Chapter 13 : Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818982/9781555818975_Chap13-1.gif /docserver/preview/fulltext/10.1128/9781555818982/9781555818975_Chap13-2.gif


There are two types of evolutionary events that impinge on bacterial genomes: microevolution (mutations and homologous recombination), which produces point mutations, and macroevolution, which results in the acquisition, loss, or rearrangement of large DNA segments ( ). Macroevolutionary events ultimately arise from the import of adaptive traits by means of mobile genetic elements (MGEs). MGEs are basically plasmids, phages, and their integrated counterparts (integrative and conjugative elements [ICEs] and prophages). Genomic islands are fossil remnants of MGEs, since they generally lost mobility by rearrangement after the initial insertion event. Nevertheless, they can sometimes still be mobilized by the recombinogenic activity of IncF plasmids ( ), among other possibilities. In summary, the dynamics of bacterial genomes can be interpreted as resulting from the microevolution of a core genome and the macroevolution of the accessory genome, i.e., the horizontal gene transfer events that give rise to the concept of a pangenome ( ).

Citation: de Toro M, Garcillán-Barcia M, de la Cruz F. 2015. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, p 219-235. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0031-2014
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Genetic map of the conjugation genes of plasmid R388. Three modules related to conjugative transfer are depicted: STB, MOB, and MPF. Genes encoded in the 18-kb fragment comprised between and (GenBank Acc. No. BR000038) are represented by arrows. Genes contained in the same operon are depicted using the same color pattern, as well as the corresponding promoters, which are represented by small arrows. Genes encoding transcription factors are outlined in black. The encoded repressors follow the same color pattern as their corresponding genes and are represented as ovals. The activity of the repressors on the promoters is indicated by lines.

Citation: de Toro M, Garcillán-Barcia M, de la Cruz F. 2015. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, p 219-235. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0031-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Distribution of plasmid sizes in the 255- plasmid collection. The figure represents the size distribution of plasmids in the collection described in Table 1 . The histogram shows the total number of plasmids corresponding to each size class (in logarithmic scale). Plasmid distribution shows a trimodal abundance curve (with calculated median sizes of 1.6, 5.1, and 87 kb). Plasmids in which a relaxase gene was detected are shown in green ( = 187), and those in which it was not, in gray ( = 68).

Citation: de Toro M, Garcillán-Barcia M, de la Cruz F. 2015. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, p 219-235. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0031-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Most frequent combinations between MOB and MPF families in . The six MOB families and four MPF families with representation in proteobacterial plasmids are shown by circles and rectangles, respectively. Existing combinations between MOB and MPF families are depicted by lines following the color code of the corresponding MOB family. The line pattern (boxed at the right of the figure) corresponds to the proteobacterial class in which the MOB-MPF element is hosted. Data were taken from Table S1 in reference .

Citation: de Toro M, Garcillán-Barcia M, de la Cruz F. 2015. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, p 219-235. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0031-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

PLACNET reconstruction of the BIDMC43a genome. The dataset was taken from Bioproject PRJNA219249 and processed by PLACNET as detailed in reference . Contigs are represented by blue nodes, while gray nodes represent reference genomes. The sizes of contig nodes are proportional to the contig length, while those of reference nodes are fixed. Colored node outlines represent contigs containing plasmid-specific protein genes (yellow, RIP proteins; red, relaxases; green, both proteins). Solid edges represent scaffold interactions, while dotted edges represent homology to references.

Citation: de Toro M, Garcillán-Barcia M, de la Cruz F. 2015. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, p 219-235. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0031-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Dendrogram of a 70-plasmid collection from Bioproject PRJNA202876. Plasmids were reconstructed using PLACNET from a collection of 19 carbapenem-resistant strains isolated from three Boston hospitals. Contigs assigned to a given plasmid were taken together; their overall proteome was extracted from the sequences and used to build a hierarchical clustering dendrogram by using the UPGMA algorithm (threshold: 70% identity and 80% coverage) ( ). Different plasmid groups were identified carrying beta-lactam and carbapenem resistance genes, as indicated by different backgrounds colors in the figure. (A) The plasmidome of the 19 carbapenem-resistant strains, identifying 10 different MOB families and 12 different Rep/Inc groups. (B) Beta-lactam and carbapenem resistance plasmids compared to their closely related reference plasmids.

Citation: de Toro M, Garcillán-Barcia M, de la Cruz F. 2015. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, p 219-235. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0031-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

Distribution of Inc/Rep types in the 255– plasmid collection. Plasmid REP types were identified as reported in references and .

Citation: de Toro M, Garcillán-Barcia M, de la Cruz F. 2015. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, p 219-235. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0031-2014
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7
Figure 7

Distribution of MOB types in the 255– plasmid collection. Plasmid MOB types were identified as reported in references and .

