1
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Zaparte A, Christopher CJ, Arnold C, Richey L, Castille A, Mistretta K, Taylor CM, Lin H, Nelson S, Kirwan JP, Apolzan JW, Campagna SR, Welsh DA. Effects of E-Cigarettes on the Lung and Systemic Metabolome in People with HIV. Metabolites 2024; 14:434. [PMID: 39195530 DOI: 10.3390/metabo14080434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024] Open
Abstract
The popularity of e-cigarettes (vaping) has soared, creating a public health crisis among teens and young adults. Chronic vaping can induce gut inflammation and reduce intestinal barrier function through the production of the proinflammatory molecule hydrogen sulfide (H2S). This is particularly concerning for people with HIV (PWH) as they already face impaired immune function and are at a higher risk for metabolic dysregulation, diabetes, and chronic liver disease. Furthermore, PWH experience unhealthy behaviors, making it crucial to understand the systemic metabolic dysregulation and pathophysiological mechanisms associated with vaping in this population. Here, we employed liquid chromatography-mass spectrometry (LC-MS)-based metabolomics to investigate the upper respiratory, circulation, and gut metabolic profiles of PWH who vape (n = 7) and smoke combustible tobacco/marijuana (n = 6) compared to control participants who did not vape or smoke (n = 10). This hypothesis-generating exploratory study revealed systemic alterations in purine, neurotransmitter, and vitamin B metabolisms and tissue-specific changes in inflammatory pathways and cryptic sulfur cycling associated with vaping and combustible tobacco/marijuana smoking in PWH. In addition, this study provides the first link between microbial-derived metabolite 2,3-dihydroxypropane-1-sulfonate (DHPS) and vaping/smoking (tobacco and marijuana)-induced metabolic dyshomeostasis in the gut. These findings highlight the importance of identifying the full biological and clinical significance of the physiological changes and risks associated with vaping.
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Affiliation(s)
- Aline Zaparte
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Courtney J Christopher
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN 37996, USA
| | - Connie Arnold
- Department of Medicine, Louisiana State University Health Sciences, Shreveport, LA 71103, USA
| | - Lauren Richey
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Adairre Castille
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Kyle Mistretta
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology, & Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Huiyi Lin
- School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Steve Nelson
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - John P Kirwan
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA 70808, USA
| | - John W Apolzan
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA 70808, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN 37996, USA
- Biological and Small Molecule Mass Spectrometry Core, University of Tennessee, 1420 Circle Drive, Knoxville, TN 37996, USA
| | - David A Welsh
- Department of Internal Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
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2
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Li Z, Pickles IB, Sharma M, Melling B, Pallasdies L, Codée JDC, Williams SJ, Overkleeft HS, Davies GJ. Detection of Sulfoquinovosidase Activity in Cell Lysates Using Activity-Based Probes. Angew Chem Int Ed Engl 2024; 63:e202401358. [PMID: 38647177 DOI: 10.1002/anie.202401358] [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: 01/19/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
The sulfolipid sulfoquinovosyl diacylglycerol (SQDG), produced by plants, algae, and cyanobacteria, constitutes a major sulfur reserve in the biosphere. Microbial breakdown of SQDG is critical for the biological utilization of its sulfur. This commences through release of the parent sugar, sulfoquinovose (SQ), catalyzed by sulfoquinovosidases (SQases). These vanguard enzymes are encoded in gene clusters that code for diverse SQ catabolic pathways. To identify, visualize and isolate glycoside hydrolase CAZY-family 31 (GH31) SQases in complex biological environments, we introduce SQ cyclophellitol-aziridine activity-based probes (ABPs). These ABPs label the active site nucleophile of this enzyme family, consistent with specific recognition of the SQ cyclophellitol-aziridine in the active site, as evidenced in the 3D structure of Bacillus megaterium SQase. A fluorescent Cy5-probe enables visualization of SQases in crude cell lysates from bacteria harbouring different SQ breakdown pathways, whilst a biotin-probe enables SQase capture and identification by proteomics. The Cy5-probe facilitates monitoring of active SQase levels during different stages of bacterial growth which show great contrast to more traditional mRNA analysis obtained by RT-qPCR. Given the importance of SQases in global sulfur cycling and in human microbiota, these SQase ABPs provide a new tool with which to study SQase occurrence, activity and stability.
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Affiliation(s)
- Zirui Li
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Isabelle B Pickles
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Benjamin Melling
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Luise Pallasdies
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jeroen D C Codée
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Herman S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
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3
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Kaur A, Pickles IB, Sharma M, Madeido Soler N, Scott NE, Pidot SJ, Goddard-Borger ED, Davies GJ, Williams SJ. Widespread Family of NAD +-Dependent Sulfoquinovosidases at the Gateway to Sulfoquinovose Catabolism. J Am Chem Soc 2023; 145:28216-28223. [PMID: 38100472 PMCID: PMC10755693 DOI: 10.1021/jacs.3c11126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
The sulfosugar sulfoquinovose (SQ) is produced by photosynthetic plants, algae, and cyanobacteria on a scale of 10 billion tons per annum. Its degradation, which is essential to allow cycling of its constituent carbon and sulfur, involves specialized glycosidases termed sulfoquinovosidases (SQases), which release SQ from sulfolipid glycoconjugates, so SQ can enter catabolism pathways. However, many SQ catabolic gene clusters lack a gene encoding a classical SQase. Here, we report the discovery of a new family of SQases that use an atypical oxidoreductive mechanism involving NAD+ as a catalytic cofactor. Three-dimensional X-ray structures of complexes with SQ and NAD+ provide insight into the catalytic mechanism, which involves transient oxidation at C3. Bioinformatic survey reveals this new family of NAD+-dependent SQases occurs within sulfoglycolytic and sulfolytic gene clusters that lack classical SQases and is distributed widely including within Roseobacter clade bacteria, suggesting an important contribution to marine sulfur cycling.
