UPEC Genomics

We have completed the full genome sequence of UTI89, a clinical E. coli isolate from a patient suffering from cystitis. We are taking advantage of this genome sequence in three distinct ways to better understand urinary tract infection.

First, using a blend of comparative genomics and molecular evolution, we are looking for functional genes and mutations that enable UPEC to cause disease in the urinary tract. We do this by looking for individual genes and amino acids that are evolving specifically under positive selection in UPEC strains. This approach gives us a new perspective on sequence data, in that we can search for functional subsets of both conserved (using crystallography and structure-function studies) and variable (using comparative genomics and molecular evolution) amino acid sequences. For example, in the figure of FimH at right, the critical subset (green) of conserved residues (dark gray) important for mannose (orange) binding is highlighted. Conversely, the functional subset (red) of variable residues (blue) is not obvious from structural analysis but can be identified becuase they are evolving under positive selection.

Second, we have designed custom UTI89 Affymetrix GeneChip arrays to better understand the transcriptional response and regulation of genes important during infection.

Finally, we are exploring proteomics using mass spectrometry, nuclear magnetic resonance, and multidimensional gel electrophoresis as additional techniques to complement the other experiments in the lab. These high throughput protein-based techniques will help not only in characterizing the molecular pathogenesis of UPEC, but may also provide novel leads for future improvements in clinical diagnosis and prognosis.