Citation: de Toro M, Garcillán-Barcia M, de la Cruz F. 2015. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, p 219-235. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0031-2014
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Ochman H,, Lawrence JG,, Groisman EA . 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405 : 299 304.[PubMed] [CrossRef]
2. de la Cruz F,, Davies J . 2000. Horizontal gene transfer and the origin of species: lessons from bacteria. Trends Microbiol 8 : 128 133.[PubMed] [CrossRef]
3. Jain R,, Rivera MC,, Moore JE,, Lake JA . 2003. Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol 20 : 1598 1602.[PubMed] [CrossRef]
4. Schubert S,, Darlu P,, Clermont O,, Wieser A,, Magistro G,, Hoffmann C,, Weinert K,, Tenaillon O,, Matic I,, Denamur E . 2009. Role of intraspecies recombination in the spread of pathogenicity islands within the Escherichia coli species. PLoS Pathog 5 : e1000257. doi:10.1371/journal.ppat.1000257. [PubMed] [CrossRef]
5. Lapierre P,, Gogarten JP . 2009. Estimating the size of the bacterial pan-genome. Trends Genet 25 : 107 110.[PubMed] [CrossRef]
6. Rasko DA,, Rosovitz MJ,, Myers GS,, Mongodin EF,, Fricke WF,, Gajer P,, Crabtree J,, Sebaihia M,, Thomson NR,, Chaudhuri R,, Henderson IR,, Sperandio V,, Ravel J . 2008. The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 190 : 6881 6893.[PubMed] [CrossRef]
7. Polz MF,, Alm EJ,, Hanage WP . 2013. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet 29 : 170 175.[PubMed] [CrossRef]
8. Nicolas-Chanoine MH,, Bertrand X,, Madec JY . 2014. Escherichia coli ST131, an intriguing clonal group. Clin Microbiol Rev 27 : 543 574.[PubMed] [CrossRef]
9. Petty NK,, Ben Zakour NL,, Stanton-Cook M,, Skippington E,, Totsika M,, Forde BM,, Phan MD,, Gomes Moriel D,, Peters KM,, Davies M,, Rogers BA,, Dougan G,, Rodriguez-Bano J,, Pascual A,, Pitout JD,, Upton M,, Paterson DL,, Walsh TR,, Schembri MA,, Beatson SA . 2014. Global dissemination of a multidrug resistant Escherichia coli clone. Proc Natl Acad Sci USA 111 : 5694 5699.[PubMed] [CrossRef]
10. Lanza VF,, de Toro M,, Garcillán-Barcia MP,, Mora A,, Blanco J,, Coque TM,, de la Cruz F . 2014. Plasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences. PLoS Genet [Epub ahead of print.] doi:10:1371/journal.pgen.1004766.
11. Partridge SR,, Zong Z,, Iredell JR . 2011. Recombination in IS26 and Tn2 in the evolution of multiresistance regions carrying blaCTX-M-15 on conjugative IncF plasmids from Escherichia coli . Antimicrob Agents Chemother 55 : 4971 4978.[PubMed] [CrossRef]
12. Nicolas-Chanoine MH,, Blanco J,, Leflon-Guibout V,, Demarty R,, Alonso MP,, Canica MM,, Park YJ,, Lavigne JP,, Pitout J,, Johnson JR . 2008. Intercontinental emergence of Escherichia coli clone O25:H4-ST131 producing CTX-M-15. J Antimicrob Chemother 61 : 273 281.[PubMed] [CrossRef]
13. Coque TM,, Novais A,, Carattoli A,, Poirel L,, Pitout J,, Peixe L,, Baquero F,, Canton R,, Nordmann P . 2008. Dissemination of clonally related Escherichia coli strains expressing extended-spectrum beta-lactamase CTX-M-15. Emerg Infect Dis 14 : 195 200.[PubMed] [CrossRef]
14. Rogers BA,, Sidjabat HE,, Paterson DL . 2011. Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain. J Antimicrob Chemother 66 : 1 14.[PubMed] [CrossRef]
15. Johnson JR,, Johnston B,, Clabots C,, Kuskowski MA,, Pendyala S,, Debroy C,, Nowicki B,, Rice J . 2010. Escherichia coli sequence type ST131 as an emerging fluoroquinolone-resistant uropathogen among renal transplant recipients. Antimicrob Agents Chemother 54 : 546 550.[PubMed] [CrossRef]
16. Morris D,, McGarry E,, Cotter M,, Passet V,, Lynch M,, Ludden C,, Hannan MM,, Brisse S,, Cormican M . 2012. Detection of OXA-48 carbapenemase in the pandemic clone Escherichia coli O25b:H4-ST131 in the course of investigation of an outbreak of OXA-48-producing Klebsiella pneumoniae . Antimicrob Agents Chemother 56 : 4030 4031.[PubMed] [CrossRef]
17. de Been M,, Lanza VF,, de Toro M,, Sharringa J,, Dohmen W,, Du Y,, Hu J,, Lei Y,, Li N,, Heederik DJJ,, Fluit AC,, Bonten MJM,, Willems RJL,, de la Cruz F,, van Schaik W . 2014. Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages. PLoS Genet [Epub ahead of print.] doi:10:1371/journal.pgen.1004776.
18. Smillie C,, Garcillan-Barcia MP,, Francia MV,, Rocha EP,, de la Cruz F . 2010. Mobility of plasmids. Microbiol Mol Biol Rev 74 : 434 452.[PubMed] [CrossRef]
