Research Topics
| H OchmanSummaryAffiliation: University of Arizona Country: USA Publications
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Publications
Psi-Phi: exploring the outer limits of bacterial pseudogenesEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 87521, USA
Genome Res 14:2273-8. 2004..Almost all (>95%) pseudogenes are restricted to only one of the genomes and are of relatively recent origin, suggesting that these bacteria possess active mechanisms to eliminate nonfunctional genes...- Evolutionary origins of genomic repertoires in bacteriaEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
PLoS Biol 3:e130. 2005..Although our analyses are limited to the gamma-Proteobacteria, these results resolve a long-standing paradox-i.e., the ability to make robust phylogenetic inferences in light of substantial LGT... - The nature and dynamics of bacterial genomesHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Science 311:1730-3. 2006..Such regions will never yield a detectable phenotype, but their identification is vital to efforts to elucidate the biological role of all the proteins within the cell... - Sex and virulence in Escherichia coli: an evolutionary perspectiveThierry Wirth
Department of Molecular Biology, Schumannstrasse 21 22, Max Planck Institut für Infektionsbiologie, 10117 Berlin, Germany
Mol Microbiol 60:1136-51. 2006..This long-term pattern of evolution was observed in genes distributed throughout the genome, and thereby is the likely result of episodic selection for strains that can escape the host immune response... - Inferring clocks when lacking rocks: the variable rates of molecular evolution in bacteriaChih Horng Kuo
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
Biol Direct 4:35. 2009..In this study, we examine the consistency of substitution rates among a set of conserved genes in diverse bacterial lineages, and address the questions regarding the validity of molecular dating... - Erosion of interaction networks in reduced and degraded genomesHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
J Exp Zool B Mol Dev Evol 308:97-103. 2007.... - A bunch of fun-guys: the whole-genome view of yeast evolutionHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 87521, USA
Trends Genet 21:1-3. 2005..The pattern of genome evolution in yeast differs from that in bacteria apparently as a result of stronger selective constraints on bacterial chromosomes... - Neutral mutations and neutral substitutions in bacterial genomesHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, USA
Mol Biol Evol 20:2091-6. 2003..These differences have resulted in conflicting interpretations of the nonselective forces that affect mutation rates... - Examining bacterial species under the specter of gene transfer and exchangeHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, 85721, USA
Proc Natl Acad Sci U S A 102:6595-9. 2005..Taken as a whole, the results derived from the analysis of complete gene inventories support several of the current means to recognize and define bacterial species... - Eyeing bacterial genomesHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Curr Opin Microbiol 6:109-13. 2003..These features have made it possible to discern the forces acting in and on bacterial genomes at levels not attainable in eukaryotes... - Exploring microbial microevolution with microarraysHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Infect Genet Evol 5:103-8. 2005..In this review, we evaluate some of the evolutionary patterns and processes affecting bacterial genomes as detected with microarrays, and also delineate the limitations and conclusions stemming from such studies... - Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomesHoward Ochman
Dept of Biochemistry and Molecular Biophysics, 233 Life Sciences South, University of Arizona, Tucson, AZ 85721, USA
Trends Genet 18:335-7. 2002..Although it is not feasible to authenticate the coding capacity of all such regions experimentally, comparisons of ORFs in related genomes can expose those that encode functional proteins... - Bacterial evolution: chromosome arithmetic and geometryHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson 85721, USA
Curr Biol 12:R427-8. 2002..Aside from its biological relevance and curiosity, this diversity calls into question the way that we define bacterial chromosomes... - Genomes on the shrinkHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Proc Natl Acad Sci U S A 102:11959-60. 2005 - Evolutionary dynamics of full genome content in Escherichia coliH Ochman
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
EMBO J 19:6637-43. 2000..Moreover, strains vary widely in their frequencies of deletions, which probably accounts for the variation in genome size within the species... - Genes lost and genes found: evolution of bacterial pathogenesis and symbiosisH Ochman
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85718, USA
Science 292:1096-9. 2001..Furthermore, pathogens and symbionts depend on similar mechanisms for interacting with hosts and show parallel trends in genome evolution... - Lateral and oblique gene transferH Ochman
