scholarly journals A novel ATP dependent dimethylsulfoniopropionate lyase in bacteria that releases dimethyl sulfide and acryloyl-CoA

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Chun-Yang Li ◽  
Xiu-Juan Wang ◽  
Xiu-Lan Chen ◽  
Qi Sheng ◽  
Shan Zhang ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Atmospheric Chemistry ◽  
Dimethyl Sulfide ◽  
Catalytic Mechanism ◽  
The Novel ◽  
Marine Environments ◽  
Biochemical Analyses ◽  
Bacteria And Fungi

Dimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule in marine environments with important roles in global sulfur and nutrient cycling. Diverse DMSP lyases in some algae, bacteria and fungi cleave DMSP to yield gaseous dimethyl sulfide (DMS), an infochemical with important roles in atmospheric chemistry. Here we identified a novel ATP-dependent DMSP lyase, DddX. DddX belongs to the acyl-CoA synthetase superfamily and is distinct from the eight other known DMSP lyases. DddX catalyses the conversion of DMSP to DMS via a two-step reaction: the ligation of DMSP with CoA to form the intermediate DMSP-CoA, which is then cleaved to DMS and acryloyl-CoA. The novel catalytic mechanism was elucidated by structural and biochemical analyses. DddX is found in several Alphaproteobacteria, Gammaproteobacteria and Firmicutes, suggesting that this new DMSP lyase may play an overlooked role in DMSP/DMS cycles.

scholarly journals Novel enzyme for dimethyl sulfide-releasing in bacteria reveals a missing route in the marine sulfur cycle

2020 ◽  
Author(s):  
Chun-Yang Li ◽  
Xiu-Juan Wang ◽  
Xiu-Lan Chen ◽  
Qi Sheng ◽  
Shan Zhang ◽  
...  
Keyword(s):  
Dimethyl Sulfide ◽  
Catalytic Mechanism ◽  
Global Climate ◽  
Sulfur Cycle ◽  
The Novel ◽  
Key Enzyme ◽  
Biochemical Analyses ◽  
Bacterial Lineages

AbstractDimethylsulfoniopropionate (DMSP) is an abundant and ubiquitous organosulfur molecule and plays important roles in the global sulfur cycle. Cleavage of DMSP produces volatile dimethyl sulfide (DMS), which has impacts on the global climate. Multiple pathways for DMSP catabolism have been identified. Here we identified yet another novel pathway, the ATP DMSP lysis pathway. The key enzyme, AcoD, is an ATP-dependent DMSP lyase. AcoD belongs to the acyl-CoA synthetase superfamily, which is totally different from other DMSP lyases, showing a new evolution route. AcoD catalyses the conversion of DMSP to DMS by a two-step reaction: the ligation of DMSP with CoA to form the intermediate DMSP-CoA, which is then cleaved to DMS and acryloyl-CoA. The novel catalytic mechanism was elucidated by structural and biochemical analyses. AcoD is widely distributed in many bacterial lineages including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Firmicutes, revealing this new pathway plays important roles in global DMSP/DMS cycles.

scholarly journals Oceanic phytoplankton are a potentially important source of benzenoids to the remote marine atmosphere

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Manon Rocco ◽  
Erin Dunne ◽  
Maija Peltola ◽  
Neill Barr ◽  
Jonathan Williams ◽  
...  
Keyword(s):  
Atmospheric Chemistry ◽  
Dimethyl Sulfide ◽  
Laboratory Culture ◽  
Marine Phytoplankton ◽  
Marine Atmosphere ◽  
Aerosol Formation ◽  
Incubation Experiments ◽  
Phytoplankton Communities ◽  
Anthropogenic Air Pollutants ◽  
Benzene Toluene

