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Berkvens A, Salinas L, Remeijer M, Planqué R, Teusink B, Bruggeman FJ. Understanding and computational design of genetic circuits of metabolic networks. Essays Biochem 2024; 68:41-51. [PMID: 38662439 PMCID: PMC11065555 DOI: 10.1042/ebc20230045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 05/01/2024]
Abstract
The expression of metabolic proteins is controlled by genetic circuits, matching metabolic demands and changing environmental conditions. Ideally, this regulation brings about a competitive level of metabolic fitness. Understanding how cells can achieve a robust (close-to-optimal) functioning of metabolism by appropriate control of gene expression aids synthetic biology by providing design criteria of synthetic circuits for biotechnological purposes. It also extends our understanding of the designs of genetic circuitry found in nature such as metabolite control of transcription factor activity, promoter architectures and transcription factor dependencies, and operon composition (in bacteria). Here, we review, explain and illustrate an approach that allows for the inference and design of genetic circuitry that steers metabolic networks to achieve a maximal flux per unit invested protein across dynamic conditions. We discuss how this approach and its understanding can be used to rationalize Escherichia coli's strategy to regulate the expression of its ribosomes and infer the design of circuitry controlling gene expression of amino-acid biosynthesis enzymes. The inferred regulation indeed resembles E. coli's circuits, suggesting that these have evolved to maximize amino-acid production fluxes per unit invested protein. We end by an outlook of the use of this approach in metabolic engineering applications.
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Affiliation(s)
- Alicia Berkvens
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
| | - Luis Salinas
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
| | - Maaike Remeijer
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
| | - Robert Planqué
- Department of Mathematics, Amsterdam Center for Dynamics and Computation, VU University, Amsterdam, NL
| | - Bas Teusink
- Systems Biology Lab, A-LIFE, AIMMS, VU University, Amsterdam, NL
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2
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Coltman BL, Rebnegger C, Gasser B, Zanghellini J. Characterising the metabolic rewiring of extremely slow growing Komagataella phaffii. Microb Biotechnol 2024; 17:e14386. [PMID: 38206275 PMCID: PMC10832545 DOI: 10.1111/1751-7915.14386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 01/12/2024] Open
Abstract
Retentostat cultivations have enabled investigations into substrate-limited near-zero growth for a number of microbes. Quantitative physiology at these near-zero growth conditions has been widely discussed, yet characterisation of the fluxome is relatively under-reported. We investigated the rewiring of metabolism in the transition of a recombinant protein-producing strain of Komagataella phaffii to glucose-limited near-zero growth rates. We used cultivation data from a 200-fold range of growth rates and comprehensive biomass composition data to integrate growth rate dependent biomass equations, generated using a number of different approaches, into a K. phaffii genome-scale metabolic model. Here, we show that a non-growth-associated maintenance value of 0.65 mmol ATP g CDW - 1 h - 1 and a growth-associated maintenance value of 108 mmol ATP g CDW - 1 lead to accurate growth rate predictions. In line with its role as energy source, metabolism is rewired to increase the yield of ATP per glucose. This includes a reduction of flux through the pentose phosphate pathway, and a greater utilisation of glycolysis and the TCA cycle. Interestingly, we observed activity of an external, non-proton translocating NADH dehydrogenase in addition to the malate-aspartate shuttle. Regardless of the method used for the generation of biomass equations, a similar, yet different, growth rate dependent rewiring was predicted. As expected, these differences between the different methods were clearer at higher growth rates, where the biomass equation provides a much greater constraint than at slower growth rates. When placed on an increasingly limited glucose diet, the metabolism of K. phaffii adapts, enabling it to continue to drive critical processes sustaining its high viability at near-zero growth rates.
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Affiliation(s)
- Benjamin Luke Coltman
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
| | - Corinna Rebnegger
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Brigitte Gasser
- CD‐Laboratory for Growth‐decoupled Protein Production in Yeast at Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Department of Biotechnology, Institute of Microbiology and Microbial BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Jürgen Zanghellini
- Austrian Centre of Industrial BiotechnologyViennaAustria
- Department of Analytical ChemistryUniversity of ViennaViennaAustria
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Alfatah M, Cui L, Goh CJH, Cheng TYN, Zhang Y, Naaz A, Wong JH, Lewis J, Poh WJ, Arumugam P. Metabolism of glucose activates TORC1 through multiple mechanisms in Saccharomyces cerevisiae. Cell Rep 2023; 42:113205. [PMID: 37792530 DOI: 10.1016/j.celrep.2023.113205] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/30/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Target of Rapamycin Complex 1 (TORC1) is a conserved eukaryotic protein complex that links the presence of nutrients with cell growth. In Saccharomyces cerevisiae, TORC1 activity is positively regulated by the presence of amino acids and glucose in the medium. However, the mechanisms underlying nutrient-induced TORC1 activation remain poorly understood. By utilizing an in vivo TORC1 activation assay, we demonstrate that differential metabolism of glucose activates TORC1 through three distinct pathways in yeast. The first "canonical Rag guanosine triphosphatase (GTPase)-dependent pathway" requires conversion of glucose to fructose 1,6-bisphosphate, which activates TORC1 via the Rag GTPase heterodimer Gtr1GTP-Gtr2GDP. The second "non-canonical Rag GTPase-dependent pathway" requires conversion of glucose to glucose 6-phosphate, which activates TORC1 via a process that involves Gtr1GTP-Gtr2GTP and mitochondrial function. The third "Rag GTPase-independent pathway" requires complete glycolysis and vacuolar ATPase reassembly for TORC1 activation. We have established a roadmap to deconstruct the link between glucose metabolism and TORC1 activation.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore.
| | - Liang Cui
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore 138602, Singapore
| | - Corinna Jie Hui Goh
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore
| | | | - Yizhong Zhang
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore
| | - Arshia Naaz
- Genome Institute of Singapore, A(∗)STAR, 60 Biopolis Street, Genome #02-01, Singapore 138672, Singapore
| | - Jin Huei Wong
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore
| | - Jacqueline Lewis
- Institute of Molecular and Cellular Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Wei Jie Poh
- Bioinformatics Institute, A(∗)STAR, 30 Biopolis Street, Singapore 138671, Singapore
| | - Prakash Arumugam
- Singapore Institute of Food and Biotechnology Innovation, A(∗)STAR, 31 Biopolis Way, Singapore 138669, Singapore; Nanyang Technological University, School of Biological Sciences, Singapore 637551, Singapore.
