Sequence analysis of the 181-kb accessory plasmid pSmeSM11b, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment

FEMS Microbiology Letters

Volumn 271, Issue 2, 2007, Pages 297-309

  Stiens, Michael ^a   Schneiker, Susanne ^a   Pühler, Alfred ^a   Schlüter, Andreas ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

Nonribosomal peptide synthesis; Plasmid transfer; repABC; Type IV secretion system

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; CARBOHYDRATE METABOLISM; CONTROLLED STUDY; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC CODE; GENOME ANALYSIS; NITROGEN FIXATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPTIDE SYNTHESIS; PLASMID; PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; RHIZOBIUM; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SINORHIZOBIUM MELILOTI;

CONJUGATION, GENETIC; GENE ORDER; GENES, BACTERIAL; MEDICAGO SATIVA; MOLECULAR SEQUENCE DATA; PLANT ROOTS; PLASMIDS; REPLICON; SEQUENCE ANALYSIS, DNA; SINORHIZOBIUM MELILOTI;

AGROBACTERIUM; FRANKIA; RHIZOBIUM; SINORHIZOBIUM MEDICAE; SINORHIZOBIUM MELILOTI;

EID: 34249037369     PISSN: 03781097     EISSN: 15746968     Source Type: Journal    
DOI: 10.1111/j.1574-6968.2007.00731.x     Document Type: Article

References (47)

