J Peter Gogarten

Summary

Affiliation: University of Connecticut
Country: USA

Publications

  1. ncbi request reprint Gene transfer: gene swapping craze reaches eukaryotes
    J Peter Gogarten
    Department of Molecular Biology, University of Connecticut, 75 North Eagleville Road, Storrs, 06269 3044, Connecticut, USA
    Curr Biol 13:R53-4. 2003
  2. pmc Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein
    Alireza G Senejani
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Int J Biol Sci 3:205-11. 2007
  3. pmc The role of reticulate evolution in creating innovation and complexity
    Kristen S Swithers
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Int J Evol Biol 2012:418964. 2012
  4. pmc Visualization of the phylogenetic content of five genomes using dekapentagonal maps
    Olga Zhaxybayeva
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Genome Biol 5:R20. 2004
  5. pmc Quartet decomposition server: a platform for analyzing phylogenetic trees
    Fenglou Mao
    Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green St, Athens, GA 30622, USA
    BMC Bioinformatics 13:123. 2012
  6. pmc Concerted gene recruitment in early plant evolution
    Jinling Huang
    Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA
    Genome Biol 9:R109. 2008
  7. pmc Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?
    Jinling Huang
    Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA
    Genome Biol 8:R99. 2007
  8. pmc Prokaryotic evolution and the tree of life are two different things
    Eric Bapteste
    UPMC, UMR CNRS 7138, 75005 Paris, France
    Biol Direct 4:34. 2009
  9. pmc Home and away- the evolutionary dynamics of homing endonucleases
    Adi Barzel
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
    BMC Evol Biol 11:324. 2011
  10. pmc A hybrid clustering approach to recognition of protein families in 114 microbial genomes
    Timothy J Harlow
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 5:45. 2004

