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Sharma V, Fedoseyenko D, Joshi S, Abdelwahed S, Begley TP. Phosphomethylpyrimidine Synthase (ThiC): Trapping of Five Intermediates Provides Mechanistic Insights on a Complex Radical Cascade Reaction in Thiamin Biosynthesis. ACS CENTRAL SCIENCE 2024; 10:988-1000. [PMID: 38799670 PMCID: PMC11117688 DOI: 10.1021/acscentsci.4c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 05/29/2024]
Abstract
Phosphomethylpyrimidine synthase (ThiC) catalyzes the conversion of AIR to the thiamin pyrimidine HMP-P. This reaction is the most complex enzyme-catalyzed radical cascade identified to date, and the detailed mechanism has remained elusive. In this paper, we describe the trapping of five new intermediates that provide snapshots of the ThiC reaction coordinate and enable the formulation of a revised mechanism for the ThiC-catalyzed reaction.
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Affiliation(s)
- Vishav Sharma
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Sumedh Joshi
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Sameh Abdelwahed
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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2
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Mooney R, Giammarini E, Corbett E, Thomson S, McKinley K, Sinisterra Sebastian P, Rodgers K, O’Donnell J, McGinness C, Roberts CW, Ramaesh K, Henriquez FL. Sodium Metabisulfite Inhibits Acanthamoeba Trophozoite Growth through Thiamine Depletion. Pathogens 2024; 13:431. [PMID: 38921729 PMCID: PMC11206890 DOI: 10.3390/pathogens13060431] [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: 04/16/2024] [Revised: 05/13/2024] [Accepted: 05/19/2024] [Indexed: 06/27/2024] Open
Abstract
Acanthamoeba keratitis (AK) is a severe infection of the cornea. Prevention and treatment are difficult due to the inefficacy of currently available compounds. The impact of many commonly used compounds for routine examinations of Acanthamoeba is unexplored but might offer insight useful in combatting AK. In this study, we demonstrate that sodium metabisulfite, a common preservation constituent of eye care solutions, was found to be active against Acanthamoeba trophozoites at concentrations lower than that commonly found in eye drops (IC50 0.03 mg/mL). We demonstrate that sodium metabisulfite depletes thiamine from growth medium and that Acanthamoeba is a thiamine auxotroph, requiring thiamine salvage for growth. The inhibitory effects of sodium metabisulfite can be overcome by thiamine supplementation. These results are consistent with the lack of key enzymes for thiamine biosynthesis in the genome of Acanthamoeba, an area which might prove exploitable using new or existing compounds. Indeed, this study highlights sodium metabisulfite as a useful inhibitor of Acanthamoeba castellanii trophozoites in vitro and that it acts, at least in part, by limiting available thiamine.
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Affiliation(s)
- Ronnie Mooney
- School of Health and Life Sciences, University of the West of Scotland Lanarkshire, Glasgow G72 0LH, UK; (R.M.)
| | - Elisa Giammarini
- School of Health and Life Sciences, University of the West of Scotland Lanarkshire, Glasgow G72 0LH, UK; (R.M.)
| | - Erin Corbett
- School of Health and Life Sciences, University of the West of Scotland Lanarkshire, Glasgow G72 0LH, UK; (R.M.)
| | - Scott Thomson
- School of Health and Life Sciences, University of the West of Scotland Lanarkshire, Glasgow G72 0LH, UK; (R.M.)
| | - Kevin McKinley
- School of Health and Life Sciences, University of the West of Scotland Lanarkshire, Glasgow G72 0LH, UK; (R.M.)
| | - Paula Sinisterra Sebastian
- School of Health and Life Sciences, University of the West of Scotland Lanarkshire, Glasgow G72 0LH, UK; (R.M.)
| | - Kiri Rodgers
- School of Health and Life Sciences, University of the West of Scotland Lanarkshire, Glasgow G72 0LH, UK; (R.M.)
| | - Jana O’Donnell
- School of Health and Life Sciences, University of the West of Scotland Lanarkshire, Glasgow G72 0LH, UK; (R.M.)
| | - Charles McGinness
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland Paisley, Glasgow PA1 2BE, UK
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Kanna Ramaesh
- NHS Greater Glasgow and Clyde, Gartnavel Hospital, Department of Ophthalmology, Glasgow G12 0YN, UK
| | - Fiona L. Henriquez
- School of Health and Life Sciences, University of the West of Scotland Lanarkshire, Glasgow G72 0LH, UK; (R.M.)