1. Barnett MJ, Fisher RF, Jones T et al 2001) Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci USA 98 : 9883 9888.
2. Beringer JE (1974) R factor transfer in Rhizobium leguminosarum. J Gen Microbiol 84 : 188 198.
3. Capela D, Barloy-Hubler F, Gouzy J et al 2001) Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc Natl Acad Sci USA 98 : 9877 9882.
4. Chao TC, Becker A, Buhrmester J, Pühler A Weidner S (2004) The Sinorhizobium meliloti fur gene regulates, with dependence on Mn(II), transcription of the sitABCD operon, encoding a metal-type transporter. J Bacteriol 186 : 3609 3620.
5. Ewing B Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8 : 186 194.
6. Ewing B, Hillier L, Wendl MC Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8 : 175 185.
7. Finan TM, Weidner S, Wong K et al 2001) The complete sequence of the 1683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc Natl Acad Sci USA 98 : 9889 9894.
8. Finking R Marahiel MA (2004) Biosynthesis of nonribosomal peptides. Annu Rev Microbiol 58 : 453 488.
9. Finn RD, Mistry J, Schuster-Bockler B et al 2006) Pfam: clans, web tools and services. Nucleic Acids Res 34 : D247 D251.
10. Galibert F, Finan TM, Long SR et al 2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293 : 668 672.
11. González V, Santamaría RI, Bustos P 2006) The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci USA 103 : 3834 3839.
12. Gordon D, Abajian C Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8 : 195 202.
13. Gordon D, Desmarais C Green P (2001) Automated finishing with autofinish. Genome Res 11 : 614 625.
14. 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.
15. Kapp D, Niehaus K, Quandt J, Müller P Pühler A (1990) Cooperative action of Rhizobium meliloti nodulation and infection mutants during the process of forming mixed infected alfalfa nodules. Plant Cell 2 : 139 151.
16. Keating TA, Ehmann DE, Kohli RM, Marshall CG, Trauger JW Walsh CT (2001) Chain termination steps in nonribosomal peptide synthetase assembly lines: directed acyl-S-enzyme breakdown in antibiotic and siderophore biosynthesis. Chembiochem 2 : 99 107.
17. Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res 29 : 4633 4642.
18. Lambalot RH, Gehring AM, Flugel RS, Zuber P, LaCelle M, Marahiel MA, Reid R, Khosla C Walsh CT (1996) A new enzyme superfamily - the phosphopantetheinyl transferases. Chem Biol 3 : 923 936.
19. Li PL Farrand SK (2000) The replicator of the nopaline-type 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.
20. Li PL, Hwang I, Miyagi H, True H Farrand SK (1999) Essential components of the Ti plasmid trb system, a type IV macromolecular transporter. J Bacteriol 181 : 5033 5041.
21. Luo ZQ, Qin Y Farrand SK (2000) The antiactivator TraM interferes with the autoinducer-dependent binding of TraR to DNA by interacting with the C-terminal region of the quorum-sensing activator. J Biol Chem 275 : 7713 7722.
22. Ma W, Charles TC Glick BR (2004) Expression of an exogenous 1-aminocyclopropane-1-carboxylate deaminase gene in Sinorhizobium meliloti increases its ability to nodulate alfalfa. Appl Environ Microbiol 70 : 5891 5897.
23. Marchler-Bauer A, Anderson JB, Cherukuri PF et al 2005) CDD: a conserved domain database for protein classification. Nucleic Acids Res 33 : D192 D196.
24. Masepohl B, Kutsche M, Riedel KU, Schmehl M, Klipp W Pühler A (1992) Functional analysis of the cysteine motifs in the ferredoxin-like protein FdxN of Rhizobium meliloti involved in symbiotic nitrogen fixation. Mol Gen Genet 233 : 33 41.
25. McLellan SR, Smallbone LA, Sibley CD Finan TM (2005) The expression of a novel antisense gene mediates incompatibility within the large repABC family of alpha-proteobacterial plasmids. Mol Microbiol 55 : 611 623.
26. Mercado-Blanco J Toro N (1996) Plasmids in rhizobia: the role of nonsymbiotic plasmids. Mol Plant-Microbe Interact 9 : 535 545.
27. Meyer F, Goesmann A, McHardy AC et al 2003) GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 31 : 2187 2195.
28. Normand P, Lapierre P, Tisa LS et al 2007) Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography. Genome Res 17 : 7 15.
29. Rolfe BG, Gresshoff PM Shine J (1980) Rapid screening for symbiotic mutants of Rhizobium and white clover. Plant Sci Lett 19 : 277 284.
30. Sambrook J, Fritsch EF Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
31. Sanjuan J Olivares J (1989) Implication of nifA in regulation of genes located on a Rhizobium meliloti cryptic plasmid that affect nodulation efficiency. J Bacteriol 171 : 4154 4161.
32. Schwieger F Tebbe CC (2000) Effect of field inoculation with Sinorhizobium meliloti L33 on the composition of bacterial communities in rhizospheres of a target plant (Medicago sativa) and a non-target plant (Chenopodium album) - linking of 16S rRNA gene-based single-strand conformation polymorphism community profiles to the diversity of cultivated bacteria. Appl Environ Microbiol 66 : 3556 3565.
33. Schwyn B Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160 : 47 56.
34. Selbitschka W, Keller M, Miethling-Graff R, Dresing U, Schwieger F, Krahn I, Homann I, Dammann-Kalinowski T, Pühler A Tebbe CC (2006) Long-term field release of bioluminescent Sinorhizobium meliloti strains to assess the influence of a recA mutation on the strains' survival. Microb Ecol 52 : 583 595.
35. Simon R (1984) High-frequency mobilization of gram-negative bacterial replicons by the in vitro constructed Tn5-mob transposon. Mol Gen Genetics 196 : 413 420.
36. Simon R, Priefer U Pühler A (1983) A broad host range mobilization system for in vivo genetic-engineering - transposon mutagenesis in gram-negative bacteria. Bio-Technology 1 : 784 791.
37. Simon R, O'Connell M, Labes M Pühler A (1986) Plasmid vectors for the genetic analysis and manipulation of rhizobia and other gram-negative bacteria. Methods Enzymol 118 : 640 659.
38. Soto MJ, Zorzano A, Mercado-Blanco J, Lepek V, Olivares J Toro N (1993) Nucleotide sequence and characterization of Rhizobium meliloti nodulation competitiveness genes nfe. J Mol Biol 229 : 570 576.
39. Stachelhaus T, Mootz HD Marahiel MA (1999) The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem Biol 6 : 493 505.
40. Stiens M, Schneiker S, Keller M, Kuhn S, Pühler A Schlüter A (2006) Sequence analysis of the 144-kilobase accessory plasmid pSmeSM11a, isolated from a dominant Sinorhizobium meliloti strain identified during a long-term field release experiment. Appl Environ Microbiol 72 : 3662 3672.
41. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND Koonin EV (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29 : 22 28.
42. Tobin MB, Fleming MD, Skatrud PL Miller JR (1990) Molecular characterization of the acyl-coenzyme A: isopenicillin N acyltransferase gene (penDE) from Penicillium chrysogenum and Aspergillus nidulans and activity of recombinant enzyme in Escherichia coli. J Bacteriol 172 : 5908 5914.
43. Tun-Garrido C, Bustos P, González V Brom S (2003) Conjugative transfer of p42a from Rhizobium etli CFN42, which is required for mobilization of the symbiotic plasmid, is regulated by quorum sensing. J Bacteriol 185 : 1681 1692.
44. Venkova-Canova T, Soberon NE, Ramirez-Romero MA Cevallos MA (2004) Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem-loop structure. Mol Microbiol 54 : 1431 1444.
45. Wheatcroft R, Mcrae DG Miller RW (1990) Changes in the Rhizobium meliloti genome and the ability to detect supercoiled plasmids during bacteroid development. Mol Plant-Microbe Interact 3 : 9 17.
46. Yeats C, Bentley S Bateman A (2003) New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor. BMC Microbiol 3 : 3.
47. Young JP, Crossman LC, Johnston AW et al 2006) The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 7 : R34.