Functional genomics of corrinoid starvation in the organohalide-respiring bacterium Dehalobacter restrictus strain PER-K23.

Aamani Rupakula,Julien Maillard,Sjef Boeren,Yue Lu,Hauke Smidt,Thomas Kruse,Christof Holliger

doi:10.3389/fmicb.2014.00751

Abstract

De novo corrinoid biosynthesis represents one of the most complicated metabolic pathways in nature. Organohalide-respiring bacteria (OHRB) have developed different strategies to deal with their need of corrinoid, as it is an essential cofactor of reductive dehalogenases, the key enzymes in OHR metabolism. In contrast to Dehalococcoides mccartyi, the genome of Dehalobacter restrictus strain PER-K23 contains a complete set of corrinoid biosynthetic genes, of which cbiH appears to be truncated and therefore non-functional, possibly explaining the corrinoid auxotrophy of this obligate OHRB. Comparative genomics within Dehalobacter spp. revealed that one (operon-2) of the five distinct corrinoid biosynthesis associated operons present in the genome of D. restrictus appeared to be present only in that particular strain, which encodes multiple members of corrinoid transporters and salvaging enzymes. Operon-2 was highly up-regulated upon corrinoid starvation both at the transcriptional (346-fold) and proteomic level (46-fold on average), in line with the presence of an upstream cobalamin riboswitch. Together, these data highlight the importance of this operon in corrinoid homeostasis in D. restrictus and the augmented salvaging strategy this bacterium adopted to cope with the need for this essential cofactor.

Highlights

Corrinoids are essential cofactors for a wide variety of enzymes that facilitate reactions including rearrangements, methyl group transfers, and reductive dehalogenation (Banerjee and Ragsdale, 2003)
The corrinoid present in the PCE reductive dehalogenase (PceA) of D. restrictus is presumably similar to the type added to the medium, i.e., cobalamin (Maillard et al, 2003)
The pathway can be divided in two branches, namely the upper corrinoid biosynthesis (UCB) and the nucleotide loop assembly (NLA), which are connected at the level of ado-cobyric acid

Summary

Introduction

Corrinoids are essential cofactors for a wide variety of enzymes that facilitate reactions including rearrangements, methyl group transfers, and reductive dehalogenation (Banerjee and Ragsdale, 2003). A recent bioinformatic study has revealed that while 76% of 540 sequenced bacterial genomes contain corrinoid-dependent enzymes, only 39% of these genomes encode the complete corrinoid biosynthesis pathway, suggesting that the salvage of corrinoids from the environment is an important process for many bacteria (Zhang et al, 2009). Both aerobic and anaerobic corrinoid biosynthesis pathways have been described showing few but significant differences, notably in tetrapyrrole ring contraction and the step at which cobalt is inserted into the ring (Scott, 2003; Moore and Warren, 2012). Corrinoid biosynthesis and salvaging in OHRB regained substantial interest in the scientific community as exemplified by the following studies: an unusual corrinoid cofactor (norpseudo-B12) has been identified in the tetrachloroethene (PCE) RDase of Sulfurospirillum multivorans (Kräutler et al, 2003); the lack of exogenous corrinoid had an effect on the RDase activity of Desulfitobacterium hafniense when cultivated with an alternative electron acceptor (Reinhold et al, 2012); many essential corrinoid biosynthetic genes have been found www.frontiersin.org

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