Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 46, 2015, Pages 14343-14347

  Anda, Mizue ^a,b   Ohtsubo, Yoshiyuki ^a   Okubo, Takashi ^a   Sugawara, Masayuki ^a   Nagata, Yuji ^a   Tsuda, Masataka ^a   Minamisawa, Kiwamu ^a   Mitsui, Hisayuki ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

Aureimonas; Chromosome; Genome rearrangement; Plasmid; Ribosomal RNA operon

Indexed keywords

RIBOSOME RNA; TRANSFER RNA; BACTERIAL RNA;

ALPHAPROTEOBACTERIA; ARTICLE; AURANTIMONADACEAE; AUREIMONAS; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL STRAIN; CHROMOSOME REARRANGEMENT; CLADISTICS; NONHUMAN; OPERON; PHYLOGENY; PLASMID; PRIORITY JOURNAL; REPLICON; GENETICS;

ALPHAPROTEOBACTERIA; OPERON; PLASMIDS; RNA, BACTERIAL; RNA, RIBOSOMAL;

EID: 84947557643     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1514326112     Document Type: Article

References (54)

1. Egan ES, Fogel MA, Waldor MK (2005) Divided genomes: Negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol Microbiol 56(5): 1129-1138.
2. Harrison PW, Lower RPJ, Kim NKD, Young JPW (2010) Introducing the bacterial 'chromid': Not a chromosome, not a plasmid. Trends Microbiol 18(4):141-148.
3. Reyes-Lamothe R, Nicolas E, Sherratt DJ (2012) Chromosome replication and segregation in bacteria. Annu Rev Genet 46:121-143.
4. Suwanto A, Kaplan S (1989) Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: Presence of two unique circular chromosomes. J Bacteriol 171(11):5850-5859.
5. Michaux S, et al. (1993) Presence of two independent chromosomes in the Brucella melitensis 16M genome. J Bacteriol 175(3):701-705.
6. Rodley PD, Römling U, Tümmler B (1995) A physical genome map of the Burkholderia cepacia type strain. Mol Microbiol 17(1):57-67.
7. Yamaichi Y, Iida T, Park K-S, Yamamoto K, Honda T (1999) Physical and genetic map of the genome of Vibrio parahaemolyticus: presence of two chromosomes in Vibrio species. Mol Microbiol 31(5):1513-1521.
8. Kunnimalaiyaan M, Stevenson DM, Zhou Y, Vary PS (2001) Analysis of the replicon region and identification of an rRNA operon on pBM400 of Bacillus megaterium QM B1551. Mol Microbiol 39(4):1010-1021.
9. Battermann A, Disse-Krömker C, Dreiseikelmann B (2003) A functional plasmid-borne rrn operon in soil isolates belonging to the genus Paracoccus. Microbiology 149(Pt 12): 3587-3593.
10. Rathsack K, Reitner J, Stackebrandt E, Tindall BJ (2011) Reclassification of Aurantimonas altamirensis (Jurado et al. 2006), Aurantimonas ureilytica (Weon et al. 2007) and Aurantimonas frigidaquae (Kim et al. 2008) as members of a new genus, Aureimonas gen. nov., as Aureimonas altamirensis gen. nov., comb. nov., Aureimonas ureilytica comb. nov. and Aureimonas frigidaquae comb. nov., and emended descriptions of the genera Aurantimonas and Fulvimarina. Int J Syst Evol Microbiol 61(Pt 11):2722-2728.
11. Anda M, et al. (2011) Isolation and genetic characterization of Aurantimonas and Methylobacterium strains from stems of hypernodulated soybeans. Microbes Environ 26(2):172-180.
12. Liu S-L, Hessel A, Sanderson KE (1993) Genomic mapping with I-Ceu I, an intronencoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci USA 90(14):6874-6878.
13. Gourse RL, Gaal T, Bartlett MS, Appleman JA, Ross W (1996) rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli. Annu Rev Microbiol 50:645-677.
14. Nieto C, Giraldo R, Fernández-Tresguerres E, Díaz R (1992) Genetic and functional analysis of the basic replicon of pPS10, a plasmid specific for Pseudomonas isolated from Pseudomonas syringae patovar savastanoi. J Mol Biol 223(2):415-426.
15. Fernández-Tresguerres ME, Martín M, García de Viedma D, Giraldo R, Díaz-Orejas R (1995) Host growth temperature and a conservative amino acid substitution in the replication protein of pPS10 influence plasmid host range. J Bacteriol 177(15): 4377-4384.
16. Giraldo R, Fernández-Tresguerres ME (2004) Twenty years of the pPS10 replicon: Insights on the molecular mechanism for the activation of DNA replication in iteroncontaining bacterial plasmids. Plasmid 52(2):69-83.
17. Giraldo R, Fernández-Tornero C, Evans PR, Díaz-Orejas R, Romero A (2003) A conformational switch between transcriptional repression and replication initiation in the RepA dimerization domain. Nat Struct Biol 10(7):565-571.
18. Weon HY, et al. (2007) Aurantimonas ureilytica sp. nov., isolated from an air sample. Int J Syst Evol Microbiol 57(Pt 8):1717-1720.
19. Mano H, Tanaka F, Nakamura C, Kaga H, Morisaki H (2007) Culturable endophytic bacterial flora of the maturing leaves and roots of rice plants (Oryza sativa) cultivated in a paddy field. Microbes Environ 22(2):175-185.
20. Pinto UM, Pappas KM, Winans SC (2012) The ABCs of plasmid replication and segregation. Nat Rev Microbiol 10(11):755-765.
21. So LY, Chen WY, Lacap-Bugler DC, Seemann M, Watt RM (2014) pZMO7-Derived shuttle vectors for heterologous protein expression and proteomic applications in the ethanol-producing bacterium Zymomonas mobilis. BMC Microbiol 14:68.
