Uri Gophna

Summary

Affiliation: Tel Aviv University
Country: Israel

Publications

  1. ncbi CRISPR loci reveal networks of gene exchange in archaea
    Avital Brodt
    Department of Molecular Microbiology and Biotechnology, George S, Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Israel
    Biol Direct 6:65. 2011
  2. ncbi CEACAM1 recognition by bacterial pathogens is species-specific
    Maike Voges
    Lehrstuhl für Zellbiologie, Universitat Konstanz, Mailbox X908, 78457 Konstanz, Germany
    BMC Microbiol 10:117. 2010
  3. ncbi Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    J Clin Microbiol 44:4136-41. 2006
  4. ncbi Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Trends Microbiol 14:64-9. 2006
  5. ncbi Lateral acquisition of genes is affected by the friendliness of their products
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
    Proc Natl Acad Sci U S A 108:343-8. 2011
  6. ncbi Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species
    Shiri Freilich
    The Blavatnik School of Computer Sciences, Faculty of Life Sciences, Ramat Aviv, Israel
    PLoS Comput Biol 6:e1000690. 2010
  7. ncbi An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes
    Adi Stern
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Syst Biol 59:212-25. 2010
  8. ncbi Native homing endonucleases can target conserved genes in humans and in animal models
    Adi Barzel
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 39:6646-59. 2011
  9. ncbi Competitive and cooperative metabolic interactions in bacterial communities
    Shiri Freilich
    Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    Nat Commun 2:589. 2011
  10. ncbi Reconstructing ancestral gene content by coevolution
    Tamir Tuller
    School of Computer Sciences, Tel Aviv University, Ramat Aviv, Israel
    Genome Res 20:122-32. 2010