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Mangel N, Fudge JB, Gruissem W, Fitzpatrick TB, Vanderschuren H. Natural Variation in Vitamin B 1 and Vitamin B 6 Contents in Rice Germplasm. FRONTIERS IN PLANT SCIENCE 2022; 13:856880. [PMID: 35444674 PMCID: PMC9014206 DOI: 10.3389/fpls.2022.856880] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/24/2022] [Indexed: 05/03/2023]
Abstract
Insufficient dietary intake of micronutrients contributes to the onset of deficiencies termed hidden hunger-a global health problem affecting approximately 2 billion people. Vitamin B1 (thiamine) and vitamin B6 (pyridoxine) are essential micronutrients because of their roles as enzymatic cofactors in all organisms. Metabolic engineering attempts to biofortify rice endosperm-a poor source of several micronutrients leading to deficiencies when consumed monotonously-have led to only minimal improvements in vitamin B1 and B6 contents. To determine if rice germplasm could be exploited for biofortification of rice endosperm, we screened 59 genetically diverse accessions under greenhouse conditions for variation in vitamin B1 and vitamin B6 contents across three tissue types (leaves, unpolished and polished grain). Accessions from low, intermediate and high vitamin categories that had similar vitamin levels in two greenhouse experiments were chosen for in-depth vitamer profiling and selected biosynthesis gene expression analyses. Vitamin B1 and B6 contents in polished seeds varied almost 4-fold. Genes encoding select vitamin B1 and B6 biosynthesis de novo enzymes (THIC for vitamin B1, PDX1.3a-c and PDX2 for vitamin B6) were differentially expressed in leaves across accessions contrasting in their respective vitamin contents. These expression levels did not correlate with leaf and unpolished seed vitamin contents, except for THIC expression in leaves that was positively correlated with total vitamin B1 contents in polished seeds. This study expands our knowledge of diversity in micronutrient traits in rice germplasm and provides insights into the expression of genes for vitamin B1 and B6 biosynthesis in rice.
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Affiliation(s)
- Nathalie Mangel
- Plant Biotechnology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jared B Fudge
- Vitamin & Environmental Stress Responses in Plants, Department of Botany and Plant Biology, Université de Genève, Geneva, Switzerland
| | - Wilhelm Gruissem
- Plant Biotechnology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Teresa B Fitzpatrick
- Vitamin & Environmental Stress Responses in Plants, Department of Botany and Plant Biology, Université de Genève, Geneva, Switzerland
| | - Hervé Vanderschuren
- Plant Biotechnology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Plant Genetics Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
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Rei Liao JY, Friso G, Forsythe ES, Michel EJS, Williams AM, Boguraev SS, Ponnala L, Sloan DB, van Wijk KJ. Proteomics, phylogenetics, and co-expression analyses indicate novel interactions in the plastid CLP chaperone-protease system. J Biol Chem 2022; 298:101609. [PMID: 35065075 PMCID: PMC8889267 DOI: 10.1016/j.jbc.2022.101609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/20/2022] Open
Abstract
The chloroplast chaperone CLPC1 unfolds and delivers substrates to the stromal CLPPRT protease complex for degradation. We previously used an in vivo trapping approach to identify interactors with CLPC1 in Arabidopsis thaliana by expressing a STREPII-tagged copy of CLPC1 mutated in its Walker B domains (CLPC1-TRAP) followed by affinity purification and mass spectrometry. To create a larger pool of candidate substrates, adaptors, or regulators, we carried out a far more sensitive and comprehensive in vivo protein trapping analysis. We identified 59 highly enriched CLPC1 protein interactors, in particular proteins belonging to families of unknown functions (DUF760, DUF179, DUF3143, UVR-DUF151, HugZ/DUF2470), as well as the UVR domain proteins EXE1 and EXE2 implicated in singlet oxygen damage and signaling. Phylogenetic and functional domain analyses identified other members of these families that appear to localize (nearly) exclusively to plastids. In addition, several of these DUF proteins are of very low abundance as determined through the Arabidopsis PeptideAtlas http://www.peptideatlas.org/builds/arabidopsis/ showing that enrichment in the CLPC1-TRAP was extremely selective. Evolutionary rate covariation indicated that the HugZ/DUF2470 family coevolved with the plastid CLP machinery suggesting functional and/or physical interactions. Finally, mRNA-based coexpression networks showed that all 12 CLP protease subunits tightly coexpressed as a single cluster with deep connections to DUF760-3. Coexpression modules for other trapped proteins suggested specific functions in biological processes, e.g., UVR2 and UVR3 were associated with extraplastidic degradation, whereas DUF760-6 is likely involved in senescence. This study provides a strong foundation for discovery of substrate selection by the chloroplast CLP protease system.
