Abstract
Anaerobic biodegradation of hydrocarbons is typically studied with newly isolated microorganisms not yet accessible to genetic manipulation. Functional genomics, viz., genome-based differential proteomics in conjunction with targeted metabolite analysis, has been instrumental for discovering a multitude of novel reactions and pathways involved in the biochemically challenging process of anaerobic hydrocarbon degradation.
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References
Bergmann F, Selesi D, Weinmaier T, Tischler P, Rattei T, Meckenstock RU (2011) Genomic insights into the metabolic potential of polycyclic aromatic hydrocarbon degrading sulfate-reducing Deltaproteobacterium N47. Environ Microbiol 13:1125–1137
Chen I-MA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, Ratner A, Huang J, Andersen E, Huntemann M, Varghese N, Hadjithomas M, Tennessen K, Nielsen T, Ivanova NA, Kyrpides NC (2016) IMG/M: integrated genome and metagenome comparative data analysis system. Nucleic Acids Res 45:D507–D516
Deutsch EW, Orchard S, Binz P-A, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR (2017) Proteomics standards initiative: fifteen years of progress and future work. J Proteome Res 16:4288. https://doi.org/10.1021/acs.jproteome.7b00370
Heintz D, Gallien S, Wischgoll S, Ullmann AK, Schaeffer C, Kretzschmar AK, van Dorsselaer A, Boll M (2009) Differential membrane proteome analysis reveals novel proteins involved in the degradation of aromatic compounds in Geobacter metallireducens. Mol Cell Proteomics 8(9):2159–2169
Kerkhof LJ, Dillon KP, Häggblom MM, McGuinness LR (2017) Profiling bacterial communities by MinION sequencing of ribosomal operons. Microbiome 5:116
Menschaert G, Fenyö D (2017) Proteogenomics from a bioinformatics angle: a growing field. Mass Spectrom Rev 36:584–599
Michas A, Vestergaard G, Trautwein K, Avramidis P, Hatzinikolaou DG, Vorgias CE, Wilkes H, Rabus R, Schloter M, Schöler A (2017) More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis. Microbiome 5:118
Nobu MK, Narihiro T, Tamaki H, Qiu Y-L, Sekiguchi Y, Woyke T, Goodwin L, Davenport KW, Kamagata Y, Liu W-T (2015) The genome of Syntrophorhabdus aromaticivorans strain UI provides new insights for syntrophic aromatic compound metabolism and electron flow. Environ Microbiol 17:4861–4872
Rabus R, Wilkes H (2020a) Functional genomics of denitrifying bacteria degrading hydrocarbons. In: Boll M (ed) Anaerobic utilization of hydrocarbons, oils and lipids. Handbook of hydrocarbon and lipid microbiology series. Springer International Publishing AG, pp 203–223
Rabus R, Wilkes H (2020b) Functional genomics of sulfate-reducing bacteria degrading hydrocarbons. In: Boll M (ed) Anaerobic utilization of hydrocarbons, oils and lipids. Handbook of hydrocarbon and lipid microbiology series. Springer International Publishing AG, pp 225–232
Rabus R, Kube M, Beck A, Widdel F, Reinhardt R (2002) Genes involved in the anaerobic degradation of ethylbenzene in a denitrifying bacterium, strain EbN1. Arch Microbiol 178:506–516
Rabus R, Kube M, Heider J, Beck A, Heitmann K, Widdel F, Reinhardt R (2005) The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch Microbiol 183:27–36
Rabus R, Wöhlbrand L, Thies D, Meyer M, Reinhold-Hurek B, Kämpfer P (2019) Aromatoleum gen. nov., a novel genus accommodating the phylogenetic lineage including Azoarcus evansii and related species, and proposal of Aromatoleum aromaticum sp. nov., Aromatoleum petrolei sp. nov., Aromatoleum bremense sp. nov., Aromatoleum toluolicum sp. nov. and Aromatoleum diolicum sp. nov. Int J Syst Evol Microbiol 69:982–997
Reuter JA, Specek DV, Snyder MP (2015) High-throughput sequencing technologies. Mol Cell 58:586–597
Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH (2017) DNA sequencing at 40: past, present and future. Nature 550:345. https://doi.org/10.1038/nature24286
Tremblay P-L, Zhang T (2020) Functional genomics of metal-reducing microbes degrading hydrocarbons. In: Boll M (ed) Anaerobic utilization of hydrocarbons, oils and lipids. Handbook of hydrocarbon and lipid microbiology series. Springer International Publishing AG, pp 233–253
Wilke A, Bischof J, Gerlach W, Glass E, Harrison T, Keegan KP, Paczian T, Trimble WL, Bagchi S, Grama A, Chaterji S, Meyer F (2016) The MG-RAST metagenomics database and portal in 2015. Nucleic Acids Res 44:D590–D594
Wöhlbrand L, Kallerhoff B, Lange D, Hufnagel P, Thiermann J, Reinhardt R, Rabus R (2007) Functional proteomic view of metabolic regulation in “Aromatoleum aromaticum” strain EbN1. Proteomics 7:2222–2239
Wöhlbrand L, Wilkes H, Halder T, Rabus R (2008) Anaerobic degradation of p-ethylphenol by “Aromatoleum aromaticum” strain EbN1: pathway, regulation and involved proteins. J Bacteriol 190:5699–5709
Wöhlbrand L, Trautwein K, Rabus R (2013) Proteomic tools for environmental microbiology – a roadmap from sample preparation to protein identification and quantification. Proteomics 13:2700–2730
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Rabus, R., Wilkes, H. (2020). Functional Genomics of Anaerobic Degradation of Hydrocarbons: An Introduction. In: Boll, M. (eds) Anaerobic Utilization of Hydrocarbons, Oils, and Lipids. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-50391-2_10
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DOI: https://doi.org/10.1007/978-3-319-50391-2_10
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