Crystal structure of Adenylylsulfate reductase from Desulfovibrio gigas suggests a potential self-regulation mechanism involving the C terminus of the beta-subunit

Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn's disease development

BACKGROUND

H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.

RESULTS

Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.

CONCLUSIONS

Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Video Abstract.

Reaction Mechanism Catalyzed by the Dissimilatory Sulfite Reductase - The Role of the Siroheme-[4FeS4] Cofactor

The present work is another part of our investigation on the pathway of dissimilatory sulfate reduction and covers a theoretical study on the reaction catalyzed by dissimilatory sulfite reductase (dSIR). dSIR is the terminal enzyme involved in this metabolic pathway, which uses the siroheme-[4Fe4S] cofactor for six-electron reduction of sulfite to sulfide. In this study we use a large cluster model containing siroheme-[4Fe4S] cofactor and protein residues involved in the direct interactions with the substrate, to get insight into the most feasible reaction mechanism and to understand the role of each considered active site component. In combination with earlier studies reported in the literature, our results lead to several interesting insights. One of the most important conclusions is that the reaction mechanism consists of three steps of two-electron reduction of sulfur and the probable role of the siroheme-[4Fe4S] cofactor is to ensure the delivery of packages of two electrons to the reactant.

Metaproteogenomic Profile of a Mesopelagic Adenylylsulfate Reductase: Course-Based Discovery Using the Ocean Protein Portal

Adenylylsulfate reductase (Apr) is a flavoprotein with a dissimilatory sulfate reductase function. Its ability to catalyze the reverse reaction in sulfur oxidizers has propelled a complex phylogenetic history of transfers with sulfate reducers and made this enzyme an important protein in ocean sulfur cycling. As part of a graduate course, we analyzed metaproteomic data from the Ocean Protein Portal and observed evidence of Apr alpha (AprA) and beta (AprB) subunits in the Central Pacific Ocean. The protein was originally taxonomically attributed toChlorobium tepidum TLS, a green sulfur bacterium. However, our phylogenomic and oceanographic contextual analysis contradicted this label, instead showing that this protein is consistent with the genomic material from the newly discovered Candidatus Lambdaproteobacteriaclass, implying that the ecological role of this lineage in oxygen minimum twilight zones is underappreciated. This study illustrates how metaproteogenomic analysis can contribute to more accurate metagenomic/proteomic annotations and comprehensive ocean biogeochemical processes conducive to course-based research experiences.

Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus

Methanothermococcus thermolithotrophicus is the only known methanogen that grows on sulfate as its sole sulfur source, uniquely uniting methanogenesis and sulfate reduction. Here we use physiological, biochemical and structural analyses to provide a snapshot of the complete sulfate reduction pathway of this methanogenic archaeon. We find that later steps in this pathway are catalysed by atypical enzymes. PAPS (3'-phosphoadenosine 5'-phosphosulfate) released by APS kinase is converted into sulfite and 3'-phosphoadenosine 5'-phosphate (PAP) by a PAPS reductase that is similar to the APS reductases of dissimilatory sulfate reduction. A non-canonical PAP phosphatase then hydrolyses PAP. Finally, the F₄₂₀-dependent sulfite reductase converts sulfite to sulfide for cellular assimilation. While metagenomic and metatranscriptomic studies suggest that the sulfate reduction pathway is present in several methanogens, the sulfate assimilation pathway in M. thermolithotrophicus is distinct. We propose that this pathway was 'mix-and-matched' through the acquisition of assimilatory and dissimilatory enzymes from other microorganisms and then repurposed to fill a unique metabolic role.

A novel sulfate-reducing and nitrogen-fixing bacterium Fundidesulfovibrio soli sp. nov., isolated from paddy soils

A strictly anaerobic sulfate-reducing strain, designated SG60^T, was isolated from paddy soil collected in Fujian Province, China. Growth of strain SG60^T was observed at 20-37 °C, pH 5.5-10.0 and 0-0.7% (w/v) NaCl. Strain SG60^T showed the highest 16S rRNA sequence similarities to the type strains of Fundidesulfovibrio magnetotacticus FSS-1^T (97.2%) and Fundidesulfovibrio putealis DSM 16056^T (96.4%). Phylogenetic trees based on the16S rRNA sequence and genome-based phylogenomic tree constructed using 120 core genes showed that strain SG60^T clustered with members of the genus Fundidesulfovibrio. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain SG60^T and the most closely related type strain F. magnetotacticus were 78.2% and 21.6%, respectively. Strain SG60^T contained MK-7 as the main respiratory quinone and anteiso-C_15:0, anteiso-C_17:1 ω9c, iso-C_16:0 and iso-C_16:1 H as the major fatty acids. Strain SG60^T produced desulfoviridin and possessed genes (nifHDK) encoding functions involved in nitrogen fixation. The genomic DNA G + C content was 65.5%. Based on the observed physiological properties, chemotaxonomic characteristics and ANI and dDDH values, strain SG60^T represents a novel species of the genus Fundidesulfovibrio, for which the name Fundidesulfovibrio soli sp. nov. is proposed. The type strain is SG60^T (= GDMCC 1.3310^T = JCM 35676^T).