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Affiliation(s)
- Arashdeep Kaur
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Isabelle B. Pickles
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Mahima Sharma
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Niccolay Madeido Soler
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nichollas E. Scott
- Department
of Microbiology and Immunology, University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Sacha J. Pidot
- Department
of Microbiology and Immunology, University
of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
| | - Ethan D. Goddard-Borger
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Spencer J. Williams
- School
of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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4
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Tanabe TS, Dahl C. HMSS2: An advanced tool for the analysis of sulphur metabolism, including organosulphur compound transformation, in genome and metagenome assemblies. Mol Ecol Resour 2023; 23:1930-1945. [PMID: 37515475 DOI: 10.1111/1755-0998.13848] [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: 05/11/2023] [Revised: 07/08/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023]
Abstract
The global sulphur cycle has implications for human health, climate change, biogeochemistry and bioremediation. The organosulphur compounds that participate in this cycle not only represent a vast reservoir of sulphur but are also used by prokaryotes as sources of energy and/or carbon. Closely linked to the inorganic sulphur cycle, it involves the interaction of prokaryotes, eukaryotes and chemical processes. However, ecological and evolutionary studies of the conversion of organic sulphur compounds are hampered by the poor conservation of the relevant pathways and their variation even within strains of the same species. In addition, several proteins involved in the conversion of sulphonated compounds are related to proteins involved in sulphur dissimilation or turnover of other compounds. Therefore, the enzymes involved in the metabolism of organic sulphur compounds are usually not correctly annotated in public databases. To address this challenge, we have developed HMSS2, a profiled Hidden Markov Model-based tool for rapid annotation and synteny analysis of organic and inorganic sulphur cycle proteins in prokaryotic genomes. Compared to its previous version (HMS-S-S), HMSS2 includes several new features. HMM-based annotation is now supported by nonhomology criteria and covers the metabolic pathways of important organosulphur compounds, including dimethylsulphoniopropionate, taurine, isethionate, and sulphoquinovose. In addition, the calculation speed has been increased by a factor of four and the available output formats have been extended to include iTol compatible data sets, and customized sequence FASTA files.
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Affiliation(s)
- 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
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5
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Li J, Sharma M, Meek R, Alhifthi A, Armstrong Z, Soler NM, Lee M, Goddard-Borger ED, Blaza JN, Davies GJ, Williams SJ. Molecular basis of sulfolactate synthesis by sulfolactaldehyde dehydrogenase from Rhizobium leguminosarum. Chem Sci 2023; 14:11429-11440. [PMID: 37886098 PMCID: PMC10599462 DOI: 10.1039/d3sc01594g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/25/2023] [Indexed: 10/28/2023] Open
Abstract
Sulfolactate (SL) is a short-chain organosulfonate that is an important reservoir of sulfur in the biosphere. SL is produced by oxidation of sulfolactaldehyde (SLA), which in turn derives from sulfoglycolysis of the sulfosugar sulfoquinovose, or through oxidation of 2,3-dihydroxypropanesulfonate. Oxidation of SLA is catalyzed by SLA dehydrogenases belonging to the aldehyde dehydrogenase superfamily. We report that SLA dehydrogenase RlGabD from the sulfoglycolytic bacterium Rhizobium leguminsarum SRDI565 can use both NAD+ and NADP+ as cofactor to oxidize SLA, and indicatively operates through a rapid equilibrium ordered mechanism. We report the cryo-EM structure of RlGabD bound to NADH, revealing a tetrameric quaternary structure and supporting proposal of organosulfonate binding residues in the active site, and a catalytic mechanism. Sequence based homology searches identified SLA dehydrogenase homologs in a range of putative sulfoglycolytic gene clusters in bacteria predominantly from the phyla Actinobacteria, Firmicutes, and Proteobacteria. This work provides a structural and biochemical view of SLA dehydrogenases to complement our knowledge of SLA reductases, and provide detailed insights into a critical step in the organosulfur cycle.
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Affiliation(s)
- Jinling Li
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York York YO10 5DD UK
| | - Richard Meek
- York Structural Biology Laboratory, Department of Chemistry, University of York York YO10 5DD UK
| | - Amani Alhifthi
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
- Chemistry Department, Faculty of Science (Female Section), Jazan University Jazan 82621 Saudi Arabia
| | - Zachary Armstrong
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
| | - Niccolay Madiedo Soler
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research Parkville Victoria 3010 Australia
| | - Mihwa Lee
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
| | - Ethan D Goddard-Borger
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research Parkville Victoria 3010 Australia
- Department of Medical Biology, University of Melbourne Parkville Victoria 3010 Australia
| | - James N Blaza
- York Structural Biology Laboratory, Department of Chemistry, University of York York YO10 5DD UK
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York York YO10 5DD UK
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne Parkville Victoria 3010 Australia
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6
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Ye Z, Wei Y, Jiang L, Zhang Y. Oxygenolytic sulfoquinovose degradation by an iron-dependent alkanesulfonate dioxygenase. iScience 2023; 26:107803. [PMID: 37731605 PMCID: PMC10507154 DOI: 10.1016/j.isci.2023.107803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 09/22/2023] Open
Abstract
Sulfoquinovose (6-deoxy-6-sulfo-D-glucose, SQ), the polar head group of sulfolipids in plants, is abundant in nature. Many bacteria degrade SQ through pathways termed sulfoglycolysis producing C3 or C2 sulfonates, while certain bacteria degrade SQ through direct oxygenolytic cleavage of the SQ C-S bond, catalyzed by a flavin-dependent alkanesulfonate monooxygenase (sulfo-ASMO pathway). Here we report bioinformatics and biochemical studies revealing an alternative mechanism for oxygenolytic cleavage of the SQ C-S bond, catalyzed by an iron and α-ketoglutarate-dependent alkanesulfonate dioxygenase (SqoD, sulfo-ASDO pathway). In both the ASMO and ASDO pathways, the product 6-dehydroglucose is reduced to glucose by NAD(P)H-dependent SquF. Marinomonas ushuaiensis, a marine bacterium, which harbors the sulfo-ASDO gene cluster is shown utilizing SQ as a carbon source for growth, accompanied by increased transcription of SqoD. The sulfo-ASDO pathway highlights the range of microbial strategies for degradation of this ubiquitous sulfo-sugar, with potential implications for sulfur recycling in different biological environments.
