Complete Genomes of the Anaerobic Degradation Specialists Aromatoleum petrolei ToN1T and Aromatoleum bremense PbN1T

The betaproteobacterial genus <i>Aromatoleum</i> comprises facultative denitrifiers specialized in the anaerobic degradation of recalcitrant organic compounds (aromatic and terpenoid). This study reports on the complete and manually annotated genomes of <i>Ar. petrolei</i> ToN1^T (5.41 Mbp) and <i>Ar. bremense</i> PbN1^T (4.38 Mbp), which cover the phylogenetic breadth of the genus <i>Aromatoleum</i> together with previously genome sequenced <i>Ar. aromaticum</i> EbN1^T [Rabus et al., Arch Microbiol. 2005 Jan;183(1):27–36]. The gene clusters for the anaerobic degradation of aromatic and terpenoid (strain ToN1^T only) compounds are scattered across the genomes of strains ToN1^T and PbN1^T. The richness in mobile genetic elements is shared with other <i>Aromatoleum</i> spp., substantiating that horizontal gene transfer should have been a major driver in shaping the genomes of this genus. The composite catabolic network of strains ToN1^T and PbN1^T comprises 88 proteins, the coding genes of which occupy 86.1 and 76.4 kbp (1.59 and 1.75%) of the respective genome. The strain-specific gene clusters for anaerobic degradation of ethyl-/propylbenzene (strain PbN1^T) and toluene/monoterpenes (strain ToN1^T) share high similarity with their counterparts in <i>Ar. aromaticum</i> strains EbN1^T and pCyN1, respectively. Glucose is degraded via the ED-pathway in strain ToN1^T, while gluconeogenesis proceeds via the reverse EMP-pathway in strains ToN1^T, PbN1^T, and EbN1^T. The diazotrophic, endophytic lifestyle of closest related genus <i>Azoarcus</i> is known to be associated with nitrogenase and type-6 secretion system (T6SS). By contrast, strains ToN1^T, PbN1^T, and EbN1^T lack <i>nif</i> genes for nitrogenase (including cofactor synthesis and enzyme maturation). Moreover, strains PbN1^T and EbN1^T do not possess <i>tss</i> genes for T6SS, while strain ToN1^T does and facultative endophytic “<i>Aromatoleum</i>” sp. CIB is known to even have both. These findings underpin the functional heterogeneity among <i>Aromatoleum</i> members, correlating with the high plasticity of their genomes.

In vivo metal selectivity of metal-dependent biosynthesis of cobalt-type nitrile hydratase in Rhodococcus bacteria: a new look at the nitrile hydratase maturation mechanism?

Metal-dependent cblA-mediated mechanism of transcription regulation of NHase could not discriminate Ni and Co, but mechanism of NHase enzyme maturation could do this.