1
|
Bhattacharya A, Samanta S, Nath AK, Ghatak A, Dey SG, Dey A. Intermediates involved in the reduction of SO 2: insight into the mechanism of sulfite reductases. Chem Commun (Camb) 2024. [PMID: 38963718 DOI: 10.1039/d4cc02124j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
Sulfite reductases (SiRs) catalyze the reduction of SO32- to H2S in biosynthetic sulfur assimilation and dissimilation of sulfate. The mechanism of the 6e-/6H+ reduction of SO32- at the siroheme cofactor is debated, and proposed intermediates involved in this 6e- reduction are yet to be spectroscopically characterized. The reaction of SO2 with a ferrous iron porphyrin is investigated, and two intermediates are trapped and characterized: an initial Fe(III)-SO22- species, which undergoes proton-assisted S-O bond cleavage to form an Fe(III)-SO species. These species are characterized using a combination of resonance Raman (with 34S-labelled SO2), EPR and DFT calculations. Results obtained help reconcile the different proposed mechanisms for the SiRs.
Collapse
Affiliation(s)
- Aishik Bhattacharya
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A & 2B, Raja SC Mullick Road, Kolkata, West Bengal PIN-700032, India.
| | - Soumya Samanta
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A & 2B, Raja SC Mullick Road, Kolkata, West Bengal PIN-700032, India.
| | - Arnab Kumar Nath
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A & 2B, Raja SC Mullick Road, Kolkata, West Bengal PIN-700032, India.
| | - Arnab Ghatak
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A & 2B, Raja SC Mullick Road, Kolkata, West Bengal PIN-700032, India.
| | - Somdatta Ghosh Dey
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A & 2B, Raja SC Mullick Road, Kolkata, West Bengal PIN-700032, India.
| | - Abhishek Dey
- School of Chemical Sciences Indian Association for the Cultivation of Science, 2A & 2B, Raja SC Mullick Road, Kolkata, West Bengal PIN-700032, India.
| |
Collapse
|
2
|
Dalcin Martins P, de Monlevad JPC, Echeveste Medrano MJ, Lenstra WK, Wallenius AJ, Hermans M, Slomp CP, Welte CU, Jetten MSM, van Helmond NAGM. Sulfide Toxicity as Key Control on Anaerobic Oxidation of Methane in Eutrophic Coastal Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:11421-11435. [PMID: 38888209 PMCID: PMC11223495 DOI: 10.1021/acs.est.3c10418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
Coastal zones account for 75% of marine methane emissions, despite covering only 15% of the ocean surface area. In these ecosystems, the tight balance between methane production and oxidation in sediments prevents most methane from escaping into seawater. However, anthropogenic activities could disrupt this balance, leading to an increased methane escape from coastal sediments. To quantify and unravel potential mechanisms underlying this disruption, we used a suite of biogeochemical and microbiological analyses to investigate the impact of anthropogenically induced redox shifts on methane cycling in sediments from three sites with contrasting bottom water redox conditions (oxic-hypoxic-euxinic) in the eutrophic Stockholm Archipelago. Our results indicate that the methane production potential increased under hypoxia and euxinia, while anaerobic oxidation of methane was disrupted under euxinia. Experimental, genomic, and biogeochemical data suggest that the virtual disappearance of methane-oxidizing archaea at the euxinic site occurred due to sulfide toxicity. This could explain a near 7-fold increase in the extent of escape of benthic methane at the euxinic site relative to the hypoxic one. In conclusion, these insights reveal how the development of euxinia could disrupt the coastal methane biofilter, potentially leading to increased methane emissions from coastal zones.
Collapse
Affiliation(s)
- Paula Dalcin Martins
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Department
of Ecosystem and Landscape Dynamics, Institute for Biodiversity and
Ecosystem Dynamics (IBED), University of
Amsterdam, Amsterdam 1098 XH, The Netherlands
| | - João P.