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4
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Montoya C, Kurylec J, Ossa A, Orrego S. Cyclic strain of poly (methyl methacrylate) surfaces triggered the pathogenicity of Candida albicans. Acta Biomater 2023; 170:415-426. [PMID: 37625677 PMCID: PMC10705016 DOI: 10.1016/j.actbio.2023.08.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/21/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Candida albicans is an opportunistic yeast and the primary etiological factor in oral candidiasis and denture stomatitis. The pathogenesis of C. albicans could be triggered by several variables, including environmental, nutritional, and biomaterial surface cues. Specifically, biomaterial interactions are driven by different surface properties, including wettability, stiffness, and roughness. Dental biomaterials experience repetitive (cyclic) stresses from chewing and biomechanical movements. Pathogenic biofilms are formed over these biomaterial surfaces under cyclic strain. This study investigated the effect of the cyclic strain (deformation) of biomaterial surfaces on the virulence of Candida albicans. Candida biofilms were grown over Poly (methyl methacrylate) (PMMA) surfaces subjected to static (no strain) and cyclic strain with different levels (ε˜x=0.1 and 0.2%). To evaluate the biomaterial-biofilm interactions, the biofilm characteristics, yeast-to-hyphae transition, and the expression of virulent genes were measured. Results showed the biofilm biomass and metabolic activity to be significantly higher when Candida adhered to surfaces subjected to cyclic strain compared to static surfaces. Examination of the yeast-to-hyphae transition showed pseudo-hyphae cells (pathogenic) in cyclically strained biomaterial surfaces, whereas static surfaces showed spherical yeast cells (commensal). RNA sequencing was used to determine and compare the transcriptome profiles of cyclically strained and static surfaces. Genes and transcription factors associated with cell adhesion (CSH1, PGA10, and RBT5), biofilm formation (EFG1), and secretion of extracellular matrix (ECM) (CRH1, ADH5, GCA1, and GCA2) were significantly upregulated in the cyclically strained biomaterial surfaces compared to static ones. Genes and transcription factors associated with virulence (UME6 and HGC1) and the secretion of extracellular enzymes (LIP, PLB, and SAP families) were also significantly upregulated in the cyclically strained biomaterial surfaces compared to static. For the first time, this study reveals a biomaterial surface factor triggering the pathogenesis of Candida albicans, which is essential for understanding, controlling, and preventing oral infections. STATEMENT OF SIGNIFICANCE: Fungal infections produced by Candida albicans are a significant contributor to various health conditions. Candida becomes pathogenic when certain environmental conditions change, including temperature, pH, nutrients, and CO2 levels. In addition, surface properties, including wettability, stiffness, and roughness, drive the interactions between Candida and biomaterials. Clinically, Candida adheres to biomaterials that are under repetitive deformation due to body movements. In this work, we revealed that when Candida adhered to biomaterial surfaces subjected to repetitive deformation, the microorganism becomes pathogenic by increasing the formation of biofilms and the expression of virulent factors related to hyphae formation and secretion of enzymes. Findings from this work could aid the development of new strategies for treating fungal infections in medical devices or implanted biomaterials.
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Affiliation(s)
- Carolina Montoya
- Department of Oral Health Sciences, Kornberg School of Dentistry, Temple University, Philadelphia, PA, United States
| | - Julia Kurylec
- Department of Oral Health Sciences, Kornberg School of Dentistry, Temple University, Philadelphia, PA, United States
| | - Alex Ossa
- Production Engineering Department, School of Engineering, Universidad EAFIT, Medellín, Colombia
| | - Santiago Orrego
- Department of Oral Health Sciences, Kornberg School of Dentistry, Temple University, Philadelphia, PA, United States; Bioengineering Department, College of Engineering, Temple University, Philadelphia, PA, United States.
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5
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Zhang X, Yu Q, Wu Y, Zhang Y, He Y, Wang R, Yu X, Li S. Glc7/PP1 dephosphorylates histone H3T11 to regulate autophagy and telomere silencing in response to nutrient availability. Cell Discov 2023; 9:71. [PMID: 37433812 DOI: 10.1038/s41421-023-00551-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/02/2023] [Indexed: 07/13/2023] Open
Abstract
How cells adapt their gene expression to nutritional changes remains poorly understood. Histone H3T11 is phosphorylated by pyruvate kinase to repress gene transcription. Here, we identify the protein phosphatase 1 (PP1), Glc7 as the enzyme that specifically dephosphorylates H3T11. We also characterize two novel Glc7-containing complexes and reveal their roles in regulating gene expression upon glucose starvation. Specifically, the Glc7-Sen1 complex dephosphorylates H3T11 to activate the transcription of autophagy-related genes. The Glc7-Rif1-Rap1 complex dephosphorylates H3T11 to derepress the transcription of telomere-proximal genes. Upon glucose starvation, Glc7 expression is up-regulated and more Glc7 translocates into the nucleus to dephosphorylate H3T11, leading to induction of autophagy and derepressed transcription of telomere-proximal genes. Furthermore, the functions of PP1/Glc7 and the two Glc7-containing complexes are conserved in mammals to regulate autophagy and telomere structure. Collectively, our results reveal a novel mechanism that regulate gene expression and chromatin structure in response to glucose availability.
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Affiliation(s)
- Xinyu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Yinsheng Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Yuan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Yi He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Rongsha Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei, China.
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei, China.
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6
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Su Y, Xu C, Shea J, DeStephanis D, Su Z. Transcriptomic changes in single yeast cells under various stress conditions. BMC Genomics 2023; 24:88. [PMID: 36829151 PMCID: PMC9960639 DOI: 10.1186/s12864-023-09184-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The stress response of Saccharomyces cerevisiae has been extensively studied in the past decade. However, with the advent of recent technology in single-cell transcriptome profiling, there is a new opportunity to expand and further understanding of the yeast stress response with greater resolution on a system level. To understand transcriptomic changes in baker's yeast S. cerevisiae cells under stress conditions, we sequenced 117 yeast cells under three stress treatments (hypotonic condition, glucose starvation and amino acid starvation) using a full-length single-cell RNA-Seq method. RESULTS We found that though single cells from the same treatment showed varying degrees of uniformity, technical noise and batch effects can confound results significantly. However, upon careful selection of samples to reduce technical artifacts and account for batch-effects, we were able to capture distinct transcriptomic signatures for different stress conditions as well as putative regulatory relationships between transcription factors and target genes. CONCLUSION Our results show that a full-length single-cell based transcriptomic analysis of the yeast may help paint a clearer picture of how the model organism responds to stress than do bulk cell population-based methods.
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Affiliation(s)
- Yangqi Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Chen Xu
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Jonathan Shea
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Darla DeStephanis
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, 28223, Charlotte, NC, USA.
