Phylogeny and compatibility: Plasmid classification in the genomics era

Archives of Microbiology

Volumn 193, Issue 5, 2011, Pages 313-321

  Petersen, Jörn ^a  

^a LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

Author keywords

Compatibility; Conjugation; Partitioning operon; Plasmid classification; Replicase; Roseobacter clade

Indexed keywords

CHROMOSOME PROTEIN; PROTEIN DNAA LIKE I; PROTEIN REPA I; PROTEIN REPA II; PROTEIN REPA IV; PROTEIN REPA V; PROTEIN REPABC 1; PROTEIN REPABC 2; PROTEIN REPABC 3; PROTEIN REPABC 5; PROTEIN REPABC 6; PROTEIN REPABC 9; PROTEIN REPB I; PROTEIN REPB II; PROTEIN REPB III; PROTEIN REPC; REPLICATION INITIATOR PROTEIN DNAA; UNCLASSIFIED DRUG;

ALPHAPROTEOBACTERIA; BACTERIAL CHROMOSOME; CLASSIFICATION; FUNCTIONAL GENOMICS; GENE REPLICATION; GENETIC COMPATIBILITY; GENETIC CONSERVATION; MICROBIAL GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLASMID; PRIORITY JOURNAL; REPLICON; SEQUENCE ANALYSIS; SHORT SURVEY; SPECIES DIFFERENCE; SPECIES DISTRIBUTION;

ALPHAPROTEOBACTERIA; CONJUGATION, GENETIC; GENOMICS; PHYLOGENY; PLASMIDS; REPLICON;

ALPHAPROTEOBACTERIA; ROSEOBACTER;

EID: 79958220279     PISSN: 03028933     EISSN: 1432072X     Source Type: Journal    
DOI: 10.1007/s00203-011-0686-9     Document Type: Short Survey

References (42)