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Affiliation(s)
- Zonghua Ye
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Department of Chemistry, Tianjin University, Tianjin 300072, P.R.China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Department of Chemistry, Tianjin University, Tianjin 300072, P.R.China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Department of Chemistry, Tianjin University, Tianjin 300072, P.R.China
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7
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Chu R, Wei Y, Liu J, Li B, Zhang J, Zhou Y, Du Y, Zhang Y. A Variant of the Sulfoglycolytic Transketolase Pathway for the Degradation of Sulfoquinovose into Sulfoacetate. Appl Environ Microbiol 2023; 89:e0061723. [PMID: 37404184 PMCID: PMC10370302 DOI: 10.1128/aem.00617-23] [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: 04/12/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
Sulfoquinovose (SQ, 6-deoxy-6-sulfo-glucose) constitutes the polar head group of plant sulfolipids and is one of the most abundantly produced organosulfur compounds in nature. Degradation of SQ by bacterial communities contributes to sulfur recycling in many environments. Bacteria have evolved at least four mechanisms for glycolytic degradation of SQ, termed sulfoglycolysis, producing C3 sulfonate (dihydroxypropanesulfonate and sulfolactate) and C2 sulfonate (isethionate) by-products. These sulfonates are further degraded by other bacteria, leading to the mineralization of the sulfonate sulfur. The C2 sulfonate sulfoacetate is widespread in the environment and is also thought to be a product of sulfoglycolysis, although the mechanistic details are yet unknown. Here, we describe a gene cluster in an Acholeplasma sp., from a metagenome derived from deeply circulating subsurface aquifer fluids (GenBank accession no. QZKD01000037), encoding a variant of the recently discovered sulfoglycolytic transketolase (sulfo-TK) pathway that produces sulfoacetate instead of isethionate as a by-product. We report the biochemical characterization of a coenzyme A (CoA)-acylating sulfoacetaldehyde dehydrogenase (SqwD) and an ADP-forming sulfoacetate-CoA ligase (SqwKL), which collectively catalyze the oxidation of the transketolase product sulfoacetaldehyde into sulfoacetate, coupled with ATP formation. A bioinformatics study revealed the presence of this sulfo-TK variant in phylogenetically diverse bacteria, adding to the variety of mechanisms by which bacteria metabolize this ubiquitous sulfo-sugar. IMPORTANCE Many bacteria utilize environmentally widespread C2 sulfonate sulfoacetate as a sulfur source, and the disease-linked human gut sulfate- and sulfite-reducing bacteria can use it as a terminal electron receptor for anaerobic respiration generating toxic H2S. However, the mechanism of sulfoacetate formation is unknown, although it has been proposed that sulfoacetate originates from bacterial degradation of sulfoquinovose (SQ), the polar head group of sulfolipids present in all green plants. Here, we describe a variant of the recently discovered sulfoglycolytic transketolase (sulfo-TK) pathway. Unlike the regular sulfo-TK pathway that produces isethionate, our biochemical assays with recombinant proteins demonstrated that a CoA-acylating sulfoacetaldehyde dehydrogenase (SqwD) and an ADP-forming sulfoacetate-CoA ligase (SqwKL) in this variant pathway collectively catalyze the oxidation of the transketolase product sulfoacetaldehyde into sulfoacetate, coupled with ATP formation. A bioinformatics study revealed the presence of this sulfo-TK variant in phylogenetically diverse bacteria and interpreted the widespread existence of sulfoacetate.
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Affiliation(s)
- Ruoxing Chu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Boran Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Jianing Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Zhou
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yunfei Du
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
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8
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Structure and mechanism of sulfofructose transaldolase, a key enzyme in sulfoquinovose metabolism. Structure 2023; 31:244-252.e4. [PMID: 36805128 DOI: 10.1016/j.str.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/15/2022] [Accepted: 01/25/2023] [Indexed: 02/19/2023]
Abstract
Sulfoquinovose (SQ) is a key component of plant sulfolipids (sulfoquinovosyl diacylglycerols) and a major environmental reservoir of biological sulfur. Breakdown of SQ is achieved by bacteria through the pathways of sulfoglycolysis. The sulfoglycolytic sulfofructose transaldolase (sulfo-SFT) pathway is used by gut-resident firmicutes and soil saprophytes. After isomerization of SQ to sulfofructose (SF), the namesake enzyme catalyzes the transaldol reaction of SF transferring dihydroxyacetone to 3C/4C acceptors to give sulfolactaldehyde and fructose-6-phosphate or sedoheptulose-7-phosphate. We report the 3D cryo-EM structure of SF transaldolase from Bacillus megaterium in apo and ligand bound forms, revealing a decameric structure formed from two pentameric rings of the protomer. We demonstrate a covalent "Schiff base" intermediate formed by reaction of SF with Lys89 within a conserved Asp-Lys-Glu catalytic triad and defined by an Arg-Trp-Arg sulfonate recognition triad. The structural characterization of the signature enzyme of the sulfo-SFT pathway provides key insights into molecular recognition of the sulfonate group of sulfosugars.
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9
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Ye Y, Yu D, Liu Q, Ma S, Zhang M, Zhao M, Xu J, Yu J. Nutritional composition of fresh carcass of turbot fed with Bacillus subtilis SMF1, B. licheniformis LMF1 and B. siamensis DL3 and its relationship with intestinal flora. Anim Feed Sci Technol 2023. [DOI: 10.1016/j.anifeedsci.2023.115627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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10
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Liu L, Chen X, Ye J, Ma X, Han Y, He Y, Tang K. Sulfoquinovose is a widespread organosulfur substrate for Roseobacter clade bacteria in the ocean. THE ISME JOURNAL 2023; 17:393-405. [PMID: 36593260 PMCID: PMC9938184 DOI: 10.1038/s41396-022-01353-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 01/03/2023]
Abstract
Sulfoquinovose (SQ) is one of the most abundant organosulfur compounds in the biosphere, and its biosynthesis and degradation can represent an important contribution to the sulfur cycle. To data, in marine environments, the microorganisms capable of metabolising SQ have remained unidentified and the sources of SQ are still uncertain. Herein, the marine Roseobacter clade bacteria (RCB) Dinoroseobacter shibae DFL 12 and Roseobacter denitrificans OCh 114 were found to grow using SQ as the sole source of carbon and energy. In the presence of SQ, we identified a set of highly up-regulated proteins encoded by gene clusters in these two organisms, of which four homologues to proteins in the SQ monooxygenase pathway of Agrobacterium fabrum C58 may confer the ability to metabolise SQ to these marine bacteria. The sulfite released from SQ desulfonation by FMN-dependent SQ monooxygenase (SmoC) may provide bacteria with reduced sulfur for assimilation, while proteins associated with sulfite production via assimilatory sulfate reduction were significantly down-regulated. Such SQ catabolic genes are restricted to a limited number of phylogenetically diverse bacterial taxa with the predominate genera belonging to the Roseobacter clade (Roseobacteraceae). Moreover, transcript analysis of Tara Oceans project and coastal Bohai Sea samples provided additional evidence for SQ metabolism by RCB. SQ was found to be widely distributed in marine phytoplankton and cyanobacteria with variable intracellular concentrations ranging from micromolar to millimolar levels, and the amounts of SQ on particulate organic matter in field samples were, on average, lower than that of dimethylsulfoniopropionate (DMSP) by one order of magnitude. Together, the phototroph-derived SQ actively metabolised by RCB represents a previously unidentified link in the marine sulfur cycle.