AbstractBenzene, toluene, ethylbenzene and xylenes can contribute to hydroxyl reactivity and secondary aerosol formation in the atmosphere. These aromatic hydrocarbons are typically classified as anthropogenic air pollutants, but there is growing evidence of biogenic sources, such as emissions from plants and phytoplankton. Here we use a series of shipborne measurements of the remote marine atmosphere, seawater mesocosm incubation experiments and phytoplankton laboratory cultures to investigate potential marine biogenic sources of these compounds in the oceanic atmosphere. Laboratory culture experiments confirmed marine phytoplankton are a source of benzene, toluene, ethylbenzene, xylenes and in mesocosm experiments their sea-air fluxes varied between seawater samples containing differing phytoplankton communities. These fluxes were of a similar magnitude or greater than the fluxes of dimethyl sulfide, which is considered to be the key reactive organic species in the marine atmosphere. Benzene, toluene, ethylbenzene, xylenes fluxes were observed to increase under elevated headspace ozone concentration in the mesocosm incubation experiments, indicating that phytoplankton produce these compounds in response to oxidative stress. Our findings suggest that biogenic sources of these gases may be sufficiently strong to influence atmospheric chemistry in some remote ocean regions.

scholarly journals Structural and Functional Analyses of Human ChaC2 in Glutathione Metabolism

Biomolecules ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 31 ◽  
Author(s):  
Yen T. K. Nguyen ◽  
Joon Sung Park ◽  
Jun Young Jang ◽  
Kyung Rok Kim ◽  
Tam T. L. Vo ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Cells ◽  
Catalytic Mechanism ◽  
Docking Study ◽  
Binding Mode ◽  
Structural Features ◽  
Glutathione Metabolism ◽  
Binding Assays ◽  
Biochemical Analyses ◽  
Functional Analyses

Glutathione (GSH) degradation plays an essential role in GSH homeostasis, which regulates cell survival, especially in cancer cells. Among human GSH degradation enzymes, the ChaC2 enzyme acts on GSH to form 5-l-oxoproline and Cys-Gly specifically in the cytosol. Here, we report the crystal structures of ChaC2 in two different conformations and compare the structural features with other known γ-glutamylcyclotransferase enzymes. The unique flexible loop of ChaC2 seems to function as a gate to achieve specificity for GSH binding and regulate the constant GSH degradation rate. Structural and biochemical analyses of ChaC2 revealed that Glu74 and Glu83 play crucial roles in directing the conformation of the enzyme and in modulating the enzyme activity. Based on a docking study of GSH to ChaC2 and binding assays, we propose a substrate-binding mode and catalytic mechanism. We also found that overexpression of ChaC2, but not mutants that inhibit activity of ChaC2, significantly promoted breast cancer cell proliferation, suggesting that the GSH degradation by ChaC2 affects the growth of breast cancer cells. Our structural and functional analyses of ChaC2 will contribute to the development of inhibitors for the ChaC family, which could effectively regulate the progression of GSH degradation-related cancers.

scholarly journals Crystal structures of γ-glutamylmethylamide synthetase provide insight into bacterial metabolism of oceanic monomethylamine

2020 ◽  
pp. jbc.RA120.015952
Author(s):  
Ning Wang ◽  
Xiu-Lan Chen ◽  
Chao Gao ◽  
Ming Peng ◽  
Peng Wang ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Catalytic Mechanism ◽  
Structural Information ◽  
Trace Gas ◽  
Microbial Genomes ◽  
Carbon And Nitrogen ◽  
Tetrahedral Intermediate ◽  
Surface Ocean ◽  
Biochemical Analyses ◽  
Global Carbon

Monomethylamine (MMA) is an important climate-active oceanic trace gas and ubiquitous in the oceans. The γ-glutamylmethylamide synthetase (GmaS) catalyzes the conversion of MMA to γ-glutamylmethylamide (GMA), the first step in MMA metabolism in many marine bacteria. The gmaS gene occurs in ~23% of microbial genomes in the surface ocean and is a validated biomarker to detect MMA-utilizing bacteria. However, the catalytic mechanism of GmaS has not been studied due to the lack of structural information. Here, the GmaS from Rhodovulum sp. 12E13 (RhGmaS) was characterized, and the crystal structures of apo-RhGmaS and RhGmaS with different ligands in five states were solved. Based on structural and biochemical analyses, the catalytic mechanism of RhGmaS was explained. ATP is first bound in RhGmaS, leading to a conformational change of a flexible loop (Lys287-Ile305), which is essential for the subsequent binding of glutamate. During the catalysis of RhGmaS, the residue Arg312 participates in polarizing the γ-phosphate of ATP and in stabilizing the γ-glutamyl phosphate intermediate; Asp177 is responsible for the deprotonation of MMA, assisting the attack of MMA on γ-glutamyl phosphate to produce a tetrahedral intermediate; and Glu186 acts as a catalytic base to abstract a proton from the tetrahedral intermediate to finally generate GMA. Sequence analysis suggested that the catalytic mechanism of RhGmaS proposed in this study has universal significance in bacteria containing GmaS. Our results provide novel insights into MMA metabolism, contributing to a better understanding of MMA catabolism in global carbon and nitrogen cycles.

