51
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Sakaki K, Ohishi K, Shimizu T, Kobayashi I, Mori N, Matsuda K, Tomita T, Watanabe H, Tanaka K, Kuzuyama T, Nishiyama M. A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Nat Chem Biol 2020; 16:415-422. [DOI: 10.1038/s41589-019-0461-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/20/2019] [Indexed: 11/09/2022]
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52
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Ascorbate and Thiamin: Metabolic Modulators in Plant Acclimation Responses. PLANTS 2020; 9:plants9010101. [PMID: 31941157 PMCID: PMC7020166 DOI: 10.3390/plants9010101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/12/2022]
Abstract
Cell compartmentalization allows incompatible chemical reactions and localised responses to occur simultaneously, however, it also requires a complex system of communication between compartments in order to maintain the functionality of vital processes. It is clear that multiple such signals must exist, yet little is known about the identity of the key players orchestrating these interactions or about the role in the coordination of other processes. Mitochondria and chloroplasts have a considerable number of metabolites in common and are interdependent at multiple levels. Therefore, metabolites represent strong candidates as communicators between these organelles. In this context, vitamins and similar small molecules emerge as possible linkers to mediate metabolic crosstalk between compartments. This review focuses on two vitamins as potential metabolic signals within the plant cell, vitamin C (L-ascorbate) and vitamin B1 (thiamin). These two vitamins demonstrate the importance of metabolites in shaping cellular processes working as metabolic signals during acclimation processes. Inferences based on the combined studies of environment, genotype, and metabolite, in order to unravel signaling functions, are also highlighted.
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Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts. Proc Natl Acad Sci U S A 2019; 116:22219-22228. [PMID: 31611373 DOI: 10.1073/pnas.1909844116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Horizontal acquisition of bacterial genes is presently recognized as an important contribution to the adaptation and evolution of eukaryotic genomes. However, the mechanisms underlying expression and consequent selection and fixation of the prokaryotic genes in the new eukaryotic setting are largely unknown. Here we show that genes composing the pathway for the synthesis of the essential vitamin B1 (thiamine) were lost in an ancestor of a yeast lineage, the Wickerhamiella/Starmerella (W/S) clade, known to harbor an unusually large number of genes of alien origin. The thiamine pathway was subsequently reassembled, at least twice, by multiple HGT events from different bacterial donors involving both single genes and entire operons. In the W/S-clade species Starmerella bombicola we obtained direct genetic evidence that all bacterial genes of the thiamine pathway are functional. The reconstructed pathway is composed by yeast and bacterial genes operating coordinately to scavenge thiamine derivatives from the environment. The adaptation of the newly acquired operons to the eukaryotic setting involved a repertoire of mechanisms until now only sparsely documented, namely longer intergenic regions, post-horizontal gene transfer (HGT) gene fusions fostering coordinated expression, gene relocation, and possibly recombination generating mosaic genes. The results provide additional evidence that HGT occurred recurrently in this yeast lineage and was crucial for the reestablishment of lost functions and that similar mechanisms are used across a broad range of eukaryotic microbes to promote adaptation of prokaryotic genes to their new environment.
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54
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Nakayoshi T, Kato K, Kurimoto E, Oda A. Possible Mechanisms of Nonenzymatic Formation of Dehydroalanine Residue Catalyzed by Dihydrogen Phosphate Ion. J Phys Chem B 2019; 123:3147-3155. [PMID: 30916562 DOI: 10.1021/acs.jpcb.8b10386] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Uncommon crosslinked amino acids have been identified in several aging tissues and are suspected to trigger various age-related diseases. Several uncommon residues are formed when the dehydroalanine (Dha) residue undergoes a nucleophilic attack by surrounding residues. Dha residues are considered to be formed by posttranslational modification of serine (Ser) and cysteine residues. In the present study, we investigated the Dha residue formation mechanism catalyzed by dihydrogen phosphate ion (H2PO4-) using quantum chemical calculations. We obtained optimized geometries using the B3LYP density functional method and carried out single-point energy calculations using the second-order Møller-Plesset perturbation method. All calculations were performed using Ace-Ser-Nme (Ace = acetyl, Nme = methylamino) as a model compound. Results of the computational analysis suggest that the mechanism underlying the Dha residue formation from Ser consists of two steps: enolization and 1,3-elimination. The H2PO4- catalyzed both reactions as a proton-relay mediator. The calculated activation barrier for Dha residue formation was estimated as 30.4 kcal mol-1. In this pathway, the catalytic H2PO4- interacts with the Ser residue α-proton, carbonyl oxygen of Ser, and C-terminal side adjacent residues, and the calculated activation energy produced was the same as the experimentally reported value for nonenzymatic modifications of amino acid residues. Therefore, our calculation suggests that H2PO4--catalyzed Ser residue dehydration can proceed nonenzymatically.
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Affiliation(s)
- Tomoki Nakayoshi
- Graduate School of Pharmacy , Meijo University , 150 Yagotoyama , Tempaku-ku, Nagoya , Aichi 468-8503 , Japan.,Institute of Medical, Pharmaceutical and Health Sciences , Kanazawa University , Kakuma-machi , Kanazawa , Ishikawa 920-1192 , Japan
| | - Koichi Kato
- Graduate School of Pharmacy , Meijo University , 150 Yagotoyama , Tempaku-ku, Nagoya , Aichi 468-8503 , Japan.,Department of Pharmacy , Kinjo Gakuin University , 2-1723 Omori , Moriyama-ku, Nagoya , Aichi 463-8521 , Japan
| | - Eiji Kurimoto
- Graduate School of Pharmacy , Meijo University , 150 Yagotoyama , Tempaku-ku, Nagoya , Aichi 468-8503 , Japan
| | - Akifumi Oda
- Graduate School of Pharmacy , Meijo University , 150 Yagotoyama , Tempaku-ku, Nagoya , Aichi 468-8503 , Japan.,Institute for Protein Research , Osaka University , 3-2 Yamadaoka, Suita , Osaka 565-0871 , Japan
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55
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Leisinger F, Burn R, Meury M, Lukat P, Seebeck FP. Structural and Mechanistic Basis for Anaerobic Ergothioneine Biosynthesis. J Am Chem Soc 2019; 141:6906-6914. [DOI: 10.1021/jacs.8b12596] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Florian Leisinger
- Department for Chemistry, University of Basel, Mattenstrasse 24a, BPR 1002, 4056, Basel, Switzerland
| | - Reto Burn
- Department for Chemistry, University of Basel, Mattenstrasse 24a, BPR 1002, 4056, Basel, Switzerland
| | - Marcel Meury
- Department for Chemistry, University of Basel, Mattenstrasse 24a, BPR 1002, 4056, Basel, Switzerland
| | - Peer Lukat
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Florian P. Seebeck
- Department for Chemistry, University of Basel, Mattenstrasse 24a, BPR 1002, 4056, Basel, Switzerland
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56
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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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57
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Amthor JS, Bar-Even A, Hanson AD, Millar AH, Stitt M, Sweetlove LJ, Tyerman SD. Engineering Strategies to Boost Crop Productivity by Cutting Respiratory Carbon Loss. THE PLANT CELL 2019; 31:297-314. [PMID: 30670486 PMCID: PMC6447004 DOI: 10.1105/tpc.18.00743] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/04/2018] [Accepted: 01/09/2019] [Indexed: 05/03/2023]
Abstract
Roughly half the carbon that crop plants fix by photosynthesis is subsequently lost by respiration. Nonessential respiratory activity leading to unnecessary CO2 release is unlikely to have been minimized by natural selection or crop breeding, and cutting this large loss could complement and reinforce the currently dominant yield-enhancement strategy of increasing carbon fixation. Until now, however, respiratory carbon losses have generally been overlooked by metabolic engineers and synthetic biologists because specific target genes have been elusive. We argue that recent advances are at last pinpointing individual enzyme and transporter genes that can be engineered to (1) slow unnecessary protein turnover, (2) replace, relocate, or reschedule metabolic activities, (3) suppress futile cycles, and (4) make ion transport more efficient, all of which can reduce respiratory costs. We identify a set of engineering strategies to reduce respiratory carbon loss that are now feasible and model how implementing these strategies singly or in tandem could lead to substantial gains in crop productivity.
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Affiliation(s)
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley 6009 WA, Australia
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Stephen D Tyerman
- ARC Centre of Excellence in Plant Energy Biology, Department of Plant Science, School of Agriculture, Food, and Wine, Waite Research Institute, University of Adelaide, Glen Osmond SA 5064, Australia
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58
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Chen Y, Chen R, Xu J, Tian Y, Xu J, Liu Y. Two New Altenusin/Thiazole Hybrids and a New Benzothiazole Derivative from the Marine Sponge-Derived Fungus Alternaria sp. SCSIOS02F49. Molecules 2018; 23:molecules23112844. [PMID: 30388842 PMCID: PMC6278658 DOI: 10.3390/molecules23112844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 01/24/2023] Open
Abstract
Two novel altenusin-thiazole hybrids named altenusinoides A and B (1 and 2), a new benzothiazole derivative (3), and three known altenusin derivatives (4–6) have been obtained from the solid culture of the marine sponge-derived fungal strain, Alternaria sp. SCSIOS02F49. The structures of these new compounds were characterized by NMR, HRESIMS, and X-ray single crystal analysis. Compounds 1 and 2 possess an unusual altenusin-thiazole-fused skeleton core (6/6/5), and compound 3 represents the first benzothiazole derivative from fungi. Compounds 4 and 5 showed significant DPPH free-radical-scavenging activities with the prominent IC50 values of 10.7 ± 0.09 μM and 100.6 ± 0.025 μM, respectively. Additionally, compound 5 exhibited COX-2 inhibitory activity with an IC50 value of 9.5 ± 0.08 μM.
