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Lei L, Alcolombri U, Tawfik DS. Biochemical Profiling of DMSP Lyases. Methods Enzymol 2018; 605:269-289. [PMID: 29909827 DOI: 10.1016/bs.mie.2018.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dimethyl sulfide (DMS) is released at rates of >107 tons annually and plays a key role in the oceanic sulfur cycle and ecology. Marine bacteria, algae, and possibly other organisms release DMS via cleavage of dimethylsulfoniopropionate (DMSP). DMSP lyases have been identified in various organisms, including bacteria, coral, and algae, thus comprising a range of gene families putatively assigned as DMSP lyases. Metagenomics may therefore provide insight regarding the presence of DMSP lyases in various marine environments, thereby promoting a better understanding of global DMS emission. However, gene counts, and even mRNA levels, do not necessarily reflect the level of DMSP cleavage activity in a given environmental sample, especially because some of the families assigned as DMSP lyases may merely exhibit promiscuous lyase activity. Here, we describe a range of biochemical profiling methods that can assign an observed DMSP lysis activity to a specific gene family. These methods include selective inhibitors and DMSP substrate analogues. Combined with genomics and metagenomics, biochemical profiling may enable a more reliable identification of the origins of DMS release in specific organisms and in crude environmental samples.
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Affiliation(s)
- Lei Lei
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Uria Alcolombri
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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2
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Lei L, Cherukuri KP, Alcolombri U, Meltzer D, Tawfik DS. The Dimethylsulfoniopropionate (DMSP) Lyase and Lyase-Like Cupin Family Consists of Bona Fide DMSP lyases as Well as Other Enzymes with Unknown Function. Biochemistry 2018; 57:3364-3377. [DOI: 10.1021/acs.biochem.8b00097] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lei Lei
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Uria Alcolombri
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Diana Meltzer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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3
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Schnicker NJ, De Silva SM, Todd JD, Dey M. Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter. Biochemistry 2017; 56:2873-2885. [DOI: 10.1021/acs.biochem.7b00099] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicholas J. Schnicker
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Saumya M. De Silva
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
| | - Jonathan D. Todd
- School
of Biological Sciences, University of East Anglia, Norwich Research
Park, Norwich NR4 7TJ, United Kingdom
| | - Mishtu Dey
- Department
of Chemistry, The University of Iowa, Iowa City, Iowa 52242, United States
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4
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Paladino A, Marchetti F, Rinaldi S, Colombo G. Protein design: from computer models to artificial intelligence. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Antonella Paladino
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Filippo Marchetti
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Silvia Rinaldi
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Giorgio Colombo
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
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5
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Alcolombri U, Lei L, Meltzer D, Vardi A, Tawfik DS. Assigning the Algal Source of Dimethylsulfide Using a Selective Lyase Inhibitor. ACS Chem Biol 2017; 12:41-46. [PMID: 28103686 DOI: 10.1021/acschembio.6b00844] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atmospheric dimethylsulfide (DMS) is massively produced in the oceans by bacteria, algae, and corals. To enable identification of DMS sources, we developed a potent mechanism-based inhibitor of the algal Alma dimethylsulfoniopropionate lyase family that does not inhibit known bacterial lyases. Its application to coral holobiont indicates that DMS originates from Alma lyase(s). This biochemical profiling may complement meta-genomics and transcriptomics to provide better understanding of the marine sulfur cycle.
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Affiliation(s)
- Uria Alcolombri
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Lei Lei
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Meltzer
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Vardi
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S. Tawfik
- Department
of Biomolecular Sciences and ‡Department of Plant and Environmental
Sciences, Weizmann Institute of Science, Rehovot, Israel
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6
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Brummett AE, Dey M. New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ. Biochemistry 2016; 55:6162-6174. [PMID: 27755868 DOI: 10.1021/acs.biochem.6b00585] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The marine microbial catabolism of dimethylsulfoniopropionate (DMSP) by the lyase pathway liberates ∼300 million tons of dimethyl sulfide (DMS) per year, which plays a major role in the biogeochemical cycling of sulfur. Recent biochemical and structural studies of some DMSP lyases, including DddQ, reveal the importance of divalent transition metal ions in assisting DMSP cleavage. While DddQ is believed to be zinc-dependent primarily on the basis of structural studies, excess zinc inhibits the enzyme. We examine the importance of iron in regulating the DMSP β-elimination reaction catalyzed by DddQ as our as-isolated purple-colored enzyme possesses ∼0.5 Fe/subunit. The UV-visible spectrum exhibited a feature at 550 nm, consistent with a tyrosinate-Fe(III) ligand-to-metal charge transfer transition. Incubation of as-isolated DddQ with added iron increases the intensity of the 550 nm peak, whereas addition of dithionite causes a bleaching as Fe(III) is reduced. Both the Fe(III) oxidized and Fe(II) reduced species are active, with similar kcat values and 2-fold differences in their Km values for DMSP. The slow turnover of Fe(III)-bound DddQ allowed us to capture a substrate-bound form of the enzyme. Our DMSP-Fe(III)-DddQ structure reveals conformational changes associated with substrate binding and shows that DMSP is positioned optimally to bind iron and is in the proximity of Tyr 120 that acts as a Lewis base to initiate catalysis. The structures of Tris-, DMSP-, and acrylate-bound forms of Fe(III)-DddQ reported here illustrate various states of the enzyme along the reaction pathway. These results provide new insights into DMSP lyase catalysis and have broader significance for understanding the mechanism of oceanic DMS production.