19. Guynet C,, Cuevas A,, Moncalian G,, de la Cruz F . 2011. The stb operon balances the requirements for vegetative stability and conjugative transfer of plasmid R388. PLoS Genet 7 : e1002073. doi:10.1371/journal.pgen.1002073. [PubMed] [CrossRef]
20. Guynet C,, de la Cruz F . 2011. Plasmid segregation without partition. Mob Genet Elements 1 : 236 241.[PubMed] [CrossRef]
21. de la Cruz F,, Frost LS,, Meyer RJ,, Zechner EL . 2010. Conjugative DNA metabolism in Gram-negative bacteria. FEMS Microbiol Rev 34 : 18 40.[PubMed] [CrossRef]
22. Francia MV,, Varsaki A,, Garcillan-Barcia MP,, Latorre A,, Drainas C,, de la Cruz F . 2004. A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev 28 : 79 100.[PubMed] [CrossRef]
23. Garcillan-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.[PubMed] [CrossRef]
24. Guglielmini J,, Quintais L,, Garcillan-Barcia MP,, de la Cruz F,, Rocha EP . 2011. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet 7 : e1002222. doi:10.1371/journal.pgen.1002222. [PubMed] [CrossRef]
25. Guasch A,, Lucas M,, Moncalian G,, Cabezas M,, Perez-Luque R,, Gomis-Ruth FX,, de la Cruz F,, Coll M . 2003. Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC. Nat Struct Biol 10 : 1002 1010.[PubMed] [CrossRef]
26. Gomis-Ruth FX,, Moncalian G,, Perez-Luque R,, Gonzalez A,, Cabezon E,, de la Cruz F,, Coll M . 2001. The bacterial conjugation protein TrwB resembles ring helicases and F1- ATPase. Nature 409 : 637 641.[PubMed] [CrossRef]
27. Chandler M,, de la Cruz F,, Dyda F,, Hickman AB,, Moncalian G,, Ton-Hoang B . 2013. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat Rev Microbiol 11 : 525 538.[PubMed] [CrossRef]
28. Francia MV,, Clewell DB,, de la Cruz F,, Moncalian G . 2013. Catalytic domain of plasmid pAD1 relaxase TraX defines a group of relaxases related to restriction endonucleases. Proc Natl Acad Sci USA 110 : 13606 13611.[PubMed] [CrossRef]
29. Low HH,, Gubellini F,, Rivera-Calzada A,, Braun N,, Connery S,, Dujeancourt A,, Lu F,, Redzej A,, Fronzes R,, Orlova EV,, Waksman G . 2014. Structure of a type IV secretion system. Nature 508 : 550 553.[PubMed] [CrossRef]
30. Cabezon E,, Ripoll-Rozada J,, Pena A,, de la Cruz F,, Arechaga I . 2014. Towards an integrated model of bacterial conjugation. FEMS Microbiol Rev. [Epub ahead of print.] doi:10.1111/1574-6976.12085. [CrossRef]
31. Guglielmini J,, Neron B,, Abby SS,, Garcillan-Barcia MP,, de la Cruz F,, Rocha EP . 2014. Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion. Nucleic Acids Res 42 : 5715 5727.[PubMed] [CrossRef]
32. Trokter M,, Felisberto-Rodrigues C,, Christie PJ,, Waksman G . 2014. Recent advances in the structural and molecular biology of type IV secretion systems. Curr Opin Struct Biol 27C : 16 23.[PubMed] [CrossRef]
33. Christie PJ,, Whitaker N,, Gonzalez-Rivera C . 2014. Mechanism and structure of the bacterial type IV secretion systems. Biochim Biophys Acta 1843 : 1578 1591.[PubMed] [CrossRef]
34. Guglielmini J,, de la Cruz F,, Rocha EP . 2013. Evolution of conjugation and type IV secretion systems. Mol Biol Evol 30 : 315 331.[PubMed] [CrossRef]
35. Bouet JY,, Nordstrom K,, Lane D . 2007. Plasmid partition and incompatibility: the focus shifts. Mol Microbiol 65 : 1405 1414.[PubMed] [CrossRef]
36. Novick RP . 1987. Plasmid incompatibility. Microbiol Rev 51 : 381 395.[PubMed]
37. Schumacher MA . 2012. Bacterial plasmid partition machinery: a minimalist approach to survival. Curr Opin Struct Biol 22 : 72 79.[PubMed] [CrossRef]
38. Diago-Navarro E,, Hernandez-Arriaga AM,, Lopez-Villarejo J,, Munoz-Gomez AJ,, Kamphuis MB,, Boelens R,, Lemonnier M,, Diaz-Orejas R . 2010. parD toxin-antitoxin system of plasmid R1: basic contributions, biotechnological applications and relationships with closely-related toxin-antitoxin systems. FEBS J 277 : 3097 3117.[PubMed] [CrossRef]
39. del Solar G,, Giraldo R,, Ruiz-Echevarria MJ,, Espinosa M,, Diaz-Orejas R . 1998. Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 62 : 434 464.[PubMed]
40. del Solar G,, Espinosa M . 2000. Plasmid copy number control: an ever-growing story. Mol Microbiol 37 : 492 500.[PubMed] [CrossRef]
41. Kolatka K,, Kubik S,, Rajewska M,, Konieczny I . 2010. Replication and partitioning of the broad-host-range plasmid RK2. Plasmid 64 : 119 134.[PubMed] [CrossRef]
42. Yano H,, Deckert GE,, Rogers LM,, Top EM . 2012. Roles of long and short replication initiation proteins in the fate of IncP-1 plasmids. J Bacteriol 194 : 1533 1543.[PubMed] [CrossRef]
