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Gelder K, Oliveira-Filho ER, García-García JD, Hu Y, Bruner SD, Hanson AD. Directed Evolution of Aerotolerance in Sulfide-Dependent Thiazole Synthases. ACS Synth Biol 2023; 12:963-970. [PMID: 36920242 PMCID: PMC10127261 DOI: 10.1021/acssynbio.2c00512] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Indexed: 03/16/2023]
Abstract
Sulfide-dependent THI4 thiazole synthases could potentially be used to replace plant cysteine-dependent suicide THI4s, whose high protein turnover rates make thiamin synthesis exceptionally energy-expensive. However, sulfide-dependent THI4s are anaerobic or microoxic enzymes and hence unadapted to the aerobic conditions in plants; they are also slow enzymes (kcat < 1 h-1). To improve aerotolerance and activity, we applied continuous directed evolution under aerobic conditions in the yeast OrthoRep system to two sulfide-dependent bacterial THI4s. Seven beneficial single mutations were identified, of which five lie in the active-site cleft predicted by structural modeling and two recapitulate features of naturally aerotolerant THI4s. That single mutations gave substantial improvements suggests that further advance under selection will be possible by stacking mutations. This proof-of-concept study established that the performance of sulfide-dependent THI4s in aerobic conditions is evolvable and, more generally, that yeast OrthoRep provides a plant-like bridge to adapt nonplant enzymes to work better in plants.
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Affiliation(s)
- Kristen
Van Gelder
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Edmar R. Oliveira-Filho
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | | | - You Hu
- Chemistry
Department, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D. Bruner
- Chemistry
Department, University of Florida, Gainesville, Florida 32611, United States
| | - Andrew D. Hanson
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
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2
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Mondal A, Lai RY, Fedoseyenko D, Giri N, Begley TP. Oxidative Dearomatization of PLP in Thiamin Pyrimidine Biosynthesis in Candida albicans. J Am Chem Soc 2023; 145:4421-4430. [PMID: 36802573 PMCID: PMC10848271 DOI: 10.1021/jacs.2c08560] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Indexed: 02/22/2023]
Abstract
The yeast thiamin pyrimidine synthase THI5p catalyzes one of the most complex organic rearrangements found in primary metabolism. In this reaction, the active site His66 and PLP are converted to thiamin pyrimidine in the presence of Fe(II) and oxygen. The enzyme is a single-turnover enzyme. Here, we report the identification of an oxidatively dearomatized PLP intermediate. We utilize oxygen labeling studies, chemical-rescue-based partial reconstitution experiments, and chemical model studies to support this identification. In addition, we also identify and characterize three shunt products derived from the oxidatively dearomatized PLP.
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Affiliation(s)
- Anushree Mondal
- Department of Chemistry, Texas A&M University, College Station, Texas77843, United States
| | | | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas77843, United States
| | | | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas77843, United States
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3
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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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4
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Lindahl PA, Vali SW. Mössbauer-based molecular-level decomposition of the Saccharomyces cerevisiae ironome, and preliminary characterization of isolated nuclei. Metallomics 2022; 14:mfac080. [PMID: 36214417 PMCID: PMC9624242 DOI: 10.1093/mtomcs/mfac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/23/2022] [Indexed: 11/25/2022]
Abstract
One hundred proteins in Saccharomyces cerevisiae are known to contain iron. These proteins are found mainly in mitochondria, cytosol, nuclei, endoplasmic reticula, and vacuoles. Cells also contain non-proteinaceous low-molecular-mass labile iron pools (LFePs). How each molecular iron species interacts on the cellular or systems' level is underdeveloped as doing so would require considering the entire iron content of the cell-the ironome. In this paper, Mössbauer (MB) spectroscopy was used to probe the ironome of yeast. MB spectra of whole cells and isolated organelles were predicted by summing the spectral contribution of each iron-containing species in the cell. Simulations required input from published proteomics and microscopy data, as well as from previous spectroscopic and redox characterization of individual iron-containing proteins. Composite simulations were compared to experimentally determined spectra. Simulated MB spectra of non-proteinaceous iron pools in the cell were assumed to account for major differences between simulated and experimental spectra of whole cells and isolated mitochondria and vacuoles. Nuclei were predicted to contain ∼30 μM iron, mostly in the form of [Fe4S4] clusters. This was experimentally confirmed by isolating nuclei from 57Fe-enriched cells and obtaining the first MB spectra of the organelle. This study provides the first semi-quantitative estimate of all concentrations of iron-containing proteins and non-proteinaceous species in yeast, as well as a novel approach to spectroscopically characterizing LFePs.
