1
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Sharma V, Fedoseyenko D, Joshi S, Abdelwahed S, Begley TP. Phosphomethylpyrimidine Synthase (ThiC): Trapping of Five Intermediates Provides Mechanistic Insights on a Complex Radical Cascade Reaction in Thiamin Biosynthesis. ACS CENTRAL SCIENCE 2024; 10:988-1000. [PMID: 38799670 PMCID: PMC11117688 DOI: 10.1021/acscentsci.4c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 05/29/2024]
Abstract
Phosphomethylpyrimidine synthase (ThiC) catalyzes the conversion of AIR to the thiamin pyrimidine HMP-P. This reaction is the most complex enzyme-catalyzed radical cascade identified to date, and the detailed mechanism has remained elusive. In this paper, we describe the trapping of five new intermediates that provide snapshots of the ThiC reaction coordinate and enable the formulation of a revised mechanism for the ThiC-catalyzed reaction.
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Affiliation(s)
- Vishav Sharma
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Sumedh Joshi
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Sameh Abdelwahed
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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2
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Chung YH, Chen TC, Yang WJ, Chen SZ, Chang JM, Hsieh WY, Hsieh MH. Ectopic expression of a bacterial thiamin monophosphate kinase enhances vitamin B1 biosynthesis in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1330-1343. [PMID: 37996996 DOI: 10.1111/tpj.16563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023]
Abstract
Plants and bacteria have distinct pathways to synthesize the bioactive vitamin B1 thiamin diphosphate (TDP). In plants, thiamin monophosphate (TMP) synthesized in the TDP biosynthetic pathway is first converted to thiamin by a phosphatase, which is then pyrophosphorylated to TDP. In contrast, bacteria use a TMP kinase encoded by ThiL to phosphorylate TMP to TDP directly. The Arabidopsis THIAMIN REQUIRING2 (TH2)-encoded phosphatase is involved in TDP biosynthesis. The chlorotic th2 mutants have high TMP and low thiamin and TDP. Ectopic expression of Escherichia coli ThiL and ThiL-GFP rescued the th2-3 mutant, suggesting that the bacterial TMP kinase could directly convert TMP into TDP in Arabidopsis. These results provide direct evidence that the chlorotic phenotype of th2-3 is caused by TDP rather than thiamin deficiency. Transgenic Arabidopsis harboring engineered ThiL-GFP targeting to the cytosol, chloroplast, mitochondrion, or nucleus accumulated higher TDP than the wild type (WT). Ectopic expression of E. coli ThiL driven by the UBIQUITIN (UBI) promoter or an endosperm-specific GLUTELIN1 (GT1) promoter also enhanced TDP biosynthesis in rice. The pUBI:ThiL transgenic rice accumulated more TDP and total vitamin B1 in the leaves, and the pGT1:ThiL transgenic lines had higher TDP and total vitamin B1 in the seeds than the WT. Total vitamin B1 only increased by approximately 25-30% in the polished and unpolished seeds of the pGT1:ThiL transgenic rice compared to the WT. Nevertheless, these results suggest that genetic engineering of a bacterial vitamin B1 biosynthetic gene downstream of TMP can enhance vitamin B1 production in rice.
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Affiliation(s)
- Yi-Hsin Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ting-Chieh Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Ju Yang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Soon-Ziet Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jia-Ming Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Wei-Yu Hsieh
- 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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3
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Ehrmann AK, Wronska AK, Perli T, de Hulster EAF, Luttik MAH, van den Broek M, Carqueija Cardoso C, Pronk JT, Daran JM. Engineering Saccharomyces cerevisiae for fast vitamin-independent aerobic growth. Metab Eng 2024; 82:201-215. [PMID: 38364997 DOI: 10.1016/j.ymben.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/08/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Chemically defined media for cultivation of Saccharomyces cerevisiae strains are commonly supplemented with a mixture of multiple Class-B vitamins, whose omission leads to strongly reduced growth rates. Fast growth without vitamin supplementation is interesting for industrial applications, as it reduces costs and complexity of medium preparation and may decrease susceptibility to contamination by auxotrophic microbes. In this study, suboptimal growth rates of S. cerevisiae CEN.PK113-7D in the absence of pantothenic acid, para-aminobenzoic acid (pABA), pyridoxine, inositol and/or biotin were corrected by single or combined overexpression of ScFMS1, ScABZ1/ScABZ2, ScSNZ1/ScSNO1, ScINO1 and Cyberlindnera fabianii BIO1, respectively. Several strategies were explored to improve growth of S. cerevisiae CEN.PK113-7D in thiamine-free medium. Overexpression of ScTHI4 and/or ScTHI5 enabled thiamine-independent growth at 83% of the maximum specific growth rate of the reference strain in vitamin-supplemented medium. Combined overexpression of seven native S. cerevisiae genes and CfBIO1 enabled a maximum specific growth rate of 0.33 ± 0.01 h-1 in vitamin-free synthetic medium. This growth rate was only 17 % lower than that of a congenic reference strain in vitamin-supplemented medium. Physiological parameters of the engineered vitamin-independent strain in aerobic glucose-limited chemostat cultures (dilution rate 0.10 h-1) grown on vitamin-free synthetic medium were similar to those of similar cultures of the parental strain grown on vitamin-supplemented medium. Transcriptome analysis revealed only few differences in gene expression between these cultures, which primarily involved genes with roles in Class-B vitamin metabolism. These results pave the way for development of fast-growing vitamin-independent industrial strains of S. cerevisiae.
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Affiliation(s)
- Anja K Ehrmann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Anna K Wronska
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Thomas Perli
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Clara Carqueija Cardoso
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
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4
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Lee KT, Liao HS, Hsieh MH. Glutamine Metabolism, Sensing and Signaling in Plants. PLANT & CELL PHYSIOLOGY 2023; 64:1466-1481. [PMID: 37243703 DOI: 10.1093/pcp/pcad054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/23/2023] [Accepted: 05/24/2023] [Indexed: 05/29/2023]
Abstract
Glutamine (Gln) is the first amino acid synthesized in nitrogen (N) assimilation in plants. Gln synthetase (GS), converting glutamate (Glu) and NH4+ into Gln at the expense of ATP, is one of the oldest enzymes in all life domains. Plants have multiple GS isoenzymes that work individually or cooperatively to ensure that the Gln supply is sufficient for plant growth and development under various conditions. Gln is a building block for protein synthesis and an N-donor for the biosynthesis of amino acids, nucleic acids, amino sugars and vitamin B coenzymes. Most reactions using Gln as an N-donor are catalyzed by Gln amidotransferase (GAT) that hydrolyzes Gln to Glu and transfers the amido group of Gln to an acceptor substrate. Several GAT domain-containing proteins of unknown function in the reference plant Arabidopsis thaliana suggest that some metabolic fates of Gln have yet to be identified in plants. In addition to metabolism, Gln signaling has emerged in recent years. The N regulatory protein PII senses Gln to regulate arginine biosynthesis in plants. Gln promotes somatic embryogenesis and shoot organogenesis with unknown mechanisms. Exogenous Gln has been implicated in activating stress and defense responses in plants. Likely, Gln signaling is responsible for some of the new Gln functions in plants.
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Affiliation(s)
- Kim-Teng Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences, The Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Hong-Sheng Liao
- 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
- Molecular and Biological Agricultural Sciences, The Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
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5
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Rocchi R, Wolkers-Rooijackers JCM, Liao Z, Tempelaars MH, Smid EJ. Strain diversity in Saccharomyces cerevisiae thiamine production capacity. Yeast 2023; 40:628-639. [PMID: 37930115 DOI: 10.1002/yea.3906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/08/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Vitamin B1 , also known as thiamine, is an important vitamin that, besides its role in human health, is converted to meat aromas upon exposure to high temperatures. Therefore, it is relevant for the production of vegan meat-like flavours. In this study, we investigated 48 Saccharomyces cerevisiae strains for their thiamine production capacity by measuring the intracellular and extracellular vitamins produced in the thiamine-free minimal medium after 72 h of growth. We found approximately an 8.2-fold difference in overall thiamine yield between the highest and lowest-producing strains. While the highest thiamine yield was 254.6 nmol/L, the highest thiamine-specific productivity was 160.9 nmol/g DW. To assess whether extracellular thiamine was due to leakage caused by cell damage, we monitored membrane permeabilization using propidium iodide (PI) staining and flow cytometry. We found a good correlation between the percentage of extracellular thiamine and PI-stained cells (Spearman's ρ = 0.85). Finally, we compared S. cerevisiae CEN.PK113-7D (wild type [WT]) to three strains evolved in a thiamine-free medium for their thiamine production capacity. On average, we saw an increase in the amount of thiamine produced. One of the evolved strains had a 49% increase in intracellular thiamine-specific productivity and a biomass increase of 20% compared with the WT. This led to a total increase in thiamine yield of 60% in this strain, reaching 208 nmol/L. This study demonstrated that it is possible to achieve thiamine overproduction in S. cerevisiae via strain selection and adaptive laboratory evolution.
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Affiliation(s)
- Rebecca Rocchi
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | | | - Zhuotong Liao
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Marcel H Tempelaars
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, Wageningen, Netherlands
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6
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Matta R, Pochampally J, Dhoddi BN, Bhookya S, Bitla S, Akkiraju AG. Synthesis, antimicrobial and antioxidant activity of triazole, pyrazole containing thiazole derivatives and molecular docking studies on COVID-19. BMC Chem 2023; 17:61. [PMID: 37330518 DOI: 10.1186/s13065-023-00965-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/26/2023] [Indexed: 06/19/2023] Open
Abstract
New series of biologically active triazole and pyrazole compounds containing 2, 4-disubstituted thiazole analogues (12a-l) were synthesized from p-hydroxy benzaldehyde and phenyl hydrazine in excellent yields and purity. All the synthesized compounds were unambiguously identified based on their spectral data analyses (IR, 1H-NMR, 13C-NMR spectra, and HRMS). The final derivatives were evaluated for their in vitro anti-microbial activity after thorough purification. Among all the tested compounds, the compound 12e, 12f and 12 k possess the highest growth inhibitory activity at MIC values of 4.8, 5.1 and 4.0 μg/ml respectively. The antioxidant properties of these compounds demonstrated and revealed remarkable activity compared to the standard antioxidant by using the DPPH free radical-scavenging assay. Moreover, molecular docking studies to evaluate the probable interactions with the catalytic domain of the gram-positive S. aureus topoisomerase IV enzyme may provide new insights for developing these new hybrids as potential antimicrobial agents. The binding affinities of compounds 12a-l were ranging from - 10.0 to - 11.0 kcal/mol with topoisomerase IV enzyme and with COVID-19 main protease binding affinities are ranging from - 8.2 to - 9.3 kcal/mol. These docking studies reveal that the compounds 12a-l could be the best inhibitors for the novel SARS Cov-2 virus and have more future in discovery of potent drug candidates.
