1
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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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2
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Rybina AA, Glushak RA, Bessonova TA, Dakhnovets AI, Rudenko AY, Ozhiganov RM, Kaznadzey AD, Tutukina MN, Gelfand MS. Phylogeny and structural modeling of the transcription factor CsqR (YihW) from Escherichia coli. Sci Rep 2024; 14:7852. [PMID: 38570624 PMCID: PMC10991401 DOI: 10.1038/s41598-024-58492-y] [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: 08/11/2023] [Accepted: 03/29/2024] [Indexed: 04/05/2024] Open
Abstract
CsqR (YihW) is a local transcription factor that controls expression of yih genes involved in degradation of sulfoquinovose in Escherichia coli. We recently showed that expression of the respective gene cassette might be regulated by lactose. Here, we explore the phylogenetic and functional traits of CsqR. Phylogenetic analysis revealed that CsqR had a conserved Met25. Western blot demonstrated that CsqR was synthesized in the bacterial cell as two protein forms, 28.5 (CsqR-l) and 26 kDa (CsqR-s), the latter corresponding to start of translation at Met25. CsqR-s was dramatically activated during growth with sulfoquinovose as a sole carbon source, and displaced CsqR-l in the stationary phase during growth on rich medium. Molecular dynamic simulations revealed two possible states of the CsqR-s structure, with the interdomain linker being represented by either a disordered loop or an ɑ-helix. This helix allowed the hinge-like motion of the N-terminal domain resulting in a switch of CsqR-s between two conformational states, "open" and "compact". We then modeled the interaction of both CsqR forms with putative effectors sulfoquinovose, sulforhamnose, sulfoquinovosyl glycerol, and lactose, and revealed that they all preferred the same pocket in CsqR-l, while in CsqR-s there were two possible options dependent on the linker structure.
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Affiliation(s)
- Anna A Rybina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205.
| | - Roman A Glushak
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119234
| | - Tatiana A Bessonova
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
| | | | - Alexander Yu Rudenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Ratislav M Ozhiganov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Anna D Kaznadzey
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Maria N Tutukina
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute of Cell Biophysics RAS (Federal Research Center "Pushchino Scientific Center for Biological Research RAS"), Pushchino, Russia, 142290
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Moscow, Russia, 121205
- Institute for Information Transmission Problems RAS, Moscow, Russia, 127051
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3
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Liu L, Gao X, Dong C, Wang H, Chen X, Ma X, Liu S, Chen Q, Lin D, Jiao N, Tang K. Enantioselective transformation of phytoplankton-derived dihydroxypropanesulfonate by marine bacteria. THE ISME JOURNAL 2024; 18:wrae084. [PMID: 38709871 PMCID: PMC11131964 DOI: 10.1093/ismejo/wrae084] [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: 01/06/2024] [Revised: 04/08/2024] [Accepted: 05/04/2024] [Indexed: 05/08/2024]
Abstract
Chirality, a fundamental property of matter, is often overlooked in the studies of marine organic matter cycles. Dihydroxypropanesulfonate (DHPS), a globally abundant organosulfur compound, serves as an ecologically important currency for nutrient and energy transfer from phytoplankton to bacteria in the ocean. However, the chirality of DHPS in nature and its transformation remain unclear. Here, we developed a novel approach using chiral phosphorus-reagent labeling to separate DHPS enantiomers. Our findings demonstrated that at least one enantiomer of DHPS is present in marine diatoms and coccolithophores, and that both enantiomers are widespread in marine environments. A novel chiral-selective DHPS catabolic pathway was identified in marine Roseobacteraceae strains, where HpsO and HpsP dehydrogenases at the gateway to DHPS catabolism act specifically on R-DHPS and S-DHPS, respectively. R-DHPS is also a substrate for the dehydrogenase HpsN. All three dehydrogenases generate stable hydrogen bonds between the chirality-center hydroxyls of DHPS and highly conserved residues, and HpsP also form coordinate-covalent bonds between the chirality-center hydroxyls and Zn2+, which determines the mechanistic basis of strict stereoselectivity. We further illustrated the role of enzymatic promiscuity in the evolution of DHPS metabolism in Roseobacteraceae and SAR11. This study provides the first evidence of chirality's involvement in phytoplankton-bacteria metabolic currencies, opening a new avenue for understanding the ocean organosulfur cycle.
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Affiliation(s)
- Le Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Xiang Gao
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Changjie Dong
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Huanyu Wang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Xiaofeng Chen
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361001, China
| | - Xiaoyi Ma
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Shujing Liu
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Dan Lin
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiang'an South Road, Xiamen 361102, China
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4
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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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5
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Sharma M, Kaur A, Madiedo Soler N, Lingford JP, Epa R, Goddard-Borger ED, Davies GJ, Williams SJ. Defining the molecular architecture, metal dependence, and distribution of metal-dependent class II sulfofructose-1-phosphate aldolases. J Biol Chem 2023; 299:105338. [PMID: 37838169 PMCID: PMC10665668 DOI: 10.1016/j.jbc.2023.105338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023] Open
Abstract
Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is a sulfosugar that is the anionic head group of plant, algal, and cyanobacterial sulfolipids: sulfoquinovosyl diacylglycerols. SQ is produced within photosynthetic tissues, forms a major terrestrial reservoir of biosulfur, and is an important species within the biogeochemical sulfur cycle. A major pathway for SQ breakdown is the sulfoglycolytic Embden-Meyerhof-Parnas pathway, which involves cleavage of the 6-carbon chain of the intermediate sulfofructose-1-phosphate (SFP) into dihydroxyacetone and sulfolactaldehyde, catalyzed by class I or II SFP aldolases. While the molecular basis of catalysis is understood for class I SFP aldolases, comparatively little is known about class II SFP aldolases. Here, we report the molecular architecture and biochemical basis of catalysis of two metal-dependent class II SFP aldolases from Hafnia paralvei and Yersinia aldovae. 3D X-ray structures of complexes with substrate SFP and product dihydroxyacetone phosphate reveal a dimer-of-dimers (tetrameric) assembly, the sulfonate-binding pocket, two metal-binding sites, and flexible loops that are implicated in catalysis. Both enzymes were metal-dependent and exhibited high KM values for SFP, consistent with their role in a unidirectional nutrient acquisition pathway. Bioinformatic analysis identified a range of sulfoglycolytic Embden-Meyerhof-Parnas gene clusters containing class I/II SFP aldolases. The class I and II SFP aldolases have mututally exclusive occurrence within Actinobacteria and Firmicutes phyla, respectively, while both classes of enzyme occur within Proteobacteria. This work emphasizes the importance of SQ as a nutrient for diverse bacterial phyla and the different chemical strategies they use to harvest carbon from this sulfosugar.
