Transcriptomic analysis of diverse green sulfur phototrophic bacteria

The Chlorobi consist mostly of anoxygenic photosynthetic microbes which are present in a wide variety of anoxic illuminated environments. While Cba. tepidum has been the model organism for Chlorobi for the last 15 years, it is not representative of the diversity of this clade. To connect the results of experiments on Cba. tepidum to other Chlorobi, comparative transcriptomics with two other strains, Chlorobium phaeobacteroides BS-1 and Chlorobium chlorochromatii CaD3, was used to identify conserved and unique genes with interesting patterns of expression. RNA-seq was used to quantify expression of the entire genome and differentially expressed genes were identified under various conditions expected to alter cellular physiology: i.e. electron donor switching or energy limitation. This global view of expression facilitated identification of genes that may be involved in poorly understood cellular processes. In Cba. tepidum, a total of seven RNA-seq libraries were sequenced, representing growth using three different electron donors. This allowed the identification of 376 protein coding genes, or 16% of the genes in the genome, that are differentially expressed between two or more libraries. To verify the predicted functional role of differentially expressed gene's products, further research is required. To this end, I made a deletion strain of one of these genes, CT1276, which encodes a hypothetical protein that is a member of protein superfamily that also contains the nitrogen fixation cofactor biosynthesis proteins NifX and NifB. This mutant was investigated for changes in sulfide tolerance, but no significant differences could be detected. The transcriptome data set for Chlorobium phaeobacteroides BS-1 includes libraries representative of growth under low light and high light, which allows for comparison of gene expression under two different energy regimes, and identification of novel adaptations for low light flux. The transcriptome data set for Chlorobium chlorochromatii CaD3 contains two libraries representing growth as part of a symbiosis and as a free living organism, which indicates several genes that may be involved in maintenance of the consortium. Transcriptomic methods have allowed insight into the physiology of Chlorobi, and resulted in data sets that can continue to be mined for many years for targets for further investigation.