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

• Published in: Nature Communications
• Main Authors: Kube, Michael, Chernikova, Tatyana N., Al-Ramahi, Yamal, Beloqui, Ana, Lopez-Cortes, Nieves, Guazzaroni, Marıa-Eugenia, Heipieper, Hermann J., Klages, Sven, Kotsyurbenko, Oleg R., Langer, Ines, Nechitaylo, Taras Y., Lunsdorf, Heinrich, Fernandez, Marisol, Juarez, Silvia, Ciordia, Sergio, Singer, Alexander, Kagan, Olga, Egorova, Olga, Petit, Pierre Alain, Stogios, Peter, Kim, Youngchang, Tchigvintsev, Anatoli, Flick, Robert, Denaro, Renata, Genovese, Maria, Albar, Juan P., Reva, Oleg N., Martınez-Gomariz, Montserrat, Tran, Hai, Ferrer, Manuel, Savchenko, Alexei, Yakunin, Alexander F., Yakimov, Michail M., Golyshina, Olga V., Reinhardt, Richard, Golyshin, Peter N.
• Format: Conference Object
• Language: English
• Published: Nature Publising Group 2013
• Subjects: Genus Oleispira; Mesophilic hydrocarbonoclastic bacteria; Antarc*; Antarctica
• Online Access: http://hdl.handle.net/2263/32319; https://doi.org/10.1038/ncomms3156

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. M.K. and P.N.G. designed the work; T.N.C. performed physiological studies; M.K., M.F., Y.A.-R., A.B., N.L.-C., M.E.G., O.R.K., T.Y.N., S.K., I.L., O.V.G., M.M.Y. R.R. and P.N.G. were associated with genome annotation; H.J.H. performed lipids and FAME analysis; M.F., M-l.F., S.J., S.C. and J.P.A performed chaperonin anti-proteome analysis; A.-x. S., O.K., O.E., P.A.P., P.S. and Y.K. were associated with structural proteomics; A.T. and R.F. were associated with functional proteomics; H.L. performed electron microscopy; R.D. performed real-time PCR; M.M.-G. and M.F. performed DIGE proteome analysis; M.G. was involved in siderophore production; O.N.R. performed genomic islands’ analysis; H.T. performed storage lipid compounds’ analysis; P.N.G. coordinated manuscript writing. Accession Codes: The genome sequence of Oleispira antarctica RB-8 has been deposited in GenBank ...