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7
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Akunuri R, Unnissa T, Vadakattu M, Bujji S, Mahammad Ghouse S, Madhavi Yaddanapudi V, Chopra S, Nanduri S. Bacterial Pyruvate Kinase: A New Potential Target to Combat Drug‐Resistant
Staphylococcus aureus
Infections. ChemistrySelect 2022. [DOI: 10.1002/slct.202201403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ravikumar Akunuri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Tanveer Unnissa
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Manasa Vadakattu
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sushmitha Bujji
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Shaik Mahammad Ghouse
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
| | - Sidharth Chopra
- Division of Molecular Microbiology and Immunology CSIR-Central Drug Research Institute (CDRI) Sitapur Road, Sector 10, Janakipuram Extension Lucknow 226 031, Uttar Pradesh India
| | - Srinivas Nanduri
- Department of Chemical Sciences National Institute of Pharmaceutical Education and Research (NIPER) Hyderabad 500 037, Telangana State India
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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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Kobayashi Y, Inokuma K, Matsuda M, Kondo A, Hasunuma T. Resveratrol production from several types of saccharide sources by a recombinant Scheffersomyces stipitis strain. Metab Eng Commun 2021; 13:e00188. [PMID: 34888140 PMCID: PMC8637140 DOI: 10.1016/j.mec.2021.e00188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/19/2021] [Accepted: 11/24/2021] [Indexed: 10/25/2022] Open
Abstract
Resveratrol is a plant-derived aromatic compound with a wide range of beneficial properties including antioxidant and anti-aging effects. The resveratrol currently available on the market is predominantly extracted from certain plants such as grape and the Japanese knotweed Polygonum cuspidatum. Due to the unstable harvest of these plants and the low resveratrol purity obtained, it is necessary to develop a stable production process of high-purity resveratrol from inexpensive feedstocks. Here, we attempted to produce resveratrol from a wide range of sugars as carbon sources by a using the genetically-engineered yeast Scheffersomyces stipitis (formerly known as Pichia stipitis), which possesses a broad sugar utilization capacity. First, we constructed the resveratrol producing strain by introducing genes coding the essential enzymes for resveratrol biosynthesis [tyrosine ammonia-lyase 1 derived from Herpetosiphon aurantiacus (HaTAL1), 4-coumarate: CoA ligase 2 derived from Arabidopsis thaliana (At4CL2), and stilbene synthase 1 derived from Vitis vinifera (VvVST1)]. Subsequently, a feedback-insensitive allele of chorismate mutase was overexpressed in the constructed strain to improve resveratrol production. The constructed strain successfully produced resveratrol from a broad range of biomass-derived sugars [glucose, fructose, xylose, N-acetyl glucosamine (GlcNAc), galactose, cellobiose, maltose, and sucrose] in shake flask cultivation. Significant resveratrol titers were detected in cellobiose and sucrose fermentation (529.8 and 668.6 mg/L after 120 h fermentation, respectively), twice above the amount obtained with glucose (237.6 mg/L). Metabolomic analysis revealed an altered profile of the metabolites involved in the glycolysis and shikimate pathways, and also of cofactors and metabolites of energy metabolisms, depending on the substrate used. The levels of resveratrol precursors such as L-tyrosine increased in cellobiose and sucrose-grown cells. The results indicate that S. stipitis is an attractive microbial platform for resveratrol production from broad types of biomass-derived sugars and the selection of suitable substrates is crucial for improving resveratrol productivity of this yeast.
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Affiliation(s)
- Yuma Kobayashi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Mami Matsuda
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.,Biomass Engineering Program, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
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11
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Reversible amyloids of pyruvate kinase couple cell metabolism and stress granule disassembly. Nat Cell Biol 2021; 23:1085-1094. [PMID: 34616026 PMCID: PMC7611853 DOI: 10.1038/s41556-021-00760-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/23/2021] [Indexed: 11/08/2022]
Abstract
Cells respond to stress by blocking translation, rewiring metabolism and forming transient messenger ribonucleoprotein assemblies called stress granules (SGs). After stress release, re-establishing homeostasis and disassembling SGs requires ATP-consuming processes. However, the molecular mechanisms whereby cells restore ATP production and disassemble SGs after stress remain poorly understood. Here we show that upon stress, the ATP-producing enzyme Cdc19 forms inactive amyloids, and that their rapid re-solubilization is essential to restore ATP production and disassemble SGs in glucose-containing media. Cdc19 re-solubilization is initiated by the glycolytic metabolite fructose-1,6-bisphosphate, which directly binds Cdc19 amyloids, allowing Hsp104 and Ssa2 chaperone recruitment and aggregate re-solubilization. Fructose-1,6-bisphosphate then promotes Cdc19 tetramerization, which boosts its activity to further enhance ATP production and SG disassembly. Together, these results describe a molecular mechanism that is critical for stress recovery and directly couples cellular metabolism with SG dynamics via the regulation of reversible Cdc19 amyloids.
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12
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Gene expression regulates metabolite homeostasis during the Crabtree effect: Implications for the adaptation and evolution of Metabolism. Proc Natl Acad Sci U S A 2021; 118:2014013118. [PMID: 33372135 DOI: 10.1073/pnas.2014013118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A key issue in both molecular and evolutionary biology has been to define the roles of genes and phenotypes in the adaptation of organisms to environmental changes. The dominant view has been that an organism's metabolic adaptations are driven by gene expression and that gene mutations, independent of the starting phenotype, are responsible for the evolution of new metabolic phenotypes. We propose an alternate hypothesis, in which the phenotype and genotype together determine metabolic adaptation both in the lifetime of the organism and in the evolutionary selection of adaptive metabolic traits. We tested this hypothesis by flux-balance and metabolic-control analysis of the relative roles of the starting phenotype and gene expression in regulating the metabolic adaptations during the Crabtree effect in yeast, when they are switched from a low- to high-glucose environment. Critical for successful short-term adaptation was the ability of the glycogen/trehalose shunt to balance the glycolytic pathway. The role of later gene expression of new isoforms of glycolytic enzymes, rather than flux control, was to provide additional homeostatic mechanisms allowing an increase in the amount and efficiency of adenosine triphosphate and product formation while maintaining glycolytic balance. We further showed that homeostatic mechanisms, by allowing increased phenotypic plasticity, could have played an important role in guiding the evolution of the Crabtree effect. Although our findings are specific to Crabtree yeast, they are likely to be broadly found because of the well-recognized similarities in glucose metabolism across kingdoms and phyla from yeast to humans.
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13
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Gassaway BM, Cardone RL, Padyana AK, Petersen MC, Judd ET, Hayes S, Tong S, Barber KW, Apostolidi M, Abulizi A, Sheetz JB, Kshitiz, Aerni HR, Gross S, Kung C, Samuel VT, Shulman GI, Kibbey RG, Rinehart J. Distinct Hepatic PKA and CDK Signaling Pathways Control Activity-Independent Pyruvate Kinase Phosphorylation and Hepatic Glucose Production. Cell Rep 2020; 29:3394-3404.e9. [PMID: 31825824 DOI: 10.1016/j.celrep.2019.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 07/31/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022] Open
Abstract
Pyruvate kinase is an important enzyme in glycolysis and a key metabolic control point. We recently observed a pyruvate kinase liver isoform (PKL) phosphorylation site at S113 that correlates with insulin resistance in rats on a 3 day high-fat diet (HFD) and suggests additional control points for PKL activity. However, in contrast to the classical model of PKL regulation, neither authentically phosphorylated PKL at S12 nor S113 alone is sufficient to alter enzyme kinetics or structure. Instead, we show that cyclin-dependent kinases (CDKs) are activated by the HFD and responsible for PKL phosphorylation at position S113 in addition to other targets. These CDKs control PKL nuclear retention, alter cytosolic PKL activity, and ultimately influence glucose production. These results change our view of PKL regulation and highlight a previously unrecognized pathway of hepatic CDK activity and metabolic control points that may be important in insulin resistance and type 2 diabetes.