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Affiliation(s)
- Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Arashdeep Kaur
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Niccolay Madiedo Soler
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - James P Lingford
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ruwan Epa
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ethan D Goddard-Borger
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
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6
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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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7
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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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8
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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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9
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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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10
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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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11
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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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12
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Remodeling of Carbon Metabolism during Sulfoglycolysis in Escherichia coli. Appl Environ Microbiol 2023; 89:e0201622. [PMID: 36728421 PMCID: PMC9972972 DOI: 10.1128/aem.02016-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Sulfoquinovose (SQ) is a major metabolite in the global sulfur cycle produced by nearly all photosynthetic organisms. One of the major pathways involved in the catabolism of SQ in bacteria such as Escherichia coli is a variant of the glycolytic Embden-Meyerhof-Parnas (EMP) pathway termed the sulfoglycolytic EMP (sulfo-EMP) pathway, which leads to the consumption of three of the six carbons of SQ and the excretion of 2,3-dihydroxypropanesulfonate (DHPS). Comparative metabolite profiling of aerobically glucose (Glc)-grown and SQ-grown E. coli cells was undertaken to identify the metabolic consequences of the switch from glycolysis to sulfoglycolysis. Sulfoglycolysis was associated with the diversion of triose phosphates (triose-P) to synthesize sugar phosphates (gluconeogenesis) and an unexpected accumulation of trehalose and glycogen storage carbohydrates. Sulfoglycolysis was also associated with global changes in central carbon metabolism, as indicated by the changes in the levels of intermediates in the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway (PPP), polyamine metabolism, pyrimidine metabolism, and many amino acid metabolic pathways. Upon entry into stationary phase and the depletion of SQ, E. coli cells utilize their glycogen, indicating a reversal of metabolic fluxes to allow glycolytic metabolism. IMPORTANCE The sulfosugar sulfoquinovose is estimated to be produced on a scale of 10 billion metric tons per annum, making it a major organosulfur species in the biosulfur cycle. The microbial degradation of sulfoquinovose through sulfoglycolysis allows the utilization of its carbon content and contributes to the biomineralization of its sulfur. However, the metabolic consequences of microbial growth on sulfoquinovose are unclear. We use metabolomics to identify the metabolic adaptations that Escherichia coli undergoes when grown on sulfoquinovose versus glucose. This revealed the increased flux into storage carbohydrates through gluconeogenesis and the reduced flux of carbon into the TCA cycle and downstream metabolism. These changes are relieved upon entry into stationary phase and reversion to glycolytic metabolism. This work provides new insights into the metabolic consequences of microbial growth on an abundant sulfosugar.
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13
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Li F, Wang J, Jiang Y, Guo Y, Liu N, Xiao S, Yao L, Li J, Zhuo C, He N, Liu B, Zhuo C. Adaptive Evolution Compensated for the Plasmid Fitness Costs Brought by Specific Genetic Conflicts. Pathogens 2023; 12:pathogens12010137. [PMID: 36678485 PMCID: PMC9861728 DOI: 10.3390/pathogens12010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
New Delhi metallo-β-lactamase (NDM)-carrying IncX3 plasmids is important in the transmission of carbapenem resistance in Escherichia coli. Fitness costs related to plasmid carriage are expected to limit gene exchange; however, the causes of these fitness costs are poorly understood. Compensatory mutations are believed to ameliorate plasmid fitness costs and enable the plasmid's wide spread, suggesting that such costs are caused by specific plasmid-host genetic conflicts. By combining conjugation tests and experimental evolution with comparative genetic analysis, we showed here that the fitness costs related to ndm/IncX3 plasmids in E. coli C600 are caused by co-mutations of multiple host chromosomal genes related to sugar metabolism and cell membrane function. Adaptive evolution revealed that mutations in genes associated with oxidative stress, nucleotide and short-chain fatty acid metabolism, and cell membranes ameliorated the costs associated with plasmid carriage. Specific genetic conflicts associated with the ndm/IncX3 plasmid in E. coli C600 involve metabolism and cell-membrane-related genes, which could be ameliorated by compensatory mutations. Collectively, our findings could explain the wide spread of IncX3 plasmids in bacterial genomes, despite their potential cost.
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Affiliation(s)
- Feifeng Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Jiong Wang
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Ying Jiang
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Yingyi Guo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Ningjing Liu
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Shunian Xiao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Likang Yao
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Jiahui Li
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Chuyue Zhuo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Nanhao He
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
| | - Baomo Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Sun Yat-sen Univesity, Guangzhou 510030, China
- Correspondence: (B.L.); (C.Z.)
| | - Chao Zhuo
- State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510030, China
- Correspondence: (B.L.); (C.Z.)
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14
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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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15
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Comparative Genomics of Escherichia coli Serotype O55:H7 Using Complete Closed Genomes. Microorganisms 2022; 10:microorganisms10081545. [PMID: 36013963 PMCID: PMC9413875 DOI: 10.3390/microorganisms10081545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/20/2022] [Accepted: 07/23/2022] [Indexed: 12/01/2022] Open
Abstract
Escherichia coli O55:H7 is a human foodborne pathogen and is recognized as the progenitor strain of E. coli O157:H7. While this strain is important from a food safety and genomic evolution standpoint, much of the genomic diversity of E. coli O55:H7 has been demonstrated using draft genomes. Here, we combine the four publicly available E. coli O55:H7 closed genomes with six newly sequenced closed genomes to provide context to this strain’s genomic diversity. We found significant diversity within the 10 E. coli O55:H7 strains that belonged to three different sequence types. The prophage content was about 10% of the genome, with three prophages common to all strains and seven unique to one strain. Overall, there were 492 insertion sequences identified within the six new sequence strains, with each strain on average containing 75 insertions (range 55 to 114). A total of 31 plasmids were identified between all isolates (range 1 to 6), with one plasmid (pO55) having an identical phylogenetic tree as the chromosome. The release and comparison of these closed genomes provides new insight into E. coli O55:H7 diversity and its ability to cause disease in humans.