1. Bartosik D, Baj J, Wlodarczyk M (1998) Molecular and functional analysis of pTAV320, a repABC-type replicon of the Paracoccus versutus composite plasmid pTAV1. Microbiology 144:3149-3157
2. Bartosik D, Szymanik M, Wysocka E (2001a) Identification of the partitioning site within the repABC-type replicon of the composite Paracoccus versutus plasmid pTAV1. J Bacteriol 183:6234-6243 (Pubitemid 34059395)
3. Bartosik D, Witkowska M, Baj J, Wlodarczyk M (2001b) Characterization and sequence analysis of the replicator region of the novel plasmid pALC1 from Paracoccus alcaliphilus. Plasmid 45:222-226 (Pubitemid 32579409)
4. Brinkhoff T, Giebel HA, Simon M (2008) Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol 189:531-539
5. Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, Threlfall EJ (2005) Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 63:219-228 (Pubitemid 41597366)
6. Cevallos MA, Cervantes-Rivera R, Gutiérrez-Ríos RM (2008) The repABC plasmid family. Plasmid 60:19-37
7. Chattoraj DK (2000) Control of plasmid DNA replication by iterons: no longer paradoxical. Mol Microbiol 37:467-476
8. Couturier M, Bex F, Bergquist PL, Maas WK (1988) Identification and classification of bacterial plasmids. Microbiol Rev 52:375-395
9. Datta N (1985) Plasmids as organisms. In: Helinski DR, Cohen SN, Clewell DB, Jackson DA, Hollaender A (eds) Plasmids in bacteria. Plenum Publishing Corp, New York, pp 3-16
10. Datta N, Hedges RW (1971) Compatibility groups among fi - R factors. Nature 234:222-223
11. Doolittle WF, Papke RT (2006) Genomics and the bacterial species problem. Genome Biol 7:116
12. Ebersbach G, Gerdes K (2005) Plasmid segregation mechanisms. Annu Rev Genet 39:453-479 (Pubitemid 43011123)
13. Figge RM, Easter J, Gober JW (2003) Productive interaction between the chromosome partitioning proteins, ParA and ParB, is required for the progression of the cell cycle in Caulobacter crescentus. Mol Microbiol 47:1225-1237 (Pubitemid 36307848)
14. Fornari CS, Watkins M, Kaplan S (1984) Plasmid distribution and analyses in Rhodopseudomonas sphaeroides. Plasmid 11:39-47
15. Fredericq P (1963) On the nature of colicinogenic factors: a review. J Theoret Biol 4:159-165
16. Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3:722-732 (Pubitemid 41195088)
17. Garcillán-Barcia MP, Francia MV, de la Cruz F (2009) The diversity of conjugative relaxases and its application in plasmid classification. FEMS Microbiol Rev 33:657-687
18. Gelvin SB (2003) Agrobacterium-mediated plant transformation: the biology behind the "gene-jockeying" tool. Microbiol Mol Biol Rev 67:16-37
19. Goodner B, Hinkle G, Gattung S, Miller N, Blanchard M, Qurollo B et al (2001) Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:2323-2328 (Pubitemid 33140550)
20. Jensen LB, Garcia-Migura L, Valenzuela AJS, Løhr M, Hasman H, Aarestrup FM (2010) A classification system for plasmids from enterococci and other Gram-positive bacteria. J Microbiol Methods 80:25-43
21. MacLellan 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 (Pubitemid 40179391)
22. MacLellan SR, Zaheer R, Sartor AL, MacLean AM, Finan TM (2006) Identification of a megaplasmid centromere reveals genetic structural diversity within the repABC family of basic replicons. Mol Microbiol 59:1559-1575
23. Messer W (2002) The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev 26:355-374
24. Moran MA, Belas R, Schell MA, González JM, Sun F, Sun S et al (2007) Ecological genomics of marine Roseobacters. Appl Environ Microbiol 73:4559-4569 (Pubitemid 47122601)
25. Moscoso M, Eritja R, Espinosa M (1997) Initiation of replication of plasmid pMV158: mechanisms of DNA strand-transfer reactions mediated by the initiator RepB protein. J Mol Biol 268:840-856 (Pubitemid 27229168)
26. Novick RP (1987) Plasmid incompatibility. Microbiol Rev 51:381-395
27. Petersen J, Brinkmann H, Pradella S (2009) Diversity and evolution of repABC type plasmids in Rhodobacterales. Environ Microbiol 11:2627-2638
28. Petersen J, Brinkmann H, Berger M, Brinkhoff T, Päuker O, Pradella S (2010) Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacterales. Mol Biol Evol (in press)
29. Phillips G, Funnell B (2004). In: Funnel BE, Phillips JG (eds) Plasmid biology. ASM Press, Washington
30. Pistorio M, Giusti MA, Del Papa MF, Draghi WO, Lozano MJ, Tejerizo GT, Lagares A (2008) Conjugal properties of the Sinorhizobium meliloti plasmid mobilome. FEMS Microbiol Ecol 65:372-382
31. Pradella S, Allgaier M, Hoch C, Päuker O, Stackebrandt E, Wagner-Döbler I (2004) Genome organization and localization of the pufLM genes of the photosynthesis reaction center in phylogenetically diverse marine Alphaproteobacteria. Appl Environ Microbiol 70:3360-3369 (Pubitemid 38745879)
32. Pradella S, Päuker O, Petersen J (2010) Genome organization of the marine Roseobacter clade member Marinovum algicola. Arch Microbiol 192:115-126
33. Ramírez-Romero MA, Soberón N, Pérez-Oseguera A, Téllez-Sosa J, Cevallos MA (2000) Structural elements required for replication and incompatibility of the Rhizobium etli symbiotic plasmid. J Bacteriol 182:3117-3124 (Pubitemid 30326926)
34. Riley MA, Lizotte-Waniewski M (2009) Population genomics and the bacterial species concept. Methods Mol Biol 532:367-377
35. Schumann W et al. (2008). In: Lipps G (ed). Plasmids: current research and future trends. Caister Academic Press, Norfolk, pp 1-263
36. Soberón N, Venkova-Canova T, Ramírez-Romero MA, Téllez-Sosa J, Cevallos MA (2004) Incompatibility and the partitioning site of the repABC basic replicon of the symbiotic plasmid from Rhizobium etli. Plasmid 51:203-216 (Pubitemid 38510367)
37. Swingley WD, Sadekar S, Mastrian SD, Matthies HJ, Hao J, Ramos H et al (2007) The complete genome sequence of Roseobacter denitrificans reveals a mixotrophic rather than photosynthetic metabolism. J Bacteriol 189:683-690
38. Thomas CM (2000) Paradigms of plasmid organization. Mol Microbiol 37:485-491
39. van den Ent F, Møller-Jensen J, Amos LA, Gerdes K, Löwe J (2002) F-actin-like filaments formed by plasmid segregation protein ParM. EMBO J 21:6935-6943
40. Wagner-Döbler I, Ballhausen B, Berger M, BrinkhoV T, Buchholz I, Bunk B et al (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae-a hitchhiker's guide to life in the sea. ISME J. 4:61-77
41. Wang Z, Jin L, Yuan Z, Wegrzyn G, Wegrzyn A (2009) Classification of plasmid vectors using replication origin, selection marker and promoter as criteria. Plasmid 61:47-51
42. Zhong Z, Caspi R, Helinski D, Knauf V, Sykes S, O'Byrne C, Shea TP, Wilkinson JE, DeLoughery C, Toukdarian A (2003) Nucleotide sequence based characterizations of two cryptic plasmids from the marine bacterium Ruegeria isolate PR1b. Plasmid 49:233-252 (Pubitemid 36561415)