R. C. de Monlevad
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Maider J. Echeveste Medrano
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Wytze Klaas Lenstra
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Utrecht 3584 CB, The Netherlands
| | - Anna Julia Wallenius
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Martijn Hermans
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Utrecht 3584 CB, The Netherlands
- Baltic
Sea Centre, Stockholm University, Stockholm 114 18, Sweden
| | - Caroline P. Slomp
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Utrecht 3584 CB, The Netherlands
| | - Cornelia Ulrike Welte
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Mike S. M. Jetten
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
| | - Niels A. G. M. van Helmond
- Department
of Microbiology, Radboud Institute for Biological and Environmental
Sciences, Radboud University, Nijmegen 6525 AJ, The Netherlands
- Department
of Earth Sciences—Geochemistry, Utrecht
University, Utrecht 3584 CB, The Netherlands
| |
Collapse
|
3
|
Esfahani BG, Walia N, Neselu K, Aragon M, Askenasy I, Wei A, Mendez JH, Stroupe ME. Dimerization of assimilatory NADPH-dependent sulfite reductase reveals elements for diflavin reductase binding at a minimal interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599029. [PMID: 38915618 PMCID: PMC11195156 DOI: 10.1101/2024.06.14.599029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Escherichia coli NADPH-dependent assimilatory sulfite reductase is responsible for fixing sulfur for incorporation into sulfur-containing biomolecules. The oxidoreductase is composed of two subunits, an NADPH, FMN, and FAD-binding diflavin reductase and an iron siroheme and Fe4S4-containing oxidase. How they interact has been an unknown for over 50 years because the complex is highly flexible, thus has been intransigent for traditional X-ray or cryo-EM structural analysis. Using a combination of the chameleon plunging system with a fluorinated lipid we overcame the challenge of preserving the minimal dimer between the subunits for high-resolution cryo-EM analysis. Here, we report the first structure of the complex between the reductase and oxidase, revealing how they interact in a minimal interface. Further, we determined the structural elements that discriminate between the pairing of a siroheme-containing oxidase with a diflavin reductase or a ferredoxin partner to channel the six electrons that reduce sulfite to sulfide.
Collapse
Affiliation(s)
- Behrouz Ghazi Esfahani
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
| | - Nidhi Walia
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
- Current Location: Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Kasahun Neselu
- New York Structural Biology Center, New York, NY, 10027, USA
| | - Mahira Aragon
- New York Structural Biology Center, New York, NY, 10027, USA
| | - Isabel Askenasy
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
- Current Location: Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Alex Wei
- New York Structural Biology Center, New York, NY, 10027, USA
| | | | - M. Elizabeth Stroupe
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
| |
Collapse
|
4
|
Ma Y, Qu Y, Yao X, Xia C, Lv M, Lin X, Zhang L, Zhang M, Hu B. Unveiling the unique role of iron in the metabolism of methanogens: A review. ENVIRONMENTAL RESEARCH 2024; 250:118495. [PMID: 38367837 DOI: 10.1016/j.envres.2024.118495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Methanogens are the main participants in the carbon cycle, catalyzing five methanogenic pathways. Methanogens utilize different iron-containing functional enzymes in different methanogenic processes. Iron is a vital element in methanogens, which can serve as a carrier or reactant in electron transfer. Therefore, iron plays an important role in the growth and metabolism of methanogens. In this paper, we cast light on the types and functions of iron-containing functional enzymes involved in different methanogenic pathways, and the roles iron play in energy/substance metabolism of methanogenesis. Furthermore, this review provides certain guiding significance for lowering CH4 emissions, boosting the carbon sink capacity of ecosystems and promoting green and low-carbon development in the future.
Collapse
Affiliation(s)
- Yuxin Ma
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ying Qu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiangwu Yao
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chujun Xia
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengjie Lv
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao Lin
- Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lili Zhang
- Beijing Enterprises Water Group Limited, Beijing, China
| | - Meng Zhang
- Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China
| | - Baolan Hu
- Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, Zhejiang, China; Department of Environmental Engineering, Zhejiang University, Hangzhou, Zhejiang, China.
