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Molecular and biochemical basis for microbial aromatic hydrocarbon degradationResearch in my laboratory is directed toward understanding the mechanisms by which different bacterial strains utilize aromatic and aliphatic compounds as carbon and energy sources. Projects in the laboratory emphasize the use of molecular genetic tools in the analysis of gene (and protein) evolution. the regulation of gene expression. the identification of intermediate compounds in catabolic pathways. and the functional analysis of the enzymes involved. The primary theme for projects in the laboratory is the examination of microbial diversity and how this affects the degradation of aromatic compounds in the environment. For instance. different bacterial strains may utilize different biochemical pathways for the degradation of the same aromatic compound. In contrast. different bacterial strains may degrade an aromatic compound by the same catabolic pathway but possess genes that have diverged widely in their nucleotide sequence. This diversity in nucleotide sequence also plays a role in the specificity and activity of the enzymes produced. Research thus focuses on a detailed biochemical. physiological. and molecular genetic investigation and comparison of different model catabolic pathways in several bacterial genera. The two main areas of emphasis are the identification of new catabolic pathways or novel genes for known catabolic pathways and the development of new tools for the rapid cloning and identification of genes involved in catabolic transformations. The laboratory is currently focusing on the degradation of polycyclic aromatic hydrocarbons by Sphingomonas. Comamonas. and Mycobacterium strains; the degradation of nitrophenols and nitrobenzoates by several different Pseudomonas species and an Arthrobacter species; the degradation of phthalates by P. cepacia. C. testosteroni. and Acinetobacter strains; and the degradation of alkanes by Pseudomonas. Acinetobacter. and several uncharacterized isolates. Selected PublicationsChang HK, Zylstra GJ. (2008) Examination and expansion of the substrate range of m-hydroxybenzoate hydroxylase. Biochem Biophys Res Commun. 371(1):149-53. Kwon NR, Chae JC, Choi KY, Yoo M, Zylstra GJ, Kim YM, Kang BS, Kim E. (2008) Identification of functionally important amino acids in a novel indigo-producing oxygenase from Rhodococcus sp. strain T104. Appl Microbiol Biotechnol. 79(3):417-22. Chae JC, Song B, Zylstra GJ. (2008) Identification of genes coding for hydrolytic dehalogenation in the metagenome derived from a denitrifying 4-chlorobenzoate degrading consortium. FEMS Microbiol Lett. 281(2):203-9. Schuler L, Ní Chadhain SM, Jouanneau Y, Meyer C, Zylstra GJ, Hols P, Agathos SN. (2008) Callaghan AV, Wawrik B, Ní Chadhain SM, Young LY, Zylstra GJ. (2008) Anaerobic alkane-degrading strain AK-01 contains two alkylsuccinate synthase genes. Biochem Biophys Res Commun. 366(1):142-8. Perry LL, Zylstra GJ. (2007) Cloning of a gene cluster involved in the catabolism of p-nitrophenol by Arthrobacter sp. strain JS443 and characterization of the p-nitrophenol monooxygenase. J Bacteriol. 189(21):7563-72. Chadhain SM, Moritz EM, Kim E, Zylstra GJ. (2007) Identification, cloning, and characterization of a multicomponent biphenyl dioxygenase from Sphingobium yanoikuyae B1. J Ind Microbiol Biotechnol. 34(9):605-13. Chae JC, Kim E, Bini E, Zylstra GJ. (2007) Comparative analysis of the catechol 2,3-dioxygenase gene locus in thermoacidophilic archaeon Sulfolobus solfataricus strain 98/2. Biochem Biophys Res Commun. 357(3):815-9. Choi KY, Kim D, Chae JC, Zylstra GJ, Kim E. (2007) Requirement of duplicated operons for maximal metabolism of phthalate by Rhodococcus sp. strain DK17. Biochem Biophys Res Commun. 357(3):766-71. Yano H, Garruto CE, Sota M, Ohtsubo Y, Nagata Y, Zylstra GJ, Williams PA, Tsuda M. (2007) Complete sequence determination combined with analysis of transposition/site-specific recombination events to explain genetic Organization of IncP-7 TOL Plasmid pWW53 and Related Mobile Genetic Elements. J Mol Biol. 369(1):11-26. Wawrik B, Kutliev D, Abdivasievna UA, Kukor JJ, Zylstra GJ, Kerkhof L. (2007) Biogeography of actinomycete communities and type II polyketide synthase genes in soils collected in New Jersey and Central Asia. Appl Environ Microbiol. 