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Affiliation(s)
- Paul A Lindahl
- Department of Chemistry, Texas A&M University, College Station, TX,USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station TX,USA
| | - Shaik Waseem Vali
- Department of Chemistry, Texas A&M University, College Station, TX,USA
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5
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Lai RY, Mondal A, Fedoseyenko D, Begley TP. Mechanistic Studies on the Single-Turnover Yeast Thiamin Pyrimidine Synthase: Characterization of the Inactive Enzyme. J Am Chem Soc 2022; 144:10711-10717. [PMID: 35675507 DOI: 10.1021/jacs.2c03322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The eukaryotic thiamin pyrimidine synthase, THI5p, has been identified as a suicidal/single-turnover enzyme that catalyzes the conversion of its active site histidine and lysine-bound pyridoxal phosphate (PLP) to the thiamin pyrimidine (HMP-P). Here we identify the histidine and PLP fragments using bottom-up proteomics and LC-MS analysis. We also identify the active form of the iron cofactor and quantitate the oxygen requirement of the THI5p reaction. This information is integrated into a mechanistic proposal for this remarkable reaction.
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Affiliation(s)
- Rung-Yi Lai
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Anushree Mondal
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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6
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García-García JD, Van Gelder K, Joshi J, Bathe U, Leong BJ, Bruner SD, Liu CC, Hanson AD. Using continuous directed evolution to improve enzymes for plant applications. PLANT PHYSIOLOGY 2022; 188:971-983. [PMID: 34718794 PMCID: PMC8825276 DOI: 10.1093/plphys/kiab500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/29/2021] [Indexed: 05/12/2023]
Abstract
Continuous directed evolution of enzymes and other proteins in microbial hosts is capable of outperforming classical directed evolution by executing hypermutation and selection concurrently in vivo, at scale, with minimal manual input. Provided that a target enzyme's activity can be coupled to growth of the host cells, the activity can be improved simply by selecting for growth. Like all directed evolution, the continuous version requires no prior mechanistic knowledge of the target. Continuous directed evolution is thus a powerful way to modify plant or non-plant enzymes for use in plant metabolic research and engineering. Here, we first describe the basic features of the yeast (Saccharomyces cerevisiae) OrthoRep system for continuous directed evolution and compare it briefly with other systems. We then give a step-by-step account of three ways in which OrthoRep can be deployed to evolve primary metabolic enzymes, using a THI4 thiazole synthase as an example and illustrating the mutational outcomes obtained. We close by outlining applications of OrthoRep that serve growing demands (i) to change the characteristics of plant enzymes destined for return to plants, and (ii) to adapt ("plantize") enzymes from prokaryotes-especially exotic prokaryotes-to function well in mild, plant-like conditions.
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Affiliation(s)
- Jorge D García-García
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Zapopan, Mexico
| | - Kristen Van Gelder
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Jaya Joshi
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Steven D Bruner
- Chemistry Department, University of Florida, Gainesville, Florida 32611
| | - Chang C Liu
- Department of Biomedical Engineering, University of California, Irvine, California 92617
- Department of Chemistry, University of California, Irvine, California 92617
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
- Author for communication:
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7
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Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases. Biochem J 2021; 478:3265-3279. [PMID: 34409984 PMCID: PMC8454699 DOI: 10.1042/bcj20210565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022]
Abstract
Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized —– but only from archaeal methanogens that are anaerobic, O2-sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O2 at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O2-sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.
