Single-taxon field measurements of bacterial gene regulation controlling DMSP fate

Abstract

The 'bacterial switch' is a proposed regulatory point in the global sulfur cycle that routes dimethylsulfoniopropionate (DMSP) to two fundamentally different fates in seawater through genes encoding either the cleavage or demethylation pathway, and affects the flux of volatile sulfur from ocean surface waters to the atmosphere. Yet which ecological or physiological factors might control the bacterial switch remains a topic of considerable debate. Here we report the first field observations of dynamic changes in expression of DMSP pathway genes by a single marine bacterial species in its natural environment. Detection of taxon-specific gene expression in Roseobacter species HTCC2255 during a month-long deployment of an autonomous ocean sensor in Monterey Bay, CA captured in situ regulation of the first gene in each DMSP pathway (dddP and dmdA) that corresponded with shifts in the taxonomy of the phytoplankton community. Expression of the demethylation pathway was relatively greater during a high-DMSP-producing dinoflagellate bloom, and expression of the cleavage pathway was greater in the presence of a mixed diatom and dinoflagellate community. These field data fit the prevailing hypothesis for bacterial DMSP gene regulation based on bacterial sulfur demand, but also suggest a modification involving oxidative stress response, evidenced as upregulation of catalase via katG, when DMSP is demethylated.

The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol

“…We investigated transcription changes using Affymetrix 14 microarrays and observed no significant changes in the expression of DMSP catabolic pathway 15 genes between HTCC1062 cells grown in the presence and absence of DMSP (see 16 Supplementary Note II). Since no changes in transcription were observed, we used isobaric tags 17 for relative and absolute quantitation (iTRAQ) to compare the proteomes of HTCC1062 18 cultures grown in the presence and absence of DMSP, confirming that proteins for both 19 pathways of DMSP catabolism are expressed constitutively (Fig. S7, Table S2).…”

“…However the presence of an alternate gene, DddP, that has weak 15 DMSP lyase activity in most SAR11 Ia.3 strains, suggests that further investigations of the 16 phenotypes of live strains will be needed before the distribution of DMSP metabolism across 17 the clade is fully understood. 18 Metabolic reconstruction with eight Pelagibacterales genomes revealed that, consistent 19 with the observation of MeSH production in HTCC1062, this and other examined 20 Pelagibacterales strains, except those in the distantly related subclade IIIa, contain homologs 7 of the dmdABC genes found in Ruegeria pomeroyi 20 ( Fig.…”

“…As predicted, E. coli transformants containing cloned HIMB5_00000220 (dddQ) 13 displayed DMSP lyase activity (Km was 56 mM, Vmax was 0.78 µmol min -1 mg protein -1 ). Strain 14 HTCC7211 and the more distantly related subclade V strain HIMB59 lacked dddK homologues, 15 but encoded gene products (respectively PB7211_1082 and HIMB59_00005110) that are ~30% 16 identical to DddP, a DMSP lyase in the M24 family of metallo-peptidases 17,18 . However, E. coli 17 transformants containing cloned PB7211_1082 (dddP-like) showed very low DMSP lyase 18 activity (0.5 ± 0.1 nmol min -1 mg -1 ), and therefore this protein may not be bona fide DMSP 19 lyases.…”

“…Strain 14 HTCC7211 and the more distantly related subclade V strain HIMB59 lacked dddK homologues, 15 but encoded gene products (respectively PB7211_1082 and HIMB59_00005110) that are ~30% 16 identical to DddP, a DMSP lyase in the M24 family of metallo-peptidases 17,18 . However, E. coli 17 transformants containing cloned PB7211_1082 (dddP-like) showed very low DMSP lyase 18 activity (0.5 ± 0.1 nmol min -1 mg -1 ), and therefore this protein may not be bona fide DMSP 19 lyases. 20 We compared the abundance of the Pelagibacterales genes for DMSP cleavage with those 21 for demethylation (dmdABC) in the Global Ocean Survey (GOS) metagenomic dataset ( Fig.…”

Deciphering ocean carbon in a changing world

“…For example, the first marine bacterial gene mediating catabolism of dimethylsulfoniopropionate (DMSP), a compound known for 50 y to be critical in the global sulfur cycle, was found in 2006 by generating transposon mutants of a marine bacterium (92), and the first phytoplankton gene mediating synthesis of DMSP was found in 2015 by shotgun proteomics of phytoplankton isolates (93). A full suite of DMSP gene discoveries is now enabling studies of the dominant transformation pathways and their regulation in the ocean (94,95). Similarly, the genes mediating marine bacterial transport and metabolism of organic compounds such as sulfonates (90,96), ectoine and hydroxyectoine (97), and methylamines and choline (31,98,99) have been recently elucidated through model organism systems.…”