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Affiliation(s)
- Raghavender Matta
- Department of Chemistry, Osmania University, Hyderabad, 500007, India
| | | | | | - Shankar Bhookya
- Department of Chemistry, Sreenidhi University, Hyderabad, 501301, India
| | - Sampath Bitla
- Department of Chemistry, Osmania University, Hyderabad, 500007, India
| | - Anjini Gayatri Akkiraju
- Molecular Medicine Lab, Department of Genetics & Biotechnology, Osmania University, Hyderabad, 500007, India
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7
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Moura Dias H, Vieira AP, de Jesus EM, de Setta N, Barros G, Van Sluys MA. Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane. PeerJ 2023; 11:e14973. [PMID: 37214086 PMCID: PMC10194071 DOI: 10.7717/peerj.14973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/07/2023] [Indexed: 05/24/2023] Open
Abstract
De novo synthesis of thiamine (vitamin B1) in plants depends on the action of thiamine thiazole synthase, which synthesizes the thiazole ring, and is encoded by the THI1 gene. Here, we investigated the evolution and diversity of THI1 in Poaceae, where C4 and C3 photosynthetic plants co-evolved. An ancestral duplication of THI1 is observed in Panicoideae that remains in many modern monocots, including sugarcane. In addition to the two sugarcane copies (ScTHI1-1 and ScTHI1-2), we identified ScTHI1-2 alleles showing differences in their sequence, indicating divergence between ScTHI1-2a and ScTHI1-2b. Such variations are observed only in the Saccharum complex, corroborating the phylogeny. At least five THI1 genomic environments were found in Poaceae, two in sugarcane, M. sinensis, and S. bicolor. The THI1 promoter in Poaceae is highly conserved at 300 bp upstream of the start codon ATG and has cis-regulatory elements that putatively bind to transcription factors associated with development, growth, development and biological rhythms. An experiment set to compare gene expression levels in different tissues across the sugarcane R570 life cycle showed that ScTHI1-1 was expressed mainly in leaves regardless of age. Furthermore, ScTHI1 displayed relatively high expression levels in meristem and culm, which varied with the plant age. Finally, yeast complementation studies with THI4-defective strain demonstrate that only ScTHI1-1 and ScTHI1-2b isoforms can partially restore thiamine auxotrophy, albeit at a low frequency. Taken together, the present work supports the existence of multiple origins of THI1 harboring genomic regions in Poaceae with predicted functional redundancy. In addition, it questions the contribution of the levels of the thiazole ring in C4 photosynthetic plant tissues or potentially the relevance of the THI1 protein activity.
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Affiliation(s)
| | | | | | - Nathalia de Setta
- Botanica/IB, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
- Universidade Federal do ABC, Sao Bernardo do Campo, Sao Paulo, Brazil
| | - Gesiele Barros
- Botanica/IB, Universidade de Sao Paulo, Sao Paulo, Sao Paulo, Brazil
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8
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Gelder K, Oliveira-Filho ER, García-García JD, Hu Y, Bruner SD, Hanson AD. Directed Evolution of Aerotolerance in Sulfide-Dependent Thiazole Synthases. ACS Synth Biol 2023; 12:963-970. [PMID: 36920242 PMCID: PMC10127261 DOI: 10.1021/acssynbio.2c00512] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Indexed: 03/16/2023]
Abstract
Sulfide-dependent THI4 thiazole synthases could potentially be used to replace plant cysteine-dependent suicide THI4s, whose high protein turnover rates make thiamin synthesis exceptionally energy-expensive. However, sulfide-dependent THI4s are anaerobic or microoxic enzymes and hence unadapted to the aerobic conditions in plants; they are also slow enzymes (kcat < 1 h-1). To improve aerotolerance and activity, we applied continuous directed evolution under aerobic conditions in the yeast OrthoRep system to two sulfide-dependent bacterial THI4s. Seven beneficial single mutations were identified, of which five lie in the active-site cleft predicted by structural modeling and two recapitulate features of naturally aerotolerant THI4s. That single mutations gave substantial improvements suggests that further advance under selection will be possible by stacking mutations. This proof-of-concept study established that the performance of sulfide-dependent THI4s in aerobic conditions is evolvable and, more generally, that yeast OrthoRep provides a plant-like bridge to adapt nonplant enzymes to work better in plants.
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Affiliation(s)
- Kristen
Van Gelder
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Edmar R. Oliveira-Filho
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | | | - You Hu
- Chemistry
Department, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D. Bruner
- Chemistry
Department, University of Florida, Gainesville, Florida 32611, United States
| | - Andrew D. Hanson
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
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9
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Mondal A, Lai RY, Fedoseyenko D, Giri N, Begley TP. Oxidative Dearomatization of PLP in Thiamin Pyrimidine Biosynthesis in Candida albicans. J Am Chem Soc 2023; 145:4421-4430. [PMID: 36802573 PMCID: PMC10848271 DOI: 10.1021/jacs.2c08560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Indexed: 02/22/2023]
Abstract
The yeast thiamin pyrimidine synthase THI5p catalyzes one of the most complex organic rearrangements found in primary metabolism. In this reaction, the active site His66 and PLP are converted to thiamin pyrimidine in the presence of Fe(II) and oxygen. The enzyme is a single-turnover enzyme. Here, we report the identification of an oxidatively dearomatized PLP intermediate. We utilize oxygen labeling studies, chemical-rescue-based partial reconstitution experiments, and chemical model studies to support this identification. In addition, we also identify and characterize three shunt products derived from the oxidatively dearomatized PLP.
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Affiliation(s)
- Anushree Mondal
- Department of Chemistry, Texas A&M University, College Station, Texas77843, United States
| | | | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas77843, United States
| | | | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas77843, United States
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10
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Thiamine and Biotin: Relevance in the Production of Volatile and Non-Volatile Compounds during Saccharomyces cerevisiae Alcoholic Fermentation in Synthetic Grape Must. Foods 2023; 12:foods12050972. [PMID: 36900489 PMCID: PMC10000645 DOI: 10.3390/foods12050972] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/17/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Vitamins are major cofactors to numerous key metabolic pathways in enological yeasts, and both thiamine and biotin, notably, are believed to be essential to yeast fermentation and growth, respectively. In order to further assess and clarify their role in winemaking, and in the resulting wine, alcoholic fermentations of a commercial Saccharomyces cerevisiae active dried yeast were conducted in synthetic media containing various concentrations of both vitamins. Growth and fermentation kinetics were monitored and proved the essential character of biotin in yeast growth, and of thiamine in fermentation. The synthetic wine volatile compounds were quantified, and notable influences of both vitamins appeared, through a striking positive effect of thiamine on the production of higher alcohols, and of biotin on fatty acids. Beyond the evidence of this influence on fermentations and on the production of volatiles, this work proves, for the first time, the impact held by vitamins on wine yeasts' exometabolome, investigated through an untargeted metabolomic analysis. This highlighted chemical differences in the composition of synthetic wines through a notably marked influence of thiamine on 46 named S. cerevisiae metabolic pathways, and especially in amino acid-associated metabolic pathways. This provides, overall, the first evidence of the impact held by both vitamins on the wine.
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11
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Noordally Z, Land L, Trichtinger C, Dalvit I, de Meyer M, Wang K, Fitzpatrick TB. Clock and riboswitch control of THIC in tandem are essential for appropriate gauging of TDP levels under light/dark cycles in Arabidopsis. iScience 2023; 26:106134. [PMID: 36866249 PMCID: PMC9972560 DOI: 10.1016/j.isci.2023.106134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/03/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Metabolic homeostasis is regulated by enzyme activities, but the importance of regulating their corresponding coenzyme levels is unexplored. The organic coenzyme thiamine diphosphate (TDP) is suggested to be supplied as needed and controlled by a riboswitch-sensing mechanism in plants through the circadian-regulated THIC gene. Riboswitch disruption negatively impacts plant fitness. A comparison of riboswitch-disrupted lines to those engineered for enhanced TDP levels suggests that time-of-day regulation of THIC expression particularly under light/dark cycles is crucial. Altering the phase of THIC expression to be synchronous with TDP transporters disrupts the precision of the riboswitch implying that temporal separation of these processes by the circadian clock is important for gauging its response. All defects are bypassed by growing plants under continuous light conditions, highlighting the need to control levels of this coenzyme under light/dark cycles. Thus, consideration of coenzyme homeostasis within the well-studied domain of metabolic homeostasis is highlighted.
