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      Draft Genome Sequence of a Versatile Hydrocarbon-Degrading Bacterium, Rhodococcus pyridinivorans Strain KG-16, Collected from Oil Fields in India

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          Abstract

          We describe here a 5.8-Mb draft genome sequence of Rhodococcus pyridinivorans strain KG-16, which was obtained from the soil samples collected from the oilfields of Krishna-Godavari basin in India. This genomic resource can provide insights into the pathways and mechanisms of hydrocarbon degradation and potentially aid in bioremediation applications.

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          Biodegradation potential of the genus Rhodococcus.

          Bronislava Uhnáková, Ludmila Martinkova, Jan Nesvera … (2008)
          A large number of aromatic compounds and organic nitriles, the two groups of compounds covered in this review, are intermediates, products, by-products or waste products of the chemical and pharmaceutical industries, agriculture and the processing of fossil fuels. The majority of these synthetic substances (xenobiotics) are toxic and their release and accumulation in the environment pose a serious threat to living organisms. Bioremediation using various bacterial strains of the genus Rhodococcus has proved to be a promising option for the clean-up of polluted sites. The large genomes of rhodococci, their redundant and versatile catabolic pathways, their ability to uptake and metabolize hydrophobic compounds, to form biofilms, to persist in adverse conditions and the availability of recently developed tools for genetic engineering in rhodococci make them suitable industrial microorganisms for biotransformations and the biodegradation of many organic compounds. The peripheral and central catabolic pathways in rhodococci are characterized for each type of aromatics (hydrocarbons, phenols, halogenated, nitroaromatic, and heterocyclic compounds) in this review. Pathways involved in the hydrolysis of nitrile pollutants (aliphatic nitriles, benzonitrile analogues) and the corresponding enzymes (nitrilase, nitrile hydratase) are described in detail. Examples of regulatory mechanisms for the expression of the catabolic genes are given. The strains that efficiently degrade the compounds in question are highlighted and examples of their use in biodegradation processes are presented.
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            The role of cytochrome P450 monooxygenases in microbial fatty acid metabolism.

            Sara Groeneboer, Wim K Soetaert, K Saerens … (2010)
            Cytochrome P450 monooxygenases (P450s) are a diverse collection of enzymes acting on various endogenous and xenobiotic molecules. Most of them catalyse hydroxylation reactions and one group of possible substrates are fatty acids and their related structures. In this minireview, the significance of P450s in microbial fatty acid conversion is described. Bacteria and yeasts possess various P450 systems involved in alkane and fatty acid degradation, and often several enzymes with different activities and specificities are retrieved in one organism. Furthermore, P450s take part in the formation of fatty acid-based secondary metabolites. Finally, there are a substantial number of microbial P450s displaying activity towards fatty acids, but to which no biological role could be assigned despite the often quite intense research. © 2010 The Authors Journal compilation © 2010 FEBS.
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              Petroleum-Degrading Enzymes: Bioremediation and New Prospects

              R. S. Peixoto, A. B. Vermelho, A. Rosado (2011)
              Anthropogenic forces, such as petroleum spills and the incomplete combustion of fossil fuels, have caused an accumulation of petroleum hydrocarbons in the environment. The accumulation of petroleum and its derivatives now constitutes an important environmental problem. Biocatalysis introduces new ways to improve the development of bioremediation strategies. The recent application of molecular tools to biocatalysis may improve bioprospecting research, enzyme yield recovery, and enzyme specificity, thus increasing cost-benefit ratios. Enzymatic remediation is a valuable alternative as it can be easier to work with than whole organisms, especially in extreme environments. Furthermore, the use of free enzymes avoids the release of exotic or genetically modified organisms (GMO) in the environment.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 11 February 2016
                Publication date Collection: Jan-Feb 2016
                Volume: 4
                Issue: 1
                Electronic Location Identifier: e01704-15
                Affiliations
                [a ]Centre for Cellular & Molecular Biology (CSIR-CCMB), Habsiguda, Hyderabad, India
                [b ]National Geophysical Research Institute (CSIR-NGRI), Habsiguda, Hyderabad, India
                Author notes
                Address correspondence to Ramesh K. Aggarwal, rameshka@ 123456ccmb.res.in .
                Article
                Publisher ID: genomeA01704-15
                DOI: 10.1128/genomeA.01704-15
                PMC ID: 4751318
                PubMed ID: 26868394
                SO-VID: a5d02bd6-7421-4cb3-b5c0-7c44bdead69c
                Copyright © Copyright © 2016 Aggarwal et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 11 December 2015
                Date accepted : 21 December 2015
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 10, Pages: 2, Words: 1212
                Funding
                Funded by: Council of Scientific and Industrial Research (CSIR) http://dx.doi.org/10.13039/501100001412
                Award ID: FYP GENESIS (Genomics and Informatics Solutions for Integrating Biology)_BSC0121
                Award Recipient : Ramesh K. Aggarwal
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date January/February 2016

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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