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Affiliation(s)
- Yaping Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Ruyan Chen
- College of Biological Science and Technology, Fuzhou University, Fuzhou 350116, China.
| | - Jinhuai Xu
- College of Biological Science and Technology, Fuzhou University, Fuzhou 350116, China.
| | - Yongqi Tian
- College of Biological Science and Technology, Fuzhou University, Fuzhou 350116, China.
| | - Jiangping Xu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica/RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China.
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59
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Fellner M, Rankin JA, Desguin B, Hu J, Hausinger RP. Analysis of the Active Site Cysteine Residue of the Sacrificial Sulfur Insertase LarE from Lactobacillus plantarum. Biochemistry 2018; 57:5513-5523. [PMID: 30157639 DOI: 10.1021/acs.biochem.8b00601] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LarE from Lactobacillus plantarum is an ATP-dependent sulfur transferase that sacrifices its Cys176 sulfur atom to form a dehydroalanine (Dha) side chain during biosynthesis of the covalently linked nickel-pincer nucleotide (NPN) cofactor (pyridinium 3-thioamide-5-thiocarboxylic acid mononucleotide) of lactate racemase. Coenzyme A (CoA) stabilizes LarE and forms a CoA-Cys176 mixed disulfide with the protein. This study presents the crystal structure of the LarE/CoA complex, revealing protein interactions with CoA that mimic those for binding ATP. CoA weakly inhibits LarE activity, and the persulfide of CoA is capable of partially regenerating functional LarE from the Dha176 form of the protein. The physiological relevance of this cycling reaction is unclear. A new form of LarE was discovered, an NPN-LarE covalent adduct, explaining prior results in which activation of the lactate racemase apoprotein required only the isolated LarE. The crystal structure of the inactive C176A variant revealed a fold essentially identical to that of wild-type LarE. Additional active site variants of LarE were created and their activities characterized, with all LarE variants analyzed in terms of the structure. Finally, the L. plantarum LarE structure was compared to a homology model of Thermoanaerobacterium thermosaccharolyticum LarE, predicted to contain three cysteine residues at the active site, and to other proteins with a similar fold and multiple active site cysteine residues. These findings suggest that some LarE orthologs may not be sacrificial but instead may catalyze sulfur transfer by using a persulfide mechanism or from a labile site on a [4Fe-4S] cluster at this position.
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Affiliation(s)
- Matthias Fellner
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joel A Rankin
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Benoît Desguin
- Institute of Life Sciences , Université catholique de Louvain , B-1348 Louvain-La-Neuve , Belgium
| | - Jian Hu
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Department of Microbiology and Molecular Genetics , Michigan State University , East Lansing , Michigan 48824 , United States
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60
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Microbial cell factories for the sustainable manufacturing of B vitamins. Curr Opin Biotechnol 2018; 56:18-29. [PMID: 30138794 DOI: 10.1016/j.copbio.2018.07.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 12/16/2022]
Abstract
Vitamins are essential compounds in human and animal diets. Their demand is increasing globally in food, feed, cosmetics, chemical and pharmaceutical industries. Most current production methods are unsustainable because they use non-renewable sources and often generate hazardous waste. Many microorganisms produce vitamins naturally, but their corresponding metabolic pathways are tightly regulated since vitamins are needed only in catalytic amounts. Metabolic engineering is accelerating the development of microbial cell factories for vitamins that could compete with chemical methods that have been optimized over decades, but scientific hurdles remain. Additional technological and regulatory issues need to be overcome for innovative bioprocesses to reach the market. Here, we review the current state of development and challenges for fermentative processes for the B vitamin group.
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61
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Hanson AD, Amthor JS, Sun J, Niehaus TD, Gregory JF, Bruner SD, Ding Y. Redesigning thiamin synthesis: Prospects and potential payoffs. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:92-99. [PMID: 29907313 DOI: 10.1016/j.plantsci.2018.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/24/2018] [Accepted: 01/31/2018] [Indexed: 05/20/2023]
Abstract
Thiamin is essential for plant growth but is short-lived in vivo and energetically very costly to produce - a combination that makes thiamin biosynthesis a prime target for improvement by redesign. Thiamin consists of thiazole and pyrimidine moieties. Its high biosynthetic cost stems from use of the suicide enzyme THI4 to form the thiazole and the near-suicide enzyme THIC to form the pyrimidine. These energetic costs lower biomass yield potential and are likely compounded by environmental stresses that destroy thiamin and hence increase the rate at which it must be made. The energy costs could be slashed by refactoring the thiamin biosynthesis pathway to eliminate the suicidal THI4 and THIC reactions. To substantiate this design concept, we first document the energetic costs of the THI4 and THIC steps in the pathway and explain how cutting these costs could substantially increase crop biomass and grain yields. We then show that a refactored pathway must produce thiamin itself rather than a stripped-down analog because the thiamin molecule cannot be simplified without losing biological activity. Lastly, we consider possible energy-efficient alternatives to the inefficient natural THI4- and THIC-mediated steps.
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Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
| | | | - Jiayi Sun
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL, USA
| | - Steven D Bruner
- Chemistry Department, University of Florida, Gainesville, FL, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, University of Florida, Gainesville, FL, USA
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62
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Jiang X, Zerfaß C, Feng S, Eichmann R, Asally M, Schäfer P, Soyer OS. Impact of spatial organization on a novel auxotrophic interaction among soil microbes. THE ISME JOURNAL 2018; 12:1443-1456. [PMID: 29572468 PMCID: PMC5955953 DOI: 10.1038/s41396-018-0095-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/31/2018] [Accepted: 02/07/2018] [Indexed: 01/21/2023]
Abstract
A key prerequisite to achieve a deeper understanding of microbial communities and to engineer synthetic ones is to identify the individual metabolic interactions among key species and how these interactions are affected by different environmental factors. Deciphering the physiological basis of species-species and species-environment interactions in spatially organized environments requires reductionist approaches using ecologically and functionally relevant species. To this end, we focus here on a defined system to study the metabolic interactions in a spatial context among the plant-beneficial endophytic fungus Serendipita indica, and the soil-dwelling model bacterium Bacillus subtilis. Focusing on the growth dynamics of S. indica under defined conditions, we identified an auxotrophy in this organism for thiamine, which is a key co-factor for essential reactions in the central carbon metabolism. We found that S. indica growth is restored in thiamine-free media, when co-cultured with B. subtilis. The success of this auxotrophic interaction, however, was dependent on the spatial and temporal organization of the system; the beneficial impact of B. subtilis was only visible when its inoculation was separated from that of S. indica either in time or space. These findings describe a key auxotrophic interaction in the soil among organisms that are shown to be important for plant ecosystem functioning, and point to the potential importance of spatial and temporal organization for the success of auxotrophic interactions. These points can be particularly important for engineering of minimal functional synthetic communities as plant seed treatments and for vertical farming under defined conditions.
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Affiliation(s)
- Xue Jiang
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Christian Zerfaß
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK
| | - Song Feng
- Los Alamos National Laboratory, Theoretical Division (T-6), Center for Nonlinear Studies, Los Alamos, NM, 87545, USA
| | - Ruth Eichmann
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
| | - Munehiro Asally
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK
| | - Patrick Schäfer
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK.
| | - Orkun S Soyer
- School of Life Sciences, The University of Warwick, Coventry, CV4 7AL, UK.
- Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry, CV4 7AL, UK.
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63
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Idris ZHC, Abidin AAZ, Subki A, Yusof ZNB. The Effect of Oxidative Stress Towards The Expression of Thiamine Biosynthesis Genes (THIC and THI1/THI4) in Oil Palm ( Elaeis guineensis). Trop Life Sci Res 2018; 29:71-85. [PMID: 29644016 PMCID: PMC5893237 DOI: 10.21315/tlsr2018.29.1.5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Thiamine is known to be an important compound in human diet and it is a cofactor required for vital metabolic processes such as acetyl-CoA biosynthesis, amino acid biosynthesis, Krebs and Calvin cycle. Besides that, thiamine has been shown to be involved in plant protection against stress. In this study, the level of expression of THIC and THI1/THI4, the genes for the first two enzymes in the thiamine biosynthesis pathway were observed when oil palm (Elaeis guineensis) was subjected to oxidative stress. Primers were designed based on the consensus sequence of thiamine biosynthesis genes obtained from Arabidopsis thaliana, Zea mays, Oryza sativa, and Alnus glutinosa. Oxidative stress were induced with various concentrations of paraquat and samplings were done at various time points post-stress induction. The expression of THIC and THI1/THI4 genes were observed via RT-PCR and qPCR analysis. The expression of THIC was increased 2-fold, while THI1/THI4 gene transcript was increased 4-fold upon induction of oxidative stress. These findings showed that oil palm responded to oxidative stress by over-expressing the genes involved in thiamine biosynthesis. These findings support the suggestion that thiamine may play an important role in plant protection against stress.