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Affiliation(s)
- Brandon M Gassaway
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Department of Systems Biology Institute, Yale University, New Haven, CT, USA
| | - Rebecca L Cardone
- Department of Internal Medicine, Yale University, New Haven, CT, USA
| | | | - Max C Petersen
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Department of Internal Medicine, Yale University, New Haven, CT, USA
| | | | | | | | - Karl W Barber
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Department of Systems Biology Institute, Yale University, New Haven, CT, USA
| | - Maria Apostolidi
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Department of Systems Biology Institute, Yale University, New Haven, CT, USA
| | | | - Joshua B Sheetz
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
| | - Kshitiz
- Department of Systems Biology Institute, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Hans R Aerni
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Department of Systems Biology Institute, Yale University, New Haven, CT, USA
| | | | | | - Varman T Samuel
- Department of Internal Medicine, Yale University, New Haven, CT, USA; Veterans Affairs Medical Center, West Haven, CT, USA
| | - Gerald I Shulman
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Richard G Kibbey
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Jesse Rinehart
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA; Department of Systems Biology Institute, Yale University, New Haven, CT, USA.
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14
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Gu Y, Ma J, Zhu Y, Ding X, Xu P. Engineering Yarrowia lipolytica as a Chassis for De Novo Synthesis of Five Aromatic-Derived Natural Products and Chemicals. ACS Synth Biol 2020; 9:2096-2106. [PMID: 32650638 PMCID: PMC7445739 DOI: 10.1021/acssynbio.0c00185] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Yarrowia
lipolytica is a novel microbial chassis
to upgrade renewable low-cost carbon feedstocks to high-value commodity
chemicals and natural products. In this work, we systematically characterized
and removed the rate-limiting steps of the shikimate pathway and achieved de novo synthesis of five aromatic chemicals in Y. lipolytica. We determined that eliminating amino
acids formation and engineering feedback-insensitive DAHP synthases
are critical steps to mitigate precursor competition and relieve the
feedback regulation of the shikimate pathway. Further overexpression
of heterologous phosphoketolase and deletion of pyruvate kinase provided
a sustained metabolic driving force that channels E4P (erythrose 4-phosphate)
and PEP (phosphoenolpyruvate) precursors through the shikimate pathway.
Precursor competing pathways and byproduct formation pathways were
also blocked by inactivating chromosomal genes. To demonstrate the
utility of our engineered chassis strain, three natural products,
2-phenylethanol (2-PE), p-coumaric acid, and violacein,
which were derived from phenylalanine, tyrosine, and tryptophan, respectively,
were chosen to test the chassis performance. We obtained 2426.22 ±
48.33 mg/L of 2-PE, 593.53 ± 28.75 mg/L of p-coumaric acid, 12.67 ± 2.23 mg/L of resveratrol, 366.30 ±
28.99 mg/L of violacein, and 55.12 ± 2.81 mg/L of deoxyviolacein
from glucose in a shake flask. The 2-PE production represents a 286-fold
increase over the initial strain (8.48 ± 0.50 mg/L). Specifically,
we obtained the highest 2-PE, violacein, and deoxyviolacein titer
ever reported from the de novo shikimate pathway
in yeast. These results set up a new stage of engineering Y. lipolytica as a sustainable biorefinery chassis
strain for de novo synthesis of aromatic compounds
with economic values.
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Affiliation(s)
- Yang Gu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jingbo Ma
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
| | - Yonglian Zhu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xinyu Ding
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Peng Xu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, United States
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15
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Liu VM, Howell AJ, Hosios AM, Li Z, Israelsen WJ, Heiden MGV. Cancer-associated mutations in human pyruvate kinase M2 impair enzyme activity. FEBS Lett 2020; 594:646-664. [PMID: 31642061 PMCID: PMC7042059 DOI: 10.1002/1873-3468.13648] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/28/2019] [Accepted: 10/15/2019] [Indexed: 12/18/2022]
Abstract
Mammalian pyruvate kinase catalyzes the final step of glycolysis, and its M2 isoform (PKM2) is widely expressed in proliferative tissues. Mutations in PKM2 are found in some human cancers; however, the effects of these mutations on enzyme activity and regulation are unknown. Here, we characterized five cancer-associated PKM2 mutations, occurring at various locations on the enzyme, with respect to substrate kinetics and activation by the allosteric activator fructose-1,6-bisphosphate (FBP). The mutants exhibit reduced maximal velocity, reduced substrate affinity, and/or altered activation by FBP. The kinetic parameters of five additional PKM2 mutants that have been used to study enzyme function or regulation also demonstrate the deleterious effects of mutations on PKM2 function. Our findings indicate that PKM2 is sensitive to many amino acid changes and support the hypothesis that decreased PKM2 activity is selected for in rapidly proliferating cells.
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Affiliation(s)
- Vivian M. Liu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
- Harvard-MIT Health Sciences and Technology Division, Harvard Medical School, Boston, MA 02115, United States
| | - Andrea J. Howell
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Aaron M. Hosios
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Zhaoqi Li
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - William J. Israelsen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
| | - Matthew G. Vander Heiden
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
- Dana-Farber Cancer Institute, Boston, MA 02115, United States
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16
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Shimizu K, Matsuoka Y. Redox rebalance against genetic perturbations and modulation of central carbon metabolism by the oxidative stress regulation. Biotechnol Adv 2019; 37:107441. [PMID: 31472206 DOI: 10.1016/j.biotechadv.2019.107441] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/04/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022]
Abstract
The micro-aerophilic organisms and aerobes as well as yeast and higher organisms have evolved to gain energy through respiration (via oxidative phosphorylation), thereby enabling them to grow much faster than anaerobes. However, during respiration, reactive oxygen species (ROSs) are inherently (inevitably) generated, and threaten the cell's survival. Therefore, living organisms (or cells) must furnish the potent defense systems to keep such ROSs at harmless level, where the cofactor balance plays crucial roles. Namely, NADH is the source of energy generation (catabolism) in the respiratory chain reactions, through which ROSs are generated, while NADPH plays important roles not only for the cell synthesis (anabolism) but also for detoxifying ROSs. Therefore, the cell must rebalance the redox ratio by modulating the fluxes of the central carbon metabolism (CCM) by regulating the multi-level regulation machinery upon genetic perturbations and the change in the growth conditions. Here, we discuss about how aerobes accomplish such cofactor homeostasis against redox perturbations. In particular, we consider how single-gene mutants (including pgi, pfk, zwf, gnd and pyk mutants) modulate their metabolisms in relation to cofactor rebalance (and also by adaptive laboratory evolution). We also discuss about how the overproduction of NADPH (by the pathway gene mutation) can be utilized for the efficient production of useful value-added chemicals such as medicinal compounds, polyhydroxyalkanoates, and amino acids, all of which require NADPH in their synthetic pathways. We then discuss about the metabolic responses against oxidative stress, where αketoacids play important roles not only for the coordination between catabolism and anabolism, but also for detoxifying ROSs by non-enzymatic reactions, as well as for reducing the production of ROSs by repressing the activities of the TCA cycle and respiration (via carbon catabolite repression). Thus, we discuss about the mechanisms (basic strategies) that modulate the metabolism from respiration to respiro-fermentative metabolism causing overflow, based on the role of Pyk activity, affecting the NADPH production at the oxidative pentose phosphate (PP) pathway, and the roles of αketoacids for the change in the source of energy generation from the oxidative phosphorylation to the substrate level phosphorylation.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio university, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan.