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Affiliation(s)
- Le Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Jianing Ye
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Xiaoyi Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Yu Han
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Yajie He
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China.
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11
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Lin H, Yu Y, Zhu L, Lai N, Zhang L, Guo Y, Lin X, Yang D, Ren N, Zhu Z, Dong Q. Implications of hydrogen sulfide in colorectal cancer: Mechanistic insights and diagnostic and therapeutic strategies. Redox Biol 2023; 59:102601. [PMID: 36630819 PMCID: PMC9841368 DOI: 10.1016/j.redox.2023.102601] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/01/2023] [Accepted: 01/02/2023] [Indexed: 01/09/2023] Open
Abstract
Hydrogen sulfide (H2S) is an important signaling molecule in colorectal cancer (CRC). It is produced in the colon by the catalytic synthesis of the colonocytes' enzymatic systems and the release of intestinal microbes, and is oxidatively metabolized in the colonocytes' mitochondria. Both endogenous H2S in colonic epithelial cells and exogenous H2S in intestinal lumen contribute to the onset and progression of CRC. The up-regulation of endogenous synthetases is thought to be the cause of the elevated H2S levels in CRC cells. Different diagnostic probes and combination therapies, as well as tumor treatment approaches through H2S modulation, have been developed in recent years and have become active area of investigation for the diagnosis and treatment of CRC. In this review, we focus on the specific mechanisms of H2S production and oxidative metabolism as well as the function of H2S in the occurrence, progression, diagnosis, and treatment of CRC. We also discuss the present challenges and provide insights into the future research of this burgeoning field.
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Affiliation(s)
- Hanchao Lin
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, China; Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute, Fudan University, China
| | - Yixin Yu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, China
| | - Le Zhu
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute, Fudan University, China
| | - Nannan Lai
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, China
| | - Luming Zhang
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, China
| | - Yu Guo
- Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute, Fudan University, China
| | - Xinxin Lin
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, China
| | - Dongqin Yang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, China.
| | - Ning Ren
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, China; Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, And Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Fudan University, China.
| | - Zhiling Zhu
- College of Materials Science and Engineering, Qingdao University of Science and Technology, China.
| | - Qiongzhu Dong
- Key Laboratory of Whole-Period Monitoring and Precise Intervention of Digestive Cancer, Shanghai Municipal Health Commission, Minhang Hospital, Fudan University, China.
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12
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Liu J, Zhao W, Gao ZW, Liu N, Zhang WH, Ling H. Effects of Exogenous Hydrogen Sulfide on Diabetic Metabolic Disorders in db/db Mice Are Associated With Gut Bacterial and Fungal Microbiota. Front Cell Infect Microbiol 2022; 12:801331. [PMID: 35425717 PMCID: PMC9001961 DOI: 10.3389/fcimb.2022.801331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/02/2022] [Indexed: 01/15/2023] Open
Abstract
The effects of hydrogen sulfide (H2S) on diabetic metabolic disorders are still controversial, and the mechanisms underlying these effects remain largely unknown. This study was conducted to investigate the potential relationship between the gut microbiota and the improvement of diabetic metabolic disorders by exogenous H2S in obese db/db mice. The db/db mice were treated with sodium hydrosulfide (NaHS) (80 μmol/kg), or vehicle for 16 weeks, respectively. We measured the serum H2S, obesity parameters, glucose homeostasis, and triglyceride. The sequencing of bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) in the cecal contents of NaHS-treated mice was performed to evaluate the gut microbial communities. We found that supplying exogenous H2S for 16 weeks significantly inhibited the increase of serum triglyceride, blood glucose, and insulin levels and altered specifically the gut bacterial microbiota structure in db/db mice. The relative abundance of some bacterial genera was correlated with the H2S or blood glucose level. Indeed, exogenous H2S increased Firmicutes and decreased Bacteroidetes at the phylum level along with changes of abundance of multifarious genera. Among them, Unclassified_Enterobacteriaceae, Prevotella, and Lactobacillus decreased and Unclassified_Ruminococcaceae, Oscillospira, Ruminococcus, Sutterella, and Desulfovibrio increased. For fungi, exogenous H2S decreased the abundance of Candida and Aspergillus. Here we demonstrated that, in diabetes, microbial dysbiosis may not be just limited to bacteria due to the inter-linked metabolic interactions among bacteria and fungi in the gut. The beneficial effects of exogenous H2S on diabetic metabolic disorders are likely associated with the alterations of specific microbiota.