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Affiliation(s)
- Jui-Yun Rei Liao
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Giulia Friso
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Evan S Forsythe
- Graduate Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Elena J S Michel
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | - Alissa M Williams
- Graduate Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Sasha S Boguraev
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA
| | | | - Daniel B Sloan
- Graduate Program in Cell and Molecular Biology, Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, New York, USA.
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Sun YJ, Cheng L. The Chemistry behind ThiC Rearrangement. Chembiochem 2021; 23:e202100385. [PMID: 34494352 DOI: 10.1002/cbic.202100385] [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: 07/31/2021] [Revised: 09/03/2021] [Indexed: 11/06/2022]
Abstract
Thiamine (vitamin B1) is crucial for life and plays a central role in metabolism. It contains thiazole and pyrimidine moieties that are constructed independently and then assembled together to generate thiamine phosphate. The study of the thiazole moiety is relatively clear, but deciphering the mechanistic enzymology of thiamine pyrimidine is more difficult. This review aims to summarize the recent research progress on ThiC rearrangement, mainly including the mechanism, related enzymes, and genes involved in the rearrangement.
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Affiliation(s)
- Ying-Jie Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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6
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Fitzpatrick TB, Chapman LM. The importance of thiamine (vitamin B 1) in plant health: From crop yield to biofortification. J Biol Chem 2020; 295:12002-12013. [PMID: 32554808 PMCID: PMC7443482 DOI: 10.1074/jbc.rev120.010918] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/17/2020] [Indexed: 12/14/2022] Open
Abstract
Ensuring that people have access to sufficient and nutritious food is necessary for a healthy life and the core tenet of food security. With the global population set to reach 9.8 billion by 2050, and the compounding effects of climate change, the planet is facing challenges that necessitate significant and rapid changes in agricultural practices. In the effort to provide food in terms of calories, the essential contribution of micronutrients (vitamins and minerals) to nutrition is often overlooked. Here, we focus on the importance of thiamine (vitamin B1) in plant health and discuss its impact on human health. Vitamin B1 is an essential dietary component, and deficiencies in this micronutrient underlie several diseases, notably nervous system disorders. The predominant source of dietary vitamin B1 is plant-based foods. Moreover, vitamin B1 is also vital for plants themselves, and its benefits in plant health have received less attention than in the human health sphere. In general, vitamin B1 is well-characterized for its role as a coenzyme in metabolic pathways, particularly those involved in energy production and central metabolism, including carbon assimilation and respiration. Vitamin B1 is also emerging as an important component of plant stress responses, and several noncoenzyme roles of this vitamin are being characterized. We summarize the importance of vitamin B1 in plants from the perspective of food security, including its roles in plant disease resistance, stress tolerance, and crop yield, and review the potential benefits of biofortification of crops with increased vitamin B1 content to improve human health.