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Affiliation(s)
- Zeenat Noordally
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Lara Land
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Celso Trichtinger
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Ivan Dalvit
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Mireille de Meyer
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Kai Wang
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland
| | - Teresa B. Fitzpatrick
- Vitamins and Environmental Stress Responses in Plants, Department of Plant Sciences, University of Geneva, 1211 Geneva, Switzerland,Corresponding author
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12
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Wooldridge R, Stone S, Pedraza A, Ray WK, Helm RF, Allen KD. The Chlamydia trachomatis p-aminobenzoate synthase CADD is a manganese-dependent oxygenase that uses its own amino acid residues as substrates. FEBS Lett 2023; 597:557-572. [PMID: 36647787 DOI: 10.1002/1873-3468.14573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 12/28/2022] [Accepted: 01/02/2023] [Indexed: 01/18/2023]
Abstract
CADD (chlamydia protein associating with death domains) is a p-aminobenzoate (pAB) synthase involved in a noncanonical route for tetrahydrofolate biosynthesis in Chlamydia trachomatis. Although previously implicated to employ a diiron cofactor, here, we show that pAB synthesis by CADD requires manganese and the physiological cofactor is most likely a heterodinuclear Mn/Fe cluster. Isotope-labeling experiments revealed that the two oxygen atoms in the carboxylic acid portion of pAB are derived from molecular oxygen. Further, mass spectrometry-based proteomic analyses of CADD-derived peptides demonstrated a glycine substitution at Tyr27, providing strong evidence that this residue is sacrificed for pAB synthesis. Additionally, Lys152 was deaminated and oxidized to aminoadipic acid, supporting its proposed role as a sacrificial amino group donor.
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Affiliation(s)
| | - Spenser Stone
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Andrew Pedraza
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - W Keith Ray
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Kylie D Allen
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
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13
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Chatterjee S, Hausinger RP. Sulfur incorporation into biomolecules: recent advances. Crit Rev Biochem Mol Biol 2022; 57:461-476. [PMID: 36403141 PMCID: PMC10192010 DOI: 10.1080/10409238.2022.2141678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/05/2022] [Accepted: 10/26/2022] [Indexed: 11/21/2022]
Abstract
Sulfur is an essential element for a variety of cellular constituents in all living organisms and adds considerable functionality to a wide range of biomolecules. The pathways for incorporating sulfur into central metabolites of the cell such as cysteine, methionine, cystathionine, and homocysteine have long been established. Furthermore, the importance of persulfide intermediates during the biosynthesis of thionucleotide-containing tRNAs, iron-sulfur clusters, thiamin diphosphate, and the molybdenum cofactor are well known. This review briefly surveys these topics while emphasizing more recent aspects of sulfur metabolism that involve unconventional biosynthetic pathways. Sacrificial sulfur transfers from protein cysteinyl side chains to precursors of thiamin and the nickel-pincer nucleotide (NPN) cofactor are described. Newer aspects of synthesis for lipoic acid, biotin, and other compounds are summarized, focusing on the requisite iron-sulfur cluster destruction. Sulfur transfers by using a noncore sulfide ligand bound to a [4Fe-4S] cluster are highlighted for generating certain thioamides and for alternative biosynthetic pathways of thionucleotides and the NPN cofactor. Thioamide formation by activating an amide oxygen atom via phosphorylation also is illustrated. The discussion of these topics stresses the chemical reaction mechanisms of the transformations and generally avoids comments on the gene/protein nomenclature or the sources of the enzymes. This work sets the stage for future efforts to decipher the diverse mechanisms of sulfur incorporation into biological molecules.
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Affiliation(s)
- Shramana Chatterjee
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Robert P. Hausinger
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
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14
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Banh ATM, Thiele B, Chlubek A, Hombach T, Kleist E, Matsubara S. Combination of long-term 13CO 2 labeling and isotopolog profiling allows turnover analysis of photosynthetic pigments in Arabidopsis leaves. PLANT METHODS 2022; 18:114. [PMID: 36183136 PMCID: PMC9526918 DOI: 10.1186/s13007-022-00946-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Living cells maintain and adjust structural and functional integrity by continual synthesis and degradation of metabolites and macromolecules. The maintenance and adjustment of thylakoid membrane involve turnover of photosynthetic pigments along with subunits of protein complexes. Quantifying their turnover is essential to understand the mechanisms of homeostasis and long-term acclimation of photosynthetic apparatus. Here we report methods combining whole-plant long-term 13CO2 labeling and liquid chromatography - mass spectrometry (LC-MS) analysis to determine the size of non-labeled population (NLP) of carotenoids and chlorophylls (Chl) in leaf pigment extracts of partially 13C-labeled plants. RESULTS The labeling chamber enabled parallel 13CO2 labeling of up to 15 plants of Arabidopsis thaliana with real-time environmental monitoring ([CO2], light intensity, temperature, relative air humidity and pressure) and recording. No significant difference in growth or photosynthetic pigment composition was found in leaves after 7-d exposure to normal CO2 (~ 400 ppm) or 13CO2 in the labeling chamber, or in ambient air outside the labeling chamber (control). Following chromatographic separation of the pigments and mass peak assignment by high-resolution Fourier-transform ion cyclotron resonance MS, mass spectra of photosynthetic pigments were analyzed by triple quadrupole MS to calculate NLP. The size of NLP remaining after the 7-d 13CO2 labeling was ~ 10.3% and ~ 11.5% for all-trans- and 9-cis-β-carotene, ~ 21.9% for lutein, ~ 18.8% for Chl a and 33.6% for Chl b, highlighting non-uniform turnover of these pigments in thylakoids. Comparable results were obtained in all replicate plants of the 13CO2 labeling experiment except for three that were showing anthocyanin accumulation and growth impairment due to insufficient water supply (leading to stomatal closure and less 13C incorporation). CONCLUSIONS Our methods allow 13CO2 labeling and estimation of NLP for photosynthetic pigments with high reproducibility despite potential variations in [13CO2] between the experiments. The results indicate distinct turnover rates of carotenoids and Chls in thylakoid membrane, which can be investigated in the future by time course experiments. Since 13C enrichment can be measured in a range of compounds, long-term 13CO2 labeling chamber, in combination with appropriate MS methods, facilitates turnover analysis of various metabolites and macromolecules in plants on a time scale of hours to days.
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Affiliation(s)
- Anh Thi-Mai Banh
- IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Björn Thiele
- IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425, Jülich, Germany
- IBG-3: Agrosphere, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Antonia Chlubek
- IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Thomas Hombach
- IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Einhard Kleist
- IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Shizue Matsubara
- IBG-2: Plant Sciences, Forschungszentrum Jülich, 52425, Jülich, Germany.
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15
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Self-sacrificial tyrosine cleavage by an Fe:Mn oxygenase for the biosynthesis of para-aminobenzoate in Chlamydia trachomatis. Proc Natl Acad Sci U S A 2022; 119:e2210908119. [PMID: 36122239 PMCID: PMC9522330 DOI: 10.1073/pnas.2210908119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chlamydia protein associating with death domains (CADD) is involved in the biosynthesis of para-aminobenzoate (pABA), an essential component of the folate cofactor that is required for the survival and proliferation of the human pathogen Chlamydia trachomatis. The pathway used by Chlamydiae for pABA synthesis differs from the canonical multi-enzyme pathway used by most bacteria that relies on chorismate as a metabolic precursor. Rather, recent work showed pABA formation by CADD derives from l-tyrosine. As a member of the emerging superfamily of heme oxygenase-like diiron oxidases (HDOs), CADD was proposed to use a diiron cofactor for catalysis. However, we report maximal pABA formation by CADD occurs upon the addition of both iron and manganese, which implicates a heterobimetallic Fe:Mn cluster is the catalytically active form. Isotopic labeling experiments and proteomics studies show that CADD generates pABA from a protein-derived tyrosine (Tyr27), a residue that is ∼14 Å from the dimetal site. We propose that this self-sacrificial reaction occurs through O2 activation by a probable Fe:Mn cluster through a radical relay mechanism that connects to the "substrate" Tyr, followed by amination and direct oxygen insertion. These results provide the molecular basis for pABA formation in C. trachomatis, which will inform the design of novel therapeutics.
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16
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Barra L, Awakawa T, Abe I. Noncanonical Functions of Enzyme Cofactors as Building Blocks in Natural Product Biosynthesis. JACS AU 2022; 2:1950-1963. [PMID: 36186570 PMCID: PMC9516700 DOI: 10.1021/jacsau.2c00391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
Enzymes involved in secondary metabolite biosynthetic pathways have typically evolutionarily diverged from their counterparts functioning in primary metabolism. They often catalyze diverse and complex chemical transformations and are thus a treasure trove for the discovery of unique enzyme-mediated chemistries. Besides major natural product classes, such as terpenoids, polyketides, and ribosomally or nonribosomally synthesized peptides, biosynthetic investigations of noncanonical natural product biosynthetic pathways often reveal functionally distinct enzyme chemistries. In this Perspective, we aim to highlight challenges and opportunities of biosynthetic investigations on noncanonical natural product pathways that utilize primary metabolites as building blocks, otherwise generally considered as enzyme cofactors. A focus is made on the discovered chemical and enzymological novelties.
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Affiliation(s)
- Lena Barra
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Takayoshi Awakawa
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ikuro Abe
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative
Research Institute of Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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17
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Hsieh WY, Wang HM, Chung YH, Lee KT, Liao HS, Hsieh MH. THIAMIN REQUIRING2 is involved in thiamin diphosphate biosynthesis and homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1383-1396. [PMID: 35791282 DOI: 10.1111/tpj.15895] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
The THIAMIN REQUIRING2 (TH2) protein comprising a mitochondrial targeting peptide followed by a transcription enhancement A and a haloacid dehalogenase domain is a thiamin monophosphate (TMP) phosphatase in the vitamin B1 biosynthetic pathway. The Arabidopsis th2-3 T-DNA insertion mutant was chlorotic and deficient in thiamin diphosphate (TDP). Complementation assays confirmed that haloacid dehalogenase domain alone was sufficient to rescue the th2-3 mutant. In pTH2:TH2-GFP/th2-3 complemented plants, the TH2-GFP was localized to the cytosol, mitochondrion, and nucleus, indicating that the vitamin B1 biosynthetic pathway extended across multi-subcellular compartments. Engineered TH2-GFP localized to the cytosol, mitochondrion, nucleus, and chloroplast, could complement the th2 mutant. Together, these results highlight the importance of intracellular TMP and thiamin trafficking in vitamin B1 biosynthesis. In an attempt to enhance the production of thiamin, we created various constructs to overexpress TH2-GFP in the cytosol, mitochondrion, chloroplast, and nucleus. Unexpectedly, overexpressing TH2-GFP resulted in an increase rather than a decrease in TMP. While studies on th2 mutants support TH2 as a TMP phosphatase, analyses of TH2-GFP overexpression lines implicating TH2 may also function as a TDP phosphatase in planta. We propose a working model that the TMP/TDP phosphatase activity of TH2 connects TMP, thiamin, and TDP into a metabolic cycle. The TMP phosphatase activity of TH2 is required for TDP biosynthesis, and the TDP phosphatase activity of TH2 may modulate TDP homeostasis in Arabidopsis.
