UWB Crest

Marine Metagenomics for New Biotechnological Applications



Previous Publications

Principal relevant papers of project partners

Ferrer M., (6 other authors) and Golyshin P.N. 2005. Novel microbial enzymes mined from the Urania deepsea hypersaline anoxic basin. Chemistry & Biology 12(8):895-904.

Beloqui A., (16 other authors) and Golyshin P.N. 2006. Novel polyphenol oxidase mined from a metagenome expression library of bovine rumen: biochemical properties, structural analysis and phylogenetic relationships. J Biol Chem 281(32):22933-22942.

Schneiker S., (28 other authors) and Golyshin P.N. 2006. Genome sequence of the ubiquitous hydrocarbondegrading marine bacterium Alcanivorax borkumensis. Nature Biotechnol 24(8):997-1004.

Ferrer M., Golyshina O.V. Beloqui A. and Golyshin P.N. 2007. Mining enzymes from extreme environments. Curr Opin Microbiol 10(3):207-214.

 Hallsworth JE*, Yakimov MM*, Golyshin P.N. and other 12 authors. 2007 Limits of life in MgCl2-containing environments: chaotropicity defines the window. Environ Microbiol. (3):801-813 (*equal contribution).

Yakimov MM, La Cono V, and other 5 authors. 2007 Primary producing prokaryotic communities of brine, interface and seawater above the halocline of deep anoxic lake L'Atalante, Eastern Mediterranean Sea. ISMEJ. 1(8):743-55

Yakimov MM, Giuliano L, Cappello S, Denaro R, Golyshin PN. 2007 Microbial community of a hydrothermal mud vent underneath the deep-sea anoxic brine lake Urania (Eastern Mediterranean).Orig Life Evol Biosph. (2):177-88.

Daffonchio D, and 23 other authors. 2006 Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline. Nature 440(7081):203-207.

Ferrer M., Golyshina O.V., Beloqui A., Golyshin P.N.* and Timmis K.N.* 2007. (*equal contribution) The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated. Nature 445(1):91-94.

Reyes-Duarte, D., et al., Angew. Chem. Int. Ed. 44:7553-7557 (2005)

Drepper, T., Eggert, T., Hummel, W., Leggewie, C., Pohl, M., Rosenau, F., Wilhelm, S., and Jaeger, K.-E. 2006 Novel biocatalysts for white biotechnology. Biotechnol J. 1:777-786

Henning, H., Leggewie, C., Pohl, M., Muller, M., Eggert, T., and Jaeger, K.-E. 2006. Identification of novel benzoylformate decarboxylases by growth selection. Appl Environ Microbiol. 72:7510-7517.

Wilhelm, S., Rosenau, F., Becker, S., Buest, S., Hausmann, S., Kolmar, H., and Jaeger K.-E. 2007. Functional cell-surface display of a lipase-specific chaperone. Chembiochem. 8:55-60

Drepper, T., Eggert, T., Circolone, F., Heck, A., Krauß, U., Guterl, J-K., Wendorff, M., Losi, A., Gärtner, W. and Jaeger, K.-E. 2007. Reporter proteins for in vivo fluorescence without oxygen. Nature Biotechnol. 25:443-445.

Meier, R., Drepper, T., Svensson, V., Jaeger K.-E., and Baumann, U. 2007. A calcium-gated lid and a large beta -roll sandwich are revealed by the crystal structure of extracellular lipase from Serratia marcescens. J Biol Chem. 282, 31477-31483.

Agogué H., F. Joux, I. Obernosterer, P. Lebaron. 2005. Resistance of marine bacterioneuston to solar radiation. Appl Environ Microbiol 71:5282-5289.

Joux F, Jeffrey WH, Lebaron P, Mitchell DL 1999. Marine bacterial isolates display diverse responses to UV-B radiation. Appl Environ Microbiol 65:3820-3827.

Obernosterer I., Catala P., Reinthaler T., Herndl G., and Lebaron P. 2005. Enhanced heterotrophic activity in the surface microlayer of the Mediterranean Sea. Aquat. Microb. Ecol. 39: 293-302.

Agogué H., Casamayor E., Bourrain M., Obernosterer I., Joux F., Herndl G. Lebaron P. 2005. A survey of bacteria inhabiting the surface microlayer of coastal ecosystems. FEMS Microb. Ecol. 54:269-280.

Urios L., Agogué H., Lesongeur F., Stackebrandt E., Lebaron P. 2006. Balneola vulgaris gen. nov. sp. Nov. a new member of the Cytophaga-Flavobacterium-Bacteroides phylum from the NW Mediterranean Sea. Int J Syst. Evol Microbiol. 56:1883-1887.

Le Breton, M., Henneke, G., Norais, C., Flament, D., Myllykallio, H., Querellou, J. and Raffin, J.-P. 2007. The heterodimeric primase from the Euryarchaea Pyrococcus abyssi: a multifunctional enzyme for initiation and repair?, J Mol Biol, 374, 5:1172-1185.

Geslin C, Gaillard M, Flament D, Rouault K, Le Romancer M, Prieur D, Erauso G. 2007. Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus abyssi. J Bacteriol. 189, 12:4510-4519

3. Le Romancer, M., M. Gaillard, C. Geslin, and Prieur D. 2007. Viruses in extreme environments. Rev Environ Sci Biotechnol 6,1-3 :17-31

Postec A., Lesongeur F., Pignet P., Ollivier B., Querellou J. and Godfroy A. 2007. Continuous enrichment cultures: insights into prokaryotic diversity and metabolic interactions in deep-sea vent chimneys. Extremophiles, 11:747-757.

