Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica

Michael Kube, Tatyana N. Chernikova, Yamal Al-Ramahi, Ana Beloqui, Nieves Lopez-Cortez, María-Eugenia Guazzaroni, Hermann J. Heipieper, Sven Klages, Oleg R. Kotsyurbenko, Ines Langer, Taras Y. Nechitaylo, Heinrich Lünsdorf, Marisol Fernández, Silvia Juárez, Sergio Ciordia, Alexander Singer, Olga Kagan, Olga Egorova, Pierre Alain Petit, Peter Stogios, Youngchang Kim, Anatoli Tchigvintsev, Robert Flick, Renata Denaro, Maria Genovese, Juan P. Albar, Oleg N. Reva, Montserrat Martínez-Gomariz, Hai Tran, Manuel Ferrer, Alexei Savchenko, Alexander F. Yakunin, Michail M. Yakimov, Olga V. Golyshina, Richard Reinhardt and Peter N. Golyshin ()
Additional contact information
Michael Kube: Max-Planck Institute for Molecular Genetics
Tatyana N. Chernikova: Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research
Yamal Al-Ramahi: Institute of Catalysis, CSIC
Ana Beloqui: Institute of Catalysis, CSIC
Nieves Lopez-Cortez: Institute of Catalysis, CSIC
María-Eugenia Guazzaroni: Institute of Catalysis, CSIC
Hermann J. Heipieper: Helmholtz Centre for Environmental Research-UFZ
Sven Klages: Max-Planck Institute for Molecular Genetics
Oleg R. Kotsyurbenko: Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research
Ines Langer: Max-Planck Institute for Molecular Genetics
Taras Y. Nechitaylo: Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research
Heinrich Lünsdorf: Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research
Marisol Fernández: Proteomic Facility, National Centre for Biotechnology, CSIC
Silvia Juárez: Proteomic Facility, National Centre for Biotechnology, CSIC
Sergio Ciordia: Proteomic Facility, National Centre for Biotechnology, CSIC
Alexander Singer: University of Toronto
Olga Kagan: University of Toronto
Olga Egorova: Midwest Center for Structural Genomics, Argonne National Laboratory
Pierre Alain Petit: C.H. Best Institute University of Toronto
Peter Stogios: C.H. Best Institute University of Toronto
Youngchang Kim: Midwest Center for Structural Genomics, Argonne National Laboratory
Anatoli Tchigvintsev: University of Toronto
Robert Flick: University of Toronto
Renata Denaro: Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina 98122, Italy
Maria Genovese: Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina 98122, Italy
Juan P. Albar: Proteomic Facility, National Centre for Biotechnology, CSIC
Oleg N. Reva: University of Pretoria
Montserrat Martínez-Gomariz: Proteomics Unit, UCM—Complutense University Madrid
Hai Tran: School of Biological Sciences, Bangor University
Manuel Ferrer: Institute of Catalysis, CSIC
Alexei Savchenko: University of Toronto
Alexander F. Yakunin: C.H. Best Institute University of Toronto
Michail M. Yakimov: Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina 98122, Italy
Olga V. Golyshina: Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research
Richard Reinhardt: Max-Planck Institute for Molecular Genetics
Peter N. Golyshin: Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research

Nature Communications, 2013, vol. 4, issue 1, 1-11

Abstract: Abstract Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis—the paradigm of mesophilic hydrocarbonoclastic bacteria—O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.

Date: 2013
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DOI: 10.1038/ncomms3156

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