Molecular dissection of bacterial acrylate catabolism – unexpected links with dimethylsulfoniopropionate catabolism and dimethyl sulfide production

Abstract

A bacterium in the genus Halomonas that grew on dimethylsulfoniopropionate (DMSP) or acrylate as sole carbon sources and that liberated the climate-changing gas dimethyl sulfide in media containing DMSP was obtained from the phylloplane of the macroalga Ulva. We identified a cluster that contains genes specifically involved in DMSP catabolism (dddD, dddT) or in degrading acrylate (acuN, acuK) or that are required to break down both substrates (dddC, dddA). Using NMR and HPLC analyses to trace 13C- or 14C-labelled acrylate and DMSP in strains of Escherichia coli with various combinations of cloned ddd and/or acu genes, we deduced that DMSP is imported by the BCCT-type transporter DddT, then converted by DddD to 3-OH-propionate (3HP), liberating dimethyl sulfide in the process. As DddD is a predicted acyl CoA transferase, there may be an earlier, unidentified catabolite of DMSP. Acrylate is also converted to 3HP, via a CoA transferase (AcuN) and a hydratase (AcuK). The 3HP is predicted to be catabolized by an alcohol dehydrogenase, DddA, to malonate semialdehyde, thence by an aldehyde dehydrogenase, DddC, to acyl CoA plus CO2. The regulation of the ddd and acu genes is unusual, as a catabolite, 3HP, was a co-inducer of their transcription. This first description of genes involved in acrylate catabolism in any organism shows that the relationship between the catabolic pathways of acrylate and DMSP differs from that which had been suggested in other bacteria.

Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate

“…It therefore provides a more expansive view of the metabolic and taxonomic basis for microbial activities compared with prevailing methods such as PCR assays, microarray approaches and single-cell techniques that target specific genes, taxa or processes. In this study, the rapid enrichment of transcripts mediating degradation of propanoate-like compounds and tricarboxylic acid cycle activity from Sargasso Sea bacterioplankton groups not known to harbor orthologs to DMSP demethylation (Howard et al, 2008) or cleavage genes (Todd et al, 2007(Todd et al, , 2010Curson et al, 2008), provides evidence for the involvement of a greater number of marine taxa in DMSP degradation. This agrees with previous findings for DMSP-S assimilation using single-cell techniques (Vila et al, 2004;Malmstrom et al, 2004a), and suggests that Bacteroidetes, Betaproteobacteria and other bacterioplankton groups either have orthologs of known DMSP-degrading genes that are not being correctly assigned, or have nonhomologous genes with similar functions in DMSP degradation that have yet to be found.…”

“…The pattern of transcript enrichment after DMSP addition suggests that the most common degradation pathway of the C3 moiety of DMSP is to acetyl-CoA by malonyl-CoA (Figure 2, see abundances of propanoate-related transcripts in Supplementary Table S5), although this is likely to be taxon-dependent and possibly temporally variable. Studies of cultured DMSP-degrading marine strains suggest that roseobacters degrade C3 compounds derived from DMSP cleavage to succinyl-CoA through the methylmalonyl pathway (C Reisch and S Gifford, personal communication), whereas a marine gammaproteobacterium strain cleaves DMSP to acetyl-CoA through 3-OH-propionyl-CoA (Todd et al, 2010). All these pathways are possible and may co-occur in seawater.…”

“…In any case, the major pathway used by marine bacteria to synthesize amino acids from DMSP-S did not clearly emerge from this analysis. Both the DMSP demethylation and cleavage pathways yield a C3 compound, possibly acrylate (Kiene and Linn, 2000b), although recent studies suggest that acryloyl-CoA or 3-OH-propionate can also be intermediates (Curson et al, 2008;Todd et al, 2010). Studies of marine and freshwater isolates have shown that some bacteria can grow on acrylate by conversion to 3-OH-propionate (Kiene, 1990;Ansede et al, 1999Ansede et al, , 2001Yoch, 2002).…”

“…dddL encodes a DMSP lyase that cleaves DMSP to DMS (Curson et al, 2008). In contrast, dddD encodes an acyl-CoA transferase that converts DMSP to 3-OH-propionate and DMS (Todd et al, 2007(Todd et al, , 2010. Finally, dddP encodes a peptidase that converts DMSP to DMS through an unknown mechanism (Todd et al, 2009).…”

The dddP gene of Roseovarius nubinhibens encodes a novel lyase that cleaves dimethylsulfoniopropionate into acrylate plus dimethyl sulfide

“…Thus, the dddD gene was originally found in some gammaproteobacteria, including Halomonas, Marinomonas, Psychrobacter and Pseudomonas (Todd et al, 2007(Todd et al, , 2009bCurson et al, 2010), but was also likely transferred by horizontal gene transfer (HGT) to other bacteria, including some 'terrestrial' strains of rhizobia and Burkholderia (Todd et al, 2007). The DddD polypeptide product is in the family of class III CoA-transferases, and its action on DMSP generates DMS plus 3-hydroxypropionate (Todd et al, 2009b). In contrast, Curson et al (2008) found that dddL, which occurs in several marine alphaproteobacteria, encodes a 'DMSP lyase', an enzyme that cleaves DMSP into acrylate plus DMS and a proton (Cantoni & Anderson, 1956;Fig.…”