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8
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Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s. Biochem J 2020; 477:2055-2069. [PMID: 32441748 DOI: 10.1042/bcj20200297] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022]
Abstract
Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsistz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mechanism in planta. Unexpectedly, transcriptome data mining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in developing grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thiazole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain-filling period.
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9
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García-García JD, Joshi J, Patterson JA, Trujillo-Rodriguez L, Reisch CR, Javanpour AA, Liu CC, Hanson AD. Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study. Life (Basel) 2020; 10:E179. [PMID: 32899502 PMCID: PMC7555113 DOI: 10.3390/life10090179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022] Open
Abstract
Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today's agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized more quickly than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cell's growth rate to the target gene's function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering.
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Affiliation(s)
| | - Jaya Joshi
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
| | - Jenelle A. Patterson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
| | - Lidimarie Trujillo-Rodriguez
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.T.-R.); (C.R.R.)
| | - Christopher R. Reisch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.T.-R.); (C.R.R.)
| | - Alex A. Javanpour
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA; (A.A.J.); (C.C.L.)
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA; (A.A.J.); (C.C.L.)
- Department of Chemistry, University of California, Irvine, CA 92617, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
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Engilberge S, Wagner T, Santoni G, Breyton C, Shima S, Franzetti B, Riobé F, Maury O, Girard E. Protein crystal structure determination with the crystallophore, a nucleating and phasing agent. J Appl Crystallogr 2019; 52:722-731. [PMID: 31396026 PMCID: PMC6662991 DOI: 10.1107/s1600576719006381] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023] Open
Abstract
Obtaining crystals and solving the phase problem remain major hurdles encountered by bio-crystallographers in their race to obtain new high-quality structures. Both issues can be overcome by the crystallophore, Tb-Xo4, a lanthanide-based molecular complex with unique nucleating and phasing properties. This article presents examples of new crystallization conditions induced by the presence of Tb-Xo4. These new crystalline forms bypass crystal defects often encountered by crystallographers, such as low-resolution diffracting samples or crystals with twinning. Thanks to Tb-Xo4's high phasing power, the structure determination process is greatly facilitated and can be extended to serial crystallography approaches.
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Affiliation(s)
- Sylvain Engilberge
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Tristan Wagner
- Microbial Protein Structure Group, Karl-von-Frisch-Strasse 10, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Gianluca Santoni
- Structural Biology Group, European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Cécile Breyton
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Seigo Shima
- Microbial Protein Structure Group, Karl-von-Frisch-Strasse 10, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Bruno Franzetti
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Francois Riobé
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Eric Girard
- Institut de Biologie Structurale, University Grenoble Alpes, CEA, CNRS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
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11
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Sun J, Sigler CL, Beaudoin GAW, Joshi J, Patterson JA, Cho KH, Ralat MA, Gregory JF, Clark DG, Deng Z, Colquhoun TA, Hanson AD. Parts-Prospecting for a High-Efficiency Thiamin Thiazole Biosynthesis Pathway. PLANT PHYSIOLOGY 2019; 179:958-968. [PMID: 30337452 PMCID: PMC6393793 DOI: 10.1104/pp.18.01085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/10/2018] [Indexed: 05/04/2023]
Abstract
Plants synthesize the thiazole precursor of thiamin (cThz-P) via THIAMIN4 (THI4), a suicide enzyme that mediates one reaction cycle and must then be degraded and resynthesized. It has been estimated that this THI4 turnover consumes 2% to 12% of the maintenance energy budget and that installing an energy-efficient alternative pathway could substantially increase crop yield potential. Available data point to two natural alternatives to the suicidal THI4 pathway: (i) nonsuicidal prokaryotic THI4s that lack the active-site Cys residue on which suicide activity depends, and (ii) an uncharacterized thiazole synthesis pathway in flowers of the tropical arum lily Caladium bicolor that enables production and emission of large amounts of the cThz-P analog 4-methyl-5-vinylthiazole (MVT). We used functional complementation of an Escherichia coli ΔthiG strain to identify a nonsuicidal bacterial THI4 (from Thermovibrio ammonificans) that can function in conditions like those in plant cells. We explored whether C. bicolor synthesizes MVT de novo via a novel route, via a suicidal or a nonsuicidal THI4, or by catabolizing thiamin. Analysis of developmental changes in MVT emission, extractable MVT, thiamin level, and THI4 expression indicated that C. bicolor flowers make MVT de novo via a massively expressed THI4 and that thiamin is not involved. Functional complementation tests indicated that C. bicolor THI4, which has the active-site Cys needed to operate suicidally, may be capable of suicidal and - in hypoxic conditions - nonsuicidal operation. T. ammonificans and C. bicolor THI4s are thus candidate parts for rational redesign or directed evolution of efficient, nonsuicidal THI4s for use in crop improvement.
