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Nowrouzi B, Torres-Montero P, Kerkhoven EJ, Martínez JL, Rios-Solis L. Rewiring Saccharomyces cerevisiae metabolism for optimised Taxol® precursors production. Metab Eng Commun 2024; 18:e00229. [PMID: 38098801 PMCID: PMC10716015 DOI: 10.1016/j.mec.2023.e00229] [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: 09/01/2023] [Revised: 10/09/2023] [Accepted: 11/04/2023] [Indexed: 12/17/2023] Open
Abstract
Saccharomyces cerevisiae has been conveniently used to produce Taxol® anticancer drug early precursors. However, the harmful impact of oxidative stress by the first cytochrome P450-reductase enzymes (CYP725A4-POR) of Taxol® pathway has hampered sufficient progress in yeast. Here, we evolved an oxidative stress-resistant yeast strain with three-fold higher titre of their substrate, taxadiene. The performance of the evolved and parent strains were then evaluated in galactose-limited chemostats before and under the oxidative stress by an oxidising agent. The interaction of evolution and oxidative stress was comprehensively evaluated through transcriptomics and metabolite profiles integration in yeast enzyme-constrained genome scale model. Overall, the evolved strain showed improved respiration, reduced overflow metabolites production and oxidative stress re-induction tolerance. The cross-protection mechanism also potentially contributed to better heme, flavin and NADPH availability, essential for CYP725A4 and POR optimal activity in yeast. The results imply that the evolved strain is a robust cell factory for future efforts towards Taxol© production.
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Affiliation(s)
- Behnaz Nowrouzi
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Pablo Torres-Montero
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Eduard J. Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - José L. Martínez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 223, Kgs. Lyngby, 2800, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, EH9 3BF, United Kingdom
- Centre for Engineering Biology, The University of Edinburgh, Edinburgh, EH9 3BD, United Kingdom
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, United Kingdom
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2
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Bysani VR, Alam AS, Bar-Even A, Machens F. Engineering and evolution of the complete Reductive Glycine Pathway in Saccharomyces cerevisiae for formate and CO 2 assimilation. Metab Eng 2024; 81:167-181. [PMID: 38040111 DOI: 10.1016/j.ymben.2023.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]
Abstract
Using captured CO2 and C1-feedstocks like formate and methanol derived from electrochemical activation of CO2 are key solutions for transforming industrial processes towards a circular carbon economy. Engineering formate and CO2-based growth in the biotechnologically relevant yeast Saccharomyces cerevisiae could boost the emergence of a formate-mediated circular bio-economy. This study adopts a growth-coupled selection scheme for modular implementation of the Reductive Glycine Pathway (RGP) and subsequent Adaptive Laboratory Evolution (ALE) to enable formate and CO2 assimilation for biomass formation in yeast. We first constructed a serine biosensor strain and then implemented the serine synthesis module of the RGP into yeast, establishing glycine and serine synthesis from formate and CO2. ALE improved the RGP-dependent growth by 8-fold. 13C-labeling experiments reveal glycine, serine, and pyruvate synthesis via the RGP, demonstrating the complete pathway activity. Further, we re-established formate and CO2-dependent growth in non-evolved biosensor strains via reverse-engineering a mutation in GDH1 identified from ALE. This mutation led to significantly more 13C-formate assimilation than in WT without any selection or overexpression of the RGP. Overall, we demonstrated the activity of the complete RGP, showing evidence for carbon transfer from formate to pyruvate coupled with CO2 assimilation.
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Affiliation(s)
- Viswanada R Bysani
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Ayesha S Alam
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Fabian Machens
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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3
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Salas-Navarrete PC, Rosas-Santiago P, Suárez-Rodríguez R, Martínez A, Caspeta L. Adaptive responses of yeast strains tolerant to acidic pH, acetate, and supraoptimal temperature. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12556-7. [PMID: 37178307 DOI: 10.1007/s00253-023-12556-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]
Abstract
Ethanol fermentations can be prematurely halted as Saccharomyces cerevisiae faces adverse conditions, such as acidic pH, presence of acetic acid, and supraoptimal temperatures. The knowledge on yeast responses to these conditions is essential to endowing a tolerant phenotype to another strain by targeted genetic manipulation. In this study, physiological and whole-genome analyses were conducted to obtain insights on molecular responses which potentially render yeast tolerant towards thermoacidic conditions. To this end, we used thermotolerant TTY23, acid tolerant AT22, and thermo-acid tolerant TAT12 strains previously generated by adaptive laboratory evolution (ALE) experiments. The results showed an increase in thermoacidic profiles in the tolerant strains. The whole-genome sequence revealed the importance of genes related to: H+, iron, and glycerol transport (i.e., PMA1, FRE1/2, JEN1, VMA2, VCX1, KHA1, AQY3, and ATO2); transcriptional regulation of stress responses to drugs, reactive oxygen species and heat-shock (i.e., HSF1, SKN7, BAS1, HFI1, and WAR1); and adjustments of fermentative growth and stress responses by glucose signaling pathways (i.e., ACS1, GPA1/2, RAS2, IRA2, and REG1). At 30 °C and pH 5.5, more than a thousand differentially expressed genes (DEGs) were identified in each strain. The integration of results revealed that evolved strains adjust their intracellular pH by H+ and acetic acid transport, modify their metabolism and stress responses via glucose signaling pathways, control of cellular ATP pools by regulating translation and de novo synthesis of nucleotides, and direct the synthesis, folding and rescue of proteins throughout the heat-shock stress response. Moreover, the motifs analysis in mutated transcription factors suggested a significant association of SFP1, YRR1, BAS1, HFI1, HSF1, and SKN7 TFs with DEGs found in thermoacidic tolerant yeast strains. KEY POINTS: • All the evolved strains overexpressed the plasma membrane H+ -ATPase PMA1 at optimal conditions • Tolerant strain TAT12 mutated genes encoding weak acid and heat response TFs HSF1, SKN7, and WAR1 • TFs HSF1 and SKN7 likely controlled the transcription of metabolic genes associated to heat and acid tolerance.
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Affiliation(s)
- Prisciluis Caheri Salas-Navarrete
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, 62209, Morelos, México
| | - Paul Rosas-Santiago
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210, Morelos, México
| | - Ramón Suárez-Rodríguez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, 62209, Morelos, México
| | - Alfredo Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210, Morelos, México
| | - Luis Caspeta
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, 62210, Morelos, México.
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4
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Ding W, Meng Q, Dong G, Qi N, Zhao H, Shi S. Metabolic engineering of threonine catabolism enables Saccharomyces cerevisiae to produce propionate under aerobic conditions. Biotechnol J 2022; 17:e2100579. [PMID: 35086163 DOI: 10.1002/biot.202100579] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Propionate is widely used as a preservative in the food and animal feed industries. Propionate is currently produced by petrochemical processes, and fermentative production of propionate remains challenging. METHODS AND RESULTS In this study, a synthetic propionate pathway was constructed in the budding yeast Saccharomyces cerevisiae, for propionate production under aerobic conditions. Through expression of tdcB and aldH from Escherichia coli and kivD from Lactococcus lactis, L-threonine was converted to propionate via 2-ketobutyrate and propionaldehyde. The resulting yeast aerobically produced 0.21 g/L propionate from glucose in a shake flask. Subsequent overexpression of pathway genes and elimination of competing pathways increased propionate production to 0.37 g/L. To further increase propionate production, carbon flux was pulled into the propionate pathway by weakened expression of pyruvate kinase (PYK1), together with overexpression of phosphoenolpyruvate carboxylase (ppc). The final propionate production reached 1.05 g/L during fed-batch fermentation in a fermenter. CONCLUSIONS AND IMPLICATIONS In this work, a yeast cell factory was constructed using synthetic biology and metabolic engineering strategies to enable propionate production under aerobic conditions. Our study demonstrates engineered S. cerevisiae as a promising alternative for the production of propionate and its derivatives. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China.,Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, No. 9, 13th Avenue, TEDA, Tianjin, 300457, China
| | - Qiongyu Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China
| | - Genlai Dong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China
| | - Nailing Qi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China
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5
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Fauziah Ma'ruf I, Sasaki Y, Kerbs A, Nießer J, Sato Y, Taniguchi H, Okano K, Kitani S, Restiawaty E, Akhmaloka, Honda K. Heterologous gene expression and characterization of two serine hydroxymethyltransferases from Thermoplasma acidophilum. Extremophiles 2021; 25:393-402. [PMID: 34196829 DOI: 10.1007/s00792-021-01238-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/24/2021] [Indexed: 12/01/2022]
Abstract
Serine hydroxymethyltransferase (SHMT) and threonine aldolase are classified as fold type I pyridoxal-5'-phosphate-dependent enzymes and engaged in glycine biosynthesis from serine and threonine, respectively. The acidothermophilic archaeon Thermoplasma acidophilum possesses two distinct SHMT genes, while there is no gene encoding threonine aldolase in its genome. In the present study, the two SHMT genes (Ta0811 and Ta1509) were heterologously expressed in Escherichia coli and Thermococcus kodakarensis, respectively, and biochemical properties of their products were investigated. Ta1509 protein exhibited dual activities to catalyze tetrahydrofolate (THF)-dependent serine cleavage and THF-independent threonine cleavage, similar to other SHMTs reported to date. In contrast, the Ta0811 protein lacks amino acid residues involved in the THF-binding motif and catalyzes only the THF-independent cleavage of threonine. Kinetic analysis revealed that the threonine-cleavage activity of the Ta0811 protein was 3.5 times higher than the serine-cleavage activity of Ta1509 protein. In addition, mRNA expression of Ta0811 gene in T. acidophilum was approximately 20 times more abundant than that of Ta1509. These observations suggest that retroaldol cleavage of threonine, mediated by the Ta0811 protein, has a major role in glycine biosynthesis in T. acidophilum.
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Affiliation(s)
- Ilma Fauziah Ma'ruf
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Department of Chemistry, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Yuka Sasaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Anastasia Kerbs
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, 33617, Bielefeld, Germany
| | - Jochen Nießer
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Institute of Bio and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Julich, Germany
| | - Yu Sato
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hironori Taniguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kenji Okano
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeru Kitani
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Elvi Restiawaty
- Chemical Engineering Process Design and Development Research Group, Faculty of Industrial Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Akhmaloka
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Department of Chemistry, Institut Teknologi Bandung, Bandung, 40132, Indonesia.,Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Jakarta, 12220, Indonesia
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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6
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Gao W, Jones TA, Rivas E. Discovery of 17 conserved structural RNAs in fungi. Nucleic Acids Res 2021; 49:6128-6143. [PMID: 34086938 PMCID: PMC8216456 DOI: 10.1093/nar/gkab355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/25/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
Many non-coding RNAs with known functions are structurally conserved: their intramolecular secondary and tertiary interactions are maintained across evolutionary time. Consequently, the presence of conserved structure in multiple sequence alignments can be used to identify candidate functional non-coding RNAs. Here, we present a bioinformatics method that couples iterative homology search with covariation analysis to assess whether a genomic region has evidence of conserved RNA structure. We used this method to examine all unannotated regions of five well-studied fungal genomes (Saccharomyces cerevisiae, Candida albicans, Neurospora crassa, Aspergillus fumigatus, and Schizosaccharomyces pombe). We identified 17 novel structurally conserved non-coding RNA candidates, which include four H/ACA box small nucleolar RNAs, four intergenic RNAs and nine RNA structures located within the introns and untranslated regions (UTRs) of mRNAs. For the two structures in the 3' UTRs of the metabolic genes GLY1 and MET13, we performed experiments that provide evidence against them being eukaryotic riboswitches.