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17
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Szatkowska R, Garcia-Albornoz M, Roszkowska K, Holman SW, Furmanek E, Hubbard SJ, Beynon RJ, Adamczyk M. Glycolytic flux in Saccharomyces cerevisiae is dependent on RNA polymerase III and its negative regulator Maf1. Biochem J 2019; 476:1053-1082. [PMID: 30885983 PMCID: PMC6448137 DOI: 10.1042/bcj20180701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 02/07/2023]
Abstract
Protein biosynthesis is energetically costly, is tightly regulated and is coupled to stress conditions including glucose deprivation. RNA polymerase III (RNAP III)-driven transcription of tDNA genes for production of tRNAs is a key element in efficient protein biosynthesis. Here we present an analysis of the effects of altered RNAP III activity on the Saccharomyces cerevisiae proteome and metabolism under glucose-rich conditions. We show for the first time that RNAP III is tightly coupled to the glycolytic system at the molecular systems level. Decreased RNAP III activity or the absence of the RNAP III negative regulator, Maf1 elicit broad changes in the abundance profiles of enzymes engaged in fundamental metabolism in S. cerevisiae In a mutant compromised in RNAP III activity, there is a repartitioning towards amino acids synthesis de novo at the expense of glycolytic throughput. Conversely, cells lacking Maf1 protein have greater potential for glycolytic flux.
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Affiliation(s)
- Roza Szatkowska
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Manuel Garcia-Albornoz
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, U.K
| | - Katarzyna Roszkowska
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Stephen W Holman
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, U.K
| | - Emil Furmanek
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Simon J Hubbard
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, U.K
| | - Robert J Beynon
- Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool, U.K
| | - Malgorzata Adamczyk
- Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
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18
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Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. mSystems 2019; 4:mSystems00170-18. [PMID: 30834327 PMCID: PMC6392091 DOI: 10.1128/msystems.00170-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/21/2019] [Indexed: 11/23/2022] Open
Abstract
Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism. Isozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are often retained over evolutionary time, suggesting that they contribute to fitness. We developed an unsupervised computational method for identifying environmental conditions under which isozymes are likely to make fitness contributions. This method analyzes published gene expression data to find specific experimental perturbations that induce differential isozyme expression. In yeast, we found that isozymes are strongly enriched in the pathways of central carbon metabolism and that many isozyme pairs show anticorrelated expression during the respirofermentative shift. Building on these observations, we assigned function to two minor central carbon isozymes, aconitase 2 (ACO2) and pyruvate kinase 2 (PYK2). ACO2 is expressed during fermentation and proves advantageous when glucose is limiting. PYK2 is expressed during respiration and proves advantageous for growth on three-carbon substrates. PYK2’s deletion can be rescued by expressing the major pyruvate kinase only if that enzyme carries mutations mirroring PYK2’s allosteric regulation. Thus, central carbon isozymes help to optimize allosteric metabolic regulation under a broad range of potential nutrient conditions while requiring only a small number of transcriptional states. IMPORTANCE Gene duplication is one of the main evolutionary paths to new protein function. Typically, duplicated genes either accumulate mutations and degrade into pseudogenes or are retained and diverge in function. Some duplicated genes, however, show long-term persistence without apparently acquiring new function. An important class of isozymes consists of those that catalyze the same reaction in the same compartment, where knockout of one isozyme causes no known functional defect. Here we present an approach to assigning specific functional roles to seemingly redundant isozymes. First, gene expression data are analyzed computationally to identify conditions under which isozyme expression diverges. Then, knockouts are compared under those conditions. This approach revealed that the expression of many yeast isozymes diverges in response to carbon availability and that carbon source manipulations can induce fitness phenotypes for seemingly redundant isozymes. A driver of these fitness phenotypes is differential allosteric enzyme regulation, indicating isozyme divergence to achieve more-optimal control of metabolism.
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19
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Jang C, Chen L, Rabinowitz JD. Metabolomics and Isotope Tracing. Cell 2019; 173:822-837. [PMID: 29727671 DOI: 10.1016/j.cell.2018.03.055] [Citation(s) in RCA: 483] [Impact Index Per Article: 96.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/21/2018] [Accepted: 03/21/2018] [Indexed: 12/15/2022]
Abstract
Great strides have been made over the past decade toward comprehensive study of metabolism. Mass spectrometry (MS) has played a central role by enabling measurement of many metabolites simultaneously. Tracking metabolite labeling from stable isotope tracers can in addition reveal pathway activities. Here, we describe the basics of metabolite measurement by MS, including sample preparation, metabolomic analysis, and data interpretation. In addition, drawing on examples of successful experiments, we highlight the ways in which metabolomics and isotope tracing can illuminate biology.
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Affiliation(s)
- Cholsoon Jang
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544, USA
| | - Li Chen
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544, USA.
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20
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Prouteau M, Loewith R. Regulation of Cellular Metabolism through Phase Separation of Enzymes. Biomolecules 2018; 8:biom8040160. [PMID: 30513998 PMCID: PMC6316564 DOI: 10.3390/biom8040160] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 01/21/2023] Open
Abstract
Metabolism is the sum of the life-giving chemical processes that occur within a cell. Proper regulation of these processes is essential for all organisms to thrive and prosper. When external factors are too extreme, or if internal regulation is corrupted through genetic or epigenetic changes, metabolic homeostasis is no longer achievable and diseases such as metabolic syndrome or cancer, aging, and, ultimately, death ensue. Metabolic reactions are catalyzed by proteins, and the in vitro kinetic properties of these enzymes have been studied by biochemists for many decades. These efforts led to the appreciation that enzyme activities can be acutely regulated and that this regulation is critical to metabolic homeostasis. Regulation can be mediated through allosteric interactions with metabolites themselves or via post-translational modifications triggered by intracellular signal transduction pathways. More recently, enzyme regulation has attracted the attention of cell biologists who noticed that change in growth conditions often triggers the condensation of diffusely localized enzymes into one or more discrete foci, easily visible by light microscopy. This reorganization from a soluble to a condensed state is best described as a phase separation. As summarized in this review, stimulus-induced phase separation has now been observed for dozens of enzymes suggesting that this could represent a widespread mode of activity regulation, rather than, or in addition to, a storage form of temporarily superfluous enzymes. Building on our recent structure determination of TOROIDs (TORc1 Organized in Inhibited Domain), the condensate formed by the protein kinase Target Of Rapamycin Complex 1 (TORC1), we will highlight that the molecular organization of enzyme condensates can vary dramatically and that future work aimed at the structural characterization of enzyme condensates will be critical to understand how phase separation regulates enzyme activity and consequently metabolic homeostasis. This information may ultimately facilitate the design of strategies to target the assembly or disassembly of specific enzymes condensates as a therapeutic approach to restore metabolic homeostasis in certain diseases.
