Structures of dimethylsulfoniopropionate‐dependent demethylase from the marine organism <i>Pelagabacter ubique</i>

Schüller, David; Reisch, Chris R.; Moran, Mary Ann; Whitman, William B.; Lanzilotta, William N.

doi:10.1002/pro.2015

Cited by 28 publications

(44 citation statements)

References 33 publications

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“…Roseobacters are a group of abundant marine bacteria known to demethylate DMSP, and Pelagibacter belongs to the SAR11 clade, whose members are highly dominant organisms in marine ecosystems, that are also well known to demethylate DMSP [11] and for which the dmdA protein structure is described. [59] The low sequence variation detected in our clone libraries, and the fact that a large fraction of bacterial dmdA taxonomic diversity was shared between all three coral host species sampled, suggest the absence of endemic dmdA assemblages or strict species-specific coral niches for DMSP demethylating bacteria within the surface mucus layer of corals. A recent study comparing free-living v. particle-associated bacterial dmdA assemblages found that most dmdA genes were shared between these two habitats, [42] again suggesting no niche diversification of dmdA gene assemblages towards distinct habitats.…”

Section: Phylogenetic Affiliation Of Bacterial Dmda Gene Assemblages mentioning

confidence: 73%

Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

Frade¹,

Schwaninger²,

Glasl³

et al. 2016

Environ. Chem.

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Environmental context. Corals produce copious amounts of dimethylsulfoniopropionate (DMSP), a sulfur compound implicated in climate regulation. We studied DMSP concentrations inside corals and unveiled the linkage between DMSP availability and the abundance of DMSP-degrading bacterial groups inhabiting the corals' surface. Our findings suggest that DMSP mediates the interplay between corals and microbes, highlighting the importance of sulfur compounds for microbial processes in corals and for the resilience of coral reef ecosystems.Abstract. Corals produce copious amounts of dimethylsulfoniopropionate (DMSP), a sulfur compound thought to play a role in structuring coral-associated bacterial communities. We tested the hypothesis that a linkage exists between DMSP availability in coral tissues and the community dynamics of bacteria in coral surface mucus. We determined DMSP concentrations in three coral species (Meandrina meandrites, Porites astreoides and Siderastrea siderea) at two sampling depths (5 and 25 m) and times of day (dawn and noon) at Curaçao, Southern Caribbean. DMSP concentration (4-409 nmol cm À2 coral surface) varied with host species-specific traits such as Symbiodinium cell abundance, but not with depth or time of sampling. Exposure of corals to air caused a doubling of their DMSP concentration. The phylogenetic affiliation of mucus-associated bacteria was examined by clone libraries targeting three main subclades of the bacterial DMSP demethylase gene (dmdA). dmdA gene abundance was determined by quantitative Polymerase Chain Reaction (qPCR) against a reference housekeeping gene (recA). Overall, a higher availability of DMSP corresponded to a lower relative abundance of the dmdA gene, but this pattern was not uniform across all host species or bacterial dmdA subclades, suggesting the existence of distinct DMSP microbial niches or varying dmdA DMSP affinities. This is the first study quantifying dmdA gene abundance in corals and linking related changes in the community dynamics of DMSP-degrading bacteria to DMSP availability. Our study suggests that DMSP mediates the regulation of microbes by the coral host and highlights the significance of sulfur compounds for microbial processes in coral reefs.

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Section: Phylogenetic Affiliation Of Bacterial Dmda Gene Assemblages mentioning

confidence: 73%

Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

Frade¹,

Schwaninger²,

Glasl³

et al. 2016

Environ. Chem.

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“…(B) Although overall architecture and H 4 folate conformation is conserved, LigM and its homologs differ to some degree in the precise folateprotein interactions that they use. Homologs shown for comparison include dimethylsulfoniopropionate(DMSP)-dependent demethylase (DmdA), which catalyzes the transfer of a methyl from DMSP to H 4 folate-N 5 (PDB ID code: 3TFJ) (27); Tm_T, a glycine cleavage system T-protein that catalyzes the formation of 5,10-methylene-H 4 folate and ammonia from an H-proteinassociated aminomethyl moiety (PDB ID code: 1WOO) (11); and dimethylglycine oxidase (DMGO), which oxidizes N,N-dimethyl glycine to form 5,10-methylene-H 4 folate (PDB ID code: 1PJ7) (20). Key interaction residues are shown in bold black type for LigM, in red type for DmdA, in blue type for Tm_T, and in green type for DMGO.…”