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 0088, USA
Curr Opin Genet Dev 11:616-9. 2001.... - Loss of DNA recombinational repair enzymes in the initial stages of genome degenerationColin Dale
Department of Biochemistry and Molecular Biophysics, University of Arizona, USA
Mol Biol Evol 20:1188-94. 2003..Similar events may be pervasive during the evolution of symbiosis because symbiont genomes typically lack recombinational repair genes and have reduced numbers of ribosomal operons... - Phylogenetics and the cohesion of bacterial genomesVincent Daubin
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ, 85721, USA
Science 301:829-32. 2003..Although comparisons of complete gene inventories indicate appreciable gain and loss of genes, orthologs available for phylogenetic reconstruction are consistent with a single tree... - Deletional bias and the evolution of bacterial genomesA Mira
Dept of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
Trends Genet 17:589-96. 2001..Here we discuss the evidence showing that deletional bias is a major force that shapes bacterial genomes... - Structural features and the persistence of acquired proteinsHema Prasad Narra
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Proteomics 8:4772-81. 2008..coli lineage were more likely to encode soluble and folded proteins, more likely to display environmental modulation of their gene expression, and by extrapolation, are more likely to be functional... - Extracting single genomes from heterogenous DNA samples: a test case with Carsonella ruddii, the bacterial symbiont of psyllids (Insecta)Colin Dale
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
J Insect Sci 5:3. 2005..The resulting libraries were highly enriched in bacterial sequences. Through the use of alternate enzymes and partial digests, this technique can be adapted to yield virtually pure DNA libraries for individual bacterial species... - The consequences of genetic drift for bacterial genome complexityChih Horng Kuo
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
Genome Res 19:1450-4. 2009..This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria... - Type III secretion systems and the evolution of mutualistic endosymbiosisColin Dale
Department of Ecology and Evolutionary Biology, Center for Insect Science, and Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721
Proc Natl Acad Sci U S A 99:12397-402. 2002..The function of inv/spa genes in maintaining symbiosis is demonstrated by the up-regulation of their expression under both in vivo and in vitro conditions that coincide with host cell invasion... - Selection on the genic location of disruptive elementsM W J van Passel
Department of Biochemistry and Molecular Biophysics, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
Trends Genet 23:601-4. 2007.... - Decoupling of genome size and sequence divergence in a symbiotic bacteriumJ J Wernegreen
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
J Bacteriol 182:3867-9. 2000..This exceptional size conservation may reflect the inability of this obligate mutualist to acquire foreign DNA and reduced selection for genetic novelty within a static intracellular environment... - Single-cell genomicsHoward Ochman
Department of Biochemistry, and Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
Environ Microbiol 9:7. 2007 - Stepwise formation of the bacterial flagellar systemRenyi Liu
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Proc Natl Acad Sci U S A 104:7116-21. 2007..These results show that core components of the bacterial flagellum originated through the successive duplication and modification of a few, or perhaps even a single, precursor gene... - Origins of flagellar gene operons and secondary flagellar systemsRenyi Liu
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
J Bacteriol 189:7098-104. 2007..These results demonstrate that the genetic basis of this ancient and structurally conserved organelle has been subject to many lineage-specific modifications... - Pea aphid as both host and vector for the phytopathogenic bacterium Pseudomonas syringaeJohn Stavrinides
Department of Ecology and Evolutionary Biology, University of Arizona, 1007 E Lowell Street, Tucson, Arizona 85721, USA
Appl Environ Microbiol 75:2230-5. 2009..These interactions illustrate that aphids can also vector bacterial pathogens and that even seemingly host-restricted pathogens can have alternative host specificities and lifestyles... - Quartet mapping and the extent of lateral transfer in bacterial genomesVincent Daubin
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, USA
Mol Biol Evol 21:86-9. 2004..Here, we focus on one of these methods, quartet mapping, and show that its application can lead to overestimation of the extent of inferred LGT in prokaryotes, particularly when applied to distantly related taxa... - The players in a mutualistic symbiosis: insects, bacteria, viruses, and virulence genesNancy A Moran
Departments of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 87521, USA
Proc Natl Acad Sci U S A 102:16919-26. 2005..defensa life cycle. We propose that, in these mutualistic symbionts, phage-borne toxin genes provide defense to the aphid host and are a basis for the observed protection against eukaryotic parasites... - Bacterial genomes as new gene homes: the genealogy of ORFans in E. coliVincent Daubin