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Affiliation(s)
- William Gao
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA
| | - Thomas A Jones
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, USA
| | - Elena Rivas
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA
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7
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Chen J, Huang XY, Salt DE, Zhao FJ. Mutation in OsCADT1 enhances cadmium tolerance and enriches selenium in rice grain. THE NEW PHYTOLOGIST 2020; 226:838-850. [PMID: 31879959 DOI: 10.1111/nph.16404] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/18/2019] [Indexed: 05/27/2023]
Abstract
How cadmium (Cd) tolerance in rice is regulated remains poorly understood. We used a forward genetic approach to investigate Cd tolerance in rice. Using a root elongation assay, we isolated a rice mutant with enhanced Cd tolerance, cadt1, from an ethyl methanesulphonate (EMS)-mutagenized population of a widely grown Indica cultivar. The mutant accumulated more Cd in roots but not in shoots and grains. Using genomic resequencing and complementation, we identified OsCADT1 as the causal gene for the mutant phenotype, which encodes a putative serine hydroxymethyltransferase. OsCADT1 protein was localized to the nucleus and the OsCADT1 gene was expressed in both roots and shoots. OsCADT1 mutation resulted in higher sulphur and selenium accumulation in the shoots and grains. Selenate influx in cadt1 was 2.4 times that of the wild-type. The mutant showed higher expression of the sulphate/selenate transporter gene OsSULTR1;1 and the sulphur-deficiency-inducible gene OsSDI1. Thiol compounds including cysteine, glutathione and phytochelatins were significantly increased in the mutant, underlying its increased Cd tolerance. Growth and grain biomass were little affected. The results suggest that OsCADT1 acts as a negative regulator of sulphate/selenate uptake and assimilation. OsCADT1 mutation increases Cd tolerance and enriches selenium in rice grains, providing a novel solution for selenium biofortification.
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Affiliation(s)
- Jie Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xin-Yuan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - David E Salt
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
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8
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You ST, Jhou YT, Kao CF, Leu JY. Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering. PLoS Biol 2019; 17:e3000433. [PMID: 31613873 PMCID: PMC6814240 DOI: 10.1371/journal.pbio.3000433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/25/2019] [Accepted: 09/27/2019] [Indexed: 11/19/2022] Open
Abstract
Cell-to-cell heterogeneity within an isogenic population has been observed in prokaryotic and eukaryotic cells. Such heterogeneity often manifests at the level of individual protein abundance and may have evolutionary benefits, especially for organisms in fluctuating environments. Although general features and the origins of cellular noise have been revealed, details of the molecular pathways underlying noise regulation remain elusive. Here, we used experimental evolution of Saccharomyces cerevisiae to select for mutations that increase reporter protein noise. By combining bulk segregant analysis and CRISPR/Cas9-based reconstitution, we identified the methyltransferase Hmt1 as a general regulator of noise buffering. Hmt1 methylation activity is critical for the evolved phenotype, and we also show that two of the Hmt1 methylation targets can suppress noise. Hmt1 functions as an environmental sensor to adjust noise levels in response to environmental cues. Moreover, Hmt1-mediated noise buffering is conserved in an evolutionarily distant yeast species, suggesting broad significance of noise regulation. Experimental evolution in yeast reveals that the methyltransferase Hmt1 functions as a mediator connecting environmental stimuli to cellular noise; Hmt1-mediated noise buffering is conserved in an evolutionarily distant yeast.
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Affiliation(s)
- Shu-Ting You
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Jhou
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
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9
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Ghanegolmohammadi F, Yoshida M, Ohnuki S, Sukegawa Y, Okada H, Obara K, Kihara A, Suzuki K, Kojima T, Yachie N, Hirata D, Ohya Y. Systematic analysis of Ca 2+ homeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles. Mol Biol Cell 2017; 28:3415-3427. [PMID: 28566553 PMCID: PMC5687040 DOI: 10.1091/mbc.e17-04-0216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 12/20/2022] Open
Abstract
We investigated the global landscape of Ca2+ homeostasis in budding yeast based on high-dimensional chemical-genetic interaction profiles. The morphological responses of 62 Ca2+-sensitive (cls) mutants were quantitatively analyzed with the image processing program CalMorph after exposure to a high concentration of Ca2+ After a generalized linear model was applied, an analysis of covariance model was used to detect significant Ca2+-cls interactions. We found that high-dimensional, morphological Ca2+-cls interactions were mixed with positive (86%) and negative (14%) chemical-genetic interactions, whereas one-dimensional fitness Ca2+-cls interactions were all negative in principle. Clustering analysis with the interaction profiles revealed nine distinct gene groups, six of which were functionally associated. In addition, characterization of Ca2+-cls interactions revealed that morphology-based negative interactions are unique signatures of sensitized cellular processes and pathways. Principal component analysis was used to discriminate between suppression and enhancement of the Ca2+-sensitive phenotypes triggered by inactivation of calcineurin, a Ca2+-dependent phosphatase. Finally, similarity of the interaction profiles was used to reveal a connected network among the Ca2+ homeostasis units acting in different cellular compartments. Our analyses of high-dimensional chemical-genetic interaction profiles provide novel insights into the intracellular network of yeast Ca2+ homeostasis.
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Affiliation(s)
| | - Mitsunori Yoshida
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yuko Sukegawa
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
- AIST-UTokyo Advanced Operand-Measurement Technology Open Innovation Laboratory, Kashiwa 277-0882, Japan
| | - Hiroki Okada
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058
| | - Keisuke Obara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
- Bioimaging Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Tetsuya Kojima
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Nozomu Yachie
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
- PRESTO, Japan Science and Technology Agency, Tokyo 102-0076, Japan
| | - Dai Hirata
- Research and Development Department, Asahi Sake Brewing Co., Nagaoka 949-5494, Japan
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
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10
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Alterations in cellular metabolism triggered by URA7 or GLN3 inactivation cause imbalanced dNTP pools and increased mutagenesis. Proc Natl Acad Sci U S A 2017; 114:E4442-E4451. [PMID: 28416670 DOI: 10.1073/pnas.1618714114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic DNA replication fidelity relies on the concerted action of DNA polymerase nucleotide selectivity, proofreading activity, and DNA mismatch repair (MMR). Nucleotide selectivity and proofreading are affected by the balance and concentration of deoxyribonucleotide (dNTP) pools, which are strictly regulated by ribonucleotide reductase (RNR). Mutations preventing DNA polymerase proofreading activity or MMR function cause mutator phenotypes and consequently increased cancer susceptibility. To identify genes not previously linked to high-fidelity DNA replication, we conducted a genome-wide screen in Saccharomyces cerevisiae using DNA polymerase active-site mutants as a "sensitized mutator background." Among the genes identified in our screen, three metabolism-related genes (GLN3, URA7, and SHM2) have not been previously associated to the suppression of mutations. Loss of either the transcription factor Gln3 or inactivation of the CTP synthetase Ura7 both resulted in the activation of the DNA damage response and imbalanced dNTP pools. Importantly, these dNTP imbalances are strongly mutagenic in genetic backgrounds where DNA polymerase function or MMR activity is partially compromised. Previous reports have shown that dNTP pool imbalances can be caused by mutations altering the allosteric regulation of enzymes involved in dNTP biosynthesis (e.g., RNR or dCMP deaminase). Here, we provide evidence that mutations affecting genes involved in RNR substrate production can cause dNTP imbalances, which cannot be compensated by RNR or other enzymatic activities. Moreover, Gln3 inactivation links nutrient deprivation to increased mutagenesis. Our results suggest that similar genetic interactions could drive mutator phenotypes in cancer cells.
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11
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Weber N, Hatsch A, Labagnere L, Heider H. Production of (S)-2-aminobutyric acid and (S)-2-aminobutanol in Saccharomyces cerevisiae. Microb Cell Fact 2017; 16:51. [PMID: 28335772 PMCID: PMC5364695 DOI: 10.1186/s12934-017-0667-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/21/2017] [Indexed: 01/09/2023] Open
Abstract
Background Saccharomyces cerevisiae (baker’s yeast) has great potential as a whole-cell biocatalyst for multistep synthesis of various organic molecules. To date, however, few examples exist in the literature of the successful biosynthetic production of chemical compounds, in yeast, that do not exist in nature. Considering that more than 30% of all drugs on the market are purely chemical compounds, often produced by harsh synthetic chemistry or with very low yields, novel and environmentally sound production routes are highly desirable. Here, we explore the biosynthetic production of enantiomeric precursors of the anti-tuberculosis and anti-epilepsy drugs ethambutol, brivaracetam, and levetiracetam. To this end, we have generated heterologous biosynthetic pathways leading to the production of (S)-2-aminobutyric acid (ABA) and (S)-2-aminobutanol in baker’s yeast. Results We first designed a two-step heterologous pathway, starting with the endogenous amino acid l-threonine and leading to the production of enantiopure (S)-2-aminobutyric acid. The combination of Bacillus subtilis threonine deaminase and a mutated Escherichia coli glutamate dehydrogenase resulted in the intracellular accumulation of 0.40 mg/L of (S)-2-aminobutyric acid. The combination of a threonine deaminase from Solanum lycopersicum (tomato) with two copies of mutated glutamate dehydrogenase from E. coli resulted in the accumulation of comparable amounts of (S)-2-aminobutyric acid. Additional l-threonine feeding elevated (S)-2-aminobutyric acid production to more than 1.70 mg/L. Removing feedback inhibition of aspartate kinase HOM3, an enzyme involved in threonine biosynthesis in yeast, elevated (S)-2-aminobutyric acid biosynthesis to above 0.49 mg/L in cultures not receiving additional l-threonine. We ultimately extended the pathway from (S)-2-aminobutyric acid to (S)-2-aminobutanol by introducing two reductases and a phosphopantetheinyl transferase. The engineered strains produced up to 1.10 mg/L (S)-2-aminobutanol. Conclusions Our results demonstrate the biosynthesis of (S)-2-aminobutyric acid and (S)-2-aminobutanol in yeast. To our knowledge this is the first time that the purely synthetic compound (S)-2-aminobutanol has been produced in vivo. This work paves the way to greener and more sustainable production of chemical entities hitherto inaccessible to synthetic biology. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0667-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nora Weber
- Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland.
