Draft Genome Sequences for Three Mercury-Methylating, Sulfate-Reducing Bacteria

Brown, Steven D.; Hurt, Richard A.; Gilmour, Cynthia C.; Elias, Dwayne A.

doi:10.1128/genomea.00618-13

Cited by 6 publications

(7 citation statements)

References 15 publications

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“…Although the number of microbes screened was small, this gene was observed to be perfectly correlated with the ability to methylate mercury and absent in any strain that had been screened and found to be a non-methylator (Parks et al, 2013). That correlation apparently still holds with the expansion of known methylators (Brown, Hurt, et al, 2013;Gilmour et al, 2013). Interestingly, all methylators are also identified as anaerobes.…”

Section: Mercury Methylationmentioning

confidence: 78%

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Rabus

Venceslau

Wöhlbrand

et al. 2015

Advances in Microbial Physiology

263

286

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Section: Mercury Methylationmentioning

confidence: 78%

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Rabus

Venceslau

Wöhlbrand

et al. 2015

Advances in Microbial Physiology

263

286

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“…Conversely, the majority of δ-proteobacteria has short cydA and cydB proteins that are evidently related to the catalytic subunits of ancestral bd oxidases of Bacillus subtilis ( Winstedt et al 1998 ). A dozen δ-proteobacteria including Desulfovibrio magneticus ( Nakazawa et al 2009 ) and Desulfococcus multivorans ( Brown et al 2013 ) have another bd oxidase, which clusters with the CIO type of α-, β-, and γ-proteobacteria, as illustrated in figure 1 . Furthermore, a phylogenetically different group of δ-proteobacteria such as Desulfobulbus propionicus has cydA sequences that are longer than those of the rest of the class, as they possess Q loop extensions similar to those of bd -I type oxidases.…”

Section: Resultsmentioning

confidence: 99%

Molecular Evolution of Cytochrome bd Oxidases across Proteobacterial Genomes

Esposti

Rosas-Pérez²,

Servín-Garcidueñas³

et al. 2015

Genome Biology and Evolution

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This work is aimed to resolve the complex molecular evolution of cytochrome bd ubiquinol oxidase, a nearly ubiquitous bacterial enzyme that is involved in redox balance and bioenergetics. Previous studies have created an unclear picture of bd oxidases phylogenesis without considering the existence of diverse types of bd oxidases. Integrated approaches of genomic and protein analysis focused on proteobacteria have generated a molecular classification of diverse types of bd oxidases, which produces a new scenario for interpreting their evolution. A duplication of the original gene cluster of bd oxidase might have occurred in the ancestors of extant α-proteobacteria of the Rhodospirillales order, such as Acidocella, from which the bd-I type of the oxidase might have diffused to other proteobacterial lineages. In contrast, the Cyanide-Insensitive Oxidase type may have differentiated into recognizable subtypes after another gene cluster duplication. These subtypes are widespread in the genomes of α-, β-, and γ-proteobacteria, with occasional instances of lateral gene transfer. In resolving the evolutionary pattern of proteobacterial bd oxidases, this work sheds new light on the basal taxa of α-proteobacteria from which the γ-proteobacterial lineage probably emerged.

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“…Sequence data were also generated using a MiSeq instrument (Illumina, San Diego, CA, USA) [16] and a paired-end approach with an approximate insert library size of 500 bp and read lengths of 151 bp, as described previously [81] and according to the manufacturer’s instructions. DNA for PacBio sequencing was sheared with G-tubes (Covaris, Inc., Woburn, MA, USA), targeting 20-kb fragments.…”

Section: Methodsmentioning

confidence: 99%

Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

Brown

Nagaraju

Utturkar

et al. 2014

Biotechnol Biofuels

134

148

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BackgroundClostridium autoethanogenum strain JA1-1 (DSM 10061) is an acetogen capable of fermenting CO, CO2 and H2 (e.g. from syngas or waste gases) into biofuel ethanol and commodity chemicals such as 2,3-butanediol. A draft genome sequence consisting of 100 contigs has been published.ResultsA closed, high-quality genome sequence for C. autoethanogenum DSM10061 was generated using only the latest single-molecule DNA sequencing technology and without the need for manual finishing. It is assigned to the most complex genome classification based upon genome features such as repeats, prophage, nine copies of the rRNA gene operons. It has a low G + C content of 31.1%. Illumina, 454, Illumina/454 hybrid assemblies were generated and then compared to the draft and PacBio assemblies using summary statistics, CGAL, QUAST and REAPR bioinformatics tools and comparative genomic approaches. Assemblies based upon shorter read DNA technologies were confounded by the large number repeats and their size, which in the case of the rRNA gene operons were ~5 kb. CRISPR (Clustered Regularly Interspaced Short Paloindromic Repeats) systems among biotechnologically relevant Clostridia were classified and related to plasmid content and prophages. Potential associations between plasmid content and CRISPR systems may have implications for historical industrial scale Acetone-Butanol-Ethanol (ABE) fermentation failures and future large scale bacterial fermentations. While C. autoethanogenum contains an active CRISPR system, no such system is present in the closely related Clostridium ljungdahlii DSM 13528. A common prophage inserted into the Arg-tRNA shared between the strains suggests a common ancestor. However, C. ljungdahlii contains several additional putative prophages and it has more than double the amount of prophage DNA compared to C. autoethanogenum. Other differences include important metabolic genes for central metabolism (as an additional hydrogenase and the absence of a phophoenolpyruvate synthase) and substrate utilization pathway (mannose and aromatics utilization) that might explain phenotypic differences between C. autoethanogenum and C. ljungdahlii.ConclusionsSingle molecule sequencing will be increasingly used to produce finished microbial genomes. The complete genome will facilitate comparative genomics and functional genomics and support future comparisons between Clostridia and studies that examine the evolution of plasmids, bacteriophage and CRISPR systems.

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Draft Genome Sequences for Three Mercury-Methylating, Sulfate-Reducing Bacteria

Cited by 6 publications

References 15 publications

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Molecular Evolution of Cytochrome bd Oxidases across Proteobacterial Genomes

Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia

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