Insights learned from pBTAi1, a 229-kb accessory plasmid from Bradyrhizobium sp. strain BTAi1 and prevalence of accessory plasmids in other Bradyrhizobium sp. strains

ISME Journal

Volumn 2, Issue 2, 2008, Pages 158-170

  Cytryn, Eddie J ^a   Jitacksorn, Siriluck ^a   Giraud, Eric ^b   Sadowsky, Michael J ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b LABORATOIRE DES SYMBIOSES TROPICALES ET MÉDITERRANÉENNES   (France)

Author keywords

Function; Genomics; Hydrogenase; Plasmids; Symbiosis

Indexed keywords

BACTERIAL PROTEIN; HYDROGENASE;

ARTICLE; BACTERIUM CONJUGATION; BRADYRHIZOBIUM; CLASSIFICATION; DNA SEQUENCE; GENETICS; GENOMICS; LEGUME; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PHYLOGENY; PLASMID; REPLICON; SYMBIOSIS;

BACTERIAL PROTEINS; BRADYRHIZOBIUM; CONJUGATION, GENETIC; FABACEAE; GENOMICS; HYDROGENASE; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLASMIDS; REPLICON; SEQUENCE ANALYSIS, DNA; SYMBIOSIS;

BRADYRHIZOBIUM; BRADYRHIZOBIUM ELKANII; BRADYRHIZOBIUM JAPONICUM; BRADYRHIZOBIUM SP.; BRADYRHIZOBIUM SP. BTAI1; THIOBACILLUS DENITRIFICANS;

EID: 38949118765     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2007.105     Document Type: Article

References (55)