Collaborators

Detail Information

Publications49

  1. ncbi CRISPR loci reveal networks of gene exchange in archaea
    Avital Brodt
    Department of Molecular Microbiology and Biotechnology, George S, Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, 69978, Israel
    Biol Direct 6:65. 2011
    ..Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism...
  2. ncbi CEACAM1 recognition by bacterial pathogens is species-specific
    Maike Voges
    Lehrstuhl für Zellbiologie, Universitat Konstanz, Mailbox X908, 78457 Konstanz, Germany
    BMC Microbiol 10:117. 2010
    ..However, it is unknown whether bacterial adhesins of human pathogens can recognize CEACAM1 orthologues from other mammals...
  3. ncbi Differences between tissue-associated intestinal microfloras of patients with Crohn's disease and ulcerative colitis
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    J Clin Microbiol 44:4136-41. 2006
    ..Imbalance in flora in Crohn's disease is probably not sufficient to cause inflammation, since microbiotas from inflamed and noninflamed tissues were of similar compositions within the same individual...
  4. ncbi Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Trends Microbiol 14:64-9. 2006
    ..Although there might be little evidence for the extensive recent transfer of genes, we demonstrate that ancient lateral gene acquisition has shaped the B. bacteriovorus genome to a great extent...
  5. ncbi Lateral acquisition of genes is affected by the friendliness of their products
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
    Proc Natl Acad Sci U S A 108:343-8. 2011
    ..We suggest that these proteins have a greater chance of forming new interactions in new species, thus integrating into existing modules. These results reveal basic principles for the incorporation of novel genes into existing systems...
  6. ncbi Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species
    Shiri Freilich
    The Blavatnik School of Computer Sciences, Faculty of Life Sciences, Ramat Aviv, Israel
    PLoS Comput Biol 6:e1000690. 2010
    ..Finally, we identify reactions that are uniquely susceptible to perturbations in human pathogens, potentially serving as novel drug-targets...
  7. ncbi An evolutionary analysis of lateral gene transfer in thymidylate synthase enzymes
    Adi Stern
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Syst Biol 59:212-25. 2010
    ..By reconstructing the ThyA and ThyX gene trees, the most likely donor of each LGT event was inferred. The role of viruses in LGT of Thy is finally discussed...
  8. ncbi Native homing endonucleases can target conserved genes in humans and in animal models
    Adi Barzel
    Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 39:6646-59. 2011
    ..We validate experimentally the predicted target specificity of candidate fungal, bacterial and archaeal HEases using cell free, yeast and archaeal assays...
  9. ncbi Competitive and cooperative metabolic interactions in bacterial communities
    Shiri Freilich
    Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    Nat Commun 2:589. 2011
    ..These findings are important for the future design of consortia optimized towards bioremediation and bio-production applications...
  10. ncbi Reconstructing ancestral gene content by coevolution
    Tamir Tuller
    School of Computer Sciences, Tel Aviv University, Ramat Aviv, Israel
    Genome Res 20:122-32. 2010
    ..Our analysis suggests that LUCA appears to have been bacterial-like and had a genome size similar to the genome sizes of many extant organisms...
  11. ncbi Extensive gene diversity in septicemic Escherichia coli strains
    Daphna Mokady
    Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
    J Clin Microbiol 43:66-73. 2005
    ..Moreover, in addition to the high level of genome plasticity, we show that the large pool of virulence genes in the septicemic strains is independent of the host, implying a high degree of zoonotic risk...
  12. ncbi Sequence features of E. coli mRNAs affect their degradation
    Gal Lenz
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
    PLoS ONE 6:e28544. 2011
    ..Notably, mRNAs of recently-acquired genes in the E. coli genome, which have a distinct nucleotide composition, tend to be highly stable. This high stability may aid the evolutionary fixation of horizontally acquired genes...
  13. ncbi Virulence factors of septicemic Escherichia coli strains
    Daphna Mokady
    Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
    Int J Med Microbiol 295:455-62. 2005
    ..The variable profile of virulence genes in septicemic E. coli strains, as well as a prevalence of mobility-related sequences point out the existence of a "mix and match" combinatorial system...
  14. ncbi Detection of spatial and temporal influences on bacterial communities in an urban stream by automated ribosomal intergenic ribosomal spacer analysis
    Amitai Or
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Israel
    Microbes Environ 26:360-6. 2011
    ..Molecular fingerprinting methods based on natural fragment length polymorphisms may therefore represent a supplementary approach for stream monitoring, alongside physico-chemical measurements...
  15. ncbi The lpf operon of invasive Escherichia coli
    Diana Ideses
    Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
    Int J Med Microbiol 295:227-36. 2005
    ..The lpf operon is expressed and is important for adherence to epithelial cells. The lpf operon was found only in four of the ExPEC strains tested and is likely to have been acquired by horizontal gene transfer...
  16. ncbi A degenerate type III secretion system from septicemic Escherichia coli contributes to pathogenesis