43. Wolk CP,, Vonshak A,, Kehoe P,, Elhai J . 1984. Construction of shuttle vectors capable of conjugative transfer from Escherichia coli to nitrogen-fixing filamentous cyanobacteria. Proc Natl Acad Sci USA 81 : 1561 1565.[PubMed] [CrossRef]
44. Dominguez W,, O’Sullivan DJ . 2013. Developing an efficient and reproducible conjugation-based gene transfer system for bifidobacteria. Microbiology 159 : 328 338.[PubMed] [CrossRef]
45. Bates S,, Cashmore AM,, Wilkins BM . 1998. IncP plasmids are unusually effective in mediating conjugation of Escherichia coli and Saccharomyces cerevisiae: involvement of the tra2 mating system. J Bacteriol 180 : 6538 6543.[PubMed]
46. Martinez-Garcia E,, Calles B,, Arevalo-Rodriguez M,, de Lorenzo V . 2011. pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes. BMC Microbiol 11 : 38. [PubMed] [CrossRef]
47. Encinas D,, Garcillan-Barcia MP,, Santos-Merino M,, Delaye L,, Moya A,, de la Cruz F . 2014. Plasmid conjugation from proteobacteria as evidence for the origin of xenologous genes in cyanobacteria. J Bacteriol 196 : 1551 1559.[PubMed] [CrossRef]
48. Watanabe T . 1963. Episome-mediated transfer of drug resistance in Enterobacteriaceae. VI. High-frequency resistance transfer system in Escherichia coli . J Bacteriol 85 : 788 794.[PubMed]
49. Stocker BAD,, Smith SM,, Ozeki H . 1963. High infectivity of Salmonella typhimurium newly infected by the colI factor. J Gen Microbiol 30 : 201 221.[CrossRef]
50. Watanabe T,, Fukasawa T . 1962. Episome-mediated transfer of drug resistance in Enterobacteriaceae. IV. Interactions between resistance transfer factor and F-factor in Escherichia coli K-12. J Bacteriol 83 : 727 735.[PubMed]
51. Watanabe T,, Nishida H,, Ogata C,, Arai T,, Sato S . 1964. Episome-mediated transfer of drug resistance in Enterobacteriaceae. VII. Two types of naturally occurring R factors. J Bacteriol 88 : 716 726.[PubMed]
52. Meynell E,, Datta N . 1965. Functional homology of the sex-factor and resistance transfer factors. Nature 207 : 884 885.[PubMed] [CrossRef]
53. Meynell E,, Meynell GG,, Datta N . 1968. Phylogenetic relationships of drug-resistance factors and other transmissible bacterial plasmids. Bacteriol Rev 32 : 55 83.[PubMed]
54. Meynell E,, Datta N . 1967. Mutant drug resistant factors of high transmissibility. Nature 214 : 885 887.[PubMed] [CrossRef]
55. Finnegan D,, Willetts N . 1973. The site of action of the F transfer inhibitor. Mol Gen Genet 127 : 307 316.[PubMed] [CrossRef]
56. Finnegan DJ,, Willetts NS . 1971. Two classes of Flac mutants insensitive to transfer inhibition by an F-like R factor. Mol Gen Genet 111 : 256 264.[PubMed] [CrossRef]
57. Timmis KN,, Andres I,, Achtman M . 1978. Fertility repression of F-like conjugative plasmids: physical mapping of the R6--5 finO and finP cistrons and identification of the finO protein. Proc Natl Acad Sci USA 75 : 5836 5840.[PubMed] [CrossRef]
58. Willetts N . 1977. The transcriptional control of fertility in F-like plasmids. J Mol Biol 112 : 141 148.[PubMed] [CrossRef]
59. Willetts NS . 1974. The kinetics of inhibition of Flac transfer by R100 in E. coli . Mol Gen Genet 129 : 123 130.[PubMed] [CrossRef]
60. Glover JNM,, Chaulk SG,, Edwards RA,, Arthur D,, Lu J,, Frost LS . 2014. The FinO family of bacterial RNA chaperones. Plasmid [Epub ahead of print.] doi:10.1016/j.plasmid.2014.07.003. [CrossRef]
61. Fong ST,, Stanisich VA . 1989. Location and characterization of two functions on RP1 that inhibit the fertility of the IncW plasmid R388. J Gen Microbiol 135 : 499 502.[PubMed]
62. Goncharoff P,, Saadi S,, Chang CH,, Saltman LH,, Figurski DH . 1991. Structural, molecular, and genetic analysis of the kilA operon of broad-host-range plasmid RK2. J Bacteriol 173 : 3463 3477.[PubMed]
63. Winans SC,, Walker GC . 1985. Fertility inhibition of RP1 by IncN plasmid pKM101. J Bacteriol 161 : 425 427.[PubMed]
64. Santini JM,, Stanisich VA . 1998. Both the fipA gene of pKM101 and the pifC gene of F inhibit conjugal transfer of RP1 by an effect on traG. J Bacteriol 180 : 4093 4101.[PubMed]
65. Cascales E,, Atmakuri K,, Liu Z,, Binns AN,, Christie PJ . 2005. Agrobacterium tumefaciens oncogenic suppressors inhibit T-DNA and VirE2 protein substrate binding to the VirD4 coupling protein. Mol Microbiol 58 : 565 579.[PubMed] [CrossRef]
66. Chen CY,, Kado CI . 1994. Inhibition of Agrobacterium tumefaciens oncogenicity by the osa gene of pSa. J Bacteriol 176 : 5697 5703.[PubMed]
