Integron gene cassettes and degradation of compounds associated with industrial waste: The case of the SydneyTar Ponds

PLoS ONE

Volumn 4, Issue 4, 2009, Pages

  Koenig, Jeremy E ^a   Sharp, Christine ^a   Dlutek, Marlena ^a   Curtis, Bruce ^a   Joss, Michael ^b   Boucher, Yan ^c   Doolittle, W Ford ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b MACQUARIE UNIVERSITY   (Australia)

^c Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INTEGRASE; PROTEIN LYSR; REGULATOR PROTEIN; TAR; UNCLASSIFIED DRUG; BACTERIAL DNA; BACTERIAL PROTEIN; LYSR PROTEIN, BACTERIA; RNA 16S; TRANSCRIPTION FACTOR;

ARTICLE; AUTOREGULATION; BIODEGRADATION; BIOREMEDIATION; CANADA; CATABOLISM; COAL MINING; CONTROLLED STUDY; ENVIRONMENTAL EXPOSURE; ESTUARY; GENE AMPLIFICATION; GENE CASSETTE; GENE FUNCTION; GENE LIBRARY; GENETIC ASSOCIATION; HORIZONTAL GENE TRANSFER; INDUSTRIAL WASTE; INTEGRON; IRON AND STEEL INDUSTRY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; POND; PROTEIN FUNCTION; REGULON; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; UNINDEXED SEQUENCE; ALGORITHM; CHEMISTRY; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; MICROBIOLOGY; PHYLOGENY;

LANGAT VIRUS;

ALGORITHMS; BACTERIAL PROTEINS; BIODEGRADATION, ENVIRONMENTAL; DNA, BACTERIAL; GENE TRANSFER, HORIZONTAL; GENETIC VARIATION; INDUSTRIAL WASTE; INTEGRONS; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION FACTORS; WATER MICROBIOLOGY;

EID: 65449187902     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005276     Document Type: Article

References (54)

