Genetic characterization of a novel rhizobial plasmid conjugation system in Rhizobium leguminosarum bv. viciae strain VF39SM

Journal of Bacteriology

Volumn 195, Issue 2, 2013, Pages 328-339

  Ding, Hao ^a   Yip, Cynthia B ^a   Hynes, Michael F ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL STRAIN; GENE CLUSTER; GENE SEQUENCE; GENE TRANSFER; GENOME; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; RHIZOBIUM LEGUMINOSARUM;

CONJUGATION, GENETIC; DNA, BACTERIAL; GENE DELETION; GENE ORDER; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; PLASMIDS; RHIZOBIUM LEGUMINOSARUM; SEQUENCE ANALYSIS, DNA;

RHIZOBIUM LEGUMINOSARUM; RHIZOBIUM LEGUMINOSARUM BV. VICIAE;

EID: 84872150205     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.01234-12     Document Type: Article

References (49)

1. Baldani JI, Weaver RW, Hynes MF, Eardly BD. 1992. Utilization of carbon substrates, electrophoretic enzyme patterns, and symbiotic performance of plasmid-cured clover rhizobia. Appl. Environ. Microbiol. 58: 2308-2314.
2. Brom S, GarcíA de los Santos A, Stepkowsky T, Flores M, Dávila G, Romero D, Palacios R. 1992. Different plasmids of Rhizobium leguminosarum bv. phaseoli are required for optimal symbiotic performance. J. Bacteriol. 174:5183-5189.
3. Finan TM, Kunkel B, De Vos GF, Signer ER. 1986. Second symbiotic megaplasmid in Rhizobium meliloti carrying exopolysaccharide and thiamine synthesis genes. J. Bacteriol. 167:66-72.
4. Hynes MF, McGregor NF. 1990. Two plasmids other than the nodulation plasmid are necessary for formation of nitrogen-fixing nodules by Rhizobium leguminosarum. Mol. Microbiol. 4:567-574.
5. Phillips DA, Sande ES, Vriezen JAC, de Bruijn FJ, Le Rudulier D, Joseph CM. 1998. A new genetic locus in Sinorhizobium meliloti is involved in stachydrine utilization. Appl. Environ. Microbiol. 64:3954-3960.
6. Streit WR, Joseph CM, Phillips DA. 1996. Biotin and other water-soluble vitamins are key growth factors for alfalfa root colonization by Rhizobium meliloti 1021. Mol. Plant Microbe Interact. 9:330-338.
7. Yost CK, Rath AM, Noel TC, Hynes MF. 2006. Characterization of genes involved in erythritol catabolism in Rhizobium leguminosarum bv. viciae. Microbiology 152:2061-2074.
8. Ding H, Hynes MF. 2009. Plasmid transfer systems in the rhizobia. Can. J. Microbiol. 55:917-927.
9. Ding H, Yip CB, Geddes BA, Oresnik IJ, Hynes MF. 2012. Glycerol utilization by Rhizobium leguminosarum requires an ABC transporter and affects competition for nodulation. Microbiology 158:1369-1378.
10. Brom S, GarcíA-delos Santos A, Cervantes L, Palacios R, Romero D. 2000. In Rhizobium etli symbiotic plasmid transfer, nodulation competitivity and cellular growth require interaction among different replicons. Plasmid 44:34-43.
11. Hooykaas PJJ, Van Brussel AAN, Den Dulk Ras H, Vanslogteren GMS, Schilperoort RA. 1981. Sym plasmid of Rhizobium trifolii expressed in different rhizobial species and Agrobacterium tumefaciens. Nature 291: 351-353.
12. Johnston AWB, Hombrecher G, Brewin NJ, Cooper MC. 1982. Two transmissible plasmids in Rhizobium leguminosarum strain 300. J. Gen. Microbiol. 128:85-93.
13. Sepúlveda E, Pérez-Mendoza D, Ramírez-Romero MA, Soto MJ, López- Lara IM, Geiger O, Sanjuán J, Brom S, Romero D. 2008. Transcriptional interference and repression modulate the conjugative ability of the symbiotic plasmid of Rhizobium etli. J. Bacteriol. 190:4189-4197.
14. Gomes-Barcellos F, Menna P, da Silva Batista JS, Hungria M. 2007. Evidence of horizontal transfer of symbiotic genes from a Bradyrhizobium japonicum inoculant strain to indigenous diazotrophs Sinorhizobium (Ensifer) fredii and Bradyrhizobium elkanii in a Brazilian savannah soil. Appl. Environ. Microbiol. 73:2635-2643.
15. Kinkle BK, Schmidt EJ. 1990. Conjugal transfer and stability of a pea symbiotic plasmid in nonsterile soil, abstr N-14, p 251. Abstr. 90th Annu. Meet. Am. Soc. Microbiol. American Society for Microbiology, Washington, DC.
16. Schofield PR, Gibson AH, Dudman WF, Watson JM. 1987. Evidence for genetic exchange and recombination of Rhizobium symbiotic plasmids in a soil population. Appl. Environ. Microbiol. 53:2942-2947.
17. Poole PS, Blyth A, Reid CJ, Walters K. 1994. Myo-inositol catabolism and catabolite regulation in Rhizobium leguminosarum bv. viciae. Microbiology 140:2787-2795.
18. Priefer UB. 1989. Genes involved in lipopolysaccharide production and symbiosis are clustered on the chromosome of Rhizobium leguminosarum biovar viciae VF39. J. Bacteriol. 171:6161-6168.
19. Giusti MA, Pistorio M, Lozano MJ, Torres Tejerizo GA, Salas ME, Martini MC, López JL, Draghi WO, Del Papa MF, Pérez-Mendoza D, Sanjuán J, Lagares A. 2012. Genetic and functional characterization of a yet-unclassified rhizobial Dtr (DNA-transfer-and-replication) region from a ubiquitous plasmid conjugal system present in Sinorhizobium meliloti, in Sinorhizobium medicae, and in other nonrhizobial Gramnegative bacteria. Plasmid 67:199-210.