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Affiliation(s)
- Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
| | - Lottie M Chapman
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
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7
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Noordally ZB, Trichtinger C, Dalvit I, Hofmann M, Roux C, Zamboni N, Pourcel L, Gas-Pascual E, Gisler A, Fitzpatrick TB. The coenzyme thiamine diphosphate displays a daily rhythm in the Arabidopsis nucleus. Commun Biol 2020; 3:209. [PMID: 32372067 PMCID: PMC7200797 DOI: 10.1038/s42003-020-0927-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/25/2020] [Indexed: 12/27/2022] Open
Abstract
In plants, metabolic homeostasis—the driving force of growth and development—is achieved through the dynamic behavior of a network of enzymes, many of which depend on coenzymes for activity. The circadian clock is established to influence coordination of supply and demand of metabolites. Metabolic oscillations independent of the circadian clock, particularly at the subcellular level is unexplored. Here, we reveal a metabolic rhythm of the essential coenzyme thiamine diphosphate (TDP) in the Arabidopsis nucleus. We show there is temporal separation of the clock control of cellular biosynthesis and transport of TDP at the transcriptional level. Taking advantage of the sole reported riboswitch metabolite sensor in plants, we show that TDP oscillates in the nucleus. This oscillation is a function of a light-dark cycle and is independent of circadian clock control. The findings are important to understand plant fitness in terms of metabolite rhythms. Noordally et al. show that the essential coenzyme thiamine diphosphate exhibits a daily rhythm in the Arabidopsis nucleus, which is driven by light-dark cycles and not by the circadian clock. This study provides insight into our understanding of the optimization of plant fitness.
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Affiliation(s)
- Zeenat B Noordally
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Celso Trichtinger
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Ivan Dalvit
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Manuel Hofmann
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Céline Roux
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Lucille Pourcel
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Elisabet Gas-Pascual
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Alexandra Gisler
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland.
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8
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Adam Z, Aviv-Sharon E, Keren-Paz A, Naveh L, Rozenberg M, Savidor A, Chen J. The Chloroplast Envelope Protease FTSH11 - Interaction With CPN60 and Identification of Potential Substrates. FRONTIERS IN PLANT SCIENCE 2019; 10:428. [PMID: 31024594 PMCID: PMC6459962 DOI: 10.3389/fpls.2019.00428] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/21/2019] [Indexed: 05/03/2023]
Abstract
FTSH proteases are membrane-bound, ATP-dependent metalloproteases found in bacteria, mitochondria and chloroplasts. The product of one of the 12 genes encoding FTSH proteases in Arabidopsis, FTSH11, has been previously shown to be essential for acquired thermotolerance. However, the substrates of this protease, as well as the mechanism linking it to thermotolerance are largely unknown. To get insight into these, the FTSH11 knockout mutant was complemented with proteolytically active or inactive variants of this protease, tagged with HA-tag, under the control of the native promoter. Using these plants in thermotolerance assay demonstrated that the proteolytic activity, and not only the ATPase one, is essential for conferring thermotolerance. Immunoblot analyses of leaf extracts, isolated organelles and sub-fractionated chloroplast membranes localized FTSH11 mostly to chloroplast envelopes. Affinity purification followed by mass spectrometry analysis revealed interaction between FTSH11 and different components of the CPN60 chaperonin. In affinity enrichment assays, CPN60s as well as a number of envelope, stroma and thylakoid proteins were found associated with proteolytically inactive FTSH11. Comparative proteomic analysis of WT and knockout plants, grown at 20°C or exposed to 30°C for 6 h, revealed a plethora of upregulated chloroplast proteins in the knockout, some of them might be candidate substrates. Among these stood out TIC40, which was stabilized in the knockout line after recovery from heat stress, and three proteins that were found trapped in the affinity enrichment assay: the nucleotide antiporter PAPST2, the fatty acid binding protein FAP1 and the chaperone HSP70. The consistent behavior of these four proteins in different assays suggest that they are potential FTSH11 substrates.
