Prof. Uri Gophna
Ph.D.: 2003, Tel-Aviv University
Phone: (Office) +972-3-640-9988
(Fax) +972-3-640-9407
E-mail:

urigo@tauex.tau.ac.il

Room#: Green 121
Member's portrait
  Personal Information
  Research Interests
  Full Publications

Personal Information

Education

1992 - 1996   Technion - Israeli Institute of Technology, Haifa, Israel, B.Sc.,

                          Biotechnology and Food Engineering - Magna Cum Laude.
1996 - 1998    Tel Aviv University, Tel Aviv, Israel, M.Sc., Biotechnology. – Magna Cum Laude.
1998 - 2003    Tel Aviv University, Tel Aviv, Israel, Ph.D. Microbiology - With Distinction.

Academic Positions
2003 - 2005       Dalhousie University, Halifax, Canada. Posdoctoral training at the W. Ford Doolittle lab

2005 - 2006       Tel Aviv University, Tel Aviv, Israel George S. Wise postdoctoral fellow.
2006 - 2007       Ph.D. level instructor Dept. of Molecular Microbiology and Biotechnology, TAU
2007 - 2012       Senior Lecturer, Dept. of Molecular Microbiology and Biotechnology, TAU

2012 -                  Associate professor, Dept. of Molecular Microbiology and Biotechnology, TAU

Honours and Awards

The Nili Rubinovich-Grossman memorial award (ISM) 2008
The George S. Wise postdoctoral fellowship 2006-2007
The Killam Postdoctoral Fellowship, 2003-2005.
The Joan and Jaim Constantiner Institute for Molecular Genetics Travel Scholarship, 2000, 2002.
The Kaplun Scholarship Award, 2002.
The Wolf Doctoral Fellowship Award, 2001.
The Award for Research and Teaching Excellence in Medicine and Life Sciences, 1998, 2000.

Research Interests

 

Understanding evolutionary processes behind bacterial adaptation has contributed to both the medical community and to evolutionary theory. Broadly, our research interests revolve around two related topics: 1. The role of lateral gene transfer (LGT) in the evolution of microorganisms and 2. The study of host-microbe interactions, with particular focus on the human gut microbiome in health and disease. We are interested in fundamental questions in microbial ecology and evolution: What are the factors that drive or limit gene flow between prokaryotic species? How does host specificity evolve? Which forces shape the population structure of microbial communities in the mammalian microbiota? Which microbial species can cause chronic diseases?

Microbial ecology in health and disease. The mammalian intestinal microbiota (formerly known as gut flora) is a complex ecosystem containing hundreds of microbial species, and bacterial cells in our body vastly outnumber our own cells. The microbiota not only contributes to the nutrition and gut development of the host but is also required for development of a healthy immune response, and is, to some degree, genetically determined. The human microbiota has been attracting tremendous interest and since there is increasing evidence supporting the involvement of the gut microbiota in several human diseases: from inflammatory bowel diseases, colorectal cancer and irritable bowel syndrome to metabolic syndrome and cardiovascular disease. However, due to its amazing complexity and the limitation of current microbe cultivation techniques, the microbiota remains a poorly understood ecosystem, in need of further research. We study the human microbiota using metagenomic techniques, and analyze samples from both healthy individuals and patients with gastric reflux disease, inflammatory bowel diseases and colorectal cancer, to try and explore the different roles the microbiota plays in these diseases.

Impact of lateral gene transfer on microbial evolution. LGT plays a crucial role in the evolution of microorganisms, including bacterial pathogens, and is a major source of genetic innovation. Many known virulence factors are the product of LGT, probably because the strong selective advantage they confer greatly increases the genes' chances of being fixed in a population. Using a variety of bioinformatic approaches we identify laterally transferred genes and study their evolution. We also investigate why some gene functions are transferred frequently while others are only rarely horizontally acquired. We are particularly interested in cases where such genes are the driving forces behind speciation in archaea and bacteria. We are also exploring inter-species recombination, a process which was believed to be extremely rare in prokaryotes, but is now known to exist in several prokaryotic groups. We have recently shown that inter-species hybrids can be formed by a natural cell fusion process in archaea and that up to 17% of the genome can be easily exchanged. The huge size of these recombined chromosome sections may explain the transfer of extremely complex adaptive traits, such as aerobic metabolism acquired by the methanogenic ancestor of extant halophilic archaea.

 

Full Publications

Refereed Articles

1. Berdichevski Y, Lamed, R., Frenkel, D., Gophna, U., Bayer, E.A., Yaron, S., Shoham, Y. and Benhar I. (1999). Matrix Assisted Refolding of Single-Chain Fv-Cellulose Binding Domain Fusion Proteins. Protein Expression and Purification. Nov;17(2): 249-59.