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Affiliation(s)
- Manoël Prouteau
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
| | - Robbie Loewith
- Department of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
- Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
- Swiss National Centre for Competence in Research (NCCR) in Chemical Biology, University of Geneva, Sciences II, Room 3-308, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland.
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21
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Xu YF, Lu W, Chen JC, Johnson SA, Gibney PA, Thomas DG, Brown G, May AL, Campagna SR, Yakunin AF, Botstein D, Rabinowitz JD. Discovery and Functional Characterization of a Yeast Sugar Alcohol Phosphatase. ACS Chem Biol 2018; 13:3011-3020. [PMID: 30240188 DOI: 10.1021/acschembio.8b00804] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Sugar alcohols (polyols) exist widely in nature. While some specific sugar alcohol phosphatases are known, there is no known phosphatase for some important sugar alcohols (e.g., sorbitol-6-phosphate). Using liquid chromatography-mass spectrometry-based metabolomics, we screened yeast strains with putative phosphatases of unknown function deleted. We show that the yeast gene YNL010W, which has close homologues in all fungi species and some plants, encodes a sugar alcohol phosphatase. We term this enzyme, which hydrolyzes sorbitol-6-phosphate, ribitol-5-phosphate, and (d)-glycerol-3-phosphate, polyol phosphatase 1 or PYP1. Polyol phosphates are structural analogs of the enediol intermediate of phosphoglucose isomerase (Pgi). We find that sorbitol-6-phosphate and ribitol-5-phosphate inhibit Pgi and that Pyp1 activity is important for yeast to maintain Pgi activity in the presence of environmental sugar alcohols. Pyp1 expression is strongly positively correlated with yeast growth rate, presumably because faster growth requires greater glycolytic and accordingly Pgi flux. Thus, yeast express the previously uncharacterized enzyme Pyp1 to prevent inhibition of glycolysis by sugar alcohol phosphates. Pyp1 may be useful for engineering sugar alcohol production.
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Affiliation(s)
- Yi-Fan Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Jonathan C. Chen
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sarah A. Johnson
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Patrick A. Gibney
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - David G. Thomas
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Greg Brown
- Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Amanda L. May
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - David Botstein
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Joshua D. Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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22
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Reznik E, Christodoulou D, Goldford JE, Briars E, Sauer U, Segrè D, Noor E. Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. Cell Rep 2018; 20:2666-2677. [PMID: 28903046 DOI: 10.1016/j.celrep.2017.08.066] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/05/2017] [Accepted: 08/19/2017] [Indexed: 12/21/2022] Open
Abstract
Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurements and the SMRN to make inferences on the sensitivity of enzymes to their regulators. Generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis.
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Affiliation(s)
- Ed Reznik
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Dimitris Christodoulou
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland
| | | | - Emma Briars
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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23
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Mei Q, Huang J, Chen W, Tang J, Xu C, Yu Q, Cheng Y, Ma L, Yu X, Li S. Regulation of DNA replication-coupled histone gene expression. Oncotarget 2017; 8:95005-95022. [PMID: 29212286 PMCID: PMC5706932 DOI: 10.18632/oncotarget.21887] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/20/2017] [Indexed: 12/21/2022] Open
Abstract
The expression of core histone genes is cell cycle regulated. Large amounts of histones are required to restore duplicated chromatin during S phase when DNA replication occurs. Over-expression and excess accumulation of histones outside S phase are toxic to cells and therefore cells need to restrict histone expression to S phase. Misregulation of histone gene expression leads to defects in cell cycle progression, genome stability, DNA damage response and transcriptional regulation. Here, we discussed the factors involved in histone gene regulation as well as the underlying mechanism. Understanding the histone regulation mechanism will shed lights on elucidating the side effects of certain cancer chemotherapeutic drugs and developing potential biomarkers for tumor cells.
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Affiliation(s)
- Qianyun Mei
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Junhua Huang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Wanping Chen
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.,Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Jie Tang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Chen Xu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Qi Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Ying Cheng
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.,Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xilan Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.,Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.,Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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24
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Gehrig S, Macpherson JA, Driscoll PC, Symon A, Martin SR, MacRae JI, Kleinjung J, Fraternali F, Anastasiou D. An engineered photoswitchable mammalian pyruvate kinase. FEBS J 2017; 284:2955-2980. [PMID: 28715126 PMCID: PMC5637921 DOI: 10.1111/febs.14175] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/24/2017] [Accepted: 07/13/2017] [Indexed: 01/06/2023]
Abstract
Changes in allosteric regulation of glycolytic enzymes have been linked to metabolic reprogramming involved in cancer. Remarkably, allosteric mechanisms control enzyme function at significantly shorter time-scales compared to the long-term effects of metabolic reprogramming on cell proliferation. It remains unclear if and how the speed and reversibility afforded by rapid allosteric control of metabolic enzymes is important for cell proliferation. Tools that allow specific, dynamic modulation of enzymatic activities in mammalian cells would help address this question. Towards this goal, we have used molecular dynamics simulations to guide the design of mPKM2 internal light/oxygen/voltage-sensitive domain 2 (LOV2) fusion at position D24 (PiL[D24]), an engineered pyruvate kinase M2 (PKM2) variant that harbours an insertion of the light-sensing LOV2 domain from Avena Sativa within a region implicated in allosteric regulation by fructose 1,6-bisphosphate (FBP). The LOV2 photoreaction is preserved in the PiL[D24] chimera and causes secondary structure changes that are associated with a 30% decrease in the Km of the enzyme for phosphoenolpyruvate resulting in increased pyruvate kinase activity after light exposure. Importantly, this change in activity is reversible upon light withdrawal. Expression of PiL[D24] in cells leads to light-induced increase in labelling of pyruvate from glucose. PiL[D24] therefore could provide a means to modulate cellular glucose metabolism in a remote manner and paves the way for studying the importance of rapid allosteric phenomena in the regulation of metabolism and enzyme control.
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Affiliation(s)
- Stefanie Gehrig
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Paul C. Driscoll
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Alastair Symon
- Instrument Prototyping Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Stephen R. Martin
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - James I. MacRae
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Jens Kleinjung
- Computational BiologyThe Francis Crick InstituteLondonUK
| | - Franca Fraternali
- Randall Division of Cell and Molecular BiophysicsKing's CollegeLondonUK
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25
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Mert MJ, Rose SH, la Grange DC, Bamba T, Hasunuma T, Kondo A, van Zyl WH. Quantitative metabolomics of a xylose-utilizing Saccharomyces cerevisiae strain expressing the Bacteroides thetaiotaomicron xylose isomerase on glucose and xylose. J Ind Microbiol Biotechnol 2017; 44:1459-1470. [PMID: 28744577 DOI: 10.1007/s10295-017-1969-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/18/2017] [Indexed: 11/26/2022]
Abstract
The yeast Saccharomyces cerevisiae cannot utilize xylose, but the introduction of a xylose isomerase that functions well in yeast will help overcome the limitations of the fungal oxido-reductive pathway. In this study, a diploid S. cerevisiae S288c[2n YMX12] strain was constructed expressing the Bacteroides thetaiotaomicron xylA (XI) and the Scheffersomyces stipitis xyl3 (XK) and the changes in the metabolite pools monitored over time. Cultivation on xylose generally resulted in gradual changes in metabolite pool size over time, whereas more dramatic fluctuations were observed with cultivation on glucose due to the diauxic growth pattern. The low G6P and F1,6P levels observed with cultivation on xylose resulted in the incomplete activation of the Crabtree effect, whereas the high PEP levels is indicative of carbon starvation. The high UDP-D-glucose levels with cultivation on xylose indicated that the carbon was channeled toward biomass production. The adenylate and guanylate energy charges were tightly regulated by the cultures, while the catabolic and anabolic reduction charges fluctuated between metabolic states. This study helped elucidate the metabolite distribution that takes place under Crabtree-positive and Crabtree-negative conditions when cultivating S. cerevisiae on glucose and xylose, respectively.