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
Genome Res 14:1036-42. 2004..Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions... - Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteinsScott R Santos
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Environ Microbiol 6:754-9. 2004..We foresee the analysis of these protein-coding regions as being complementary to ribosomal DNA for answering questions pertaining to bacterial identification, classification, phylogenetics and evolution... - Start-up entities in the origin of new genesVincent Daubin
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Curr Opin Genet Dev 14:616-9. 2004..This invention of such novel functions seems to be founded on a strategy that secures the short-term survival of parasitic elements and thereby contributes to the renovation of gene repertoires in their host... - The effect of chromosome geometry on genetic diversityPradeep Reddy Marri
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Genetics 179:511-6. 2008..Collectively, our findings indicate that chromosome topology does not contribute significantly to either allelic or genotypic diversity and that the evolution of linear chromosomes is not based on a facility to recombine... - Gene location and bacterial sequence divergenceAlex Mira
Department of Ecology and Evolutionary Biology, University of Arizona, Tuscon 85721, USA
Mol Biol Evol 19:1350-8. 2002.... - Intracellular symbionts of sharpshooters (Insecta: Hemiptera: Cicadellinae) form a distinct clade with a small genomeNancy A Moran
Department of Ecology and Evolutionary Biology, Biological Sciences West 310, University of Arizona, Tucson 85721, USA
Environ Microbiol 5:116-26. 2003..A new genus and species name, 'Candidatus Baumannia cicadellinicola' (sp. nov.) is proposed for this newly characterized clade of symbiotic bacteria... - Gene decay in archaeaM W J van Passel
Department of Biochemistry and Molecular Biophysics, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA
Archaea 2:137-43. 2007..Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes... - Calibrating bacterial evolutionH Ochman
Department of Ecology, University of Arizona, Tucson, AZ 85721, USA
Proc Natl Acad Sci U S A 96:12638-43. 1999..However, there is evidence that bacteria have a constant genome-wide mutation rate on an evolutionary time scale but that this rate differs dramatically from the rate estimated by experimental methods... - The fate of new bacterial genesChih Horng Kuo
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
FEMS Microbiol Rev 33:38-43. 2009..This review summarizes the methods for identifying new genes in bacterial genomes and examines the features that promote the retention and elimination of these evolutionary novelties... - Effect of chromosome location on bacterial mutation ratesRichard Ellis Hudson
Department of Ecology and Evolutionary Biology, 310 Biosciences West, University of Arizona, Tucson, AZ 85721, USA
Mol Biol Evol 19:85-92. 2002..At all loci, regardless of chromosome location, T.A --> G.C transversions were more frequent than A.T --> G.C transitions during the exponential phase... - The emergence and fate of horizontally acquired genes in Escherichia coliMark W J van Passel
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona, United States of America
PLoS Comput Biol 4:e1000059. 2008..With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates... - Transcription increases multiple spontaneous point mutations in Salmonella entericaRichard Ellis Hudson
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Nucleic Acids Res 31:4517-22. 2003..Transitions occurred at roughly twice the rate of transversions, similar to results from sequence comparisons; however, several individual transversions are more frequent than the least common transition... - Of what use is sex to bacteria?Hema Prasad Narra
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
Curr Biol 16:R705-10. 2006.... - Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genomeTyler Jarvik
Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85718, USA
J Bacteriol 192:560-7. 2010.... - Recognizing the pseudogenes in bacterial genomesEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 87521, USA
Nucleic Acids Res 33:3125-32. 2005.... - Reconciling the many faces of lateral gene transferJeffrey G Lawrence
Trends Microbiol 10:1-4. 2002
Research Grants
- Genome Erosion in Infectious MicroorganismsHoward Ochman; Fiscal Year: 2007..abstract_text> ..
- EVOLUTIONARY GENETICS OF BACTERIAL CHROMOSOMESHoward Ochman; Fiscal Year: 2000..coli that have be serially transferred for more than 10,000 generations (obtained from the laboratory of Richard Lenski). ..
- Elucidating the origins and functions of unknown genesHoward Ochman; Fiscal Year: 2009..By combining experimental and bioinformatic approaches, the present proposal will analyze the origins, functions and structural properties of ORFans, and how they have assumed key roles in cellular function. ..