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Affiliation(s)
- Zach Adam
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Zach Adam,
| | - Elinor Aviv-Sharon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alona Keren-Paz
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Leah Naveh
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mor Rozenberg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alon Savidor
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX, United States
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Holliday GL, Akiva E, Meng EC, Brown SD, Calhoun S, Pieper U, Sali A, Booker SJ, Babbitt PC. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain. Methods Enzymol 2018; 606:1-71. [PMID: 30097089 DOI: 10.1016/bs.mie.2018.06.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The radical SAM superfamily contains over 100,000 homologous enzymes that catalyze a remarkably broad range of reactions required for life, including metabolism, nucleic acid modification, and biogenesis of cofactors. While the highly conserved SAM-binding motif responsible for formation of the key 5'-deoxyadenosyl radical intermediate is a key structural feature that simplifies identification of superfamily members, our understanding of their structure-function relationships is complicated by the modular nature of their structures, which exhibit varied and complex domain architectures. To gain new insight about these relationships, we classified the entire set of sequences into similarity-based subgroups that could be visualized using sequence similarity networks. This superfamily-wide analysis reveals important features that had not previously been appreciated from studies focused on one or a few members. Functional information mapped to the networks indicates which members have been experimentally or structurally characterized, their known reaction types, and their phylogenetic distribution. Despite the biological importance of radical SAM chemistry, the vast majority of superfamily members have never been experimentally characterized in any way, suggesting that many new reactions remain to be discovered. In addition to 20 subgroups with at least one known function, we identified additional subgroups made up entirely of sequences of unknown function. Importantly, our results indicate that even general reaction types fail to track well with our sequence similarity-based subgroupings, raising major challenges for function prediction for currently identified and new members that continue to be discovered. Interactive similarity networks and other data from this analysis are available from the Structure-Function Linkage Database.
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States.
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Elaine C Meng
- Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, United States
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Sara Calhoun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Graduate Program in Biophysics, University of California, San Francisco, CA, United States
| | - Ursula Pieper
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States
| | - Squire J Booker
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States; Department of Chemistry, The Pennsylvania State University, University Park, PA, United States; The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute, University of California, San Francisco, CA, United States.
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10
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Wilcoxen J, Bruender NA, Bandarian V, Britt RD. A Radical Intermediate in Bacillus subtilis QueE during Turnover with the Substrate Analogue 6-Carboxypterin. J Am Chem Soc 2018; 140:1753-1759. [PMID: 29303575 DOI: 10.1021/jacs.7b10860] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
7-Carboxy-7-deazaguanine (CDG) synthase (QueE), a member of the radical S-deoxyadenosyl-l-methionine (SAM) superfamily of enzymes, catalyzes a radical-mediated ring rearrangement required to convert 6-carboxy-5,6,7,8-tetrahydropterin (CPH4) into CDG, forming the 7-dezapurine precursor to all pyrrolopyrimidine metabolites. Members of the radical SAM superfamily bind SAM to a [4Fe-4S] cluster, leveraging the reductive cleavage of SAM by the cluster to produce a highly reactive 5'-deoxyadenosyl radical which initiates chemistry by H atom abstraction from the substrate. QueE has recently been shown to use 6-carboxypterin (6-CP) as an alternative substrate, forming 6-deoxyadenosylpterin as the product. This reaction has been proposed to occur by radical addition between 5'-dAdo· and 6-CP, which upon oxidative decarboxylation yields the modified pterin. Here, we present spectroscopic evidence for a 6-CP-dAdo radical. The structure of this intermediate is determined by characterizing its electronic structure by continuous wave and pulse electron paramagnetic resonance spectroscopy.
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Affiliation(s)
- Jarett Wilcoxen
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
| | - Nathan A Bruender
- Department of Chemistry and Biochemistry, St. Cloud State University , St. Cloud, Minnesota 56301, United States
| | - Vahe Bandarian
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis , Davis, California 95616, United States
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11
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Mangel N, Fudge JB, Fitzpatrick TB, Gruissem W, Vanderschuren H. Vitamin B1 diversity and characterization of biosynthesis genes in cassava. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3351-3363. [PMID: 28859374 PMCID: PMC5853225 DOI: 10.1093/jxb/erx196] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 05/22/2017] [Indexed: 05/06/2023]
Abstract
Vitamin B1, which consists of the vitamers thiamin and its phosphorylated derivatives, is an essential micronutrient for all living organisms because it is required as a metabolic cofactor in several enzymatic reactions. Genetic diversity of vitamin B1 biosynthesis and accumulation has not been investigated in major crop species other than rice and potato. We analyzed cassava germplasm for accumulation of B1 vitamers. Vitamin B1 content in leaves and roots of 41 cassava accessions showed significant variation between accessions. HPLC analyses of B1 vitamers revealed distinct profiles in cassava leaves and storage roots, with nearly equal relative levels of thiamin pyrophosphate and thiamin monophosphate in leaves, but mostly thiamin pyrophosphate in storage roots. Unusually, the cassava genome has two genes encoding the 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate synthase, THIC (MeTHIC1 and MeTHIC2), both of which carry a riboswitch in the 3'-UTR, as well as the adenylated thiazole synthase, THI1 (MeTHI1a and MeTHI1b). The THIC and THI1 genes are expressed at very low levels in storage roots compared with the accumulation of vitamin B1, indicating only limited biosynthesis de novo therein. In leaves, vitamin B1 content is negatively correlated with THIC and THI1 expression levels, suggesting post-transcriptional regulation of THIC by the riboswitch present in the 3'-UTR of the THIC mRNA and regulation of THI1 by promoter activity or alternative post-transcriptional mechanisms.