1. Albrecht SL, Maier RJ, Hanus FJ, Russell SA, Emerich DW, Evans HJ. (1979). Hydrogenase in Rhizobium japonicum increases nitrogen fixation by nodulated soybeans. Science 203: 1255-1257.
2. Baginsky C, Brito B, Imperial J, Manuel Palacios J, Ruiz-Argüeso T. (2002). Diversity and evolution of
3. hydrogenase systems in rhizobia. Appl Environ Microbiol 68: 4915-4924.
4. Barnett MJ, Fisher RF, Jones T, Komp C, Abola AP, Barloy-Hubler F et al. (2001). Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci USA 14: 9883-9888.
5. Barton BM, Harding GP, Zuccarelli AJ. (1995). A general method for detecting and sizing large plasmids. Anal Biochem 226: 235-240.
6. Beller HR, Chain PS, Letain TE, Chakicherla A, Larimer FW, Richardson PM et al. (2006). The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 188: 1473-1488.
7. Belogurov AA, Delver EP, Agafonova OV, Belogurova NG, Lee LY, Kado CI. (2000). Antirestriction protein ard (type C) encoded by IncW plasmid psa has a high similarity to the 'protein transport' domain of TraC1 primase of promiscuous plasmid RP4. J Mol Biol 296: 969-977.
8. Bignell C, Thomas CM. (2001). The bacterial ParA-ParB partitioning proteins. J Biotechnol 13: 1-34.
9. Birren B, Lai E. (1993). Pulsed Field Gel Electrophoresis a Practical Approach. Academic Press Inc.: USA, ISBN 0-12-101290-5.
10. Brito B, Baginsky C, Palacios JM, Cabrera E, Ruiz-Argueso T, Imperial J. (2005). Biodiversity of uptake hydrogenase systems from legume endosymbiotic bacteria. Biochem Soc Trans 33: 33-35.
11. Calteau A, Gouy M, Perrière G. (2005). Horizontal transfer of two opérons coding for hydrogenases between bacteria and archaea. J Mol Evol 60: 557-565.
12. Casalot L, Rousset M. (2001). Maturation of the [NiFe] hydrogenases. Trends Microbiol 9: 228-237.
13. Cevallos MA, Porta H, Izquierdo J, Tun-Garrido C, Garciade-los-Santos A, Davila G et al. (2002). Rhizobium etli CFN42 contains at least three plasmids of the repABC family: a structural and evolutionary analysis. Plasmid 48: 104-116.
14. Evans HJ, Harker AR, Papen H, Russell SA, Hanus FJ, Zuber M. (1987). Physiology, biochemistry, and genetics of the uptake hydrogenase in rhizobia. Annu Rev Microbiol 41: 335-361.
15. Felsenstein J. (1989). PHYLIP - phylogeny inference package (Version 3.2). Cladistics 5: 164-166.
16. Francki KT, Chang BJ, Mee BJ, Collignon PJ, Susai V, Keese PK. (2000). Identification of genes associated with copper tolerance in an adhesion-defective mutant of Aeromonas veronii biovar sobria. FEMS Immunol Med Microbiol 29: 115-121.
17. Giraud E, Fleischman D. (2004). Nitrogen-fixing symbiosis between photosynthetic bacteria and legumes. Photosynth Res 82: 115-130.
18. Giraud E, Moulin L, Vallenet D, Barbe V, Cytryn E, Avarre JC et al. (2007). Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science 316: 1307-1312.
19. Gonzalez V, Santamaria RI, Bustos P, Hernandez-Gonzalez I, Medrano-Soto A, Moreno-Hagelsieb G et al. (2006). The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA 7: 3834-3839.
20. Gottfert M, Rothlisberger S, Kundig C, Beck C, Marty R, Hennecke H. (2001). Potential symbiosis-specific genes uncovered by sequencing a 410-kilobase DNA region of the Bradyrhizobium japonicum chromosome. J Bacteriol 183: 1405-1412.
21. Gross DC, Vidaver AK, Klucas RV. (1979). Plasmids, biological properties and efficacy of nitrogen fixation in Rhizobium japonicum strains indigenous to alkaline soils. J Gen Microbiol 114: 257-266.
22. He X, Chang W, Pierce DL, Seib LO, Wagner J, Fuqua C. (2003). Quorum sensing in Rhizobium sp. strain NGR 234 regulates conjugal transfer (tra) gene expression and influences growth rate. J Bacteriol 185: 809-822.
23. Itoh Y, Watson JM, Haas D, Leisinger T. (1984). Genetic and molecular characterization of the Pseudomonas plasmid pVS1. Plasmid 11: 206-220.
24. Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S et al. (2002). Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA 110. DNA Res 9: 189-197.
25. Keyser HH, van Berkum P, Weber DF. (1982). A comparative study of the physiology of symbioses formed by Rhizobium japonicum with Glycine max, Vigna unguiculata, and Macroptilium atropurpurem. Plant Physiol 70: 1626-1630.
26. Lane DJ. (1991). 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds). Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons: New York, pp 115-175.
27. Li PL, Farrand SK. (2000). The replicator of the nopalinetype Ti plasmid pTiC58 is a member of the repABC family and is influenced by the TraR-dependent quorum-sensing regulatory system. J Bacteriol 182: 179-188.
28. Lim CK, Cooksey DA. (1993). Characterization of chromosomal homologs of the plasmid-borne copper resistance operon of Pseudomonas syringae. J Bacteriol 175: 4492-4498.
29. Martínez E, Palacios R, Sánchez F. (1987). Nitrogen-fixing nodules induced by Agrobacterium tumefaciens harboring Rhizobium phaseoli plasmids. J Bacteriol 169: 2828-2834.
