Ralf Koebnik - Curriculum vitae

Ralf's Photo

Personal data

  • Year of birth: 1961
  • Nationality: German

Profession

  • Directeur de recherche at the Institut de Recherche pour le Développement in Montpellier. Since 2006.
  • Senior scientist at the Martin Luther University of Halle-Wittenberg, Institute of Genetics, Laboratory of Prof. Dr. Ulla Bonas. 2001-2006.
  • Postdoctoral fellow (backed by a DFG Habilitation grant) at the Martin Luther University of Halle-Wittenberg, Institute of Genetics, Laboratory of Prof. Dr. Ulla Bonas. 1999-2001.
  • Postdoctoral fellow (backed by a DFG research grant) at the Biocenter Basel, Department of Molecular Microbiology, Laboratory of Prof. Dr. Jurg P. Rosenbusch. 1996-1999.
  • Research associate (Postdoc) at the Max Planck Institute for Biology in Tübingen, Department of Microbiology (head: Prof. Dr. Ulf Henning). 1992-1996.
  • Scientific employee at the pharmaceutical "Germed" Research Center for Biotechnology in Berlin. 1986-1989.

Education

  • Habilitation in genetics at the Martin Luther University of Halle-Wittenberg. Title: "Structure and function of β-structured membrane proteins". 2001.
  • Participation in the EMBO practical course on Protein Design on Computers at the EMBL (Heidelberg, Germany). 1994.
  • Ph.D. student at the Eberhard Karls University of Tübingen, Department of Microbiology and Membrane Physiology, supervised by Profs. Dr. Volkmar Braun and Dr. Klaus Hantke. Thesis title: "Ferrichrome uptake in bacteria: Membrane topology of the ferrichrome receptor from Escherichia coli and structures of the ferrichrome receptor and of the TonB protein from Yersinia enterocolitica". 1990-1992.
  • Diploma with Prof. Dr. Rudolf Hagemann in the principal subjects General Genetics and Molecular Biology and Special Genetics of Procaryotes. 1986.
  • Diploma work at the Central Institute for Molecular Biology of the Academy of Sciences of the G.D.R. (today's Max Delbrueck Center for Molecular Medicine), Berlin-Buch, supervised by Prof. Dr. Dierck-Hartmut Liebscher. Title: "Expression of prochymosin in Escherichia coli". 1985-1986.
  • Study of Biology/Genetics at the Martin Luther University of Halle-Wittenberg. 1981-1986.
  • Abitur at a special school on mathematics and natural sciences (Heinrich-Hertz-Gymnasium) in Berlin. 1975-1979.
  • Primary school in Berlin. 1967-1975.

Military service

  • 1979-1981

Research interests

Since 1990, I investigate the structure, function, assembly, and dynamics of bacterial outer membrane proteins. For this purpose, I used the proteins OmpA (a protein of structural importance), OmpF (a non-specific porin), LamB (a specific porin), and FhuA (a TonB-dependent receptor) from Escherichia coli as model systems. In particular, OmpA served as a paradigm for the design of artificial membrane proteins. In 1999, I started to work on the type III secretion mechanism of the plant pathogenic bacterium Xanthomonas campestris. From 2002 to 2005, I was coordinating the annotation of the Xanthomonas campestris genome sequence at the Institute of Genetics of the Martin Luther University of Halle-Wittenberg (Laboratory of Prof. Dr. Ulla Bonas) and since then I went into comparative genomics and data mining in order to identify novel pathogenicity factors. In 2006, I launched a new research project focussing on the interaction between rice pathogenic Xanthomonas oryzae and its host plant.

For this project, which was launched at the Institut de Recherche pour le Développement in Montpellier, I am looking for enthusiastic masters and PhD students with interest in molecular biology, protein biochemistry, transcriptomics and/or proteomics, either on the bacterial or on the plant side.

Teaching duties

From 2000 to 2006, I organized practical courses in basic and advanced genetics. Furthermore, I gave lectures and seminars in genetics, microbiology, plant biotechnology, phytopathology and bioinformatics, all at the Martin Luther University of Halle-Wittenberg.