67. Farrand S,, Kado CI,, Ireland CR . 1981. Suppression of tumorigenicity by the IncW R plasmid pSa in Agrobacterium tumefaciens . Mol Gen Genet 181 : 44 51.[CrossRef]
68. Skippington E,, Ragan MA . 2011. Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev 35 : 707 735.[PubMed] [CrossRef]
69. Garcillan-Barcia MP,, de la Cruz F . 2008. Why is entry exclusion an essential feature of conjugative plasmids? Plasmid 60 : 1 18.[PubMed] [CrossRef]
70. Schuurmans JM,, van Hijum SA,, Piet JR,, Handel N,, Smelt J,, Brul S,, ter Kuile BH . 2014. Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains. Plasmid 72 : 1 8.[PubMed] [CrossRef]
71. Garcia-Quintanilla M,, Ramos-Morales F,, Casadesus J . 2008. Conjugal transfer of the Salmonella enterica virulence plasmid in the mouse intestine. J Bacteriol 190 : 1922 1927.[PubMed] [CrossRef]
72. Stecher B,, Denzler R,, Maier L,, Bernet F,, Sanders MJ,, Pickard DJ,, Barthel M,, Westendorf AM,, Krogfelt KA,, Walker AW,, Ackermann M,, Dobrindt U,, Thomson NR,, Hardt WD . 2012. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae . Proc Natl Acad Sci USA 109 : 1269 1274.[PubMed] [CrossRef]
73. 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.[PubMed] [CrossRef]
74. Gotz A,, Pukall R,, Smit E,, Tietze E,, Prager R,, Tschape H,, van Elsas JD,, Smalla K . 1996. Detection and characterization of broad-host-range plasmids in environmental bacteria by PCR. Appl Environ Microbiol 62 : 2621 2628.[PubMed]
75. Alvarado A,, Garcillan-Barcia MP,, de la Cruz F . 2012. A degenerate primer MOB typing (DPMT) method to classify gamma-proteobacterial plasmids in clinical and environmental settings. PLoS One 7 : e40438. doi:10.1371/journal.pone.0040438. [PubMed] [CrossRef]
76. Garcillan-Barcia MP,, de la Cruz F . 2013. Ordering the bestiary of genetic elements transmissible by conjugation. Mob Genet Elements 3 : e24263. doi:10.4161/mge.24263. [PubMed] [CrossRef]
77. Garcillan-Barcia MP,, Ruiz del Castillo B,, Alvarado A,, de la Cruz F,, Martinez-Martinez L . 2014. Degenerate primer MOB typing of multiresistant clinical isolates of E. coli uncovers new plasmid backbones. Plasmid [Epub ahead of print.] doi:10:1016/j.plasmid.2014.11.003.
78. Miyamoto M,, Motooka D,, Gotoh K,, Imai T,, Yoshitake K,, Goto N,, Iida T,, Yasunaga T,, Horii T,, Arakawa K,, Kasahara M,, Nakamura S . 2014. Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes. BMC Genomics 15 : 699. [PubMed] [CrossRef]
79. Liu L,, Li Y,, Li S,, Hu N,, He Y,, Pong R,, Lin D,, Lu L,, Law M . 2012. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012 : 251364. [PubMed] [CrossRef]
80. Brolund A,, Franzen O,, Melefors O,, Tegmark-Wisell K,, Sandegren L . 2013. Plasmidome-analysis of ESBL-producing Escherichia coli using conventional typing and high-throughput sequencing. PLoS One 8 : e65793. doi:10.1371/journal.pone.0065793. [PubMed] [CrossRef]
81. Smoot ME,, Ono K,, Ruscheinski J,, Wang PL,, Ideker T . 2011. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27 : 431 432.[PubMed] [CrossRef]
82. Leverstein-van Hall MA,, Dierikx CM,, Cohen Stuart J,, Voets GM,, van den Munckhof MP,, van Essen-Zandbergen A,, Platteel T,, Fluit AC,, van de Sande-Bruinsma N,, Scharinga J,, Bonten MJ,, Mevius DJ . 2011. Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains. Clin Microbiol Infect 17 : 873 880.[PubMed] [CrossRef]
83. Kluytmans JA,, Overdevest IT,, Willemsen I,, Kluytmans-van den Bergh MF,, van der Zwaluw K,, Heck M,, Rijnsburger M,, Vandenbroucke-Grauls CM,, Savelkoul PH,, Johnston BD,, Gordon D,, Johnson JR . 2013. Extended-spectrum beta-lactamase-producing Escherichia coli from retail chicken meat and humans: comparison of strains, plasmids, resistance genes, and virulence factors. Clin Infect Dis 56 : 478 487.[PubMed] [CrossRef]
84. Datta N,, Hughes VM . 1983. Plasmids of the same Inc groups in Enterobacteria before and after the medical use of antibiotics. Nature 306 : 616 617.[PubMed] [CrossRef]
85. Carattoli A . 2013. Plasmids and the spread of resistance. Int J Med Microbiol 303 : 298 304.[PubMed] [CrossRef]
86. Carattoli A,, Zankari E,, Garcia-Fernandez A,, Voldby Larsen M,, Lund O,, Villa L,, Moller Aarestrup F,, Hasman H . 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58 : 3895 3903.[PubMed] [CrossRef]