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Affiliation(s)
- Wei-Yu Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Hsin-Mei Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Hsin Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kim-Teng Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
| | - Hong-Sheng Liao
- 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
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica, Taipei, 11529, Taiwan
- Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, 40227, Taiwan
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18
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Effects of tryptophan and phenylalanine on tryptophol production in Saccharomyces cerevisiae revealed by transcriptomic and metabolomic analyses. J Microbiol 2022; 60:832-842. [DOI: 10.1007/s12275-022-2059-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 10/18/2022]
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19
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Peres da Silva R, Brock M. NIH4215: A mutation-prone thiamine auxotrophic clinical Aspergillus fumigatus isolate. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:908343. [PMID: 37746208 PMCID: PMC10512395 DOI: 10.3389/ffunb.2022.908343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/30/2022] [Indexed: 09/26/2023]
Abstract
Aspergillus fumigatus is the main cause of life-threatening invasive aspergillosis. Despite the availability of various antifungals, therapy remains challenging and requires further studies. Accordingly, the clinical A. fumigatus isolate NIH4215 deriving from a fatal case of human pulmonary aspergillosis has frequently been used in drug efficacy studies. Unexpectedly, our initial attempts to generate a bioluminescent reporter of strain NIH4215 for in vivo drug efficacy studies failed, as NIH4215 was unable to grow on defined minimal medium. Subsequent analyses discovered a previously undescribed thiamine auxotrophy of strain NIH4215 and transformation with thiamine biosynthesis genes from A. fumigatus strain Af293 identified the nmt1 gene as cause of the thiamine auxotrophy. Sequencing of the defective nmt1 gene revealed the loss of a cysteine codon within an essential iron-binding motif. Subsequently, the wild-type nmt1 gene was successfully used to generate a bioluminescent reporter strain in NIH4215 by simultaneously deleting the akuB locus. The resulting bioluminescent ΔakuB strains showed a high frequency of homologous integration as confirmed by generation of pyrG and niaD deletion mutants. When tested in a Galleria mellonella infection model, neither thiamine auxotrophy nor the deletion of the akuB locus had a significant effect on virulence. However, besides thiamine auxotrophy, sectors with altered morphology and albino mutants frequently arose on colony edges of strain NIH4215 and its derivatives, and stable albino mutants were successfully isolated. A proposed increased mutation rate of NIH4215 was confirmed by screening for spontaneous occurrence of fluoorotic acid resistant mutants. Independent mutations in the pyrG and pyrE gene were identified in the fluoroorotic acid resistant NIH4215 isolates and the frequency of mutation was by at least one order of magnitude higher than that observed for the clinical A. fumigatus isolate CBS144.89. In summary, despite its virulence in animal models, strain NIH4215 is a thiamine auxotroph and prone to accumulate mutations. Our results suggest that thiamine biosynthesis is dispensable for host infection and mutation-prone strains such as NIH4215 could potentially facilitate the evolution of azole resistant strains as increasingly observed in the environment.
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Affiliation(s)
| | - Matthias Brock
- University of Nottingham, School of Life Sciences, University Park, Nottingham, United Kingdom
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20
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Lai RY, Mondal A, Fedoseyenko D, Begley TP. Mechanistic Studies on the Single-Turnover Yeast Thiamin Pyrimidine Synthase: Characterization of the Inactive Enzyme. J Am Chem Soc 2022; 144:10711-10717. [PMID: 35675507 DOI: 10.1021/jacs.2c03322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The eukaryotic thiamin pyrimidine synthase, THI5p, has been identified as a suicidal/single-turnover enzyme that catalyzes the conversion of its active site histidine and lysine-bound pyridoxal phosphate (PLP) to the thiamin pyrimidine (HMP-P). Here we identify the histidine and PLP fragments using bottom-up proteomics and LC-MS analysis. We also identify the active form of the iron cofactor and quantitate the oxygen requirement of the THI5p reaction. This information is integrated into a mechanistic proposal for this remarkable reaction.
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Affiliation(s)
- Rung-Yi Lai
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Anushree Mondal
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Tadhg P Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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21
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Abdulghani M, Iram R, Chidrawar P, Bhosle K, Kazi R, Patil R, Kharat K, Zore G. Proteomic profile of Candida albicans biofilm. J Proteomics 2022; 265:104661. [PMID: 35728770 DOI: 10.1016/j.jprot.2022.104661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 11/25/2022]
Abstract
Candida albicans biofilms are characterized by structural and cellular heterogeneity that confers antifungal resistance and immune evasion. Despite this, biofilm formation remains poorly understood. In this study, we used proteomic analysis to understand biofilm formation in C. albicans related to morphophysiological and architectural features. LC-MS/MS analysis revealed that 64 proteins were significantly modulated, of which 31 were upregulated and 33 were downregulated. The results indicate that metabolism (25 proteins), gene expression (13 proteins), stress response (7 proteins), and cell wall (5 proteins) composition are modulated. The rate of oxidative phosphorylation (OxPhos) and biosynthesis of UDP-N-acetylglucosamine, vitamin B6, and thiamine increased, while the rate of methionine biosynthesis decreased. There was a significant modification of the cell wall architecture due to higher levels of Sun41, Pir1 and Csh1 and increased glycosylation of proteins. It was observed that C. albicans induces hyphal growth by upregulating the expression of genes involved in cAMP-PKA and MAPK pathways. This study is significant in that it suggests an increase in OxPhos and alteration of cell wall architecture that could be contributing to the recalcitrance of C. albicans cells growing in biofilms. Nevertheless, a deeper investigation is needed to explore it further. SIGNIFICANCE: Candida sps is included in the list of pathogens with potential drug resistance threat due to the increased frequency especially colonization of medical devices, and tissues among the patients, in recent years. Significance of our study is that we are reporting traits like modulation in cell wall composition, amino acid and vitamin biosynthesis and importantly energy generation (OxPhos) etc. These traits could be conferring antifungal resistance, host immune evasion etc. and thus survival, in addition to facilitating biofilm formation. These findings are expected to prime the further studies on devising potent strategy against biofilm growth among the patients.
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Affiliation(s)
- Mazen Abdulghani
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - Rasiqua Iram
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - Priti Chidrawar
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - Kajal Bhosle
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India
| | - Rubina Kazi
- Division of Biochemical Sciences, CSIR-NCL, Pune 8, MS, India
| | - Rajendra Patil
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MS, India
| | - Kiran Kharat
- Department of Biotechnology, Deogiri College, Aurangabad, MS, India
| | - Gajanan Zore
- School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, MS, India.
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22
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Molina RS, Rix G, Mengiste AA, Alvarez B, Seo D, Chen H, Hurtado J, Zhang Q, Donato García-García J, Heins ZJ, Almhjell PJ, Arnold FH, Khalil AS, Hanson AD, Dueber JE, Schaffer DV, Chen F, Kim S, Ángel Fernández L, Shoulders MD, Liu CC. In vivo hypermutation and continuous evolution. NATURE REVIEWS. METHODS PRIMERS 2022; 2:37. [PMID: 37073402 PMCID: PMC10108624 DOI: 10.1038/s43586-022-00130-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Rosana S. Molina
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
| | - Gordon Rix
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Amanuella A. Mengiste
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Beatriz Alvarez
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Daeje Seo
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Haiqi Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Juan Hurtado
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Qiong Zhang
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jorge Donato García-García
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Av. General Ramon Corona 2514, Nuevo Mexico, C.P. 45138, Zapopan, Jalisco, Mexico
| | - Zachary J. Heins
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Patrick J. Almhjell
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Frances H. Arnold
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ahmad S. Khalil
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David V. Schaffer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California Berkeley and San Francisco, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Fei Chen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seokhee Kim
- Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea
| | - Luis Ángel Fernández
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, Campus UAM Cantoblanco, 28049 Madrid, Spain
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, CA 92617, USA
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23
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Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:e2121362119. [PMID: 35549553 PMCID: PMC9171785 DOI: 10.1073/pnas.2121362119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Photoinhibitory high light stress in plants leads to increases in markers of protein degradation and transcriptional up-regulation of proteases and proteolytic machinery, but protein homeostasis (proteostasis) of most enzymes is largely maintained under high light, so we know little about the metabolic consequences of it beyond photosystem damage. We developed a technique to look for rapid protein turnover events in response to high light through 13C partial labeling and detailed peptide mass spectrometry. This analysis reveals a light-induced transcriptional program for nuclear-encoded genes, beyond the regulation of photosystem II, to replace key protein degradation targets in plants and ensure proteostasis under high light stress. Photoinhibitory high light stress in Arabidopsis leads to increases in markers of protein degradation and transcriptional up-regulation of proteases and proteolytic machinery, but proteostasis is largely maintained. We find significant increases in the in vivo degradation rate for specific molecular chaperones, nitrate reductase, glyceraldehyde-3 phosphate dehydrogenase, and phosphoglycerate kinase and other plastid, mitochondrial, peroxisomal, and cytosolic enzymes involved in redox shuttles. Coupled analysis of protein degradation rates, mRNA levels, and protein abundance reveal that 57% of the nuclear-encoded enzymes with higher degradation rates also had high light–induced transcriptional responses to maintain proteostasis. In contrast, plastid-encoded proteins with enhanced degradation rates showed decreased transcript abundances and must maintain protein abundance by other processes. This analysis reveals a light-induced transcriptional program for nuclear-encoded genes, beyond the regulation of the photosystem II (PSII) D1 subunit and the function of PSII, to replace key protein degradation targets in plants and ensure proteostasis under high light stress.