2. Gophna, U., Oelschlaeger, T.A., Hacker, J. and Ron, E.Z. (2001). Yersinia HPI In Septicemic Escherichia coli Strains Isolated From Diverse Hosts. FEMS Microbiology Letters Mar;196(1): 57-60.

3. Gophna, U. Barlev, M., Seijffers, R., Hacker, J. and Ron, E.Z. (2001). Curli Mediated Internalization of Escherichia coli by Eukaryotic Cells. Infection and Immunity 2001 69(4): 2659-65.

4. Gophna, U., Barlev, M., Hacker, J. and Ron. E.Z. (2001). Internalization of Escherichia coli serotype O78 by Eukaryotic Cells. The Infectious Disease Review. Supplement 3: 37-42.

5. Gophna, U., Oelschlaeger, T.A., Hacker, J. and Ron, E.Z. (2002). Role of Fibronectin in Curli-Mediated Internalization. FEMS Microbiology Letters. Jun;212(1): 55-8.

6. Gophna, U., Parket, A., Hacker, J., and Ron, E.Z. (2003). A Novel ColV Plasmid Encoding Type IV Pili. Microbiology. 149: 177-184.

7. Adiri, R.S., Gophna U., and Ron, E.Z. (2003). Multilocus Sequence Typing (MLST) of Escherichia coli O78 Strains. FEMS Microbiology Letters. May; 222(2): 199-203. (joint first author)

8. Hacham,Y., Gophna U., and Amir R. (2003). In Vivo Analysis of Various Substrates Utilized by Cystathionine {gamma}-Synthase and O-Acetylhomoserine Sulfhydrylase in Methionine Biosynthesis. Mol Biol Evol. 20(9): 1513-1520.

9. Gophna, U, Ron, E.Z., and Graur, D. (2003). Bacterial Type III Secretion Systems are Ancient and Evolved by Multiple Horizontal Transfer Events. Gene. 312: 151-163.

10. Gophna, U., Charlebois, R.L., Doolittle, W.F. (2004) Have archaeal genes contributed to bacterial virulence? Trends in Microbiology. 12(5):213-219.

11. Gophna, U., Ideses, D., Rosen, R., Grundland, A., and Ron, E.Z. (2004) OmpA of Septicemic Escherichia coli O78: Secretion and Convergent Evolution. International Journal of Medical Microbiology. 294(6): 373-381.

12. Gophna, U., Doolittle, W.F., and Charlebois, R.L. (2005) Weighted Genome Trees: Refinements and Applications. Journal of Bacteriology. 187(4):1305-16.

13. Mokady, D., Gophna, U., and Ron, E.Z. (2005) Extensive Gene Diversity in Septicemic Escherichia coli Strains. Journal of Clinical Microbiology. 43(1):66-73.

14. Gophna, U., Bapteste, E., Doolittle W.F., Biran D., and Ron E.Z. Evolutionary Plasticity of Methionine Biosynthesis. Gene. 355:48-57.

15. Ideses, D, Biran, D., Gophna, U., Levy-Nissenbaum, O., and Ron, E.Z. Identification and Characterization of the LPF operon of invasive Escherichia coli. International Journal of Medical Microbiology. 295: 227-236.

16. Cherny, I., Rockah, L., Levy-Nissenbaum, O., Gophna, U., Ron, E.Z., and Gazit, U. (2005) The Formation of Escherichia coli Curli Amyloid Fibrils is Mediated by Prion-Like Peptide Repeats. Journal of Molecular Biology. 352(2):245-52.

17. Ideses, D, Gophna, U., Paitan, Y. Chaudhuri, R.R., Pallen, M.J., and Ron, E.Z. (2005) A Degenerate Type-III Secretion System from Septicemic Escherichia coli Contributes to Pathogenesis. Journal of Bacteriology. 187(23):8164-8171.

18. Gophna, U., Thompson, J.R., Boucher, Y., and Doolittle, W.F. (2006) Complex Histories of Genes Encoding 3-Hydroxy-3-Methylglutaryl-CoenzymeA Reductase. Molecular Biology and Evolution. 23(1):168-178.

19. Gophna, U., Charlebois, R.L., Doolittle, W.F. (2006) Lateral Gene Transfer in Bdellovibrio bacteriovorus. Trends in Microbiology. 14(2): 64-69. Recommended by faculty of 1000.

20. Gophna, U., Sommerfeld, K., Gophna, S., Doolittle., W.F., Veldhuyzen van Zanten., S.J.O. (2006) Differences between Crohn's disease and ulcerative colitis patients in tissue-associated intestinal microflora. Journal of Clinical Microbiology. 44: 4136-4141.

21. Wellner, A., Lurie, M., Gophna, U. (2007). Complexity, connectivity, and duplicability as barriers to lateral gene transfer. Genome Biology 8:R156.

