Genome analysis of Thauera chlorobenzoica strain 3CB-1T, a halobenzoate-degrading bacterium isolated from aquatic sediment

Louie, Tiffany S.; Pavlik, Elizabeth Jane; Häggblom, Max M.

doi:10.1007/s00203-021-02497-y

Cited by 7 publications

(1 citation statement)

References 40 publications

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“…The fact that R. palustris CGA009 Δ badM can grow on 3-CBA indicates that native CoA ligases have activity against 3-CBA. This is surprising because the ability to degrade 3-CBA is thought to be restricted to bacterial strains that encode a CoA ligase that has increased activity with 3-CBA (6, 18). R. palustris CGA009 and RCB100 encode three CoA ligases involved in anaerobic aromatic compound degradation: benzoyl-CoA ligase, BadA 4-hydroxybenzoyl-CoA ligase, HbaA; and cyclohexanecarboxylate-CoA ligase, AliA.…”

Section: Discussionmentioning

confidence: 99%

Evolution ofRhodopseudomonas palustristo degrade halogenated aromatic compounds involves changes in pathway regulation and enzyme specificity

Haq,

Christensen,

Fixen

2023

Preprint

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Halogenated aromatic compounds are used in a variety of industrial applications but can be harmful to humans and animals when released into the environment. Microorganisms that degrade halogenated aromatic compounds anaerobically have been isolated but the evolutionary path that they may have taken to acquire this ability is not well understood. A strain of the purple nonsulfur bacterium,Rhodopseudomonas palustris, RCB100, can use 3-chlorobenzoate (3-CBA) as a carbon source whereas a closely related strain, CGA009, cannot. To reconstruct the evolutionary events that enabled RCB100 to degrade 3-CBA, we selected for and isolated a CGA009 strain capable of growing on 3-CBA, although not as well as RCB100. Comparative whole-genome sequencing of the evolved strain and RCB100 revealed large deletions encompassingbadM, a transcriptional repressor of genes for anaerobic benzoate degradation. It was previously shown that in strain RCB100, a single nucleotide change in an alicyclic acid coenzyme A ligase gene, namedaliA, gives rise to a variant AliA enzyme that has high activity with 3-CBA. When we introduced the RCB100aliAallele and abadMdeletion intoR. palustrisCGA009, it grew on 3-CBA at a similar rate as RCB100. This work provides an example of pathway evolution that includes a variant of a promiscuous enzyme with enhanced substrate specificity and a regulatory mutation that leads to constitutive expression of a pathway that does not regulate the promiscuous enzyme.ImportanceBiodegradation of man-made compounds often involves the activity of promiscuous enzymes whose native substrate is structurally similar to the man-made compound. Based on the enzymes involved, it is possible to predict what microorganisms are likely involved in biodegradation of anthropogenic compounds. However, there are examples of organisms that contain the required enzyme(s) and yet cannot metabolize these compounds. We found that even when the purple nonsulfur bacterium,Rhodopseudomonas palustris, encodes all the enzymes required for degradation of a halogenated aromatic compound, it is unable to metabolize that compound. Using adaptive evolution, we found a regulatory mutation and a variant of promiscuous enzyme with increased substrate specificity were required, but the ability to metabolize a halogenated aromatic compound also resulted in reduced fitness on another aromatic compound. This work provides insight into how an environmental isolated evolved to use halogenated aromatic compounds and the potential ecological trade-offs associated with this adaptation.

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Section: Discussionmentioning

confidence: 99%

Evolution ofRhodopseudomonas palustristo degrade halogenated aromatic compounds involves changes in pathway regulation and enzyme specificity

Haq,

Christensen,

Fixen

2023

Preprint

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Naturally Occurring Organohalogen Compounds—A Comprehensive Review

Gribble

2023

Progress in the Chemistry of Organic Natural Products

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Characterization by 16S Amplicon Sequencing of Bacterial Communities Overall and During the Maturation Process of Peloids in Two Spas of an Italian Thermal Complex

Paduano,

Marchesi,

Valeriani

et al. 2024

Microb Ecol

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Peloids are made by mixing clay materials with thermo-mineral waters, enriched with organic substances from microorganisms during maturation. Their beneficial properties may depend on clay minerals, water characteristics, and microbial components, although strong evidence is lacking. Next Generation Sequencing (NGS) allows a comprehensive approach to studying the entire microbial community, including cultivable and uncultivable bacteria. Our study aims to characterize, by NGS, the bacterial community overall and during the maturation process of thermal muds in two spas (A-B) of an Italian thermal complex. Peloids were produced from sulfurous-bromine-iodine thermal water and clay material: natural mud for spa A and sterile clay for spa B. Thermal waters and peloids at different maturation stages (2/4/6 months) were analyzed for microbiome characterization by 16S amplicon sequencing. Biodiversity profiles showed a low level of similarity between peloids and water used for their maturation. Peloids from spa A showed greater microbial richness than those from spa B, suggesting that natural mud with an existing bacterial community leads to greater biodiversity than sterile clay. Genera involved in sulfur metabolism were prevalent in both spas, as expected considering peloids matured in sulfide-rich water. For all three maturation stages, the prevalent genera were Thiobacillus and Pelobacter in spa A and Thiobacillus , Thauera , Pelobacter , and Desulfuromonas in spa B. Richness and diversity indices showed that the community seemed to stabilize after 2–4 months. The 16S amplicon sequencing to study bacterial communities enables the identification of a biological signature that characterizes a specific thermal matrix, defining its therapeutic and cosmetic properties. The bacterial composition of peloids is affected by the thermal water and the type of clay material used in their formulation and maturation. Supplementary Information The online version contains supplementary material available at 10.1007/s00248-024-02469-x.

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Genome analysis of Thauera chlorobenzoica strain 3CB-1T, a halobenzoate-degrading bacterium isolated from aquatic sediment

Cited by 7 publications

References 40 publications

Evolution ofRhodopseudomonas palustristo degrade halogenated aromatic compounds involves changes in pathway regulation and enzyme specificity

Evolution ofRhodopseudomonas palustristo degrade halogenated aromatic compounds involves changes in pathway regulation and enzyme specificity

Naturally Occurring Organohalogen Compounds—A Comprehensive Review

Characterization by 16S Amplicon Sequencing of Bacterial Communities Overall and During the Maturation Process of Peloids in Two Spas of an Italian Thermal Complex

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