DddY is a bacterial dimethylsulfoniopropionate lyase representing a new cupin enzyme superfamily with unknown primary function

Abstract

Dimethylsulfide (DMS) is released at rates of >10 7 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms, release DMS via cleavage of dimethylsulfoniopropionate (DMSP). Different genes encoding proteins with DMSP lyase activity are known belonging to different superfamilies and exhibiting highly variable levels of DMSP lyase activity. DddY shows the highest activity among all reported bacterial lyases yet is poorly characterized. Here, we describe the characterization of recombinant DddY is from different marine bacteria. We found that DddY activity demands a transition metal ion cofactor. DddY also shares two sequence motifs with other bacterial lyases assigned as cupin-like enzymes, DddQ, DddL, DddK, and DddW. These cupin motif residues are essential for DddY activity, as for the other cupin DMSP lyases, and all these enzymes are characterized by a common metalchelator inhibitor (TPEN). Analysis of all sequences carrying these cupin motifs defined a superfamily: Cupin-DLL (DMSP lyases and lyase-like). The DMSP lyase families are sporadically distributed suggesting that DMSP lyases evolved within this superfamily independently along multiple lineages. However, the specific activity levels, genomic context analysis, and systematic profiling of substrate selectivity as described in the accompanying paper, indicate that for only some of these families, most distinctly DddY and DddL, DMSP lyase is the primary, native activity. In other families, foremost DddQ, DMSP lyase seems to be merely a promiscuous activity. The native function of DddQ, and of nearly all members of this newly identified Cupin-DLL superfamily, remains unknown.All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

Novel Insights Into Bacterial Dimethylsulfoniopropionate Catabolism in the East China Sea

“…KORDI-100, and one metagenome assembled Synechococcus genome ( Synechococcus sp. TMED20) (Lei et al, 2017) have a putative DMSP lyase gene, this being dddY -like gene. Thus, Cyanobacteria are not believed to be significant DMSP catabolisers.…”

Uptake of Dimethylsulfoniopropionate (DMSP) by Natural Microbial Communities of the Great Barrier Reef (GBR), Australia

“…To date, only one sequenced cyanobacterial strain, Synechococcus sp. KORDI-100, has been found to have a DMSP lyase gene [ 77 ]. Given that Prochlorococcus and SAR11 were present in high relative abundances at both sites, the fact that DMSP showed higher accumulated in the small fraction of the outer reef, suggests that rather than differences in microbial community composition, it was the metabolic state of the community driving this difference, whereby the bacterial community of the outer reef site were preferentially taking up DMSPd to meet their sulfur and carbon demands for growth [ 21 , 27 ].…”