scholarly journals Structure-Function Analysis Indicates that an Active-Site Water Molecule Participates in Dimethylsulfoniopropionate Cleavage by DddK

2019 ◽  
Vol 85 (8) ◽  
Author(s):  
Ming Peng ◽  
Xiu-Lan Chen ◽  
Dian Zhang ◽  
Xiu-Juan Wang ◽  
Ning Wang ◽  
...  
Keyword(s):  
Water Molecule ◽  
Active Site ◽  
Dimethyl Sulfide ◽  
Catalytic Mechanism ◽  
Heterotrophic Bacteria ◽  
Function Analysis ◽  
Cloud Condensation Nuclei ◽  
Oxidation Products ◽  
Condensation Nuclei ◽  
Marine Heterotrophic Bacteria

ABSTRACT The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram quantities in marine environments and has important roles in global sulfur and carbon cycling. Many marine microorganisms catabolize DMSP via DMSP lyases, generating the climate-active gas dimethyl sulfide (DMS). DMS oxidation products participate in forming cloud condensation nuclei and, thus, may influence weather and climate. SAR11 bacteria are the most abundant marine heterotrophic bacteria; many of them contain the DMSP lyase DddK, and their dddK transcripts are relatively abundant in seawater. In a recently described catalytic mechanism for DddK, Tyr64 is predicted to act as the catalytic base initiating the β-elimination reaction of DMSP. Tyr64 was proposed to be deprotonated by coordination to the metal cofactor or its neighboring His96. To further probe this mechanism, we purified and characterized the DddK protein from Pelagibacter ubique strain HTCC1062 and determined the crystal structures of wild-type DddK and its Y64A and Y122A mutants (bearing a change of Y to A at position 64 or 122, respectively), where the Y122A mutant is complexed with DMSP. The structural and mutational analyses largely support the catalytic role of Tyr64, but not the method of its deprotonation. Our data indicate that an active water molecule in the active site of DddK plays an important role in the deprotonation of Tyr64 and that this is far more likely than coordination to the metal or His96. Sequence alignment and phylogenetic analysis suggest that the proposed catalytic mechanism of DddK has universal significance. Our results provide new mechanistic insights into DddK and enrich our understanding of DMS generation by SAR11 bacteria. IMPORTANCE The climate-active gas dimethyl sulfide (DMS) plays an important role in global sulfur cycling and atmospheric chemistry. DMS is mainly produced through the bacterial cleavage of marine dimethylsulfoniopropionate (DMSP). When released into the atmosphere from the oceans, DMS can be photochemically oxidized into DMSO or sulfate aerosols, which form cloud condensation nuclei that influence the reflectivity of clouds and, thereby, global temperature. SAR11 bacteria are the most abundant marine heterotrophic bacteria, and many of them contain DMSP lyase DddK to cleave DMSP, generating DMS. In this study, based on structural analyses and mutational assays, we revealed the catalytic mechanism of DddK, which has universal significance in SAR11 bacteria. This study provides new insights into the catalytic mechanism of DddK, leading to a better understanding of how SAR11 bacteria generate DMS.

scholarly journals Global airborne microbial communities controlled by surrounding landscapes and wind conditions

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Romie Tignat-Perrier ◽  
Aurélien Dommergue ◽  
Alban Thollot ◽  
Christoph Keuschnig ◽  
Olivier Magand ◽  
...  
Keyword(s):  
Particulate Matter ◽  
High Altitude ◽  
Microbial Communities ◽  
Atmospheric Chemistry ◽  
Sampling Site ◽  
Temporal Stability ◽  
Fungal Species ◽  
The World ◽  
Bacteria And Fungi ◽  
Over Time