73(9):2982-9. Rozhkova-Novosad EA, Chae JC, Zylstra GJ, Bertrand EM, Alexander-Ozinskas M, Deng D, Moe LA, van Beilen JB, Danahy M, Groves JT, Austin RN. (2007) Profiling mechanisms of alkane hydroxylase activity in vivo using the diagnostic substrate norcarane. Chem Biol. 14(2):165-72. Poulain AJ, Ni Chadhain SM, Ariya PA, Amyot M, Garcia E, Campbell PG, Zylstra GJ, Barkay T. (2007) Potential for mercury reduction by microbes in the high arctic. Appl Environ Microbiol. 73(7):2230-8. Bae HW, Kim D, Choi KY, Kwon NR, Chae JC, Zylstra GJ, Koh SC, Lee CH, Kim E. (2007) Functional identification of p-cumate operons in the terpene-degrading Rhodococcus sp. strain T104. FEMS Microbiol Lett. 266(1):54-9. Choi KY, Zylstra GJ, Kim E. (2007) Benzoate catabolite repression of the phthalate degradation pathway in Rhodococcus sp. strain DK17. Appl Environ Microbiol. 73(4):1370-4. Chae JC, Zylstra GJ. (2006) 4-Chlorobenzoate uptake in Comamonas sp. strain DJ-12 is mediated by a tripartite ATP-independent periplasmic transporter. J Bacteriol. 188(24):8407-12. Ni Chadhain SM. Norman RS. Pesce KV. Kukor JJ. Zylstra GJ. (2006) Microbial dioxygenase gene population shifts during polycyclic aromatic hydrocarbon biodegradation. Appl Environ Microbiol. 72(6):4078-87. Chae JC. Kim CK. Zylstra GJ. (2005) Characterization of two small cryptic plasmids from Pseudomonas sp. strain S-47. Biochem Biophys Res Commun. 338(3):1600-6. Choi KY. Kim D. Sul WJ. Chae JC. Zylstra GJ. Kim YM. Kim E. (2005) Molecular and biochemical analysis of phthalate and terephthalate degradation by Rhodococcus sp. strain DK17. FEMS Microbiol Lett. 252(2):207-13. Jang JY. Kim D. Bae HW. Choi KY. Chae JC. Zylstra GJ. Kim YM. Kim E. (2005) Isolation and characterization of a rhodococcus species strain able to grow on ortho- and para-xylene. J Microbiol. 43(4):325-30. Wawrik. B.. L. Kerkhof. G. J. Zylstra. and J. J. Kukor. 2005. Identification of unique type II polyketide synthase genes in soil. Appl. Env. Microbiol. 71(5):2232-8. Kim. D.. Chae. J-C. Zylstra. GJ. Sohn. H-Y. Kwon. G-S and Kim. E. (2005). Identification of two-component regulatory genes involved in o-xylene degradation by Rhodococcus sp. strain DK17. J. Microbiol. 43:49-53. Cho. O.. Choi. KY. Zylstra. GJ. Kim. Y-S. Kim. S-K. Lee. JH. Sohn. H-Y. Kwon. G-S. Kim. YM and Kim. E. 2005. Catabolic role of a three-component salicylate oxygenase from Sphingomonas yanoikuyae B1 in polycyclic aromatic hydrocarbon degradation. Biochem. Biophys. Res. Commun. 327:656-662. Kim. D.. Chae. J-C. Jang. J-Y. Zylstra. GJ. Kim. YM. Kang. BS. and Kim. E. (2005). Functional characterization and molecular modeling of methylcatechol 2,3-dioxygenase from o-xylene-degrading Rhodococcus sp. strain DK17. Biochem. Biophys. Res. Commun. 326:880-886. Caballero. A.. Esteve-Núñez. A. Zylstra. GJ. and Ramos. JL. (2005). Assimilation of nitrogen from nitrite and trinitrotoluene in Pseudomonas putida JLR11. J. Bacteriol. 187:396-399. Kim. D.. Chae. J-C. Zylstra. GJ. Kim. Y-S. Kim. SK. Nam. MH. Kim. YM and E. Kim. E. (2004). Identification of a novel dioxygenase involved in metabolism of o-xylene. toluene. and ethylbenzene by Rhodococcus sp. strain DK17. Appl. Environ. Microbiol. 70:7086-7092. Dennis. J. J.. and Zylstra. GJ. (2004). Complete sequence and genetic organization of pDTG1. the 83 kilobase naphthalene degradation plasmid from Pseudomonas putida strain NCIB 9816-4. J. Mol. Biol. 341:753-768 Williams. P. A.. Jones. RM and Zylstra. GJ. (2004). Genomics of Catabolic Plasmids. p. 165-196. In J. L. Ramos (ed.). Pseudomonas Volume 1: Genomics. Lifestyle. and Molecular Architecture. Kluwer Academic / Plenum Publishers. New York. Palleroni. N. J.. Port. AM. Chang. H-K and Zylstra. GJ. (2004). Hydrocarboniphaga effusa gen. nov.. sp. nov.. a novel member of the gamma-Proteobacteria active in alkane and aromatic hydrocarbon degradation. Int. J. Syst. Evol. Microbiol. 54:1203-1207. |
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