Rabus R, Kube M, Heider J, Beck A, Heitmann K, Widdel F et al.. The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1. Arch Microbiol 183: 27-36

Max Planck Institut für Marine Mikrobiologie, Celsiusstrasse 1, 28359, Bremen, Germany.
Archives of Microbiology (Impact Factor: 1.67). 02/2005; 183(1):27-36. DOI: 10.1007/s00203-004-0742-9
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ABSTRACT Recent research on microbial degradation of aromatic and other refractory compounds in anoxic waters and soils has revealed that nitrate-reducing bacteria belonging to the Betaproteobacteria contribute substantially to this process. Here we present the first complete genome of a metabolically versatile representative, strain EbN1, which metabolizes various aromatic compounds, including hydrocarbons. A circular chromosome (4.3 Mb) and two plasmids (0.21 and 0.22 Mb) encode 4603 predicted proteins. Ten anaerobic and four aerobic aromatic degradation pathways were recognized, with the encoding genes mostly forming clusters. The presence of paralogous gene clusters (e.g., for anaerobic phenylacetate oxidation), high sequence similarities to orthologs from other strains (e.g., for anaerobic phenol metabolism) and frequent mobile genetic elements (e.g., more than 200 genes for transposases) suggest high genome plasticity and extensive lateral gene transfer during metabolic evolution of strain EbN1. Metabolic versatility is also reflected by the presence of multiple respiratory complexes. A large number of regulators, including more than 30 two-component and several FNR-type regulators, indicate a finely tuned regulatory network able to respond to the fluctuating availability of organic substrates and electron acceptors in the environment. The absence of genes required for nitrogen fixation and specific interaction with plants separates strain EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary material on sequence and annotation are provided at the Web page

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Available from: Johann Heider, Sep 29, 2015
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    • "Even with the complete genome sequences of microorganisms with the potential for bioremediation studies are not accelerating in a rapid manner (Heidelberg et al., 2002; Tiedje and Shewanella, 2002; Golyshin et al., 2003; Rabus et al., 2005; Seshadri et al., 2005). With the completed genome sequences, it is possible to analyze the expression of all genes in each genome under various environmental conditions using wholegenome DNA microarrays (Muffler et al., 2002; Schut et al., 2003; Gao et al., 2004). "
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    Biodegradation and Bioremediation, 2014 edited by Prof. Masood Ahmad, 08/2014: chapter Recent Advances in the Field of Bioremediation: pages 1-42; Studium Press LLC, U.S.A.., ISBN: 1-62699-026-3
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    • "Aromatoleum aromaticum EbN1 (Rabus et al. 2005), Azoarcus sp. KH32C (Nishizawa et al. 2012), Azoarcus sp. "
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    ABSTRACT: Here, shotgun metagenomic sequencing was conducted to reveal the hydrogen-oxidizing autotrophic-denitrifying metabolism in an enriched Thauera-dominated consortium. A draft genome named Thauera R4 of over 90 % completeness (3.8 Mb) was retrieved mainly by a coverage-defined binning method from 3.5 Gb paired-end Illumina reads. We identified 1,263 genes (accounting for 33 % of total genes in the finished genome of Thauera aminoaromatica MZ1T) with average nucleotide identity of 87.6 % shared between Thauera R4 and T. aminoaromatica MZ1T. Although Thauera R4 and T. aminoaromatica shared quite similar nitrogen metabolism and a high nucleotide similarity (98.8 %) in their 16S ribosomal RNA genes, they showed different functional potentials in several important environmentally relevant processes. Unlike T. aminoaromatica MZ1T, Thauera R4 carries an operon of [NiFe]-hydrogenase (EC catalyzing molecular hydrogen oxidation in nitrate-rich solution. Moreover, Thauera R4 is a mixtrophic bacterium possessing key enzymes for autotrophic CO2-fixation and heterotrophic acetate assimilation metabolism. This Thauera R4 bin provides another genetic reference to better understand the niches of Thauera and demonstrates a model pipeline to reveal functional profiles and reconstruct novel and dominant genomes from a simplified mixed culture in environmental studies.
    Applied Microbiology and Biotechnology 04/2014; 98(15). DOI:10.1007/s00253-014-5756-x · 3.34 Impact Factor
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    • "BclA activates benzoate aerobically and anaerobically but also catalyses 2-aminobenzoyl-CoA formation in T. aromatica (Schühle et al., 2003). In contrast, in other denitrifying microorganisms, such as Azoarcus/'Aromatoleum' strains (Rabus et al., 2005; Carmona et al., 2009), as well as in the phototroph R. palustris (Egland et al., 1995), every catabolic cluster appears to have its own specific CoA ligase gene, e.g. the bzdA and bclA genes from the "
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    ABSTRACT: The mbd cluster encoding genes of the 3-methylbenzoyl-CoA pathway involved in the anaerobic catabolism of 3-methylbenzoate and m-xylene was characterized for the first time in the denitrifying β-Proteobacterium Azoarcus sp. CIB. The mbdA gene product was identified as a 3-methylbenzoate-CoA ligase required for 3-methylbenzoate activation; its substrate spectrum was unique in activating all three methylbenzoate isomers. An inducible 3-methylbenzoyl-CoA reductase (mbdONQP gene products), displaying significant amino acid sequence similarities to known class I benzoyl-CoA reductases catalysed the ATP-dependent reduction of 3-methylbenzoyl-CoA to a methyldienoyl-CoA. The mbdW gene encodes a methyldienoyl-CoA hydratase that hydrated the methyldienoyl-CoA to a methyl-6-hydroxymonoenoyl-CoA compound. The mbd cluster also contains the genes predicted to be involved in the subsequent steps of the 3-methylbenzoyl-CoA pathway as well as the electron donor system for the reductase activity. Whereas the catabolic mbd genes are organized in two divergent inducible operons, the putative mbdR regulatory gene was transcribed separately and showed constitutive expression. The efficient expression of the mbd genes required the oxygen-dependent AcpR activator, and it was subject of carbon catabolite repression by some organic acids and amino acids. Sequence analyses suggest that the mbd gene cluster was recruited by Azoarcus sp. CIB through horizontal gene transfer.
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