Metagenome analysis reveals yet unexplored reductive dechlorinating potential of <i><scp>D</scp>ehalobacter</i> sp. <scp>E</scp>1 growing in co‐culture with <i><scp>S</scp>edimentibacter</i> sp.

Maphosa, Farai; Passel, Mark W. J. van; Vos, Willem M. de; Smidt, Hauke

doi:10.1111/j.1758-2229.2012.00376.x

Cited by 47 publications

(52 citation statements)

References 58 publications

(86 reference statements)

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“…Strain CF could also grow without corrinoid supplementation (Figure 1b). Consistent with these observations, genomes of strains CF, DCA (Tang et al, 2016) and UNSWDHB (Deshpande et al, 2013) all possess a complete cobinamide biosynthesis pathway, whereas strains PER-K23 (Rupakula et al, 2013) and E1 (Maphosa et al, 2012) do not. However, to date, no direct evidence for de novo corrinoid synthesis by Dehalobacter exists.…”

Section: Corrinoid Biosynthesissupporting

confidence: 67%

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates

et al. 2016

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Two novel chlorinated alkane-respiring Dehalobacter restrictus strains CF and DCA were isolated from the same enrichment culture, ACT-3, and characterized. The closed genomes of these highly similar sister strains were previously assembled from metagenomic sequence data and annotated. The isolation of the strains enabled experimental verification of predicted annotations, particularly focusing on irregularities or predicted gaps in central metabolic pathways and cofactor biosynthesis. Similar to D. restrictus strain PER-K23, strains CF and DCA require arginine, histidine and threonine for growth, although the corresponding biosynthesis pathways are predicted to be functional. Using strain CF to experimentally verify annotations, we determined that the predicted defective serine biosynthesis pathway can be rescued with a promiscuous serine hydroxymethyltransferase. Strain CF grew without added thiamine although the thiamine biosynthesis pathway is predicted to be absent; intracellular thiamine diphosphate, the cofactor of carboxylases in central metabolism, was not detected in cell extracts. Thus, strain CF may use amino acids to replenish central metabolites, portending entangled metabolite exchanges in ACT-3. Consistent with annotation, strain CF possesses a functional corrinoid biosynthesis pathway, demonstrated by increasing corrinoid content during growth and guided cobalamin biosynthesis in corrinoid-free medium. Chloroform toxicity to corrinoid-producing methanogens and acetogens may drive the conservation of corrinoid autotrophy in Dehalobacter strains. Heme detection in strain CF cell extracts suggests the 'archaeal' heme biosynthesis pathway also functions in anaerobic Firmicutes. This study reinforces the importance of incorporating enzyme promiscuity and cofactor availability in genome-scale functional predictions and identifies essential nutrient interdependencies in anaerobic dechlorinating microbial communities.

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Section: Corrinoid Biosynthesissupporting

confidence: 67%

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates

et al. 2016

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“…Consistent with this expectation, a draft genome for Dehalobacter sp. E1 was recently elucidated based on metagenome analysis of a defined co-culture [22]. The availability of OHRB genomes has allowed comparative genomic studies within genera [15,23] as well as across phyla [6].…”

Section: Organohalide Respirationmentioning

confidence: 99%

“…The genome of Dehalogenimonas lykanthroporepellens strain BL-DC-9, the only sequenced Dehalogenimonas, contains 19 rdhA genes [17,66]. The presence of multiple rdhA genes is also a feature in the Dehalobacter genus, with up to 24 complete putative rdhA genes within sequenced Dehalobacter genomes [21,22,67].…”

Section: Reductive Dehalogenasesmentioning

confidence: 99%

Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases

Hug

Maphosa

Leys

et al. 2013

Phil. Trans. R. Soc. B

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255

272

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Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.

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“…Another striking feature is the high conservation degree of RdhA proteins between D. restrictus and the newly available RdhA sequences identified in the metagenome of the b-HCH dechlorinating co-culture containing Dehalobacter sp. E1 (DhbE1 in figure 3) [10]. Indeed, five of nine DhbE1 proteins have identical counterparts in D. restrictus (99 -100% sequence identity), whereas three RdhA have highly similar homologues (70-92% identity) in D. restrictus.…”

Section: (I) Multiple Reductive Dehalogenase Homologue Gene Clusters mentioning

confidence: 99%

The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics

Rupakula

Kruse

Boeren

et al. 2013

Phil. Trans. R. Soc. B

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Dehalobacter restrictus strain PER-K23 is an obligate organohalide respiring bacterium, which displays extremely narrow metabolic capabilities. It grows only via coupling energy conservation to anaerobic respiration of tetra- and trichloroethene with hydrogen as sole electron donor. Dehalobacter restrictus represents the paradigmatic member of the genus Dehalobacter , which in recent years has turned out to be a major player in the bioremediation of an increasing number of organohalides, both in situ and in laboratory studies. The recent elucidation of the D. restrictus genome revealed a rather elaborate genome with predicted pathways that were not suspected from its restricted metabolism, such as a complete corrinoid biosynthetic pathway, the Wood–Ljungdahl (WL) pathway for CO 2 fixation, abundant transcriptional regulators and several types of hydrogenases. However, one important feature of the genome is the presence of 25 reductive dehalogenase genes, from which so far only one, pceA , has been characterized on genetic and biochemical levels. This study describes a multi-level functional genomics approach on D. restrictus across three different growth phases. A global proteomic analysis allowed consideration of general metabolic pathways relevant to organohalide respiration, whereas the dedicated genomic and transcriptomic analysis focused on the diversity, composition and expression of genes associated with reductive dehalogenases.

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Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in co‐culture with Sedimentibacter sp.

Cited by 47 publications

References 58 publications

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates

Refined experimental annotation reveals conserved corrinoid autotrophy in chloroform-respiring Dehalobacter isolates

Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases

The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics

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