Mechanism of Changes in Goaf Water Hydrogeochemistry: A Case Study of the Menkeqing Coal Mine

Goaf water in mining areas is widely found in China's coal mines. To clarify the hydrogeochemical characteristics of goaf water and the influence mechanism of water-rock interaction and further reveal microbial action on the formation of goaf water quality, the goaf water in the Menkeqing coal mine was taken as the object, and physical modeling was used to simulate the process of the real goaf changing from an oxygen-sufficient environment to an anoxic environment with the rise of groundwater level in this work. The experimental results showed that the water-rock interaction in the goaf was mainly the dissolution-precipitation of minerals in the rocks of the caving zone and fracture zone, cation exchange, and oxidation of pyrite in the coal layer. The primary sources of Na⁺ and K⁺ in the goaf water were the dissolution and reverse ion exchange of silicate minerals such as albite and potassium feldspar, while Ca²⁺ and Mg²⁺ mainly from the dissolution of minerals such as calcium feldspar, calcite, and chlorite. The oxidation of pyrite in coal was the main reason for the increase in SO₄^2- concentration, the enhancement of reduction, and the decrease in pH and DO (dissolved oxygen) in the goaf water. Relative abundance of sulfate-reducing bacteria (SRB) in goaf (e.g., Desulfosporosinus, Desulfobacterium, etc.) increased gradually, inhibiting the increase in SO₄^2- concentration in goaf water through the devulcanization of SRB. The inverse hydrogeochemical modeling was performed using PHREEQC for two stages of the simulation experiment: 0-30 days and 30-300 days. The simulation results show that the water-rock action in the formation of goaf water mainly occurred in the simulation experiment's early stage (0-30 days), and the mineral dissolution is dominant throughout the experimental stage. The results of the study provide a theoretical reference for the prediction of highly mineralized water pollution in goaf and its prevention and control.

Molecular dynamics simulations of aqueous systems of inhibitor candidates for adenosine-5’-phosphosufate reductase

Molecular dynamics (MD) simulations were used to evaluate some chelating agents as potential candidates to inhibitors for dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Molecular docking methods were used to evaluate the best binding modes of these molecules to the enzyme at two binding sites: of the substrate (enzyme active site) by mean the redocking protocol of substrate; and of one of the [Fe₄S₄]²⁺ groups by mean of the clusterization protocol. The best docking poses were selected by criteria such as low energy and RMSD (redocking) and the cluster with the higher number of similar poses (clusterization), which were submitted to MD simulations. RMSD, RDF, and hydrogen bonds results revelated that all ligands left the cube site, while in the active site, some ligands remained in their docking region, pointing to the enzyme active site as the best target for the selected ligands. The binding energy results of ligands hydroxamic acid (HXA) and catechol (CAT) showed that they bonded favorably to the enzyme and key residues of the active site contributed significantly to the protein-ligand bind, indicating HAX and CAT may compete with the substrate for interactions with these residues and displaying potential as candidates for experimental studies about APSrAB inhibitors.Communicated by Ramaswamy H. Sarma.

Development of parameters compatible with the CHARMM36 force field for [Fe4S4]2+ clusters and molecular dynamics simulations of adenosine-5'-phosphosulfate reductase in GROMACS 2019

DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [Fe₄S₄]²⁺ that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [Fe₄S₄]²⁺ through the CHARMM36 force field.

Reaction mechanism catalyzed by the dissimilatory adenosine 5'-phosphosulfate reductase. Adenosine 5'-monophosphate inhibitor and key role of arginine 317 in switching the course of catalysis

The present research is a continuation of our work on dissimilatory reduction pathway of sulfate - involved in biogeochemical sulfur turnover. Adenosine 5'-phosphosulfate reductase (APSR) is the second enzyme in the dissimilatory pathway of the sulfate to sulfide reduction. It reversibly catalyzes formation of the sulfite anion (HSO₃^-) from adenosine 5'-phosphosulfate (APS) - the activated form of sulfate provided by ATP sulfurylase (ATPS). Two electrons required for this redox reaction derive from reduced FAD cofactor, which is suggested to be involved directly in the catalysis by formation of FADH-SO₃^- intermediate. The present work covers quantum-mechanical (QM) studies on APSR reaction performed for eight models of APSR active site. The cluster models were constructed based on two crystal structures (PDB codes: 2FJA and 2FJB), differing in conformation of Arg317 active site residue. The described results indicated the most feasible mechanism of APSR forward reaction, including formation of FADH_N-SO₃^- adduct (with proton on N5 atom of isoalloxazine), tautomerization of FADH_N-SO₃^- to FADH_O-SO₃^- (with proton on CO moiety of isoalloxazine), and its reductive cleavage to oxidized FAD and sulfite anion. The reverse reaction proceeds in the backward direction. It is suggested that it requires two AMP molecules, one acting as a substrate and another as an inhibitor of forward reaction, which forces change of Arg317 conformation from "arginine in" (2FJA) to "arginine out" (2FJB). Important role of Arg317 in switching the course of the APSR catalytic reaction is revealed by changing the direction of thermodynamic driving force. The presented research also shows the importance of the protonation pattern of the reduced FAD cofactor and protein residues within the active site.

Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation

To solve the competition problem of acidophilic bacteria and sulfate-reducing bacteria in the practical application of mine tailing bioremediation, research into the mechanisms of using different nutrients to adjust the microbial community was conducted. Competition experiments involving acidophilic bacteria and sulfate-reducing bacteria were performed by supplementing the media with yeast extract, tryptone, lactate, and glucose. The physiochemical properties were determined, and the microbial community structure and biomass were investigated using MiSeq sequencing and qRT-PCR, respectively. Four nutrients had different remediation mechanisms and yielded different remediation effects. Yeast extract and tryptone (more than 1.6 g/L) promoted sulfate-reducing bacteria and inhibited acidophilic bacteria. Lactate inhibited both sulfate-reducing and acidophilic bacteria. Glucose promoted acidophilic bacteria more than sulfate-reducing bacteria. Yeast extract was the best choice for adjusting the microbial community and bioremediation, followed by tryptone. Lactate kept the physiochemical properties stable or made slight improvements; however, glucose was not suitable for mine tailing remediation. Different nutrients had significant effects on the abundance of the second enzyme of the sulfate-reducing pathway (p < 0.05), which is the rate-limiting step of sulfate-reducing pathways. Nutrients changed the remediation effects effectively by adjusting the microbial community and the abundance of the sulfate-reducing rate-limiting enzyme.

Electron transfer between the QmoABC membrane complex and adenosine 5'-phosphosulfate reductase

The dissimilatory adenosine 5'-phosphosulfate reductase (AprAB) is a key enzyme in the sulfate reduction pathway that catalyzes the reversible two electron reduction of adenosine 5'-phosphosulfate (APS) to sulfite and adenosine monophosphate (AMP). The physiological electron donor for AprAB is proposed to be the QmoABC membrane complex, coupling the quinone-pool to sulfate reduction. However, direct electron transfer between these two proteins has never been observed. In this work we demonstrate for the first time direct electron transfer between the Desulfovibrio desulfuricans ATCC 27774 QmoABC complex and AprAB. Cyclic voltammetry conducted with the modified Qmo electrode and AprAB in the electrolyte solution presented the Qmo electrochemical signature with two additional well-defined one electron redox processes, attributed to the AprAB FAD redox behavior. Moreover, experiments performed under catalytic conditions using the QmoABC modified electrode, with AprAB and APS in solution, show a catalytic current peak develop in the cathodic wave, attributed to substrate reduction, and which is not observed in the absence of QmoABC. Substrate dependence conducted with different electrode preparations (with and without immobilized Qmo) demonstrated that the QmoABC complex is essential for efficient electron delivery to AprAB, in order to sustain catalysis. These results confirm the role of Qmo in electron transfer to AprAB.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.

The sulfate-rich and extreme saline sediment of the ephemeral tirez lagoon: a biotope for acetoclastic sulfate-reducing bacteria and hydrogenotrophic methanogenic archaea

Our goal was to examine the composition of methanogenic archaea (MA) and sulfate-reducing (SRP) and sulfur-oxidizing (SOP) prokaryotes in the extreme athalassohaline and particularly sulfate-rich sediment of Tirez Lagoon (Spain). Thus, adenosine-5′-phosphosulfate (APS) reductase α (aprA) and methyl coenzyme M reductase α (mcrA) gene markers were amplified given that both enzymes are specific for SRP, SOP, and MA, respectively. Anaerobic populations sampled at different depths in flooded and dry seasons from the anoxic sediment were compared qualitatively via denaturing gradient gel electrophoresis (DGGE) fingerprint analysis. Phylogenetic analyses allowed the detection of SRP belonging to Desulfobacteraceae, Desulfohalobiaceae, and Peptococcaceae in ∂-proteobacteria and Firmicutes and SOP belonging to Chromatiales/Thiotrichales clade and Ectothiorhodospiraceae in γ-proteobacteria as well as MA belonging to methylotrophic species in Methanosarcinaceae and one hydrogenotrophic species in Methanomicrobiaceae. We also estimated amino acid composition, GC content, and preferential codon usage for the AprA and McrA sequences from halophiles, nonhalophiles, and Tirez phylotypes. Even though our results cannot be currently conclusive regarding the halotolerant strategies carried out by Tirez phylotypes, we discuss the possibility of a plausible “salt-in” signal in SRP and SOP as well as of a speculative complementary haloadaptation between salt-in and salt-out strategies in MA.