1. Stokes HW, Hall RM (1989) A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol Microbiol 3: 1669-1683.
2. Collis CM, Stokes HW, Hall RM (2002) Integron-encoded IntI integrases preferentially recognize the adjacent cognate attI site in recombination with a 59-be site. Mol Microbiol. pp 1415-1427.
3. Chen CY, Wu KM, Chang YC, Chang CH, Tsai HC, et al. (2003) Comparative genome analysis of Vibrio vulnificus, a marine pathogen. Genome Res 13: 2577-2587.
4. Rowe-Magnus DA, Guerout AM, Biskri L, Bouige P, Mazel D (2003) Comparative analysis of superintegrons: engineering extensive genetic diversity in the Vibrionaceae. Genome Res 13: 428-442.
5. Levesque C, Brassard S, Lapointe J, Roy PH (1994) Diversity and relative strength of tandem promoters for the antibiotic-resistance genes of several integrons. Gene 142: 49-54.
6. Boucher Y, Labbate M, Koenig JE, Stokes HW (2007) Integrons: mobilizable platforms that promote genetic diversity in bacteria. Trends Microbiol 15: 301-309.
7. Mazel D (2006) Integrons: agents of bacterial evolution. Nat Rev Microbiol 4: 608-620.
8. Wright MS, Baker-Austin C, Lindell AH, Stepanauskas R, Stokes HW, et al. (2008) Influence of industrial contamination on mobile genetic elements: class 1 integron abundance and gene cassette structure in aquatic bacterial communities. ISME J 2: 417-428.
9. Furimsky E (2002) Sydney tar ponds: some problems in quantifying toxic waste. Environ Manage 30: 872-879.
10. Atwell P HP, Kozak J, Morin K (1982) Ambient Air PAH Study in Sydney Nova Scotia. Environmental Protection Services: Environment Canada.
11. Lambert TW, Lane S (2004) Lead, arsenic, and polycyclic aromatic hydrocarbons in soil and house dust in the communities surrounding the Sydney, Nova Scotia, tar ponds. Environ Health Perspect 112: 35-41.
12. Band P CM, Henry J, Zielinski J, Jiang H, Semenciw R (2003) Mortality Rates within Sydney, Nova Scotia, by Exposure Areas to Airborne Coke Ovens and Steel Mill Emissions. Health Canada. pp 1961-1988.
13. Guernsey JR, Dewar R, Weerasinghe S, Kirkland S, Veugelers PJ (2000) Incidence of cancer in Sydney and Cape Breton County, Nova Scotia 1979-1997. Can J Public Health 91: 285-292.
14. Dodds L, Seviour R (2001) Congenital anomalies and other birth outcomes among infants born to women living near a hazardous waste site in Sydney, Nova Scotia. Can J Public Health 92: 331-334.
15. Stokes HW, Holmes AJ, Nield BS, Holley MP, Nevalainen KM, et al. (2001) Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA. Appl Environ Microbiol 67: 5240-5246.
16. Holmes AJ, Gillings MR, Nield BS, Mabbutt BC, Nevalainen KM, et al. (2003) The gene cassette metagenome is a basic resource for bacterial genome evolution. Environ Microbiol 5: 383-394.
17. Koenig JE, Boucher Y, Charlebois RL, Nesbo C, Zhaxybayeva O, et al. (2008) Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments. Environ Microbiol.
18. Ferry JG (1992) Methane from acetate. J Bacteriol 174: 5489-5495.
19. Lovley DR (2001) Bioremediation. Anaerobes to the rescue. Science 293: 1444-1446.
20. Jackson BE, Bhupathiraju VK, Tanner RS, Woese CR, McInerney MJ (1999) Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms. Arch Microbiol 171: 107-114.
21. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
22. Hong SH, Bunge J, Jeon SO, Epstein SS (2006) Predicting microbial species richness. Proc Natl Acad Sci U S A 103: 117-122.
23. Elsaied H, Stokes HW, Nakamura T, Kitamura K, Fuse H, et al. (2007) Novel and diverse integron integrase genes and integron-like gene cassettes are prevalent in deep-sea hydrothermal vents. Environ Microbiol 9: 2298-2312.
24. Nemergut DR, Martin AP, Schmidt SK (2004) Integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution. Appl Environ Microbiol 70: 1160-1168.
25. Chao A (1984) Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11: 265-270.
26. Schell MA (1993) Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47: 597-626.
27. Rothmel RK, Aldrich TL, Houghton JE, Coco WM, Ornston LN, et al. (1990) Nucleotide sequencing and characterization of Pseudomonas putida catR: a positive regulator of the catBC operon is a member of the LysR family. J Bacteriol 172: 922-931.
28. Coco WM, Rothmel RK, Henikoff S, Chakrabarty AM (1993) Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida. J Bacteriol 175: 417-427.
29. Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GS, et al. (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 23: 873-878.
30. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
31. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, et al. (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36: D480-484.
32. Timmis KN, Pieper DH (1999) Bacteria designed for bioremediation. Trends Biotechnol 17: 200-204.
33. Lawrence JG, Roth JR (1996) Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143: 1843-1860.
34. Zhang J, Rosenberg HF, Nei M (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A 95: 3708-3713.
35. Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, et al. (2006) Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genet 2: e214. doi:10.1371/journal.pgen.0020214.
36. Katz LA, Curtis EA, Pfunder M, Landweber LF (2000) Characterization of novel sequences from distantly related taxa by walking PCR. Mol Phylogenet Evol 14: 318-321.
37. Huson DH, Auch AF, Qi J, Schuster SC (2007) MEGAN analysis of metagenomic data. Genome Res 17: 377-386.
38. Qiu R, Zhao B, Liu J, Huang X, Li Q, et al. (2008) Sulfate reduction and copper precipitation by a Citrobacter sp. isolated from a mining area. J Hazard Mater.
39. JDAC LE (2000) Phase II/III Environmental Site Assessment Muggah Creek Watershed Sydney, Nova Scotia. Nova Scotia Department of Transportation and Public Works.
40. Atlas RM (2005) Handbook of media for environmental microbiology, 2nd ed. Francis T, ed. 664 p.
41. Baker GC, Smith JJ, Cowan DA (2003) Review and re-analysis of domain-specific 16S primers. J Microbiol Methods 55: 541-555.
42. 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.
43. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
44. Gordon D (2004) Viewing and Editing Assembled Sequences Using Consed. Current Protocols in Bioinformatics 11.2.1-11.2.43.
45. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
46. Saldanha AJ (2004) Java Treeview - extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
47. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
48. Guindon S, Lethiec F, Duroux P, Gascuel O (2005) PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 33: W557-559.
49. Gillings M, Boucher Y, Labbate M, Holmes A, Krishnan S, et al. (2008) The evolution of class 1 integrons and the rise of antibiotic resistance. J Bacteriol 190: 5095-5100.
50. Stamatakis A (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 2688-2690.
51. Ferraroni M, Kolomytseva MP, Solyanikova IP, Scozzafava A, Golovleva LA, et al. (2006) Crystal structure of 3-chlorocatechol 1,2-dioxygenase key enzyme of a new modified ortho-pathway from the Gram-positive Rhodococcus opacus 1CP grown on 2-chlorophenol. J Mol Biol 360: 788-799.
52. Ornston LN (1966) The conversion of catechol and protocatechuate to beta-ketoadipate by Pseudomonas putida. 3. Enzymes of the catechol pathway. J Biol Chem 241: 3795-3799.
53. Shen X, Liu S (2005) Key enzymes of the protocatechuate branch of the beta-ketoadipate pathway for aromatic degradation in Corynebacterium glutamicum. Sci China C Life Sci 48: 241-249.
54. Platt A, Shingler V, Taylor SC, Williams PA (1995) The 4-hydroxy-2-oxovalerate aldolase and acetaldehyde dehydrogenase (acylating) encoded by the nahM and nahO genes of the naphthalene catabolic plasmid pWW60-22 provide further evidence of conservation of meta-cleavage pathway gene sequences. Microbiology 141 (Pt 9): 2223-2233.