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Affiliation(s)
- Jian Liu
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Wei Zhao
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Zi-Wei Gao
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Ning Liu
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Wei-Hua Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin, China
- *Correspondence: Hong Ling, ; Wei-Hua Zhang,
| | - Hong Ling
- Department of Microbiology, Harbin Medical University, Harbin, China
- Wu Lien-Teh Institute, Harbin Medical University, Harbin, China
- Heilongjiang Provincial Key Laboratory of Infection and Immunity, Harbin, China
- Key Laboratory of Pathogen Biology, Harbin, China
- *Correspondence: Hong Ling, ; Wei-Hua Zhang,
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13
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Snow AJ, Sharma M, Lingford JP, Zhang Y, W.-Y.Mui J, Epa R, Goddard-Borger ED, Williams SJ, Davies GJ. The sulfoquinovosyl glycerol binding protein SmoF binds and accommodates plant sulfolipids. Curr Res Struct Biol 2022; 4:51-58. [PMID: 35341160 PMCID: PMC8940949 DOI: 10.1016/j.crstbi.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 10/26/2022] Open
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14
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Kaur A, van der Peet PL, Mui JWY, Herisse M, Pidot S, Williams SJ. Genome sequences of Arthrobacter spp. that use a modified sulfoglycolytic Embden-Meyerhof-Parnas pathway. Arch Microbiol 2022; 204:193. [PMID: 35201431 PMCID: PMC8873060 DOI: 10.1007/s00203-022-02803-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 12/04/2022]
Abstract
Sulfoglycolysis pathways enable the breakdown of the sulfosugar sulfoquinovose and environmental recycling of its carbon and sulfur content. The prototypical sulfoglycolytic pathway is a variant of the classical Embden–Meyerhof–Parnas (EMP) pathway that results in formation of 2,3-dihydroxypropanesulfonate and was first described in gram-negative Escherichia coli. We used enrichment cultures to discover new sulfoglycolytic bacteria from Australian soil samples. Two gram-positive Arthrobacter spp. were isolated that produced sulfolactate as the metabolic end-product. Genome sequences identified a modified sulfoglycolytic EMP gene cluster, conserved across a range of other Actinobacteria, that retained the core sulfoglycolysis genes encoding metabolic enzymes but featured the replacement of the gene encoding sulfolactaldehyde (SLA) reductase with SLA dehydrogenase, and the absence of sulfoquinovosidase and sulfoquinovose mutarotase genes. Excretion of sulfolactate by these Arthrobacter spp. is consistent with an aerobic saprophytic lifestyle. This work broadens our knowledge of the sulfo-EMP pathway to include soil bacteria.
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Affiliation(s)
- Arashdeep Kaur
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Phillip L van der Peet
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Janice W-Y Mui
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Marion Herisse
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Sacha Pidot
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3000, Australia
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
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15
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Buret AG, Allain T, Motta JP, Wallace JL. Effects of Hydrogen Sulfide on the Microbiome: From Toxicity to Therapy. Antioxid Redox Signal 2022; 36:211-219. [PMID: 33691464 PMCID: PMC8861923 DOI: 10.1089/ars.2021.0004] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/13/2022]
Abstract
Significance: Hydrogen sulfide (H2S), an important regulator of physiology and health, helps resolve inflammation and promotes tissue repair in the gastrointestinal tract. Recent Advances: Gut microbiota live as a multispecies biofilm in close interaction with the upper mucus layer lining the epithelium. The relative abundance, spatial organization, and function of these microorganisms affect a broad range of health outcomes. This article provides a state-of-the-art review of our understanding of the cross talk between H2S, the gut microbiota, and health. H2S can have toxic or therapeutic effects, depending on its concentration and source. When produced at excessive concentrations by local microbiota, H2S may cause mucus disruption and inflammation and contribute to development of cancer. In contrast, low levels of endogenous or exogenous H2S directly stabilize mucus layers, prevent fragmentation and adherence of the microbiota biofilm to the epithelium, inhibit the release of invasive pathobionts, and help resolve inflammation and tissue injury. Although scarce, research findings suggest that dietary H2S obtained from plants or ingestion of the H2S precursor, L-cysteine, may also modulate the abundance and function of microbiota. Critical Issues: A critical issue is the lack of understanding of the metagenomic, transcriptomic, and proteomic alterations that characterize the interactions between H2S and gut microbiota to shape health outcomes. Future Directions: The ambivalent roles of H2S in the gut offer a fertile ground for research on such critical issues. The findings will improve our understanding of how H2S modulates the microbiota to affect body function and will help identify novel therapeutic strategies. Antioxid. Redox Signal. 36, 211-219.
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Affiliation(s)
- Andre G. Buret
- Host–Parasite Interactions Program, Inflammation Research Network, Biological Sciences, University of Calgary, Calgary, Canada
- Antibe Therapeutics, Inc., Toronto, Canada
| | - Thibault Allain
- Host–Parasite Interactions Program, Inflammation Research Network, Biological Sciences, University of Calgary, Calgary, Canada
| | - Jean-Paul Motta
- Institute of Digestive Health Research, IRSD, INSERM U1220, Toulouse, France
| | - John L. Wallace
- Host–Parasite Interactions Program, Inflammation Research Network, Biological Sciences, University of Calgary, Calgary, Canada
- Antibe Therapeutics, Inc., Toronto, Canada
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16
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Oxidative desulfurization pathway for complete catabolism of sulfoquinovose by bacteria. Proc Natl Acad Sci U S A 2022; 119:2116022119. [PMID: 35074914 PMCID: PMC8795539 DOI: 10.1073/pnas.2116022119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2021] [Indexed: 12/31/2022] Open
Abstract
Sulfoquinovose, a sulfosugar derivative of glucose, is produced by most photosynthetic organisms and contains up to half of all sulfur in the biosphere. Several pathways for its breakdown are known, though they provide access to only half of the carbon in sulfoquinovose and none of its sulfur. Here, we describe a fundamentally different pathway within the plant pathogen Agrobacterium tumefaciens that features oxidative desulfurization of sulfoquinovose to access all carbon and sulfur within the molecule. Biochemical and structural analyses of the pathway’s key proteins provided insights how the sulfosugar is recognized and degraded. Genes encoding this sulfoquinovose monooxygenase pathway are present in many plant pathogens and symbionts, alluding to a possible role for sulfoquinovose in plant host–bacteria interactions. Catabolism of sulfoquinovose (SQ; 6-deoxy-6-sulfoglucose), the ubiquitous sulfosugar produced by photosynthetic organisms, is an important component of the biogeochemical carbon and sulfur cycles. Here, we describe a pathway for SQ degradation that involves oxidative desulfurization to release sulfite and enable utilization of the entire carbon skeleton of the sugar to support the growth of the plant pathogen Agrobacterium tumefaciens. SQ or its glycoside sulfoquinovosyl glycerol are imported into the cell by an ATP-binding cassette transporter system with an associated SQ binding protein. A sulfoquinovosidase hydrolyzes the SQ glycoside and the liberated SQ is acted on by a flavin mononucleotide-dependent sulfoquinovose monooxygenase, in concert with an NADH-dependent flavin reductase, to release sulfite and 6-oxo-glucose. An NAD(P)H-dependent oxidoreductase reduces the 6-oxo-glucose to glucose, enabling entry into primary metabolic pathways. Structural and biochemical studies provide detailed insights into the recognition of key metabolites by proteins in this pathway. Bioinformatic analyses reveal that the sulfoquinovose monooxygenase pathway is distributed across Alpha- and Betaproteobacteria and is especially prevalent within the Rhizobiales order. This strategy for SQ catabolism is distinct from previously described pathways because it enables the complete utilization of all carbons within SQ by a single organism with concomitant production of inorganic sulfite.