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16
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Novel indole-mediated potassium ion import system confers a survival advantage to the Xanthomonadaceae family. THE ISME JOURNAL 2022; 16:1717-1729. [PMID: 35319020 DOI: 10.1038/s41396-022-01219-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/02/2022] [Accepted: 03/07/2022] [Indexed: 12/30/2022]
Abstract
Interspecific and intraspecific communication systems of microorganisms are involved in the regulation of various stress responses in microbial communities. Although the significance of signaling molecules in the ubiquitous family Xanthomonadaceae has been reported, the role bacterial communications play and their internal mechanisms are largely unknown. Here, we use Lysobacter enzymogenes, a member of Xanthomonadaceae, to identify a novel potassium ion import system, LeKdpXFABC. This import system participates in the indole-mediated interspecies signaling pathway and matters in environmental adaptation. Compared with the previously reported kdpFABC of Escherichia coli, LekdpXFABC contains a novel indispensable gene LekdpX and is directly regulated by the indole-related two-component system QseC/B. QseC autophosphorylation is involved in this process. The operon LekdpXFABC widely exists in Xanthomonadaceae. Moreover, indole promotes antimicrobial product production at the early exponential phase. Further analyses show that indole enhances potassium ion adsorption on the cell surface by upregulating the production of O-antigenic polysaccharides. Finally, we confirm that LeKdpXFABC mediation by indole is subject to the intraspecific signaling molecules DSFs, of which the biosynthesis genes always exist together with LekdpXFABC. Therefore, as a new idea, the signal collaborative strategy of indole and DSFs might ensure the persistent fitness advantage of Xanthomonadaceae in variable environments.
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17
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Yan L, Liu Y. Mechanistic Insights into the Anaerobic Degradation of Globally Abundant Dihydroxypropanesulfonate Catalyzed by the DHPS-Sulfolyase (HpsG). J Chem Inf Model 2022; 62:2880-2888. [PMID: 35583151 DOI: 10.1021/acs.jcim.2c00174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
2(S)-Dihydroxypropanesulfonate (DHPS) is the main abundant organosulfonate in the biosphere generated by the microbial degradation of the abundant organosulfur species 6-deoxy-6-sulfo-d-glucopyranose (sulfoquinovose, SQ). Massive amounts of DHPS can also be produced by the highly abundant oceanic diatoms. The quantity of degradation DHPS is so large that it has become an important part of the earth's sulfur. The recently characterized O2-sensitive glycyl radical enzyme DHPS-sulfolyase HpsG in anaerobic bacteria was found to be capable of cleaving the C-S bond of DHPS under anaerobic conditions. However, the detailed degradation mechanism is still unclear. Here, on the basis of the crystal structure of HpsG, we constructed the computational model and performed QM/MM calculations to illuminate the anaerobic degradation mechanism of DHPS. Our calculations revealed that the degradation reaction follows an unusual radical-dependent mechanism that does not require a conserved Glu464 to deprotonate the C2 hydroxyl of substrate to promote the C-S cleavage; instead, after the first hydrogen abstraction triggered by the thiyl radical (Cys462), the C-S bond in 2(S)-dihydroxypropanesulfonate can directly collapse. Thus, conserved Glu464 mainly plays a role in stabilizing the substrate and reaction intermediate by forming a hydrogen bond. After the release of the sulfonic acid group from the protein environment, the deprotonated Glu464 spontaneously accepts a proton from the C2 hydroxyl of the substrate radical. Our findings clarified an unusual C-S cleavage mechanism involved in the DHPS degradation reaction catalyzed by GREs.
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Affiliation(s)
- Lijuan Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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18
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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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19
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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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20
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Burchill L, Zudich L, van der Peet PL, White JM, Williams SJ. Synthesis of the Alkylsulfonate Metabolites Cysteinolic Acid, 3-Amino-2-hydroxypropanesulfonate, and 2,3-Dihydroxypropanesulfonate. J Org Chem 2022; 87:4333-4342. [PMID: 35199527 DOI: 10.1021/acs.joc.2c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chiral hydroxy- and aminohydroxysulfonic acids are widespread in the marine and terrestrial environment. Here we report simple methods for the synthesis of d- and l-cysteinolic acid (from (Boc-d-Cys-OH)2 and (Boc-l-Cys-OH)2, respectively), R- and S-3-amino-2-hydroxypropanesulfonate (from S- and R-epichlorohydrin, respectively), and R- and S-2,3-dihydroxypropanesulfonate (from S- and R-epichlorohydrin, respectively). d-Cysteinolate bile salts were generated by coupling with cholic and chenodeoxycholic acids. A series of single-crystal 3D X-ray structures confirmed the absolute configurations of the aminosulfonates. By comparison of optical rotation, we assign naturally occurring 3-amino-2-hydroxypropanesulfonate from Gateloupia livida as possessing the R-configuration. This simple synthetic approach will support future studies of the occurrence, chemotaxonomic distribution, and metabolism of these alkylsulfonates.
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Affiliation(s)
- Laura Burchill
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Luca Zudich
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Phillip L van der Peet
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jonathan M White
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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21
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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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22
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Ubiquitous Occurrence of a Biogenic Sulfonate in Marine Environment. SUSTAINABILITY 2022. [DOI: 10.3390/su14031240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The biogenic sulfonate 2,3-dihydroxypropane-1-sulfonate (DHPS) is a vital metabolic currency between phytoplankton and bacteria in marine environments. However, the occurrence and quantification of DHPS in the marine environment has not been well-characterized. In this study, we used targeted metabolomics to determine the concentration of DHPS in the Pearl River Estuary, an in situ costal mesocosm ecosystem and a hydrothermal system off Kueishantao Island. The results suggested that DHPS occurred ubiquitously in the marine environment, even in shallow-sea hydrothermal systems, at a level comparable to that of dimethylsulfoniopropionate. The concentration of DHPS was closely related to phytoplankton community composition and was especially associated with the abundance of diatoms. Epsilonproteobacteria were considered as the most likely producers of DHPS in shallow-sea hydrothermal systems. This work expands current knowledge on sulfonates and presents a new viewpoint on the sulfur cycle in hydrothermal systems.