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Affiliation(s)
- Zainor Hafisah Che Idris
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Aisamuddin Ardi Zainal Abidin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Atiqah Subki
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Zetty Norhana Balia Yusof
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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64
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Shimizu M. NAD +/NADH homeostasis affects metabolic adaptation to hypoxia and secondary metabolite production in filamentous fungi. Biosci Biotechnol Biochem 2018; 82:216-224. [PMID: 29327656 DOI: 10.1080/09168451.2017.1422972] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Filamentous fungi are used to produce fermented foods, organic acids, beneficial secondary metabolites and various enzymes. During such processes, these fungi balance cellular NAD+:NADH ratios to adapt to environmental redox stimuli. Cellular NAD(H) status in fungal cells is a trigger of changes in metabolic pathways including those of glycolysis, fermentation, and the production of organic acids, amino acids and secondary metabolites. Under hypoxic conditions, high NADH:NAD+ ratios lead to the inactivation of various dehydrogenases, and the metabolic flow involving NAD+ is down-regulated compared with normoxic conditions. This review provides an overview of the metabolic mechanisms of filamentous fungi under hypoxic conditions that alter the cellular NADH:NAD+ balance. We also discuss the relationship between the intracellular redox balance (NAD/NADH ratio) and the production of beneficial secondary metabolites that arise from repressing the HDAC activity of sirtuin A via Nudix hydrolase A (NdxA)-dependent NAD+ degradation.
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Affiliation(s)
- Motoyuki Shimizu
- a Faculty of Agriculture, Department of Applied Biological Chemistry , Meijo University , Nagoya , Japan
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Minhas AP, Tuli R, Puri S. Pathway Editing Targets for Thiamine Biofortification in Rice Grains. FRONTIERS IN PLANT SCIENCE 2018; 9:975. [PMID: 30042775 PMCID: PMC6048418 DOI: 10.3389/fpls.2018.00975] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Thiamine deficiency is common in populations consuming polished rice as a major source of carbohydrates. Thiamine is required to synthesize thiamine pyrophosphate (TPP), an essential cofactor of enzymes of central metabolism. Its biosynthesis pathway has been partially elucidated and the effect of overexpression of a few genes such as thi1 and thiC, on thiamine accumulation in rice has been reported. Based on current knowledge, this review focuses on the potential of gene editing in metabolic engineering of thiamine biosynthesis pathway to improve thiamine in rice grains. Candidate genes, suitable for modification of the structural part to evolve more efficient versions of enzymes in the pathway, are discussed. For example, adjacent cysteine residues may be introduced in the catalytic domain of thi4 to improve the turn over activity of thiamine thiazole synthase 2. Motif specific editing to modify promoter regulatory regions of genes is discussed to modulate gene expression. Editing cis acting regulatory elements in promoter region can shift the expression of transporters and thiamine binding proteins to endosperm. This can enhance dietary availability of thiamine from rice grains. Differential transcriptomics on rice varieties with contrasting grain thiamine and functional genomic studies will identify more strategic targets for editing in future. Developing functionally enhanced foods by biofortification is a sustainable approach to make diets wholesome.
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Abstract
Vitamin B1 (thiamin) is a cofactor for critical enzymatic processes and is scarce in surface oceans. Several eukaryotic marine algal species thought to rely on exogenous thiamin are now known to grow equally well on the precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), including the haptophyte Emiliania huxleyi Because the thiamin biosynthetic capacities of the diverse and ecologically important haptophyte lineage are otherwise unknown, we investigated the pathway in transcriptomes and two genomes from 30 species representing six taxonomic orders. HMP synthase is missing in data from all studied taxa, but the pathway is otherwise complete, with some enzymatic variations. Experiments on axenic species from three orders demonstrated that equivalent growth rates were supported by 1 µM HMP or thiamin amendment. Cellular thiamin quotas were quantified in the oceanic phytoplankter E. huxleyi using the thiochrome assay. E. huxleyi exhibited luxury storage in standard algal medium [(1.16 ± 0.18) × 10-6 pmol thiamin cell-1], whereas quotas in cultures grown under more environmentally relevant thiamin and HMP supplies [(2.22 ± 0.07) × 10-7 or (1.58 ± 0.14) × 10-7 pmol thiamin cell-1, respectively] were significantly lower than luxury values and prior estimates. HMP and its salvage-related analog 4-amino-5-aminomethyl-2-methylpyrimidine (AmMP) supported higher growth than thiamin under environmentally relevant supply levels. These compounds also sustained growth of the stramenopile alga Pelagomonas calceolata Together with identification of a salvage protein subfamily (TENA_E) in multiple phytoplankton, the results indicate that salvaged AmMP and exogenously acquired HMP are used by several groups for thiamin production. Our studies highlight the potential importance of thiamin pathway intermediates and their analogs in shaping phytoplankton community structure.IMPORTANCE The concept that vitamin B1 (thiamin) availability in seawater controls the productivity and structure of eukaryotic phytoplankton communities has been discussed for half a century. We examined B1 biosynthesis and salvage pathways in diverse phytoplankton species. These comparative genomic analyses as well as experiments show that phytoplankton thought to require exogenous B1 not only utilize intermediate compounds to meet this need but also exhibit stronger growth on these compounds than on thiamin. Furthermore, oceanic phytoplankton have lower cellular thiamin quotas than previously reported, and salvage of intermediate compounds is likely a key mechanism for meeting B1 requirements under environmentally relevant scenarios. Thus, several lines of evidence now suggest that availability of specific precursor molecules could be more important in structuring phytoplankton communities than the vitamin itself. This understanding of preferential compound utilization and thiamin quotas will improve biogeochemical model parameterization and highlights interaction networks among ocean microbes.
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Helliwell KE. The roles of B vitamins in phytoplankton nutrition: new perspectives and prospects. THE NEW PHYTOLOGIST 2017; 216:62-68. [PMID: 28656633 DOI: 10.1111/nph.14669] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/05/2017] [Indexed: 06/07/2023]
Abstract
Contents 62 I. 62 II. 63 III. 63 IV. 66 V. 66 VI. 67 67 References 67 SUMMARY: B vitamins play essential roles in central metabolism. These organic water-soluble molecules act as, or as part of, coenzymes within the cell. Unlike land plants, many eukaryotic algae are auxotrophic for certain B vitamins. Recent progress in algal genetic resources and environmental chemistry have promoted a renewal of interest in the role of vitamins in governing phytoplankton dynamics, and illuminated amazing versatility in phytoplankton vitamin metabolism. Accumulating evidence demonstrates metabolic complexity in the production and bioavailability of different vitamin forms, coupled with specialized acquisition strategies to salvage and remodel vitamin precursors. Here, I describe recent advances and discuss how they redefine our view of the way in which vitamins are cycled in aquatic ecosystems and their importance in structuring phytoplankton communities.
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Affiliation(s)
- Katherine E Helliwell
- The Marine Biological Association, The Laboratory, Citadel Hill, Plymouth, PL1 2PB, UK
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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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Peng Z, Bu J, McLuckey SA. The Generation of Dehydroalanine Residues in Protonated Polypeptides: Ion/Ion Reactions for Introducing Selective Cleavages. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1765-1774. [PMID: 28497355 PMCID: PMC5681889 DOI: 10.1007/s13361-017-1672-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/02/2017] [Accepted: 03/19/2017] [Indexed: 06/07/2023]
Abstract
We examine a gas-phase approach for converting a subset of amino acid residues in polypeptide cations to dehydroalanine (Dha). Subsequent activation of the modified polypeptide ions gives rise to specific cleavage N-terminal to the Dha residue. This process allows for the incorporation of selective cleavages in the structural characterization of polypeptide ions. An ion/ion reaction within the mass spectrometer between a multiply protonated polypeptide and the sulfate radical anion introduces a radical site into the multiply protonated polypeptide reactant. Subsequent collisional activation of the polypeptide radical cation gives rise to radical side chain loss from one of several particular amino acid side chains (e.g., leucine, asparagine, lysine, glutamine, and glutamic acid) to yield a Dha residue. The Dha residues facilitate preferential backbone cleavages to produce signature c- and z-ions, demonstrated with cations derived from melittin, mechano growth factor (MGF), and ubiquitin. The efficiencies for radical side chain loss and for subsequent generation of specific c- and z-ions have been examined as functions of precursor ion charge state and activation conditions using cations of ubiquitin as a model for a small protein. It is noted that these efficiencies are not strongly dependent on ion trap collisional activation conditions but are sensitive to precursor ion charge state. Moderate to low charge states show the greatest overall yields for the specific Dha cleavages, whereas small molecule losses (e.g., water/ammonia) dominate at the lowest charge states and proton catalyzed amide bond cleavages that give rise to b- and y-ions tend to dominate at high charge states. Graphical Abstract ᅟ.
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Affiliation(s)
- Zhou Peng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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Structural insights into the catalytic mechanism of a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family, LarE. Proc Natl Acad Sci U S A 2017; 114:9074-9079. [PMID: 28784764 DOI: 10.1073/pnas.1704967114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The lar operon in Lactobacillus plantarum encodes five Lar proteins (LarA/B/C/D/E) that collaboratively synthesize and incorporate a niacin-derived Ni-containing cofactor into LarA, an Ni-dependent lactate racemase. Previous studies have established that two molecules of LarE catalyze successive thiolation reactions by donating the sulfur atom of their exclusive cysteine residues to the substrate. However, the catalytic mechanism of this very unusual sulfur-sacrificing reaction remains elusive. In this work, we present the crystal structures of LarE in ligand-free and several ligand-bound forms, demonstrating that LarE is a member of the N-type ATP pyrophosphatase (PPase) family with a conserved N-terminal ATP PPase domain and a unique C-terminal domain harboring the putative catalytic site. Structural analysis, combined with structure-guided mutagenesis, leads us to propose a catalytic mechanism that establishes LarE as a paradigm for sulfur transfer through sacrificing its catalytic cysteine residue.