Collaborators

Detail Information

Publications56

  1. ncbi request reprint Gene transfer: gene swapping craze reaches eukaryotes
    J Peter Gogarten
    Department of Molecular Biology, University of Connecticut, 75 North Eagleville Road, Storrs, 06269 3044, Connecticut, USA
    Curr Biol 13:R53-4. 2003
    ..The mechanisms and frequencies of these transfers remain the subject of speculation, but the findings provide ample reason to seriously consider interspecies gene transfer as an important evolutionary process in eukaryotes...
  2. pmc Structural stability and endonuclease activity of a PI-SceI GFP-fusion protein
    Alireza G Senejani
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Int J Biol Sci 3:205-11. 2007
    ..However, the endonuclease activity of the newly engineered protein was different from the wild-type protein in that it required the presence of Mn(2+) and not Mg(2+) metal cations for activity...
  3. pmc The role of reticulate evolution in creating innovation and complexity
    Kristen S Swithers
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Int J Evol Biol 2012:418964. 2012
    ..We discuss how these different evolutionary processes contribute to generating innovation and complexity...
  4. pmc Visualization of the phylogenetic content of five genomes using dekapentagonal maps
    Olga Zhaxybayeva
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Genome Biol 5:R20. 2004
    ..Analyses of genomes representing five photosynthetic bacterial phyla and of the prokaryotic contributions to the eukaryotic cell illustrate the utility of the methods...
  5. pmc Quartet decomposition server: a platform for analyzing phylogenetic trees
    Fenglou Mao
    Department of Biochemistry and Molecular Biology, University of Georgia, 120 Green St, Athens, GA 30622, USA
    BMC Bioinformatics 13:123. 2012
    ..This approach was shown to be useful in several studies of completely sequenced microbial genomes...
  6. pmc Concerted gene recruitment in early plant evolution
    Jinling Huang
    Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA
    Genome Biol 9:R109. 2008
    ..However, no systematic studies on the scope of anciently acquired genes and their impact on macroevolution are currently available in eukaryotes...
  7. pmc Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?
    Jinling Huang
    Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858, USA
    Genome Biol 8:R99. 2007
    ..This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria...
  8. pmc Prokaryotic evolution and the tree of life are two different things
    Eric Bapteste
    UPMC, UMR CNRS 7138, 75005 Paris, France
    Biol Direct 4:34. 2009
    ..In the following we will consider this circumstance from philosophical, scientific, and epistemological perspectives, surmising that phylogeny opted for a single model as a holdover from the Modern Synthesis of evolution...
  9. pmc Home and away- the evolutionary dynamics of homing endonucleases
    Adi Barzel
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, 69978, Israel
    BMC Evol Biol 11:324. 2011
    ....
  10. pmc A hybrid clustering approach to recognition of protein families in 114 microbial genomes
    Timothy J Harlow
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
    BMC Bioinformatics 5:45. 2004
    ..g. as the result of matches to so-called promiscuous domains. Use of the Markov Cluster algorithm avoids this non-specificity, but does not preserve topological or threshold information about protein families...
  11. pmc PentaPlot: a software tool for the illustration of genome mosaicism
    Lutz Hamel
    Department of Computer Science and Statistics, University of Rhode Island, Kingston, RI 02881, USA
    BMC Bioinformatics 6:139. 2005
    ..PentaPlot is a software tool that computes such dekapentagonal maps given an appropriate probability support matrix...
  12. pmc The intein of the Thermoplasma A-ATPase A subunit: structure, evolution and expression in E. coli
    A G Senejani
    Department of Molecular and Cell Biology, University of Connecticut, 75 North Eagleville Rd Storrs, CT 06269 3044, USA
    BMC Biochem 2:13. 2001
    ..In addition to this splicing activity, most reported inteins also contain an endonuclease domain that is important in intein propagation...
  13. ncbi request reprint Horizontal gene transfer, genome innovation and evolution
    J Peter Gogarten
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 3125, USA
    Nat Rev Microbiol 3:679-87. 2005
    ....
  14. pmc Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements
    J Peter Gogarten
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 31258, USA
    BMC Evol Biol 6:94. 2006
    ..BMC Evol Biol 2006, 6:42) provide important stepping stones towards integrated studies on how these parasitic elements evolve through time together with, or despite, their hosts...
  15. ncbi request reprint Inteins: structure, function, and evolution
    J Peter Gogarten
    Department of Molecular and Cell Biology, University of Connecticut, 75 North Eagleville Road, Storrs 06269 3044, USA
    Annu Rev Microbiol 56:263-87. 2002
    ..In particular, this review considers inteins as selfish or parasitic genetic elements, a point of view that explains many otherwise puzzling aspects of inteins...
  16. pmc A rooted net of life
    David Williams
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Biol Direct 6:45. 2011
    ..Given sufficient evidence, edges may then be differentiated as those representing vertical lines of inheritance within lineages and those representing horizontal genetic transfers or endosymbioses between lineages...
  17. pmc Genome sequence of Thermotoga sp. strain RQ2, a hyperthermophilic bacterium isolated from a geothermally heated region of the seafloor near Ribeira Quente, the Azores
    Kristen S Swithers
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 3125, USA
    J Bacteriol 193:5869-70. 2011
    ..This operon is also found in Thermotoga naphthophila strain RKU-10 but no other Thermotogales. These are the first reported PTS transporters in the Thermotogales...
  18. ncbi request reprint Genome mosaicism and organismal lineages
    Olga Zhaxybayeva
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Trends Genet 20:254-60. 2004
  19. pmc Thermotoga lettingae can salvage cobinamide to synthesize vitamin B12
    Nicholas C Butzin
