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

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 under accession core FO203512. Protein structures have deposited in PDB under accession codes 3QVM (a/b hydrolase, OLEAN_C08020), 3QVQ (phosphodiesterase, OLEAN_C20330), 3M16 (transaldolase, OLEAN_C18160), 3LQY (isochorismatase, OLEAN_C07660), 3LNP (amidohydrolase, OLEAN_C13880), 3V77/3L53 (fumarylacetoacetate isomerase/hydrolase, OLEAN_C35840), 3VCR/3LAB (2-keto-3-deoxy-6-phosphogluconate aldolase, OLEAN_C25130), 3IRU (phoshonoacetaldehyde hydrolase, OLEAN_C33610), 3I4Q (inorganic pyrophosphatase, OLEAN_C30460), 3LMB (protein with unknown function, OLEAN_C10530). 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 ...