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71
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Hsieh WY, Liao JC, Wang HT, Hung TH, Tseng CC, Chung TY, Hsieh MH. The Arabidopsis thiamin-deficient mutant pale green1 lacks thiamin monophosphate phosphatase of the vitamin B 1 biosynthesis pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:145-157. [PMID: 28346710 DOI: 10.1111/tpj.13552] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/20/2017] [Accepted: 03/21/2017] [Indexed: 05/24/2023]
Abstract
Thiamin diphosphate (TPP, vitamin B1 ) is an essential coenzyme present in all organisms. Animals obtain TPP from their diets, but plants synthesize TPPde novo. We isolated and characterized an Arabidopsis pale green1 (pale1) mutant that contained higher concentrations of thiamin monophosphate (TMP) and less thiamin and TPP than the wild type. Supplementation with thiamin, but not the thiazole and pyrimidine precursors, rescued the mutant phenotype, indicating that the pale1 mutant is a thiamin-deficient mutant. Map-based cloning and whole-genome sequencing revealed that the pale1 mutant has a mutation in At5g32470 encoding a TMP phosphatase of the TPP biosynthesis pathway. We further confirmed that the mutation of At5g32470 is responsible for the mutant phenotypes by complementing the pale1 mutant with constructs overexpressing full-length At5g32470. Most plant TPP biosynthetic enzymes are located in the chloroplasts and cytosol, but At5g32470-GFP localized to the mitochondrion of the root, hypocotyl, mesophyll and guard cells of the 35S:At5g32470-GFP complemented plants. The subcellular localization of a functional TMP phosphatase suggests that the complete vitamin B1 biosynthesis pathway may involve the chloroplasts, mitochondria and cytosol in plants. Analysis of PALE1 promoter-uidA activity revealed that PALE1 is mainly expressed in vascular tissues of Arabidopsis seedlings. Quantitative RT-PCR analysis of TPP biosynthesis genes and genes encoding the TPP-dependent enzymes pyruvate dehydrogenase, α-ketoglutarate dehydrogenase and transketolase revealed that the transcript levels of these genes were upregulated in the pale1 mutant. These results suggest that endogenous levels of TPP may affect the expression of genes involved in TPP biosynthesis and TPP-dependent enzymes.
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Affiliation(s)
- Wei-Yu Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jo-Chien Liao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsin-Tzu Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzu-Huan Hung
- Biotechnology Division, Taiwan Agricultural Research Institute, Taichung, 41362, Taiwan
| | - Ching-Chih Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Tsui-Yun Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ming-Hsiun Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
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72
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Desguin B, Soumillion P, Hausinger RP, Hols P. Unexpected complexity in the lactate racemization system of lactic acid bacteria. FEMS Microbiol Rev 2017; 41:S71-S83. [DOI: 10.1093/femsre/fux021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022] Open
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Abstract
Synthetic methods inspired by Nature often offer unique advantages including mild conditions and biocompatibility with aqueous media. Inspired by an ergothioneine biosynthesis protein EgtB, a mononuclear non-haem iron enzyme capable of catalysing the C-S bond formation and sulfoxidation, herein, we discovered a mild and metal-free C-H sulfenylation/intramolecular rearrangement cascade reaction employing an internally oxidizing O-N bond as a directing group. Our strategy accommodates a variety of oxyamines with good site selectivity and intrinsic oxidative properties. Combining an O-N bond with an X-S bond generates a C-S bond and an S=N bond rapidly. The newly discovered cascade reaction showed excellent chemoselectivity and a wide substrate scope for both oxyamines and sulfenylation reagents. We demonstrated the biocompatibility of the C-S bond coupling reaction by applying a coumarin-based fluorogenic probe in bacterial lysates. Finally, the C-S bond coupling reaction enabled the first fluorogenic formation of phospholipids, which self-assembled to fluorescent vesicles in situ.
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74
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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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75
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Ferens FG, Spicer V, Krokhin OV, Motnenko A, Summers WA, Court DA. A deletion variant partially complements a porin-less strain of Neurospora crassa. Biochem Cell Biol 2017; 95:318-327. [DOI: 10.1139/bcb-2016-0166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mitochondrial porin, the voltage-dependent anion channel, plays an important role in metabolism and other cellular functions within eukaryotic cells. To further the understanding of porin structure and function, Neurospora crassa wild-type porin was replaced with a deletion variant lacking residues 238–242 (238porin). 238porin was assembled in the mitochondrial outer membrane, but the steady state levels were only about 3% of those of the wild-type protein. The strain harbouring 238porin displayed cytochrome deficiencies and expressed alternative oxidase. Nonetheless, it exhibited an almost normal linear growth rate. Analysis of mitochondrial proteomes from a wild-type strain FGSC9718, a strain lacking porin (ΔPor-1), and one expressing only 238porin, revealed that the major differences between the variant strains were in the levels of subunits of the NADH:ubiquinone oxidoreductase (complex I) of the electron transport chain, which were reduced only in the ΔPor-1 strain. These, and other proteins related to electron flow and mitochondrial biogenesis, are differentially affected by relative porin levels.
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Affiliation(s)
- Fraser G. Ferens
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Victor Spicer
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Oleg V. Krokhin
- Department of Internal Medicine & Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Anna Motnenko
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - William A.T. Summers
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Deborah A. Court
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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76
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Wei WJ, Siegbahn PEM, Liao RZ. Theoretical Study of the Mechanism of the Nonheme Iron Enzyme EgtB. Inorg Chem 2017; 56:3589-3599. [PMID: 28277674 DOI: 10.1021/acs.inorgchem.6b03177] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
EgtB is a nonheme iron enzyme catalyzing the C-S bond formation between γ-glutamyl cysteine (γGC) and N-α-trimethyl histidine (TMH) in the ergothioneine biosynthesis. Density functional calculations were performed to elucidate and delineate the reaction mechanism of this enzyme. Two different mechanisms were considered, depending on whether the sulfoxidation or the S-C bond formation takes place first. The calculations suggest that the S-O bond formation occurs first between the thiolate and the ferric superoxide, followed by homolytic O-O bond cleavage, very similar to the case of cysteine dioxygenase. Subsequently, proton transfer from a second-shell residue Tyr377 to the newly generated iron-oxo moiety takes place, which is followed by proton transfer from the TMH imidazole to Tyr377, facilitated by two crystallographically observed water molecules. Next, the S-C bond is formed between γGC and TMH, followed by proton transfer from the imidazole CH moiety to Tyr377, which was calculated to be the rate-limiting step for the whole reaction, with a barrier of 17.9 kcal/mol in the quintet state. The calculated barrier for the rate-limiting step agrees quite well with experimental kinetic data. Finally, this proton is transferred back to the imidazole nitrogen to form the product. The alternative thiyl radical attack mechanism has a very high barrier, being 25.8 kcal/mol, ruling out this possibility.
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Affiliation(s)
- Wen-Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
| | - Per E M Siegbahn
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-10691 Stockholm, Sweden
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology , Wuhan 430074, China
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Li L, Nelson CJ, Trösch J, Castleden I, Huang S, Millar AH. Protein Degradation Rate in Arabidopsis thaliana Leaf Growth and Development. THE PLANT CELL 2017; 29:207-228. [PMID: 28138016 PMCID: PMC5354193 DOI: 10.1105/tpc.16.00768] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/12/2017] [Accepted: 01/30/2017] [Indexed: 05/04/2023]
Abstract
We applied 15N labeling approaches to leaves of the Arabidopsis thaliana rosette to characterize their protein degradation rate and understand its determinants. The progressive labeling of new peptides with 15N and measuring the decrease in the abundance of >60,000 existing peptides over time allowed us to define the degradation rate of 1228 proteins in vivo. We show that Arabidopsis protein half-lives vary from several hours to several months based on the exponential constant of the decay rate for each protein. This rate was calculated from the relative isotope abundance of each peptide and the fold change in protein abundance during growth. Protein complex membership and specific protein domains were found to be strong predictors of degradation rate, while N-end amino acid, hydrophobicity, or aggregation propensity of proteins were not. We discovered rapidly degrading subunits in a variety of protein complexes in plastids and identified the set of plant proteins whose degradation rate changed in different leaves of the rosette and correlated with leaf growth rate. From this information, we have calculated the protein turnover energy costs in different leaves and their key determinants within the proteome.
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Affiliation(s)
- Lei Li
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Clark J Nelson
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Josua Trösch
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Ian Castleden
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - Shaobai Huang
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley 6009, Western Australia, Australia
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A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea. J Bacteriol 2017; 199:JB.00743-16. [PMID: 27920295 DOI: 10.1128/jb.00743-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 11/28/2016] [Indexed: 01/15/2023] Open
Abstract
Thiamine (vitamin B1) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamine biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages in the Crenarchaeota phylum as well as in the Halobacteria and Thermococci classes of the Euryarchaeota ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain, which is similar to the archaeal thiamine phosphate synthase ThiN. By using comparative genomics, we predicted ThiR-binding DNA motifs and reconstructed ThiR regulons in 67 genomes representing all above-mentioned lineages. The predicted ThiR-binding motifs are characterized by palindromic symmetry with several distinct lineage-specific consensus sequences. In addition to thiamine biosynthesis genes, the reconstructed ThiR regulons include various transporters for thiamine and its precursors. Bioinformatics predictions were experimentally validated by in vitro DNA-binding assays with the recombinant ThiR protein from the hyperthermophilic archaeon Metallosphaera yellowstonensis MK1. Thiamine phosphate and, to some extent, TPP and hydroxyethylthiazole phosphate were required for the binding of ThiR to its DNA targets, suggesting that ThiR is derepressed by limitation of thiamine phosphates. The thiamine phosphate-binding residues previously identified in ThiN are highly conserved in ThiR regulators, suggesting a conserved mechanism for effector recognition. IMPORTANCE Thiamine pyrophosphate is a cofactor for many essential enzymes for glucose and energy metabolism. Thiamine or vitamin B1 biosynthesis and its transcriptional regulation in Archaea are poorly understood. We applied the comparative genomics approach to identify a novel family of regulators for the transcriptional control of thiamine metabolism genes in Archaea and reconstructed the respective regulons. The predicted ThiR regulons in archaeal genomes control the majority of thiamine biosynthesis genes. The reconstructed regulon content suggests that numerous uptake transporters for thiamine and/or its precursors are encoded in archaeal genomes. The ThiR regulon was experimentally validated by DNA-binding assays with Metallosphaera spp. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in diverse lineages of Archaea.