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17
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Snow AJD, Burchill L, Sharma M, Davies GJ, Williams SJ. Sulfoglycolysis: catabolic pathways for metabolism of sulfoquinovose. Chem Soc Rev 2021; 50:13628-13645. [PMID: 34816844 DOI: 10.1039/d1cs00846c] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Sulfoquinovose (SQ), a derivative of glucose with a C6-sulfonate, is produced by photosynthetic organisms and is the headgroup of the sulfolipid sulfoquinovosyl diacylglycerol. The degradation of SQ allows recycling of its elemental constituents and is important in the global sulfur and carbon biogeochemical cycles. Degradation of SQ by bacteria is achieved through a range of pathways that fall into two main groups. One group involves scission of the 6-carbon skeleton of SQ into two fragments with metabolic utilization of carbons 1-3 and excretion of carbons 4-6 as dihydroxypropanesulfonate or sulfolactate that is biomineralized to sulfite/sulfate by other members of the microbial community. The other involves the complete metabolism of SQ by desulfonylation involving cleavage of the C-S bond to release sulfite and glucose, the latter of which can enter glycolysis. The discovery of sulfoglycolytic pathways has revealed a wide range of novel enzymes and SQ binding proteins. Biochemical and structural characterization of the proteins and enzymes in these pathways have illuminated how the sulfonate group is recognized by Nature's catalysts, supporting bioinformatic annotation of sulfoglycolytic enzymes, and has identified functional and structural relationships with the pathways of glycolysis.
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Affiliation(s)
- Alexander J D Snow
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.
| | - Laura Burchill
- School of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, UK.
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Parkville, Victoria 3010, Australia. .,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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18
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Liu J, Wei Y, Ma K, An J, Liu X, Liu Y, Ang EL, Zhao H, Zhang Y. Mechanistically Diverse Pathways for Sulfoquinovose Degradation in Bacteria. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04321] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Kailiang Ma
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Junwei An
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xumei Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yinbo Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669, Singapore
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
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19
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An J, Wei Y, Liu J, Lui Ang E, Zhao H, Zhang Y. Biochemical Investigation of 3-Sulfopropionaldehyde Reductase HpfD. Chembiochem 2021; 22:2862-2866. [PMID: 34410031 DOI: 10.1002/cbic.202100316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 08/15/2021] [Indexed: 11/09/2022]
Abstract
Sulfoquinovose is the polar headgroup of plant sulfolipids and is a globally abundant organosulfur compound, and its degradation by bacteria is an important component of the sulfur cycle. Sulfoquinovose degradation by certain bacteria, including Escherichia coli, produces dihydroxypropanesulfonate (DHPS), which is further converted by anaerobic bacteria into 3-hydroxypropanesulfonate (3-HPS), through the catalytic action of DHPS dehydratase (a member of the glycyl radical enzyme family), and sulfopropionaldehyde reductase HpfD (a member of the metal-dependent alcohol dehydrogenase family). Here we report biochemical investigation of Hungatella hathewayi HpfD. In addition to 3-HPS, HpfD also displayed high catalytic activities for NAD+ -dependent oxidation of 4-hydroxybutanesulfonate (4-HBS) and γ-hydroxybutyrate (GHB). The highest activity was obtained with Fe2+ or Mn2+ as the divalent metal cofactor. Bioinformatics studies suggest that, in addition to DHPS degradation, 3-HPS and γ-aminobutyrate (GABA) degradations also involve HpfD homologs.
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Affiliation(s)
- Junwei An
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, 61801, USA
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, P. R. China.,Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China
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20
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Fan L, Li F, Chen X, Dong X, Hu G, Song C, Meng S, Li D, Chen J. Metagenomics analysis reveals the distribution and communication of antibiotic resistance genes within two different red swamp crayfish Procambarus clarkii cultivation ecosystems. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117144. [PMID: 33930822 DOI: 10.1016/j.envpol.2021.117144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/01/2021] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
Antibiotic resistance genes (ARGs) are emerging contaminants that pose a potential risk to human health worldwide. In this study, a metagenomic analysis was performed to investigate the distribution of ARGs in paddy field ecosystems, crayfish monoculture pond ecosystems, and rice-crayfish cultivation field ecosystems. The results showed that MacB and BcrA are two dominant ARGs, and macrolide is the dominant antibiotic not only in the water, but also in the sediment and gut of crayfish, in both the crayfish monoculture and the rice-crayfish cultivation ecosystems. Meanwhile, some lower-abundance ARGs in the water and sediment of crayfish cultivation ecosystems were significantly different in their abundance than those in rice paddy fields, and the ARGs in crayfish culture system and rice paddy fields showed even higher dissimilarities of diversity. Comprehensive analysis with redundancy analysis(RDA)and the distribution of dominant ARGs showed that the dissimilarity was related to the higher concentrations of total nitrogen (TN), total phosphorus (TP), chlorophyll a (Chla), permanganate index (CODMn), and nitrate in the water of rice paddy fields, and was related to the higher contents of N, P, K, and organic matter (OM) in the sediment of rice paddy fields. The source trackers of ARGs within the crayfish cultivation ponds and the rice-crayfish cultivation fields showed that the sediment in crayfish cultivation ponds mainly played the role of the 'sink' for ARGs, and the water and gut of crayfish mutually contributed to the high rates of ARGs. The ARG contribution rates of crayfish gut and sediment decreased and increased, respectively, in rice-crayfish cultivation fields and in crayfish monoculture ponds, which might be related to the lower crayfish biomass and the lower water depth in rice-crayfish cultivation fields.