Meet me at

Publications

  • Pesce, C., J.M. Jacobs, E. Berthelot, M. Perret, T. Vancheva, C. Bragard, and R. Koebnik (2017). Comparative genomics identifies a novel conserved protein, HpaT, in proteobacterial type III secretion systems that do not possess the putative translocon protein HrpF. Front. Microbiol. 8: 1177.
  • Langlois, P.A., J. Snelling, J.P. Hamilton, C. Bragard, R. Koebnik, V. Verdier, L.R. Triplett, J. Blom, N.A. Tisserat, and J.E. Leach (2017). Characterization of the Xanthomonas translucens complex using draft genomes, comparative genomics, phylogenetic analysis, and diagnostic LAMP assays. Phytopathology 107: 519-527.
  • Zuluaga, P., B. Szurek, R. Koebnik, T. Kroj, and J.B. Morel (2017). Effector mimics and integrated decoys, the never-ending arms race between rice and Xanthomonas oryzae. Front. Plant Sci. 8: 431.
  • Blanvillain-Baufumé, S., M. Reschke, M. Solé, F. Auguy, H. Doucoure, B. Szurek, D. Meynard, M. Portefaix, S. Cunnac, E. Guiderdoni, J. Boch, and R. Koebnik (2017). Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14-inducing TAL effectors. Plant Biotechnol. J. 15: 306-317.
  • Kini, K., R. Agnimonhan, O. Afolabi, B. Milan, B. Soglonou, V. Gbogbo, R. Koebnik, and D. Silué (2017). First report of a new bacterial leaf blight of rice caused by Pantoea ananatis and Pantoea stewartii in Benin. Plant Disease 101: 242.
  • Kini, K., R. Agnimonhan, O. Afolabi, B. Soglonou, D. Silué, and R. Koebnik (2017). First report of a new bacterial leaf blight of rice caused by Pantoea ananatis and Pantoea stewartii in Togo. Plant Disease 101: 241.
  • Barak, J.D., T. Vancheva, P. Lefeuvre, J.B. Jones, S. Timilsina, G.V. Minsavage, G.E. Vallad, and R. Koebnik (2016). Whole-genome sequences of Xanthomonas euvesicatoria strains clarify taxonomy and reveal a stepwise erosion of type 3 effectors. Front. Plant Sci. 7: 1805.
  • Hutin, M., S. Césari, V. Chalvon, C. Michel, T.T. Tran, J. Boch, R. Koebnik, B. Szurek, B., and T. Kroj (2016). Ectopic activation of the rice NLR heteropair RGA4/RGA5 confers resistance to bacterial blight and bacterial leaf streak diseases. Plant J. 88: 43-55.
  • Robéne, I., S. Bolot, O. Pruvost, M. Arlat, L.D. Noël, S. Carr¸re, M.A. Jacques, R. Koebnik, and L. Gagnevin (2016). High-Quality draft genome sequences of two Xanthomonas pathotype strains infecting aroid plants. Genome Announc. 4: e00902-16.
  • Jacques, M.A., M. Arlat, A. Boulanger, T. Boureau, S. Carrère, S. Cesbron, N.W. Chen, S. Cociancich, A. Darrasse, N. Denancé, M. Fischer-Le Saux, L. Gagnevin, R. Koebnik, E. Lauber, L.D. Noël, I. Pieretti, P. Portier, O. Pruvost, A. Rieux, I. Robène, M. Royer, B. Szurek, V. Verdier, and C. Vernière (2016) Using ecology, physiology, and genomics to understand host specificity in Xanthomonas. Annu. Rev. Phytopathol. 54: 163-187.
  • Grau, J., M. Reschke, A. Erkes, J. Streubel, R. Morgan, G. Wilson, R. Koebnik, and J. Boch (2016). AnnoTALE: bioinformatics tools for identification, annotation, and nomenclature of TALEs from Xanthomonas genomic sequences. Sci. Rep. 6: 21077.
  • Roux, B., S. Bolot, E. Guy, N. Denancé, M. Lautier, M.F. Jardinaud, M. Fischer-Le Saux, P. Portier, M.A. Jacques, L. Gagnevin, O. Pruvost, E. Lauber, M. Arlat, S. Carrère, R. Koebnik, and L.D. Noël (2015) Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome. BMC Genomics 16: 975.
