Diversity of Cobalamin Riboswitches in the Corrinoid-Producing Organohalide Respirer Desulfitobacterium hafniense

Abstract

The strategic adaptation of prokaryotes in polluted niches involves the efficient regulation of their metabolism. The obligate anaerobe and metabolically versatile Desulfitobacterium hafniense reductively dechlorinates halogenated organic compounds (socalled organohalides). Some D. hafniense strains carry out organohalide respiration (OHR), a process which requires the use of corrinoid as a cofactor in reductive dehalogenases, the key enzymes in OHR. We report here the diversity of the cobalamin riboswitches that possibly regulate the corrinoid metabolism for D. hafniense. The analysis of available D. hafniense genomes indicates the presence of 18 cobalamin riboswitches located upstream of genes whose products are mainly involved in corrinoid biosynthesis and transport. To obtain insight into their function, the secondary structures of three of these RNA elements were predicted by Mfold, as well as analyzed by in-line probing. These RNA elements both display diversity in their structural elements and exhibit various affinities toward adenosylcobalamin that possibly relates to their role in the regulation of corrinoid metabolism. Furthermore, adenosylcobalamin-induced in vivo repression of RNA synthesis of the downstream located genes indicates that the corrinoid transporters and biosynthetic enzymes in D. hafniense strain TCE1 are regulated at the transcriptional level. Taken together, the riboswitch-mediated regulation of the complex corrinoid metabolism in D. hafniense could be of crucial significance in environments polluted with organohalides both to monitor their intracellular corrinoid level and to coexist with corrinoid-auxotroph OHR bacteria.

Ecophysiology and environmental distribution of organohalide-respiring bacteria

“…Desulfitobacterium hafniense [74,301] or Geobacter lovleyi [128] cyanocobalamin to support optimal TCE dechlorination rates and growth yield [324], a value that is similar to what was observed for D. restrictus. Therefore, and in addition to the ecogenomic biomarkers defined by Maphosa et al [13], one could consider the physiological threshold of corrinoid concentration as a possible diagnostic tool to delineate the reductive dechlorination potential by corrinoid-auxotrophic OHRB in anaerobic environments.…”

“…Corrinoid co-factors were found in all studied reductive dehalogenases except for the chlorobenzoate RDase functionally characterized from Desulfomonile tiedjei that harbors a heme cofactor [255]. Some facultative OHRB such as Sulfurospirillum multivorans [297], Geobacter lovleyi [128] and Desulfitobacterium hafniense [74,301] [67,261]. Cobalamin is routinely supplied in the growth media during the isolation and maintenance of D. restrictus PER-K23 T in the laboratory, and it is tempting to speculate that the frameshift mutation in cbiH gene arose during long-term cultivation under cobalamin-rich conditions, and decay of the corrinoid biosynthesis pathway as an unused but costly trait.…”

“…These five sequences were manually refined in a similar way as done previously for the Cbl-RS sequences of Desulfitobacterium hafniense [301]. The alignment of structurally conserved regions of D.…”

“…Sequence maximum likelihood tree analysis was done with MEGA5 [307]. Cobalamin riboswitches (Cbl-RS) were identified using Rfam [308] and initially aligned using ClustalX and then corrected manually as described earlier [301]. Comparative genome analysis was performed using the Artemis…”

“…Functional genomics of corrinoid starvation in the organohalide-respiring bacterium Dehalobacter restrictus strain PER-K23 [20,74,301,302].…”