22. Ishikawa K, Handa N, Kobayashi I (2009) Cleavage of a model DNA replication fork by a Type I restriction endonuclease. Nucleic Acids Res 37(11):3531-3544.
23. Ishikawa K, Handa N, Sears L, Raleigh EA, Kobayashi I (2011) Cleavage of a model DNA replication fork by a methyl-specific endonuclease. Nucleic Acids Res 39(13): 5489-5498.
24. Kaneko T, et al. (2002) Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res 9(6):189-197.
25. Kiss A, Sain B, Venetianer P (1977) The number of rRNA genes in Escherichia coli. FEBS Lett 79(1):77-79.
26. LaFauci G, Widom RL, Eisner RL, Jarvis ED, Rudner R (1986) Mapping of rRNA genes with integrable plasmids in Bacillus subtilis. J Bacteriol 165(1):204-214.
27. Condon C, Liveris D, Squires C, Schwartz I, Squires CL (1995) rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation. J Bacteriol 177(14):4152-4156.
28. Ikeda S, et al. (2010) Community shifts of soybean stem-associated bacteria responding to different nodulation phenotypes and N levels. ISME J 4(3):315-326.
29. Boisvert F-M, van Koningsbruggen S, Navascués J, Lamond AI (2007) The multifunctional nucleolus. Nat Rev Mol Cell Biol 8(7):574-585.
30. Kitahara K, Miyazaki K (2013) Revisiting bacterial phylogeny: Natural and experimental evidence for horizontal gene transfer of 16S rRNA. Mob Genet Elements 3(1): e24210.
31. Ohtsubo Y, Maruyama F, Mitsui H, Nagata Y, Tsuda M (2012) Complete genome sequence of Acidovorax sp. strain KKS102, a polychlorinated-biphenyl degrader. J Bacteriol 194(24):6970-6971.
32. Angiuoli SV, et al. (2008) Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 12(2):137-141.
33. Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M (2008) GenomeMatcher: A graphical user interface for DNA sequence comparison. BMC Bioinformatics 9:376.
34. Conesa A, et al. (2005) Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674-3676.
35. Mulder N, Apweiler R (2007) InterPro and InterProScan: Tools for protein sequence classification and comparison. Methods Mol Biol 396:59-70.
36. Tamura K, et al. (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739.
37. Lagesen K, et al. (2007) RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100-3108.
38. Langille MG, Brinkman FS (2009) IslandViewer: An integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25(5): 664-665.
39. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS (2011) PHAST: A fast phage search tool. Nucleic Acids Res 39(Web Server issue, Suppl 2):W347-W352.
40. Varani AM, Siguier P, Gourbeyre E, Charneau V, Chandler M (2011) ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol 12(3): R30.
41. Gustafson AM, O'Connell KP, Thomashow MF (2002) Regulation of Sinorhizobium meliloti 1021 rrnA-reporter gene fusions in response to cold shock. Can J Microbiol 48(9):821-830.
42. MacLellan SR, MacLean AM, Finan TM (2006) Promoter prediction in the rhizobia. Microbiology 152(Pt 6):1751-1763.
43. Condon C, Squires C, Squires CL (1995) Control of rRNA transcription in Escherichia coli. Microbiol Rev 59(4):623-645.
44. Brosius J, Dull TJ, Sleeter DD, Noller HF (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148(2):107-127.
45. Lobry JR (1996) Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol 13(5):660-665.
46. Brassinga AKC, Siam R, Marczynski GT (2001) Conserved gene cluster at replication origins of the a-proteobacteria Caulobacter crescentus and Rickettsia prowazekii. J Bacteriol 183(5):1824-1829.
47. Bigot S, Sivanathan V, Possoz C, Barre F-X, Cornet F (2007) FtsK, a literate chromosome segregation machine. Mol Microbiol 64(6):1434-1441.
48. Carnoy C, Roten C-A (2009) The dif/Xer recombination systems in proteobacteria. PLoS One 4(9):e6531.
49. Cole C, Barber JD, Barton GJ (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36(Web Server issue, Suppl 2):W197-W201.
50. Jurado V, Gonzalez JM, Laiz L, Saiz-Jimenez C (2006) Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave. Int J Syst Evol Microbiol 56(Pt 11):2583-2585.
51. Kim MS, Hoa KT, Baik KS, Park SC, Seong CN (2008) Aurantimonas frigidaquae sp. nov., isolated from a water-cooling system. Int J Syst Evol Microbiol 58(Pt 5):1142-1146.
52. Denner EB, et al. (2003) Aurantimonas coralicida gen. nov., sp. nov., the causative agent of white plague type II on Caribbean scleractinian corals. Int J Syst Evol Microbiol 53(Pt 4):1115-1122.
53. Anderson CR, et al. (2009) Aurantimonas manganoxydans, sp. nov. and Aurantimonas litoralis, sp. nov.: Mn(II) oxidizing representatives of a globally distributed clade of alpha-Proteobacteria from the order Rhizobiales. Geomicrobiol J 26(3):189-198.
54. Cho JC, Giovannoni SJ (2003) Fulvimarina pelagi gen. nov., sp. nov., a marine bacterium that forms a deep evolutionary lineage of descent in the order "Rhizobiales". Int J Syst Evol Microbiol 53(Pt 6):1853-1859.