Systems biology of motile mycoplasmas

The mycoplasmas are a reductively evolved group of Gram-positive related bacteria that lack cell walls and have small genome sizes. Despite minimal genetic resources, they have diverse phenotypes including pathogenicity and gliding motility. Their simplicity makes them extremely attractive candidates for the emerging field of systems biology. This thesis explores the mechanism of gliding motility, examines the protein composition of a mycoplasma cell at an organism-wide level, and reports the genome sequence of Mycoplasma mobile, the species with the most robust gliding motility. The thesis is divided into three sections. In the first section, M. mobile is subjected to pharmacological treatments and biochemical measurements to establish that the energy source for gliding is the hydrolysis of adenosine triphosphate (ATP). It was also found that exogenous protein is required to potentiate gliding on glass surfaces. In the second section, methods are developed to determine the proteins that are present in cells of M. pneumoniae with respect to genomic predictions. This novel technique, termed proteogenomic mapping, resulted in the discovery of new proteins that had not been previously annotated and was able to detect an undocumented modification to an M. pneumoniae protein. In the third section, proteogenomic mapping and genomic sequencing are applied together to report the genome and annotation of M. mobile. Analysis of the genome focused on the identification of motility genes, but other significant results were encountered such as a long repeating unit of DNA sequence that codes for highly similar yet unique proteins and evidence of horizontal gene transfer. In addition to being the most deeply sequenced genus of organisms to date, the results in this thesis give them the highest degree of proteomic coverage as well (88% and 80% for M. mobile and M. pneumoniae, respectively). Taken together, this thesis presents a fine-level view of the motility subsystem and a broad-level view of the overall protein composition of motile mycoplasmas.