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Affiliation(s)
- M J Mert
- Unit for Environmental Sciences and Management: Microbiology, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - S H Rose
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - D C la Grange
- Unit for Environmental Sciences and Management: Microbiology, North-West University, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - T Bamba
- Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - T Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - A Kondo
- Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodaicho, Nada-ku, Kobe, 657-8501, Japan
| | - W H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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26
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Wang L, Liu S, Ding Y, Yuan SS, Ho YY, Tseng GC. Meta-analytic framework for liquid association. Bioinformatics 2017; 33:2140-2147. [PMID: 28334340 PMCID: PMC6044323 DOI: 10.1093/bioinformatics/btx138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 02/11/2017] [Accepted: 03/09/2017] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association (LA) is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). LA detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation and limited sample size. With the rapid development of microarray and NGS technology, LA analysis combining multiple gene expression studies can provide more accurate and stable results. RESULTS In this article, we proposed two meta-analytic approaches for LA analysis (MetaLA and MetaMLA) to combine multiple transcriptomic studies. To compensate demanding computing, we also proposed a two-step fast screening algorithm for more efficient genome-wide screening: bootstrap filtering and sign filtering. We applied the methods to five Saccharomyces cerevisiae datasets related to environmental changes. The fast screening algorithm reduced 98% of running time. When compared with single study analysis, MetaLA and MetaMLA provided stronger detection signal and more consistent and stable results. The top triplets are highly enriched in fundamental biological processes related to environmental changes. Our method can help biologists understand underlying regulatory mechanisms under different environmental exposure or disease states. AVAILABILITY AND IMPLEMENTATION A MetaLA R package, data and code for this article are available at http://tsenglab.biostat.pitt.edu/software.htm. CONTACT ctseng@pitt.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lin Wang
- School of Statistics, Capital University of Economics and Business, Fengtai, Beijing, China
| | - Silvia Liu
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shin-sheng Yuan
- Institute of Statistical Science, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yen-Yi Ho
- Department of Statistics, College of Arts and Sciences, University of South Carolina, Columbia, SC, USA
| | - George C Tseng
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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27
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Choi J, Rajagopal A, Xu YF, Rabinowitz JD, O’Shea EK. A systematic genetic screen for genes involved in sensing inorganic phosphate availability in Saccharomyces cerevisiae. PLoS One 2017; 12:e0176085. [PMID: 28520786 PMCID: PMC5435139 DOI: 10.1371/journal.pone.0176085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/05/2017] [Indexed: 01/10/2023] Open
Abstract
Saccharomyces cerevisiae responds to changes in extracellular inorganic phosphate (Pi) availability by regulating the activity of the phosphate-responsive (PHO) signaling pathway, enabling cells to maintain intracellular levels of the essential nutrient Pi. Pi-limitation induces upregulation of inositol heptakisphosphate (IP7) synthesized by the inositol hexakisphosphate kinase Vip1, triggering inhibition of the Pho80/Pho85 cyclin-cyclin dependent kinase (CDK) complex by the CDK inhibitor Pho81, which upregulates the PHO regulon through the CDK target and transcription factor Pho4. To identify genes that are involved in signaling upstream of the Pho80/Pho85/Pho81 complex and how they interact with each other to regulate the PHO pathway, we performed genome-wide screens with the synthetic genetic array method. We identified more than 300 mutants with defects in signaling upstream of the Pho80/Pho85/Pho81 complex, including AAH1, which encodes an adenine deaminase that negatively regulates the PHO pathway in a Vip1-dependent manner. Furthermore, we showed that even in the absence of VIP1, the PHO pathway can be activated under prolonged periods of Pi starvation, suggesting complexity in the mechanisms by which the PHO pathway is regulated.
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Affiliation(s)
- Joonhyuk Choi
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Abbhirami Rajagopal
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Yi-Fan Xu
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Erin K. O’Shea
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States of America
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28
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Yu Q, Tong C, Luo M, Xue X, Mei Q, Ma L, Yu X, Mao W, Kong L, Yu X, Li S. Regulation of SESAME-mediated H3T11 phosphorylation by glycolytic enzymes and metabolites. PLoS One 2017; 12:e0175576. [PMID: 28426732 PMCID: PMC5398556 DOI: 10.1371/journal.pone.0175576] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/28/2017] [Indexed: 12/15/2022] Open
Abstract
Cancer cells prefer aerobic glycolysis, but little is known about the underlying mechanism. Recent studies showed that the rate-limiting glycolytic enzymes, pyruvate kinase M2 (PKM2) directly phosphorylates H3 at threonine 11 (H3T11) to regulate gene expression and cell proliferation, revealing its non-metabolic functions in connecting glycolysis and histone modifications. We have reported that the yeast homolog of PKM2, Pyk1 phosphorylates H3T11 to regulate gene expression and oxidative stress resistance. But how glycolysis regulates H3T11 phosphorylation remains unclear. Here, using a series of glycolytic enzyme mutants and commercial available metabolites, we investigated the role of glycolytic enzymes and metabolites on H3T11 phosphorylation. Mutation of glycolytic genes including phosphoglucose isomerase (PGI1), enolase (ENO2), triosephosphate isomerase (TPI1), or folate biosynthesis enzyme (FOL3) significantly reduced H3T11 phosphorylation. Further study demonstrated that glycolysis regulates H3T11 phosphorylation by fueling the substrate, phosphoenonylpyruvate and the coactivator, FBP to Pyk1. Thus, our results provide a comprehensive view of how glycolysis modulates H3T11 phosphorylation.
