Chapter 31
Diversity and Role of Bacterial Integron/Gene Cassette Metagenome in Extreme Marine Environments
Hosam Elsaied,
Akihiko Maruyama,
Hosam Elsaied
National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
Search for more papers by this authorAkihiko Maruyama
National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
Search for more papers by this authorHosam Elsaied,
Akihiko Maruyama,
Hosam Elsaied
National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
Search for more papers by this authorAkihiko Maruyama
National Institute of Advanced Industrial Science and Technology, Ibaraki, Japan
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorSummary
This chapter contains sections titled:
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Introduction
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Internet Resources
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References
INTERNET RESOURCES
- DDBJ clustal W analyses (http://clustalw.ddbj.nig.ac. jp/top-e.html)
- DDBJ blast (http://blast.ddbj.nig.ac.jp/top-e.html)
- REFERENCES
- Ahmed A, Kawaguchi F, Shimamoto T. 2006. Class 2 integrons in Vibrio cholerae. J. Med. Microbiol. 55: 643–644.
- Barlow R, Gobius K. 2006. Diverse class 2 integrons in bacteria from beef cattle sources. J. Antimicrob. Chemother. 58: 1133–1138.
- Biskri L, Bouvier A, Gue'rout M, Boisnard S, Mazel D. 2005. Comparative study of class 1 integron and Vibrio cholerae superintegron integrase activities. J. Bacteriol. 187: 1740–1750.
- Cavanaugh C. 1983. Symbiotic chemoautotrophic bacteria in marine invertebrates from sulfide-rich habitats. Nature 302: 58.
- Cherry R, Desbruyeres D, Heyraud N. 1992. High levels of radioactivity in hydrothermal vent polychaetes. C. R. Acad. Sci. Paris Ser. III 315: 21–26.
- Collis C, Hall R. 1995. Expression of antibiotic resistance genes in the integrated cassettes of integrons. Antimicrob. Agents Chemother. 39: 155–162.
- Duplessis M, Ziebis W, Gros O, Caro A, Robidart J, Felbeck H. 2004. Respiration strategies utilized by the gill endosymbiont from the host Lucinid Codakia orbicularis [Bivalvia: Lucinidae]. Appl. Environ. Microbiol. 70: 4144–4150.
- Elsaied H, Stokes H, Nakamura T, Kitamura K, Fuse H, Maruyama A. 2007. Novel and diverse integron integrase genes and integron-like gene cassettes are prevalent in deep-sea hydrothermal vents. Environ. Microbiol. 9: 2298–2312.
- Esposito D, Scocca J. 1997. The integrase family of tyrosine recombinases: Evolution of a conserved active site domain. Nucleic Acids Res. 25: 3605–3614.
- Felbeck H, Childress J, Somero G. 1981. Calvin Benson cycle and sulfide oxidation enzymes in animals from sulfied-rich habitats. Nature 293: 291–293.
- Gillings M, Krishnan S, Worden P, Hardwick S. 2008. Recovery of diverse genes for class 1 integron-integrases from environmental DNA samples. FEMS Microbiol. Lett. 287: 56–62.
- Grainge I, Jayaram M. 1999. The integrase family of recombinase: Organization and function of the active site. Mol. Microbiol. 33: 449–456.
- Grynberg M, Godzik A. 2004. NERD: a DNA processing-related domain present in the anthrax virulence plasmid, pXO1. TRENDS Biochem. Sciences 29: 106–110.
- Hall R, Brookes D, Stokes H. 1991. Site-specific insertion of genes into integrons: Role of the 59-base element and determination of the recombination cross-over point. Mol. Microbiol. 5: 1941–1959.
- Hou S, Saw J, Lee K, Freitas T, Belisle C, Kawarabayasi Y, et al. 2004. Genome sequence of the deep-sea g-Proteobacterium idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy. Proc. Natl. Acad. Sci. USA 101: 18036–18041.