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23
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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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24
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Chen X, Liu L, Gao X, Dai X, Han Y, Chen Q, Tang K. Metabolism of chiral sulfonate compound 2,3-dihydroxypropane-1-sulfonate (DHPS) by Roseobacter bacteria in marine environment. ENVIRONMENT INTERNATIONAL 2021; 157:106829. [PMID: 34425483 DOI: 10.1016/j.envint.2021.106829] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
The sulfonate compound 2,3-dihydroxypropane-1-sulfonate (DHPS) is one of the most abundant organic sulfur compounds in the biosphere. DHPS derived from dietary intake could be transformed into sulfide by intestinal microbiota and thus impacts human health. However, little is known about its sulfur transformation and subsequent impacts in marine environment. In this study, laboratory-culturing was combined with targeted metabolomic, chemical fluorescence probing, and comparative proteomic methods to examine the bioavailability of chiral DHPS (R and S isomers) for bacteria belonging to the marine Roseobacter clade. The metabolic potential of DHPS in bacteria was further assessed based on genomic analysis. Roseobacter members Ruegeria pomeroyi DSS-3, Dinoroseobacter shibae DFL 12, and Roseobacter denitrificans OCh 114 could utilize chiral DHPS for growth, producing sulfite. They all contained a similar gene cluster for DHPS metabolism but differed in the genes encoding enzymes for desulfonation. There was no significant difference in the growth rate and DHPS consumption rate for R. pomeroyi DSS-3 between R- and S-DHPS cultures, with few proteins expressed differentially were found. Proteomic data suggested that a series of hydrogenases oxidized DHPS, after which desulfonation could proceed via three distinct enzymatic pathways. Strain R. pomeroyi DSS-3 completed the desulfonation via L-cysteate sulfo-lyase, while D. shibae DFL 12 and R. denitrificans OCh 114 primarily utilized sulfolactate sulfo-lyase, and sulfopyruvate decarboxylase followed by sulfoacetaldehyde acetyltransferase, respectively, to complete desulfonation releasing the sulfonate-moiety. The sulfite could be further oxidized or incorporated into sulfate assimilation, indicated by the proteomic data. Furthermore, DHPS metabolic pathways were found primarily in marine bacterial groups, including the majority of sequenced Roseobacter genomes. Our results suggest that chiral DHPS, as a vital reduced sulfur reservoir, could be metabolized by marine bacteria, providing a resource for bacterial growth, rather than acting as a source of toxic sulfide within the marine ecosystem.
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Affiliation(s)
- Xiaofeng Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Xiang Gao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Xi Dai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Yu Han
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Xiamen University, Xiamen 361102, Fujian, PR China.
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25
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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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26
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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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27
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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: 20] [Impact Index Per Article: 6.7] [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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28
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Shimada T, Ogasawara H, Kobayashi I, Kobayashi N, Ishihama A. Single-Target Regulators Constitute the Minority Group of Transcription Factors in Escherichia coli K-12. Front Microbiol 2021; 12:697803. [PMID: 34220787 PMCID: PMC8249747 DOI: 10.3389/fmicb.2021.697803] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
The identification of regulatory targets of all transcription factors (TFs) is critical for understanding the entire network of genome regulation. A total of approximately 300 TFs exist in the model prokaryote Escherichia coli K-12, but the identification of whole sets of their direct targets is impossible with use of in vivo approaches. For this end, the most direct and quick approach is to identify the TF-binding sites in vitro on the genome. We then developed and utilized the gSELEX screening system in vitro for identification of more than 150 E. coli TF-binding sites along the E. coli genome. Based on the number of predicted regulatory targets, we classified E. coli K-12 TFs into four groups, altogether forming a hierarchy ranging from a single-target TF (ST-TF) to local TFs, global TFs, and nucleoid-associated TFs controlling as many as 1,000 targets. Using the collection of purified TFs and a library of genome DNA segments from a single and the same E. coli K-12, we identified here a total of 11 novel ST-TFs, CsqR, CusR, HprR, NorR, PepA, PutA, QseA, RspR, UvrY, ZraR, and YqhC. The regulation of single-target promoters was analyzed in details for the hitherto uncharacterized QseA and RspR. In most cases, the ST-TF gene and its regulatory target genes are adjacently located on the E. coli K-12 genome, implying their simultaneous transfer in the course of genome evolution. The newly identified 11 ST-TFs and the total of 13 hitherto identified altogether constitute the minority group of TFs in E. coli K-12.
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Affiliation(s)
| | - Hiroshi Ogasawara
- Research Center for Supports to Advanced Science, Division of Gene Research, Shinshu University, Nagano, Japan.,Research Center for Fungal and Microbial Dynamism, Shinshu University, Nagano, Japan
| | - Ikki Kobayashi
- School of Agriculture, Meiji University, Kawasaki, Japan
| | - Naoki Kobayashi
- Department of Frontier Science, Hosei University, Koganei, Japan
| | - Akira Ishihama
- Department of Frontier Science, Hosei University, Koganei, Japan.,Micro-Nano Technology Research Center, Hosei University, Koganei, Japan
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29
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Pan Q, Li Z, Ju X, Hou C, Xiao Y, Shi R, Fu C, Danchin A, You C. Escherichia coli segments its controls on carbon-dependent gene expression into global and specific regulations. Microb Biotechnol 2021; 14:1084-1106. [PMID: 33650807 PMCID: PMC8085971 DOI: 10.1111/1751-7915.13776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 01/20/2023] Open
Abstract
How bacteria adjust gene expression to cope with variable environments remains open to question. Here, we investigated the way global gene expression changes in E. coli correlated with the metabolism of seven carbon substrates chosen to trigger a large panel of metabolic pathways. Coarse-grained analysis of gene co-expression identified a novel regulation pattern: we established that the gene expression trend following immediately the reduction of growth rate (GR) was correlated to its initial expression level. Subsequent fine-grained analysis of co-expression demonstrated that the Crp regulator, coupled with a change in GR, governed the response of most GR-dependent genes. By contrast, the Cra, Mlc and Fur regulators governed the expression of genes responding to non-glycolytic substrates, glycolytic substrates or phosphotransferase system transported sugars following an idiosyncratic way. This work allowed us to expand additional genes in the panel of gene complement regulated by each regulator and to elucidate the regulatory functions of each regulator comprehensively. Interestingly, the bulk of genes controlled by Cra and Mlc were, respectively, co-regulated by Crp- or GR-related effect and our quantitative analysis showed that each factor took turns to work as the primary one or contributed equally depending on the conditions.