87. Hoffmann M,, Zhao S,, Pettengill J,, Luo Y,, Monday SR,, Abbott J,, Ayers SL,, Cinar HN,, Muruvanda T,, Li C,, Allard MW,, Whichard J,, Meng J,, Brown EW,, McDermott PF . 2014. Comparative genomic analysis and virulence differences in closely related Salmonella enterica serotype Heidelberg isolates from humans, retail meats, and animals. Genome Biol Evol 6 : 1046 1068.[PubMed] [CrossRef]
88. Avila P,, Nunez B,, de la Cruz F . 1996. Plasmid R6K contains two functional oriTs which can assemble simultaneously in relaxosomes in vivo . J Mol Biol 261 : 135 143.[PubMed] [CrossRef]
89. Egawa R,, Hirota Y . 1962. Inhibition of fertility by multiple drug-resistance in Escherichia coli K-12. Jpn J Genet 37 : 66 69.[CrossRef]
90. Edwards S,, Meynell GG . 1968. General method for isolating de-repressed bacterial sex factors. Nature 219 : 869 870.[PubMed] [CrossRef]
91. Fernandez-Lopez R,, Del Campo I,, Revilla C,, Cuevas A,, de la Cruz F . 2014. Negative feedback and transcriptional overshooting in a regulatory network for horizontal gene transfer. PLoS Genet 10 : e1004171. doi:10.1371/journal.pgen.1004171. [PubMed] [CrossRef]
92. Haft RJ,, Mittler JE,, Traxler B . 2009. Competition favours reduced cost of plasmids to host bacteria. ISME J 3 : 761 769.[PubMed] [CrossRef]
93. Will WR,, Frost LS . 2006. Characterization of the opposing roles of H-NS and TraJ in transcriptional regulation of the F-plasmid tra operon. J Bacteriol 188 : 507 514.[PubMed] [CrossRef]
94. Silverman PM,, Rother S,, Gaudin H . 1991. Arc and Sfr functions of the Escherichia coli K-12 arcA gene product are genetically and physiologically separable. J Bacteriol 173 : 5648 5652.[PubMed]
95. Strohmaier H,, Noiges R,, Kotschan S,, Sawers G,, Hogenauer G,, Zechner EL,, Koraimann G . 1998. Signal transduction and bacterial conjugation: characterization of the role of ArcA in regulating conjugative transfer of the resistance plasmid R1. J Mol Biol 277 : 309 316.[PubMed] [CrossRef]
96. Camacho EM,, Casadesus J . 2002. Conjugal transfer of the virulence plasmid of Salmonella enterica is regulated by the leucine-responsive regulatory protein and DNA adenine methylation. Mol Microbiol 44 : 1589 1598.[PubMed] [CrossRef]
97. Camacho EM,, Casadesus J . 2005. Regulation of traJ transcription in the Salmonella virulence plasmid by strand-specific DNA adenine hemimethylation. Mol Microbiol 57 : 1700 1718.[PubMed] [CrossRef]
98. Starcic M,, Zgur-Bertok D,, Jordi BJ,, Wosten MM,, Gaastra W,, van Putten JP . 2003. The cyclic AMP-cyclic AMP receptor protein complex regulates activity of the traJ promoter of the Escherichia coli conjugative plasmid pRK100. J Bacteriol 185 : 1616 1623.[PubMed] [CrossRef]
99. Starcic-Erjavec M,, van Putten JP,, Gaastra W,, Jordi BJ,, Grabnar M,, Zgur-Bertok D . 2003. H-NS and Lrp serve as positive modulators of traJ expression from the Escherichia coli plasmid pRK100. Mol Genet Genomics 270 : 94 102.[PubMed] [CrossRef]
100. Camacho EM,, Serna A,, Madrid C,, Marques S,, Fernandez R,, de la Cruz F,, Juarez A,, Casadesus J . 2005. Regulation of finP transcription by DNA adenine methylation in the virulence plasmid of S almonella enterica . J Bacteriol 187 : 5691 5699.[PubMed] [CrossRef]
101. Lau-Wong IC,, Locke T,, Ellison MJ,, Raivio TL,, Frost LS . 2008. Activation of the Cpx regulon destabilizes the F plasmid transfer activator, TraJ, via the HslVU protease in Escherichia coli . Mol Microbiol 67 : 516 527.[PubMed] [CrossRef]
102. Wong JJ,, Lu J,, Glover JN . 2012. Relaxosome function and conjugation regulation in F-like plasmids: a structural biology perspective. Mol Microbiol 85 : 602 617.[PubMed] [CrossRef]
103. Toleman MA,, Walsh TR . 2011. Combinatorial events of insertion sequences and ICE in Gram-negative bacteria. FEMS Microbiol Rev 35 : 912 935.[PubMed] [CrossRef]
104. Parks AR,, Peters JE . 2009. Tn7 elements: engendering diversity from chromosomes to episomes. Plasmid 61 : 1 14.[PubMed] [CrossRef]
105. De Gelder L,, Ponciano JM,, Joyce P,, Top EM . 2007. Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology 153 : 452 463.[PubMed] [CrossRef]
106. Heuer H,, Fox RE,, Top EM . 2007. Frequent conjugative transfer accelerates adaptation of a broad-host-range plasmid to an unfavorable Pseudomonas putida host. FEMS Microbiol Ecol 59 : 738 748.[PubMed] [CrossRef]
107. Dahlberg C,, Chao L . 2003. Amelioration of the cost of conjugative plasmid carriage in Eschericha coli K12. Genetics 165 : 1641 1649.[PubMed]