Rouillon C, Henneke G, Flament D, Querellou J, and Raffin JP. 2007. DNA polymerase switching on homotrimeric PCNA at the replication fork of the euryarchaea Pyrococcus abyssi. J Mol Biol.369, 2:343-55.

Proudfoot M, (11 other authors), Savchenko A.L. Yakunin A.F. 2008. Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain. J Mol Biol 375(1):301-315.

Nocek B, & other 9 authors. 2007. Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus - a member of a new family of non-ribosomal peptide synthases. J Mol Biol. 372(2):456-69.

Kuznetsova E., (12 other authors) and Yakunin A.F. 2006. Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family. J Biol Chem. 281(47):36149-36161.

Nocek B., Cuff M., Evdokimova E., Edwards A., Joachimiak A., Savchenko A. 2006. 1.6 A crystal structure of a PA2721 protein from P. aeruginosa--a potential drug-resistance protein. Proteins. 63(4):1102-1105.

Yakunin AF, Yee AA, Savchenko A., Edwards A.M., Arrowsmith C.H. 2004 Structural proteomics: a tool for genome annotation. Curr Opin Chem Biol. 8(1):42-48.

Fuchs, B.M., and other 9 authors. 2007. Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis. Proc Natl Acad Sci USA 104:2891-2896.

Mussmann, M., and other 15 authors. 2007. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS. Biol. 5:1923-1937.

Richter, M., and 6 other authors. 2007. Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function. J Bacteriol189:4899-4910.

Woebken, D., H. Teeling, Wecker P., Dumitriu A., Kostadinov I., Delong E.F., Amann R. and Gloeckner

F.O. 2007. From the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes. ISME J. 1:419-435.

Woyke, T., H. Teeling, and 17 other authors. 2006. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 443:950-955.

Lombó,F.; & other 8 authors. 2006. Deciphering the Biosynthesis Pathway of the Antitumor Thiocoraline from a Marine Actinomycete and Its Expression in Two Streptomyces Species. ChembioChem. 7: 366-76.

Velasco A., & other 10 authors. 2005. Molecular characterization of the safracin biosynthetic pathway from Pseudomonas fluorescens A2-2: designing new cytotoxic compounds Mol Microbiol. 56: 144-154.

Carballo JL; Naranjo S; Kukurtzu B; de La Calle F; Hernandez-Zanuy A. 2000. Production of Ecteinascidia turbinata (Ascidiacea: Perophoridae) for obtaining anticancer compounds. Journal of the World Aquaculture Society 31: 481-490

Cuevas,C.; Perez,M.; & other 12 authors. 2000. Synthesis of ecteinascidin ET-743 and phthalascidin Pt-650 from cyanosafracin B  Org Lett 2: 2545-2548.

Fernandez-Chimeno,R.I.; & other 5 authors. 2000. IB-96212, a novel cytotoxic macrolide produced by a marine Micromonospora. I. Taxonomy, fermentation, isolation and biological activities 2000. J Antibiot. 53: 474-478.

Andexer, J., von Langermann, J., Mell, A., Bocola, M., Kragl, U., Eggert, T. and Pohl, M. 2007. An R-selective hydroxynitrile lyase from A. thaliana with an !/"-hydrolase fold. Angew Chem Int Ed. 46: 8679-81.

Drepper, T., Eggert, T., (…), (…) and Jaeger, K.-E. 2007. In vivo fluorescence without oxygen: Novel

fluorescence reporters for anaerobic systems. Nat. Biotechnol. 25: 443-445.

Reetz, M.T., Puls, M., Carballeira, J.D., Vogel, A., Jaeger, K.-E., Eggert, T., Thiel, W., Bocola, M. and Otte, N. 2007. Learning from directed evolution: further lessons from theoretical investigations into kooperative mutations in lipase enantioselectivity. ChemBioChem.8: 106-112.

Andexer, J., Guterl, J.-K., Pohl, M. and Eggert, T. 2006. A High-throughput screening assay for hydroxynitrile lyase activity. Chem Commun. 40: 4201-4203.

Brockmeier, U., (…), and Eggert, T. 2006. Systematic screening of all signal peptides from B. subtilis: a powerful strategy in optimizing heterologous protein secretion in Gram-positive bacteria. J Mol Biol362: 393-402.

Jean C., Hernandez-Pigeon H, Blanc A., Charveron M., and Laurent G. 2007. Epidermal growth factor receptor pathway mitigates UVA-induced G2/M arrest in keratinocyte cells. J Invest Dermatol. 127:2418-24.

Hernandez-Pigeon H, Jean C., Charruyer A., Haure MJ, Baudouin C., Charveron M., Quillet-Mary A., and Laurent G. 2007. UVA induces granzyme B in human keratinocytes through MIF: implication in extracellular matrix remodeling. J Biol Chem. 282:8157-64.

Hernandez-Pigeon H, Jean C., Charruyer A., Haure MJ, Titeux M., Tonasso L., Quillet-Mary A., Baudouin C., Charveron M., and Laurent G. 2006. Human keratinocytes acquire cellular cytotoxicity under UV-B irradiation. Implication of granzyme B and perforin. J Biol Chem. 281:13525-32.

Courdavault S., C. Baudouin, M. Charveron, B. Canguilhem, A. Favier, J. Cadet and T. Douki. 2005. Repair of the three main types of bipyrimidine DNA photoproducts in human keratinocytes exposed to UVB and UVA radiations. DNA Repair, 4:836-844.