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Hanson AD, Beaudoin GA, McCarty DR, Gregory JF. Does Abiotic Stress Cause Functional B Vitamin Deficiency in Plants? PLANT PHYSIOLOGY 2016; 172:2082-2097. [PMID: 27807106 PMCID: PMC5129723 DOI: 10.1104/pp.16.01371] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/19/2016] [Indexed: 05/20/2023]
Abstract
B vitamins are the precursors of essential metabolic cofactors but are prone to destruction under stress conditions. It is therefore a priori reasonable that stressed plants suffer B vitamin deficiencies and that certain stress symptoms are metabolic knock-on effects of these deficiencies. Given the logic of these arguments, and the existence of data to support them, it is a shock to realize that the roles of B vitamins in plant abiotic stress have had minimal attention in the literature (100-fold less than hormones) and continue to be overlooked. In this article, we therefore aim to explain the connections among B vitamins, enzyme cofactors, and stress conditions in plants. We first outline the chemistry and biochemistry of B vitamins and explore the concept of vitamin deficiency with the help of information from mammals. We then summarize classical and recent evidence for stress-induced vitamin deficiencies and for plant responses that counter these deficiencies. Lastly, we consider potential implications for agriculture.
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Affiliation(s)
- Andrew D Hanson
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Guillaume A Beaudoin
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Donald R McCarty
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
| | - Jesse F Gregory
- Horticultural Sciences Department (A.D.H., G.A.B., D.R.M) and Food Science and Human Nutrition Department (J.F.G.), University of Florida, Gainesville, Florida 32611-0690
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Nagae M, Parniske M, Kawaguchi M, Takeda N. The Thiamine Biosynthesis Gene THI1 Promotes Nodule Growth and Seed Maturation. PLANT PHYSIOLOGY 2016; 172:2033-2043. [PMID: 27702844 PMCID: PMC5100774 DOI: 10.1104/pp.16.01254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/29/2016] [Indexed: 05/16/2023]
Abstract
Thiamine (vitamin B1) is essential for living organisms. Unlike animals, plants can synthesize thiamine. In Lotus japonicus, the expression of two thiamine biosynthesis genes, THI1 and THIC, was enhanced by inoculation with rhizobia but not by inoculation with arbuscular mycorrhizal fungi. THIC and THI2 (a THI1 paralog) were expressed in uninoculated leaves. THI2-knockdown plants and the transposon insertion mutant thiC had chlorotic leaves. This typical phenotype of thiamine deficiency was rescued by an exogenous supply of thiamine. In wild-type plants, THI1 was expressed mainly in roots and nodules, and the thi1 mutant had green leaves even in the absence of exogenous thiamine. THI1 was highly expressed in actively dividing cells of nodule primordia. The thi1 mutant had small nodules, and this phenotype was rescued by exogenous thiamine and by THI1 complementation. Exogenous thiamine increased nodule diameter, but the level of arbuscular mycorrhizal colonization was unaffected in the thi1 mutant or by exogenous thiamine. Expression of symbiotic marker genes was induced normally, implying that mainly nodule growth was delayed in the thi1 mutant. Furthermore, this mutant formed many immature seeds with reduced seed weight. These results indicate that thiamine biosynthesis mediated by THI1 enhances nodule enlargement and is required for seed development in L. japonicus.
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Affiliation(s)
- Miwa Nagae
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan (M.N., M.K., N.T.)
- Genetics, Faculty of Biology, University of Munich, 82152 Martinsried, Germany (M.P.); and
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan (M.K., N.T.)
| | - Martin Parniske
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan (M.N., M.K., N.T.)
- Genetics, Faculty of Biology, University of Munich, 82152 Martinsried, Germany (M.P.); and
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan (M.K., N.T.)
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan (M.N., M.K., N.T.)
- Genetics, Faculty of Biology, University of Munich, 82152 Martinsried, Germany (M.P.); and
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan (M.K., N.T.)
| | - Naoya Takeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Myodaiji, Okazaki, Aichi 444-8585, Japan (M.N., M.K., N.T.);
- Genetics, Faculty of Biology, University of Munich, 82152 Martinsried, Germany (M.P.); and
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan (M.K., N.T.)
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81
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Goyer A. Thiamin biofortification of crops. Curr Opin Biotechnol 2016; 44:1-7. [PMID: 27750185 DOI: 10.1016/j.copbio.2016.09.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 09/08/2016] [Accepted: 09/14/2016] [Indexed: 12/25/2022]
Abstract
Thiamin is essential for human health. While plants are the ultimate source of thiamin in most human diets, staple foods like white rice have low thiamin content. Therefore, populations whose diets are mainly based on low-thiamin staple crops suffer from thiamin deficiency. Biofortification of rice grain by engineering the thiamin biosynthesis pathway has recently been attempted, with up to 5-fold increase in thiamin content in unpolished seeds. However, polished seeds that retain only the starchy endosperm had similar thiamin content than that of non-engineered plants. Various factors such as limited supply of precursors, limited activity of thiamin biosynthetic enzymes, dependence on maternal tissues to supply thiamin, or lack of thiamin stabilizing proteins may have hindered thiamin increase in the endosperm.
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Affiliation(s)
- Aymeric Goyer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, United States; Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston, OR 97838, United States.
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82
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Pilo AL, Peng Z, McLuckey SA. The dehydroalanine effect in the fragmentation of ions derived from polypeptides. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:857-866. [PMID: 27484024 PMCID: PMC5068825 DOI: 10.1002/jms.3831] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 05/11/2023]
Abstract
The fragmentation of peptides and proteins upon collision-induced dissociation (CID) is highly dependent on sequence and ion type (e.g. protonated, deprotonated, sodiated, odd electron, etc.). Some amino acids, for example aspartic acid and proline, have been found to enhance certain cleavages along the backbone. Here, we show that peptides and proteins containing dehydroalanine, a non-proteinogenic amino acid with an unsaturated side-chain, undergo enhanced cleavage of the N-Cα bond of the dehydroalanine residue to generate c- and z-ions. Because these fragment ion types are not commonly observed upon activation of positively charged even-electron species, they can be used to identify dehydroalanine residues and localize them within the peptide or protein chain. While dehydroalanine can be generated in solution, it can also be generated in the gas phase upon CID of various species. Oxidized S-alkyl cysteine residues generate dehydroalanine upon activation via highly efficient loss of the alkyl sulfenic acid. Asymmetric cleavage of disulfide bonds upon collisional activation of systems with limited proton mobility also generates dehydroalanine. Furthermore, we show that gas-phase ion/ion reactions can be used to facilitate the generation of dehydroalanine residues via, for example, oxidation of S-alkyl cysteine residues and conversion of multiply-protonated peptides to radical cations. In the latter case, loss of radical side-chains to generate dehydroalanine from some amino acids gives rise to the possibility for residue-specific backbone cleavage of polypeptide ions. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Zhou Peng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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83
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Shimizu M, Masuo S, Itoh E, Zhou S, Kato M, Takaya N. Thiamine synthesis regulates the fermentation mechanisms in the fungus Aspergillus nidulans. Biosci Biotechnol Biochem 2016; 80:1768-75. [DOI: 10.1080/09168451.2016.1158631] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Thiamine pyrophosphate (TPP) is a critical cofactor and its biosynthesis is under the control of TPP availability. Here we disrupted a predicted thiA gene of the fungus Aspergillus nidulans and demonstrated that it is essential for synthesizing cellular thiamine. The thiamine riboswitch is a post-transcriptional mechanism for TPP to repress gene expression and it is located on A. nidulans thiA pre-messenger RNA. The thiA riboswitch was not fully derepressed under thiamine-limited conditions, and fully derepressed under environmental stressors. Upon exposure to hypoxic stress, the fungus accumulated more ThiA and NmtA proteins, and more thiamine than under aerobic conditions. The thiA gene was required for the fungus to upregulate hypoxic branched-chain amino acids and ethanol fermentation that involve enzymes containing TPP. These findings indicate that hypoxia modulates thiA expression through the thiamine riboswitch, and alters cellular fermentation mechanisms by regulating the activity of the TPP enzymes.