| | - Anaëlle Hatsch
- Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland
| | | | - Harald Heider
- Evolva SA, Duggingerstrasse 23, 4153, Reinach, Switzerland
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12
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Hirato Y, Tokuhisa M, Tanigawa M, Ashida H, Tanaka H, Nishimura K. Cloning and characterization of d-threonine aldolase from the green alga Chlamydomonas reinhardtii. PHYTOCHEMISTRY 2017; 135:18-23. [PMID: 28038776 DOI: 10.1016/j.phytochem.2016.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/07/2016] [Accepted: 12/14/2016] [Indexed: 06/06/2023]
Abstract
d-Threonine aldolase (DTA) catalyzes the pyridoxal 5'-phosphate (PLP)-dependent interconversion of d-threonine and glycine plus acetaldehyde. The enzyme is a powerful tool for the stereospecific synthesis of various β-hydroxy amino acids in synthetic organic chemistry. In this study, DTA from the green alga Chlamydomonas reinhardtii was discovered and characterized, representing the first report to describe the existence of eukaryotic DTA. DTA was overexpressed in recombinant Escherichia coli BL21 (DE3) cells; the specific activity of the enzyme in the cell-free extract was 0.8 U/mg. The recombinant enzyme was purified to homogeneity by ammonium sulfate fractionation, DEAE-Sepharose, and Mono Q column chromatographies (purified enzyme 7.0 U/mg). For the cleavage reaction, the optimal temperature and pH were 70 °C and pH 8.4, respectively. The enzyme demonstrated 90% of residual activity at 50 °C for 1 h. The enzyme catalyzed the synthesis of d- and d-allo threonine from a mixture of glycine and acetaldehyde (the diastereomer excess of d-threonine was 18%). DTA was activated by several divalent metal ions, including manganese, and was inhibited by PLP enzyme inhibitors and metalloenzyme inhibitors.
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Affiliation(s)
- Yuki Hirato
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan
| | - Mayumi Tokuhisa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan
| | - Minoru Tanigawa
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan
| | - Hiroyuki Ashida
- Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Shimane University, Nishikawatsu 1060, Matsue, Shimane, 690-8504, Japan
| | - Hiroyuki Tanaka
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Seta, Shiga, 520-2192, Japan
| | - Katsushi Nishimura
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda-Surugadai, Chiyoda-Ku, Tokyo, 101-8308, Japan; Department of Biotechnology and Materials Chemistry, Junior College, Nihon University, 7-24-1Narashinodai, Funabashi, Chiba, 274-8501, Japan.
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Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae. Metab Eng Commun 2016; 3:153-163. [PMID: 29468121 PMCID: PMC5779720 DOI: 10.1016/j.meteno.2016.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 03/17/2016] [Accepted: 05/10/2016] [Indexed: 01/23/2023] Open
Abstract
Genome-scale metabolic models (GEMs) can be used to evaluate genotype-phenotype relationships and their application to microbial strain engineering is increasing in popularity. Some of the algorithms used to simulate the phenotypes of mutant strains require the determination of a wild-type flux distribution. However, the accuracy of this reference, when calculated with flux balance analysis, has not been studied in detail before. Here, the wild-type simulations of selected GEMs for Saccharomyces cerevisiae have been analysed and most of the models tested predicted erroneous fluxes in central pathways, especially in the pentose phosphate pathway. Since the problematic fluxes were mostly related to areas of the metabolism consuming or producing NADPH/NADH, we have manually curated all reactions including these cofactors by forcing the use of NADPH/NADP+ in anabolic reactions and NADH/NAD+ for catabolic reactions. The curated models predicted more accurate flux distributions and performed better in the simulation of mutant phenotypes. The flux distributions of the genome-scale models of Saccharomyces cerevisiae were evaluated Most of the tested models showed fluxes inconsistent with experimental data A manual curation process was performed on all reactions including NADH or NADPH The curated models showed flux distributions more consistent with experimental data Phenotype simulations improved when the curated flux distributions were used
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14
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Wu XY, Zhou GC, Chen YX, Wu P, Liu LW, Ma FF, Wu M, Liu CC, Zeng YJ, Chu AE, Hang YY, Chen JQ, Wang B. Soybean Cyst Nematode Resistance Emerged via Artificial Selection of Duplicated Serine Hydroxymethyltransferase Genes. FRONTIERS IN PLANT SCIENCE 2016; 7:998. [PMID: 27458476 PMCID: PMC4937839 DOI: 10.3389/fpls.2016.00998] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/24/2016] [Indexed: 05/17/2023]
Abstract
A major soybean (Forrest cultivar) quantitative trait locus (QTL) gene, Rhg4, which controls resistance to soybean cyst nematodes (SCN), encodes the enzyme serine hydroxylmethyltransferase (SHMT). The resistant allele possesses two critical missense mutations (P130R and N358Y) compared to that of the sensitive allele, rhg4. To understand the evolutionary history of this gene, sequences of 117 SHMT family members from 18 representative plant species were used to reconstruct their phylogeny. According to this phylogeny, the plant SHMT gene family can be divided into two groups and four subgroups (Ia, Ib, IIa, and IIb). Belonging to the Subgroup Ia lineage, the rhg4 gene evolved from a recent duplication event in Glycine sp.. To further explore how the SCN-resistant allele emerged, both the rhg4 gene and its closest homolog, the rhg4h gene, were isolated from 33 cultivated and 68 wild soybean varieties. The results suggested that after gene duplication, the soybean rhg4 gene accumulated a higher number of non-synonymous mutations than rhg4h. Although a higher number of segregating sites and gene haplotypes were detected in wild soybeans than in cultivars, the SCN-resistant Rhg4 allele (represented by haplotype 4) was not found in wild varieties. Instead, a very similar allele, haplotype 3, was observed in wild soybeans at a frequency of 7.4%, although it lacked the two critical non-synonymous substitutions. Taken together, these findings support that the SCN-resistant Rhg4 allele likely emerged via artificial selection during the soybean domestication process, based on a SCN-sensitive allele inherited from wild soybeans.
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Affiliation(s)
- Xiao-Yi Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
| | - Guang-Can Zhou
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, NanjingChina
| | - Yun-Xia Chen
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
| | - Ping Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
| | - Li-Wei Liu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
| | - Fang-Fang Ma
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
| | - Mian Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
| | - Cheng-Chen Liu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
| | - Ying-Jie Zeng
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
| | - Alexander E. Chu
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UTUSA
| | - Yue-Yu Hang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, NanjingChina
| | - Jian-Qun Chen
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
- *Correspondence: Bin Wang, Jian-Qun Chen,
| | - Bin Wang
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, NanjingChina
- *Correspondence: Bin Wang, Jian-Qun Chen,
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15
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Liu G, Zhang M, Mo T, He L, Zhang W, Yu Y, Zhang Q, Ding W. Metabolic flux analysis of the halophilic archaeon Haladaptatus paucihalophilus. Biochem Biophys Res Commun 2015; 467:1058-62. [PMID: 26441084 DOI: 10.1016/j.bbrc.2015.09.174] [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: 09/14/2015] [Accepted: 09/30/2015] [Indexed: 11/30/2022]
Abstract
This work reports the (13)C-assisted metabolic flux analysis of Haladaptatus paucihalophilus, a halophilic archaeon possessing an intriguing osmoadaption mechanism. We showed that the carbon flow is through the oxidative tricarboxylic acid (TCA) cycle whereas the reductive TCA cycle is not operative in H. paucihalophilus. In addition, both threonine and the citramalate pathways contribute to isoleucine biosynthesis, whereas lysine is synthesized through the diaminopimelate pathway and not through the α-aminoadipate pathway. Unexpected, the labeling patterns of glycine from the cells grown on [1-(13)C]pyruvate and [2-(13)C]pyruvate suggest that, unlike all the organisms investigated so far, in which glycine is produced exclusively from the serine hydroxymethyltransferase (SHMT) pathway, glycine biosynthesis in H. paucihalophilus involves different pathways including SHMT, threonine aldolase (TA) and the reverse reaction of glycine cleavage system (GCS), demonstrating for the first time that other pathways instead of SHMT can also make a significant contribution to the cellular glycine pool. Transcriptional analysis confirmed that both TA and GCS genes were transcribed in H. paucihalophilus, and the transcriptional level is independent of salt concentrations in the culture media. This study expands our understanding of amino acid biosynthesis and provides valuable insights into the metabolism of halophilic archaea.
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Affiliation(s)
- Guangxiu Liu
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou, 730000, China
| | - Manxiao Zhang
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou, 730000, China
| | - Tianlu Mo
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Lian He
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou, 730000, China
| | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Wei Ding
- Key Laboratory of Desert and Desertification, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou, 730000, China; Department of Chemistry, Fudan University, Shanghai, 200433, China.
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16
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Li S, Swanson SK, Gogol M, Florens L, Washburn MP, Workman JL, Suganuma T. Serine and SAM Responsive Complex SESAME Regulates Histone Modification Crosstalk by Sensing Cellular Metabolism. Mol Cell 2015; 60:408-21. [PMID: 26527276 DOI: 10.1016/j.molcel.2015.09.024] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 08/14/2015] [Accepted: 09/25/2015] [Indexed: 12/30/2022]
Abstract
Pyruvate kinase M2 (PKM2) is a key enzyme for glycolysis and catalyzes the conversion of phosphoenolpyruvate (PEP) to pyruvate, which supplies cellular energy. PKM2 also phosphorylates histone H3 threonine 11 (H3T11); however, it is largely unknown how PKM2 links cellular metabolism to chromatin regulation. Here, we show that the yeast PKM2 homolog, Pyk1, is a part of a novel protein complex named SESAME (Serine-responsive SAM-containing Metabolic Enzyme complex), which contains serine metabolic enzymes, SAM (S-adenosylmethionine) synthetases, and an acetyl-CoA synthetase. SESAME interacts with the Set1 H3K4 methyltransferase complex, which requires SAM synthesized from SESAME, and recruits SESAME to target genes, resulting in phosphorylation of H3T11. SESAME regulates the crosstalk between H3K4 methylation and H3T11 phosphorylation by sensing glycolysis and glucose-derived serine metabolism. This leads to auto-regulation of PYK1 expression. Thus, our study provides insights into the mechanism of regulating gene expression, responding to cellular metabolism via chromatin modifications.