Section: Resultsmentioning

confidence: 99%

“…Beyond LigM's unconventional use of glutamine residues in binding H 4 folate, there are several additional striking differences between the residue topology of LigM's H 4 folate-binding site and those of its closest structural homologs Tm_T (rmsd: 2.4 Å, 23% sequence identity) (11); Arthrobacter globiformis dimethylglycine oxidase (DMGO) (rmsd: 2.7 Å, 21% sequence identity) (20); and dimethylsulfoniopropionate (DMSP)-dependent demethylase (DmdA) (rmsd: 3.2 Å, 20% sequence identity) (27). Notably, LigM contains phenylalanines (Phe110, Phe188) and a tryptophan (Trp256) in place of three key Tm_T tyrosines (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Utilization of a tryptophan for H 4 folate binding is unique to LigM. DmdA also contains a tryptophan (Trp197); however Trp197 plays a greater role in facilitating an interaction with DmdA's second substrate, DMSP, than it does with H 4 folate (27). Furthermore, LigM differs in the residue composition of the innermost portion of the H 4 folate-binding cavity.…”

Section: Resultsmentioning

confidence: 99%

“…Markedly different, LigM contains Tyr247 in this position, which, at 5.65 Å from H 4 folate, is not poised for direct interaction with H 4 folate. In DmdA, this innermost region of the channel houses Ser122, which interacts directly with H 4 folate at N 1 , N 8 , and the pteridine amine and is expected to greatly influence the nucleophilicity of H 4 folate-N 5 (27). These differences in pteridine ring coordination may reflect differences in precise mechanism and target substrates of these enzymes, quite possibly influencing the nucleophilic strength of H 4 folate-N 5 (LigM, DmdA) or N 5 /N 10 (Tm_T, DMGO) and suggesting differences in both the mechanism and mode of priming H 4 folate-N 5 for nucleophilic attack.…”

Section: Resultsmentioning

confidence: 99%

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Structure of arylO-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

Kohler

Mills

Adams

et al. 2017

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

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Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, was previously available. LigM-catalyzed demethylation enables further modification and ring opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. Here, we characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. These results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.demethylase | biocatalysis | aryl metabolism | tetrahydrofolate | lignin D emethylation reactions are found throughout biology, impacting a wide range of cellular processes from metabolism and energy generation to genetic imprinting and DNA repair (1-3). Reflective of such extensive application, there is an immense diversity in the mechanisms used by demethylases, the enzymes responsible for catalyzing methyl transfer reactions. Intriguingly, only roughly 1% of identified demethylases have been characterized at a structural level (4), and those that have vary substantially in protein fold, making it difficult to discern the structural basis and catalytic determinants for this key biocatalytic process based on function alone.Aryl demethylation is of particular interest because it is an essential first step in the modification, and ultimately metabolism, of aromatic compounds under aerobic conditions. Because of its importance, a wide variety of aryl demethylase systems have been identified from aryl compound-using soil and marine bacteria. These organisms are uniquely capable of metabolizing aromatic waste and natural breakdown products such as those derived f...

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Aerobic Bacterial Catabolism of Dimethylsulfoniopropionate

Boden

Hutt

2018

Aerobic Utilization of Hydrocarbons, Oils and Lipids

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Dimethylsulfoniopropionate (DMSP) is an organosulfur zwitterion produced by various marine algae and Bacteria as an osmolyte, cryoprotectant, defense molecule, and antioxidant. In the marine environment in particular, it can be degraded by the Bacteria in various ways. In this chapter we cover the biochemistry and physiology of the various pathways of DMSP catabolism, including the three core enzymes DMSP dethiomethylase (EC 4.4.1.3, the so-called DMSP lyase), DMSP demethylase (EC 2.1.1.269), and DMSP CoA transferase/lyase (EC 2.3.1.x). Six isoenzyme classes of DMSP dethiomethylase have been purified and confirmed in marine Bacteria thus far, with a further isoenzyme found in algae that may also occur in Bacteriathese are all discussed in detail. Methodologies for enzyme assays and the synthesis of DMSP hydrochloride are given, including those for radio-and stable-isotope labelling.

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Structures of dimethylsulfoniopropionate‐dependent demethylase from the marine organism Pelagabacter ubique

Abstract: Dimethylsulfoniopropionate (DMSP) is a ubiquitous algal metabolite and common carbon and sulfur source for marine bacteria.

Cited by 28 publications

References 33 publications

Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

Dimethylsulfoniopropionate in corals and its interrelations with bacterial assemblages in coral surface mucus

Structure of arylO-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

Aerobic Bacterial Catabolism of Dimethylsulfoniopropionate

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