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Affiliation(s)
- Qing Pan
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao, ShandongChina
| | - Zongjin Li
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Xian Ju
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Chaofan Hou
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Yunzhu Xiao
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Ruoping Shi
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Engineering Research Center of Biomass Resources and EnvironmentQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao, ShandongChina
| | - Antoine Danchin
- Kodikos Labs/Stellate TherapeuticsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen UniversityShenzhen, GuangdongChina
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30
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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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31
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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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32
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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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33
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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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34
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Sokaribo AS, Perera SR, Sereggela Z, Krochak R, Balezantis LR, Xing X, Lam S, Deck W, Attah-Poku S, Abbott DW, Tamuly S, White AP. A GMMA-CPS-Based Vaccine for Non-Typhoidal Salmonella. Vaccines (Basel) 2021; 9:vaccines9020165. [PMID: 33671372 PMCID: PMC7922415 DOI: 10.3390/vaccines9020165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/16/2022] Open
Abstract
Non-typhoidal Salmonella are a major cause of gastroenteritis worldwide, as well as causing bloodstream infections in sub-Saharan Africa with a high fatality rate. No vaccine is currently available for human use. Current vaccine development strategies are focused on capsular polysaccharides (CPS) present on the surface of non-typhoidal Salmonella. This study aimed to boost the amount of CPS purified from S. Typhimurium for immunization trials. Random mutagenesis with Tn10 transposon increased the production of CPS colanic acid, by 10-fold compared to wildtype. Immunization with colanic acid or colanic acid conjugated to truncated glycoprotein D or inactivated diphtheria toxin did not induce a protective immune response in mice. However, immunization with Generalized Modules for Membrane Antigens (GMMAs) isolated from colanic acid overproducing isolates reduced Salmonella colonization in mice. Our results support the development of a GMMA-CPS-based vaccine against non-typhoidal Salmonella.
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Affiliation(s)
- Akosiererem S. Sokaribo
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Sumudu R. Perera
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Zoe Sereggela
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Ryan Krochak
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Lindsay R. Balezantis
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
| | - Xiaohui Xing
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J4B1, Canada; (X.X.); (D.W.A.)
| | - Shirley Lam
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
| | - William Deck
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
| | - Sam Attah-Poku
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
| | - Dennis Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J4B1, Canada; (X.X.); (D.W.A.)
| | - Shantanu Tamuly
- Department of Veterinary Biochemistry, College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati 781022, Assam, India;
| | - Aaron P. White
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK S7N5E3, Canada; (A.S.S.); (S.R.P.); (Z.S.); (R.K.); (L.R.B.); (S.L.); (W.D.); (S.A.-P.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N5E5, Canada
- Correspondence: ; Tel.: +01-306-966-7485
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35
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Peretó J. Transmetabolism: the non-conformist approach to biotechnology. Microb Biotechnol 2021; 14:41-44. [PMID: 33119190 PMCID: PMC7888464 DOI: 10.1111/1751-7915.13691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/03/2022] Open
Affiliation(s)
- Juli Peretó
- Department of Biochemistry and Molecular BiologyUniversity of ValenciaInstitute for Integrative Systems Biology I2SysBio (University of Valencia‐CSIC)Darwin Bioprospecting Excellence SL, Parc Científic de la Universitat de ValènciaPaternaSpain
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36
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Poh WH, Lin J, Colley B, Müller N, Goh BC, Schleheck D, El Sahili A, Marquardt A, Liang Y, Kjelleberg S, Lescar J, Rice SA, Klebensberger J. The SiaABC threonine phosphorylation pathway controls biofilm formation in response to carbon availability in Pseudomonas aeruginosa. PLoS One 2020; 15:e0241019. [PMID: 33156827 PMCID: PMC7647112 DOI: 10.1371/journal.pone.0241019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/06/2020] [Indexed: 12/17/2022] Open
Abstract
The critical role of bacterial biofilms in chronic human infections calls for novel anti-biofilm strategies targeting the regulation of biofilm development. However, the regulation of biofilm development is very complex and can include multiple, highly interconnected signal transduction/response pathways, which are incompletely understood. We demonstrated previously that in the opportunistic, human pathogen P. aeruginosa, the PP2C-like protein phosphatase SiaA and the di-guanylate cyclase SiaD control the formation of macroscopic cellular aggregates, a type of suspended biofilms, in response to surfactant stress. In this study, we demonstrate that the SiaABC proteins represent a signal response pathway that functions through a partner switch mechanism to control biofilm formation. We also demonstrate that SiaABCD functionality is dependent on carbon substrate availability for a variety of substrates, and that upon carbon starvation, SiaB mutants show impaired dispersal, in particular with the primary fermentation product ethanol. This suggests that carbon availability is at least one of the key environmental cues integrated by the SiaABCD system. Further, our biochemical, physiological and crystallographic data reveals that the phosphatase SiaA and its kinase counterpart SiaB balance the phosphorylation status of their target protein SiaC at threonine 68 (T68). Crystallographic analysis of the SiaA-PP2C domain shows that SiaA is present as a dimer. Dynamic modelling of SiaA with SiaC suggested that SiaA interacts strongly with phosphorylated SiaC and dissociates rapidly upon dephosphorylation of SiaC. Further, we show that the known phosphatase inhibitor fumonisin inhibits SiaA mediated phosphatase activity in vitro. In conclusion, the present work improves our understanding of how P. aeuruginosa integrates specific environmental conditions, such as carbon availability and surfactant stress, to regulate cellular aggregation and biofilm formation. With the biochemical and structural characterization of SiaA, initial data on the catalytic inhibition of SiaA, and the interaction between SiaA and SiaC, our study identifies promising targets for the development of biofilm-interference drugs to combat infections of this aggressive opportunistic pathogen.