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24
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Strobbe S, Verstraete J, Fitzpatrick TB, Faustino M, Lourenço TF, Oliveira MM, Stove C, Van Der Straeten D. A novel panel of yeast assays for the assessment of thiamin and its biosynthetic intermediates in plant tissues. THE NEW PHYTOLOGIST 2022; 234:748-763. [PMID: 35037254 PMCID: PMC9303440 DOI: 10.1111/nph.17974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Thiamin (or thiamine), known as vitamin B1, represents an indispensable component of human diets, being pivotal in energy metabolism. Thiamin research depends on adequate vitamin quantification in plant tissues. A recently developed quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) method is able to assess the level of thiamin, its phosphorylated entities and its biosynthetic intermediates in the model plant Arabidopsis thaliana, as well as in rice. However, their implementation requires expensive equipment and substantial technical expertise. Microbiological assays can be useful in deter-mining metabolite levels in plant material and provide an affordable alternative to MS-based analysis. Here, we evaluate, by comparison to the LC-MS/MS reference method, the potential of a carefully chosen panel of yeast assays to estimate levels of total vitamin B1, as well as its biosynthetic intermediates pyrimidine and thiazole in Arabidopsis samples. The examined panel of Saccharomyces cerevisiae mutants was, when implemented in microbiological assays, capable of correctly assigning a series of wild-type and thiamin biofortified Arabidopsis plant samples. The assays provide a readily applicable method allowing rapid screening of vitamin B1 (and its biosynthetic intermediates) content in plant material, which is particularly useful in metabolic engineering approaches and in germplasm screening across or within species.
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Affiliation(s)
- Simon Strobbe
- Laboratory of Functional Plant BiologyDepartment of BiologyGhent UniversityK.L. Ledeganckstraat 35B‐9000GentBelgium
| | - Jana Verstraete
- Laboratory of ToxicologyDepartment of BioanalysisGhent UniversityOttergemsesteenweg 460B‐9000GentBelgium
| | - Teresa B. Fitzpatrick
- Vitamins and Environmental Stress Responses in PlantsDepartment of Botany and Plant BiologyUniversity of GenevaQuai E. Ansermet 301211GenevaSwitzerland
| | - Maria Faustino
- Instituto de Tecnologia Química e Biológica António XavierUniversidade NOVA de LisboaPlant Functional Genomics – GPlantS LabAv. da República2780‐157OeirasPortugal
| | - Tiago F. Lourenço
- Instituto de Tecnologia Química e Biológica António XavierUniversidade NOVA de LisboaPlant Functional Genomics – GPlantS LabAv. da República2780‐157OeirasPortugal
| | - M. Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António XavierUniversidade NOVA de LisboaPlant Functional Genomics – GPlantS LabAv. da República2780‐157OeirasPortugal
| | - Christophe Stove
- Laboratory of ToxicologyDepartment of BioanalysisGhent UniversityOttergemsesteenweg 460B‐9000GentBelgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant BiologyDepartment of BiologyGhent UniversityK.L. Ledeganckstraat 35B‐9000GentBelgium
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Colinas M, Fitzpatrick TB. Coenzymes and the primary and specialized metabolism interface. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102170. [PMID: 35063913 DOI: 10.1016/j.pbi.2021.102170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
In plants, primary and specialized metabolism have classically been distinguished as either essential for growth or required for survival in a particular environment. Coenzymes (organic cofactors) are essential for growth but their importance to specialized metabolism is often not considered. In line with the recent proposal of viewing primary and specialized metabolism as an integrated whole rather than segregated lots with a defined interface, we highlight here the importance of collating information on the regulation of coenzyme supply with metabolic demands using examples of vitamin B derived coenzymes. We emphasize that coenzymes can have enormous influence on the outcome of metabolic as well as engineered pathways and should be taken into account in the era of synthetic biology.
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Affiliation(s)
- Maite Colinas
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 80, D-07745 Jena, Germany.
| | - 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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Exchange of Vitamin B 1 and Its Biosynthesis Intermediates Shapes the Composition of Synthetic Microbial Cocultures and Reveals Complexities of Nutrient Sharing. J Bacteriol 2022; 204:e0050321. [PMID: 35357164 DOI: 10.1128/jb.00503-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Microbial communities occupy diverse niches in nature, and community members routinely exchange a variety of nutrients among themselves. While large-scale metagenomic and metabolomic studies shed some light on these exchanges, the contribution of individual species and the molecular details of specific interactions are difficult to track. In this study, we follow the exchange of vitamin B1 (thiamin) and its intermediates between microbes within synthetic cocultures of Escherichia coli and Vibrio anguillarum. Thiamin contains two moieties, 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) and 4-methyl-5-(2-hydroxyethyl)thiazole (THZ), which are synthesized by distinct pathways using enzymes ThiC and ThiG, respectively, and then coupled by ThiE to form thiamin. Even though E. coli ΔthiC, ΔthiE, and ΔthiG mutants are thiamin auxotrophs, we observed that cocultures of ΔthiC-ΔthiE and ΔthiC-ΔthiG mutants are able to grow in a thiamin-deficient medium, whereas the ΔthiE-ΔthiG coculture does not. Further, the exchange of thiamin and its intermediates in V. anguillarum cocultures and in mixed cocultures of V. anguillarum and E. coli revealed that there exist specific patterns for thiamin metabolism and exchange among these microbes. Our findings show that HMP is shared more frequently than THZ, concurrent with previous observations that free HMP and HMP auxotrophy is commonly found in various environments. Furthermore, we observe that the availability of exogenous thiamin in the media affects whether these strains interact with each other or grow independently. These findings collectively underscore the importance of the exchange of essential metabolites as a defining factor in building and modulating synthetic or natural microbial communities. IMPORTANCE Vitamin B1 (thiamin) is an essential nutrient for cellular metabolism. Microorganisms that are unable to synthesize thiamin either fully or in part exogenously obtain it from their environment or via exchanges with other microbial members in their community. In this study, we created synthetic microbial cocultures that rely on sharing thiamin and its biosynthesis intermediates and observed that some of them are preferentially exchanged. We also observed that the coculture composition is dictated by the production and/or availability of thiamin and its intermediates. Our studies with synthetic cocultures provide the molecular basis for understanding thiamin sharing among microorganisms and lay out broad guidelines for setting up synthetic microbial cocultures by using the exchange of an essential metabolite as their foundation.
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García-García JD, Van Gelder K, Joshi J, Bathe U, Leong BJ, Bruner SD, Liu CC, Hanson AD. Using continuous directed evolution to improve enzymes for plant applications. PLANT PHYSIOLOGY 2022; 188:971-983. [PMID: 34718794 PMCID: PMC8825276 DOI: 10.1093/plphys/kiab500] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/29/2021] [Indexed: 05/12/2023]
Abstract
Continuous directed evolution of enzymes and other proteins in microbial hosts is capable of outperforming classical directed evolution by executing hypermutation and selection concurrently in vivo, at scale, with minimal manual input. Provided that a target enzyme's activity can be coupled to growth of the host cells, the activity can be improved simply by selecting for growth. Like all directed evolution, the continuous version requires no prior mechanistic knowledge of the target. Continuous directed evolution is thus a powerful way to modify plant or non-plant enzymes for use in plant metabolic research and engineering. Here, we first describe the basic features of the yeast (Saccharomyces cerevisiae) OrthoRep system for continuous directed evolution and compare it briefly with other systems. We then give a step-by-step account of three ways in which OrthoRep can be deployed to evolve primary metabolic enzymes, using a THI4 thiazole synthase as an example and illustrating the mutational outcomes obtained. We close by outlining applications of OrthoRep that serve growing demands (i) to change the characteristics of plant enzymes destined for return to plants, and (ii) to adapt ("plantize") enzymes from prokaryotes-especially exotic prokaryotes-to function well in mild, plant-like conditions.
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Affiliation(s)
- Jorge D García-García
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Zapopan, Mexico
| | - Kristen Van Gelder
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Jaya Joshi
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Steven D Bruner
- Chemistry Department, University of Florida, Gainesville, Florida 32611
| | - Chang C Liu
- Department of Biomedical Engineering, University of California, Irvine, California 92617
- Department of Chemistry, University of California, Irvine, California 92617
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
- Author for communication:
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Dastmalchi M. Suicide prevention for enzymes using continuous directed evolution. PLANT PHYSIOLOGY 2022; 188:924-925. [PMID: 34791471 PMCID: PMC8825248 DOI: 10.1093/plphys/kiab526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Mehran Dastmalchi
- Department of Plant Science, McGill University, Montreal, QC H9X 3V9, Canada
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29
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Bathe U, Leong BJ, McCarty DR, Henry CS, Abraham PE, Wilson MA, Hanson AD. The Moderately (D)efficient Enzyme: Catalysis-Related Damage In Vivo and Its Repair. Biochemistry 2021; 60:3555-3565. [PMID: 34729986 DOI: 10.1021/acs.biochem.1c00613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Enzymes have in vivo life spans. Analysis of life spans, i.e., lifetime totals of catalytic turnovers, suggests that nonsurvivable collateral chemical damage from the very reactions that enzymes catalyze is a common but underdiagnosed cause of enzyme death. Analysis also implies that many enzymes are moderately deficient in that their active-site regions are not naturally as hardened against such collateral damage as they could be, leaving room for improvement by rational design or directed evolution. Enzyme life span might also be improved by engineering systems that repair otherwise fatal active-site damage, of which a handful are known and more are inferred to exist. Unfortunately, the data needed to design and execute such improvements are lacking: there are too few measurements of in vivo life span, and existing information about the extent, nature, and mechanisms of active-site damage and repair during normal enzyme operation is too scarce, anecdotal, and speculative to act on. Fortunately, advances in proteomics, metabolomics, cheminformatics, comparative genomics, and structural biochemistry now empower a systematic, data-driven approach for identifying, predicting, and validating instances of active-site damage and its repair. These capabilities would be practically useful in enzyme redesign and improvement of in-use stability and could change our thinking about which enzymes die young in vivo, and why.
