An improved method for including upper size range plasmids in metamobilomes

PLoS ONE

Volumn 9, Issue 8, 2014, Pages

  Norman, Anders ^a,b   Riber, Leise ^a   Luo, Wenting ^a   Li, Li Li ^a   Hansen, Lars Hestbjerg ^a,c   Sørensen, Søren Johannes ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c AARHUS UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM CONJUGATION; BIOLOGY; GENE AMPLIFICATION; GENETICS; GENOME SIZE; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; PLASMID;

COMPUTATIONAL BIOLOGY; CONJUGATION, GENETIC; GENE AMPLIFICATION; GENOME SIZE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PLASMIDS;

EID: 84905918111     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0104405     Document Type: Article

References (43)

1. Norman A, Hansen LH, Sørensen SJ (2009) Conjugative plasmids: vessels of the communal gene pool. Philos Trans R Soc Lond B Biol Sci 364: 2275-2289. doi:10.1098/rstb.2009.0037.
2. Wright GD (2007) The antibiotic resistome: the nexus of chemical and genetic diversity. Nat Rev Micro 5: 175-186. doi:10.1038/nrmicro1614.
3. Schlüter A, Szczepanowski R, Pühler A, Top EM (2007) Genomics of IncP-1 antibiotic resistance plasmids isolated from wastewater treatment plants provides evidence for a widely accessible drug resistance gene pool. FEMS Microbiol Rev 31: 449-477. doi:10.1111/j.1574-6976.2007.00074.x. (Pubitemid 46920252)
4. Sørensen SJ, Bailey M, Hansen LH, Kroer N, Wuertz S (2005) Studying plasmid horizontal transfer in situ: a critical review. Nat Rev Micro 3: 700-710. doi:10.1038/nrmicro1232. (Pubitemid 41195086)
5. Garcillán-Barcia MP, Alvarado A, de la Cruz F (2011) Identification of bacterial plasmids based on mobility and plasmid population biology. FEMS Microbiol Rev 35: 936-956. doi:10.1111/j.1574-6976.2011.00291.x.
6. Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, et al. (2005) Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 63: 219-228. doi:10.1016/j.mimet.2005.03.018. (Pubitemid 41597366)
7. Alvarado A, Garcillán-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.
8. Top E, De Smet I, Verstraete W, Dijkmans R, Mergeay M (1994) Exogenous Isolation of Mobilizing Plasmids from Polluted Soils and Sludges. Appl Environ Microbiol 60: 831-839. (Pubitemid 24077970)
9. Szczepanowski R, Bekel T, Goesmann A, Krause L, Krömeke H, et al. (2008) Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology. J Biotechnol 136: 54-64. doi:10.1016/j.jbiotec. 2008.03.020.
10. Rosario K, Breitbart M (2011) Exploring the viral world through metagenomics. Curr Opin Virol 1: 289-297. doi:10.1016/j.coviro.2011.06.004.
11. Walker A (2012) Welcome to the plasmidome. Nat Rev Micro 10: 379-379. doi:10.1038/nrmicro2804.
12. Li LL, Norman A, Hansen LH, Sørensen SJ (2012) Metamobilomics - expanding our knowledge on the pool of plasmid encoded traits in natural environments using high-throughput sequencing. Clin Microbiol Infect 18: 5-7. doi:10.1111/j.1469-0691.2012.03862.x.
13. Jørgensen TS, Xu Z, Hansen MA, Sørensen SJ, Hansen LH (2014) Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome. PLoS ONE 9: e87924. doi:10.1371/journal.pone.0087924.
14. Zhang T, Zhang XX, Ye L (2011) Plasmid Metagenome Reveals High Levels of Antibiotic Resistance Genes and Mobile Genetic Elements in Activated Sludge. PLoS ONE 6: e26041. doi:10.1371/journal.pone.0026041.
15. Sentchilo V, Mayer AP, Guy L, Miyazaki R, Green Tringe S, et al. (2013) Community-wide plasmid gene mobilization and selection. ISME J 7: 1173-1186.
16. Mukai T, Matsubara K, Takagi Y (1973) Isolation of Circular DNA Molecules from Whole Cellular DNA by Use of ATP-Dependent Deoxyribonuclease. Proc Natl Acad Sci U S A 70: 2884-2887.
17. Kav AB, Benhar I, Mizrahi I (2013) A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches. J Microbiol Methods 95: 272-279. doi:10.1016/j.mimet.2013.09.008.
18. Dean FB, Nelson JR, Giesler TL, Lasken RS (2001) Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification. Genome Res 11: 1095-1099. doi:10.1101/gr.180501. (Pubitemid 32834553)
19. Kav AB, Sasson G, Jami E, Doron-Faigenboim A, Benhar I, et al. (2012) Insights into the bovine rumen plasmidome. Proc Natl Acad Sci U S A 109: 5452-5457. doi:10.1073/pnas.1116410109.
20. Bolivar F, Rodriguez RL, Greene PJ, Betlach MC, Heyneker HL, et al. (1977) Construction and characterization of new cloning vehicle. II. A multipurpose cloning system. Gene 2: 95-113. doi:10.1016/0378-1119(77)90000-2. (Pubitemid 9021046)