108. Humphrey B,, Thomson NR,, Thomas CM,, Brooks K,, Sanders M,, Delsol AA,, Roe JM,, Bennett PM,, Enne VI . 2012. Fitness of Escherichia coli strains carrying expressed and partially silent IncN and IncP1 plasmids. BMC Microbiol 12 : 53. [PubMed] [CrossRef]
109. Carattoli A . 2009. Resistance plasmid families in Enterobacteriaceae . Antimicrob Agents Chemother 53 : 2227 2238.[PubMed] [CrossRef]
110. de Toro M,, Rojo-Bezares B,, Vinue L,, Undabeitia E,, Torres C,, Saenz Y . 2010. In vivo selection of aac(6′)-Ib-cr and mutations in the gyrA gene in a clinical qnrS1-positive Salmonella enterica serovar Typhimurium DT104B strain recovered after fluoroquinolone treatment. J Antimicrob Chemother 65 : 1945 1949.[PubMed] [CrossRef]
111. Garcia-Fernandez A,, Fortini D,, Veldman K,, Mevius D,, Carattoli A . 2009. Characterization of plasmids harbouring qnrS1, qnrB2 and qnrB19 genes in Salmonella . J Antimicrob Chemother 63 : 274 281.[PubMed] [CrossRef]
112. San Millan A,, Escudero JA,, Gutierrez B,, Hidalgo L,, Garcia N,, Llagostera M,, Dominguez L,, Gonzalez-Zorn B . 2009. Multiresistance in Pasteurella multocida is mediated by coexistence of small plasmids. Antimicrob Agents Chemother 53 : 3399 3404.[PubMed] [CrossRef]
113. Lorenzo-Diaz F,, Fernandez-Lopez C,, Garcillan-Barcia MP,, Espinosa M . 2014. Bringing them together: plasmid pMV158 rolling circle replication and conjugation under an evolutionary perspective. Plasmid 74 : 15 31.[PubMed] [CrossRef]
114. Rijavec M,, Budic M,, Mrak P,, Muller-Premru M,, Podlesek Z,, Zgur-Bertok D . 2007. Prevalence of ColE1-like plasmids and colicin K production among uropathogenic Escherichia coli strains and quantification of inhibitory activity of colicin K. Appl Environ Microbiol 73 : 1029 1032.[PubMed] [CrossRef]
115. Tan Y,, Riley MA . 1997. Nucleotide polymorphism in colicin E2 gene clusters: evidence for nonneutral evolution. Mol Biol Evol 14 : 666 673.[PubMed] [CrossRef]
116. Watson RJ,, Vernet T,, Visentin LP . 1985. Relationships of the Col plasmids E2, E3, E4, E5, E6, and E7: restriction mapping and colicin gene fusions. Plasmid 13 : 205 210.[PubMed] [CrossRef]
117. Gregorova D,, Pravcova M,, Karpiskova R,, Rychlik I . 2002. Plasmid pC present in Salmonella enterica serovar Enteritidis PT14b strains encodes a restriction modification system. FEMS Microbiol Lett 214 : 195 198.[PubMed] [CrossRef]
118. Zakharova MV,, Beletskaya IV,, Denjmukhametov MM,, Yurkova TV,, Semenova LM,, Shlyapnikov MG,, Solonin AS . 2002. Characterization of pECL18 and pKPN2: a proposed pathway for the evolution of two plasmids that carry identical genes for a type II restriction-modification system. Mol Genet Genomics 267 : 171 178.[PubMed] [CrossRef]
119. Mruk I,, Sektas M,, Kaczorowski T . 2001. Characterization of pEC156, a ColE1-type plasmid from Escherichia coli E1585-68 that carries genes of the EcoVIII restriction-modification system. Plasmid 46 : 128 139.[PubMed] [CrossRef]
120. Miller CA,, Cohen SN . 1978. Phenotypically cryptic EcoRI endonuclease activity specified by the ColE1 plasmid. Proc Natl Acad Sci USA 75 : 1265 1269.[PubMed] [CrossRef]
121. Cabezon E,, Sastre JI,, de la Cruz F . 1997. Genetic evidence of a coupling role for the TraG protein family in bacterial conjugation. Mol Gen Genet 254 : 400 406.[PubMed] [CrossRef]
122. Camps M . 2010. Modulation of ColE1-like plasmid replication for recombinant gene expression. Recent Pat DNA Gene Seq 4 : 58 73.[PubMed] [CrossRef]
123. Fukuoh A,, Iwasaki H,, Ishioka K,, Shinagawa H . 1997. ATP-dependent resolution of R-loops at the ColE1 replication origin by Escherichia coli RecG protein, a Holliday junction-specific helicase. EMBO J 16 : 203 209.[PubMed] [CrossRef]
124. Xu FF,, Gaggero C,, Cohen SN . 2002. Polyadenylation can regulate ColE1 type plasmid copy number independently of any effect on RNAI decay by decreasing the interaction of antisense RNAI with its RNAII target. Plasmid 48 : 49 58.[PubMed] [CrossRef]
125. Dasgupta S,, Masukata H,, Tomizawa J . 1987. Multiple mechanisms for initiation of ColE1 DNA replication: DNA synthesis in the presence and absence of ribonuclease H. Cell 51 : 1113 1122.[PubMed] [CrossRef]
126. Jung YH,, Lee Y . 1995. RNases in ColE1 DNA metabolism. Mol Biol Rep 22 : 195 200.[PubMed] [CrossRef]
127. Colloms SD,, McCulloch R,, Grant K,, Neilson L,, Sherratt DJ . 1996. Xer-mediated site-specific recombination in vitro . EMBO J 15 : 1172 1181.[PubMed]