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Affiliation(s)
- Adam E Brummett
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
| | - Mishtu Dey
- Department of Chemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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7
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Burns AS, Bullock HA, Smith C, Huang Q, Whitman WB, Moran MA. Small RNAs expressed during dimethylsulfoniopropionate degradation by a model marine bacterium. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:763-773. [PMID: 27337503 DOI: 10.1111/1758-2229.12437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 06/06/2023]
Abstract
The fate of the sulfur moiety of dimethylsulfoniopropionate (DMSP) depends on the 'bacterial switch', a regulatory point between two metabolic pathways with different biogeochemical endpoints. Studies have focused on transcriptional patterns of known genes to determine physiological and environmental factors affecting this switch, but post-transcriptional regulation has been under-studied. Here we use a model bacterium containing both pathways to look for transcription of non-coding regulatory small RNAs (sRNAs) during DMSP metabolism. RNA-seq analysis of Ruegeria pomeroyi DSS-3 grown with DMSP, metabolic intermediates of DMSP degradation (MMPA or acetate), or methionine revealed 182 putative sRNAs, with 46 showing differential expression during growth on DMSP. A knockout mutant constructed for an upregulated sRNA had a phenotype that differed in its use of the two degradation pathways. Because transcription patterns of many differentially expressed sRNAs were not correlated with the transcription of their putative target gene, their effects on DMSP degradation would not be observable in the transcriptome. Overall, our results indicate that sRNAs are crucial but largely cryptic actors in regulating DMSP metabolism in this model marine bacterium and potentially other bacterial groups involved in the surface ocean sulfur cycle.
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Affiliation(s)
- Andrew S Burns
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Hannah A Bullock
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Christa Smith
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Qiuyuan Huang
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | | | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
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8
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Enzymatic breakage of dimethylsulfoniopropionate — a signature molecule for life at sea. Curr Opin Chem Biol 2016; 31:58-65. [DOI: 10.1016/j.cbpa.2016.01.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/11/2016] [Accepted: 01/15/2016] [Indexed: 11/18/2022]
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9
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Wang P, Chen X, Li C, Gao X, Zhu D, Xie B, Qin Q, Zhang X, Su H, Zhou B, Xun L, Zhang Y. Structural and molecular basis for the novel catalytic mechanism and evolution of
DddP
, an abundant peptidase‐like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold. Mol Microbiol 2015; 98:289-301. [DOI: 10.1111/mmi.13119] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Peng Wang
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Xiu‐Lan Chen
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Chun‐Yang Li
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Xiang Gao
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - De‐yu Zhu
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Bin‐Bin Xie
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Qi‐Long Qin
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Xi‐Ying Zhang
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Hai‐Nan Su
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Bai‐Cheng Zhou
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
| | - Lu‐ying Xun
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
| | - Yu‐Zhong Zhang
- State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China
- Marine Biotechnology Research Center Shandong University Jinan 250100 China
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10
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Alcolombri U, Ben-Dor S, Feldmesser E, Levin Y, Tawfik DS, Vardi A. MARINE SULFUR CYCLE. Identification of the algal dimethyl sulfide-releasing enzyme: A missing link in the marine sulfur cycle. Science 2015; 348:1466-9. [PMID: 26113722 DOI: 10.1126/science.aab1586] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Algal blooms produce large amounts of dimethyl sulfide (DMS), a volatile with a diverse signaling role in marine food webs that is emitted to the atmosphere, where it can affect cloud formation. The algal enzymes responsible for forming DMS from dimethylsulfoniopropionate (DMSP) remain unidentified despite their critical role in the global sulfur cycle. We identified and characterized Alma1, a DMSP lyase from the bloom-forming algae Emiliania huxleyi. Alma1 is a tetrameric, redox-sensitive enzyme of the aspartate racemase superfamily. Recombinant Alma1 exhibits biochemical features identical to the DMSP lyase in E. huxleyi, and DMS released by various E. huxleyi isolates correlates with their Alma1 levels. Sequence homology searches suggest that Alma1 represents a gene family present in major, globally distributed phytoplankton taxa and in other marine organisms.
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Affiliation(s)
- Uria Alcolombri
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel. Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit, Biological Services, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ester Feldmesser
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yishai Levin
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
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11
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Alcolombri U, Laurino P, Lara-Astiaso P, Vardi A, Tawfik DS. DddD Is a CoA-Transferase/Lyase Producing Dimethyl Sulfide in the Marine Environment. Biochemistry 2014; 53:5473-5. [DOI: 10.1021/bi500853s] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Uria Alcolombri
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Paola Laurino
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Pedro Lara-Astiaso
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Vardi
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S. Tawfik
- Department
of Biological Chemistry and ‡Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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12
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Reply to Tawfik et al.: DddQ is a dimethylsulfoniopropionate lyase involved in dimethylsulfoniopropionate catabolism in marine bacterial cells. Proc Natl Acad Sci U S A 2014; 111:E2080. [PMID: 24967457 DOI: 10.1073/pnas.1403460111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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