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Affiliation(s)
- Shanshan Li
- Stowers Institute for Medical Research, 1000 E. 50(th) Street, Kansas City, MO 64110, USA
| | - Selene K Swanson
- Stowers Institute for Medical Research, 1000 E. 50(th) Street, Kansas City, MO 64110, USA
| | - Madelaine Gogol
- Stowers Institute for Medical Research, 1000 E. 50(th) Street, Kansas City, MO 64110, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, 1000 E. 50(th) Street, Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, 1000 E. 50(th) Street, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, 1000 E. 50(th) Street, Kansas City, MO 64110, USA
| | - Tamaki Suganuma
- Stowers Institute for Medical Research, 1000 E. 50(th) Street, Kansas City, MO 64110, USA.
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17
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Comparative proteomic analysis of engineered Saccharomyces cerevisiae with enhanced free fatty acid accumulation. Appl Microbiol Biotechnol 2015; 100:1407-1420. [PMID: 26450510 DOI: 10.1007/s00253-015-7028-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/13/2015] [Accepted: 09/20/2015] [Indexed: 01/27/2023]
Abstract
The engineered Saccharomyces cerevisiae strain △faa1△faa4 [Acot5s] was demonstrated to accumulate more free fatty acids (FFA) previously. Here, comparative proteomic analysis was performed to get a global overview of metabolic regulation in the strain. Over 500 proteins were identified, and 82 of those proteins were found to change significantly in the engineered strains. Proteins involved in glycolysis, acetate metabolism, fatty acid synthesis, TCA cycle, glyoxylate cycle, the pentose phosphate pathway, respiration, transportation, and stress response were found to be upregulated in △faa1△faa4 [Acot5s] as compared to the wild type. On the other hand, proteins involved in glycerol, ethanol, ergosterol, and cell wall synthesis were downregulated. Taken together with our metabolite analysis, our results showed that the disruption of Faa1 and Faa4 and expression of Acot5s in the engineered strain △faa1△faa4 [Acot5s] not only relieved the feedback inhibition of fatty acyl-CoAs on fatty acid synthesis, but also caused a major metabolic rearrangement. The rearrangement redirected carbon flux toward the pathways which generate the essential substrates and cofactors for fatty acid synthesis, such as acetyl-CoA, ATP, and NADPH. Therefore, our results help shed light on the mechanism for the increased production of fatty acids in the engineered strains, which is useful in providing information for future studies in biofuel production.
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18
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Liu G, Zhang M, Chen X, Zhang W, Ding W, Zhang Q. Evolution of Threonine Aldolases, a Diverse Family Involved in the Second Pathway of Glycine Biosynthesis. J Mol Evol 2015; 80:102-7. [DOI: 10.1007/s00239-015-9667-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 01/21/2015] [Indexed: 10/24/2022]
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Torto-Alalibo T, Purwantini E, Lomax J, Setubal JC, Mukhopadhyay B, Tyler BM. Genetic resources for advanced biofuel production described with the Gene Ontology. Front Microbiol 2014; 5:528. [PMID: 25346727 PMCID: PMC4193338 DOI: 10.3389/fmicb.2014.00528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/22/2014] [Indexed: 12/12/2022] Open
Abstract
Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary. The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology () project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. Here we review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.
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Affiliation(s)
- Trudy Torto-Alalibo
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Endang Purwantini
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Jane Lomax
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome CampusCambridge, UK
| | - João C. Setubal
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Department of Biological Sciences, Oregon State UniversityCorvallis, OR, USA
| | - Brett M. Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Center for Genome Research and Biocomputing, Oregon State UniversityCorvallis, OR, USA
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Suzuki T, Sugiyama M, Wakazono K, Kaneko Y, Harashima S. Lactic-acid stress causes vacuolar fragmentation and impairs intracellular amino-acid homeostasis in Saccharomyces cerevisiae. J Biosci Bioeng 2012; 113:421-30. [DOI: 10.1016/j.jbiosc.2011.11.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 10/20/2011] [Accepted: 11/09/2011] [Indexed: 11/24/2022]
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21
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High-level production of tetraacetyl phytosphingosine (TAPS) by combined genetic engineering of sphingoid base biosynthesis and L-serine availability in the non-conventional yeast Pichia ciferrii. Metab Eng 2012; 14:172-84. [DOI: 10.1016/j.ymben.2011.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 11/29/2011] [Accepted: 12/02/2011] [Indexed: 11/20/2022]
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22
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Chiba Y, Terada T, Kameya M, Shimizu K, Arai H, Ishii M, Igarashi Y. Mechanism for folate-independent aldolase reaction catalyzed by serine hydroxymethyltransferase. FEBS J 2011; 279:504-14. [PMID: 22141341 DOI: 10.1111/j.1742-4658.2011.08443.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serine hydroxymethyltransferase catalyzes the cleavage of β-hydroxyamino acids into glycine and aldehydes in the absence of tetrahydrofolate. The enzyme accepts various β-hydroxyamino acids as the substrate of this reaction. The reaction rate varies depending on the substituent and stereochemistry at the Cβ atom: the erythro forms and the β-phenyl substituent are preferred over the threo forms and the β-methyl substituent, respectively. Although several mechanisms have been proposed, what determines the substrate preference remains unclear. We first performed quantum mechanical calculations to assess the validity of the reaction mechanisms. The results indicate that the retro-aldol mechanism starting with abstraction of the proton from the β-hydroxyl group is plausible. This also suggests that Cα-Cβ bond cleavage is the rate-limiting step. We next measured the dependence of the rate constants on temperature with four representative substrates and calculated the activation energies and pre-exponential factors from the Arrhenius plots. The activation energies of the erythro forms were lower than those of the threo forms. The β-phenyl substituent lowered the activation energy in the threo form, whereas it did not alter the activation energy but increased the pre-exponential factor in the erythro form. We present a unified model to explain the origin of the substituent and stereochemical preferences by combining the theoretical and experimental results. A possible biological role of the tetrahydrofolate-independent activity in thermophiles is also discussed.
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Affiliation(s)
- Yoko Chiba
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
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Inositol phosphate kinase Vip1p interacts with histone chaperone Asf1p in Saccharomyces cerevisiae. Mol Biol Rep 2011; 39:4989-96. [PMID: 22160571 DOI: 10.1007/s11033-011-1295-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 11/30/2011] [Indexed: 12/25/2022]
Abstract
Histone eviction and deposition are critical steps in many nuclear processes. The histone H3/H4 chaperone Asf1p is highly conserved and is involved in DNA replication, DNA repair, and transcription. To identify the factors concerned with anti-silencing function 1 (ASF1), we purified Asf1p-associated factors from the yeast Saccharomyces cerevisiae by a GST pull-down experiment, and mass spectrometry analysis was performed. Several factors are specifically associated with Asf1p, including Vip1p. VIP1 is conserved from yeast to humans and encodes inositol hexakisphoshate and inositol heptakisphosphate kinase. Vip1p interacted with Asf1p as a dimer or in a complex with another protein(s). Deletion of VIP1 did not affect the interaction between Asf1p and other Asf1p-associated factors. An in vitro GST pull-down assay indicated a direct interaction between Asf1p and Vip1p, and the interaction between the two factors in vivo was detected by an immunoprecipitation experiment. Furthermore, genetic experiments revealed that VIP1 disruption increased sensitivity to 6-azauracil (6-AU), but not to DNA-damaging reagents in wild-type and ASF1-deleted strains. It is thought that 6-AU decreases nucleotide levels and reduces transcription elongation. These observations suggest that the association of Asf1p and Vip1p may be implicated in transcription elongation.
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Ji Y, Hebbring S, Zhu H, Jenkins GD, Biernacka J, Snyder K, Drews M, Fiehn O, Zeng Z, Schaid D, Mrazek DA, Kaddurah-Daouk R, Weinshilboum RM. Glycine and a glycine dehydrogenase (GLDC) SNP as citalopram/escitalopram response biomarkers in depression: pharmacometabolomics-informed pharmacogenomics. Clin Pharmacol Ther 2010; 89:97-104. [PMID: 21107318 DOI: 10.1038/clpt.2010.250] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Major depressive disorder (MDD) is a common psychiatric disease. Selective serotonin reuptake inhibitors (SSRIs) are an important class of drugs used in the treatment of MDD. However, many patients do not respond adequately to SSRI therapy. We used a pharmacometabolomics-informed pharmacogenomic research strategy to identify citalopram/escitalopram treatment outcome biomarkers. Metabolomic assay of plasma samples from 20 escitalopram remitters and 20 nonremitters showed that glycine was negatively associated with treatment outcome (P = 0.0054). This observation was pursued by genotyping tag single-nucleotide polymorphisms (SNPs) for genes encoding glycine synthesis and degradation enzymes, using 529 DNA samples from SSRI-treated MDD patients. The rs10975641 SNP in the glycine dehydrogenase (GLDC) gene was associated with treatment outcome phenotypes. Genotyping for rs10975641 was carried out in 1,245 MDD patients in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study, and its presence was significant (P = 0.02) in DNA taken from these patients. These results highlight a possible role for glycine in SSRI response and illustrate the use of pharmacometabolomics to "inform" pharmacogenomics.
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Affiliation(s)
- Y Ji
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
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25
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Jouhten P, Pitkänen E, Pakula T, Saloheimo M, Penttilä M, Maaheimo H. 13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose. BMC SYSTEMS BIOLOGY 2009; 3:104. [PMID: 19874611 PMCID: PMC2776023 DOI: 10.1186/1752-0509-3-104] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 10/29/2009] [Indexed: 11/17/2022]
Abstract
Background The filamentous fungus Trichoderma reesei is an important host organism for industrial enzyme production. It is adapted to nutrient poor environments where it is capable of producing large amounts of hydrolytic enzymes. In its natural environment T. reesei is expected to benefit from high energy yield from utilization of respirative metabolic pathway. However, T. reesei lacks metabolic pathway reconstructions and the utilization of the respirative pathway has not been investigated on the level of in vivo fluxes. Results The biosynthetic pathways of amino acids in T. reesei supported by genome-level evidence were reconstructed with computational carbon path analysis. The pathway reconstructions were a prerequisite for analysis of in vivo fluxes. The distribution of in vivo fluxes in both wild type strain and cre1, a key regulator of carbon catabolite repression, deletion strain were quantitatively studied by performing 13C-labeling on both repressive carbon source glucose and non-repressive carbon source sorbitol. In addition, the 13C-labeling on sorbitol was performed both in the presence and absence of sophorose that induces the expression of cellulase genes. Carbon path analyses and the 13C-labeling patterns of proteinogenic amino acids indicated high similarity between biosynthetic pathways of amino acids in T. reesei and yeast Saccharomyces cerevisiae. In contrast to S. cerevisiae, however, mitochondrial rather than cytosolic biosynthesis of Asp was observed under all studied conditions. The relative anaplerotic flux to the TCA cycle was low and thus characteristic to respiratory metabolism in both strains and independent of the carbon source. Only minor differences were observed in the flux distributions of the wild type and cre1 deletion strain. Furthermore, the induction of the hydrolytic gene expression did not show altered flux distributions and did not affect the relative amino acid requirements or relative anabolic and respirative activities of the TCA cycle. Conclusion High similarity between the biosynthetic pathways of amino acids in T. reesei and yeast S. cerevisiae was concluded. In vivo flux distributions confirmed that T. reesei uses primarily the respirative pathway also when growing on the repressive carbon source glucose in contrast to Saccharomyces cerevisiae, which substantially diminishes the respirative pathway flux under glucose repression.
