| Hydrogen gas (H2) is a clean-burning fuel and energy source that can be produced biologically by bacteria. Photosynthetic bacteria are especially promising as biocatalysts for H2 production because energy from light can be used to drive this thermodynamically difficult process. The photosynthetic bacterium Rhodopseudomonas draws on the functioning of three major metabolic modules to produce H2. These are photophosphorylation to generate ATP from light, carbon compound catabolism to generate electrons, and nitrogenase, an enzyme that combines electrons from carbon compounds with protons from water to generate H2 by an ATP-intensive process. Each of metabolic modules is complicated and when considered together it is clear that H2 production requires the integration of dozens of metabolic reactions. For example, acquisition of metals needed for synthesis of a functional nitrogenase is not easily identified as being associated with H2 production. To identify a full set of genes from Rhodopseudomonas involved in H2 production, I compared the genomes and transcriptomes of 16 closely related strains of Rhodopseudomonas . In addition, I constructed co-expression networks of a set of 7 other less closely related Rhodopseudomonas strains and correlated gene expression modules with nitrogenase activities and H2 production yields of the strains. I identified a set of 54 genes that were highly expressed in all 16 closely related strains grown under the H2-producing condition in high light. These are candidates for genes that contribute to H2 production. The co-expression analysis suggested that expression of nitrogenase genes is an essential but not a limiting factor for H 2 production. In contrast, the expression of light-harvesting genes appeared to be important for H2 production under high and low light. In the process of generating data for this thesis, I developed an easy-to-use integrated tool for processing RNA-seq data, called Xpression. This tool is well suited to analyze gene expression data generated from bacteria and Achaea and should be useful to research laboratories that do not routinely carry out gene expression studies. |