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Affiliation(s)
- Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Mark A Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611, United States
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30
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Gray HB, Winkler JR. Functional and protective hole hopping in metalloenzymes. Chem Sci 2021; 12:13988-14003. [PMID: 34760183 PMCID: PMC8565380 DOI: 10.1039/d1sc04286f] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/20/2021] [Indexed: 01/19/2023] Open
Abstract
Electrons can tunnel through proteins in microseconds with a modest release of free energy over distances in the 15 to 20 Å range. To span greater distances, or to move faster, multiple charge transfers (hops) are required. When one of the reactants is a strong oxidant, it is convenient to consider the movement of a positively charged "hole" in a direction opposite to that of the electron. Hole hopping along chains of tryptophan (Trp) and tyrosine (Tyr) residues is a critical function in several metalloenzymes that generate high-potential intermediates by reactions with O2 or H2O2, or by activation with visible light. Examination of the protein structural database revealed that Tyr/Trp chains are common protein structural elements, particularly among enzymes that react with O2 and H2O2. In many cases these chains may serve a protective role in metalloenzymes by deactivating high-potential reactive intermediates formed in uncoupled catalytic turnover.
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Affiliation(s)
- Harry B Gray
- Beckman Institute, California Institute of Technology 1200 E California Boulevard Pasadena CA 19925 USA
| | - Jay R Winkler
- Beckman Institute, California Institute of Technology 1200 E California Boulevard Pasadena CA 19925 USA
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Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases. Biochem J 2021; 478:3265-3279. [PMID: 34409984 PMCID: PMC8454699 DOI: 10.1042/bcj20210565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022]
Abstract
Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized —– but only from archaeal methanogens that are anaerobic, O2-sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O2 at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O2-sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.
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Joshi J, Mimura M, Suzuki M, Wu S, Gregory JF, Hanson AD, McCarty DR. The Thiamin-Requiring 3 Mutation of Arabidopsis 5-Deoxyxylulose-Phosphate Synthase 1 Highlights How the Thiamin Economy Impacts the Methylerythritol 4-Phosphate Pathway. FRONTIERS IN PLANT SCIENCE 2021; 12:721391. [PMID: 34421975 PMCID: PMC8377734 DOI: 10.3389/fpls.2021.721391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 06/01/2023]
Abstract
The thiamin-requiring mutants of Arabidopsis have a storied history as a foundational model for biochemical genetics in plants and have illuminated the central role of thiamin in metabolism. Recent integrative genetic and biochemical analyses of thiamin biosynthesis and utilization imply that leaf metabolism normally operates close to thiamin-limiting conditions. Thus, the mechanisms that allocate thiamin-diphosphate (ThDP) cofactor among the diverse thiamin-dependent enzymes localized in plastids, mitochondria, peroxisomes, and the cytosol comprise an intricate thiamin economy. Here, we show that the classical thiamin-requiring 3 (th3) mutant is a point mutation in plastid localized 5-deoxyxylulose synthase 1 (DXS1), a key regulated enzyme in the methylerythritol 4-phosphate (MEP) isoprene biosynthesis pathway. Substitution of a lysine for a highly conserved glutamate residue (E323) located at the subunit interface of the homodimeric enzyme conditions a hypomorphic phenotype that can be rescued by supplying low concentrations of thiamin in the medium. Analysis of leaf thiamin vitamers showed that supplementing the medium with thiamin increased total ThDP content in both wild type and th3 mutant plants, supporting a hypothesis that the mutant DXS1 enzyme has a reduced affinity for the ThDP cofactor. An unexpected upregulation of a suite of biotic-stress-response genes associated with accumulation of downstream MEP intermediate MEcPP suggests that th3 causes mis-regulation of DXS1 activity in thiamin-supplemented plants. Overall, these results highlight that the central role of ThDP availability in regulation of DXS1 activity and flux through the MEP pathway.
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Affiliation(s)
- Jaya Joshi
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Manaki Mimura
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Japan
| | - Masaharu Suzuki
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Shan Wu
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jesse F. Gregory
- Department Food Science and Human Nutrition, University of Florida, Gainesville, FL, United States
| | - Andrew D. Hanson
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Donald R. McCarty
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
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Mavrommati M, Daskalaki A, Papanikolaou S, Aggelis G. Adaptive laboratory evolution principles and applications in industrial biotechnology. Biotechnol Adv 2021; 54:107795. [PMID: 34246744 DOI: 10.1016/j.biotechadv.2021.107795] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/11/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022]
Abstract
Adaptive laboratory evolution (ALE) is an innovative approach for the generation of evolved microbial strains with desired characteristics, by implementing the rules of natural selection as presented in the Darwinian Theory, on the laboratory bench. New as it might be, it has already been used by several researchers for the amelioration of a variety of characteristics of widely used microorganisms in biotechnology. ALE is used as a tool for the deeper understanding of the genetic and/or metabolic pathways of evolution. Another important field targeted by ALE is the manufacturing of products of (high) added value, such as ethanol, butanol and lipids. In the current review, we discuss the basic principles and techniques of ALE, and then we focus on studies where it has been applied to bacteria, fungi and microalgae, aiming to improve their performance to biotechnological procedures and/or inspect the genetic background of evolution. We conclude that ALE is a promising and efficacious method that has already led to the acquisition of useful new microbiological strains in biotechnology and could possibly offer even more interesting results in the future.
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Affiliation(s)
- Maria Mavrommati
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece; Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - Alexandra Daskalaki
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece
| | - Seraphim Papanikolaou
- Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - George Aggelis
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece.
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Müller-Schüssele SJ, Bohle F, Rossi J, Trost P, Meyer AJ, Zaffagnini M. Plasticity in plastid redox networks: evolution of glutathione-dependent redox cascades and glutathionylation sites. BMC PLANT BIOLOGY 2021; 21:322. [PMID: 34225654 PMCID: PMC8256493 DOI: 10.1186/s12870-021-03087-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/08/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Flexibility of plant metabolism is supported by redox regulation of enzymes via posttranslational modification of cysteine residues, especially in plastids. Here, the redox states of cysteine residues are partly coupled to the thioredoxin system and partly to the glutathione pool for reduction. Moreover, several plastid enzymes involved in reactive oxygen species (ROS) scavenging and damage repair draw electrons from glutathione. In addition, cysteine residues can be post-translationally modified by forming a mixed disulfide with glutathione (S-glutathionylation), which protects thiol groups from further oxidation and can influence protein activity. However, the evolution of the plastid glutathione-dependent redox network in land plants and the conservation of cysteine residues undergoing S-glutathionylation is largely unclear. RESULTS We analysed the genomes of nine representative model species from streptophyte algae to angiosperms and found that the antioxidant enzymes and redox proteins belonging to the plastid glutathione-dependent redox network are largely conserved, except for lambda- and the closely related iota-glutathione S-transferases. Focussing on glutathione-dependent redox modifications, we screened the literature for target thiols of S-glutathionylation, and found that 151 plastid proteins have been identified as glutathionylation targets, while the exact cysteine residue is only known for 17% (26 proteins), with one or multiple sites per protein, resulting in 37 known S-glutathionylation sites for plastids. However, 38% (14) of the known sites were completely conserved in model species from green algae to flowering plants, with 22% (8) on non-catalytic cysteines. Variable conservation of the remaining sites indicates independent gains and losses of cysteines at the same position during land plant evolution. CONCLUSIONS We conclude that the glutathione-dependent redox network in plastids is highly conserved in streptophytes with some variability in scavenging and damage repair enzymes. Our analysis of cysteine conservation suggests that S-glutathionylation in plastids plays an important and yet under-investigated role in redox regulation and stress response.
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Affiliation(s)
- Stefanie J Müller-Schüssele
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany.
- Present Address: Department of Biology, Technische Universität Kaiserslautern, 67663, Kaiserslautern, Germany.
| | - Finja Bohle
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Jacopo Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Paolo Trost
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Friedrich-Ebert-Allee 144, 53113, Bonn, Germany
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
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Jin D, Sun B, Zhao W, Ma J, Zhou Q, Han X, Mei Y, Fan Y, Pei Y. Thiamine-biosynthesis genes Bbpyr and Bbthi are required for conidial production and cell wall integrity of the entomopathogenic fungus Beauveria bassiana. J Invertebr Pathol 2021; 184:107639. [PMID: 34139258 DOI: 10.1016/j.jip.2021.107639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 01/29/2023]
Abstract
Beauveria bassiana is an important entomopathogenic fungus used to control a variety of insect pests. Conidia are the infective propagules of the fungus. However, some important factors that influence conidiation are still to be investigated. In this study, a mutant with decreased conidial production and hyphal growth was identified from a random T-DNA insertional library of B. bassiana. The corresponding gene (Bbthi) for this mutation encodes a putative thiazole synthase. Thiazole and pyrimidine are structural components of thiamine (vitamin B1), which is an essential nutrient for all forms of life. Disruption of Bbthi, Bbpyr, a putative pyrimidine synthetic gene, or both in B. bassiana results in a significant decrease of thiamine content. Loss of Bbthi and Bbpyr function significantly decreased the conidial production and hyphal growth, as well as disrupted the integrity of conidial cell wall. However, the defect of Bbpyr and Bbthi does not decrease the virulence of B. bassiana. Our results indicate the importance of thiamine biosynthesis in conidiation of B. bassiana, and provide useful information to produce conidia of entomopathogenic fungi for biocontrol of insect pests.
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Affiliation(s)
- Dan Jin
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Binda Sun
- Biotechnology Research Center, Southwest University, Chongqing, China; Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University (Third Military Medical University), China
| | - Wenqi Zhao
- Biotechnology Research Center, Southwest University, Chongqing, China; Institute of Medicine and Equipment for High Altitude Region, College of High Altitude Military Medicine, Army Medical University (Third Military Medical University), China
| | - Jincheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Qiuyue Zhou
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Xuemeng Han
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Yalin Mei
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Yanhua Fan
- Biotechnology Research Center, Southwest University, Chongqing, China
| | - Yan Pei
- Biotechnology Research Center, Southwest University, Chongqing, China.