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Affiliation(s)
- Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Fajun Li
- Shandong Peninsula Engineering Research Center of Comprehensive Brine Utilization, Weifang University of Science and Technology, Shouguang, 262700, China
| | - Xi Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Xinxu Dong
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, China
| | - Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, China
| | - Dandan Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, China
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi, 214081, China; Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, China.
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21
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Xue CX, Lin H, Zhu XY, Liu J, Zhang Y, Rowley G, Todd JD, Li M, Zhang XH. DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data. Front Microbiol 2021; 12:698286. [PMID: 34408730 PMCID: PMC8367434 DOI: 10.3389/fmicb.2021.698286] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/05/2021] [Indexed: 12/15/2022] Open
Abstract
Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.
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Affiliation(s)
- Chun-Xu Xue
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Heyu Lin
- School of Earth Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Xiao-Yu Zhu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Yunhui Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Gary Rowley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jonathan D. Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
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22
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Abstract
Sulfonates include diverse natural products and anthropogenic chemicals and are widespread in the environment. Many bacteria can degrade sulfonates and obtain sulfur, carbon, and energy for growth, playing important roles in the biogeochemical sulfur cycle. Cleavage of the inert sulfonate C-S bond involves a variety of enzymes, cofactors, and oxygen-dependent and oxygen-independent catalytic mechanisms. Sulfonate degradation by strictly anaerobic bacteria was recently found to involve C-S bond cleavage through O2-sensitive free radical chemistry, catalyzed by glycyl radical enzymes (GREs). The associated discoveries of new enzymes and metabolic pathways for sulfonate metabolism in diverse anaerobic bacteria have enriched our understanding of sulfonate chemistry in the anaerobic biosphere. An anaerobic environment of particular interest is the human gut microbiome, where sulfonate degradation by sulfate- and sulfite-reducing bacteria (SSRB) produces H2S, a process linked to certain chronic diseases and conditions.
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Affiliation(s)
- Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore 138669
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology; and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China;
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23
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Hanson BT, Dimitri Kits K, Löffler J, Burrichter AG, Fiedler A, Denger K, Frommeyer B, Herbold CW, Rattei T, Karcher N, Segata N, Schleheck D, Loy A. Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut. ISME JOURNAL 2021; 15:2779-2791. [PMID: 33790426 PMCID: PMC8397734 DOI: 10.1038/s41396-021-00968-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/01/2021] [Accepted: 03/17/2021] [Indexed: 12/26/2022]
Abstract
Responses of the microbiota to diet are highly personalized but mechanistically not well understood because many metabolic capabilities and interactions of human gut microorganisms are unknown. Here we show that sulfoquinovose (SQ), a sulfonated monosaccharide omnipresent in green vegetables, is a selective yet relevant substrate for few but ubiquitous bacteria in the human gut. In human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia used recently identified pathways to cooperatively catabolize SQ with 2,3-dihydroxypropane-1-sulfonate as a transient intermediate to hydrogen sulfide (H2S), a key intestinal metabolite with disparate effects on host health. SQ-degradation capability is encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. However, re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and H2S production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, demonstrating that these microbial functions are core attributes of the human gut. The discovery of green-diet-derived SQ as an exclusive microbial nutrient and an additional source of H2S in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.
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Affiliation(s)
- Buck T Hanson
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,FFoQSI GmbH, Austrian Competence Centre for Feed and Food Quality Safety & Innovation, Tulln, Austria
| | - K Dimitri Kits
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Jessica Löffler
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anna G Burrichter
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | | | - Karin Denger
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Benjamin Frommeyer
- Department of Biology, University of Konstanz, Konstanz, Germany.,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Craig W Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy
| | - David Schleheck
- Department of Biology, University of Konstanz, Konstanz, Germany. .,Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany.
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. .,Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
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24
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Sharma M, Abayakoon P, Epa R, Jin Y, Lingford JP, Shimada T, Nakano M, Mui JWY, Ishihama A, Goddard-Borger ED, Davies GJ, Williams SJ. Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis. ACS CENTRAL SCIENCE 2021; 7:476-487. [PMID: 33791429 PMCID: PMC8006165 DOI: 10.1021/acscentsci.0c01285] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Indexed: 06/12/2023]
Abstract
The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on Earth and is metabolized by bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolizes SQ to produce dihydroxyacetone phosphate and sulfolactaldehyde and is analogous to the classical Embden-Meyerhof-Parnas glycolysis pathway for the metabolism of glucose-6-phosphate, though the former only provides one C3 fragment to central metabolism, with excretion of the other C3 fragment as dihydroxypropanesulfonate. Here, we report a comprehensive structural and biochemical analysis of the three core steps of sulfoglycolysis catalyzed by SQ isomerase, sulfofructose (SF) kinase, and sulfofructose-1-phosphate (SFP) aldolase. Our data show that despite the superficial similarity of this pathway to glycolysis, the sulfoglycolytic enzymes are specific for SQ metabolites and are not catalytically active on related metabolites from glycolytic pathways. This observation is rationalized by three-dimensional structures of each enzyme, which reveal the presence of conserved sulfonate binding pockets. We show that SQ isomerase acts preferentially on the β-anomer of SQ and reversibly produces both SF and sulforhamnose (SR), a previously unknown sugar that acts as a derepressor for the transcriptional repressor CsqR that regulates SQ-utilization. We also demonstrate that SF kinase is a key regulatory enzyme for the pathway that experiences complex modulation by the metabolites SQ, SLA, AMP, ADP, ATP, F6P, FBP, PEP, DHAP, and citrate, and we show that SFP aldolase reversibly synthesizes SFP. This body of work provides fresh insights into the mechanism, specificity, and regulation of sulfoglycolysis and has important implications for understanding how this biochemistry interfaces with central metabolism in prokaryotes to process this major repository of biogeochemical sulfur.
