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

Kirkwood, Mark; Brun, Nick E. Le; Todd, Jonathan D.; Johnston, Andrew

doi:10.1099/mic.0.038927-0

Cited by 51 publications

(61 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…strain K (likely P. globosa) by Stefels & Dijkhuizen (1996), but are within the range of that previously reported for in vitro DMSP lyase activity in other prymnesiophyte extracts, including 3 different strains of Gephyrocapsa oceanica (pH 5) (Franklin et al 2010) and 4 strains of Emiliania huxleyi (pH 4 to 6) (Steinke et al 1998(Steinke et al , 2000. The lyases from P. globosa and P. antarctica also had lower pH optima than found in the green macroalga Ulva curvata (pH 8) (de Souza et al 1996), or in the bacteria Roseovarius nubinhibens (pH 6) (Kirkwood et al 2010) and Alcaligenes sp. strain M3A (pH 8) (de Souza & Yoch 1995a).…”

Section: Resultssupporting

confidence: 84%

“…They have been found in marine algae, including phytoplankton (Steinke et al , 1998, and in a variety of different bacteria (de Souza & Yoch 1995a) in which 6 different DMSP lyase proteins (DddD, DddL, DddP, DddQ, DddW and DddY) have been identified (Todd et al 2007, Curson et al 2008, Kirkwood et al 2010. All these proteins except DddD catalyze cleavage of DMSP into acrylate and DMS.…”

Section: Resale or Republication Not Permitted Without Written Consenmentioning

confidence: 99%

“…The proteins of bacterial DMSP lyase, DddL, DddQ and DddW contain metal binding cupin pockets (Curson et al 2008. However, the DddP protein of the bacterium Roseovarius nubinhibens was not affected by EDTA, indicating no requirement of a metal cofactor for DMSP lyase activity (Kirkwood et al 2010). It was reported that the in vitro DMSP lyase activity in the alga Polysiphonia paniculata (Nishiguchi & Goff 1995) was partially inhibited by EDTA, PMSF and pCMB, and was not affected by Ca 2+ and Mg…”

mentioning

confidence: 99%

See 2 more Smart Citations

Comparative functional characteristics of DMSP lyases extracted from polar and temperate Phaeocystis species

Mohapatra¹,

Rellinger²,

Kieber³

et al. 2013

Aquat. Biol.

View full text Add to dashboard Cite

Members of the marine phytoplankton genus Phaeocystis (Prymnesiophyceae) produce large amounts of the intracellular osmolyte DMSP and they are known to also produce lyase enzymes that cleave DMSP into the biogeochemically important trace gas DMS. The functional characteristics of DMSP lyase activity in Phaeocystis spp. are not well known. We characterized DMSP lyase activity in extracts from 2 ecologically important species from this genus, the mesophile P. globosa (strain CCMP629) and the psychrophile P. antarctica (strain CCMP1374). Results from whole cell extracts showed that both algal species were potent producers of DMSP lyase, with Michaelis-Menten constant (K m ) and maximum reaction velocity (V max , respectively, for P. antarctica. The optimal DMSP lyase activity was recorded at pH 4 and 30°C for P. globosa, and at pH 5 and 20°C for P. antarctica. The half-life of the DMSP lyase of P. globosa was 210 min at 25°C, which was longer than that of the P. antarctica enzyme (61.9 min). First-order kinetic analysis of DMSP lyase thermal denaturation demonstrated that the activation energy, free energy, enthalpy and entropy of denaturation in P. antarctica extracts were lower than for P. globosa extracts, confirming that the P. antarctica DMSP lyase was more thermolabile than the lyase from the temperate strain. Inhibitor tests with metals, a chelator (EDTA) and a serine binding agent (PMSF) suggested that the DMSP lyases from both Phaeocystis species were metalloenzymes with serine and sulfhydryl groups at the active site. The acidic pH optima for the Phaeocystis strains are consistent with findings from other Prymnesiophyceae, and we speculate that this may reflect adaptation to an acidic sub-cellular location for the DMSP lyase. KEY WORDS:Dimethylsulfide · Dimethylsulfoniopropionate · DMSP · DMSP lyase · Prymnesiophyte · Psychrophile Resale or republication not permitted without written consent of the publisherAquat Biol 18: 185-195, 2013 186 via the enzyme DMSP demethylase to 3-(methylmercapto) propionic acid (MMPA). In a subsequent reaction, MMPA either undergoes demethylation to form 3-mercaptopropionic acid and/or demethiolation to form methanethiol (Reisch et al. 2011). In the second pathway, DMSP lyase (EC 4.4.1.3) catalyzes the lysis of DMSP into dimethylsulfide (DMS), acrylate and a proton. There is worldwide interest in evaluating the biochemical and molecular mechanisms involved in the regulation of enzymatic cleavage of DMSP to DMS because DMS is an important component of the global sulfur cycle and a potential climate-active trace gas. DMS is supersaturated in all surface ocean waters and, once transferred to the atmosphere, it rapidly oxidizes to dimethylsulfoxide, methanesulfonate (MSA) or sulfate. Sulfur-containing, acidic aerosols derived from these compounds can affect the Earth's climate system by scattering incoming sunlight and contributing to the population of aerosol particles that act as cloud condensation nuclei (Charlson et al. 1987, Simó 2001.DMSP lyases are the key...

show abstract

Section: Resultssupporting

confidence: 84%

Section: Resale or Republication Not Permitted Without Written Consenmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Comparative functional characteristics of DMSP lyases extracted from polar and temperate Phaeocystis species

Mohapatra¹,

Rellinger²,

Kieber³

et al. 2013

Aquat. Biol.