22. Kreimer A., Borenstein, E., Gophna, U., and Ruppin., E. (2008) The Evolution of Modularity in Bacterial Metabolic Networks. PNAS. 105(19): 6976-6981.

23. Wellner A., and Gophna U. (2008) Neutrality of foreign subunits in an experimental model of lateral gene transfer. Molecular Biology and Evolution 25(9): 1835-1840.


24. Cohen, O., Stern, A., Rubinstein, N. Gophna, U., and Pupko, T. (2008) A likelihood Framework to Analyze Phyletic Patterns. Philosophical Transactions of the Royal Society of London B. Biological Sciences 363(1512):3903-11.


25. Albert, E.J., Sommerfeld, K., Gophna, S., Marshall, J.A., and Gophna, U. (2009) The Gut Microbiota of Toll-Like Receptor 2 Mutant Mice Exhibits Lineage Specific Modifications. Environmental Microbiology Reports 1(1):65-70.


26. Freilich, S., Kreimer, A., Borenstein, E.A., Yosef, N., Sharan, R., Gophna, U. and Ruppin, E. (2009) Metabolic-network driven analysis of bacterial ecological strategies. Genome Biology 5;10(6):R61.


27. Tuller, T., Birin, H. Gophna, U., Kupiec, M., and Ruppin, E. (2010) Reconstructing ancestral gene content by co-evolution. Genome Research. 20(1):122-32.

28. Stern, A., Mayrose, I., Penn, O., Shaul, S., Gophna, U., and Pupko, T. (2010). An Evolutionary Analysis of lateral gene transfer in thymidylate synthase enzymes. Systematic Biology 59(2): 212-225.

29. Freilich, S., Kreimer, A., Borenstein, E.A., Gophna, U., Sharan, R., and Ruppin, E. (2010). Decoupling environment-dependent and independent genetic robustness across bacterial species. PLOS Computational Biology 26; 6(2): e1000690

30. Kovacs, A., Yacoby, K., and Gophna, U. (2010) A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Research in Microbiology 161: 162-167.

31. Freilich, S., Kreimer, A., Meilijson, I., Gophna, U., Sharan, R., and Ruppin, E. (2010) The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Research 38(12):3857-68.

32. Voges, M., Bachmann, V., Kammerer, R., Gophna, U., and Hauck, C.R. (2010) CEACAM1 recognition by bacterial pathogens is species-specific. BMC Microbiology 10(1):117.

33. Lurie-Weinberger, M. Gomez-Valero, L., Merault, N., Glöckner, G., Buchrieser, C., and Gophna, U. (2010) The origins of eukaryotic-like genes in Legionella pneumophila. International Journal of Medical Microbiology 300: 470–481.

34. Omer, S., Kovacs, A., Mazor, Y., and Gophna U. (2010) Integration of a foreign gene into a native complex does not impair fitness in an experimental model of lateral gene transfer. Molecular Biology and Evolution 27: 2441-2445.

35. Weingart, U., Persi, E., Gophna, U., and Horn, D. (2010) Deriving enzymatic signatures from short read data. BMC Bioinformatics 11:390.

36. Katz, C., Cohen-Or, Y., Gophna, U*., and Ron, E.Z.*. (2010) The ubiquitous conserved glycopeptidase Gcp prevents accumulation of toxic glycated proteins. 1(3): e00195-10. *equal contribution.

37. Gophna, U. and Ofran, Y. (2011) Lateral Acquisition of Genes is affected by the Friendliness of their Products. PNAS. 108(1):343-8.

38. Naor, A., Lazary, R., Barzel, A., Papke, R.T., and Gophna, U. (2011) In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii. PLoS One. 6(1): e15833.

39. Kovacs, A., Ben-Jacob, N., Tayem, H. Halperin, E. Iraqi, F.A. and Gophna U. (2011) Genotype is a Stronger Determinant than Sex of the Mouse Gut Microbiota. Microbial Ecology. 61(2):423-8

40. Cohen O., Gophna, U., and Pupko, T. (2011) The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Molecular Biology and Evolution. 28: 1481-1489

41. Zurel, D. Benayahu, Y., Or, A., Kovacs, A., and Gophna, U. (2011) Composition and dynamics of gill microbiota of the invasive Indo-Pacific oyster Chama pacifica in the eastern Mediterranean Sea. Environmental Microbiology. 13:1467-76. Cover.

42. Tuller, T., Girshovich, Y., Sella, Y., Kreimer, A., Freilich, S. Kupiec, M., Gophna, U*., and Ruppin, E*. (2011). Associations between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Research. 39 (11): 4743-4755. * equal contribution
NAR featured article. Featured Articles represent the top 5% of NAR papers in terms of originality, significance and scientific excellence.

43. Zhang, X., Kupiec, M., Gophna, U., and Tuller, T. (2011) Analysis of Co-evolving Gene Families Using Evolutionarily Reciprocal Orthologous Modules. Genome Biology and Evolution. 3: 413-423.