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Affiliation(s)
- Wee-Han Poh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jianqing Lin
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research, Singapore, Singapore
| | - Brendan Colley
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicolai Müller
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Konstanz, Germany
| | - Boon Chong Goh
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - David Schleheck
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Konstanz, Germany
| | - Abbas El Sahili
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Andreas Marquardt
- Konstanz Research School Chemical Biology, Departments of Chemistry and Biology, University of Konstanz, Konstanz, Germany
| | - Yang Liang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- The ithree Institute, The University of Technology Sydney, Sydney, Australia
| | - Janosch Klebensberger
- University of Stuttgart, Institute of Biochemistry and Technical Biochemistry, Stuttgart, Germany
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37
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Haange SB, Groeger N, Froment J, Rausch T, Burkhardt W, Gonnermann S, Braune A, Blaut M, von Bergen M, Rolle-Kampczyk U. Multiplexed Quantitative Assessment of the Fate of Taurine and Sulfoquinovose in the Intestinal Microbiome. Metabolites 2020; 10:E430. [PMID: 33114761 PMCID: PMC7692227 DOI: 10.3390/metabo10110430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 12/25/2022] Open
Abstract
(1) Introduction: Sulfonates, which can be diet- or host-derived, are a class of compounds detected in the gut, are involved in host-microbiome interactions and have several health effects. Our aim was to develop a method to quantify five of the sulfonates in the intestine and apply it in a simplified human microbiome model. These were taurine, its metabolic precursor cysteate and one of its degradation products isethionate, as well as sulfoquinovose and one of its most relevant degradation products 2,3-dihydroxy-1-propanesulfonate. (2) Methods: An extraction and sample preparation method was developed, without the need for derivatization. To detect and quantify the extracted sulfonates, a multiplexed LC-MS/MS-MRM method was established. (3) Results: The accuracy and precision of the method were within GLP-accepted parameters (www.ema.europa.eu). To apply this method in a pilot study, we spiked either taurine or sulfoquinovose into an in vitro simplified human microbiota model with and without Bilophila wadsworthia, a known sulfonate utilizer. The results revealed that only the culture with B. wadsworthia was able to degrade taurine, with isethionate as an intermediate. After spiking the communities with sulfoquinovose, the results revealed that the simplified human microbiome model was able to degrade sulfoquinovose to 2,3-dihydroxypropane-1-sulfonate, which was probably catalyzed by Escherichia coli. In the community with B. wadsworthia, the 2,3-dihydroxypropane-1-sulfonate produced was further degraded by B. wadsworthia to sulfide. (4) Conclusions: We successfully developed a method for sulfonate quantification and applied it in a first pilot study.
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Affiliation(s)
- Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
| | - Nicole Groeger
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
| | - Jean Froment
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
| | - Theresa Rausch
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Wiebke Burkhardt
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Svenja Gonnermann
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Annett Braune
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Michael Blaut
- Research Group Intestinal Microbiology, Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, 14558 Nuthetal, Germany; (T.R.); (W.B.); (S.G.); (A.B.); (M.B.)
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, 04103 Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (N.G.); (J.F.); (M.v.B.)
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38
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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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Frommeyer B, Fiedler AW, Oehler SR, Hanson BT, Loy A, Franchini P, Spiteller D, Schleheck D. Environmental and Intestinal Phylum Firmicutes Bacteria Metabolize the Plant Sugar Sulfoquinovose via a 6-Deoxy-6-sulfofructose Transaldolase Pathway. iScience 2020; 23:101510. [PMID: 32919372 PMCID: PMC7491151 DOI: 10.1016/j.isci.2020.101510] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/04/2020] [Accepted: 08/25/2020] [Indexed: 01/22/2023] Open
Abstract
Bacterial degradation of the sugar sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) produced by plants, algae, and cyanobacteria, is an important component of the biogeochemical carbon and sulfur cycles. Here, we reveal a third biochemical pathway for primary SQ degradation in an aerobic Bacillus aryabhattai strain. An isomerase converts SQ to 6-deoxy-6-sulfofructose (SF). A novel transaldolase enzyme cleaves the SF to 3-sulfolactaldehyde (SLA), while the non-sulfonated C3-(glycerone)-moiety is transferred to an acceptor molecule, glyceraldehyde phosphate (GAP), yielding fructose-6-phosphate (F6P). Intestinal anaerobic bacteria such as Enterococcus gilvus, Clostridium symbiosum, and Eubacterium rectale strains also express transaldolase pathway gene clusters during fermentative growth with SQ. The now three known biochemical strategies for SQ catabolism reflect adaptations to the aerobic or anaerobic lifestyle of the different bacteria. The occurrence of these pathways in intestinal (family) Enterobacteriaceae and (phylum) Firmicutes strains further highlights a potential importance of metabolism of green-diet SQ by gut microbial communities to, ultimately, hydrogen sulfide.
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Affiliation(s)
- Benjamin Frommeyer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | | | | | - Buck T. Hanson
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Wien, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090 Wien, Austria
| | - Paolo Franchini
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Dieter Spiteller
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
| | - David Schleheck
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, 78457 Konstanz, Germany
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40
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A Sulfoglycolytic Entner-Doudoroff Pathway in Rhizobium leguminosarum bv. trifolii SRDI565. Appl Environ Microbiol 2020; 86:AEM.00750-20. [PMID: 32444469 DOI: 10.1128/aem.00750-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/14/2020] [Indexed: 01/05/2023] Open
Abstract
Rhizobia are nitrogen-fixing bacteria that engage in symbiotic relationships with plant hosts but can also persist as free-living bacteria in the soil and rhizosphere. Here, we show that free-living Rhizobium leguminosarum SRDI565 can grow on the sulfosugar sulfoquinovose (SQ) or the related glycoside SQ-glycerol using a sulfoglycolytic Entner-Doudoroff (sulfo-ED) pathway, resulting in production of sulfolactate (SL) as the major metabolic end product. Comparative proteomics supports the involvement of a sulfo-ED operon encoding an ABC transporter, sulfo-ED enzymes, and an SL exporter. Consistent with an oligotrophic lifestyle, proteomics data revealed little change in expression of the sulfo-ED proteins during growth on SQ versus mannitol, a result confirmed through biochemical assay of sulfoquinovosidase activity in cell lysates. Metabolomics analysis showed that growth on SQ involves gluconeogenesis to satisfy metabolic requirements for glucose-6-phosphate and fructose-6-phosphate. Metabolomics analysis also revealed the unexpected production of small amounts of sulfofructose and 2,3-dihydroxypropanesulfonate, which are proposed to arise from promiscuous activities of the glycolytic enzyme phosphoglucose isomerase and a nonspecific aldehyde reductase, respectively. The discovery of a rhizobium isolate with the ability to degrade SQ builds our knowledge of how these important symbiotic bacteria persist within soil.IMPORTANCE Sulfonate sulfur is a major form of organic sulfur in soils but requires biomineralization before it can be utilized by plants. Very little is known about the biochemical processes used to mobilize sulfonate sulfur. We show that a rhizobial isolate from soil, Rhizobium leguminosarum SRDI565, possesses the ability to degrade the abundant phototroph-derived carbohydrate sulfonate SQ through a sulfoglycolytic Entner-Doudoroff pathway. Proteomics and metabolomics demonstrated the utilization of this pathway during growth on SQ and provided evidence for gluconeogenesis. Unexpectedly, off-cycle sulfoglycolytic species were also detected, pointing to the complexity of metabolic processes within cells under conditions of sulfoglycolysis. Thus, rhizobial metabolism of the abundant sulfosugar SQ may contribute to persistence of the bacteria in the soil and to mobilization of sulfur in the pedosphere.