- Koenig J, Boucher Y, Charlebois R, Nesbø C, Zhaxybayeva O, et al. 2008. Integron-associated gene cassettes in Halifax Harbour: Assessment of a mobile gene pool in marine sediments. Environ. Microbiol. 10: 1024–1038.
- Koenig J, Sharp C, Dlutek M, Curtis B, Joss M, Boucher Y, Doolittle W. 2009. Integron gene cassettes and degradation of compounds associated with industrial waste: the case of the Sydney Tar Ponds. PLoS ONE 4(4): e5276.
- Lee R, Childress J. 1994. Assimilation of inorganic nitrogen by chemoautotrophic and methanotrophic symbioses. Appl. Environ. Microbiol. 60: 1852–1858.
- Magee E, Richardson C, Hughes R, Cummings J. 2000. Contribution of dietary protein to sulfide production in the large intestine: An in vitro and a controlled feeding study in humans. Am. J. Clin. Nutr. 72: 1488–1494.
- Marquez C, Labbate M, Ingold A, Chowdhury P, Ramírez M, et al. 2008. Recovery of a functional class 2 integron from an Escherichia coli strain mediating a urinary tract infection. Antimicrob. Agents Chemother. 52: 4153–4154.
- Mazel D, Dychinco B, Webb V, Davies J. 1998. A distinctive class of integron in the Vibrio cholerae genome. Science 280: 605–608.
- Mazel D. 2006. Integrons: agents of bacterial evolution. Nat. Rev. Microbiol. 4: 608–620.
- Messier N, Roy B. 2001. Integron integrases possess a unique additional domain necessary for activity. J. Bacteriol. 183: 6699–6706.
- Minic Z, Herve G. 2004. Biochemical and enzymological aspects of the symbiosis between the deep-sea tubeworm Riftia pachyptila and its bacterial endosymbiont. Eur. J. Biochem. 271: 3093–3102.
- Nandi S, Maurer J, Hofacre C, Summers A. 2004. Gram positive bacteria are a major reservoir of class 1 antibiotic resistance integrons in poultry litter. Proc. Natl. Acad. Sci. USA 101: 7118–7122.
- Nield B, Holmes A, Gillings M, Recchia G, Mabbutt B, Nevalainen K, Stokes H. 2001. Recovery of new integron classes from environmental DNA. FEMS Microbiol. Lett. 195: 59–65.
- Ochman H, Lawrence J, Groisman EA. 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299–304.
- Pruski A, Dixon D. 2003. Toxic vents and DNA damage: First evidence from a naturally contaminated deep-sea environment. Aquat. Toxicol. 64: 1–13.
- Rodríguez-Minguela C, Apajalahti J, Chai B, Cole J, Tiedje J. 2009. Worldwide prevalence of class 2 integrases outside the clinical setting is associated with human impact. Appl. Environ. Microbiol. 75: 5100–5110.
- Shoemaker N, Vlamakis H, Hayes K, Salyers A. 2001. Evidence for extensive resistance gene transfer among Bacteroides spp. and among Bacteroides and other genera in the human colon. Appl. Environ. Microbiol. 67: 561–568.
- Smalla K, Krogerrecklenfort E, Heuer H, Dejonghe W, Top E, et al. 2000. PCR-based detection of mobile genetic elements in total community DNA. Microbiology 146: 1256–1257.
- Stokes H, Hall R. 1989. A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: Integrons. Mol. Microbiol. 3: 1669–1683.
- Stokes H, O'Gorman D, Recchia G, Parsekhian M, Hall R. 1997. Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol. Microbiol. 26: 731–745.
- Stokes H, Holmes A, Nield B, Holley M, Nevalainen K, Mabbutt B, Gillings M. 2001. Gene cassette PCR: Sequence-independent recovery of entire genes from environmental DNA. Appl. Environ. Microbiol. 67: 5240–5246.
- Wright M, Baker-Austin C, Lindell A, Stepanauskas R, Stokes H, McArthur J. 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.
- Xu H, Davies J, Miao V. 2007. Molecular characterization of class 3 integrons from Delftia spp. J. Bacteriol. 17: 6276–6283.