    Diana Ideses
    Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Israel
    J Bacteriol 187:8164-71. 2005
    ..These results are the first demonstration of the importance of ETT2 for pathogenesis...
  17. ncbi The large-scale organization of the bacterial network of ecological co-occurrence interactions
    Shiri Freilich
    Blavatnik School of Computer Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
    Nucleic Acids Res 38:3857-68. 2010
    ..Here, we demonstrate its utility for predicting cooperation and inhibition within communities...
  18. ncbi Deriving enzymatic and taxonomic signatures of metagenomes from short read data
    Uri Weingart
    School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel
    BMC Bioinformatics 11:390. 2010
    ..Relative amounts of different EC categories define the enzymatic spectrum, without the need to perform genomic assemblies of short reads...
  19. ncbi Complexity, connectivity, and duplicability as barriers to lateral gene transfer
    Alon Wellner
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel, 69978
    Genome Biol 8:R156. 2007
    ....
  20. ncbi Metabolic-network-driven analysis of bacterial ecological strategies
    Shiri Freilich
    The Blavatnik School of Computer Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
    Genome Biol 10:R61. 2009
    ....
  21. ncbi In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii
    Adit Naor
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 6:e15833. 2011
    ....
  22. ncbi Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen
    Mor N Lurie-Weinberger
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Genomics 99:52-8. 2012
    ..Thus, bacterial genes contributed to the host-adaptation by allowing a larger variety of surface structures and increasing the efficiency of metal ion uptake in the competitive gut niche...
  23. ncbi Integration of a foreign gene into a native complex does not impair fitness in an experimental model of lateral gene transfer
    Shira Omer
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
    Mol Biol Evol 27:2441-5. 2010
    ..We conclude that LGT of complex subunits may be neutral even when the transferred subunit can integrate into the host complex and that this neutrality can be a fertile ground for selective forces once the environment changes...
  24. ncbi Association between translation efficiency and horizontal gene transfer within microbial communities
    Tamir Tuller
    Faculty of Mathematics and Computer Science, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Blavatnik School of Computer Science, School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Nucleic Acids Res 39:4743-55. 2011
    ..Our results also suggest that frequent HGT may be a homogenizing force that increases the similarity in the tRNA pools of organisms within the same community...
  25. ncbi A likelihood framework to analyse phyletic patterns
    Ofir Cohen
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Philos Trans R Soc Lond B Biol Sci 363:3903-11. 2008
    ..Our methodology was applied to analyse a large corpus of data, consisting of 4873 gene families spanning 63 species and revealed novel insights regarding the evolutionary nature of genome-wide gain and loss dynamics...
  26. ncbi Neutrality of foreign complex subunits in an experimental model of lateral gene transfer
    Alon Wellner
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
    Mol Biol Evol 25:1835-40. 2008
    ..We conclude that LGT of complex subunits may be mostly neutral and that forces operating against gene retention appear to be moderate...
  27. ncbi OmpA of a septicemic Escherichia coli O78--secretion and convergent evolution
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
    Int J Med Microbiol 294:373-81. 2004
    ..Support for this assumption was obtained from experiments indicating that addition of exogenous, purified OmpA reduces killing of bacteria by NE...
  28. ncbi Low species barriers in halophilic archaea and the formation of recombinant hybrids
    Adit Naor
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
    Curr Biol 22:1444-8. 2012
    ..These results show that recombination barriers may be more permissive in halophilic archaea than they are in bacteria...
  29. ncbi The origins of eukaryotic-like proteins in Legionella pneumophila
    Mor N Lurie-Weinberger
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
    Int J Med Microbiol 300:470-81. 2010
    ..Information on selection patterns and eukaryotic-like status was combined as a novel approach to predict type IV secretion system effectors of Legionella, which represent promising targets for future study...
  30. ncbi Composition and dynamics of the gill microbiota of an invasive Indo-Pacific oyster in the eastern Mediterranean Sea
    Dror Zurel
    The Porter School of Environmental Studies, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
    Environ Microbiol 13:1467-76. 2011
    ..We suggest that this conserved association between bacteria and oyster reflects either a symbiosis between the oyster host and some of its bacteria, a co-invasion of both parties, or both...
  31. ncbi Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel 69978
    Gene 312:151-63. 2003
    ....
  32. ncbi The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer
    Ofir Cohen
    Department of Cell Research and Immunology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
    Mol Biol Evol 28:1481-9. 2011
    ..In contrast, we found that connectivity is an important and a statistically significant factor in determining transferability when proteins with a similar function are compared...
