genome architecture changes in Azospirillum. J Bacteriol 188:5364-5373
46. Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R (2006) Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinform 7:142
47. Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K, Hurst GB, Hayes-McDonald W, Robertson JS, Barbe V, Calteau A, Rouy Z, Mangenot S, Prigent-Combaret C, Normand P, Boyer M, Siguier P, Dessaux Y, Elmerich C, Condemine G, Krishnen G, Kennedy I, Paterson AH, Gonza'lez V, Mavingui P, Zhulin I (2011) Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet 7:e1002430
48. Yamaguchi T, Tsutsumi F, Putnoky P, Fukuhara M, Nakamura T (2009) pH-dependent regulation of the multi-subunit cation/ proton antiporter Pha1 system from Sinorhizobium meliloti. Microbiology 155:2750-2756