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Affiliation(s)
- Motoyuki Shimizu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Faculty of Agriculture, Department of Applied Biological Chemistry, Meijo University, Nagoya, Japan
| | - Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Eriko Itoh
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shengmin Zhou
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Masashi Kato
- Faculty of Agriculture, Department of Applied Biological Chemistry, Meijo University, Nagoya, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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84
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Jhulki I, Chanani PK, Abdelwahed SH, Begley TP. A Remarkable Oxidative Cascade That Replaces the Riboflavin C8 Methyl with an Amino Group during Roseoflavin Biosynthesis. J Am Chem Soc 2016; 138:8324-7. [PMID: 27331868 PMCID: PMC5610575 DOI: 10.1021/jacs.6b02469] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Roseoflavin is a naturally occurring riboflavin analogue with antibiotic properties. It is biosynthesized from riboflavin in a reaction involving replacement of the C8 methyl with a dimethylamino group. Herein we report the identification of a flavin-dependent enzyme that converts flavin mononucleotide (FMN) and glutamate to 8-amino-FMN via the intermediacy of 8-formyl-FMN. A mechanistic proposal for this remarkable transformation is proposed.
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Affiliation(s)
- Isita Jhulki
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Prem K. Chanani
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Sameh H. Abdelwahed
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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85
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Martinis J, Gas-Pascual E, Szydlowski N, Crèvecoeur M, Gisler A, Bürkle L, Fitzpatrick TB. Long-Distance Transport of Thiamine (Vitamin B1) Is Concomitant with That of Polyamines. PLANT PHYSIOLOGY 2016; 171:542-53. [PMID: 27006489 PMCID: PMC4854701 DOI: 10.1104/pp.16.00009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/20/2016] [Indexed: 05/03/2023]
Abstract
Thiamine (vitamin B1) is ubiquitous and essential for cell energy supply in all organisms as a vital metabolic cofactor, known for over a century. In plants, it is established that biosynthesis de novo is taking place predominantly in green tissues and is furthermore limited to plastids. Therefore, transport mechanisms are required to mediate the movement of this polar metabolite from source to sink tissue to activate key enzymes in cellular energy generating pathways but are currently unknown. Similar to thiamine, polyamines are an essential set of charged molecules required for diverse aspects of growth and development, the homeostasis of which necessitates long-distance transport processes that have remained elusive. Here, a yeast-based screen allowed us to identify Arabidopsis (Arabidopsis thaliana) PUT3 as a thiamine transporter. A combination of biochemical, physiological, and genetic approaches permitted us to show that PUT3 mediates phloem transport of both thiamine and polyamines. Loss of function of PUT3 demonstrated that the tissue distribution of these metabolites is altered with growth and developmental consequences. The pivotal role of PUT3 mediated thiamine and polyamine homeostasis in plants, and its importance for plant fitness is revealed through these findings.
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Affiliation(s)
- Jacopo Martinis
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (J.M., E.G.-P., N.S., M.C., A.G., T.B.F.); andInstitute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland (L.B.)
| | - Elisabet Gas-Pascual
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (J.M., E.G.-P., N.S., M.C., A.G., T.B.F.); andInstitute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland (L.B.)
| | - Nicolas Szydlowski
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (J.M., E.G.-P., N.S., M.C., A.G., T.B.F.); andInstitute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland (L.B.)
| | - Michèle Crèvecoeur
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (J.M., E.G.-P., N.S., M.C., A.G., T.B.F.); andInstitute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland (L.B.)
| | - Alexandra Gisler
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (J.M., E.G.-P., N.S., M.C., A.G., T.B.F.); andInstitute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland (L.B.)
| | - Lukas Bürkle
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (J.M., E.G.-P., N.S., M.C., A.G., T.B.F.); andInstitute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland (L.B.)
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland (J.M., E.G.-P., N.S., M.C., A.G., T.B.F.); andInstitute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland (L.B.)
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86
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Nickel-pincer cofactor biosynthesis involves LarB-catalyzed pyridinium carboxylation and LarE-dependent sacrificial sulfur insertion. Proc Natl Acad Sci U S A 2016; 113:5598-603. [PMID: 27114550 DOI: 10.1073/pnas.1600486113] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lactate racemase enzyme (LarA) of Lactobacillus plantarum harbors a (SCS)Ni(II) pincer complex derived from nicotinic acid. Synthesis of the enzyme-bound cofactor requires LarB, LarC, and LarE, which are widely distributed in microorganisms. The functions of the accessory proteins are unknown, but the LarB C terminus resembles aminoimidazole ribonucleotide carboxylase/mutase, LarC binds Ni and could act in Ni delivery or storage, and LarE is a putative ATP-using enzyme of the pyrophosphatase-loop superfamily. Here, we show that LarB carboxylates the pyridinium ring of nicotinic acid adenine dinucleotide (NaAD) and cleaves the phosphoanhydride bond to release AMP. The resulting biscarboxylic acid intermediate is transformed into a bisthiocarboxylic acid species by two single-turnover reactions in which sacrificial desulfurization of LarE converts its conserved Cys176 into dehydroalanine. Our results identify a previously unidentified metabolic pathway from NaAD using unprecedented carboxylase and sulfur transferase reactions to form the organic component of the (SCS)Ni(II) pincer cofactor of LarA. In species where larA is absent, this pathway could be used to generate a pincer complex in other enzymes.
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87
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Hayashi M, Kijima Y, Tazuya-Murayama K, Yamada K. The Biosynthesis of the Thiazole Moiety of Thiamin in the Archaeon Halobacterium salinarum. J Nutr Sci Vitaminol (Tokyo) 2016; 61:270-4. [PMID: 26226965 DOI: 10.3177/jnsv.61.270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The biosynthetic pathways of the thiazole moiety of thiamin were studied in the archaeon Halobacterium salinarum. Thiamin is generated by the union of 4-amino-5-hydroxymethyl-2-methylpyrimidine (pyrimidine) and 5-(2-hydroxyethyl)-4-methylthiazole (thiazole). The biosynthesis of thiazole is different in facultative anaerobes, aerobes and eukaryotes. In eukaryotes, the C-4, -4', -5, -5' and -5" of the thiazole is biosynthesized from nicotinamide adenine dinucleotide (NAD), with cysteine as S donor and the C-2 and N atoms of glycine. In facultative anaerobic bacteria, such as Escherichia coli, the precursors of the thiazole are the N and C-2 atoms from tyrosine and C-4, -4', -5, -5' and -5" from 1-deoxy-D-xylurose-5-phosphate, again with cysteine as S donor. In aerobic bacteria, such as Bacillus subtilis, L-tyrosine is replaced by glycine. In Archaea, known as the third domain of life, the biosynthetic pathway of thiamin has not yet been elucidated. In the present study in the archaeon H. salinarum, it was shown that both the N and C-2 from glycine are incorporated into the thiazole, rather than the N atom coming from L-tyrosine. These results show that thiazole biosynthesis in H. salinarum more closely resembles the biosynthetic pathway found in eukaryotes.
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Affiliation(s)
- Maria Hayashi
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University
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88
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Sirota FL, Maurer-Stroh S, Eisenhaber B, Eisenhaber F. Single-residue posttranslational modification sites at the N-terminus, C-terminus or in-between: To be or not to be exposed for enzyme access. Proteomics 2016; 15:2525-46. [PMID: 26038108 PMCID: PMC4745020 DOI: 10.1002/pmic.201400633] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 04/17/2015] [Accepted: 05/29/2015] [Indexed: 11/30/2022]
Abstract
Many protein posttranslational modifications (PTMs) are the result of an enzymatic reaction. The modifying enzyme has to recognize the substrate protein's sequence motif containing the residue(s) to be modified; thus, the enzyme's catalytic cleft engulfs these residue(s) and the respective sequence environment. This residue accessibility condition principally limits the range where enzymatic PTMs can occur in the protein sequence. Non‐globular, flexible, intrinsically disordered segments or large loops/accessible long side chains should be preferred whereas residues buried in the core of structures should be void of what we call canonical, enzyme‐generated PTMs. We investigate whether PTM sites annotated in UniProtKB (with MOD_RES/LIPID keys) are situated within sequence ranges that can be mapped to known 3D structures. We find that N‐ or C‐termini harbor essentially exclusively canonical PTMs. We also find that the overwhelming majority of all other PTMs are also canonical though, later in the protein's life cycle, the PTM sites can become buried due to complex formation. Among the remaining cases, some can be explained (i) with autocatalysis, (ii) with modification before folding or after temporary unfolding, or (iii) as products of interaction with small, diffusible reactants. Others require further research how these PTMs are mechanistically generated in vivo.
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Affiliation(s)
- Fernanda L Sirota
- Bioinformatics Institute (BII), Agency for Science and Technology (A*STAR), Matrix, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science and Technology (A*STAR), Matrix, Singapore.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science and Technology (A*STAR), Matrix, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science and Technology (A*STAR), Matrix, Singapore.,Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore.,School of Computer Engineering (SCE), Nanyang Technological University (NTU), Singapore
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89
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Wang L, Ye, Liu H, Liu X, Wei C, Huang Y, Liu Y, Tu J. Both overexpression and suppression of an Oryza sativa NB-LRR-like gene OsLSR result in autoactivation of immune response and thiamine accumulation. Sci Rep 2016; 6:24079. [PMID: 27052628 PMCID: PMC4823736 DOI: 10.1038/srep24079] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/18/2016] [Indexed: 01/27/2023] Open
Abstract
Tight and accurate regulation of immunity and thiamine biosynthesis is critical for proper defence mechanisms and several primary metabolic cycles in plants. Although thiamine is known to enhance plant defence by priming, the mechanism by which thiamine biosynthesis responds to immune signals remains poorly understood. Here we identified a novel rice (Oryza sativa L.) NB-LRR gene via an insertion mutation, this mutant confesses a low seed setting phenotype and the corresponding genetic locus was named OsLSR (Low seed setting related). Comparing with wildtype plant, both overexpression and suppression of OsLSR lead to the autoactivation of the rice immune system and accumulation of thiamine, which result in a great fitness cost and yield penalty. Moreover, when fused with eGFP at their C terminus, two fragments, OsLSR1-178 and OsLSR464-546, localized to chloroplasts where thiamine is produced. Our result suggests that OsLSR differs from traditional NB-LRR genes. Its expression is closely related to the immune status and thiamine level in plant cells and should be maintained within a narrow range for rice growth.