View full text Add to dashboard Cite

show abstract

“…HTCC2181 lacks the tdm gene required for TMAO metabolism, but it can oxidize TMAO to CO 2 , as demonstrated previously (12). Similarly, multiple enzymes responsible for the cleavage of the compatible osmolyte dimethylsulfoniopropionate into the climate-active gas dimethylsulfide have now been identified (36,49).…”

Section: Discussionmentioning

confidence: 69%

Trimethylamine N -oxide metabolism by abundant marine heterotrophic bacteria

Lidbury

Murrell

Chen

2014

Proc. Natl. Acad. Sci. U.S.A.

136

191

View full text Add to dashboard Cite

Trimethylamine N-oxide (TMAO) is a common osmolyte found in a variety of marine biota and has been detected at nanomolar concentrations in oceanic surface waters. TMAO can serve as an important nutrient for ecologically important marine heterotrophic bacteria, particularly the SAR11 clade and marine Roseobacter clade (MRC). However, the enzymes responsible for TMAO catabolism and the membrane transporter required for TMAO uptake into microbial cells have yet to be identified. We show here that the enzyme TMAO demethylase (Tdm) catalyzes the first step in TMAO degradation. This enzyme represents a large group of proteins with an uncharacterized domain (DUF1989). The function of TMAO demethylase in a representative from the SAR11 clade (strain HIMB59) and in a representative of the MRC (Ruegeria pomeroyi DSS-3) was confirmed by heterologous expression of tdm (the gene encoding Tdm) in Escherichia coli. In R. pomeroyi, mutagenesis experiments confirmed that tdm is essential for growth on TMAO. We also identified a unique ATP-binding cassette transporter (TmoXWV) found in a variety of marine bacteria and experimentally confirmed its specificity for TMAO through marker exchange mutagenesis and lacZ reporter assays of the promoter for genes encoding this transporter. Both Tdm and TmoXWV are particularly abundant in natural seawater assemblages and actively expressed, as indicated by a number of recent metatranscriptomic and metaproteomic studies. These data suggest that TMAO represents a significant, yet overlooked, nutrient for marine bacteria. (1) and is predicted to have a number of important physiological roles (2). In marine elasmobranchs (sharks and rays), TMAO accumulates at high concentrations (up to 500 mM), helping to offset the destabilizing effects of urea on cellular proteins (1, 3, 4). TMAO can be metabolized to small methylated amines, for example, tri-, di-, and monomethylamine (TMA, DMA, and MMA, respectively). These volatile organic N compounds are precursors of marine aerosols and the potent greenhouse gas nitrous oxide in the marine atmosphere (5). In anoxic sediments or pockets of hypoxic conditions, such as in marine snow, they are precursors for the potent greenhouse gas methane (6). In marine surface waters, TMAO concentrations can reach up to 79 nM; however, owing to the technical difficulties associated with quantifying TMAO in seawater, reports of in situ concentrations of TMAO are limited (7,8). In a previously published study in which TMAO and TMA were quantified in the marine environment, TMAO had a higher average concentration throughout the water column and over a seasonal cycle (8).TMAO is a well-studied terminal electron acceptor for anaerobic microbial respiration (9, 10), but its catabolism in aerobic surface seawater is not well understood. Recent studies have shown that TMAO in the Sargasso Sea is predominantly oxidized by bacterioplankton as an energy source (11) and that the marine methylotrophic bacterium Methylophilales sp. HTCC2181 oxidizes TMAO to CO 2 to generate energy (1...

show abstract

“…Indeed, some individual bacterial strains have multiple ways to catabolize DMSP. For example, Ruegeria pomeroyi DSS-3 contains DmdA, the DMSP demethylase (Howard et al, 2006), plus two genes, dddQ and dddP, that encode DMSP lyases that cleave DMSP into DMS plus acrylate, although they are in wholly different polypeptide families (Todd et al, 2009Kirkwood et al, 2010).…”

mentioning

confidence: 99%

DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria pomeroyi DSS-3

et al. 2011

Self Cite

View full text Add to dashboard Cite

Ruegeria pomeroyi DSS-3 is a model Roseobacter marine bacterium, particularly regarding its catabolism of dimethylsulfoniopropionate (DMSP), an abundant anti-stress molecule made by marine phytoplankton. We found a novel gene, dddW, which encodes a DMSP lyase that cleaves DMSP into acrylate plus the environmentally important volatile dimethyl sulfide (DMS). Mutations in dddW reduced, but did not abolish DMS production. Transcription of dddW was greatly enhanced by pre-growth of cells with DMSP, via a LysR-type regulator. Close DddW homologs occur in only one other Roseobacter species, and there are no close homologs and only a few related sequences in metagenomes of marine bacteria. In addition to DddW, R. pomeroyi DSS-3 had been shown to have two other, different, DMSP lyases, DddP and DddQ, plus an enzyme that demethylates DMSP, emphasizing the importance of this substrate for this model bacterium.

show abstract

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

Cited by 51 publications

References 36 publications

Comparative functional characteristics of DMSP lyases extracted from polar and temperate Phaeocystis species

Comparative functional characteristics of DMSP lyases extracted from polar and temperate Phaeocystis species

Trimethylamine N -oxide metabolism by abundant marine heterotrophic bacteria

DddW, a third DMSP lyase in a model Roseobacter marine bacterium, Ruegeria pomeroyi DSS-3

Contact Info

Product

Resources

About