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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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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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