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Strobbe S, Verstraete J, Stove C, Van Der Straeten D. Metabolic engineering of rice endosperm towards higher vitamin B1 accumulation. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1253-1267. [PMID: 33448624 PMCID: PMC8196658 DOI: 10.1111/pbi.13545] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/01/2020] [Indexed: 05/07/2023]
Abstract
Rice is a major food crop to approximately half of the human population. Unfortunately, the starchy endosperm, which is the remaining portion of the seed after polishing, contains limited amounts of micronutrients. Here, it is shown that this is particularly the case for thiamin (vitamin B1). Therefore, a tissue-specific metabolic engineering approach was conducted, aimed at enhancing the level of thiamin specifically in the endosperm. To achieve this, three major thiamin biosynthesis genes, THIC, THI1 and TH1, controlled by strong endosperm-specific promoters, were employed to obtain engineered rice lines. The metabolic engineering approaches included ectopic expression of THIC alone, in combination with THI1 (bigenic) or combined with both THI1 and TH1 (trigenic). Determination of thiamin and thiamin biosynthesis intermediates reveals the impact of the engineering approaches on endosperm thiamin biosynthesis. The results show an increase of thiamin in polished rice up to threefold compared to WT, and stable upon cooking. These findings confirm the potential of metabolic engineering to enhance de novo thiamin biosynthesis in rice endosperm tissue and aid in steering future biofortification endeavours.
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Affiliation(s)
- Simon Strobbe
- Laboratory of Functional Plant BiologyDepartment of BiologyGhent UniversityGentBelgium
| | - Jana Verstraete
- Laboratory of ToxicologyDepartment of BioanalysisGhent UniversityGentBelgium
| | - Christophe Stove
- Laboratory of ToxicologyDepartment of BioanalysisGhent UniversityGentBelgium
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The number of catalytic cycles in an enzyme's lifetime and why it matters to metabolic engineering. Proc Natl Acad Sci U S A 2021; 118:2023348118. [PMID: 33753504 PMCID: PMC8020674 DOI: 10.1073/pnas.2023348118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The continuous replacement of enzymes and other proteins appropriates up to half the maintenance energy budget in microorganisms and plants. High enzyme replacement rates therefore cut the productivity of biosystems ranging from microbial fermentations to crops. However, yardsticks to assess what drives enzyme protein replacement and guidelines on how to reduce it are lacking. Accordingly, we compared enzymes’ life spans across kingdoms using a new yardstick (catalytic cycles until replacement [CCR]) and related CCR to enzyme reaction chemistry. We concluded that 1) many enzymes fail due to collateral damage from the reaction they catalyze, and 2) such damage and its attendant enzyme replacement costs are mitigable by engineering and are therefore promising targets for synthetic biology. Metabolic engineering uses enzymes as parts to build biosystems for specified tasks. Although a part’s working life and failure modes are key engineering performance indicators, this is not yet so in metabolic engineering because it is not known how long enzymes remain functional in vivo or whether cumulative deterioration (wear-out), sudden random failure, or other causes drive replacement. Consequently, enzymes cannot be engineered to extend life and cut the high energy costs of replacement. Guided by catalyst engineering, we adopted catalytic cycles until replacement (CCR) as a metric for enzyme functional life span in vivo. CCR is the number of catalytic cycles that an enzyme mediates in vivo before failure or replacement, i.e., metabolic flux rate/protein turnover rate. We used estimated fluxes and measured protein turnover rates to calculate CCRs for ∼100–200 enzymes each from Lactococcus lactis, yeast, and Arabidopsis. CCRs in these organisms had similar ranges (<103 to >107) but different median values (3–4 × 104 in L. lactis and yeast versus 4 × 105 in Arabidopsis). In all organisms, enzymes whose substrates, products, or mechanisms can attack reactive amino acid residues had significantly lower median CCR values than other enzymes. Taken with literature on mechanism-based inactivation, the latter finding supports the proposal that 1) random active-site damage by reaction chemistry is an important cause of enzyme failure, and 2) reactive noncatalytic residues in the active-site region are likely contributors to damage susceptibility. Enzyme engineering to raise CCRs and lower replacement costs may thus be both beneficial and feasible.
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Hsieh P, Chung Y, Lee K, Wang S, Lu C, Hsieh M. The rice PALE1 homolog is involved in the biosynthesis of vitamin B1. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:218-220. [PMID: 32777168 PMCID: PMC7868968 DOI: 10.1111/pbi.13465] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 07/10/2020] [Accepted: 08/02/2020] [Indexed: 05/04/2023]
Affiliation(s)
- Ping‐Han Hsieh
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Yi‐Hsin Chung
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Kim‐Teng Lee
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Shi‐Yun Wang
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
| | - Chung‐An Lu
- Department of Life SciencesNational Central UniversityTaoyuanTaiwan
| | - Ming‐Hsiun Hsieh
- Institute of Plant and Microbial BiologyAcademia SinicaTaipeiTaiwan
- Department of Life SciencesNational Central UniversityTaoyuanTaiwan
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Labuschagne P, Divol B. Thiamine: a key nutrient for yeasts during wine alcoholic fermentation. Appl Microbiol Biotechnol 2021; 105:953-973. [PMID: 33404836 DOI: 10.1007/s00253-020-11080-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/18/2020] [Accepted: 12/27/2020] [Indexed: 12/27/2022]
Abstract
Alcoholic fermentation is a crucial step of winemaking, during which yeasts convert sugars to alcohol and also produce or biotransform numerous flavour compounds. In this context, nutrients are essential compounds to support yeast growth and ultimately ensure complete fermentation, as well as optimized production of flavour compounds over that of off-flavour compounds. In particular, the vitamin thiamine not only plays an essential cofactor role for several enzymes involved in various metabolic pathways, including those leading to the production of wine-relevant flavour compounds, but also aids yeast survival via thiamine-dependent stress protection functions. Most yeast species are able to both assimilate exogenous thiamine into the cell and synthesize thiamine de novo. However, the mechanism and level of thiamine accumulation depend on several factors. This review provides an in-depth overview of thiamine utilization and metabolism in the model yeast species Saccharomyces cerevisiae, as well as the current knowledge on (1) the intracellular functions of thiamine, (2) the balance between and regulation of uptake and synthesis of thiamine and (3) the multitude of factors influencing thiamine availability and utilization. For the latter, a particular emphasis is placed on conditions occurring during wine fermentation. The adequacy of thiamine concentration in grape must to ensure successful fermentation is discussed together with the effect of thiamine concentration on fermentation kinetics and on wine sensory properties. This knowledge may serve as a resource to optimise thiamine concentrations for optimal industrial application of yeasts. KEY POINTS: • Thiamine uptake is preferred over biosynthesis and is transcriptionally repressed. • Multiple factors affect thiamine synthesis, availability and uptake for wine yeast. • Thiamine availability impacts fermentation kinetics and wine's sensory properties.
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Affiliation(s)
- Pwj Labuschagne
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Private Bag X1, Matieland, 7602, South Africa
| | - B Divol
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Private Bag X1, Matieland, 7602, South Africa.
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Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s. Biochem J 2020; 477:2055-2069. [PMID: 32441748 DOI: 10.1042/bcj20200297] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022]
Abstract
Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsistz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mechanism in planta. Unexpectedly, transcriptome data mining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in developing grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thiazole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain-filling period.
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Deciphering potential inhibitors targeting THI4 of Fusarium solani sp. to combat fungal keratitis: An integrative computational approach. Comput Biol Chem 2020; 88:107350. [DOI: 10.1016/j.compbiolchem.2020.107350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 12/27/2022]
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An Unusual Route for p-Aminobenzoate Biosynthesis in Chlamydia trachomatis Involves a Probable Self-Sacrificing Diiron Oxygenase. J Bacteriol 2020; 202:JB.00319-20. [PMID: 32967910 DOI: 10.1128/jb.00319-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/23/2020] [Indexed: 11/20/2022] Open
Abstract
Chlamydia trachomatis lacks the canonical genes required for the biosynthesis of p-aminobenzoate (pABA), a component of essential folate cofactors. Previous studies revealed a single gene from C. trachomatis, the CT610 gene, that rescues Escherichia coli ΔpabA, ΔpabB, and ΔpabC mutants, which are otherwise auxotrophic for pABA. CT610 shares low sequence similarity to nonheme diiron oxygenases, and the previously solved crystal structure revealed a diiron active site. Genetic studies ruled out several potential substrates for CT610-dependent pABA biosynthesis, including chorismate and other shikimate pathway intermediates, leaving the actual precursor(s) unknown. Here, we supplied isotopically labeled potential precursors to E. coli ΔpabA cells expressing CT610 and found that the aromatic portion of tyrosine was highly incorporated into pABA, indicating that tyrosine is a precursor for CT610-dependent pABA biosynthesis. Additionally, in vitro enzymatic experiments revealed that purified CT610 exhibits low pABA synthesis activity under aerobic conditions in the absence of tyrosine or other potential substrates, where only the addition of a reducing agent such as dithiothreitol appears to stimulate pABA production. Furthermore, site-directed mutagenesis studies revealed that two conserved active site tyrosine residues are essential for the pABA synthesis reaction in vitro Thus, the current data are most consistent with CT610 being a unique self-sacrificing enzyme that utilizes its own active site tyrosine residue(s) for pABA biosynthesis in a reaction that requires O2 and a reduced diiron cofactor.IMPORTANCE Chlamydia trachomatis is the most reported sexually transmitted infection in the United States and the leading cause of infectious blindness worldwide. Unlike many other intracellular pathogens that have undergone reductive evolution, C. trachomatis is capable of de novo biosynthesis of the essential cofactor tetrahydrofolate using a noncanonical pathway. Here, we identify the biosynthetic precursor to the p-aminobenzoate (pABA) portion of folate in a process that requires the CT610 enzyme from C. trachomatis We further provide evidence that CT610 is a self-sacrificing or "suicide" enzyme that uses its own amino acid residue(s) as the substrate for pABA synthesis. This work provides the foundation for future investigation of this chlamydial pABA synthase, which could lead to new therapeutic strategies for C. trachomatis infections.