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
    Appl Environ Microbiol 79:7006-12. 2013
    ..These results suggest that Thermotogales species can use the BtuFCD transporter to import both B12 and cobinamide, even if they cannot salvage cobinamide. ..
  20. pmc Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements
    Kristen S Swithers
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269 3125, USA
    BMC Evol Biol 9:303. 2009
    ..Here we provide quantitative statistical support from an analyses of proteins that host inteins, group I introns, group II introns and spliceosomal introns across all three domains of life...
  21. ncbi request reprint Rooting the ribosomal tree of life
    Gregory P Fournier
    Department of Molecular and Cell Biology, University of Connecticut, CT, USA
    Mol Biol Evol 27:1792-801. 2010
    ....
  22. pmc Filling the gaps in the genomic landscape
    David Williams
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269 3125, USA
    Genome Biol 11:103. 2010
    ..A new initiative provides comparative genomicists with a more complete picture of genome diversity. Here we discuss the improved sampling strategy...
  23. pmc Vitamin B(12) synthesis and salvage pathways were acquired by horizontal gene transfer to the Thermotogales
    Kristen S Swithers
    Department of Molecular and Cell Biology, University of Connecticut, CT, USA
    Genome Biol Evol 4:730-9. 2012
    ..Genes in T. africanus with apparent B(12) riboswitches were found to be down-regulated in the presence of vitamin B(12) consistent with their roles in B(12) synthesis and cobinamide salvage...
  24. pmc Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologs
    Amanda K Petrus
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 7:e40236. 2012
    ..These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath...
  25. ncbi request reprint Cladogenesis, coalescence and the evolution of the three domains of life
    Olga Zhaxybayeva
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
    Trends Genet 20:182-7. 2004
    ..Each contemporary molecule has its own history that traces back to an individual molecular cenancestor. However, these molecular ancestors were likely to be present in different organisms and at different times...
  26. pmc Trees in the web of life
    Kristen S Swithers
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    J Biol 8:54. 2009
    ....
  27. pmc BranchClust: a phylogenetic algorithm for selecting gene families
    Maria S Poptsova
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    BMC Bioinformatics 8:120. 2007
    ....
  28. pmc Biased gene transfer and its implications for the concept of lineage
    Cheryl P Andam
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Biol Direct 6:47. 2011
    ..In the presence of horizontal gene transfer (HGT), the concepts of lineage and genealogy in the microbial world become more ambiguous because chimeric genomes trace their ancestry from a myriad of sources, both living and extinct...
  29. pmc Reassessment of the lineage fusion hypothesis for the origin of double membrane bacteria
    Kristen S Swithers
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 6:e23774. 2011
    ..We conclude that the signal detected in James Lake's analysis in part results from a systematic artifact due to group size and diversity combined with low levels of horizontal gene transfer...
  30. ncbi request reprint Ancient gene duplications and the root(s) of the tree of life
    Olga Zhaxybayeva
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 31258, USA
    Protoplasma 227:53-64. 2005
    ....
  31. pmc Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life
    Gregory P Fournier
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 31258, USA
    Philos Trans R Soc Lond B Biol Sci 364:2229-39. 2009
    ..Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history...
  32. doi request reprint Using comparative genome analysis to identify problems in annotated microbial genomes
    Maria S Poptsova
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Microbiology 156:1909-17. 2010
    ..Researchers need to be aware of the existing errors in the annotation of even well-studied genomes, such as Escherichia coli, and consider additional quality control for their results...
  33. pmc Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants
    Nicholas C Butzin
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 8:e84300. 2013
    ....
  34. pmc The power of phylogenetic approaches to detect horizontally transferred genes
    Maria S Poptsova
    Department of Molecular and Cell Biology, University of Connecticut, CT, USA
    BMC Evol Biol 7:45. 2007
    ..Are the detected transfers mainly false positives, or are they the tip of an iceberg of many transfer events most of which go undetected by current methods?..
  35. pmc Quantifying homologous replacement of loci between haloarchaeal species
    David Williams
    Department of Molecular and Cell Biology, University of Connecticut, CT, USA
    Genome Biol Evol 4:1223-44. 2012
    ....
  36. ncbi request reprint Spliceosomal introns: new insights into their evolution
    Olga Zhaxybayeva
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269 3125, USA
    Curr Biol 13:R764-6. 2003
    ..Only a small subset of the analyzed introns was present in the common ancestor of plants, fungi, animals and Plasmodium...
  37. pmc Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales
    Kenneth M Noll
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    BMC Evol Biol 8:7. 2008
    ..We examined deep phylogenetic relationships among the mal genes of these hyperthermophiles and their close relatives to look for evidence of shared ancestry...
  38. doi request reprint Estimating the size of the bacterial pan-genome
    Pascal Lapierre
    University of Connecticut Biotechnology Center, 91 North Eagleville Road, Storrs, CT 06269 3149, USA
    Trends Genet 25:107-10. 2009
    ..Our findings indicate that the pan-genome of the bacterial domain is of infinite size (the Bacteria as a whole have an open pan-genome) and that approximately 250 genes per genome belong to the extended bacterial core genome...
  39. pmc Biased gene transfer mimics patterns created through shared ancestry
    Cheryl P Andam
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    Proc Natl Acad Sci U S A 107:10679-84. 2010