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Affiliation(s)
- Jiayi Sun
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Cindy L Sigler
- Department of Environmental Horticulture, University of Florida, Gainesville, Florida 32611
| | | | - Jaya Joshi
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Jenelle A Patterson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Keun H Cho
- Department of Environmental Horticulture, University of Florida, Gainesville, Florida 32611
| | - Maria A Ralat
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida 32611
| | - Jesse F Gregory
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, Florida 32611
| | - David G Clark
- Department of Environmental Horticulture, University of Florida, Gainesville, Florida 32611
| | - Zhanao Deng
- Gulf Coast Research and Education Center, Department of Environmental Horticulture, University of Florida, Wimauma, Florida 33598
| | - Thomas A Colquhoun
- Department of Environmental Horticulture, University of Florida, Gainesville, Florida 32611
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
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12
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The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism. Microbiol Mol Biol Rev 2018; 83:83/1/e00040-18. [PMID: 30567937 DOI: 10.1128/mmbr.00040-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ribosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its "big brother" phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups, Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.
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13
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Meir Z, Osherov N. Vitamin Biosynthesis as an Antifungal Target. J Fungi (Basel) 2018; 4:E72. [PMID: 29914189 PMCID: PMC6023522 DOI: 10.3390/jof4020072] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 12/18/2022] Open
Abstract
The large increase in the population of immunosuppressed patients, coupled with the limited efficacy of existing antifungals and rising resistance toward them, have dramatically highlighted the need to develop novel drugs for the treatment of invasive fungal infections. An attractive possibility is the identification of possible drug targets within essential fungal metabolic pathways not shared with humans. Here, we review the vitamin biosynthetic pathways (vitamins A⁻E, K) as candidates for the development of antifungals. We present a set of ranking criteria that identify the vitamin B2 (riboflavin), B5 (pantothenic acid), and B9 (folate) biosynthesis pathways as being particularly rich in new antifungal targets. We propose that recent scientific advances in the fields of drug design and fungal genomics have developed sufficiently to merit a renewed look at these pathways as promising sources for the development of novel classes of antifungals.
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Affiliation(s)
- Zohar Meir
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel.
| | - Nir Osherov
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv 69978, Israel.
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14
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Song Z, Pan J, Xie L, Gong G, Han S, Zhang W, Hu Y. Expression, Purification, and Activity of ActhiS, a Thiazole Biosynthesis Enzyme from Acremonium chrysogenum. BIOCHEMISTRY (MOSCOW) 2017; 82:852-860. [PMID: 28918750 DOI: 10.1134/s0006297917070112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Thiamine pyrophosphate is an essential coenzyme in all organisms. Its biosynthesis involves independent syntheses of the precursors, pyrimidine and thiazole, which are then coupled. In our previous study with overexpressed and silent mutants of ActhiS (thiazole biosynthesis enzyme from Acremonium chrysogenum), we found that the enzyme level correlated with intracellular thiamine content in A. chrysogenum. However, the exact structure and function of ActhiS remain unclear. In this study, the enzyme-bound ligand was characterized as the ADP adduct of 5-(2-hydroxyethyl)-4-methylthiazole-2-carboxylic acid (ADT) using HPLC and 1H NMR. The ligand-free ActhiS expressed in M9 minimal medium catalyzed conversion of NAD+ and glycine to ADT in the presence of iron. Furthermore, the C217 residue was identified as the sulfur donor for the thiazole moiety. These observations confirm that ActhiS is a thiazole biosynthesis enzyme in A. chrysogenum, and it serves as a sulfur source for the thiazole moiety.