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Affiliation(s)
- Mahima Sharma
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Palika Abayakoon
- School
of Chemistry and Bio21 Molecular Science
and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ruwan Epa
- School
of Chemistry and Bio21 Molecular Science
and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yi Jin
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - James P. Lingford
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tomohiro Shimada
- School
of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Masahiro Nakano
- Institute
for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Janice W.-Y. Mui
- School
of Chemistry and Bio21 Molecular Science
and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia
| | - Akira Ishihama
- Micro-Nano
Technology Research Center, Hosei University, Koganei, Tokyo, Japan
| | - Ethan D. Goddard-Borger
- ACRF
Chemical Biology Division, The Walter and
Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia
- Department
of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gideon J. Davies
- York
Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Spencer J. Williams
- School
of Chemistry and Bio21 Molecular Science
and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia
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25
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Burkhardt W, Rausch T, Klopfleisch R, Blaut M, Braune A. Impact of dietary sulfolipid-derived sulfoquinovose on gut microbiota composition and inflammatory status of colitis-prone interleukin-10-deficient mice. Int J Med Microbiol 2021; 311:151494. [PMID: 33711649 DOI: 10.1016/j.ijmm.2021.151494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/12/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
The interplay between diet, intestinal microbiota and host is a major factor impacting health. A diet rich in unsaturated fatty acids has been reported to stimulate the growth of Bilophila wadsworthia by increasing the proportion of the sulfonated bile acid taurocholate (TC). The taurine-induced overgrowth of B. wadsworthia promoted the development of colitis in interleukin-10-deficient (IL-10-/-) mice. This study aimed to investigate whether intake of the sulfonates sulfoquinovosyl diacylglycerols (SQDG) with a dietary supplement or their degradation product sulfoquinovose (SQ), stimulate the growth of B. wadsworthia in a similar manner and, thereby, cause intestinal inflammation. Conventional IL-10-/- mice were fed a diet supplemented with the SQDG-rich cyanobacterium Arthrospira platensis (Spirulina). SQ or TC were orally applied to conventional IL-10-/- mice and gnotobiotic IL-10-/- mice harboring a simplified human intestinal microbiota with or without B. wadsworthia. Analyses of inflammatory parameters revealed that none of the sulfonates induced severe colitis, but both, Spirulina and TC, induced expression of pro-inflammatory cytokines in cecal mucosa. Cell numbers of B. wadsworthia decreased almost two orders of magnitude by Spirulina feeding but slightly increased in gnotobiotic SQ and conventional TC mice. Changes in microbiota composition were observed in feces as a result of Spirulina or TC feeding in conventional mice. In conclusion, the dietary sulfonates SQDG and their metabolite SQ did not elicit bacteria-induced intestinal inflammation in IL-10-/- mice and, thus, do not promote colitis.
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Affiliation(s)
- Wiebke Burkhardt
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Theresa Rausch
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Robert Klopfleisch
- Institute of Veterinary Pathology, Freie Universitaet Berlin, Berlin, Germany
| | - Michael Blaut
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany; Institute of Nutritional Sciences, University of Potsdam, Nuthetal, Germany
| | - Annett Braune
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany.
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26
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Glowacki RWP, Martens EC. If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria. J Bacteriol 2020; 203:JB.00481-20. [PMID: 33168637 PMCID: PMC8092160 DOI: 10.1128/jb.00481-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to persist, successful bacterial inhabitants of the human gut need to adapt to changing nutrient conditions, which are influenced by host diet and a variety of other factors. For members of the Bacteroidetes and several other phyla, this has resulted in diversification of a variety of enzyme-based systems that equip them to sense and utilize carbohydrate-based nutrients from host, diet, and bacterial origin. In this review, we focus first on human gut Bacteroides and describe recent findings regarding polysaccharide utilization loci (PULs) and the mechanisms of the multi-protein systems they encode, including their regulation and the expanding diversity of substrates that they target. Next, we highlight previously understudied substrates such as monosaccharides, nucleosides, and Maillard reaction products that can also affect the gut microbiota by feeding symbionts that possess specific systems for their metabolism. Since some pathogens preferentially utilize these nutrients, they may represent nutrient niches competed for by commensals and pathogens. Finally, we address recent work to describe nutrient acquisition mechanisms in other important gut species such as those belonging to the Gram-positive anaerobic phyla Actinobacteria and Firmicutes, as well as the Proteobacteria Because gut bacteria contribute to many aspects of health and disease, we showcase advances in the field of synthetic biology, which seeks to engineer novel, diet-controlled nutrient utilization pathways within gut symbionts to create rationally designed live therapeutics.
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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27
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Liu Y, Wei Y, Zhou Y, Ang EL, Zhao H, Zhang Y. A transaldolase-dependent sulfoglycolysis pathway in Bacillus megaterium DSM 1804. Biochem Biophys Res Commun 2020; 533:1109-1114. [PMID: 33036753 DOI: 10.1016/j.bbrc.2020.09.124] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 01/17/2023]
Abstract
Sulfoquinovose (6-deoxy-6-sulfoglucose, SQ) is a component of sulfolipids found in the photosynthetic membranes of plants and other photosynthetic organisms, and is one of the most abundant organosulfur compounds in nature. Microbial degradation of SQ, termed sulfoglycolysis, constitutes an important component of the biogeochemical sulfur cycle. Two sulfoglycolysis pathways have been reported, with one resembling the Embden-Meyerhof-Parnas (sulfo-EMP) pathway, and the other resembling the Entner-Doudoroff (sulfo-ED) pathway. Here we report a third sulfoglycolysis pathway in the bacterium Bacillus megaterium DSM 1804, in which sulfosugar cleavage is catalyzed by the transaldolase SqvA, which converts 6-deoxy-6-sulfofructose and glyceraldehyde 3-phosphate into fructose -6-phosphate and (S)-sulfolactaldehyde. Variations of this transaldolase-dependent sulfoglycolysis (sulfo-TAL) pathway are present in diverse bacteria, and add to the diversity of mechanisms for the degradation of this abundant organosulfur compound.
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Affiliation(s)
- Yinbo Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Yan Zhou
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, IL, 61801, USA.
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China.
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