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Affiliation(s)
- Liangchao Wang
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Ye
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Huachun Liu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Xuejiao Liu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Chuchu Wei
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Yuqing Huang
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Yujun Liu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
| | - Jumin Tu
- Institute of Crop Science, Zhejiang University, Yu-Hang-Tang Road No 866, Hangzhou, 310058, China
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90
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Zhang X, Eser BE, Chanani PK, Begley TP, Ealick SE. Structural Basis for Iron-Mediated Sulfur Transfer in Archael and Yeast Thiazole Synthases. Biochemistry 2016; 55:1826-38. [PMID: 26919468 PMCID: PMC4811699 DOI: 10.1021/acs.biochem.6b00030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Thiamin diphosphate is an essential cofactor in all forms of life and plays a key role in amino acid and carbohydrate metabolism. Its biosynthesis involves separate syntheses of the pyrimidine and thiazole moieties, which are then coupled to form thiamin monophosphate. A final phosphorylation produces the active form of the cofactor. In most bacteria, six gene products are required for biosynthesis of the thiamin thiazole. In yeast and fungi only one gene product, Thi4, is required for thiazole biosynthesis. Methanococcus jannaschii expresses a putative Thi4 ortholog that was previously reported to be a ribulose 1,5-bisphosphate synthase [Finn, M. W. and Tabita, F. R. (2004) J. Bacteriol., 186, 6360-6366]. Our structural studies show that the Thi4 orthologs from M. jannaschii and Methanococcus igneus are structurally similar to Thi4 from Saccharomyces cerevisiae. In addition, all active site residues are conserved except for a key cysteine residue, which in S. cerevisiae is the source of the thiazole sulfur atom. Our recent biochemical studies showed that the archael Thi4 orthologs use nicotinamide adenine dinucleotide, glycine, and free sulfide to form the thiamin thiazole in an iron-dependent reaction [Eser, B., Zhang, X., Chanani, P. K., Begley, T. P., and Ealick, S. E. (2016) J. Am. Chem. Soc. , DOI: 10.1021/jacs.6b00445]. Here we report X-ray crystal structures of Thi4 from M. jannaschii complexed with ADP-ribulose, the C205S variant of Thi4 from S. cerevisiae with a bound glycine imine intermediate, and Thi4 from M. igneus with bound glycine imine intermediate and iron. These studies reveal the structural basis for the iron-dependent mechanism of sulfur transfer in archael and yeast thiazole synthases.
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Affiliation(s)
- Xuan Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Bekir E. Eser
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Prem K. Chanani
- Department of Chemistry, Texas A&M University, College Station, Texas 77843
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843,To whom correspondence should be addressed at the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853. Telephone: (607) 255-7961. Fax: (607) 255-1227. ,
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853,To whom correspondence should be addressed at the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853. Telephone: (607) 255-7961. Fax: (607) 255-1227. ,
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91
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Iosue CL, Attanasio N, Shaik NF, Neal EM, Leone SG, Cali BJ, Peel MT, Grannas AM, Wykoff DD. Partial Decay of Thiamine Signal Transduction Pathway Alters Growth Properties of Candida glabrata. PLoS One 2016; 11:e0152042. [PMID: 27015653 PMCID: PMC4807840 DOI: 10.1371/journal.pone.0152042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 02/21/2016] [Indexed: 12/31/2022] Open
Abstract
The phosphorylated form of thiamine (Vitamin B1), thiamine pyrophosphate (TPP) is essential for the metabolism of amino acids and carbohydrates in all organisms. Plants and microorganisms, such as yeast, synthesize thiamine de novo whereas animals do not. The thiamine signal transduction (THI) pathway in Saccharomyces cerevisiae is well characterized. The ~10 genes required for thiamine biosynthesis and uptake are transcriptionally upregulated during thiamine starvation by THI2, THI3, and PDC2. Candida glabrata, a human commensal and opportunistic pathogen, is closely related to S. cerevisiae but is missing half of the biosynthetic pathway, which limits its ability to make thiamine. We investigated the changes to the THI pathway in C. glabrata, confirming orthologous functions. We found that C. glabrata is unable to synthesize the pyrimidine subunit of thiamine as well as the thiamine precursor vitamin B6. In addition, THI2 (the gene encoding a transcription factor) is not present in C. glabrata, indicating a difference in the transcriptional regulation of the pathway. Although the pathway is upregulated by thiamine starvation in both species, C. glabrata appears to upregulate genes involved in thiamine uptake to a greater extent than S. cerevisiae. However, the altered regulation of the THI pathway does not alter the concentration of thiamine and its vitamers in the two species as measured by HPLC. Finally, we demonstrate potential consequences to having a partial decay of the THI biosynthetic and regulatory pathway. When the two species are co-cultured, the presence of thiamine allows C. glabrata to rapidly outcompete S. cerevisiae, while absence of thiamine allows S. cerevisiae to outcompete C. glabrata. This simplification of the THI pathway in C. glabrata suggests its environment provides thiamine and/or its precursors to cells, whereas S. cerevisiae is not as reliant on environmental sources of thiamine.
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Affiliation(s)
- Christine L. Iosue
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Nicholas Attanasio
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Noor F. Shaik
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Erin M. Neal
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Sarah G. Leone
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Brian J. Cali
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Michael T. Peel
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Amanda M. Grannas
- Department of Chemistry, Villanova University, Villanova, Pennsylvania, United States of America
| | - Dennis D. Wykoff
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
- * E-mail:
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92
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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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93
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Wang Y, Wang J, Yu S, Wang F, Ma H, Yue C, Liu M, Deng Z, Huang Y, Qu X. Identifying the Minimal Enzymes for Unusual Carbon-Sulfur Bond Formation in Thienodolin Biosynthesis. Chembiochem 2016; 17:799-803. [PMID: 26854280 DOI: 10.1002/cbic.201500670] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Yaya Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Jiali Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Shuqi Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Fan Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Hongmin Ma
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Changwu Yue
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences, 1 Beichen West Road; Beijing 100101 China
- Guizhou Key Laboratory of Microbial Resources and Drug Development; Zunyi Medical College, 201 Dalian Road; Zunyi 563003 China
| | - Minghao Liu
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences, 1 Beichen West Road; Beijing 100101 China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
| | - Ying Huang
- State Key Laboratory of Microbial Resources; Institute of Microbiology; Chinese Academy of Sciences, 1 Beichen West Road; Beijing 100101 China
| | - Xudong Qu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery; Ministry of Education, School of Pharmaceutical Sciences; Wuhan University; 185 Donghu Road Wuhan 430071 China
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94
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Dong W, Thomas N, Ronald PC, Goyer A. Overexpression of Thiamin Biosynthesis Genes in Rice Increases Leaf and Unpolished Grain Thiamin Content But Not Resistance to Xanthomonas oryzae pv. oryzae. FRONTIERS IN PLANT SCIENCE 2016; 7:616. [PMID: 27242822 PMCID: PMC4861732 DOI: 10.3389/fpls.2016.00616] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/22/2016] [Indexed: 05/06/2023]
Abstract
Thiamin diphosphate (ThDP), also known as vitamin B1, serves as an enzymatic cofactor in glucose metabolism, the Krebs cycle, and branched-chain amino acid biosynthesis in all living organisms. Unlike plants and microorganisms, humans are not able to synthesize ThDP de novo and must obtain it from their diet. Staple crops such as rice are poor sources of thiamin. Hence, populations that mainly consume rice commonly suffer thiamin deficiency. In addition to thiamin's nutritional function, studies in rice have shown that some thiamin biosynthesis genes are involved in resistance to Xanthomonas oryzae, which causes a serious disease in rice fields. This study shows that overexpression of two thiamin biosynthesis genes, 4-methyl-5-β-hydroxyethylthiazole phosphate synthase and 4-amino-2-methyl-5-hydroxymethylpyrimidine phosphate synthase, involved in the first steps of the thiazole and pyrimidine synthesis branches, respectively, increased thiamin content up to fivefold in unpolished seeds that retain the bran. However, thiamin levels in polished seeds with removed bran were similar to those found in polished control seeds. Plants with higher accumulation of thiamin did not show enhanced resistance to X. oryzae. These results indicate that stacking of two traits can enhance thiamin accumulation in rice unpolished grain. We discuss potential roadblocks that prevent thiamin accumulation in the endosperm.