  • Pesce, C., S. Bolot, E. Berthelot, C. Bragard, S. Cunnac, M. Fischer-Le Saux, P. Portier, M. Arlat, L. Gagnevin, M.A. Jacques, L.D. Noël, S. Carrère, and R. Koebnik (2015) Draft genome sequence of the Xanthomonas translucens pv. graminis pathotype strain CFBP 2053. Genome Announc. 3: e01174-15.
  • Hutin, M., F. Sabot, A. Ghesquière, R. Koebnik, and B. Szurek (2015). A knowledge-based molecular screen uncovers a broad spectrum OsSWEET14 resistance allele to bacterial blight from wild rice. Plant J. 84: 694-703.
  • Afolabi, O., R. Amoussa, M. Bilé, A. Oludare, V. Gbogbo, L. Poulin, R. Koebnik, B. Szurek, and D. Silué (2015). First report of bacterial leaf blight of rice caused by Xanthomonas oryzae pv. oryzae in Benin. Plant Disease 100: 515.
  • Jacobs, J.M., C. Pesce, P. Lefeuvre, and R. Koebnik (2015). Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. Front. Plant Sci. 6: 431.
  • Tran, T.T., N. Nguyen, N. Phan, H.T. Nguyen, B. Szurek, R. Koebnik, H. Le Huy, C. Ha Viet, and S. Cunnac (2015). Confirmation of bacterial leaf streak of rice caused by Xanthomonas oryzae pv. oryzicola in Vietnam. Plant Disease 99: 1853.
  • Pesce, C., S. Bolot, S. Cunnac, P. Portier, M. Fischer-Le Saux, M.A. Jacques, L. Gagnevin, M. Arlat, L.D. Noël, S. Carrère, C. Bragard, and R. Koebnik (2015). High-Quality draft genome sequence of the Xanthomonas translucens pv. cerealis pathotype strain CFBP 2541. Genome Announc. 3: e01574-14.
  • Vancheva, T., N. Bogatzevska, P. Moncheva, P. Lefeuvre, and R. Koebnik (2015). Draft genome sequences of two Xanthomonas vesicatoria strains from the Balkan Peninsula. Genome Announc. 3: e01558-14.
  • Vancheva, T., P. Lefeuvre, N. Bogatzevska, P. Moncheva, and R. Koebnik (2015). Draft genome sequences of two Xanthomonas euvesicatoria strains from the Balkan Peninsula. Genome Announc. 3: e01528-14.
  • Poulin, L., P. Grygiel, M. Magne, L. Gagnevin, L.M. Rodriguez-R, N. Forero Serna, S. Zhao, M. El Rafii, S. Dao, C. Tekete, I. Wonni, O. Koita, O. Pruvost, V. Verdier, C. Vernière, and R. Koebnik (2015). New multilocus variable-number tandem-repeat analysis tool for surveillance and local epidemiology of bacterial leaf blight and bacterial leaf streak of rice caused by Xanthomonas oryzae. Appl. Environ. Microbiol. 81: 688-698.
  • Afolabi, O., B. Milan, L. Poulin, J. Ongom, B. Szurek, R. Koebnik, and D. Silué (2014). First report of Xanthomonas oryzae pv. oryzicola causing bacterial leaf streak of rice in Uganda. Plant Disease 98: 1579.
  • Afolabi, O., B. Milan, R. Amoussa, R. Koebnik, L. Poulin, B. Szurek, G. Habarugira, J. Bigirimana, and D. Silué (2014). First report of Xanthomonas oryzae pv. oryzicola causing bacterial leaf streak of rice in Burundi. Plant Disease 98: 1426.
  • Poulin, L., H. Raveloson, M. Sester, L.M. Raboin, D. Silué, R. Koebnik, and B. Szurek (2014): Confirmation of bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola on rice in Madagascar. Plant Disease 98: 1423.
  • Triplett, L., R. Koebnik, V. Verdier, and J.E. Leach (2014): The Genomics of Xanthomonas oryzae. In: Genomics of Plant-Associated Bacteria (Eds. D.C. Gross, A. Lichens-Park, and C. Kole); Springer, Heidelberg, New York, Dordrecht, London; pp. 127-150.
  • Gagnevin, L., S. Bolot, J.L. Gordon, O. Pruvost, C. Vernière, I. Robène, M. Arlat, L.D. Noël, S. Carrère, M.A. Jacques, and R. Koebnik (2014): Draft genome sequence of Xanthomonas axonopodis pv. allii strain CFBP 6369. Genome Announc. 2: e00727-14.