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García-García JD, Joshi J, Patterson JA, Trujillo-Rodriguez L, Reisch CR, Javanpour AA, Liu CC, Hanson AD. Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study. Life (Basel) 2020; 10:E179. [PMID: 32899502 PMCID: PMC7555113 DOI: 10.3390/life10090179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022] Open
Abstract
Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today's agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized more quickly than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cell's growth rate to the target gene's function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering.
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Affiliation(s)
| | - Jaya Joshi
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
| | - Jenelle A. Patterson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
| | - Lidimarie Trujillo-Rodriguez
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.T.-R.); (C.R.R.)
| | - Christopher R. Reisch
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32603, USA; (L.T.-R.); (C.R.R.)
| | - Alex A. Javanpour
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA; (A.A.J.); (C.C.L.)
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, CA 92617, USA; (A.A.J.); (C.C.L.)
- Department of Chemistry, University of California, Irvine, CA 92617, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
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Fitzpatrick TB, Chapman LM. The importance of thiamine (vitamin B 1) in plant health: From crop yield to biofortification. J Biol Chem 2020; 295:12002-12013. [PMID: 32554808 PMCID: PMC7443482 DOI: 10.1074/jbc.rev120.010918] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/17/2020] [Indexed: 12/14/2022] Open
Abstract
Ensuring that people have access to sufficient and nutritious food is necessary for a healthy life and the core tenet of food security. With the global population set to reach 9.8 billion by 2050, and the compounding effects of climate change, the planet is facing challenges that necessitate significant and rapid changes in agricultural practices. In the effort to provide food in terms of calories, the essential contribution of micronutrients (vitamins and minerals) to nutrition is often overlooked. Here, we focus on the importance of thiamine (vitamin B1) in plant health and discuss its impact on human health. Vitamin B1 is an essential dietary component, and deficiencies in this micronutrient underlie several diseases, notably nervous system disorders. The predominant source of dietary vitamin B1 is plant-based foods. Moreover, vitamin B1 is also vital for plants themselves, and its benefits in plant health have received less attention than in the human health sphere. In general, vitamin B1 is well-characterized for its role as a coenzyme in metabolic pathways, particularly those involved in energy production and central metabolism, including carbon assimilation and respiration. Vitamin B1 is also emerging as an important component of plant stress responses, and several noncoenzyme roles of this vitamin are being characterized. We summarize the importance of vitamin B1 in plants from the perspective of food security, including its roles in plant disease resistance, stress tolerance, and crop yield, and review the potential benefits of biofortification of crops with increased vitamin B1 content to improve human health.
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Affiliation(s)
- Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
| | - Lottie M Chapman
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
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Adaptive Laboratory Evolution and Reverse Engineering of Single-Vitamin Prototrophies in Saccharomyces cerevisiae. Appl Environ Microbiol 2020; 86:AEM.00388-20. [PMID: 32303542 PMCID: PMC7267190 DOI: 10.1128/aem.00388-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/11/2020] [Indexed: 01/28/2023] Open
Abstract
Many strains of Saccharomyces cerevisiae, a popular platform organism in industrial biotechnology, carry the genetic information required for synthesis of biotin, thiamine, pyridoxine, para-aminobenzoic acid, pantothenic acid, nicotinic acid, and inositol. However, omission of these B vitamins typically leads to suboptimal growth. This study demonstrates that, for each individual B vitamin, it is possible to achieve fast vitamin-independent growth by adaptive laboratory evolution (ALE). Identification of mutations responsible for these fast-growing phenotypes by whole-genome sequencing and reverse engineering showed that, for each compound, a small number of mutations sufficed to achieve fast growth in its absence. These results form an important first step toward development of S. cerevisiae strains that exhibit fast growth on inexpensive, fully supplemented mineral media that only require complementation with a carbon source, thereby reducing costs, complexity, and contamination risks in industrial yeast fermentation processes. Quantitative physiological studies on Saccharomyces cerevisiae commonly use synthetic media (SM) that contain a set of water-soluble growth factors that, based on their roles in human nutrition, are referred to as B vitamins. Previous work demonstrated that in S. cerevisiae CEN.PK113-7D, requirements for biotin were eliminated by laboratory evolution. In the present study, this laboratory strain was shown to exhibit suboptimal specific growth rates when either inositol, nicotinic acid, pyridoxine, pantothenic acid, para-aminobenzoic acid (pABA), or thiamine was omitted from SM. Subsequently, this strain was evolved in parallel serial-transfer experiments for fast aerobic growth on glucose in the absence of individual B vitamins. In all evolution lines, specific growth rates reached at least 90% of the growth rate observed in SM supplemented with a complete B vitamin mixture. Fast growth was already observed after a few transfers on SM without myo-inositol, nicotinic acid, or pABA. Reaching similar results in SM lacking thiamine, pyridoxine, or pantothenate required more than 300 generations of selective growth. The genomes of evolved single-colony isolates were resequenced, and for each B vitamin, a subset of non-synonymous mutations associated with fast vitamin-independent growth was selected. These mutations were introduced in a non-evolved reference strain using CRISPR/Cas9-based genome editing. For each B vitamin, the introduction of a small number of mutations sufficed to achieve a substantially increased specific growth rate in non-supplemented SM that represented at least 87% of the specific growth rate observed in fully supplemented complete SM. IMPORTANCE Many strains of Saccharomyces cerevisiae, a popular platform organism in industrial biotechnology, carry the genetic information required for synthesis of biotin, thiamine, pyridoxine, para-aminobenzoic acid, pantothenic acid, nicotinic acid, and inositol. However, omission of these B vitamins typically leads to suboptimal growth. This study demonstrates that, for each individual B vitamin, it is possible to achieve fast vitamin-independent growth by adaptive laboratory evolution (ALE). Identification of mutations responsible for these fast-growing phenotypes by whole-genome sequencing and reverse engineering showed that, for each compound, a small number of mutations sufficed to achieve fast growth in its absence. These results form an important first step toward development of S. cerevisiae strains that exhibit fast growth on inexpensive, fully supplemented mineral media that only require complementation with a carbon source, thereby reducing costs, complexity, and contamination risks in industrial yeast fermentation processes.
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46
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Biochemical characterisation and application of keratinase from Bacillus thuringiensis MT1 to enable valorisation of hair wastes through biosynthesis of vitamin B-complex. Int J Biol Macromol 2020; 153:561-572. [PMID: 32151720 DOI: 10.1016/j.ijbiomac.2020.03.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/22/2023]
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Abstract
At least two types of pincer complexes are known to exist in biology. A metal-pyrroloquinolone quinone (PQQ) cofactor was first identified in bacterial methanol dehydrogenase, and later also found in selected short-chain alcohol dehydrogenases of other microorganisms. The PQQ-associated metal can be calcium, magnesium, or a rare earth element depending on the enzyme sequence. Synthesis of this organic ligand requires a series of accessory proteins acting on a small peptide, PqqA. Binding of metal to PQQ yields an ONO-type pincer complex. More recently, a nickel-pincer nucleotide (NPN) cofactor was discovered in lactate racemase, LarA. This cofactor derives from nicotinic acid adenine dinucleotide via action of a carboxylase/hydrolase, sulfur transferase, and nickel insertase, resulting in an SCS-type pincer complex. The NPN cofactor likely occurs in selected other racemases and epimerases of bacteria, archaea, and a few eukaryotes.
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Affiliation(s)
- Jorge Nevarez
- Department of Chemistry, 578 South Shaw Lane, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Aiko Turmo
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Jian Hu
- Department of Chemistry, 578 South Shaw Lane, Michigan State University, East Lansing, Michigan 48824 (USA).,Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA)
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, 603 Wilson Road, Room 212, Michigan State University, East Lansing, Michigan 48824 (USA).,Department of Microbiology and Molecular Genetics, 567 Wilson Road, 2215 Biomedical Physical Sciences, Michigan State University, East Lansing, Michigan 48824 (USA)
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Noordally ZB, Trichtinger C, Dalvit I, Hofmann M, Roux C, Zamboni N, Pourcel L, Gas-Pascual E, Gisler A, Fitzpatrick TB. The coenzyme thiamine diphosphate displays a daily rhythm in the Arabidopsis nucleus. Commun Biol 2020; 3:209. [PMID: 32372067 PMCID: PMC7200797 DOI: 10.1038/s42003-020-0927-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/25/2020] [Indexed: 12/27/2022] Open
Abstract
In plants, metabolic homeostasis—the driving force of growth and development—is achieved through the dynamic behavior of a network of enzymes, many of which depend on coenzymes for activity. The circadian clock is established to influence coordination of supply and demand of metabolites. Metabolic oscillations independent of the circadian clock, particularly at the subcellular level is unexplored. Here, we reveal a metabolic rhythm of the essential coenzyme thiamine diphosphate (TDP) in the Arabidopsis nucleus. We show there is temporal separation of the clock control of cellular biosynthesis and transport of TDP at the transcriptional level. Taking advantage of the sole reported riboswitch metabolite sensor in plants, we show that TDP oscillates in the nucleus. This oscillation is a function of a light-dark cycle and is independent of circadian clock control. The findings are important to understand plant fitness in terms of metabolite rhythms. Noordally et al. show that the essential coenzyme thiamine diphosphate exhibits a daily rhythm in the Arabidopsis nucleus, which is driven by light-dark cycles and not by the circadian clock. This study provides insight into our understanding of the optimization of plant fitness.
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Affiliation(s)
- Zeenat B Noordally
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Celso Trichtinger
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Ivan Dalvit
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Manuel Hofmann
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Céline Roux
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Lucille Pourcel
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Elisabet Gas-Pascual
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Alexandra Gisler
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Teresa B Fitzpatrick
- Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland.
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Perli T, Wronska AK, Ortiz‐Merino RA, Pronk JT, Daran J. Vitamin requirements and biosynthesis in Saccharomyces cerevisiae. Yeast 2020; 37:283-304. [PMID: 31972058 PMCID: PMC7187267 DOI: 10.1002/yea.3461] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term "vitamin" is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.
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Affiliation(s)
- Thomas Perli
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Anna K. Wronska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | - Jack T. Pronk
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jean‐Marc Daran
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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50
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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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