Molecular and biochemical basis for microbial aromatic hydrocarbon degradation
Research in my laboratory is directed toward understanding the mechanisms by which different bacterial strains utilize aromatic 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 different bacterial genera.
Specific areas of research include:
- site-directed modification of enzymes to understand their function and to perhaps enhance their ability to transform aromatic compounds to oxygenated intermediates,
- analysis of gene regulation and how this can be used to enhance microbial biodegradation of xenobiotic compounds in the environment,
- design and use of molecular probes to track genes and their expression in the environment, and
- construction of hybrid catabolic pathways for the degradation of recalcitrant compounds.
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 the degradation of phthalates by P. cepacia, C. testosteroni, and Acinetobacter.
- Chai B, Tsoi TV, Iwai S, Liu C, Fish JA, Gu C, Johnson TA, Zylstra G, Teppen BJ, Li H, Hashsham SA, Boyd SA, Cole JR, Tiedje JM. 2016. Sphingomonas wittichiiStrain RW1 genome-wide gene expression shifts in response to dioxins and clay. PloS one 11:e0157008. DOI PubMed
- Ambrose, K. V., Z. Tian, Y. Wang, J. Smith, G. Zylstra, B. Huang, and F. C. Belanger. 2015. Functional characterization of salicylate hydroxylase from the fungal endophyte Epichloe festucae. Nature Sci Rep 5:10939. DOI
- Masuda, H., Y. Shiwa, H. Yoshikawa, and G. J. Zylstra. 2014. Draft Genome Sequence of the Versatile Alkane-Degrading Bacterium Aquabacterium sp. Strain NJ1. Genome Announc 2:e01271-01214. DOI
- Theisen, J., G. J. Zylstra, and N. Yee. 2013. Genetic evidence for a molybdopterin-containing tellurate reductase. Appl. Environ. Microbiol. 79:3171-3175. PubMed
- Masuda, H., K. McClay, R. J. Steffan, and G. J. Zylstra. 2012. Biodegradation of tetrahydrofuran and 1,4-dioxane by souble diiron monooxygenase in Pseudonocardia sp. strain ENV478. J. Mol. Microbiol. Biotechnol. 22:312-316. PubMed
- Chang, H. K., G. J. Zylstra, and J.-C. Chae. 2012. Genome sequence of n-alkane degrading Hydrocarboniphaga effusa strain AP103T (ATCC BAA-332T). J. Bacteriol. 194:5120. PubMed
- Yoo, M., D. Kim, K. Y. Choi, J. C. Chae, G. J. Zylstra, and E. Kim. 2012. Draft genome sequence and comparative analysis of the superb aromatic hydrocarbon degrader Rhodococcus sp. strain DK17. J. Bacteriol. 194:4440. PubMed
- Masuda, H., K. McClay, R. J. Steffan, and G. J. Zylstra. 2012. Characterization of three propane-inducible oxygenases in Mycobacterium sp. strain ENV421. Lett. Appl. Microbiol. 55:175-81. PubMed
- Callaghan, A. V., B. E. L. Morris, I. A. C. Pereira, M. J. McInerney, R. N. Austin, J. T. Groves, J. J. Kukor, J. M. Suflita, L. Y. Young , G. J. Zylstra, and B. Wawrik. 2012. The genome sequence of Desulfatibacillum alkenivorans AK-01: a blueprint for anaerobic alkane oxidation. Env. Microbiol. 14:101-13. PubMed