  • Trujillo B, C.A., N. Arias-Rojas, L. Poulin, C.A. Medina, A. Tapiero, S. Restrepo, R. Koebnik, and A.J. Bernal (2014): Population typing of the causal agent of cassava bacterial blight in the Eastern Plains of Colombia using two types of molecular markers. BMC Microbiol. 14: 161.
  • Pruvost, O., M. Magne, K. Boyer, A. Leduc, C. Tourterel, C. Drevet, V. Ravigné, L. Gagnevin, F. Guérin, F. Chiroleu, R. Koebnik, V. Verdier, and C. Vernière (2014): A MLVA genotyping scheme for global surveillance of the citrus pathogen Xanthomonas citri pv. citri suggests a worldwide geographical expansion of a single genetic lineage. PLoS One 9: e98129.
  • Wonni, I., B. Cottyn, L. Detemmerman, S. Dao, L. Ouedraogo, S. Sarra, C. Tekete, S. Poussier, R. Corral, L. Triplett, O. Koita, R. Koebnik, J. Leach, B. Szurek, M. Maes, and V. Verdier (2014): Analysis of Xanthomonas oryzae pv. oryzicola population in Mali and Burkina Faso reveals a high level of genetic and pathogenic diversity. Phytopathology 104: 520-531.
  • Robin, G.P., E. Ortiz, B. Szurek, J.P. Brizard, and R. Koebnik (2014): Comparative proteomics reveal new HrpX-regulated proteins of Xanthomonas oryzae pv. oryzae. J. Proteomics 97: 256-264.
  • Bahar, O., R. Pruitt, D.D. Luu, B. Schwessinger, A. Daudi, F. Liu, R. Ruan, L. Fontaine-Bodin, R. Koebnik, and P. Ronald (2014): The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles. PeerJ 2: e242.
  • Darrasse, A., S. Bolot, L. Serres-Giardi, E. Charbit, T. Boureau, M. Fisher-Le Saux, M. Briand, M. Arlat, L. Gagnevin, R. Koebnik, L.D. Noël, S. Carrère, and M.A. Jacques (2013): High-quality draft genome sequences of Xanthomonas axonopodis pv. glycines strains CFBP 2526 and CFBP 7119. Genome Announc. 1: e01036-13.
  • Jacques, M.A., S. Bolot, E. Charbit, A. Darrasse, M. Briand, M. Arlat, L. Gagnevin, R. Koebnik, L.D. Noël, P. Portier, S. Carrère, and T. Boureau (2013): High-quality draft genome sequence of Xanthomonas alfalfae subsp. alfalfae strain CFBP 3836. Genome Announc. 1: e01035-13.
  • Arrieta-Ortiz, M.L., L.M. Rodríguez-R, A.L. Pérez-Quintero, L. Poulin, A.C. Díaz, N. Arias Rojas, C. Trujillo, M. Restrepo Benavides, R. Bart, J. Boch, T. Boureau, A. Darrasse, P. David, T. Dugé de Bernonville, P. Fontanilla, L. Gagnevin, F. Guérin, M.A. Jacques, E. Lauber, P. Lefeuvre, C. Medina, E. Medina, N. Montenegro, A. Muñoz Bodnar, L.D. Noël, J.F. Ortiz Quiñones, D. Osorio, C. Pardo, P.B. Patil, S. Poussier, O. Pruvost, I. Robène-Soustrade, R.P. Ryan, J. Tabima, O.G. Urrego Morales, C. Vernière, S. Carrere, V. Verdier, B. Szurek, S. Restrepo, C. López, R. Koebnik, and A. Bernal (2013) Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. manihotis strain CIO151. PLoS One 8: e79704.
  • Darrasse, A., S. Carrère, V. Barbe, T. Boureau, M.L. Arrieta-Ortiz, S. Bonneau, M. Briand, C. Brin, S. Cociancich, K. Durand, S. Fouteau, L. Gagnevin, F. Guérin, E. Guy, A. Indiana, R. Koebnik, E. Lauber, A. Munoz, L.D. Noël, I. Pieretti, S. Poussier, O. Pruvost, I. Robène-Soustrade, P. Rott, M. Royer, L. Serres-Giardi, B. Szurek, M.A. van Sluys, V. Verdier, C. Vernière, M. Arlat, C. Manceau, M.A. Jacques (2013): Genome sequence of Xanthomonas fuscans subsp. fuscans strain 4834-R reveals that flagellar motility is not a general feature of xanthomonads. BMC Genomics 14: 761.
