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ABSTRACT: Anaerobic trichloroethene-dechlorinating enrichment culture

PROVIDER: PRJNA1172988 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR30995600_1.fastq.gz	Fastqsanger.gz
	SRR30995600_2.fastq.gz	Fastqsanger.gz
	SRR30995601_1.fastq.gz	Fastqsanger.gz
	SRR30995601_2.fastq.gz	Fastqsanger.gz
	SRR30995602_1.fastq.gz	Fastqsanger.gz

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Project description:The aim of this study is to obtain a systems level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven draft genomes were binned from the metagenomes. At an early stage (2 d), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment with exogenous cobalamin compared to the one without cobalamin addition. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid-producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted qPCR analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin. Furthermore, Dehalococcoides' corrinoid salvaging and modification pathway was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles of members of dechlorinating communities under cobalamin-limited conditions.

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Project description:The organohalide-respiring Sulfurospirillum multivorans uses chlorinated ethenes as electron acceptors for growth under anoxic conditions. However, little is known about the interaction of these substrates with proteins. Here, we apply thermal proteome profiling (TPP) to analyze enzyme-trichloroethene interactions. TPP is commonly used to investigate protein-ligand binding through protein melting curve shifts. Several modifications in the protocol, e.g. performing the incubation under anaerobic conditions and increasing the temperature range up to 97°C, improved the detection range and allowed the investigation of oxygen-sensitive proteins. Enzymatic reductive dehalogenation was prevented by omitting the electron donor during incubations. This enabled detecting the interaction of the tetrachloroethene reductive dehalogenase PceA with trichloroethene and confirms the enzyme’s specificity for this substrate. Another 19 proteins showed significant melting curve shifts with trichloroethene, pointing to other proteins directly or indirectly interacting with trichloroethene. Interestingly, a putative response regulator reacted similarly towards trichloroethene, which is potentially in line with its proposed role in regulating trichloroethene respiration. The TPP approach is here proven to facilitate the identification of substrate-enzyme interactions of strictly anaerobic reductive dehalogenases and probably their regulators. This strategy can be used to identify yet unknown substrate specificities and potential signal-sensing proteins in other difficult to study bacteria.

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