  33. ncbi The formation of Escherichia coli curli amyloid fibrils is mediated by prion-like peptide repeats
    Izhack Cherny
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    J Mol Biol 352:245-52. 2005
    ..Since mammal prion, yeast prion, and curli protein are evolutionarily distinct, the conserved peptide repeats most likely define an optimized self-association motif that was independently evolved by diverse systems...
  34. ncbi Extensive Inter-Domain Lateral Gene Transfer in the Evolution of the Human Commensal Methanosphaera stadtmanae
    Mor Nadia Lurie-Weinberger
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University Tel Aviv, Israel
    Front Genet 3:182. 2012
    ..stadtmanae to a host-dependent lifestyle by allowing a larger variation in surface structures and increasing transport efficiency in the gut niche which is diverse and competitive...
  35. ncbi The evolution of modularity in bacterial metabolic networks
    Anat Kreimer
    School of Mathematical Science, Tel Aviv University, Tel Aviv 69978, Israel
    Proc Natl Acad Sci U S A 105:6976-81. 2008
    ..This reveals a trend of modularity decrease from ancestors to descendants that is likely the outcome of niche specialization and the incorporation of peripheral metabolic reactions...
  36. ncbi Genotype is a stronger determinant than sex of the mouse gut microbiota
    Amir Kovacs
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
    Microb Ecol 61:423-8. 2011
    ..These findings imply that genetic polymorphisms help shape the intestinal microbiota of mammals and consequently could affect host susceptibility to diseases...
  37. ncbi Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions
    Adi Barzel
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel, 69978
    Biochem Soc Trans 39:169-73. 2011
    ..In particular, the fitness effects of harbouring an intein/HEN can be tested in direct competition assays, providing additional insights that will improve current evolutionary models...
  38. ncbi A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness
    Amir Kovacs
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
    Res Microbiol 161:192-7. 2010
    ....
  39. ncbi Role of fibronectin in curli-mediated internalization
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
    FEMS Microbiol Lett 212:55-8. 2002
    ..The ability of curli fibers to bind fibronectin can therefore be linked to virulence...
  40. ncbi In situ transplant analysis of free-living bacteria in a lotic ecosystem
    Amitai Or
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University Ramat Aviv, Tel Aviv 69978, Israel
    Res Microbiol 164:262-9. 2013
    ..Nevertheless, introducing free-living bacteria from the human-impacted section into the freshwater section resulted in a profile more similar to the latter, indicating a profound niche influence on these microbial assemblages...
  41. ncbi A genetic investigation of the KEOPS complex in halophilic Archaea
    Adit Naor
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
    PLoS ONE 7:e43013. 2012
    ..volcanii. Deletion of pcc1 led to pleiotropic phenotypes, including decreased growth rate, reduced levels of t(6)A modification, and elevated levels of intra-cellular glycation products...
  42. ncbi Fine-scale temporal dynamics of a fragmented lotic microbial ecosystem
    Amitai Or
    Department of Molecular Microbiology and Biotechnology, George S Wise Faculty of Life Sciences, Tel Aviv University
    Sci Rep 2:207. 2012
    ..Thus, our results show that microbial ecosystems can change rapidly, but re-establish a new equilibrium relatively quickly...
  43. ncbi Multilocus sequence typing (MLST) of Escherichia coli O78 strains
    Roni S Adiri
    Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
    FEMS Microbiol Lett 222:199-203. 2003
    ..Preliminary, but significant, results indicate that clonal division in E. coli O78 strains is host independent, and closely related clones reside in different hosts. There was a positive correlation between virulence and clonal origin...
  44. ncbi A novel ColV plasmid encoding type IV pili
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
    Microbiology 149:177-84. 2003
    ..As type IV pili of Gram-negative bacteria are involved in several stages of infection, their presence on a ColV virulence plasmid could expand the repertoire of pathogenesis-related genes...
  45. ncbi Weighted genome trees: refinements and applications
    Uri Gophna
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia
    J Bacteriol 187:1305-16. 2005
    ..Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution...
  46. ncbi Evolutionary plasticity of methionine biosynthesis
    Uri Gophna
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1X5
    Gene 355:48-57. 2005
    ..This study illustrates how diverse molecular solutions can fulfill a conserved function in living beings...
  47. ncbi Complex histories of genes encoding 3-hydroxy-3-methylglutaryl-CoenzymeA reductase
    Uri Gophna
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
    Mol Biol Evol 23:168-78. 2006
    ..We demonstrate that even in Vibrio species, where HMGR is not clustered with other genes to form an operon or a metabolic cluster, it is under strong purifying selection...
  48. ncbi Have archaeal genes contributed to bacterial virulence?
    Uri Gophna
    Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada
    Trends Microbiol 12:213-9. 2004
  49. ncbi Virulence and the heat shock response
    Uri Gophna
    Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel 69978
    Int J Med Microbiol 292:453-61. 2003
    ..The cross talk between heat shock and virulence genes is discussed...