| |
Collapse
|
5
|
Kümpel C, Grosser M, Tanabe TS, Dahl C. Fe/S proteins in microbial sulfur oxidation. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119732. [PMID: 38631440 DOI: 10.1016/j.bbamcr.2024.119732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/26/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024]
Abstract
Iron-sulfur clusters serve as indispensable cofactors within proteins across all three domains of life. Fe/S clusters emerged early during the evolution of life on our planet and the biogeochemical cycle of sulfur is one of the most ancient and important element cycles. It is therefore no surprise that Fe/S proteins have crucial roles in the multiple steps of microbial sulfur metabolism. During dissimilatory sulfur oxidation in prokaryotes, Fe/S proteins not only serve as electron carriers in several steps, but also perform catalytic roles, including unprecedented reactions. Two cytoplasmic enzyme systems that oxidize sulfane sulfur to sulfite are of particular interest in this context: The rDsr pathway employs the reverse acting dissimilatory sulfite reductase rDsrAB as its key enzyme, while the sHdr pathway utilizes polypeptides resembling the HdrA, HdrB and HdrC subunits of heterodisulfide reductase from methanogenic archaea. Both pathways involve components predicted to bind unusual noncubane Fe/S clusters acting as catalysts for the formation of disulfide or sulfite. Mapping of Fe/S cluster machineries on the sulfur-oxidizing prokaryote tree reveals that ISC, SUF, MIS and SMS are all sufficient to meet the Fe/S cluster maturation requirements for operation of the sHdr or rDsr pathways. The sHdr pathway is dependent on lipoate-binding proteins that are assembled by a novel pathway, involving two Radical SAM proteins, namely LipS1 and LipS2. These proteins coordinate sulfur-donating auxiliary Fe/S clusters in atypical patterns by three cysteines and one histidine and act as lipoyl synthases by jointly inserting two sulfur atoms to an octanoyl residue. This article is part of a Special Issue entitled: Biogenesis and Function of Fe/S proteins.
Collapse
Affiliation(s)
- Carolin Kümpel
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Martina Grosser
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Tomohisa Sebastian Tanabe
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Christiane Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany.
| |
Collapse
|
6
|
Müller MC, Lemaire ON, Kurth JM, Welte CU, Wagner T. Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations. Commun Biol 2024; 7:111. [PMID: 38243071 PMCID: PMC10799026 DOI: 10.1038/s42003-023-05726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/19/2023] [Indexed: 01/21/2024] Open
Abstract
Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.
Collapse
Affiliation(s)
- Marie-Caroline Müller
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Olivier N Lemaire
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia M Kurth
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Microcosm Earth Center, Philipps-University Marburg and Max Planck Institute for Terrestrial Microbiology, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
| |
Collapse
|
7
|
Jespersen M, Wagner T. Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus. Nat Microbiol 2023:10.1038/s41564-023-01398-8. [PMID: 37277534 DOI: 10.1038/s41564-023-01398-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/26/2023] [Indexed: 06/07/2023]
Abstract
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.
Collapse
Affiliation(s)
- Marion Jespersen
- Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Tristan Wagner
- Microbial Metabolism Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
| |
Collapse
|
8
|
Lemaire ON, Belhamri M, Wagner T. Structural and biochemical elucidation of class I hybrid cluster protein natively extracted from a marine methanogenic archaeon. Front Microbiol 2023; 14:1179204. [PMID: 37250035 PMCID: PMC10210160 DOI: 10.3389/fmicb.2023.1179204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/03/2023] [Indexed: 05/31/2023] Open
Abstract
Whilst widespread in the microbial world, the hybrid cluster protein (HCP) has been paradoxically a long-time riddle for microbiologists. During three decades, numerous studies on a few model organisms unravelled its structure and dissected its metal-containing catalyst, but the physiological function of the enzyme remained elusive. Recent studies on bacteria point towards a nitric oxide reductase activity involved in resistance during nitrate and nitrite reduction as well as host infection. In this study, we isolated and characterised a naturally highly produced HCP class I from a marine methanogenic archaeon grown on ammonia. The crystal structures of the enzyme in a reduced and partially oxidised state, obtained at a resolution of 1.45 and 1.36-Å, respectively, offered a precise picture of the archaeal enzyme intimacy. There are striking similarities with the well-studied enzymes from Desulfovibrio species regarding sequence, kinetic parameters, structure, catalyst conformations, and internal channelling systems. The close phylogenetic relationship between the enzymes from Methanococcales and many Bacteria corroborates this similarity. Indeed, Methanococcales HCPs are closer to these bacterial homologues than to any other archaeal enzymes. The relatively high constitutive production of HCP in M. thermolithotrophicus, in the absence of a notable nitric oxide source, questions the physiological function of the enzyme in these ancient anaerobes.
Collapse
|