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Affiliation(s)
- Paula Jouhten
- VTT Technical Research Centre of Finland, Espoo, Finland.
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Jander G, Joshi V. Aspartate-Derived Amino Acid Biosynthesis in Arabidopsis thaliana. THE ARABIDOPSIS BOOK 2009; 7:e0121. [PMID: 22303247 PMCID: PMC3243338 DOI: 10.1199/tab.0121] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The aspartate-derived amino acid pathway in plants leads to the biosynthesis of lysine, methionine, threonine, and isoleucine. These four amino acids are essential in the diets of humans and other animals, but are present in growth-limiting quantities in some of the world's major food crops. Genetic and biochemical approaches have been used for the functional analysis of almost all Arabidopsis thaliana enzymes involved in aspartate-derived amino acid biosynthesis. The branch-point enzymes aspartate kinase, dihydrodipicolinate synthase, homoserine dehydrogenase, cystathionine gamma synthase, threonine synthase, and threonine deaminase contain well-studied sites for allosteric regulation by pathway products and other plant metabolites. In contrast, relatively little is known about the transcriptional regulation of amino acid biosynthesis and the mechanisms that are used to balance aspartate-derived amino acid biosynthesis with other plant metabolic needs. The aspartate-derived amino acid pathway provides excellent examples of basic research conducted with A. thaliana that has been used to improve the nutritional quality of crop plants, in particular to increase the accumulation of lysine in maize and methionine in potatoes.
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Affiliation(s)
- Georg Jander
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853 USA
- Address correspondence to
| | - Vijay Joshi
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853 USA
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27
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Palumbo MC, Colosimo A, Giuliani A, Farina L. Essentiality is an emergent property of metabolic network wiring. FEBS Lett 2007; 581:2485-9. [PMID: 17493616 DOI: 10.1016/j.febslet.2007.04.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 04/20/2007] [Accepted: 04/20/2007] [Indexed: 11/15/2022]
Abstract
The topological bases of essentiality in the yeast metabolic network from the perspective of double mutations are the subject of this study. A strong relationship between essentiality and the 'missing alternative' topological property is shown in terms of the presence of multiple genes synthesizing the same enzyme, supplementary enzymes participating in the same metabolic reaction, and availability of other pathways in the graph connecting the separated nodes after the knockouts. We demonstrate that the 'missing alternative' paradigm is sufficient to explain the generation of essentiality for double mutations in which each single deleted element is non-essential.
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28
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Joshi V, Laubengayer KM, Schauer N, Fernie AR, Jander G. Two Arabidopsis threonine aldolases are nonredundant and compete with threonine deaminase for a common substrate pool. THE PLANT CELL 2006; 18:3564-75. [PMID: 17172352 PMCID: PMC1785404 DOI: 10.1105/tpc.106.044958] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Amino acids are not only fundamental protein constituents but also serve as precursors for many essential plant metabolites. Although amino acid biosynthetic pathways in plants have been identified, pathway regulation, catabolism, and downstream metabolite partitioning remain relatively uninvestigated. Conversion of Thr to Gly and acetaldehyde by Thr aldolase (EC 4.1.2.5) was only recently shown to play a role in plant amino acid metabolism. Whereas one Arabidopsis thaliana Thr aldolase (THA1) is expressed primarily in seeds and seedlings, the other (THA2) is expressed in vascular tissue throughout the plant. Metabolite profiling of tha1 mutants identified a >50-fold increase in the seed Thr content, a 50% decrease in seedling Gly content, and few other significant metabolic changes. By contrast, homozygous tha2 mutations cause a lethal albino phenotype. Rescue of tha2 mutants and tha1 tha2 double mutants by overproduction of feedback-insensitive Thr deaminase (OMR1) shows that Gly formation by THA1 and THA2 is not essential in Arabidopsis. Seed-specific expression of feedback-insensitive Thr deaminase in both tha1 and tha2 Thr aldolase mutants greatly increases seed Ile content, suggesting that these two Thr catabolic enzymes compete for a common substrate pool.
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Affiliation(s)
- Vijay Joshi
- Boyce Thompson Institute for Plant Research, Ithaca, New York 14853, USA
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29
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Lu P, Rangan A, Chan SY, Appling DR, Hoffman DW, Marcotte EM. Global metabolic changes following loss of a feedback loop reveal dynamic steady states of the yeast metabolome. Metab Eng 2006; 9:8-20. [PMID: 17049899 DOI: 10.1016/j.ymben.2006.06.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 05/27/2006] [Accepted: 06/20/2006] [Indexed: 11/16/2022]
Abstract
Metabolic enzymes control cellular metabolite concentrations dynamically in response to changing environmental and intracellular conditions. Such real-time feedback regulation suggests the global metabolome may sample distinct dynamic steady states, forming "basins of stability" in the energy landscape of possible metabolite concentrations and enzymatic activities. Using metabolite, protein and transcriptional profiling, we characterize three dynamic steady states of the yeast metabolome that form by perturbing synthesis of the universal methyl donor S-adenosylmethionine (AdoMet). Conversion between these states is driven by replacement of serine with glycine+formate in the media, loss of feedback inhibition control by the metabolic enzyme Met13, or both. The latter causes hyperaccumulation of methionine and AdoMet, and dramatic global compensatory changes in the metabolome, including differences in amino acid and sugar metabolism, and possibly in the global nitrogen balance, ultimately leading to a G1/S phase cell cycle delay. Global metabolic changes are not necessarily accompanied by global transcriptional changes, and metabolite-controlled post-transcriptional regulation of metabolic enzymes is clearly evident.
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Affiliation(s)
- Peng Lu
- Center for Systems and Synthetic Biology, University of Texas, 1 University Station, Austin, TX 78712-0159, USA
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30
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Subramanian M, Qiao WB, Khanam N, Wilkins O, Der SD, Lalich JD, Bognar AL. Transcriptional regulation of the one-carbon metabolism regulon in Saccharomyces cerevisiae by Bas1p. Mol Microbiol 2005; 57:53-69. [PMID: 15948949 DOI: 10.1111/j.1365-2958.2005.04663.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanisms mediating responses to glycine withdrawal in budding yeast were studied using a genome-wide profiling approach. A striking pattern of repressed expression of genes with an enrichment for those involved in one-carbon metabolism and AMP biosynthesis was revealed. Sequence analysis of the promoters for the most severely repressed genes identified a conserved sequence, TGACTC, a known binding site for the transcription factors Gcn4p and Bas1p. Loss of BAS1 abolished or significantly reduced the repression of these genes in response to glycine removal but this phenotype was much less apparent in the absence of BAS2 or GCN4. Addition of a Bas1p-LexA fusion protein to a strain with a LexAop-LacZ fusion showed a strong glycine effect both in a BAS2 and a bas2 background. A Bas1p-VP16 fusion protein activated expression in a bas1bas2 strain but no glycine effect was observed while a Bas1p-Bas2p fusion protein activated expression to a lesser extent with a slight stimulation by glycine. These results suggest that glycine affects Bas1p activation of transcription rather than DNA binding and that Bas2p is not required for this affect. Glycine withdrawal repressed many of the same genes as addition of adenine, a process known to be dependent on Bas1p. However, the glycine response is independent of adenine repression, because glycine regulation occurs normally in ade strains. We did not see any difference in the degree of stimulation by glycine in the presence or absence of adenine even in Ade+ strains. Glycine regulation was also found to be dependent on an intact SHM2 gene, which encodes cytoplasmic serine hydroxymethyltransferase. A reporter plasmid containing a DNA sequence from the GCV2 promoter which confers glycine regulation on heterologous genes was introduced into the yeast deletion set to screen for genes required for glycine regulation. A number of genes, including BAS1 were required for activation by glycine but only the SHM2 gene was required for repression in the absence of glycine. We also showed that regulation of the SHM2 promoter by glycine requires Bas1p but not Bas2p or Gcn4p using a beta-galactosidase reporter. The response of the promoter to glycine required an intact SHM2 gene but was restored in a shm2 strain by addition of formate to the medium.
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Affiliation(s)
- Mohan Subramanian
- Department of Medical Genetics and Microbiology, University of Toronto, Medical Sciences Building Room 4383, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
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31
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Edgar AJ. Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene. BMC Genomics 2005; 6:32. [PMID: 15757516 PMCID: PMC555945 DOI: 10.1186/1471-2164-6-32] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2004] [Accepted: 03/09/2005] [Indexed: 11/24/2022] Open
Abstract
Background There are three pathways of L-threonine catabolism. The enzyme L-threonine aldolase (TA) has been shown to catalyse the conversion of L-threonine to yield glycine and acetaldehyde in bacteria, fungi and plants. Low levels of TA enzymatic activity have been found in vertebrates. It has been suggested that any detectable activity is due to serine hydroxymethyltransferase and that mammals lack a genuine threonine aldolase. Results The 7-exon murine L-threonine aldolase gene (GLY1) is located on chromosome 11, spanning 5.6 kb. The cDNA encodes a 400-residue protein. The protein has 81% similarity with the bacterium Thermotoga maritima TA. Almost all known functional residues are conserved between the two proteins including Lys242 that forms a Schiff-base with the cofactor, pyridoxal-5'-phosphate. The human TA gene is located at 17q25. It contains two single nucleotide deletions, in exons 4 and 7, which cause frame-shifts and a premature in-frame stop codon towards the carboxy-terminal. Expression of human TA mRNA was undetectable by RT-PCR. In mice, TA mRNA was found at low levels in a range of adult tissues, being highest in prostate, heart and liver. In contrast, serine/threonine dehydratase, another enzyme that catabolises L-threonine, is expressed very highly only in the liver. Serine dehydratase-like 1, also was most abundant in the liver. In whole mouse embryos TA mRNA expression was low prior to E-15 increasing more than four-fold by E-17. Conclusion Mice, the western-clawed frog and the zebrafish have transcribed threonine aldolase/GLY1 genes, but the human homolog is a non-transcribed pseudogene. Serine dehydratase-like 1 is a putative L-threonine catabolising enzyme.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Chromosome Mapping
- Cloning, Molecular
- Codon, Terminator
- Computational Biology
- Crystallography, X-Ray
- DNA, Complementary/metabolism
- Embryo, Mammalian/metabolism
- Exons
- Gene Deletion
- Gene Expression Regulation, Developmental
- Glycine Hydroxymethyltransferase/genetics
- Glycine Hydroxymethyltransferase/metabolism
- Humans
- Liver/metabolism
- Lysine/chemistry
- Mice
- Molecular Sequence Data
- Open Reading Frames
- Protein Structure, Tertiary
- Pseudogenes
- Pyridoxal Phosphate/chemistry
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Species Specificity
- Time Factors
- Tissue Distribution
- Transcription, Genetic
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Affiliation(s)
- Alasdair J Edgar
- Department of Craniofacial Development, King's College, London, UK.