128. Zaleski P,, Wolinowska R,, Strzezek K,, Lakomy A,, Plucienniczak A . 2006. The complete sequence and segregational stability analysis of a new cryptic plasmid pIGWZ12 from a clinical strain of Escherichia coli . Plasmid 56 : 228 232.[PubMed] [CrossRef]
129. Takechi S,, Matsui H,, Itoh T . 1995. Primer RNA synthesis by plasmid-specified Rep protein for initiation of ColE2 DNA replication. EMBO J 14 : 5141 5147.[PubMed]
130. Takechi S,, Yasueda H,, Itoh T . 1994. Control of ColE2 plasmid replication: regulation of Rep expression by a plasmid-coded antisense RNA. Mol Gen Genet 244 : 49 56.[PubMed] [CrossRef]
131. Butler MS,, Cooper MA . 2011. Antibiotics in the clinical pipeline in 2011. J Antibiotics 64 : 413 425.[PubMed] [CrossRef]
132. Cooper MA,, Shlaes D . 2011. Fix the antibiotics pipeline. Nature 472 : 32. [PubMed] [CrossRef]
133. Brolund A,, Sundqvist M,, Kahlmeter G,, Grape M . 2010. Molecular characterisation of trimethoprim resistance in Escherichia coli and Klebsiella pneumoniae during a two year intervention on trimethoprim use. PLoS One 5 : e9233. doi:10.1371/journal.pone.0009233. [CrossRef]
134. Sundqvist M,, Geli P,, Andersson DI,, Sjolund-Karlsson M,, Runehagen A,, Cars H,, Abelson-Storby K,, Cars O,, Kahlmeter G . 2009. Little evidence for reversibility of trimethoprim resistance after a drastic reduction in trimethoprim use. J Antimicrob Chemother 65 : 350 360.[PubMed] [CrossRef]
135. Yates CM,, Shaw DJ,, Roe AJ,, Woolhouse ME,, Amyes SG . 2006. Enhancement of bacterial competitive fitness by apramycin resistance plasmids from non-pathogenic Escherichia coli . Biol Lett 2 : 463 465.[PubMed] [CrossRef]
136. Perez-Mendoza D,, de la Cruz F . 2009. Escherichia coli genes affecting recipient ability in plasmid conjugation: are there any? BMC Genomics 10 : 71. [PubMed] [CrossRef]
137. Baquero F,, Coque TM,, de la Cruz F . 2011. Ecology and evolution as targets: the need for novel eco-evo drugs and strategies to fight antibiotic resistance. Antimicrob Agents Chemother 55 : 3649 3660.[PubMed] [CrossRef]
138. Novotny C,, Knight WS,, Brinton CC Jr . 1968. Inhibition of bacterial conjugation by ribonucleic acid and deoxyribonucleic acid male-specific bacteriophages. J Bacteriol 95 : 314 326.[PubMed]
139. Ou JT . 1973. Inhibition of formation of Escherichia coli mating pairs by f1 and MS2 bacteriophages as determined with a Coulter counter. J Bacteriol 114 : 1108 1115.[PubMed]
140. Palchoudhury SR,, Iyer VN . 1969. Loss of an episomal fertility factor following the multiplication of coliphage M13. Mol Gen Genet 105 : 131 139.[PubMed] [CrossRef]
141. Cullum J,, Collins JF,, Broda P . 1978. Factors affecting the kinetics of progeny formation with F′lac in Escherichia coli K12. Plasmid 1 : 536 544.[PubMed] [CrossRef]
142. Lin A,, Jimenez J,, Derr J,, Vera P,, Manapat ML,, Esvelt KM,, Villanueva L,, Liu DR,, Chen IA . 2011. Inhibition of bacterial conjugation by phage M13 and its protein g3p: quantitative analysis and model. PLoS One 6 : e19991. [PubMed] [CrossRef]
143. Garcillan-Barcia MP,, Jurado P,, Gonzalez-Perez B,, Moncalian G,, Fernandez LA,, de la Cruz F . 2007. Conjugative transfer can be inhibited by blocking relaxase activity within recipient cells with intrabodies. Mol Microbiol 63 : 404 416.[PubMed] [CrossRef]
144. Fernandez-Lopez R,, Machon C,, Longshaw CM,, Martin S,, Molin S,, Zechner EL,, Espinosa M,, Lanka E,, de la Cruz F . 2005. Unsaturated fatty acids are inhibitors of bacterial conjugation. Microbiology 151 : 3517 3526.[PubMed] [CrossRef]
145. Smith MA,, Coincon M,, Paschos A,, Jolicoeur B,, Lavallee P,, Sygusch J,, Baron C . 2012. Identification of the binding site of Brucella VirB8 interaction inhibitors. Chem Biol 19 : 1041 1048.[PubMed] [CrossRef]
146. Zhou Y,, Call DR,, Broschat SL . 2013. Using protein clusters from whole proteomes to construct and augment a dendrogram. Adv Bioinformatics 2013 : 191586. [PubMed] [CrossRef]
147. Villa L,, Garcia-Fernandez A,, Fortini D,, Carattoli A . 2010. Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants. J Antimicrob Chemother 65 : 2518 2529.[PubMed] [CrossRef]


Generic image for table
Table 1

Genomes sequenced to establish the plasmid collection

Citation: de Toro M, Garcillán-Barcia M, de la Cruz F. 2015. Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Plasmids, p 219-235. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0031-2014

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error