Structural and molecular basis for the novel catalytic mechanism and evolution of <scp>DddP</scp>, an abundant peptidase‐like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold

Wang, Peng; Chen, Xiu-Lan; Li, Chun-Yang; Gao, Xiang; Zhu, Deyu; Xie, Bin-Bin; Qin, Qi‐Long; Zhang, Xiying; Su, Hai-Nan; Zhou, Biao; Xun, Luying; Zhang, Yuzhong

doi:10.1111/mmi.13119

Cited by 38 publications

(62 citation statements)

References 42 publications

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“…The crystal structures of DddP and DddQ from Ruegeria lacuscaerulensis and DddP from Roseobacter denitrificans have been solved (Li et al, 2013; Wang et al, 2015). Data gathered from the available structures suggests that subtle changes in the active sites of these lyases make sulfur containing substrates, like DMSP, the preferred substrates for these enzymes.…”

Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

“…Typically, an M24 peptidase hydrolyzes C-N bonds. DddP, however, cleaves C-S bonds (Todd et al, 2009; Wang et al, 2015). Wang and coworkers expressed the recombinant R. lacuscaerulensis dddP in E. coli and found it displayed no measurable activity toward the M24 peptidase substrate valine-proline, but it did exhibit DMSP lyase activity, producing acrylate and DMS (Wang et al, 2015).…”

Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

“…DddP, however, cleaves C-S bonds (Todd et al, 2009; Wang et al, 2015). Wang and coworkers expressed the recombinant R. lacuscaerulensis dddP in E. coli and found it displayed no measurable activity toward the M24 peptidase substrate valine-proline, but it did exhibit DMSP lyase activity, producing acrylate and DMS (Wang et al, 2015). DddP is a homodimeric protein in which one monomer has a metal center containing Fe, while the other monomer generally contains Fe, but may also contain Ni, Zn, or Cu instead (Hehemann et al, 2014; Wang et al, 2015).…”

Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

“…Wang and coworkers expressed the recombinant R. lacuscaerulensis dddP in E. coli and found it displayed no measurable activity toward the M24 peptidase substrate valine-proline, but it did exhibit DMSP lyase activity, producing acrylate and DMS (Wang et al, 2015). DddP is a homodimeric protein in which one monomer has a metal center containing Fe, while the other monomer generally contains Fe, but may also contain Ni, Zn, or Cu instead (Hehemann et al, 2014; Wang et al, 2015). The explanation for the change in substrate preference and activity appears to be due to the change of the active ion from Co or Mn coordinated by five residues in the M24 peptidases to Fe coordinated by six residues in DddP.…”

Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

“…The explanation for the change in substrate preference and activity appears to be due to the change of the active ion from Co or Mn coordinated by five residues in the M24 peptidases to Fe coordinated by six residues in DddP. The two metal ions in DddP are coordinated with three aspartates, two glutamates, and a histidine residue, which are conserved in the known functional DddPs (Hehemann et al, 2014; Wang et al, 2015). The substitution of any of the active site residues for alanine in DddP results in the elimination of DMSP lyase activity, indicating that all six are necessary for activity (Kirkwood et al, 2010; Wang et al, 2015).…”

Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

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Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria

2017

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The elucidation of the pathways for dimethylsulfoniopropionate (DMSP) synthesis and metabolism and the ecological impact of DMSP have been studied for nearly 70 years. Much of this interest stems from the fact that DMSP metabolism produces the climatically active gas dimethyl sulfide (DMS), the primary natural source of sulfur to the atmosphere. DMSP plays many important roles for marine life, including use as an osmolyte, antioxidant, predator deterrent, and cryoprotectant for phytoplankton and as a reduced carbon and sulfur source for marine bacteria. DMSP is hypothesized to have become abundant in oceans approximately 250 million years ago with the diversification of the strong DMSP producers, the dinoflagellates. This event coincides with the first genome expansion of the Roseobacter clade, known DMSP degraders. Structural and mechanistic studies of the enzymes of the bacterial DMSP demethylation and cleavage pathways suggest that exposure to DMSP led to the recruitment of enzymes from preexisting metabolic pathways. In some cases, such as DmdA, DmdD, and DddP, these enzymes appear to have evolved to become more specific for DMSP metabolism. By contrast, many of the other enzymes, DmdB, DmdC, and the acrylate utilization hydratase AcuH, have maintained broad functionality and substrate specificities, allowing them to carry out a range of reactions within the cell. This review will cover the experimental evidence supporting the hypothesis that, as DMSP became more readily available in the marine environment, marine bacteria adapted enzymes already encoded in their genomes to utilize this new compound.

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Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

Section: Enzymatic Cleavage Of Dmspmentioning

confidence: 99%

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Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria

2017

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

Wang

et al. 2020

J Basic Microbiol

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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.

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Sulfur isotope fractionations constrain the biological cycling of dimethylsulfoniopropionate in the upper ocean

Osorio-Rodriguez

Razo-Mejia

Dalleska

et al. 2021

Limnology & Oceanography

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The rapid turnover of dimethylsulfoniopropionate (DMSP), likely the most relevant dissolved organic sulfur compound in the surface ocean, makes it pivotal to understand the cycling of organic sulfur. Dimethylsulfoniopropionate is mainly synthesized by phytoplankton, and it can be utilized as carbon and sulfur sources by marine bacteria or cleaved by bacteria or algae to produce the volatile compound dimethylsulfide (DMS), involved in the formation of sulfate aerosols. The fluxes between the consumption (i.e., demethylation) and cleavage pathways are thought to depend on community interactions and their sulfur demand. However, a quantitative assessment of the sulfur partitioning between each of these pathways is still missing. Here, we report for the first time the sulfur isotope fractionations by enzymes involved in DMSP degradation with different catalytic mechanisms, expressed heterologously in Escherichia coli. We show that the residual DMSP from the demethylation pathway is 2.7‰ enriched in δ 34 S relative to the initial DMSP, and that the fractionation factor ( 34 ε) of the cleavage pathways varies between À1 and À9‰. The incorporation of these fractionation factors into mass balance calculations constrains the biological fates of DMSP in seawater, supports the notion that demethylation dominates over cleavage in marine environments, and could be used as a proxy for the dominant pathways of degradation of DMSP by marine microbial communities.

show abstract

Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase‐like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold

Cited by 38 publications

References 42 publications

Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria

Evolution of Dimethylsulfoniopropionate Metabolism in Marine Phytoplankton and Bacteria

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

Sulfur isotope fractionations constrain the biological cycling of dimethylsulfoniopropionate in the upper ocean

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