Molecular detection and phylogenetic analysis of the catechol 1,2-dioxygenase gene from Gordonia spp.

Systematic and Applied Microbiology

Volumn 32, Issue 5, 2009, Pages 291-300

  Shen, Fo Ting ^a   Lin, Jyun Liang ^a   Huang, Chieh Chen ^a   Ho, Ying Ning ^a   Arun, A B ^a   Young, Li Sen ^b   Young, Chiu Chung ^a  

^a NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

^b YUANPEI UNIVERSITY   (Taiwan)

Author keywords

Catechol 1,2 dioxygenase gene (catA gene); Gordonia; Oil contaminated soil; Phylogeny

Indexed keywords

AMINO ACID; CATECHOL 1,2 DIOXYGENASE; DNA TOPOISOMERASE (ATP HYDROLYSING) B;

ACTINOBACTERIA; AMINO ACID SEQUENCE; ARTICLE; BIOREMEDIATION; CATABOLISM; CONTROLLED STUDY; ENZYME SUBSTRATE; FRAMESHIFT MUTATION; GENE AMPLIFICATION; GENE DELETION; GENE SEGREGATION; GENETIC CONSERVATION; GENETIC VARIABILITY; GORDONIA; GORDONIA AMICALIS; GORDONIA RHIZOSPHERA; GORDONIA SPUTI; MARKER GENE; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; RNA TRANSLATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; UNINDEXED SEQUENCE;

BACTERIAL PROTEINS; CATECHOL 1,2-DIOXYGENASE; CLUSTER ANALYSIS; DNA PRIMERS; DNA, BACTERIAL; FRAMESHIFT MUTATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; THEACEAE;

ACTINOBACTERIA; GORDONIA AMICALIS; GORDONIA RHIZOSPHERA; GORDONIA SPUTI;

EID: 67650450189     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2009.04.002     Document Type: Article

References (26)

1. Arenskötter M., Bröker D., and Steinbüchel A. Biology of the metabolically diverse genus Gordonia. Appl. Environ. Microbiol. 70 (2004) 3195-3204
2. Cavalca L., Dell'Amico E., and Andreoni V. Intrinsic bioremediability of an aromatic hydrocarbon-polluted groundwater: diversity of bacterial population and toluene monooxygenase genes. Appl. Microbiol. Biotechnol. 64 (2004) 576-587
3. Chandler D.P., and Brockman F.J. Estimating biodegradative gene numbers at a JP-5 contaminated site using PCR. Appl. Biochem. Biotechnol. 57/58 (1996) 971-982
4. Cheung P.Y., and Kinkle B.K. Mycobacterium diversity and pyrene mineralization in petroleum-contaminated soils. Appl. Environ. Microbiol. 67 (2001) 2222-2229
5. Fleming J.T., Sanseverino J., and Sayler G.S. Quantitative relationship between naphthalene catabolic gene frequency and expression in predicting PAH degradation in soils at town gas manufacturing sites. Environ. Sci. Technol. 27 (1993) 1068-1074
6. Hamann C., Hegemann J., and Hildebrandt A. Detection of polycyclic aromatic hydrocarbon degradation genes in different soil bacteria by polymerase chain reaction and DNA hybridization. FEMS Microbiol. Lett. 173 (1999) 255-263
7. Tamura K., Dudley J., Nei M., and Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24 (2007) 1596-1599
8. Lloyd-Jones G., Laurie A.D., Hunter D.W.F., and Fraser R. Analysis of catabolic genes for naphthalene and phenanthrene degradation in contaminated New Zealand soils. FEMS Microbiol. Ecol. 29 (1999) 69-79
9. Milcic-Terzic J., Lopez-Vidal Y., Vrvic M.M., and Saval S. Detection of catabolic genes in indigenous microbial consortia isolated from a diesel-contaminated soil. Bioresour. Technol. 78 (2001) 47-54
10. Morton B.R. Chloroplast DNA codon usage. Evidence for selection at the psbA locus based on tRNA availability,. J. Mol. Evol. 27 (1993) 273-280
11. Peplies J., Kottmann R., Ludwig W., and Glöckner F.O. A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst. Appl. Microbiol. 31 (2008) 251-257
12. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
13. Sei K., Asano K., Tateishi N., Mori K., Ike M., and Fujita M. Design of PCR primers and gene probes for the general detection of bacterial populations capable of degrading aromatic compounds via catechol cleavage pathways. J. Biosci. Bioeng. 88 (1999) 542-550
14. Sharp P.M., Tuohy T.M.F., and Mosurski K.R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 14 (1986) 5125-5143
15. Shen F.T., Ho M.J., Huang H.R., Arun A.B., Rekha P.D., and Young C.C. Molecular detection and phylogenetic characterization of Gordonia species in heavily oil-contaminated soils. Res. Microbiol. 159 (2008) 522-529
16. Shen F.T., Lu H.L., Lin J.L., Huang W.S., Arun A.B., and Young C.C. Phylogenetic analysis of members of the metabolically diverse genus Gordonia based on proteins encoding the gyrB gene. Res. Microbiol. 157 (2006) 367-375
17. Shen F.T., and Young C.C. Rapid detection and identification of the metabolically diverse genus Gordonia by 16S rRNA-gene-targeted genus-specific primers. FEMS Microbiol. Lett. 250 (2005) 221-227
18. Stamatakis A., Hoover P., and Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst. Biol. 75 (2008) 758-771
19. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 (1989) 585-595
20. Táncsics A., Szoboszlay S., Kriszt B., Kukolya J., Baka E., Márialigeti K., and Révész S. Applicability of the functional gene catechol 1,2-dioxygenase as a biomarker in the detection of BTEX-degrading Rhodococcus species. J. Appl. Microbiol. (2008) 10.1111/j.1365-2672.2008.03832.x
21. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
22. Veselý M., Knoppová M., Nešvera J., and Pátek M. Analysis of catRABC operon for catechol degradation from phenol-degrading Rhodococcus erythropolis. Appl. Microbiol. Biotechnol. 76 (2007) 159-168
23. Watts D., and MacBeath J.R. Automated fluorescent DNA sequencing on the ABI PRISM 310 Genetic Analyzer. Methods Mol. Biol. 167 (2001) 153-170
24. Whyte L.G., Bourbonniere L., and Greer C.W. Biodegradation of petroleum hydrocarbons by psychrotrophic Pseudomonas strains possessing both alkane (alk) and naphthalene (nah) catabolic pathways. Appl. Environ. Microbiol. 63 (1997) 3719-3723
25. Young C.C., Lin T.C., Yeh M.S., Shen F.T., and Chang J.S. Identification and kinetic characteristics of an indigenous diesel-degrading Gordonia alkanivorans strain. World J. Microbiol. Biotechnol. 21 (2005) 1409-1414
26. Zhou H.W., Guo C.L., Wong Y.S., and Tam N.F.Y. Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments. FEMS Microbiol. Lett. 262 (2006) 148-157