Ahsan Islam

From

Ahsan Islam

Supervisor: Krishna Mahadevan and Elizabeth Edwards, Department of Chemical Engineering and Applied Chemistry

WiP Seminar, 18 September 2008

Genome-scale modeling of the metabolism of Dehalococcoides bacteria: from genome to pan-genome

Dehalococcoides are important for the bioremediation of chlorinated solvent contaminated sites. However, how this dehalogenating capability has been acquired and employed by these microbes is not well understood, specifically at the metabolism level. In addition, the low growth yield of these bacteria is a major impediment to faster bioremediation process. Hence, genome-scale reconstruction of the entire metabolic network and subsequent modeling of Dehalococcoides will be beneficial to understanding and overcoming these issues. Moreover, such a model is an excellent platform for exploring the metabolic capability of a microbe as well as for generating experimentally testable hypotheses regarding the microbe’s physiology. Hence in this presentation, I’ll talk about a genome-scale reconstruction of the entire metabolic network and subsequent modeling of Dehalococcoides species strain CBDB1, a dechlorinating bacterium unique for its metabolic niche of degrading toxic and persistent ground water pollutants. In addition, I’ll also talk about the Dehalococcoides pan-metabolic model that has been developed using strain CBDB1 metabolic model and the published genome sequences of 4 Dehalococcoides isolates –Dehalococcoides sp. strain CBDB1, Dehalococcoides ethenogenes strain 195, Dehalococcoides sp. strain BAV1, Dehalococcoides sp. strain VS. The pan-model reveals the remarkable similarities exist among the isolates from the context of core metabolic processes.

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