    ..We conclude that the observed phylogenetic pattern reflects both vertical inheritance and biased HGT and that the signal caused by common organismal descent is difficult to distinguish from the signal due to biased gene transfer...
  40. pmc An improved probability mapping approach to assess genome mosaicism
    Olga Zhaxybayeva
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269 3125, USA
    BMC Genomics 4:37. 2003
    ..Here we extend the probability mapping approach by improving taxon sampling of the analyzed datasets, and by using bootstrap support values, a more conservative tool to assess reliability...
  41. doi request reprint Biased gene transfer in microbial evolution
    Cheryl P Andam
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, Connecticut 06269 3125, USA
    Nat Rev Microbiol 9:543-55. 2011
    ..We also discuss the role of biased gene transfer in the formation of taxonomically recognizable natural groups in the tree or net of life...
  42. pmc Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia
    Gregory P Fournier
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269 31258, USA
    J Bacteriol 190:1124-7. 2008
    ..This event likely occurred within the last 475 million years, causing profound changes in planetary methane biogeochemistry...
  43. pmc Inferring the ancient history of the translation machinery and genetic code via recapitulation of ribosomal subunit assembly orders
    Gregory P Fournier
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 5:e9437. 2010
    ..Furthermore, we find that this ordering produces several trends in specific amino acid usages compatible with models of genetic code evolution...
  44. pmc Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales
    Cheryl P Andam
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Rd, Storrs, CT 06269 3125, USA
    BMC Evol Biol 12:85. 2012
    ..During the course of evolution, HGT has played an essential role in the origin and dissemination of genetic and metabolic novelty...
  45. ncbi request reprint Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species
    Pascal Lapierre
    Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT 06269 3125, USA
    Syst Appl Microbiol 29:15-23. 2006
    ..For all the Thermus and Deinococcus species surveyed, including Thermus scotoductus, cultures that were free of contamination only contained an A/V-type ATP synthases...
  46. pmc Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data
    Adam C Silver
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
    PLoS ONE 6:e16751. 2011
    ..Instead, the detection of genes critical in the adaptation to specific niches may help to reveal the physiological specialization of these strains...
  47. ncbi request reprint Prokaryotic evolution in light of gene transfer
    J Peter Gogarten
    Department of Molecular and Cell Biology, University of Connecticut, CT, USA
    Mol Biol Evol 19:2226-38. 2002
    ....
  48. pmc Genome sequence of Kosmotoga olearia strain TBF 19.5.1, a thermophilic bacterium with a wide growth temperature range, isolated from the Troll B oil platform in the North Sea
    Kristen S Swithers
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    J Bacteriol 193:5566-7. 2011
    ..Its genome sequence reveals extensive gene gains and a large content of mobile genetic elements. It also contains putative hydrogenase genes that have no homologs in the other member of the Thermotogales...
  49. ncbi request reprint Signature of a primitive genetic code in ancient protein lineages
    Gregory P Fournier
    Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269 3125, USA
    J Mol Evol 65:425-36. 2007
    ..Thus, expansion of the genetic code likely set the stage for the transition from RNA-based to protein-based life...
  50. ncbi request reprint A hyperconserved protein in Prochlorococcus and marine Synechococcus
    Olga Zhaxybayeva
    Department of Biochemistry and Molecular Biology, Dalhousie University, NS, Canada
    FEMS Microbiol Lett 274:30-4. 2007
    ..Comparative analyses indicate that the hyperconserved protein, which may be involved in interactions with nucleic acids, is under stabilizing selection and has resided in these genomes since the last common ancestor of the group...
  51. ncbi request reprint The evolution of eukaryotes
    William Martin
    Science 316:542-3; author reply 542-3. 2007
  52. ncbi request reprint Whole-genome analysis of photosynthetic prokaryotes
    Jason Raymond
    Department of Chemistry and Biochemistry, Arizona State University ASU, Tempe, AZ 85287 1604, USA
    Science 298:1616-20. 2002
    ..Our results explain incoherencies in previous data-limited phylogenetic analyses of phototrophic bacteria and indicate that the core components of photosynthesis have been subject to lateral transfer...
  53. pmc Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach
    Jason Raymond
    Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287 1604, USA
    Philos Trans R Soc Lond B Biol Sci 358:223-30. 2003
    ..A small plurality phylogenetic signal was observed, which may be a core of remnant genes not subject to HGT, or may result from a propensity for gene exchange between two or more of the photosynthetic organisms compared...
  54. pmc Evolutionary and diagnostic implications of intragenomic heterogeneity in the 16S rRNA gene in Aeromonas strains
    Alessia Morandi
    Institute for Infectious Diseases, University of Berne, Switzerland
    J Bacteriol 187:6561-4. 2005
    ..5%. The SSU copies from Aeromonas veronii LMG13695 clustered with sequences from four Aeromonas species. These results demonstrate intragenomic heterogeneity of SSU and suggest caution when using SSU to identify aeromonads...
  55. pmc Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events
    Olga Zhaxybayeva
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
    Genome Res 16:1099-108. 2006
    ..However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases...
  56. ncbi request reprint Were arachnids the first to use combinatorial peptide libraries?
    Brianna L Sollod
    Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06032 3305, USA
    Peptides 26:131-9. 2005
    ..This gene-based combinatorial peptide library strategy appears to have been first implemented by arachnids almost 400 million years ago, long before cone snails evolved a similar mechanism for generating peptide diversity...