McHardy, A.C., Goesmann, A., Phler, A. The nucleotide sequence of the A. borkumensis SK2 genome was submitted to GenBank under accession number AM286690. The A. borkumensis SK2 genome encodes a number of proteins putatively involved in metabolic reactions of potential biotechnological interest, including eight hydrolases of the haloacid dehydrogenase/epoxide family, two determinants for dienelactone hydrolases (ABO_1618 and ABO_1886), three for deacylases, 36 for various cytochrome proteins and 30 for oxidoreductases. Genome Res. Thus, the genome encodes for a broad spectrum of systems for the catabolism of hydrocarbons, giving it a competitive advantage over other oil-degrading marine microbial communities. et al. The A. borkumensis SK2 AlkB1 alkane hydroxylase efficiently oxidizes medium-chain alkanes (C5 to C12). Microbiol. Gordon, D., Desmarais, C. & Green, P. Automated finishing with Autofinish. The A. borkumensis SK2 chromosome harbors 16 pil genes related to Type IV pili, which mediate the formation of biofilms and are involved in surface translocations27. Owing to the low solubility of hydrocarbons in water, bacterial degradation takes place mainly at the hydrocarbon-water interface. These keywords were added by machine and not by the authors. Toren, A., Orr, E., Paitan, Y., Ron, E.Z. 3 online). One of the most dramatic polluting events was the spill of oil from the supertanker Prestige, which sank off the Galician coast of Spain, releasing an estimated 17,000 tons of heavy fuel oil1. The main microbes which are usually used in bioremediation are- Pseudomonas putida, Dechloromonas aromatica, Deinococcus radiodurans, Methylibium petroleiphilum, Alcanivorax borkumensis, h chrysosporium. 269, 1978719795 (1994). The tree is rooted with the methyl-CoM-reductase subunit A from Methanolubus tindarius (gbU22244). Interestingly, various elements of heavy metal cation efflux transport systems were identified within a putative transposon (Supplementary Results 1 online). CORDIS website requires JavaScript enabled in order to work properly. Sixteen groups of bacteria were enriched within the plume, particularly the Oceanospirillales (a group that includes Alcanivorax who we've already met). Appl Environ Microbiol 68: 55375548. Microbial biodegradation is the use of bioremediation and biotransformation methods to harness the naturally occurring ability of microbial xenobiotic metabolism to degrade, transform or accumulate environmental pollutants, including hydrocarbons (e.g. "Blueprint of an Oil-eating Bacterium." Curation and annotation of the genome was done by using the annotation system GenDB40. Genome analysis yielded unprecedented insights into the bacterium's capacity for (i) n-alkane degradation, including metabolism, biosurfactant production and biofilm formation, (ii) scavenging of nutrients and cofactors in the oligotrophic marine environment and (iii) coping with various habitat-specific stress factors. - 68.183.91.154. Syutsubo, K., Kishira, H. & Harayama, S. Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains. Dyksterhouse, S.E., Gray, J.P., Herwig, R.P., Lara, J.C. & Staley, J.T. et al. Biochim Biophys Acta 1393: 5762. Schneiker S, Dos Santos VAPM, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Phler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhlter FJ, Weidner S, Kaiser O, Golyshin PN (2006) Genome sequence ofthe ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Bacteria; Phylum: Proteobacteria; Class: Gammaproteobacteria; Order: Oceanospirillales; Family: Alcanivoracaceae. (PDF 115 kb), Phylogenetic tree of AlkB1 protein homologues of A.borkumensis SK2 identified in the 'nr' database including sequences from the Sargassos Sea environmental shotgun library. This article is distributed under the terms of the Creative Commons Attribution-Non-Commercial-Share Alike license (http://creativecommons.org/licenses/by-nc-sa/3.0/), which permits distribution, and reproduction in any medium, provided the original author and source are credited. You are using a browser version with limited support for CSS. contributed to the annotation, R.D. OmpA proteins, the active constituents of the biosurfactant alasan, have been demonstrated to efficiently emulsify hydrocarbons25 and to be produced by a number of oil-degrading -Proteobacteria26. & Rosenberg, E. The active component of the bioemulsifier alasan from Acinetobacter radioresistens KA53 is an OmpA-like protein. Acad. Maintenance of sustainable marine and coastal ecosystems urgently requires the development of effective measures to reduce oil pollution and mitigate its environmental impact. contributed to the gene prediction, F.M. contributed to the detailed analysis of genome features and production of genome visualizations, J.S.S. [1] Fernandez-Martinez, Javier, Maria J. Pujalte, Jesus Garcia-Martinez, Manuel Mata, Esperanza Garay, and Francisco Rodriguez-Valera. PubMed Central Les bactries dgradant les hydrocarbures se nourrissent des hydrocarbures contenus dans les gouttelettes d'huile, les dcomposant en composs inorganiques. USA 98, 435440 (2001). The A. borkumensis SK2 genome has a number of regions with atypical GC content. & Witholt, B. Diversity of alkane hydroxylase systems in the environment. Ewing, B., Hillier, L., Wendl, M. & Green, P. Base-calling of automated sequencer traces using phred. A. borkumensis SK2's most distinctive feature is its ability to grow efficiently and almost exclusively on alkanes2,5,11,12. Kim BH, Kim HG, Bae GI, Bang IS, Bang SH, Choi JH, Park YK (2004) Expression of cspH upon nutrient up-shift in Salmonella enterica serovar Typhimurium. The remaining 514 coding sequences comprise 316 conserved hypothetical and 198 of unknown function (Fig. Klappenbach JA, Dunbar JM, Schmidt TM (2000) rRNA operon copy number reflects ecological strategies of bacteria. ABO_0201 (P450(c)) clusters in an operon-like structure with genes encoding a ferredoxin (fdx, ABO_0200), an alcohol dehydrogenase (alkJ2, ABO_0202), a FAD-dependent oxidoreductase (ABO_0203) and an AraC transcriptional regulator gene (ABO_0199) (Fig. Biochimie 78, 364369 (1996). Chem. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Finally, 32,428 high-quality reads, a total of 11,472 (2.0 X), 13,052 (2.3 X), and 7,904 (1.4 X) end sequences from libraries of 1 kb, 23 kb and 8 kb, respectively, were established (X's indicate genome equivalents). %PDF-1.5 % Article Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium. Medical Microbiology Services. Mohanty BK, Kushner SR (2003) Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Please enable JavaScript. Read more. This work was supported by grants of the German Federal Ministry of Education and Research (031U113D, 031U213D) and 0313105 in the frame of the GenoMik network Genome Research on Bacteria Relevant for Agriculture, Environment and Biotechnology. K.T. A. borkumensis is an unusual, rod-shaped marine -proteobacterium able to grow on a highly restricted spectrum of substrates, predominantly alkanes2. Sci. Mix well. A. borkumensis forms stable emulsions of hydrocarbon in water and produces biosurfactants23. Biochemical Engineering Journal , 2018; 132: 279 DOI: 10.1016/j.bej.2018.01.014 Cite This Page : It encodes three cytochromes: ABO_2384 for P450(a), and two paralogous genes ABO_2288 P450(b) and ABO_0201 P450(c). Collectively, 1,471 sequencing reads were added to the shotgun assembly for finishing and polishing of the genomic sequence. 6, 264273 (2004). Appl Environ Microbiol 70: 26032613. \uRd^j``(t"S;TeZ Sample type/isolated from: seawater sediment sample [Ref. et al. & van Beilen, J.B. Functional analysis of alkane hydroxylases from Gram-negative and Gram-positive bacteria. Microbiol. : #4326 . 4. The A. borkumensis SK2 genome has many determinants for the biosynthesis, export, modification and polymerization of exopolysaccharides putatively involved in biofilm formation. In seawater with high concentrations of n-alkanes (as a result of oil spills, natural oil fields, and/or processing plants), Alcanivorax quickly becomes the predominant microbial community and is found in higher populations when compared to Alcanivorax in unpolluted seawater. The versatility and wider spectrum for hydrocarbon utilization clearly provides A. borkumensis SK2 a competitive advantage over other members of oil-degrading marine microbial communities. contributed to the maintenance and improvement of GenDB web interface, A.C.McH. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Environ. Google Scholar. ), Bioinformatics & Pattern Discovery Group, IBM Thomas J Watson Research Center, Yorktown Heights, New York, 10598, USA, Manuel Ferrer,Alice C McHardy&Daniela Regenhardt, Division Biogeochemistry, Research Centre Rossendorf, Dresden, D-01314, Germany, You can also search for this author in Genome Res. burning of fossil fuels, plant and animal respiration, decaying process. contributed to the data analysis, J.B. contributed to the annotation, T.N.C. It thrives in aerobic and halophilic environments. "Genome Sequence of the Ubiquitous Hydrocarbon-degrading Marine Bacterium Alcanivorax Borkumensis." Genome Res. Alcanivorax borkumensis is a rod-shaped bacteria that relies on oil to provide it with energy. Its genome specifies a number of systems for the catabolism of hydrocarbons (Figs. Environ. In: Timmis, K.N. Altschul, S.F. Schneiker, S. et al. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. When conditions in these moderately halophilic environments are right, Alcanivorax may make up 80-90% of the oil-degrading microbes present in the area [4]. Where multiple homologous transporters with similar substrate predictions exist, the number of that type of protein is indicated in parentheses. contributed to the annotation, A.G. contributed to the automatic and manual annotation and the coordination of software development for genome analysis, O.V.G. Importantly, both alkane hydroxylase systems are located close to the origin of replication of the chromosome (Supplementary Fig. They hope that their new understanding of the biochemistry of the micro-organism will lead to the development of new, effective, environmentally friendly methods to clean up oil-contaminated waters. International Journal of Systematic and Evolutionary Microbiology 53 (2003): 331-338. However, genes for the synthesis of other organic compatible solutes, such as trehalose, di-inositol phosphate or mannosylglycerate, were not identified. Gene 33, 103119 (1985). It is found in low numbers in all oceans of the world and becomes abundant in oil-contaminated waters. Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. 1.Cells of A. borkumensis were cultivated aerobically at 30C and 150 rpm for 60 h in ONR7a medium containing 1% (wt/vol) sodium pyruvate or 0.5% (wt/vol) hexadecane as the sole carbon source.Cells of A. jadensis were cultivated at 30C and 150 rpm for 96 h in . . Export of sodium ions at the expense of the proton gradient is performed by a variety of sodium/proton antiporters, including the multisubunit Na+/H+ antiporter (mnhABCDEFG genes, ABO_2653-2658), as well as NhaD (ABO_0238), NhaB (ABO_1226), NhaP (ABO_1404) and NhaC (ABO_2329) (Fig. Identification of an amino acid position that determines the substrate range of integral membrane alkane hydroxylases. Nucleic Acids Res. Biophys. 2 online). Microbiol. Citation in PubAg 50; Full Text 6; Journal. Accuracy assessment. Microbe Descriptions - Read online for free. Accordingly, and in addition to the uptake systems for glutamate (gltP, ABO_1478, gltS, ABO_1616) and choline/betaine (ABO_0232, ABO_0637 and ABO_0808), the A. borkumensis SK2 genome contains the genetic determinants for the biosynthesis of glutamate (gltA, ABO_1501, gltB, ABO_2229, gltD, ABO_2228 and gltX, ABO_1509), ectoine (ectABC, ABO_2150_2152) and (putatively) betaine (ABO_0886) (Fig. & Rosenberg, E. Natural roles of biosurfactants. Gordon, D., Abajian, C. & Green, P. Consed: A graphical tool for sequence finishing. These biosurfactants are anionic glucolipids carrying four fatty acids of varying chain lengths11. Ochsner UA, Fiechter A, Reiser J (1994) Isolation, characterization, and expression in Escherichia coliof the Pseudomonas aeruginosa rhlAB genes encoding a rhamnosyltransferase involved in rhamnolipid biosurfactant synthesis. Alcanivorax was one of the types of bacteria that Todd and his group found in the Challenger Deep. initiated the project and contributed to conception of the work and manuscript writing, F.-J.V. El sitio web de CORDIS requiere tener activado JavaScript para funcionar correctamente. It has been detected worldwide in places such as the Mediterranean Sea, Pacific Ocean, and the Arctic Sea [4]. It's genome consists of a single circular chromosome with 3,120,143 base pairs and an average G+C content of 54.7%.
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