  • Royer, M., R. Koebnik, M. Marguerettaz, V. Barbe, G.P. Robin, C. Brin, S. Carrere, C. Gomez, M. Hügelland, G. Völler, J. Noëll, I. Pieretti, S. Rausch, V. Verdier, S. Poussier, P. Rott, R.D. Süssmuth, R.D., and S. Cociancich (2013): Genome mining reveals the genus Xanthomonas to be a promising reservoir for new bioactive non-ribosomally synthesized peptides. BMC Genomics 14: 658.
  • Bolot, S., A. Munoz Bodnar, S. Cunnac, E. Ortiz, B. Szurek, L.D. Noël, M. Arlat, M.A. Jacques, L. Gagnevin, P. Portier, M. Fischer-Le Saux, S. Carrere, and R. Koebnik (2013): Draft genome sequence of the Xanthomonas cassavae type strain CFBP 4642. Genome Announc. 1: e00679-13.
  • Cunnac, S., S. Bolot, N. Forero Serna, E. Ortiz, B. Szurek, L.D. Noël, M. Arlat, M.A. Jacques, L. Gagnevin, S. Carrere, M. Nicole, and R. Koebnik (2013) High-quality draft genome sequences of two Xanthomonas citri pv. malvacearum strains. Genome Announc. 1: e00674-13.
  • Streubel, J., C. Pesce, M. Hutin, R. Koebnik, J. Boch, and B. Szurek (2013): Five phylogenetically close rice SWEET genes confer TAL effector-mediated susceptibility to Xanthomonas oryzae pv. oryzae. New Phytol. 200: 808-819.
  • Pérez-Quintero, A.L., L.M. Rodriguez-R, A. Dereeper, C. López, R. Koebnik, B. Szurek, and S. Cunnac (2013): An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. PLoS One 8: e68464.
  • Zhao, S., W.L. Mo, F. Wu, W. Tang, J.L. Tang, B. Szurek, V. Verdier, R. Koebnik, and J.X. Feng (2013): Identification of non-TAL effectors in Xanthomonas oryzae pv. oryzae Chinese strain 13751 and analysis of their role in the bacterial virulence. World J. Microbiol. Biotechnol. 29: 733-744.
  • Castiblanco, L.F., J. Gil, A. Rojas, D. Osorio, S. Gutiérrez, A. Muñoz-Bodnar, A.L. Perez-Quintero, R. Koebnik, B. Szurek, C. López, S. Restrepo, V. Verdier, and A.J. Bernal (2013): TALE1 from Xanthomonas axonopodis pv. manihotis acts as a transcriptional activator in plant cells and is important for pathogenicity in cassava plants. Mol. Plant Pathol. 14: 84-95.
  • Pieretti, I., M. Royer, V. Barbe, S. Carrere, R. Koebnik, A. Couloux, A. Darrasse, J. Gouzy, M.A. Jacques, E. Lauber, C. Manceau, S. Mangenot, S. Poussier, B. Segurens, B. Szurek, V. Verdier, M. Arlat, D.W. Gabriel, P. Rott, and S. Cociancich (2012): Genomic insights into strategies used by Xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels. BMC Genomics 13: 658.
  • Zhao, S., L. Poulin, L.M. Rodriguez-R, N. Forero Serna, S.Y. Liu, I. Wonni, B. Szurek, V. Verdier, J.E. Leach, Y.Q. He, J.X. Feng, and R. Koebnik (2012): Development of a variable number of tandem repeats typing sscheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola. Phytopathology 102: 948-956.
  • Hajri, A., C. Brin, S. Zhao, P. David, J.X. Feng, R. Koebnik, B. Szurek, V. Verdier, T. Boureau, and S. Poussier (2012): Multilocus sequence analysis and type three effector repertoires mining provide new insights into evolutionary history and virulence of Xanthomonas oryzae. Mol. Plant Pathol. 13: 288-302.
  • R. Koebnik, and M. Lindeberg (2012): Comparative genomics and evolution of bacterial type III effectors. In: Effectors in Plant-Microbe Interactions (Eds. F. Martin, S. Kamoun); John Wiley & Sons, Inc.; pp. 55-76.