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Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate. Proc Natl Acad Sci U S A 2020; 117:15599-15608. [PMID: 32571930 DOI: 10.1073/pnas.2003434117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
2(S)-dihydroxypropanesulfonate (DHPS) is a microbial degradation product of 6-deoxy-6-sulfo-d-glucopyranose (sulfoquinovose), a component of plant sulfolipid with an estimated annual production of 1010 tons. DHPS is also at millimolar levels in highly abundant marine phytoplankton. Its degradation and sulfur recycling by microbes, thus, play important roles in the biogeochemical sulfur cycle. However, DHPS degradative pathways in the anaerobic biosphere are not well understood. Here, we report the discovery and characterization of two O2-sensitive glycyl radical enzymes that use distinct mechanisms for DHPS degradation. DHPS-sulfolyase (HpsG) in sulfate- and sulfite-reducing bacteria catalyzes C-S cleavage to release sulfite for use as a terminal electron acceptor in respiration, producing H2S. DHPS-dehydratase (HpfG), in fermenting bacteria, catalyzes C-O cleavage to generate 3-sulfopropionaldehyde, subsequently reduced by the NADH-dependent sulfopropionaldehyde reductase (HpfD). Both enzymes are present in bacteria from diverse environments including human gut, suggesting the contribution of enzymatic radical chemistry to sulfur flux in various anaerobic niches.
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42
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Iglesias MJ, Soengas R, Martins CB, Correia MJ, Ferreira JD, Santos LMA, Ortiz FL. Chemotaxonomic Profiling Through NMR 1. JOURNAL OF PHYCOLOGY 2020; 56:521-539. [PMID: 31876290 DOI: 10.1111/jpy.12959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/11/2019] [Indexed: 06/10/2023]
Abstract
A metabolite screening of cyanobacteria was performed by nuclear magnetic resonance (NMR) analysis of the soluble material obtained through sequential extraction of the biomass with three different extractive ability solvents (hexane, ethyl acetate, and methanol). Twenty-five strains from the Coimbra Collection of Algae (ACOI) belonging to different orders in the botanical code that represent three subsections of the Stainer-Rippka classification were used. The 1 H NMR spectra of hexane extracts showed that only two strains of Nostoc genus accumulated triacylglycerols. Monogalactosyldiacylglycerols and digalactosyldiacylglycerols were the major components of the ethyl acetate extracts in a mono- to digalactosyldiacylglycerols ratio of 4.5 estimated by integration of the signals at δ 3.99 and 3.94 ppm (sn3 glycerol methylene). Oligosaccharides of sucrose and mycosporine-like amino acids, among other polar metabolites, were detected in the methanolic extracts. Strains of Nostocales order contained heterocyst glycolipids, whereas sulphoquinovosyldiacylglycerols were absent in one of the studied strains (Microchaete tenera ACOI 1451). Phosphathidylglycerol was identified as the major phospholipid in the methanolic extracts together with minor amounts of phosphatidylcholine based on 1 H, 31 P 2D correlation experiments. Chemotaxonomic information could be easily obtained through the analysis of the δ 3.0-0.5 ppm (fatty acid distribution) and δ 1.2-1.1 ppm (terminal methyl groups of the aglycons in heterocyst glycolipids) regions of the 1 H NMR spectra of the ethyl acetate and methanol extracts, respectively.
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Affiliation(s)
- María José Iglesias
- Área de Química Orgánica, Research Centre CIAIMBITAL, Universidad de Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Raquel Soengas
- Área de Química Orgánica, Research Centre CIAIMBITAL, Universidad de Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Clara B Martins
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Maria João Correia
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Joana D Ferreira
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Lilia M A Santos
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Fernando López Ortiz
- Área de Química Orgánica, Research Centre CIAIMBITAL, Universidad de Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
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Sharma M, Abayakoon P, Lingford JP, Epa R, John A, Jin Y, Goddard-Borger ED, Davies GJ, Williams SJ. Dynamic Structural Changes Accompany the Production of Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase. ACS Catal 2020. [DOI: 10.1021/acscatal.9b04427] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Palika Abayakoon
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne, Parkville, Victoria 3010, Australia
| | - 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
| | - Ruwan Epa
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alan John
- 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
| | - Yi Jin
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - 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, Heslington, York YO10 5DD, United Kingdom
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute University of Melbourne, Parkville, Victoria 3010, Australia
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Zhang Y, Mui JWY, Arumaperuma T, Lingford JP, Goddard-Borger ED, White JM, Williams SJ. Concise synthesis of sulfoquinovose and sulfoquinovosyl diacylglycerides, and development of a fluorogenic substrate for sulfoquinovosidases. Org Biomol Chem 2020; 18:675-686. [PMID: 31894821 DOI: 10.1039/c9ob02540e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The sulfolipid sulfoquinovosyl diacylglycerol (SQDG) and its headgroup, the sulfosugar sulfoquinovose (SQ), are estimated to harbour up to half of all organosulfur in the biosphere. SQ is liberated from SQDG and related glycosides by the action of sulfoquinovosidases (SQases). We report a 10-step synthesis of SQDG that we apply to the preparation of saturated and unsaturated lipoforms. We also report an expeditious synthesis of SQ and (13C6)SQ, and X-ray crystal structures of sodium and potassium salts of SQ. Finally, we report the synthesis of a fluorogenic SQase substrate, methylumbelliferyl α-d-sulfoquinovoside, and examination of its cleavage kinetics by two recombinant SQases. These compounds will assist in dissecting the role of sulfoglycolysis in the biogeochemical sulfur cycle and understanding the molecular basis of sulfoglycolysis.
