Howard Ochman
Professor of Biochemistry, and Molecular and Cellular Biology
Ph.D. 1984, University of Rochester
Molecular evolution of bacterial genes and genomes.
Research Interests
My research attempts to elucidate the factors that influence the generation and maintenance of variation in bacterial genomes.
Due to the small size, absence of introns, paucity of highly repetitive DNA, and maintenance of gene order in divergent taxa, the bacterial genome has traditionally been viewed as being evolutionarily conserved. However, naturally occurring strains of E. coli vary in genome size, and our research analyzes polymorphic regions to determine the rates and patterns of chromosome evolution. Furthermore, enteric bacteria display considerable diversity in biochemical characteristics, host range, and patterns of virulence, suggesting that large-scale changes have occurred within the genomes of these species since they diverged. We are presently examining DNA sequences that are unique to Salmonella in an attempt to discover the molecular, genetic, and phenotypic characteristics that define bacterial species. As a result of the analyses of species-specific sequences, we have defined two pathogenicity islands responsible for virulence properties of Salmonella.
One of the more fundamental assumptions of molecular evolution is that mutations occur at random throughout the genome. Although this premise underlies most empirical and theoretical studies in this field, several lines of evidence suggest that mutations do not occur in a purely random manner. Due to the antiparallel orientation of complementary strands, DNA replication is an asymmetric process; and since the mechanisms for replicating the two strands differ, it is possible for the rate and pattern of mutations to differ on the two strands. The aims of this research are to determine if the leading and lagging strands of DNA have unequal mutation rates, and to ascertain the degree to which biases in substitution rates are influenced by genomic location and base composition.
Selected Publications
Marri, P.R, L.K. Harris, K. Houmiel, S.C. Slater and H. Ochman (2008) The effect of chromosome geometry on genetic diversity. Genetics, in press
Stavrinides, J. and H. Ochman (2008) Phylogenetic methods and inferences in microbial evolution. Encyclopedia of Microbiology, Elsevier
Liu, R. and H. Ochman (2007) Stepwise formation of the bacterial flagellar system. Proc. Natl. Acad. Sci. USA 104: 7116-7121.
Ochman, H., R. Liu and E.P.C. Rocha (2007). Erosion of interaction networks in reduced and degraded genomes. J. Experimental. Zool. 308B: 97-103.
van Passel, M.W.J., C. S. Smillie and H. Ochman (2007) Gene decay in Archaea. Archaea 2: 137-142.
Narra, H.P. and H. Ochman (2006) Of what use is sex to bacteria? Current Biology 16: R705-R710
Ochman, H. and L. Davalos (2006) The nature and dynamics of bacterial genomes. Science 311: 1730-1734.
Wirth, T., Falush, D., Lan, R., Colles, F., Mensa, P., Wieler, L.H., Karch, H., Reeves, P., Maiden, M.C.J., Ochman, H. and M. Achtman (2006) Sex and virulence in Escherichia coli: an evolutionary perspective. Molec. Microbiol. 60: 1136-1151.
Daubin, V. and H. Ochman (2004) Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli. Genome Research14: 1036-1042.
Daubin, V. and H. Ochman (2004) Recognizing lateral gene transfer by quartet mapping. Molec. Biol. Evol. 21: 48-51.
Daubin, V. and H. Ochman (2004) Start-up entities in the evolution of new genes. Curr. Opin. Genet. Devel., in press.
Lerat, E. and H. Ochman (2004) Y-F: Exploring the outer limits of bacterial pseudogenes. Genome Research, in press.
Santos, S.R. and H. Ochman (2004) Identification and phylogenetic sorting of bacterial lineages using universally conserved genes and proteins.Environ. Microbiol. 6: 754-759.
Dale, C., B. Wang, N.A. Moran and H. Ochman (2003) Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration in mutualistic bacterial endosymbionts.Molec. Biol. Evol. 20: 1188-1194.
Daubin, V., N.A. Moran, and H. Ochman (2003) Phylogenetics and the cohesion of bacterial genomes. Science 301: 829-832.
Hudson, R.E., U. Bergthorsson, and H. Ochman (2003) Transcription increases a broad spectrum of spontaneous mutations in bacteria.Nucleic Acids Res. 31: 4517-4522.
Ochman, H. (2003) Neutral mutations and neutral substitutions in bacterial genomes. Molec. Biol. Evol. 20: 2091-2096
Ochman, H. and S. R. Santos (2003) Eyeing bacterial genomes.Curr. Op. Microbiol. 6: 109-113.