  • Bogdanove, A.J., R. Koebnik, H. Lu, A. Furutani, S.V. Angiuoli, P.B. Patil, M.A. Van Sluys, R.P. Ryan, D.F. Meyer, S.W. Han, G. Aparna, M. Rajaram, A.L. Delcher, A.M. Phillippy, D. Puiu, M.C. Schatz, M. Shumway, D.D. Sommer, C. Trapnell, F. Benahmed, G. Dimitrov, R. Madupu, D. Radune, S. Sullivan, G. Jha, H. Ishihara, S.W. Lee, A. Pandey, V. Sharma, M. Sriariyanun, B. Szurek, C.M. Vera-Cruz, K.S. Dorman, P.C. Ronald, V. Verdier, J.M. Dow, R.V. Sonti, S. Tsuge, V. Brendel, P.D. Rabinowicz, D. Kelley, R. Madapu, D. Radune, Y.S. Seo, J.E. Leach, F.F. White, and S.L. Salzberg (2011): Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. J. Bacteriol. 193: 5450-5464.
  • Yu, Y., J. Streubel, S. Balzergue, A. Champion, J. Boch, R. Koebnik, J.X. Feng, V. Verdier, and B. Szurek (2011): Colonization of rice leaf blades by an African strain of Xanthomonas oryzae pv. oryzae depends on a new TAL effector which induces the rice nodulin-3 Os11N3 gene. Mol. Plant Microbe Interact. 24: 1102-1113.
  • Mhedbi-Hajri, N., M.A. Jacques, R. Koebnik (2011): Adhesion mechanisms of plant-pathogenic Xanthomonadaceae. Adv. Exp. Med. Biol. 715: 71-89.
  • Potnis, N., K. Krasileva, V. Chow, N.F. Almeida, P.B. Patil, R.P. Ryan, M. Sharlach, F. Behlau, J.M. Dow, M.T. Momol, F.F. White, J.F. Preston, B.A. Vinatzer, R. Koebnik, J.C. Setubal, D.J. Norman, B.J. Staskawicz, and J.B. Jones (2011): Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper. BMC Genomics 12: 146.
  • Berger, C., G.P. Robin, U. Bonas, and R. Koebnik (2010): Membrane topology of conserved components of the type III secretion system from the plant pathogen Xanthomonas campestris pv. vesicatoria. Microbiology 156: 1963-1974.
  • Pieretti, I., M. Royer, V. Barbe, S. Carrere, R. Koebnik, S. Cociancich, A. Couloux, A. Darrasse, J. Gouzy, M.A. Jacques, E. Lauber, C. Manceau, S. Mangenot, S. Poussier, B. Segurens, B. Szurek, V. Verdier, M. Arlat, and P. Rott (2009): The complete genome sequence of Xanthomonas albilineans provides new insights into the reductive genome evolution of the xylem-limited Xanthomonadaceae. BMC Genomics 10: 616.
  • Ryan, R.P., R. Koebnik, B. Szurek, T. Boureau, A. Bernal, A. Bogdanove, and J.M. Dow (2009): Passing GO (gene ontology) in plant pathogen biology: a report from the Xanthomonas Genomics Conference. Cell. Microbiol. 11: 1689-1696.
  • White, F.F., N. Potnis, J.B. Jones, and R. Koebnik (2009): The type III effectors of Xanthomonas. Mol. Plant Pathol. 10: 749-766.
  • Gross, R., C.A. Guzman, M. Sebaihia, V.A. dos Santos, D.H. Pieper, R. Koebnik, M. Lechner, D. Bartels, J. Buhrmester, J.V. Choudhuri, T. Ebensen, L. Gaigalat, S. Herrmann, A.N. Khachane, C. Larisch, S. Link, B. Linke, F. Meyer, S. Mormann, D. Nakunst, C. Rückert, S. Schneiker-Bekel, K. Schulze, F.J. Vorhölter, T. Yevsa, J.T. Engle, W.E. Goldman, A. Pühler, U.B. Göbel, A. Goesmann, H. Blöcker, O. Kaiser, and R. Martinez-Arias (2008): The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics 9: 449.
  • Salzberg, S.L., D.D. Sommer, M.C. Schatz, A.M. Phillippy, P.D. Rabinowicz, S. Tsuge, A. Furutani, H. Ochiai, A.L. Delcher, D. Kelley, R. Madupu, D. Puiu, D. Radune, M. Shumway, C. Trapnell, G. Aparna, G. Jha, A. Pandey, P.B. Patil, H. Ishihara, D.F. Meyer, B. Szurek, V. Verdier, R. Koebnik, J.M. Dow, R.P. Ryan, H. Hirata, S. Tsuyumu, S.W. Lee, Y.S. Seo, M. Sriariyanum, P.C. Ronald, R.V. Sonti, M.A. Van Sluys, J.E. Leach, F.F. White, and A.J. Bogdanove (2008): Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics 9: 204.
