Genome Sequence, Proteome Profile, and Identification of a Multiprotein Reductive Dehalogenase Complex in Dehalogenimonas alkenigignens Strain BRE15M

Abstract

Bacteria of the genus Dehalogenimonas respire with vicinally halogenated alkanes via dihaloelimination. We aimed to describe involved proteins and their supermolecular organization. Metagenomic sequencing of a Dehalogenimonas-containing culture resulted in a 1.65 Mbp draft genome of Dehalogenimonas alkenigignens strain BRE15M. It contained 31 full-length reductive dehalogenase homologous genes (rdhA), but only eight had cognate rdhB gene coding for membrane-anchoring proteins. Shotgun proteomics of cells grown with 1,2-dichloropropane as an electron acceptor identified 1152 proteins representing more than 60% of the total proteome. Ten RdhA proteins were detected, including a DcpA ortholog, which was the strongest expressed RdhA. Blue native gel electrophoresis (BNE) demonstrating maximum activity was localized in a protein complex of 146–242 kDa. Protein mass spectrometry revealed the presence of DcpA, its membrane-anchoring protein DcpB, two hydrogen uptake hydrogenase subunits (HupL and HupS), an iron–sulfur protein (HupX), and subunits of a redox protein with a molybdopterin-binding motif (OmeA and OmeB) in the complex. BNE after protein solubilization with different detergent concentrations revealed no evidence for an interaction between the putative respiratory electron input module (HupLS) and the OmeA/OmeB/HupX module. All detected RdhAs comigrated with the organohalide respiration complex. Based on genomic and proteomic analysis, we propose quinone-independent respiration in Dehalogenimonas.

Dual C–Br Isotope Fractionation Indicates Distinct Reductive Dehalogenation Mechanisms of 1,2-Dibromoethane in Dehalococcoides- and Dehalogenimonas-Containing Cultures

“…Two enrichment cultures with different bacterial populations were used for in vivo laboratory batch experiments with respiring cells. The Dehalogenimonas-containing culture used in this study was derived from sediments obtained from the Besòs River (Spain); the genome of this strain was recently sequenced and annotated, and it was denominated Dehalogenimonas alkenigignens strain BRE15M . The composition of this consortium is shown in the Supporting Information (Figure S1).…”

“…The Dehalogenimonas -containing culture used in this study was derived from sediments obtained from the Besòs River (Spain); the genome of this strain was recently sequenced and annotated, and it was denominated Dehalogenimonas alkenigignens strain BRE15M. 27 The composition of this consortium is shown in the Supporting Information ( Figure S1 ). Further information regarding enzymatic assays with cell suspensions, cell harvesting, DNA extraction, and 16S rRNA gene amplicon sequencing is provided in Supporting Information .…”

Respiratory protein interactions in Dehalobacter sp. strain 8M revealed through genomic and native proteomic analyses

“…Another explanation for the occurrence of the RdhA protein in the 150 kDa region is that RdhA is part of a larger respiratory complex. Such a respiratory multiprotein complex has been found in Dehalococcoides mccartyi strain CBDB1 (Kublik et al, 2016) and Dehalogenimonas alkenigignens strain BRE15M (Trueba-Santiso et al, 2021). In these complexes, however, a complex iron-sulfurmolybdoprotein (CISM) acts as a scaffold or relay for electron transport between hydrogenase and reductive dehalogenase, obviating quinone involvement.…”

Dehalogenimonas etheniformans sp. nov., a formate-oxidizing, organohalide-respiring bacterium isolated from grape pomace

“…A shared feature of sequenced Dehalogenimonas and Dehalococcoides genomes is the presence of multiple, nonidentical reductive dehalogenase A (rdhA) genes [5,[20][21][22][23][24][25][26][27][28][29]. Dehalococcoides mccartyi 195 T and the type strains of previously described species of the genus Dehalogenimonas harbour between 18 and 29 rdhA genes (Table 1).…”