Abstract The atmosphere is an important route for transporting and disseminating microorganisms over short and long distances. Understanding how microorganisms are distributed in the atmosphere is critical due to their role in public health, meteorology and atmospheric chemistry. In order to determine the dominant processes that structure airborne microbial communities, we investigated the diversity and abundance of both bacteria and fungi from the PM10 particle size (particulate matter of 10 micrometers or less in diameter) as well as particulate matter chemistry and local meteorological characteristics over time at nine different meteorological stations around the world. The bacterial genera Bacillus and Sphingomonas as well as the fungal species Pseudotaeniolina globaosa and Cladophialophora proteae were the most abundant taxa of the dataset, although their relative abundances varied greatly based on sampling site. Bacterial and fungal concentration was the highest at the high-altitude and semi-arid plateau of Namco (China; 3.56 × 106 ± 3.01 × 106 cells/m3) and at the high-altitude and vegetated mountain peak Storm-Peak (Colorado, USA; 8.78 × 104 ± 6.49 × 104 cells/m3), respectively. Surrounding ecosystems, especially within a 50 km perimeter of our sampling stations, were the main contributors to the composition of airborne microbial communities. Temporal stability in the composition of airborne microbial communities was mainly explained by the diversity and evenness of the surrounding landscapes and the wind direction variability over time. Airborne microbial communities appear to be the result of large inputs from nearby sources with possible low and diluted inputs from distant sources.

PLP undergoes conformational changes during the course of an enzymatic reaction

2014 ◽  
Vol 70 (2) ◽  
pp. 596-606 ◽  
Author(s):  
Ho-Phuong-Thuy Ngo ◽  
Nuno M. F. S. A. Cerqueira ◽  
Jin-Kwang Kim ◽  
Myoung-Ki Hong ◽  
Pedro Alexandrino Fernandes ◽  
...  
Keyword(s):  
Conformational Change ◽  
Conformational Changes ◽  
Catalytic Mechanism ◽  
Enzymatic Reaction ◽  
Nucleophilic Attack ◽  
The Novel ◽  
X Ray ◽  
X Ray Crystallography ◽  
Starting Point ◽  
High Level

Numerous enzymes, such as the pyridoxal 5′-phosphate (PLP)-dependent enzymes, require cofactors for their activities. Using X-ray crystallography, structural snapshots of the L-serine dehydratase catalytic reaction of a bacterial PLP-dependent enzyme were determined. In the structures, the dihedral angle between the pyridine ring and the Schiff-base linkage of PLP varied from 18° to 52°. It is proposed that the organic cofactor PLP directly catalyzes reactions by active conformational changes, and the novel catalytic mechanism involving the PLP cofactor was confirmed by high-level quantum-mechanical calculations. The conformational change was essential for nucleophilic attack of the substrate on PLP, for concerted proton transfer from the substrate to the protein and for directing carbanion formation of the substrate. Over the whole catalytic cycle, the organic cofactor catalyzes a series of reactions, like the enzyme. The conformational change of the PLP cofactor in catalysis serves as a starting point for identifying the previously unknown catalytic roles of organic cofactors.

scholarly journals Conserved bases for the initial cyclase in gibberellin biosynthesis: from bacteria to plants

2019 ◽  
Vol 476 (18) ◽  
pp. 2607-2621 ◽  
Author(s):  
Cody Lemke ◽  
Kevin C. Potter ◽  
Samuel Schulte ◽  
Reuben J. Peters
Keyword(s):  
Catalytic Mechanism ◽  
Phylogenetic Analyses ◽  
Gibberellin Biosynthesis ◽  
Associated Bacteria ◽  
Functional Conservation ◽  
Microbe Interactions ◽  
Bacteria And Fungi ◽  
Product Outcome ◽  
Insight Into ◽  
Ga Biosynthesis

Abstract All land plants contain at least one class II diterpene cyclase (DTC), which utilize an acid-base catalytic mechanism, for the requisite production of ent-copalyl diphosphate (ent-CPP) in gibberellin A (GA) phytohormone biosynthesis. These ent-CPP synthases (CPSs) are hypothesized to be derived from ancient bacterial origins and, in turn, to have given rise to the frequently observed additional DTCs utilized in more specialized plant metabolism. However, such gene duplication and neo-functionalization has occurred repeatedly, reducing the utility of phylogenetic analyses. Support for evolutionary scenarios can be found in more specific conservation of key enzymatic features. While DTCs generally utilize a DxDD motif as the catalytic acid, the identity of the catalytic base seems to vary depending, at least in part, on product outcome. The CPS from Arabidopsis thaliana has been found to utilize a histidine-asparagine dyad to ligate a water molecule that serves as the catalytic base, with alanine substitution leading to the production of 8β-hydroxy-ent-CPP. Here this dyad and effect of Ala substitution is shown to be specifically conserved in plant CPSs involved in GA biosynthesis, providing insight into plant DTC evolution and assisting functional assignment. Even more strikingly, while GA biosynthesis arose independently in plant-associated bacteria and fungi, the catalytic base dyad also is specifically found in the relevant bacterial, but not fungal, CPSs. This suggests functional conservation of CPSs from bacteria to plants, presumably reflecting an early role for derived diterpenoids in both plant development and plant–microbe interactions, eventually leading to GA, and a speculative evolutionary scenario is presented.