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32
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Jander G, Norris SR, Joshi V, Fraga M, Rugg A, Yu S, Li L, Last RL. Application of a high-throughput HPLC-MS/MS assay to Arabidopsis mutant screening; evidence that threonine aldolase plays a role in seed nutritional quality. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2004; 39:465-75. [PMID: 15255874 DOI: 10.1111/j.1365-313x.2004.02140.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Beyond their essential function as the building blocks of proteins, amino acids contribute to many aspects of plant biochemistry and physiology. Despite this, there are relatively large gaps in our understanding of the biochemical pathways and regulation of amino acid synthesis in plants. A rapid (1.5 min versus 20-90 min for standard methods) HPLC-MS/MS assay for separating 19 amino acids was developed for quantifying levels of free amino acids in plant tissue. This assay was used to determine the free amino acid content in the seeds of 10,000 randomly mutagenized Arabidopsis lines, and 322 Arabidopsis lines with increased levels of one or more amino acids were identified. The heritability of the mutant phenotype was confirmed for 43 lines with increased seed levels of the aspartate-derived amino acids Ile, Lys, Thr, or Met. Genetic mapping and DNA sequencing identified a mutation in an Arabidopsis threonine aldolase (AT1G08630, EC 4.1.2.5) as the cause of increased seed Thr levels in one mutant. The assay that was developed for this project has broad applicability to Arabidopsis and other plant species.
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Affiliation(s)
- Georg Jander
- Cereon Genomics, 45 Sidney Street, Cambridge, MA 02139, USA.
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33
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Alvarez-Vasquez F, Sims KJ, Hannun YA, Voit EO. Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models. J Theor Biol 2004; 226:265-91. [PMID: 14643642 DOI: 10.1016/j.jtbi.2003.08.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
For the first time, kinetic information from the literature was collected and used to construct integrative dynamical mathematical models of sphingolipid metabolism. One model was designed primarily with kinetic equations in the tradition of Michaelis and Menten whereas the other two models were designed as alternative power-law models within the framework of Biochemical Systems Theory. Each model contains about 50 variables, about a quarter of which are dependent (state) variables, while the others are independent inputs and enzyme activities that are considered constant. The models account for known regulatory signals that exert control over the pathway. Standard mathematical testing, repeated revisiting of the literature, and numerous rounds of amendments and refinements resulted in models that are stable and rather insensitive to perturbations in inputs or parameter values. The models also appear to be compatible with the modest amount of experimental experience that lends itself to direct comparisons. Even though the three models are based on different mathematical representations, they show dynamic responses to a variety of perturbations and changes in conditions that are essentially equivalent for small perturbations and similar for large perturbations. The kinetic information used for model construction and the models themselves can serve as a starting point for future analyses and refinements.
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Affiliation(s)
- Fernando Alvarez-Vasquez
- Department of Biometry and Epidemiology, Medical University of South Carolina, 303K Cannon place, 135 Cannon St, Charleston, SC 29425-2503, USA
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34
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Gelling CL, Piper MDW, Hong SP, Kornfeld GD, Dawes IW. Identification of a novel one-carbon metabolism regulon in Saccharomyces cerevisiae. J Biol Chem 2003; 279:7072-81. [PMID: 14645232 DOI: 10.1074/jbc.m309178200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glycine specifically induces genes encoding subunits of the glycine decarboxylase complex (GCV1, GCV2, and GCV3), and this is mediated by a fall in cytoplasmic levels of 5,10-methylenetetrahydrofolate caused by inhibition of cytoplasmic serine hydroxymethyltransferase. Here it is shown that this control system extends to genes for other enzymes of one-carbon metabolism and de novo purine biosynthesis. Northern analysis of the response to glycine demonstrated that the induction of the GCV genes and the induction of other amino acid metabolism genes are temporally distinct. The genome-wide response to glycine revealed that several other genes are rapidly co-induced with the GCV genes, including SHM2, which encodes cytoplasmic serine hydroxymethyltransferase. These results were refined by examining transcript levels in an shm2Delta strain (in which cytoplasmic 5,10-methylenetetrahydrofolate levels are reduced) and a met13Delta strain, which lacks the main methylenetetrahydrofolate reductase activity of yeast and is effectively blocked at consumption of 5,10-methylene tetrahydrofolate for methionine synthesis. Glycine addition also caused a substantial transient disturbance to metabolism, including a sequence of changes in induction of amino acid biosynthesis and respiratory chain genes. Analysis of the glycine response in the shm2Delta strain demonstrated that apart from the one-carbon regulon, most of these transient responses were not contingent on a disturbance to one-carbon metabolism. The one-carbon response is distinct from the Bas1p purine biosynthesis regulon and thus represents the first example of transcriptional regulation in response to activated one-carbon status.
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Affiliation(s)
- Cristy L Gelling
- Ramaciotti Centre for Gene Function Analysis and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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35
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Yang Y, Meier UT. Genetic interaction between a chaperone of small nucleolar ribonucleoprotein particles and cytosolic serine hydroxymethyltransferase. J Biol Chem 2003; 278:23553-60. [PMID: 12700234 DOI: 10.1074/jbc.m300695200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Srp40p is a nonessential yeast nucleolar protein proposed to function as a chaperone for over 100 small nucleolar ribonucleoprotein particles that are required for rRNA maturation. To verify and expand on its function, genetic screens were performed for the identification of genes that were lethal when mutated in a SRP40 null background (srp40Delta). Unexpectedly, mutation of both cytosolic serine hydroxymethyltransferase (SHM2) and one-carbon tetrahydrofolate synthase (ADE3) was required to achieve synthetic lethality with srp40Delta. Shm2p and Ade3p are cytoplasmic enzymes producing 5,10-methylene tetrahydrofolate in convergent pathways as the primary source for cellular one-carbon groups. Nonetheless, point mutants of Shm2p that were catalytically inactive (i.e. failed to rescue the methionine auxotrophy of a shm2Delta ade3 strain) complemented the synthetic lethal phenotype, thus revealing a novel metabolism-independent function of Shm2p. The same Shm2p mutants exacerbated a giant cell phenotype observed in the shm2Delta ade3 strain suggesting a catalysis-independent role for Shm2p in cell size control, possibly through regulation of ribosome biogenesis via SRP40. Additionally, we show that the Sm-like protein Lsm5p, which as part of Lsm complexes participates in cytosolic and nuclear RNA processing and degradation pathways, is a multicopy suppressor of the synthetic lethality and of the specific depletion of box H/ACA small nucleolar RNAs from the srp40Delta shm2 ade3 strain. Finally, rat Nopp140 restored growth and stability of box H/ACA snoRNAs after genetic depletion of SRP40 in the synthetic lethal strain indicating that it is indeed the functional homolog of yeast Srp40p.
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Affiliation(s)
- Yunfeng Yang
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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36
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Koren A, Ben-Aroya S, Steinlauf R, Kupiec M. Pitfalls of the synthetic lethality screen in Saccharomyces cerevisiae: an improved design. Curr Genet 2003; 43:62-9. [PMID: 12684846 DOI: 10.1007/s00294-003-0373-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2002] [Revised: 12/19/2002] [Accepted: 12/19/2002] [Indexed: 10/25/2022]
Abstract
The colony color assay in yeast enables the visual identification of plasmid-loss events. In combination with a plasmid-dependence assay, it is commonly used to identify synthetic interactions between functionally related genes. Frequently, the plasmid carries the ADE3 gene and mutants are recognized as red colonies that fail to produce sectors. In these assays, a high percentage of false-positives is obtained, most of which result from synthetic lethality with the ade3 mutation. Here, we study the nature of these mutants. We report that mutations in the HIP1 and SHM1 genes exhibit synthetic lethality with ade3 deletions. A similar interaction is found between the fur1 and ura3 mutations. Lethality in the absence of the mitochondrial Shm1 and the cytoplasmic Ade3 enzymes indicates that, under certain circumstances, these cellular compartments cooperate in carrying out essential metabolic processes. In addition, we report the identification of a truncated ADE3 allele with a unique coloration phenotype and show that it can be used to improve synthetic lethal screens.
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Affiliation(s)
- Amnon Koren
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Ramat Aviv, Israel
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37
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Kielkopf CL, Burley SK. X-ray Structures of Threonine Aldolase Complexes: Structural Basis of Substrate Recognition†,‡. Biochemistry 2002; 41:11711-20. [PMID: 12269813 DOI: 10.1021/bi020393+] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
L-Threonine acetaldehyde-lyase (threonine aldolase, TA) is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a secondary glycine biosynthetic pathway. X-ray structures of Thermatoga maritima TA have been determined as the apo-enzyme at 1.8 A resolution and bound to substrate L-allo-threonine and product glycine at 1.9 and 2.0 A resolution, respectively. Despite low pairwise sequence identities, TA is a member of aspartate aminotransferase (AATase) fold family of PLP enzymes. The enzyme forms a 222 homotetramer with the PLP cofactor bound via a Schiff-base linkage to Lys199 within a domain interface. The structure reveals bound calcium and chloride ions that appear to contribute to catalysis and oligomerization, respectively. Although L-threonine and L-allo-threonine are substrates for T. maritima TA, enzymatic assays revealed a strong preference for L-allo-threonine. Structures of the external aldimines with substrate/product reveal a pair of histidines that may provide flexibility in substrate recognition. Variation in the threonine binding pocket may explain preferences for L-allo-threonine versus L-threonine among TA family members.