  • Weber, E., C. Berger, U. Bonas, and R. Koebnik (2007): Refinement of the Xanthomonas campestris pv. vesicatoria hrpD and hrpE operon structure. Mol. Plant Microbe Interact. 20: 559-567.
  • Johansson, M.U., S. Alioth, K. Hu, R. Walser, R. Koebnik, and K. Pervushin (2007): A minimal transmembrane beta-barrel platform protein studied by Nuclear Magnetic Resonance. Biochemistry 46: 1128-1140.
  • Koebnik, R., A. Krüger, F. Thieme, A. Urban, and U. Bonas (2006): Specific binding of the Xanthomonas campestris pv. vesicatoria AraC-type transcriptional activator HrpX to plant-inducible promoter boxes. J. Bacteriol. 188: 7652-7660.
  • Weber, E., and R. Koebnik (2006): Positive selection of the Hrp pilin HrpE of the plant pathogen Xanthomonas. J. Bacteriol. 188: 1405-1410.
  • Thieme, F., R. Koebnik, T. Bekel, C. Berger, J. Boch, D. Büttner, C. Caldana, L. Gaigalat, A. Goesmann, S. Kay, O. Kirchner, C. Lanz, B. Linke, A.C. McHardy, F. Meyer, G. Mittenhuber, D.H. Nies, U. Niesbach-Klösgen, T. Patschkowski, C. Rückert, O. Rupp, S. Schneiker, S.C. Schuster, F. Vorhölter, E. Weber, A. Pühler, U. Bonas, D. Bartels, and O. Kaiser (2005): Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J. Bacteriol. 187: 7254-7266.
  • Weber, E., and R. Koebnik (2005): Domain structure of HrpE, the Hrp pilus subunit of Xanthomonas campestris pv. vesicatoria. J. Bacteriol. 187: 6175-6186.
  • Koebnik, R. (2005): TonB-dependent trans-envelope signalling: the exception or the rule? Trends Microbiol. 13: 343-347.
  • Weber, E., T. Ojanen-Reuhs, E. Huguet, G. Hause, M. Romantschuk, T.K. Korhonen, U. Bonas, and R. Koebnik (2005): The type III-dependent Hrp pilus is required for productive interaction of Xanthomonas campestris pv. vesicatoria with pepper host plants. J. Bacteriol. 187: 2458-2468.
  • Koebnik, R. (2001): The role of bacterial pili in protein and DNA translocation. Trends Microbiol. 9: 586-590.
  • Van Gelder, P. , R. Dutzler, F. Dumas, R. Koebnik, and T. Schirmer (2001): Sucrose transport through maltoporin mutants of Escherichia coli. Protein Eng. 14: 943-948.
  • Dumas, F., S. Frank, R. Koebnik, E. Maillet, A. Lustig, and P. Van Gelder (2000): Extended sugar slide function for the periplasmic coiled coil domain of ScrY. J. Mol. Biol. 300: 687-695.
  • Koebnik, R., K.P. Locher, and P. Van Gelder (2000): Structure and function of bacterial outer membrane proteins: Barrels in a nutshell. Mol. Microbiol. 37: 239-253.
  • Dumas, F., R. Koebnik, M. Winterhalter, and P. Van Gelder (2000): Sugar transport through maltoporin of Escherichia coli. Role of polar tracks. J. Biol. Chem. 275: 19747-19751.
  • Koebnik, R. (1999): OmpA. In: Encyclopedia of Molecular Biology (Ed. Thomas E. Creighton); John Wiley & Sons, Inc., New York, Chichester, Weinheim, Brisbane, Singapore, Toronto; pp. 1701-1707.
  • Koebnik, R. (1999): Structural and functional roles of the surface-exposed loops of the beta-barrel membrane protein OmpA from Escherichia coli. J. Bacteriol. 181: 3688-3694.
  • Koebnik, R. (1999): Membrane assembly of the E. coli outer membrane protein OmpA: Exploring sequence constraints on transmembrane beta-strands. J. Mol. Biol. 285: 1801-1810.
  • Locher, K.P., B. Rees, R. Koebnik, A. Mitschler, L. Moulinier, J.P. Rosenbusch, and D. Moras (1998): Transmembrane signaling across the ligand-gated FhuA receptor: Crystal structures of free and ferrichrome-bound states reveal allosteric changes. Cell 95: 771-778.
