Identification of a functional dddD‐Rh for dimethyl sulfide production in the Antarctic Rhodococcus sp. NJ‐530

Abstract

Dimethylsulfoniopropionate (DMSP) is widespread in the oceans, and its biological metabolite, dimethyl sulfide (DMS), plays an important role in the atmosphere. The Antarctic region has become a hotspot in DMS studies due to the high spatial and temporal variability in DMS(P) concentration, but the level of bacterial DMS production remains unclear. In this study, a bacterium isolated from Antarctic floating ice, Rhodococcus sp. NJ‐530, was found to metabolize DMSP into DMS, and the rate of DMS production was measured as 3.96 pmol·mg protein−1·h−1. Rhodococcus sp. NJ‐530 had a DddD‐Rh enzyme containing two CaiB domains, which belonged to the CoA‐transferase III superfamily. However, the DddD‐Rh had a molecular weight of 73.21 kDa, which was very different from previously characterized DddD enzymes in sequence and evolution. In vitro assays showed that DddD‐Rh was functional in the presence of acetyl‐CoA. This was the first functional DddD from Gram‐positive Actinobacteria. Moreover, a quantitative real‐time polymerase chain reaction revealed that high temperature facilitated the expression of dddD‐Rh, and changes of salinity had little effect on it. This study adds new evidence to the bacterial DMS production in the Southern Ocean and provides a basis for investigating the metabolic mechanism of DMSP in extreme environments.

Recent insights into oceanic dimethylsulfoniopropionate biosynthesis and catabolism

“…Recently, a DddD‐Rh enzyme encoded by dddD‐Rh gene found on the plasmid Actinobacteria Rhodococcus sp. NJ‐530 has been identified and it is very distant from the known DMSP lyase DddD in sequence and evolution (Wang et al ., 2020). The crystal structure of DMSP lyase DddD has not been resolved yet, and the structural homology using Swiss‐Model (Arnold et al ., 2006) identified DddD's active site residues.…”

“…According to this, the anticipated topology of DddD lyase enzyme is made up of two CaiB‐like intertwined domains joined through a long polypeptide linker. This model also suggested that the C‐domain contains the catalytic aspartate that performs CoA transfer in all class III CoA‐transferases, whereas the N domain contains a short insertion (LGSSY, residues 165–169) (Alcolombri et al ., 2014; Wang et al ., 2020). A catalytic cycle has been purposed, in which DMSP and acetyl CoA react via an acetylated enzyme intermediate to form a DMSP covalent intermediate complex (DMSP–Enzyme CoASH), which can be employed in two alternative ways.…”