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Affiliation(s)
| | - Jared B Fudge
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | | | - Hervé Vanderschuren
- Department of Biology, ETH Zurich, Zurich, Switzerland
- AgroBioChem Department, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Makins C, Ghosh S, Román-Meléndez GD, Malec PA, Kennedy RT, Marsh ENG. Does Viperin Function as a Radical S-Adenosyl-l-methionine-dependent Enzyme in Regulating Farnesylpyrophosphate Synthase Expression and Activity? J Biol Chem 2016; 291:26806-26815. [PMID: 27834682 DOI: 10.1074/jbc.m116.751040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/31/2016] [Indexed: 01/09/2023] Open
Abstract
Viperin is an endoplasmic reticulum-associated antiviral responsive protein that is highly up-regulated in eukaryotic cells upon viral infection through both interferon-dependent and independent pathways. Viperin is predicted to be a radical S-adenosyl-l-methionine (SAM) enzyme, but it is unknown whether viperin actually exploits radical SAM chemistry to exert its antiviral activity. We have investigated the interaction of viperin with its most firmly established cellular target, farnesyl pyrophosphate synthase (FPPS). Numerous enveloped viruses utilize cholesterol-rich lipid rafts to bud from the host cell membrane, and it is thought that by inhibiting FPPS activity (and therefore cholesterol synthesis), viperin retards viral budding from infected cells. We demonstrate that, consistent with this hypothesis, overexpression of viperin in human embryonic kidney cells reduces the intracellular rate of accumulation of FPPS but does not inhibit or inactivate FPPS. The endoplasmic reticulum-localizing, N-terminal amphipathic helix of viperin is specifically required for viperin to reduce cellular FPPS levels. However, although viperin reductively cleaves SAM to form 5'-deoxyadenosine in a slow, uncoupled reaction characteristic of radical SAM enzymes, this cleavage reaction is independent of FPPS. Furthermore, mutation of key cysteinyl residues ligating the catalytic [Fe4S4] cluster in the radical SAM domain, surprisingly, does not abolish the inhibitory activity of viperin against FPPS; indeed, some mutations potentiate viperin activity. These observations imply that viperin does not act as a radical SAM enzyme in regulating FPPS.
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Affiliation(s)
- Caitlyn Makins
- From the Departments of Chemistry and.,Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | | | | | | | | | - E Neil G Marsh
- From the Departments of Chemistry and .,Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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Mehta AP, Abdelwahed SH, Fenwick MK, Hazra AB, Taga ME, Zhang Y, Ealick SE, Begley TP. Anaerobic 5-Hydroxybenzimidazole Formation from Aminoimidazole Ribotide: An Unanticipated Intersection of Thiamin and Vitamin B₁₂ Biosynthesis. J Am Chem Soc 2015; 137:10444-7. [PMID: 26237670 PMCID: PMC4753784 DOI: 10.1021/jacs.5b03576] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Comparative genomics of the bacterial thiamin pyrimidine synthase (thiC) revealed a paralogue of thiC (bzaF) clustered with anaerobic vitamin B12 biosynthetic genes. Here we demonstrate that BzaF is a radical S-adenosylmethionine enzyme that catalyzes the remarkable conversion of aminoimidazole ribotide (AIR) to 5-hydroxybenzimidazole (5-HBI). We identify the origin of key product atoms and propose a reaction mechanism. These studies represent the first step in solving a long-standing problem in anaerobic vitamin B12 assembly and reveal an unanticipated intersection of thiamin and vitamin B12 biosynthesis.