  • Phale, P.S., A. Philippsen, T. Kiefhaber, R. Koebnik, V.P. Phale, T. Schirmer, and J.P. Rosenbusch (1998): Stability of trimeric OmpF porin: the contributions of the latching loop L2. Biochem. 37: 15663-15670.
  • Prilipov, A., P.S. Phale, R. Koebnik, C. Widmer, and J.P. Rosenbusch (1998): Identification and characterization of two quiescent porin genes, nmpC and ompN, in E. coli BE. J. Bacteriol. 180: 3388-3392.
  • Prilipov, A., P.S. Phale, P. Van Gelder, J.P. Rosenbusch, and R. Koebnik (1998): Coupling site-directed mutagenesis with high-level expression: Large scale production of mutant porins from E. coli. FEMS Microbiol. Lett. 163: 65-72.
  • Koebnik, R. (1996): In vivo membrane assembly of split variants of the E. coli outer membrane protein OmpA. EMBO J. 15: 3529-3537.
  • Koebnik, R. (1995): Proposal for a peptidoglycan-associating alpha-helical motif in the C-terminal regions of some bacterial cell-surface proteins. Mol. Microbiol. 16: 1269-1270.
  • Koebnik, R., and L. Krämer (1995): Membrane assembly of circularly permuted variants of the E. coli outer membrane protein OmpA. J. Mol. Biol. 250: 617-626.
  • Bahar, I., M. Buck, M. Helmer Citterich, A. Dahm, L.-O. Essen, P. Fariselli, A. Finkelstein, R. Hooft, T. Hubbard, R. Koebnik, Y. Kuroda, A.M. Lesk, J. Luo, L.M. Mayr, J. Moult, K. Mueller, F.R. Ortigao, J. Osuna, A. Reinhardt, C. Sander, A. Tramontano, B. Vallone, and G. Vriend (1994): ProDes94: Protein design on computers. BIOcomputing Technical Document 8, EMBL Heidelberg.
  • Ried, G., R. Koebnik, I. Hindennach, B. Mutschler, and U. Henning (1994): Membrane topology and assembly of the outer membrane protein OmpA of Escherichia coli K-12. Mol. Gen. Genet. 243: 127-135.
  • Henning, U., and R. Koebnik (1994): Outer membrane proteins of Escherichia coli: mechanism of sorting and regulation of synthesis. In: New Comprehensive Biochem., Vol. 27: Bacterial Cell Wall (Eds. J.-M. Ghuysen, R. Hakenbeck); Elsevier Science Publishers B.V.; pp. 381-395.
  • Koebnik, R. (1993): The structural organization of TonB-dependent receptors. Trends Microbiol. 1: 201.
  • Koebnik, R. (1993): The molecular interaction between components of the TonB-ExbBD-dependent and of the TolQRA-dependent bacterial uptake systems. Mol. Microbiol. 9: 219.
  • Bäumler, A.J., R. Koebnik, I. Stojiljkovic, J. Heesemann, V. Braun, and K. Hantke (1993): Survey on newly characterized iron uptake systems of Yersinia enterocolitica. Zbl. Bakteriol. - Int. J. Med. Microbiol. 278: 416-424.
  • Koebnik, R., A.J. Bäumler, J. Heesemann, V. Braun, and K. Hantke (1993): The TonB protein of Yersinia enterocolitica and its interaction with TonB-box proteins. Mol. Gen. Genet. 237: 152-160.
  • Koebnik, R., K. Hantke, and V. Braun (1993): The TonB-dependent ferrichrome receptor FcuA of Yersinia enterocolitica: evidence against a strict co-evolution of receptor structure and substrate specificity. Mol. Microbiol. 7: 383-393.
  • Koebnik, R., and V. Braun (1993): Insertion derivatives containing segments of up to 16 amino acids identify surface and periplasm-exposed regions of the FhuA outer membrane receptor of Escherichia coli K-12. J. Bacteriol. 175: 826-839.
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    Institut de Recherche pour le Développement
    Interactions Plantes Microorganismes Environnement
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