scholarly journals Kinetics of dimethyl sulfide (DMS) reactions with isoprene-derived Criegee intermediates studied with direct UV absorption

2020 ◽  
Author(s):  
Mei-Tsan Kuo ◽  
Isabelle Weber ◽  
Christa Fittschen ◽  
Jim Jr-Min Lin
Keyword(s):  
Atmospheric Chemistry ◽  
Dimethyl Sulfide ◽  
Relative Rate ◽  
Chem Phys ◽  
High Reactivity ◽  
Rate Coefficients ◽  
Visible Absorption ◽  
Criegee Intermediates ◽  
The Individual ◽  
Kinetics Of

Abstract. Criegee intermediates (CIs) are formed in the ozonolysis of unsaturated hydrocarbons and play a role in atmospheric chemistry as a non-photolytic OH source or a strong oxidant. Using a relative rate method in an ozonolysis experiment, Newland et al. [Atmos. Chem. Phys., 15, 9521–9536, 2015] reported high reactivity of isoprene-derived Criegee intermediates towards dimethyl sulfide (DMS) relative to that towards SO2 with the ratio of the rate coefficients kDMS+CI / kSO2+CI = 3.5 ± 1.8. Here we reinvestigated the kinetics of DMS reactions with two major Criegee intermediates formed in isoprene ozonolysis, CH2OO and methyl vinyl ketone oxide (MVKO). The individual CI was prepared following reported photolytic method with suitable (diiodo) precursors in the presence of O2. The concentration of CH2OO or MVKO was monitored directly in real time through their intense UV-visible absorption. Our results indicate the reactions of DMS with CH2OO and MVKO are both very slow; the upper limits of the rate coefficients are 4 orders of magnitude smaller than that reported by Newland et al. These results suggest that the ozonolysis experiment could be complicated such that interpretation should be careful and these CIs would not oxidize atmospheric DMS at any substantial level.

scholarly journals Structural insights into TSC complex assembly and GAP activity on Rheb

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Huirong Yang ◽  
Zishuo Yu ◽  
Xizi Chen ◽  
Jiabei Li ◽  
Ningning Li ◽  
...  
Keyword(s):  
Tuberous Sclerosis ◽  
Catalytic Mechanism ◽  
Coiled Coil ◽  
Small Gtpase ◽  
Dimerization Domain ◽  
Gtp Hydrolysis ◽  
Complex Assembly ◽  
Complex Functions ◽  
Biochemical Analyses ◽  
Hydrolysis Of

AbstractTuberous sclerosis complex (TSC) integrates upstream stimuli and regulates cell growth by controlling the activity of mTORC1. TSC complex functions as a GTPase-activating protein (GAP) towards small GTPase Rheb and inhibits Rheb-mediated activation of mTORC1. Mutations in TSC genes cause tuberous sclerosis. In this study, the near-atomic resolution structure of human TSC complex reveals an arch-shaped architecture, with a 2:2:1 stoichiometry of TSC1, TSC2, and TBC1D7. This asymmetric complex consists of two interweaved TSC1 coiled-coil and one TBC1D7 that spans over the tail-to-tail TSC2 dimer. The two TSC2 GAP domains are symmetrically cradled within the core module formed by TSC2 dimerization domain and central coiled-coil of TSC1. Structural and biochemical analyses reveal TSC2 GAP-Rheb complimentary interactions and suggest a catalytic mechanism, by which an asparagine thumb (N1643) stabilizes γ-phosphate of GTP and accelerate GTP hydrolysis of Rheb. Our study reveals mechanisms of TSC complex assembly and GAP activity.

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