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Affiliation(s)
- Angad P. Mehta
- Department of Chemistry, Texas A&M University, College Station, TX-77843, USA
| | - Sameh H. Abdelwahed
- Department of Chemistry, Texas A&M University, College Station, TX-77843, USA
- herapeutic chemistry department, National research center, Dokki, Cario, Egypt
| | - Michael K. Fenwick
- Department of Chemistry and Chemical Biology, Cornell University, 120 Baker Lab, Ithaca, New York 14853, USA
| | - Amrita B. Hazra
- Department of Plant and Microbial Biology, University of California, Berkeley, USA
| | - Michiko E. Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, USA
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, 120 Baker Lab, Ithaca, New York 14853, USA
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, 120 Baker Lab, Ithaca, New York 14853, USA
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, TX-77843, USA
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14
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Shibata N, Toraya T. Molecular architectures and functions of radical enzymes and their (re)activating proteins. J Biochem 2015; 158:271-92. [PMID: 26261050 DOI: 10.1093/jb/mvv078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/22/2015] [Indexed: 02/07/2023] Open
Abstract
Certain proteins utilize the high reactivity of radicals for catalysing chemically challenging reactions. These proteins contain or form a radical and therefore named 'radical enzymes'. Radicals are introduced by enzymes themselves or by (re)activating proteins called (re)activases. The X-ray structures of radical enzymes and their (re)activases revealed some structural features of these molecular apparatuses which solved common enigmas of radical enzymes—i.e. how the enzymes form or introduce radicals at the active sites, how they use the high reactivity of radicals for catalysis, how they suppress undesired side reactions of highly reactive radicals and how they are (re)activated when inactivated by extinction of radicals. This review highlights molecular architectures of radical B12 enzymes, radical SAM enzymes, tyrosyl radical enzymes, glycyl radical enzymes and their (re)activating proteins that support their functions. For generalization, comparisons of the recently reported structures of radical enzymes with those of canonical radical enzymes are summarized here.
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Affiliation(s)
- Naoki Shibata
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan and
| | - Tetsuo Toraya
- Department of Bioscience and Biotechnology, Graduate School of Natural Science and Technology, Okayama University, Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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15
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Non-canonical active site architecture of the radical SAM thiamin pyrimidine synthase. Nat Commun 2015; 6:6480. [PMID: 25813242 PMCID: PMC4389238 DOI: 10.1038/ncomms7480] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/30/2015] [Indexed: 01/04/2023] Open
Abstract
Radical S-adenosylmethionine (SAM) enzymes use a [4Fe-4S] cluster to generate a 5'-deoxyadenosyl radical. Canonical radical SAM enzymes are characterized by a β-barrel-like fold and SAM anchors to the differentiated iron of the cluster, which is located near the amino terminus and within the β-barrel, through its amino and carboxylate groups. Here we show that ThiC, the thiamin pyrimidine synthase in plants and bacteria, contains a tethered cluster-binding domain at its carboxy terminus that moves in and out of the active site during catalysis. In contrast to canonical radical SAM enzymes, we predict that SAM anchors to an additional active site metal through its amino and carboxylate groups. Superimposition of the catalytic domains of ThiC and glutamate mutase shows that these two enzymes share similar active site architectures, thus providing strong evidence for an evolutionary link between the radical SAM and adenosylcobalamin-dependent enzyme superfamilies.
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16
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Fitzpatrick TB, Thore S. Complex behavior: from cannibalism to suicide in the vitamin B1 biosynthesis world. Curr Opin Struct Biol 2014; 29:34-43. [DOI: 10.1016/j.sbi.2014.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 10/24/2022]
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17
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Broderick JB, Duffus B, Duschene KS, Shepard EM. Radical S-adenosylmethionine enzymes. Chem Rev 2014; 114:4229-317. [PMID: 24476342 PMCID: PMC4002137 DOI: 10.1021/cr4004709] [Citation(s) in RCA: 589] [Impact Index Per Article: 58.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Joan B. Broderick
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Benjamin
R. Duffus
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Kaitlin S. Duschene
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Eric M. Shepard
- Department of Chemistry and
Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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