Functional robustness of a polycyclic aromatic hydrocarbon metabolic network examined in a nidA aromatic ring-hydroxylating oxygenase mutant of Mycobacterium vanbaalenii PYR-1

Applied and Environmental Microbiology

Volumn 78, Issue 10, 2012, Pages 3715-3723

  Kim, Seong Jae ^a   Song, Jaekyeong ^a   Kweon, Ohgew ^a,c   Holland, Ricky D ^b   Kim, Dae Wi ^a   Kim, Jongnam ^a   Yu, Li Rong ^b   Cerniglia, Carl E ^a  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^b National Institute of Animal Science   (South Korea)

^c University of Arkansas at Little Rock ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEGRADATION RATE; FLUORANTHENE; FUNCTIONAL MODULES; IN-VIVO; INITIAL OXIDATION; METABOLIC NETWORK; OXYGENASES; PAH MIXTURES; PROTEOME ANALYSIS; WHOLE CELL; WILD TYPES;

ANTHRACENE; AROMATIC COMPOUNDS; HIGH PRESSURE LIQUID CHROMATOGRAPHY;

DEGRADATION;

BACTERIAL PROTEIN; OXYGENASE; POLYCYCLIC AROMATIC HYDROCARBON; PROTEOME;

BACTERIUM; DEGRADATION; ENZYME ACTIVITY; FLUORANTHENE; LIQUID CHROMATOGRAPHY; METABOLISM; PAH; PROTEOMICS; PYRENE;

ARTICLE; CHEMISTRY; CULTURE MEDIUM; ENZYMOLOGY; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MYCOBACTERIUM; TRANSPOSON;

BACTERIAL PROTEINS; CULTURE MEDIA; DNA TRANSPOSABLE ELEMENTS; GENE DELETION; GENE EXPRESSION PROFILING; METABOLIC NETWORKS AND PATHWAYS; MUTAGENESIS, INSERTIONAL; MYCOBACTERIUM; OXYGENASES; POLYCYCLIC HYDROCARBONS, AROMATIC; PROTEOME;

MYCOBACTERIUM VANBAALENII PYR-1;

EID: 84861173121     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.07798-11     Document Type: Article

References (36)

