Genome British Columbia - Genome Genomics

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Completed

Microbial Envirogenomics

Project Leaders:
Julian Davies, Lindsay Eltis, William Mohn

Lead Institution:
University of British Columbia

Research Funding Program:
Competition I

Technology Applications:
Bioremediation, biotransformation, "green" chemistry

Project Website:
Rhodococcus Genome Project

The Microbial Envirogenomics project elucidates and exploits the physiology and functioning of environmentally important bacteria through genomic approaches, starting with Rhodococcus RHA1. Rhodococci are soil bacteria with unique and diverse capabilities, leading to several possible applications in environmental, pharmaceutical, chemical and industrial bioremediation. The strain RHA1 is remarkably effective at breaking down complex and toxic compounds; plus it can grow on numerous substrates, produce unique compounds and even desulfurize coal. The research team has completed sequencing the genome of RHA1 and is now using expression and protein datasets with bioinformatics analysis to determine the metabolic machinery within Rhodococcus. This work furthers the understanding of RHA1 and related organisms and greatly facilitates engineering of RHA1 for the development of various environmentally sustainable and efficient industrial applications.

Bacteria are critical to the global elemental cycles that sustain all other life in the biosphere. Microorganisms comprise the majority of organisms on earth, their total biomass is approximately equal to that of plants and they represent most of the existing genetic and physiological diversity. Bacteria are also an important source of biocatalysts for industrial processes and bioremediation, the removal of toxic chemical contaminants from polluted environments using microbial processes. Despite their significance, the basic biology of most bacteria is unknown.

In the initial phase of the project, the sequence of RHA1 was determined and the researchers are now reconstructing metabolic pathways. Gene inactivation studies and arrayed expression libraries will be used to systematically evaluate gene function.

The project also analyses the response to starvation and various other environment stresses. Proteomic and microarray studies were performed on RHA1 growing on, or in the presence of, specific environmental pollutants. This provides novel insights into how pathways interact to degrade compounds and other processes required for pollutant degradation, such as pollutant sensing and uptake.

This research on RHA1 accelerates the development of genomics tools to study and engineer Gram positive microorganisms. Advances in understanding soil bacteria greatly contribute to the improvement of land management for agriculture and forestry. In addition to providing a well-characterized vector for bioremediation, this work will facilitate engineering RHA1 for diverse commercial applications.

Project Publications
Anderton MC, Bhakta S, Besra GS, Je avons P, Eltis LD, a nd Sim E. (2006). Characterisation of the putative operon containing arylamine N -acetyltransferase (nat) in Mycobacterium bovis BCG. Molecular Microbioogyl, 59 ,181-192.

Denef V.J. , Klappenbach J.A., Patrauchan M.A., Florizone C., Rodrigues J.L.M. , Tsoi T.V., Verstraete W., Eltis L.D. & Tiedje J.M. (2006). Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Applied and Environmental Microbiology, 72 , 585-595 .

Denef V.J., Patrauchan M.A., Florizone C., Park J., Tsoi T.V., Verstraete W., Tiedje J.M., Eltis L.D. (2005). Growth substrate and phase specific expression of biphenyl, benzoate and C1 metabolic pathways in Burkholderia xenovorans LB400. Journal of Bacteriology, 187 (23), 7996-8005.

Navarro-Llorens J.M., Patrauchan M.A., Stewart G.R., Davies J., Eltis L.D. & Mohn W.W. (2005). The catabolism of Phenylacetic Acid in Rhodococcus RHA1. Journal of Bacteriology, 187 (13), 4497-4504.

Patrauchan M.A., Florizone C., Dosanjh M., Mohn W.W., Davies J. & Eltis L.D. (2005).The catabolism of benzoate and phthalate by a shared ß-ketoadipate pathway in Rhodococcus RHA1. Journal of Bacteriology, 187 (12), 4050-4063.

Warren R., Hsiao W.W.L., Kudo H., Myhre M., Dosanjh M., Petrescu A., Kobayashi H., Shimizu S., Miyauchi K., Masai E., Yang G. , Stott J.M., Schein J.E., Shin H., Khattra J., Smailus D., Butterfield Y.S., Siddiqui A., Holt R., Marra M.A., Jones S.J.M., Mohn W.W., Brinkman F.S.L., Fukuda M., Davies J., & Eltis LD. (2004). Functional Characterization of a Catabolic Plasmid from Polychlorinated-Biphenyl-Degrading Rhodococcus sp. Strain RHA1. Journal of Bacteriology, 186 (22),7783-7795.