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Affiliation(s)
- Clara L Kielkopf
- Laboratories of Molecular Biophysics and Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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38
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Ramesh V, Köhrer C, RajBhandary UL. Expression of Escherichia coli methionyl-tRNA formyltransferase in Saccharomyces cerevisiae leads to formylation of the cytoplasmic initiator tRNA and possibly to initiation of protein synthesis with formylmethionine. Mol Cell Biol 2002; 22:5434-42. [PMID: 12101237 PMCID: PMC133937 DOI: 10.1128/mcb.22.15.5434-5442.2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Protein synthesis in eukaryotic cytoplasm and in archaebacteria is initiated with methionine, whereas, that in eubacteria and in eukaryotic organelles, such as mitochondria and chloroplasts, is initiated with formylmethionine. In view of this clear distinction, we have investigated whether protein synthesis in the eukaryotic cytoplasm can be initiated with formylmethionine, and, if so, what the consequences are to the cell. For this purpose, we have expressed in an inducible manner the Escherichia coli methionyl-tRNA formyltransferase (MTF) in the cytoplasm of the yeast Saccharomyces cerevisiae. Expression of active MTF, but not of an inactive mutant, leads to formylation of methionine attached to the yeast cytoplasmic initiator tRNA to the extent of about 70%. As a consequence, the yeast strain grows slowly. Coexpression of the E. coli polypeptide deformylase (DEF), which removes the formyl group from the N-terminal formylmethionine in a polypeptide, rescues the slow-growth phenotype, whereas, coexpression of an inactive mutant of DEF does not. These results suggest that the cytoplasmic protein-synthesizing system of yeast, like that of eubacteria, can at least to some extent utilize formylated initiator Met-tRNA to initiate protein synthesis and that initiation of proteins with formylmethionine leads to the slow-growth phenotype. Removal of the formyl group in these proteins by DEF would explain the rescue of the slow-growth phenotype.
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Affiliation(s)
- Vaidyanathan Ramesh
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Holmes WB, Appling DR. Cloning and characterization of methenyltetrahydrofolate synthetase from Saccharomyces cerevisiae. J Biol Chem 2002; 277:20205-13. [PMID: 11923304 DOI: 10.1074/jbc.m201242200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The folate derivative 5-formyltetrahydrofolate (folinic acid; 5-CHO-THF) was discovered over 40 years ago, but its role in metabolism remains poorly understood. Only one enzyme is known that utilizes 5-CHO-THF as a substrate: 5,10-methenyltetrahydrofolate synthetase (MTHFS). A BLAST search of the yeast genome using the human MTHFS sequence revealed a 211-amino acid open reading frame (YER183c) with significant homology. The yeast enzyme was expressed in Escherichia coli, and the purified recombinant enzyme exhibited kinetics similar to previously purified MTHFS. No new phenotype was observed in strains disrupted at MTHFS or in strains additionally disrupted at the genes encoding one or both serine hydroxymethyltransferases (SHMT) or at the genes encoding one or both methylenetetrahydrofolate reductases. However, when the MTHFS gene was disrupted in a strain lacking the de novo folate biosynthesis pathway, folinic acid (5-CHO-THF) could no longer support the folate requirement. We have thus named the yeast gene encoding methenyltetrahydrofolate synthetase FAU1 (folinic acid utilization). Disruption of the FAU1 gene in a strain lacking both 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase isozymes (ADE16 and ADE17) resulted in a growth deficiency that was alleviated by methionine. Genetic analysis suggested that intracellular accumulation of the purine intermediate AICAR interferes with a step in methionine biosynthesis. Intracellular levels of 5-CHO-THF were determined in yeast disrupted at FAU1 and other genes encoding folate-dependent enzymes. In fau1 disruptants, 5-CHO-THF was elevated 4-fold over wild-type yeast. In yeast lacking MTHFS along with both AICAR transformylases, 5-CHO-THF was elevated 12-fold over wild type. 5-CHO-THF was undetectable in strains lacking SHMT activity, confirming SHMT as the in vivo source of 5-CHO-THF. Taken together, these results indicate that S. cerevisiae harbors a single, nonessential, MTHFS activity. Growth phenotypes of multiply disrupted strains are consistent with a regulatory role for 5-CHO-THF in one-carbon metabolism and additionally suggest a metabolic interaction between the purine and methionine pathways.
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Affiliation(s)
- William B Holmes
- Department of Chemistry and Biochemistry, the Institute for Cellular and Molecular Biology, and the Biochemical Institute, University of Texas, Austin 78712, USA
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Woldman Y, Appling DR. A general method for determining the contribution of split pathways in metabolite production in the yeast Saccharomyces cerevisiae. Metab Eng 2002; 4:170-81. [PMID: 12009796 DOI: 10.1006/mben.2001.0221] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe a simple method using (13)C labeling and NMR spectroscopy to determine the flux contributions of alternative pathways in Saccharomyces cerevisiae that produce the same metabolite with identical labeling patterns. Cells were incubated with a (13)C-labeled precursor for one of the branches, and the absolute enrichment of the product and its metabolic precursor(s) was quantified. The ratio of the absolute enrichment of the product to that of its precursor reflects the contribution of the pathway. The method was applied to the biosynthesis of glycine in yeast, which can occur from threonine via threonine aldolase or from serine via serine hydroxymethyltransferase. [2-(13)C]Aspartate and [2-(13)C]serine were used as labeled precursors for the threonine aldolase and serine hydroxymethyltransferase pathways, respectively. The data show that in cells possessing both pathways, the serine hydroxymethyltransferase pathway contributes 65-75% of the total glycine production. In comparison with other approaches, this method provides an inexpensive, flexible alternative to determining the flux contributions of split pathways under controlled conditions and should have wide applicability in the metabolic engineering of microorganisms.
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Affiliation(s)
- Yakov Woldman
- Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
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41
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Nigavekar SS, Cannon JF. Characterization of genes that are synthetically lethal with ade3 or leu2 in Saccharomyces cerevisiae. Yeast 2002; 19:115-22. [PMID: 11788966 DOI: 10.1002/yea.807] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Combinations of two non-lethal mutations that result in cell death are synthetically lethal. Such a genetic relationship suggests a functional interaction between the corresponding gene products. Frequently, an ade2 ade3 colony-sectoring assay is used to screen for synthetic lethal mutants. In these screens, mutants are sought that fail to lose a plasmid that bears a gene of interest. However, a subset of mutants is often found that is dependent on plasmid components other than the target gene. To understand the mechanism of this dependence, we characterized those mutants that, although prevalent in most mutant hunts, are usually discarded. Using a LEU2-ADE3 plasmid, plasmid-dependent mutations were found in the SHM2, PTR3, BAP2 and SSY1 genes. Double shm2 ade3 mutants are non-viable because the two pathways for tetrahydrofolate synthesis are blocked. Mutations in PTR3, BAP2 and SSY1 disrupt sensing and transport of extracellular leucine. Therefore, ptr3, bap2 or ssy1 mutants must be leucine prototrophs to grow on rich media. In light of these findings, we propose modifications that should improve the efficiency of synthetic lethal screening procedures.
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Affiliation(s)
- Shraddha S Nigavekar
- Department of Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO 65212, USA
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42
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Lim SH, Choi JS, Park EY. Microbial production of riboflavin using riboflavin overproducers,Ashbya gossypii, Bacillus subtilis, andCandida famate: An overview. BIOTECHNOL BIOPROC E 2001. [DOI: 10.1007/bf02931951] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Maaheimo H, Fiaux J, Cakar ZP, Bailey JE, Sauer U, Szyperski T. Central carbon metabolism of Saccharomyces cerevisiae explored by biosynthetic fractional (13)C labeling of common amino acids. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:2464-79. [PMID: 11298766 DOI: 10.1046/j.1432-1327.2001.02126.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Aerobic and anaerobic central metabolism of Saccharomyces cerevisiae cells was explored in batch cultures on a minimal medium containing glucose as the sole carbon source, using biosynthetic fractional (13)C labeling of proteinogenic amino acids. This allowed, firstly, unravelling of the network of active central pathways in cytosol and mitochondria, secondly, determination of flux ratios characterizing glycolysis, pentose phosphate cycle, tricarboxylic acid cycle and C1-metabolism, and thirdly, assessment of intercompartmental transport fluxes of pyruvate, acetyl-CoA, oxaloacetate and glycine. The data also revealed that alanine aminotransferase is located in the mitochondria, and that amino acids are synthesized according to documented pathways. In both the aerobic and the anaerobic regime: (a) the mitochondrial glycine cleavage pathway is active, and efflux of glycine into the cytosol is observed; (b) the pentose phosphate pathways serve for biosynthesis only, i.e. phosphoenolpyruvate is entirely generated via glycolysis; (c) the majority of the cytosolic oxaloacetate is synthesized via anaplerotic carboxylation of pyruvate; (d) the malic enzyme plays a key role for mitochondrial pyruvate metabolism; (e) the transfer of oxaloacetate from the cytosol to the mitochondria is largely unidirectional, and the activity of the malate-aspartate shuttle and the succinate-fumarate carrier is low; (e) a large fraction of the mitochondrial pyruvate is imported from the cytosol; and (f) the glyoxylate cycle is inactive. In the aerobic regime, 75% of mitochondrial oxaloacetate arises from anaplerotic carboxylation of pyruvate, while in the anaerobic regime, the tricarboxylic acid cycle is operating in a branched fashion to fulfill biosynthetic demands only. The present study shows that fractional (13)C labeling of amino acids represents a powerful approach to study compartmented eukaryotic systems.
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Affiliation(s)
- H Maaheimo
- Department of Chemistry, University at Buffalo, The State University of New York, NY, USA
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Gombert AK, Moreira dos Santos M, Christensen B, Nielsen J. Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J Bacteriol 2001; 183:1441-51. [PMID: 11157958 PMCID: PMC95019 DOI: 10.1128/jb.183.4.1441-1451.2001] [Citation(s) in RCA: 277] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2000] [Accepted: 11/23/2000] [Indexed: 11/20/2022] Open
Abstract
The network structure and the metabolic fluxes in central carbon metabolism were characterized in aerobically grown cells of Saccharomyces cerevisiae. The cells were grown under both high and low glucose concentrations, i.e., either in a chemostat at steady state with a specific growth rate of 0.1 h(-1) or in a batch culture with a specific growth rate of 0.37 h(-1). Experiments were carried out using [1-(13)C]glucose as the limiting substrate, and the resulting summed fractional labelings of intracellular metabolites were measured by gas chromatography coupled to mass spectrometry. The data were used as inputs to a flux estimation routine that involved appropriate mathematical modelling of the central carbon metabolism of S. cerevisiae. The results showed that the analysis is very robust, and it was possible to quantify the fluxes in the central carbon metabolism under both growth conditions. In the batch culture, 16.2 of every 100 molecules of glucose consumed by the cells entered the pentose-phosphate pathway, whereas the same relative flux was 44.2 per 100 molecules in the chemostat. The tricarboxylic acid cycle does not operate as a cycle in batch-growing cells, in contrast to the chemostat condition. Quantitative evidence was also found for threonine aldolase and malic enzyme activities, in accordance with published data. Disruption of the MIG1 gene did not cause changes in the metabolic network structure or in the flux pattern.