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Affiliation(s)
- Zhihui Song
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, Shanghai, 201203, China.
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ThiN as a Versatile Domain of Transcriptional Repressors and Catalytic Enzymes of Thiamine Biosynthesis. J Bacteriol 2017; 199:JB.00810-16. [PMID: 28115546 DOI: 10.1128/jb.00810-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/14/2017] [Indexed: 01/21/2023] Open
Abstract
Thiamine biosynthesis is commonly regulated by a riboswitch mechanism; however, the enzymatic steps and regulation of this pathway in archaea are poorly understood. Haloferax volcanii, one of the representative archaea, uses a eukaryote-like Thi4 (thiamine thiazole synthase) for the production of the thiazole ring and condenses this ring with a pyrimidine moiety synthesized by an apparent bacterium-like ThiC (2-methyl-4-amino-5-hydroxymethylpyrimidine [HMP] phosphate synthase) branch. Here we found that archaeal Thi4 and ThiC were encoded by leaderless transcripts, ruling out a riboswitch mechanism. Instead, a novel ThiR transcription factor that harbored an N-terminal helix-turn-helix (HTH) DNA binding domain and C-terminal ThiN (TMP synthase) domain was identified. In the presence of thiamine, ThiR was found to repress the expression of thi4 and thiC by a DNA operator sequence that was conserved across archaeal phyla. Despite having a ThiN domain, ThiR was found to be catalytically inactive in compensating for the loss of ThiE (TMP synthase) function. In contrast, bifunctional ThiDN, in which the ThiN domain is fused to an N-terminal ThiD (HMP/HMP phosphate [HMP-P] kinase) domain, was found to be interchangeable for ThiE function and, thus, active in thiamine biosynthesis. A conserved Met residue of an extended α-helix near the active-site His of the ThiN domain was found to be important for ThiDN catalytic activity, whereas the corresponding Met residue was absent and the α-helix was shorter in ThiR homologs. Thus, we provide new insight into residues that distinguish catalytic from noncatalytic ThiN domains and reveal that thiamine biosynthesis in archaea is regulated by a transcriptional repressor, ThiR, and not by a riboswitch.IMPORTANCE Thiamine pyrophosphate (TPP) is a cofactor needed for the enzymatic activity of many cellular processes, including central metabolism. In archaea, thiamine biosynthesis is an apparent chimera of eukaryote- and bacterium-type pathways that is not well defined at the level of enzymatic steps or regulatory mechanisms. Here we find that ThiN is a versatile domain of transcriptional repressors and catalytic enzymes of thiamine biosynthesis in archaea. Our study provides new insight into residues that distinguish catalytic from noncatalytic ThiN domains and reveals that archaeal thiamine biosynthesis is regulated by a ThiN domain transcriptional repressor, ThiR, and not by a riboswitch.
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Eser BE, Zhang X, Chanani PK, Begley TP, Ealick SE. From Suicide Enzyme to Catalyst: The Iron-Dependent Sulfide Transfer in Methanococcus jannaschii Thiamin Thiazole Biosynthesis. J Am Chem Soc 2016; 138:3639-42. [PMID: 26928142 PMCID: PMC4805478 DOI: 10.1021/jacs.6b00445] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria and yeast utilize different strategies for sulfur incorporation in the biosynthesis of the thiamin thiazole. Bacteria use thiocarboxylated proteins. In contrast, Saccharomyces cerevisiae thiazole synthase (THI4p) uses an active site cysteine as the sulfide source and is inactivated after a single turnover. Here, we demonstrate that the Thi4 ortholog from Methanococcus jannaschii uses exogenous sulfide and is catalytic. Structural and biochemical studies on this enzyme elucidate the mechanistic details of the sulfide transfer reactions.
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Affiliation(s)
- Bekir E. Eser
- Zirve University, Department of Medical Biochemistry, Emine-Bahaeddin Nakıboglu School of Medicine, Gaziantep 27260, Turkey
| | - Xuan Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Prem K. Chanani
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
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