1. Brezna B, Khan AA, Cerniglia CE. 2003. Molecular characterization of dioxygenases from polycyclic aromatic hydrocarbon-degrading Mycobacterium spp. FEMS Microbiol. Lett. 223:177-183.
2. Cébron A, Norini MP, Beguiristain T, Leyval C. 2008. Real-time PCR quantification of PAH-ring hydroxylating dioxygenase (PAH-RHDalpha) genes from Gram positive and Gram negative bacteria in soil and sediment samples. J. Microbiol. Methods 73:148-159.
3. Debruyn JM, Chewning CS, Sayler GS. 2007. Comparative quantitative prevalence of mycobacteria and functionally abundant nidA, nahAc, and nagAc dioxygenase genes in coal tar contaminated sediments. Environ. Sci. Technol. 41:5426-5432.
4. Goude R, Parish T. 2008. Electroporation of mycobacteria. In Parish T, Brown AC (ed), Mycobacteria protocols. Humana Press, Totowa, NJ.
5. Heitkamp MA, Cerniglia CE. 1988. Mineralization of polycyclic aromatic hydrocarbons by a bacterium isolated from sediment below an oil field. Appl. Environ. Microbiol. 54:1612-1614.
6. Heitkamp MA, Cerniglia CE. 1989. Polycyclic aromatic hydrocarbon degradation by a Mycobacterium sp. in microcosms containing sediment and water from a pristine ecosystem. Appl. Environ. Microbiol. 55:1968-1973.
7. Hermans J, Boschloo JG, de Bont JAM. 1990. Transformation of Mycobacterium aurum by electroporation: the use of glycine, lysozyme and isonicotinic acid hydrazide in enhancing transformation efficiency. FEMS Microbiol. Lett. 72:221-224.
8. Kelley I, Cerniglia CE. 1995. Degradation of a mixture of highmolecular-weight polycyclic aromatic hydrocarbons by a Mycobacterium strain PYR-1. J. Soil Contam. 4:77-91.
9. Kelley I, Freeman JP, Evans FE, Cerniglia CE. 1991. Identification of a carboxylic acid metabolite from the catabolism of fluoranthene by a Mycobacterium sp. Appl. Environ. Microbiol. 57:636-641.
10. Khan AA, Kim SJ, Paine DD, Cerniglia CE. 2002. Classification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Mycobacterium sp. strain PYR-1, as Mycobacterium vanbaalenii sp. nov. Int. J. Syst. Evol. Microbiol. 52:1997-2002.
11. Khan AA, et al. 2001. Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl. Environ. Microbiol. 67:3577-3585.
12. Kieser T, Bibb JM, Buttner MJ, Chater KF, Hopwood DA. 2000. Practical Streptomyces genetics. John Innes Foundation, Norwich, United Kingdom.
13. Kim SJ, Kweon O, Cerniglia CE. 2010. Degradation of polycyclic aromatic hydrocarbons by Mycobacterium strains, p 1865-1880. In Timmis KN (ed), Handbook of hydrocarbon and lipid microbiology, vol 3. Springer, Braunschweig, Germany.
14. Kim SJ, Kweon O, Cerniglia CE. 2009. Proteomic applications to elucidate bacterial aromatic hydrocarbon metabolic pathways. Curr. Opin. Microbiol. 12:301-309.
15. Kim SJ, et al. 2006. Molecular cloning and expression of genes encoding a novel dioxygenase involved in low- and high-molecular-weight polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Appl. Environ. Microbiol. 72:1045-1054.
16. Kim SJ, Kweon O, Jones RC, Edmondson RD, Cerniglia CE. 2008. Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 19:859-881.
17. Kim SJ, et al. 2007. Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology. J. Bacteriol. 189:464-472.
18. Kim YH, Engesser KH, Cerniglia CE. 2005. Numerical and genetic analysis of polycyclic aromatic hydrocarbon-degrading mycobacteria. Microb. Ecol. 50:110-119.
19. Kim YH, Freeman JP, Moody JD, Engesser KH, Cerniglia CE. 2005. Effects of pH on the degradation of phenanthrene and pyrene by Mycobacterium vanbaalenii PYR-1. Appl. Microbiol. Biotechnol. 67:275-285.
20. Kiyohara H, Nagao K, Yana K. 1982. Rapid screen for bacteria degrading water-insoluble, solid hydrocarbons on agar plates. Appl. Environ. Microbiol. 43:454-457.
21. Krivobok S, et al. 2003. Identification of pyrene-induced proteins in Mycobacterium sp. strain 6PY1: evidence for two ring-hydroxylating dioxygenases. J. Bacteriol. 185:3828-3841.
22. Kweon O, et al. 2008. A new classification system for bacterial Rieske nonheme iron aromatic ring-hydroxylating oxygenases. BMC Biochem. 9:11.
23. Kweon O, Kim SJ, Cerniglia CE. 2010. Genomic view of mycobacterial high molecular weight polycyclic aromatic hydrocarbon degradation, p 1165-1178. In Timmis KN (ed), Handbook of hydrocarbon and lipid microbiology, vol 2. Springer, Braunschweig, Germany.
24. Kweon O, Kim S-J, Freeman JP. 2010. Substrate specificity and structural characteristics of the novel Rieske nonheme iron aromatic ringhydroxylating oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1. mBio 1(2):e00135-10. doi:10.1128/mBio.00135-10.
25. Kweon O, et al. 2011. Polycyclic aromatic hydrocarbon-metabolic network in Mycobacterium vanbaalenii PYR-1. J. Bacteriol. 193:4326-4337.
26. Kweon O, et al. 2007. A polyomic approach to elucidate the fluoranthene degradative pathway in Mycobacterium vanbaalenii PYR-1. J. Bacteriol. 189:4635-4647.
27. Liang Y, et al. 2006. Study of biochemical pathways and enzymes involved in pyrene degradation by Mycobacterium sp. strain KMS. Appl. Environ. Microbiol. 72:7821-7828.
28. Miller CD, et al. 2004. Isolation and characterization of polycyclic aromatic hydrocarbon-degrading Mycobacterium isolates from soil. Microb. Ecol. 48:230-238.
29. Moody JD, Freeman JP, Cerniglia CE. 2005. Degradation of benz[a]anthracene by Mycobacterium vanbaalenii strain PYR-1. Biodegradation 16: 513-526.
30. Moody JD, Freeman JP, Fu PP, Cerniglia CE. 2004. Degradation of benzo[a]pyrene by Mycobacterium vanbaalenii PYR-1. Appl. Environ. Microbiol. 70:340-345.
31. Moody JD, Fu PP, Freeman JP, Cerniglia CE. 2003. Regio- and stereoselective metabolism of 7,12-dimethylbenz[a]anthracene by Mycobacterium vanbaalenii PYR-1. Appl. Environ. Microbiol. 69:3924-3931.
32. Pagnout C, et al. 2007. Isolation and characterization of a gene cluster involved in PAH degradation in Mycobacterium sp. strain SNP11: expression in Mycobacterium smegmatis mc2155. Res. Microbiol. 158:175-186.
33. Rehmann K, Noll HP, Steinberg CE, Kettrup AA. 1998. Pyrene degradation by Mycobacterium sp. strain KR2. Chemosphere 36:2977-2992.
34. Sho M, Hamel C, Greer CW. 2004. Two distinct gene clusters encode pyrene degradation in Mycobacterium sp. strain S65. FEMS Microbiol. Ecol. 48:209-220.
35. Stingley RL, Khan AA, Cerniglia CE. 2004. Molecular characterization of a phenanthrene degradation pathway in Mycobacterium vanbaalenii PYR-1. Biochem. Biophys. Res. Commun. 322:133-146.
36. Vila J, et al. 2001. Identification of a novel metabolite in the degradation of pyrene by Mycobacterium sp. strain AP1: actions of the isolate on twoand three-ring polycyclic aromatic hydrocarbons. Appl. Environ. Microbiol. 67:5497-5505.