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Affiliation(s)
- A K Gombert
- Center for Process Biotechnology, Department of Biotechnology, Technical University of Denmark, DK-2800, Lyngby, Denmark
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45
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Snell K, Baumann U, Byrne PC, Chave KJ, Renwick SB, Sanders PG, Whitehouse SK. The genetic organization and protein crystallographic structure of human serine hydroxymethyltransferase. ADVANCES IN ENZYME REGULATION 2000; 40:353-403. [PMID: 10828359 DOI: 10.1016/s0065-2571(99)00035-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- K Snell
- Section of Structural Biology, Institute of Cancer Research, University of London, SW7 3RP, London, UK.
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46
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Dickert S, Pierik AJ, Linder D, Buckel W. The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cinnamate by Clostridium sporogenes. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:3874-84. [PMID: 10849007 DOI: 10.1046/j.1432-1327.2000.01427.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phenyllactate dehydratase from Clostridium sporogenes grown anaerobically on L-phenylalanine catalyses the reversible syn-dehydration of (R)-phenyllactate to (E)-cinnamate. Purification yielded a heterotrimeric enzyme complex (130 +/- 15 kDa) composed of FldA (46 kDa), FldB (43 kDa) and FldC (40 kDa). By re-chromatography on Q-Sepharose, the major part of FldA could be separated and identified as oxygen insensitive cinnamoyl-CoA:phenyllactate CoA-transferase, whereas the transferase depleted trimeric complex retained oxygen sensitive phenyllactate dehydratase activity and contained about one [4Fe-4S] cluster. The dehydratase activity required 10 microM FAD, 0.4 mM ATP, 2.5 mM MgCl2, 0.1 mM NADH, 5 microM cinnamoyl-CoA and small amounts of cell-free extract (10 microg protein per mL) similar to that known for 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. The N-terminus of the homogenous FldA (39 amino acids) is homologous to that of CaiB (39% sequence identity) involved in carnitine metabolism in Escherichia coli. Both enzymes are members of an emerging group of CoA-transferases which exhibit high substrate specificity but apparently do not form enzyme CoA-ester intermediates. It is concluded that dehydration of (R)-phenyllactate to (E)-cinnamate proceeds in two steps, a CoA-transfer from cinnamoyl-CoA to phenyllactate, catalysed by FldA, followed by the dehydration of phenyllactyl-CoA, catalysed by FldB and FldC, whereby the noncovalently bound prosthetic group cinnamoyl-CoA is regenerated. This demonstrates the necessity of a 2-hydroxyacyl-CoA intermediate in the dehydration of 2-hydroxyacids. The transient CoA-ester formation during the dehydration of phenyllactate resembles that during citrate cleavage catalysed by bacterial citrate lyase, which contain a derivative of acetyl-CoA covalently bound to an acyl-carrier-protein (ACP).
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Affiliation(s)
- S Dickert
- Laboratorium für Mikrobiologie, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
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47
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McClung CR, Hsu M, Painter JE, Gagne JM, Karlsberg SD, Salomé PA. Integrated temporal regulation of the photorespiratory pathway. Circadian regulation of two Arabidopsis genes encoding serine hydroxymethyltransferase. PLANT PHYSIOLOGY 2000; 123:381-92. [PMID: 10806255 PMCID: PMC59012 DOI: 10.1104/pp.123.1.381] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/1999] [Accepted: 01/18/2000] [Indexed: 05/18/2023]
Abstract
The photorespiratory pathway is comprised of enzymes localized within three distinct cellular compartments: chloroplasts, peroxisomes, and mitochondria. Photorespiratory enzymes are encoded by nuclear genes, translated in the cytosol, and targeted into these distinct subcellular compartments. One likely means by which to regulate the expression of the genes encoding photorespiratory enzymes is coordinated temporal control. We have previously shown in Arabidopsis that a circadian clock regulates the expression of the nuclear genes encoding both chloroplastic (Rubisco small subunit and Rubisco activase) and peroxisomal (catalase) components of the photorespiratory pathway. To determine whether a circadian clock also regulates the expression of genes encoding mitochondrial components of the photorespiratory pathway, we characterized a family of Arabidopsis serine hydroxymethyltransferase (SHM) genes. We examined mRNA accumulation for two of these family members, including one probable photorespiratory gene (SHM1) and a second gene expressed maximally in roots (SHM4), and show that both exhibit circadian oscillations in mRNA abundance that are in phase with those described for other photorespiratory genes. In addition, we show that SHM1 mRNA accumulates in light-grown seedlings, although this response is probably an indirect consequence of the induction of photosynthesis and photorespiration by illumination.
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Affiliation(s)
- C R McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755-3576, USA.
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48
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DeSouza L, Shen Y, Bognar AL. Disruption of cytoplasmic and mitochondrial folylpolyglutamate synthetase activity in Saccharomyces cerevisiae. Arch Biochem Biophys 2000; 376:299-312. [PMID: 10775416 DOI: 10.1006/abbi.2000.1741] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Similar to other eukaryotes, yeasts have parallel pathways of one-carbon metabolism in the cytoplasm and mitochondria and have folylpolyglutamate synthetase activity in both compartments. The gene encoding folylpolyglutamate synthetase is MET7 (also referred to as MET23) on chromosome XV and appears to encode both the cytoplasmic and mitochondrial forms of the enzyme. In order to determine the metabolic roles of both forms of folylpolyglutamate synthetase, we disrupted the met7 gene and determined that the strain is a methionine auxotroph and an adenine and thymidine auxotroph when grown in the presence of sulfanilamide. The met7 mutant becomes petite under normal growth conditions but can be maintained with a grande phenotype if the strain is tup and all media are supplemented with dTMP. A met7 gly1 strain is auxotrophic for glycine when grown on glucose but prototrophic when grown on glycerol. A met7 ser1 strain cannot use glycine to suppress the serine auxotrophy of the ser1 phenotype. A met7 shm2 strain is nonviable. In order to disrupt just the mitochondrial folylpolyglutamate synthetase activity, we constructed mutants with an inactivated chromosomal MET7 gene complemented by genes that express only cytoplasmic folylpolyglutamate synthetase, including the Lactobacillus casei folC gene and the yeast MET7 gene with its mitochondrial leader sequence deleted (MET7Deltam). All the genes providing cytoplasmic folylpolyglutamate synthetase complemented the methionine auxotrophy as well as the synthetic lethality of the shm2 strain and the synthetic glycine auxotrophy of the gly1 strain. The strains lacking the mitochondrial folylpolyglutamate synthetase had longer doubling times than the isogenic wild-type strains but retained the function of the mitochondrial folate-dependent enzymes to produce formate, serine, and glycine. Mutants complemented by the bacterial folC gene or by the MET7Deltam gene on a 2mu plasmid remained grande without the tup mutation and supplementation and dTMP. Mutants complemented by the MET7Deltam gene integrated in single copy became petites under those conditions, indicating a deficiency in dTMP production but this is likely due to lower expression of cytoplasmic folylpolyglutamate synthetase by the MET7Deltam gene.
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Affiliation(s)
- L DeSouza
- Department of Medical Genetics and Microbiology, Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
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Rao NA, Talwar R, Savithri HS. Molecular organization, catalytic mechanism and function of serine hydroxymethyltransferase--a potential target for cancer chemotherapy. Int J Biochem Cell Biol 2000; 32:405-16. [PMID: 10762066 DOI: 10.1016/s1357-2725(99)00126-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Serine hydroxymethyltransferase, a pyridoxal-5'-phosphate dependent enzyme, catalyzes the retro-aldol cleavage of serine to yield glycine and the hydroxymethyl group is transferred to 5,6,7,8-tetrahydrofolate to generate 5,10-methylene-H4-folate. The enzyme plays a pivotal role in channeling metabolites between amino acid and nucleotide metabolism. Dihydrofolate reductase and thymidylate synthase have been favorite targets for the development of anticancer drugs. However, development of resistance to drugs, due to a variety of reasons, has necessitated the identification of alternate targets for cancer chemotherapy and serine hydroxymethyltransferase is one such potential target. A detailed study of the kinetics of interaction of serine and folate analogs with this enzyme revealed several unique features that can be exploited for the design of new chemotherapeutic agents. The pathways for the reversible unfolding of the dimeric Escherichia coli and the tetrameric sheep liver enzyme, although different, revealed a requirement for the cofactor in the final step for generating an active enzyme. The gly A gene of Escherichia coli has been shown to code for this enzyme. Analysis of available gene sequences indicate that serine hydroxymethyltransferase is one of the most highly conserved proteins. The isolation of the cDNA clones for the enzyme and their overexpression in heterologous systems has enabled the probing of the molecular mechanisms of catalysis and the role of lysine, arginine and histidine in cofactor, substrate(s) binding and in maintaining the structure of the protein. Recently, the three-dimensional structure of the human liver serine hydroxymethyltransferase has been published. This, along with the information already available, provides a framework for the rational design of drugs targeted specifically towards this enzyme.
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Affiliation(s)
- N A Rao
- Department of Biochemistry, Indian Institute of Science, Bangalore
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50
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Ogawa H, Gomi T, Fujioka M. Serine hydroxymethyltransferase and threonine aldolase: are they identical? Int J Biochem Cell Biol 2000; 32:289-301. [PMID: 10716626 DOI: 10.1016/s1357-2725(99)00113-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Serine hydroxymethyltransferase, a pyridoxal phosphate-dependent enzyme, catalyses the interconversion of serine and glycine, both of which are major sources of one-carbon units necessary for the synthesis of purine, thymidylate, methionine, and so on. Threonine aldolase catalyzes the pyridoxal phosphate-dependent, reversible reaction between threonine and acetaldehyde plus glycine. No extensive studies have been carried out on threonine aldolase in animal tissues, and it has long been believed that serine hydroxymethyltransferase and threonine aldolase are the same, i.e. one entity. This is based on the finding that rabbit liver serine hydroxymethyltransferase possesses some threonine aldolase activity. Recently, however, many kinds of threonine aldolase and corresponding genes were isolated from micro-organisms, and these enzymes were shown to be distinct from serine hydroxymethyltransferase. The experiments with isolated hepatocytes and cell-free extracts from various animals revealed that threonine is degraded mainly through the pathway initiated by threonine 3-dehydrogenase, and there is little or no contribution by threonine aldolase. Thus, although serine hydroxymethyltransferase from some mammalian livers exhibits a low threonine aldolase activity, the two enzymes are distinct from each other and mammals lack the "genuine" threonine aldolase.
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Affiliation(s)
- H Ogawa
- Department of Biochemistry, Faculty of Medicine, Toyama Medical and Pharmaceutical University, Japan.
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