30. Masterson RV, Russel PR, Atherly AG. (1982). Nitrogen fixation (nif) genes and large plasmids of Rhizobium japonicum. J Bacteriol 152: 928-931.
31. Mercado-Blanco J, Toro N. (1996). Plasmids in rhizobia: the role of nonsymbiotic plasmids. Mol Plant-Microb Interact 9: 535-545.
32. Mergeay M, Monchy S, Vallaeys T, Auquier V, Benotmane A, Bertin P et al. (1995). Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiol Rev 27: 385-410.
33. Merrick MJ, Edwards RA. (1995). Nitrogen control in bacteria. Microbiol Rev 59: 604-622.
34. Mills SD, Lim CK, Cooksey DA. (1994). Purification and characterization of CopR, a transcriptional activator protein that binds to a conserved domain (cop box) in copper-inducible promoters of Pseudomonas syringae. Mol Gen Genet 15: 341-351.
35. Monchy S, Benotmane MA, Wattiez R, van Aelst S, Auquier V, Borremans B et al. (2006). Transcriptomic and proteomic analyses of the pMOL30-encoded copper resistance in Cupriavidus metallidurans strain CH34. Microbiology 152: 1765-1776.
36. Pappas KM, Winans SC. (2003). A LuxR-type regulator from Agrobacterium tumefaciens elevates Ti plasmid copy number by activating transcription of plasmid replication genes. Mol Microbiol 48: 1059-1073.
37. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, Read TD et al. (2002). The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci USA 99: 13148-13153.
38. Ramirez-Romero M, Soberón N, Pérez-Oseguera A, TéllezSosa J, Cevallos MA. (2000). Structural elements required for replication and incompatibility of the Rhizobium etli symbiotic plasmid. J Bacteriol 182: 3117-31124.
39. Ramirez-Romero MA, Tellez-Sosa J, Barrios H, PerezOseguera A, Rosas V, Cevallos MA. (2001). RepA negatively autoregulates the transcription of the repABC operon of the Rhizobium etli symbiotic plasmid basic replicon. Mol Microbiol 42: 195-204.
40. Rensing C, Grass G. (2003). Escherichia coli mechanisms of copper homeostasis in a changing environment. FEMS Microbiol Rev 27: 197-213.
41. Rozen S, Skaletsky HJ. (2000). Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds). Bioinformatics Methods and Protocols: Methods in Molecular Biology. Humana Press: Totowa, NJ, pp 365-386.
42. Sadowsky MJ, Cregan PB, Göttfert M, Sharma A, Gerhold D, Rodriguez-Quinones F et al. (1991). The Bradyrhizobium japonicum nolA gene and its involvement in the genotype-specific nodulation of soybeans. Proc Natl Acad Sci USA 88: 637-641.
43. Sadowsky MJ, Kosslak RM, Madrzak CJ, Golinska B, Cregan PB. (1995). Restriction of nodulation by Bradyrhizobium japonicum is mediated by factors present in the roots of Glycine max. Appl Environ Microbiol 61: 832-836.
44. Sadowsky MJ, Tully RE, Cregan PB, Keyser HH. (1987). Genetic diversity in Bradyrhizobium japonicum serogroup 123 and its relation to genotype-specific nodulation of soybeans. Appl Environ Microbiol 53: 2624-2630.
45. Sajjaphan K, Shapir N, Wackett LP, Palmer M, Blackmon B, Tomkins J et al. (2006). Arthrobacter aurescens TC1 atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional in Escherichia coli. Appl Environ Microbiol 70: 4402-4407.
46. Sawada H, Kuykendall LD, Young JM. (2003). Changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts. J Gen Appl Microbiol 49: 155-179.
47. Somasagaran P, Hoben H. (1994). Handbook for Rhizobium: Methods in Legume-Rhizobium Technology. Springer: Berlin Heidelberg New York.
48. Stiens M, Schneiker S, Keller M, Kuhn S, Puhler A, Schluter A. (2006). Sequence analysis of the 144-kilobase accessory plasmid pSmeSMlla, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment. Appl Environ Microbiol 72: 3662-3672.
49. Stowers MD, Eaglesham ARJ. (1983). A stem-nodulating Rhizobium with physiological characteristics of both fast and slow growers. J Gen Microbiol 129: 3651-3655.
50. Summerfield AS, Huxley PA, Minchin FR. (1977). Plant husbandry and management techniques for growing grain legumes under simulated conditions in controlled environment. Expl Tropical Agric 13: 81-92.
51. Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, Cruveiller S et al. (2006). MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34: 53-65.
52. van Berkùm P, Leibold JM, Eardly BD. (2006). Proposal for combining Bradyrhizobium spp. (Aeschynomene indica) with Blastobacter denitrificans and to transfer Blastobacter denitrificans (Hirsch and Muller, 1985) to the genus Bradyrhizobium as Bradyrhizobium denitrificans (comb. nov.). Syst Appl Microbiol 29: 207-215.
53. Wang ET, van Berkum P, Sui XH, Beyene D, Chen WX, Martinez-Romero E. (1999). Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov. Int J Syst Bacteriol 1: 51-65.
54. Watson RJ, Heys R. (2006). Replication regions of Sinorhizobium meliloti plasmids. Plasmid 55: 87-98.
55. Young JP, Crossman LC, Johnston AW, Thomson NR, Ghazoui ZF, Hull KH et al. (2006). The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 7: R34; doi:10.1186/gb-2006-7-4-r34.