20. Hynes MF, Simon R, Pühler A. 1985. The development of plasmid-free strains of Agrobacterium tumefaciens by using incompatibility with a Rhizobium meliloti plasmid to eliminate pAtC58. Plasmid 13:99-105.
21. Hynes MF, Brucksch K, Priefer U. 1988. Melanin production encoded by a cryptic plasmid in a Rhizobium leguminosarum strain. Arch. Microbiol. 150:326-332.
22. Beringer JE. 1974. R factor transfer in Rhizobium leguminosarum. J. Gen. Microbiol. 84:188-198.
23. Robertsen BK, Aman P, Darvill AG, McNeil M, Albersheim P. 1981. Host-symbiont interactions. V. The structure of acidic extracellular polysaccharides secreted by Rhizobium leguminosarum and Rhizobium trifolii. Plant Physiol. 67:389-400.
24. Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
25. Yost CK, Rochepeau P, Hynes MF. 1998. Rhizobium leguminosarum contains a group of genes that appear to code for methyl-accepting chemotaxis proteins. Microbiology 144:1945-1956.
26. Jones JDG, Gutterson N. 1987. An efficient mobilizable cosmid vector pRK7813 and its use in a rapid method for marker exchange in Pseudomonas fluorescens strain Hv37a. Gene 61:299-306.
27. Quandt J, Hynes MF. 1993. Versatile suicide vectors which allow direct selection for gene replacement in gram-negative bacteria. Gene 127:15-21.
28. Simon R, Priefer U, Pühler A. 1983. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gramnegative bacteria. Nat. Biotechnol. 1:784-791.
29. Rochepeau P, Selinger LB, Hynes MF. 1997. Transposon-like structure of a new plasmid-encoded restriction-modification system in Rhizobium leguminosarum VF39SM. Mol. Gen. Genet. 256:387-396.
30. Beringer JE, Beynon JL, Buchanan-Wollaston AV, Johnston AWB. 1978. Transfer of drug-resistance transposon Tn5 to Rhizobium. Nature 276:633-634.
31. Ruvkun GB, Ausubel FM. 1981. A general method for site-directed mutagenesis in prokaryotes. Nature 289:85-88.
32. Alexeyev MF, Shokolenko IN, Croughan TP. 1995. Improved anti- biotic-resistance gene cassettes and omega elements for Escherichia coli vector construction and in vitro deletion/insertion mutagenesis. Gene 160:63-67.
33. Selbitschka W, Arnold W, Priefer UB, Rottschaefer T, Schmidt M, Simon R, Pühler A. 1991. Characterization of recA genes and recA mutants of Rhizobium meliloti and Rhizobium leguminosarum biovar viciae. Mol. Gen. Genet. 229:86-95.
34. Yost CK, Del Bel KL, Quandt J, Hynes MF. 2004. Rhizobium leguminosarum methyl-accepting chemotaxis protein genes are down-regulated in the pea nodule. Arch. Microbiol. 182:505-513.
35. Fellay R, Frey J, Krisch H. 1987. Interposon mutagenesis of soil and water bacteria: a family of DNA fragments designed for in vitro insertional mutagenesis of gram-negative bacteria. Gene 52:147-154.
36. Farrand SK, O'Morchoe SP, McCutchan J. 1989. Construction of an Agrobacterium tumefaciens C58 recA mutant. J. Bacteriol. 171:5314-5321.
37. Reeve WG, Tiwari RP, Worsley PS, Dilworth MJ, Glenn AR, Howieson JG. 1999. Constructs for insertional mutagenesis, transcriptional signal localization and gene regulation studies in root nodule and other bacteria. Microbiology 145:1307-1316.
38. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
39. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
40. Chaudhuri RR, Loman NJ, Snyder LAS, Bailey CM, Stekel DJ, Pallen MJ. 2008. xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Res. 36:D543-D546.
41. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673-679.
42. 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.
43. Lagesen K, Hallin P, Rodland EA, Staerfeldt Rognes H-HT, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35:3100-3108.
44. Quandt J, Clark RG, Venter AP, Clark SR, Twelker S, Hynes MF. 2004. Modified RP4 and Tn5-Mob derivatives for facilitated manipulation of large plasmids in Gram-negative bacteria. Plasmid 52:1-12.
45. Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop RMI, Peterson KM. 1995. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175-176.
46. Danino VE, Wilkinson A, Edwards A, Downie JA. 2003. Recipientinduced transfer of the symbiotic plasmid pRL1JI in Rhizobium leguminosarum bv. viciae is regulated by a quorum-sensing relay. Mol. Microbiol. 50:511-525.
47. Manoil C, Rosenbusch JP. 1982. Conjugation deficient mutants of Escherichia coli distinguish classes of functions of the outer membrane OmpA protein. Mol. Gen. Genet. 187:148-156.
48. Pérez-Mendoza D, de la Cruz F. 2009. Escherichia coli genes affecting recipient ability in plasmid conjugation: are there any? BMC Genomics 10:71. doi:10.1186/1471-2164-10-71.
49. Ramsay JP, Major AS, Komarovsky VM, Sullivan JT, Dy RL, Hynes MF, Salmond GP, Ronson CW. 26 October 2012. A widely conserved molecular switch controls quorum sensing and symbiosis island transfer in Mesorhizobium loti through expression of a novel antiactivator. Mol. Microbiol. [Epub ahead of print.] doi:10.1111/mmi.12079.