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Affiliation(s)
- Wei Dong
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Hermiston Agricultural Research and Extension Center, Oregon State UniversityHermiston, OR, USA
| | - Nicholas Thomas
- Department of Plant Pathology, University of California, DavisDavis, CA, USA
| | - Pamela C. Ronald
- Department of Plant Pathology, University of California, DavisDavis, CA, USA
| | - Aymeric Goyer
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Hermiston Agricultural Research and Extension Center, Oregon State UniversityHermiston, OR, USA
- *Correspondence: Aymeric Goyer,
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95
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Dong W, Stockwell VO, Goyer A. Enhancement of Thiamin Content in Arabidopsis thaliana by Metabolic Engineering. PLANT & CELL PHYSIOLOGY 2015; 56:2285-96. [PMID: 26454882 DOI: 10.1093/pcp/pcv148] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 10/02/2015] [Indexed: 05/06/2023]
Abstract
Thiamin is an essential nutrient in the human diet. Severe thiamin deficiency leads to beriberi, a lethal disease which is common in developing countries. Thiamin biofortification of staple food crops is a possible strategy to alleviate thiamin deficiency-related diseases. In plants, thiamin plays a role in the response to abiotic and biotic stresses, and data from the literature suggest that boosting thiamin content could increase resistance to stresses. Here, we tested an engineering strategy to increase thiamin content in Arabidopsis. Thiamin is composed of a thiazole ring linked to a pyrimidine ring by a methylene bridge. THI1 and THIC are the first committed steps in the synthesis of the thiazole and pyrimidine moieties, respectively. Arabidopsis plants were transformed with a vector containing the THI1-coding sequence under the control of a constitutive promoter. Total thiamin leaf content in THI1 plants was up approximately 2-fold compared with the wild type. THI1-overexpressing lines were then crossed with pre-existing THIC-overexpressing lines. Resulting THI1 × THIC plants accumulated up to 3.4- and 2.6-fold more total thiamin than wild-type plants in leaf and seeds, respectively. After inoculation with Pseudomonas syringae, THI1 × THIC plants had lower populations than the wild-type control. However, THI1 × THIC plants subjected to various abiotic stresses did not show any visible or biochemical changes compared with the wild type. We discuss the impact of engineering thiamin biosynthesis on the nutritional value of plants and their resistance to biotic and abiotic stresses.
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Affiliation(s)
- Wei Dong
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S First Street, Hermiston, OR 97838, USA Present address: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Virginia O Stockwell
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA
| | - Aymeric Goyer
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97330, USA Hermiston Agricultural Research and Extension Center, Oregon State University, 2121 S First Street, Hermiston, OR 97838, USA
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96
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Paulo JA, O'Connell JD, Gaun A, Gygi SP. Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. Mol Biol Cell 2015; 26:4063-74. [PMID: 26399295 PMCID: PMC4710237 DOI: 10.1091/mbc.e15-07-0499] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/18/2015] [Indexed: 12/27/2022] Open
Abstract
A mass spectrometry–based tandem mass tag 9-plex strategy was used to determine alterations in relative protein abundance due to three carbon sources—glucose, galactose, and raffinose. More than 4700 proteins were quantified across all nine samples; 1003 demonstrated statistically significant differences in abundance in at least one condition. The global proteomic alterations in the budding yeast Saccharomyces cerevisiae due to differences in carbon sources can be comprehensively examined using mass spectrometry–based multiplexing strategies. In this study, we investigate changes in the S. cerevisiae proteome resulting from cultures grown in minimal media using galactose, glucose, or raffinose as the carbon source. We used a tandem mass tag 9-plex strategy to determine alterations in relative protein abundance due to a particular carbon source, in triplicate, thereby permitting subsequent statistical analyses. We quantified more than 4700 proteins across all nine samples; 1003 proteins demonstrated statistically significant differences in abundance in at least one condition. The majority of altered proteins were classified as functioning in metabolic processes and as having cellular origins of plasma membrane and mitochondria. In contrast, proteins remaining relatively unchanged in abundance included those having nucleic acid–related processes, such as transcription and RNA processing. In addition, the comprehensiveness of the data set enabled the analysis of subsets of functionally related proteins, such as phosphatases, kinases, and transcription factors. As a resource, these data can be mined further in efforts to understand better the roles of carbon source fermentation in yeast metabolic pathways and the alterations observed therein, potentially for industrial applications, such as biofuel feedstock production.
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Affiliation(s)
- Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | | | - Aleksandr Gaun
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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97
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Colinas M, Fitzpatrick TB. Natures balancing act: examining biosynthesis de novo, recycling and processing damaged vitamin B metabolites. CURRENT OPINION IN PLANT BIOLOGY 2015; 25:98-106. [PMID: 26005929 DOI: 10.1016/j.pbi.2015.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/22/2015] [Accepted: 05/01/2015] [Indexed: 05/06/2023]
Abstract
Plants use B vitamin compounds as cofactors for metabolism. Biosynthesis de novo of these metabolites in plants is almost fully elucidated. However, salvaging of precursors as well as cofactor derivatives is only being unraveled. Furthermore, processing of these compounds when damaged by cellular activities to prevent deleterious effects on metabolism is emerging. Recent investigations indicate that the role of B vitamins goes beyond metabolism and are being linked with epigenetic traits, specific developmental cues, the circadian clock, as well as abiotic and biotic stress responses. More in depth investigations on the regulation of the provision of these compounds through biosynthesis de novo, salvage and transport is suggesting that plants may share the cost of this load by division of labor.
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Affiliation(s)
- Maite Colinas
- Department of Botany and Plant Biology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
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98
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Liu Y, Zhang W, Xie L, Liu H, Gong G, Zhu B, Hu Y. Acthi, a thiazole biosynthesis enzyme, is essential for thiamine biosynthesis and CPC production in Acremonium chrysogenum. Microb Cell Fact 2015; 14:50. [PMID: 25886533 PMCID: PMC4416257 DOI: 10.1186/s12934-015-0235-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/30/2015] [Indexed: 11/13/2022] Open
Abstract
Background The filamentous fungus Acremonium chrysogenum is an important industrial fungus and is used in the production of the β-lactam antibiotic cephalosporin C. Little is known regarding the molecular and biological mechanisms of how this industrial strain was improved by mutagenesis and molecular breeding. Comparative proteomics is one of the most powerful methods to evaluate the influence of gene expression on metabolite production. Results In this study, we used comparative proteomics to investigate the molecular mechanisms involved in the biosynthesis of cephalosporin C between a high-producer (HY) strain and a wide-type (WT) strain. We found that the expression levels of thiamine biosynthesis-related enzymes, including the thiazole biosynthesis enzyme (Acthi), pyruvate oxidase, flavin adenine dinucleotide (FAD)-dependent oxidoreductase and sulfur carrier protein-thiS, were up-regulated in the HY strain. An Acthi-silencing mutant of the WT strain grew poorly on chemically defined medium (MMC) in the absence of thiamine, and its growth was recovered on MMC medium supplemented with thiamine. The intracellular thiamine content was changed in the Acthi silencing or over-expression mutants. In addition, we demonstrated that the manipulation of the Acthi gene can affect the hyphal growth of Acremonium chrysogenum, the transcription levels of cephalosporin C biosynthetic genes, the quantification levels of precursor amino acids for cephalosporin C synthesis and the expression levels of thiamine diphosphate-dependent enzymes. Over-expression of Acthi can significantly increase the cephalosporin C yield in both the WT strain and the HY mutant strain. Conclusions Using comparative proteomics, four differently expressed proteins were exploited, whose functions may be involved in thiamine diphosphate metabolism. Among these proteins, the thiazole biosynthesis enzyme (ActhiS) may play an important role in cephalosporin C biosynthesis. Our studies suggested that Acthi might be involved in the transcriptional regulation of cephalosporin C biosynthesis. Therefore, the thiamine metabolic pathway could be a potential target for the molecular breeding of this cephalosporin C producer for industrial applications.
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Affiliation(s)
- Yan Liu
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, 1599 Zhangheng Road, Shanghai, 201203, China. .,Shanghai Institute of Pharmaceutical Industry, 1320 Beijing Road (W), Shanghai, 200040, China.
| | - Wei Zhang
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, 1599 Zhangheng Road, Shanghai, 201203, China.
| | - Liping Xie
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, 1599 Zhangheng Road, Shanghai, 201203, China.
| | - Hong Liu
- Shanghai Institute of Pharmaceutical Industry, 1320 Beijing Road (W), Shanghai, 200040, China. .,Present address: Luye Pharma Group Ltd., Yantai, Shandong, 264003, China.
| | - Guihua Gong
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, 1599 Zhangheng Road, Shanghai, 201203, China.
| | - Baoquan Zhu
- Shanghai Institute of Pharmaceutical Industry, 1320 Beijing Road (W), Shanghai, 200040, China.
| | - Youjia Hu
- China State Institute of Pharmaceutical Industry, Zhangjiang Institute, 1599 Zhangheng Road, Shanghai, 201203, China.
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99
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Goncharenko KV, Vit A, Blankenfeldt W, Seebeck FP. Struktur der Sulfoxid-Synthase EgtB aus der Ergothionein- Biosynthese. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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100
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Goncharenko KV, Vit A, Blankenfeldt W, Seebeck FP. Structure of the sulfoxide synthase EgtB from the ergothioneine biosynthetic pathway. Angew Chem Int Ed Engl 2015; 54:2821-4. [PMID: 25597398 DOI: 10.1002/anie.201410045] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 01/09/2023]
Abstract
The non-heme iron enzyme EgtB catalyzes O2 -dependent C-S bond formation between γ-glutamyl cysteine and N-α-trimethyl histidine as the central step in ergothioneine biosynthesis. Both, the catalytic activity and the architecture of EgtB are distinct from known sulfur transferases or thiol dioxygenases. The crystal structure of EgtB from Mycobacterium thermoresistibile in complex with γ-glutamyl cysteine and N-α-trimethyl histidine reveals that the two substrates and three histidine residues serve as ligands in an octahedral iron binding site. This active site geometry is consistent with a catalytic mechanism in which C-S bond formation is initiated by an iron(III)-complexed thiyl radical attacking the imidazole ring of N-α-trimethyl histidine.
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Affiliation(s)
- Kristina V Goncharenko
- Department for Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel (Switzerland)
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