44. Barzel, A., Privman, E., Peeri , M., Naor, A., Shachar, E., Burstein, D., Lazary, R., Gophna, U., Pupko, T., and Kupiec, M. (2011) Native homing endonucleases can specifically cleave conserved genes in humans and in animal models. Nucleic Acids Research. 39(15):6646-59.

45. Or, A. and Gophna, U. (2011) Detection of Spatial and temporal influences on bacterial communities in an urban stream by automated ribosomal intergenic spacer analysis. Microbes and Environments. 26(4):360-6.


46. Lenz, G., Doron-Faigenboim, A. Ron, E.Z., Tuller, T., and Gophna, U. (2011) Sequence features of Escherichia coli mRNAs determine their stability. PLoS One 6(12):e28544.


47. Freilich, S., Zarecki, R., Eilam, O., Shtifman-Segal, E., Henry, C.S., Kupiec, M., Gophna, U., Sharan, R., and Ruppin, E. (2011) Competitive and cooperative metabolic interactions in bacterial communities. Nature Communications. 2:589. doi: 10.1038/ncomms1597.


48 Brodt A., Lurie-Weinberger M.N. and Gophna, U. (2011). CRISPR Loci Reveal Networks of Gene Exchange in Archaea. Biology Direct. 6(1):65.


49 Dan, M., Gottesman, T., Tzivian A., Schwartz, O., Gophna, U., and Rokney, A. (2012) Sexually transmitted Escherichia coli urethritis and orchi-epididymitis. Sexually Transmitted Diseases. 39(1):16-17.


50 Lurie-Weinberger M.N., Peeri, M., and Gophna, U. (2012). Contribution of lateral gene transfer to the gene repertoire of a gut-adapted methanogen. Genomics. 99(1):52-58.


51 Or, A., Shtrasler, L. and Gophna, U. Fine-Scale Temporal Dynamics of a fragmented microbial ecosystem. (2012). Scientific Reports. 2:207.


52. Naor, A., Lapierre, P., Meavrech, M., Papke, R.T., and Gophna, U. Low Species Barriers in Halophilic Archaea and the Formation of a Recombinant Hybrid. Current Biology 22:1-5.


53. Keren, N., Naftali, T., Kovacs, A., Konikoff, F.M. and Gophna, U. Can Colonoscopy Aspirates be a Substitute for Fecal Samples in Analyses of the Intestinal Microbiota? Bioscience of Microbiota, Food and Health. (accepted)


54. Zurel, D., Gophna, U., and Benayahu, Y. Parity and disparity between two Chama oysters: The reproductive biology of the Indo-Pacific C. pacifica Broderip 1835, invasive to the Mediterranean Sea; and C. savignyi Lamy, 1921, indigenous to the Red Sea. Marine Ecology. (accepted)

Reviews
1. Gophna, U. and Ron, E.Z. (2003). Virulence and the Heat Shock Response. International Journal of Medical Microbiology. 292(7-8): 453-461.

2. Mokady, D., Gophna, U., and Ron, E.Z. (2005) Virulence Factors of Septicemic Escherichia coli Strains. International Journal of Medical Microbiology. 295(6-7): 455-62.

3. Gophna, U. (2009) Complexity Apparently Is Not a Barrier to Lateral Gene Transfers. Microbe. 4 (12): 549-53.

4. Barzel, A., Naor, A., Privman, E., Kupiec, M. and Gophna, U. (2011) Homing endonucleases residing within inteins – evolutionary puzzles awaiting genetic solutions. Biochemical Society Transactions. 39(1):169-173.

5. Gophna, U. (2011). The guts of dietary habits. Science. 334(6052):45-6.

Chapters in books
1. Pallen, M.J. and Gophna, U. (2007) Bacterial Flagella and Type III Secretion: Case Studies in the Evolution of Complexity, in Volff J.N. (ed): Genome Dynamics, Gene and Protein Evolution. Karger, Basel. vol 3, 30-47.

2. Keren, N. and Gophna, U. (in press) The intestinal microbiota and intestinal disease: irritable bowel syndrome, in Rosenberg, E.& Gophna U. eds.: Beneficial Microorganisms in Multicellular Life Forms. Springer, Heidelberg.

3. Kovacs, A. and Gophna, U. (in press) The intestinal microbiota and intestinal disease: inflammatory bowel disease in Rosenberg, E.& Gophna U. eds.: Beneficial Microorganisms in Multicellular Life Forms. Springer, Heidelberg.

Patents
1. Barzel, A.,Privman, E., Burstein, D., Gophna, U., Kupiec, M., and Pupko, T. (2009) Method for Searching for Homing Endonucleases, their Genes and their Targets. International patent No. PCT/IL2009/000172.


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