21. Sengeløv G, Kristensen KJ, Sørensen AH, Kroer N, Sørensen SJ (2001) Effect of Genomic Location on Horizontal Transfer of a Recombinant Gene Cassette Between Pseudomonas Strains in the Rhizosphere and Spermosphere of Barley Seedlings. Curr Microbiol 42: 160-167. doi:10.1007/s002840010197.
22. Pan X, Urban AE, Palejev D, Schulz V, Grubert F, et al. (2008) A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proc Natl Acad Sci U S A 105: 15499-15504. doi:10.1073/pnas. 0808028105.
23. Fierer N, Jackson JA, Vilgalys R, Jackson RB (2005) Assessment of Soil Microbial Community Structure by Use of Taxon-Specific Quantitative PCR Assays. Appl Environ Microbiol 71: 4117-4120. doi:10.1128/AEM.71.7.4117-4120.2005. (Pubitemid 40980588)
24. Kampmann ML, Fordyce SL, Ávila-Arcos MC, Rasmussen M, Willerslev E, et al. (2011) A simple method for the parallel deep sequencing of full influenza A genomes. J Virol Methods 178: 243-248. doi:10.1016/j.jviromet.2011. 09.001.
25. Peng Y, Leung HCM, Yiu SM, Chin FYL (2011) Meta-IDBA: a de Novo assembler for metagenomic data. Bioinformatics 27: i94-i101. doi:10.1093/bioinformatics/ btr216.
26. Zerbino DR, Birney E (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829. doi:10.1101/gr.074492. 107. (Pubitemid 351645072)
27. Hyatt D, Chen GL, LoCascio P, Land M, Larimer F, et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
28. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. doi:10.1093/ bioinformatics/btp324.
29. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, et al. (2012) The Pfam protein families database. Nucleic Acids Res 40: D290-D301. doi:10.1093/nar/gkr1065.
30. Jones BV, Marchesi JR (2007) Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Meth 4: 55-61. doi:10.1038/nmeth964. (Pubitemid 46029477)
31. Blanco L, Bernad A, Lázaro JM, Martín G, Garmendia C, et al. (1989) Highly efficient DNA synthesis by the phage phi 29 DNA polymerase. Symmetrical mode of DNA replication. J Biol Chem 264: 8935-8940. (Pubitemid 19151620)
32. Figurski DH, Meyer RJ, Helinski DR (1979) Suppression of Co1E1 replication properties by the Inc P-1 plasmid RK2 in hybrid plasmids constructed in vitro. J Mol Biol 133: 295-318.
33. Bahl MI, Hansen LH, Goesmann A, Sørensen SJ (2007) The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established α, β and δ sub-groups. Plasmid 58: 31-43. doi:10.1016/j.plasmid.2006.11. 007. (Pubitemid 46874585)
34. Lin-Chao S, Bremer H (1986) Effect of the bacterial growth rate on replication control of plasmid pBR322 in Escherichia coli. Mol Gen Genet 203: 143-149. doi:10.1007/BF00330395. (Pubitemid 16078945)
35. Bahl MI, Hansen LH, Sørensen SJ (2007) Impact of conjugal transfer on the stability of IncP-1 plasmid pKJK5 in bacterial populations. FEMS Microbiol Lett 266: 250-256. doi:10.1111/j.1574-6968.2006.00536.x. (Pubitemid 44952574)
36. Bahl MI, Sørensen SJ, Hestbjerg Hansen L (2004) Quantification of plasmid loss in Escherichia coli cells by use of flow cytometry. FEMS Microbiol Lett 232: 45-49. doi:10.1016/S0378-1097(04)00015-1. (Pubitemid 38328733)
37. Warburton PJ, Allan E, Hunter S, Ward J, Booth V, et al. (2011) Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease, using transposon-aided capture (TRACA). FEMS Microbiol Ecol 78: 349-354. doi:10.1111/j.1574-6941.2011.01166.x.
38. Del Solar G, Giraldo R, Ruiz-Echevarría MJ, Espinosa M, Díaz-Orejas R (1998) Replication and Control of Circular Bacterial Plasmids. Microbiol Mol Biol Rev 62: 434-464. (Pubitemid 28270281)
39. Thomas CM, Meyer R, Helinski DR (1980) Regions of broad-host-range plasmid RK2 which are essential for replication and maintenance. J Bacteriol 141: 213-222. (Pubitemid 10097651)
40. Meyer R (2009) Replication and conjugative mobilization of broad host-range IncQ plasmids. Plasmid 62: 57-70. doi:10.1016/j.plasmid.2009.05.001.
41. Motallebi-Veshareh M, Rouch DA, Thomas CM (1990) A family of ATPases involved in active partitioning of diverse bacterial plasmids. Mol Microbiol 4: 1455-1463. doi:10.1111/j.1365-2958.1990.tb02056.x.
42. Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EPC, de la Cruz F (2010) Mobility of plasmids. Microbiol Mol Biol Rev 74: 434-452. doi:10.1128/MMBR.00020-10.
43. Santos CL, Tavares F, Thioulouse J, Normand P (2009) A phylogenomic analysis of bacterial helix-turn-helix transcription factors. FEMS Microbiol Rev 33: 411-429. doi:10.1111/j.1574-6976.2008.00154.x.