The diversity of organisms on Earth is largely determined by the differences in genes that they contain in their genome. Even with the apparent diversity outwardly displayed by all organisms, there are significant numbers of genes that are shared throughout. Genome sequencing of thousands of organisms in recent years has revealed an enormous database of gene sequences that code for many previously unknown proteins. From humans to plants to fungi and bacteria, a large proportion of the genes encoded with in these organisms have no known function. The goal of this research is to identify genes in the purple photosynthetic bacterium Rhodobacter sphaeroides, clone these genes, express and purify the proteins that are encoded in these genes, and then characterize the functions of the purified proteins. Knowledge of the function of these genes will give significant insight which may allow for engineering of the bacteria for clean energy, or identify new functions which would be used in unforeseen medical, environmental or engineering applications.
R. sphaeroides is a purple photosynthetic bacterium that has been well-studied for many years. The Rhodobacter species growth modes include aerobic and anaerobic respiration, anaerobic photosynthesis, fermentation, use of diverse organic carbon sources, or use of carbon dioxide (CO2) as the sole carbon source both aerobically and anaerobically. Purple photosynthetic bacteria have been isolated from a variety of soils, plants, and aqueous environments ranging from fresh water to salt water and temperatures from hot springs to polar ice caps. Because the physiology of R. sphaeroides is well known, this makes it an ideal candidate for a gene knockout study because observation of different physiological phenotypes would allow the function of the deleted gene to be elucidated.
Sequence analysis of a purple photosynthetic bacterium R. sphaeroides reveals several protein sequences that are uncharacterized and are highly conserved among bacteria such as Escherichia coli, Staphylococcus aureus, Xanthomonas axonopodis, Bradyrhizobium japonicum, Rhodopirellula baltica, Gluconobacter oxydans, Pseudomonas syringae, Shigella sonnei, Tenacibaculum, Flavobacterium, Blastopirellula marina, Rickettsiella grylli, Mesorhizobium, Streptomyces ambofaciens, Enterobacter spp., Planctomyces maris, and Klebsiella pneumoniae. The primary objectives of the project are to clone the genes encoding several highly conserved proteins and to express and purify the proteins of which the genes encode, and characterize the biochemical properties of the proteins.
Genomic sequences are just the beginning of our understanding of how organisms work. Even with detailed annotation of genomes in which sequences of DNA from one organism are compared to other DNA sequences of different organisms, not all genes and their respective gene products can be correctly identified. In fact, numerous instances exist where annotation reveals many genes to be "unknown function" or "hypothetical protein." This is why individual gene study is a necessary and potentially rewarding process in which new previously unidentified functions will be discovered for the first time.