Bacterial Molecular Evolution

Selection-Driven Gene Inactivation

For a protein-coding gene to persist, selection must favor a functional protein in the long term. Nevertheless, premature stop codons in some genes appear to be positively selected under some circumstances. The identities of affected genes shed light on both the evolutionary phenomenon and the genes themselves.

Determinants of Position-Specific Mutation Rates

Nucleotide positions in a genome exhibit different rates of mutation. Previous work on this project characterized the high C→T mutation rate at 5-methyl C residues in bacteria, and used this to infer methylation patterns. Other work revealed that N4 methylation of C by a particular Type III restriction-modification system is associated with extremely high C→A mutation rate. Additional hypermutation phenomena are under study.

Short-Term Effects of Selection on Coding Sequences

The evolution of coding sequences and their protein products is most commonly studied by comparison of sequences from different species, with divergence times of millions of years. Comparison of sequences from tight genetic clusters of bacteria, with divergence times of years to decades, provides a very different perspective on protein evolution.

Evolution of Pathogen Characteristics

Genetic differences within a bacterial species can have phenotypic consequences that are relevant to disease. Reconstruction of genetic changes that have occurred recently can elucidate the evolution of disease-causing and other important traits on a relatively short time scale (years or decades).