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Affiliation(s)
- Yunyang Zhang
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Janice W-Y Mui
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Thimali Arumaperuma
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia.
| | - James P Lingford
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3010, Australia and Department of Medical Biology, 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 and Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jonathan M White
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute and University of Melbourne, Parkville, Victoria 3010, Australia.
| | - 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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Affiliation(s)
- Beth T Williams
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK.
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Abstract
Marine microorganisms play crucial roles in Earth's element cycles through the production and consumption of organic matter. One of the elements whose fate is governed by microbial activities is sulfur, an essential constituent of biomass and a crucial player in climate processes. With sulfur already being well studied in the ocean in its inorganic forms, organic sulfur compounds are emerging as important chemical links between marine phytoplankton and bacteria. The high concentration of inorganic sulfur in seawater, which can readily be reduced by phytoplankton, provides a freely available source of sulfur for biomolecule synthesis. Mechanisms such as exudation and cell lysis release these phytoplankton-derived sulfur metabolites into seawater, from which they are rapidly assimilated by marine bacteria and archaea. Energy-limited bacteria use scavenged sulfur metabolites as substrates or for the synthesis of vitamins, cofactors, signalling compounds and antibiotics. In this Review, we examine the current knowledge of sulfur metabolites released into and taken up from the marine dissolved organic matter pool by microorganisms, and the ecological links facilitated by their diversity in structures, oxidation states and chemistry.
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Weissenbach J. Exploring biochemical diversity in bacteria. AN ACAD BRAS CIENC 2019; 91:e20190252. [PMID: 31365611 DOI: 10.1590/0001-3765201920190252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/18/2019] [Indexed: 11/21/2022] Open
Abstract
The various descriptors of biochemical diversity and an evaluation of its status of knowledge are briefly outlined. Using a few examples from in house research projects, I illustrate strategies used to increase this knowledge. Because bacteria represent an extremely diverse domain of life and carry out the widest known range of biochemical transformations, this mini-review focusses on bacteria.
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Affiliation(s)
- Jean Weissenbach
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
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Sulfonate-based networks between eukaryotic phytoplankton and heterotrophic bacteria in the surface ocean. Nat Microbiol 2019; 4:1706-1715. [PMID: 31332382 DOI: 10.1038/s41564-019-0507-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/06/2019] [Indexed: 01/29/2023]
Abstract
In the surface ocean, phytoplankton transform inorganic substrates into organic matter that fuels the activity of heterotrophic microorganisms, creating intricate metabolic networks that determine the extent of carbon recycling and storage in the ocean. Yet, the diversity of organic molecules and interacting organisms has hindered detection of specific relationships that mediate this large flux of energy and matter. Here, we show that a tightly coupled microbial network based on organic sulfur compounds (sulfonates) exists among key lineages of eukaryotic phytoplankton producers and heterotrophic bacterial consumers in the North Pacific Subtropical Gyre. We find that cultured eukaryotic phytoplankton taxa produce sulfonates, often at millimolar internal concentrations. These same phytoplankton-derived sulfonates support growth requirements of an open-ocean isolate of the SAR11 clade, the most abundant group of marine heterotrophic bacteria. Expression of putative sulfonate biosynthesis genes and sulfonate abundances in natural plankton communities over the diel cycle link sulfonate production to light availability. Contemporaneous expression of sulfonate catabolism genes in heterotrophic bacteria highlights active cycling of sulfonates in situ. Our study provides evidence that sulfonates serve as an ecologically important currency for nutrient and energy exchange between microbial autotrophs and heterotrophs, highlighting the importance of organic sulfur compounds in regulating ecosystem function.
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Sulfur metabolites that facilitate oceanic phytoplankton-bacteria carbon flux. ISME JOURNAL 2019; 13:2536-2550. [PMID: 31227817 DOI: 10.1038/s41396-019-0455-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/08/2019] [Accepted: 05/03/2019] [Indexed: 11/09/2022]
Abstract
Unlike biologically available nitrogen and phosphorus, which are often at limiting concentrations in surface seawater, sulfur in the form of sulfate is plentiful and not considered to constrain marine microbial activity. Nonetheless, in a model system in which a marine bacterium obtains all of its carbon from co-cultured phytoplankton, bacterial gene expression suggests that at least seven dissolved organic sulfur (DOS) metabolites support bacterial heterotrophy. These labile exometabolites of marine dinoflagellates and diatoms include taurine, N-acetyltaurine, isethionate, choline-O-sulfate, cysteate, 2,3-dihydroxypropane-1-sulfonate (DHPS), and dimethylsulfoniopropionate (DMSP). Leveraging from the compounds identified in this model system, we assessed the role of sulfur metabolites in the ocean carbon cycle by mining the Tara Oceans dataset for diagnostic genes. In the 1.4 million bacterial genome equivalents surveyed, estimates of the frequency of genomes harboring the capability for DOS metabolite utilization ranged broadly, from only 1 out of every 190 genomes (for the C2 sulfonate isethionate) to 1 out of every 5 (for the sulfonium compound DMSP). Bacteria able to participate in DOS transformations are dominated by Alphaproteobacteria in the surface ocean, but by SAR324, Acidimicrobiia, and Gammaproteobacteria at mesopelagic depths, where the capability for utilization occurs in higher frequency than in surface bacteria for more than half the sulfur metabolites. The discovery of an abundant and diverse suite of marine bacteria with the genetic capacity for DOS transformation argues for an important role for sulfur metabolites in the pelagic ocean carbon cycle.
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Saburi W, Sato S, Hashiguchi S, Muto H, Iizuka T, Mori H. Enzymatic characteristics of d-mannose 2-epimerase, a new member of the acylglucosamine 2-epimerase superfamily. Appl Microbiol Biotechnol 2019; 103:6559-6570. [DOI: 10.1007/s00253-019-09944-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/20/2019] [Accepted: 05/25/2019] [Indexed: 11/30/2022]
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