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Affiliation(s)
- Qi Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Chong Tong
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Mingdan Luo
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Xiangyan Xue
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Qianyun Mei
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Lixin Ma
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Xiaolan Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Wuxiang Mao
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Lingbao Kong
- Department of HumanPopulation Genetics, Human Aging Research Institute and School of Life Science, Nanchang University, Nanchang, China
| | - Xilan Yu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
- * E-mail: (XY); (SL)
| | - Shanshan Li
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources,College of Life Sciences, Hubei University, Wuhan, Hubei, China
- * E-mail: (XY); (SL)
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29
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Non-metabolic functions of glycolytic enzymes in tumorigenesis. Oncogene 2016; 36:2629-2636. [PMID: 27797379 DOI: 10.1038/onc.2016.410] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/05/2016] [Accepted: 09/05/2016] [Indexed: 12/19/2022]
Abstract
Cancer cells reprogram their metabolism to meet the requirement for survival and rapid growth. One hallmark of cancer metabolism is elevated aerobic glycolysis and reduced oxidative phosphorylation. Emerging evidence showed that most glycolytic enzymes are deregulated in cancer cells and play important roles in tumorigenesis. Recent studies revealed that all essential glycolytic enzymes can be translocated into nucleus where they participate in tumor progression independent of their canonical metabolic roles. These noncanonical functions include anti-apoptosis, regulation of epigenetic modifications, modulation of transcription factors and co-factors, extracellular cytokine, protein kinase activity and mTORC1 signaling pathway, suggesting that these multifaceted glycolytic enzymes not only function in canonical metabolism but also directly link metabolism to epigenetic and transcription programs implicated in tumorigenesis. These findings underscore our understanding about how tumor cells adapt to nutrient and fuel availability in the environment and most importantly, provide insights into development of cancer therapy.
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30
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Hackett SR, Zanotelli VRT, Xu W, Goya J, Park JO, Perlman DH, Gibney PA, Botstein D, Storey JD, Rabinowitz JD. Systems-level analysis of mechanisms regulating yeast metabolic flux. Science 2016; 354:aaf2786. [PMID: 27789812 PMCID: PMC5414049 DOI: 10.1126/science.aaf2786] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 09/23/2016] [Indexed: 07/25/2023]
Abstract
Cellular metabolic fluxes are determined by enzyme activities and metabolite abundances. Biochemical approaches reveal the impact of specific substrates or regulators on enzyme kinetics but do not capture the extent to which metabolite and enzyme concentrations vary across physiological states and, therefore, how cellular reactions are regulated. We measured enzyme and metabolite concentrations and metabolic fluxes across 25 steady-state yeast cultures. We then assessed the extent to which flux can be explained by a Michaelis-Menten relationship between enzyme, substrate, product, and potential regulator concentrations. This revealed three previously unrecognized instances of cross-pathway regulation, which we biochemically verified. One of these involved inhibition of pyruvate kinase by citrate, which accumulated and thereby curtailed glycolytic outflow in nitrogen-limited yeast. Overall, substrate concentrations were the strongest driver of the net rates of cellular metabolic reactions, with metabolite concentrations collectively having more than double the physiological impact of enzymes.
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Affiliation(s)
- Sean R Hackett
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | | | - Wenxin Xu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan Goya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Junyoung O Park
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - David H Perlman
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Patrick A Gibney
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - John D Storey
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Center for Statistics and Machine Learning, Princeton University, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA. Department of Chemistry, Princeton University, Princeton, NJ 08544, USA.
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31
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Zhu XL, Wang QM. Application of fecal markers in inflammatory bowel disease. Shijie Huaren Xiaohua Zazhi 2016; 24:902-908. [DOI: 10.11569/wcjd.v24.i6.902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel disease (IBD) includes ulcerative colitis (UC) and Crohn's disease (CD). The diagnosis and assessment of inflammation activity principally rely on endoscopy combined with pathological biopsy. Fecal biomarkers possess advantages including non-invasion, simplicity, fastness and repeatability, and they are effective in judging inflammation activity, monitoring illness status, distinguishing organic and functional diseases as well as assessing treatment outcome. Various fecal biomarkers of IBD including fecal calprotectin, lactoferrin, M-2 type pyruvate kinase, S100A12 and myeloperoxidase are summarized in this paper.
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32
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Noy T, Vergnolle O, Hartman TE, Rhee KY, Jacobs WR, Berney M, Blanchard JS. Central Role of Pyruvate Kinase in Carbon Co-catabolism of Mycobacterium tuberculosis. J Biol Chem 2016; 291:7060-9. [PMID: 26858255 DOI: 10.1074/jbc.m115.707430] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) displays a high degree of metabolic plasticity to adapt to challenging host environments. Genetic evidence suggests thatMtbrelies mainly on fatty acid catabolism in the host. However,Mtbalso maintains a functional glycolytic pathway and its role in the cellular metabolism ofMtbhas yet to be understood. Pyruvate kinase catalyzes the last and rate-limiting step in glycolysis and theMtbgenome harbors one putative pyruvate kinase (pykA, Rv1617). Here we show thatpykAencodes an active pyruvate kinase that is allosterically activated by glucose 6-phosphate (Glc-6-P) and adenosine monophosphate (AMP). Deletion ofpykApreventsMtbgrowth in the presence of fermentable carbon sources and has a cidal effect in the presence of glucose that correlates with elevated levels of the toxic catabolite methylglyoxal. Growth attenuation was also observed in media containing a combination of short chain fatty acids and glucose and surprisingly, in media containing odd and even chain fatty acids alone. Untargeted high sensitivity metabolomics revealed that inactivation of pyruvate kinase leads to accumulation of phosphoenolpyruvate (P-enolpyruvate), citrate, and aconitate, which was consistent with allosteric inhibition of isocitrate dehydrogenase by P-enolpyruvate. This metabolic block could be relieved by addition of the α-ketoglutarate precursor glutamate. Taken together, our study identifies an essential role of pyruvate kinase in preventing metabolic block during carbon co-catabolism inMtb.
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Affiliation(s)
- Tahel Noy
- From the Departments of Biochemistry and
| | | | - Travis E Hartman
- the Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021
| | - Kyu Y Rhee
- the Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10021
| | - William R Jacobs
- the Department of Microbiology and Immunology, Howard Hughes Medical Institute at Albert Einstein College of Medicine, New York, New York 10461, and Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York 10461
| | - Michael Berney
- Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York 10461,
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33
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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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34
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Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data. Cell Syst 2015; 1:270-82. [DOI: 10.1016/j.cels.2015.09.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 08/12/2015] [Accepted: 09/30/2015] [Indexed: 11/20/2022]
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35
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Kochanowski K, Sauer U, Noor E. Posttranslational regulation of microbial metabolism. Curr Opin Microbiol 2015; 27:10-7. [PMID: 26048423 DOI: 10.1016/j.mib.2015.05.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/04/2015] [Accepted: 05/08/2015] [Indexed: 10/23/2022]
Abstract
Fluxes in microbial metabolism are controlled by various regulatory layers that alter abundance or activity of metabolic enzymes. Recent studies suggest a division of labor between these layers: transcriptional regulation mostly controls the allocation of protein resources, passive flux regulation by enzyme saturation and thermodynamics allows rapid responses at the expense of higher protein cost, and posttranslational regulation is utilized by cells to directly take control of metabolic decisions. We present recent advances in elucidating the role of these regulatory layers, focusing on posttranslational modifications and allosteric interactions. As the systematic mapping of posttranslational regulatory events has now become possible, the next challenge is to identify those regulatory events that are functionally relevant under a given condition.
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Affiliation(s)
- Karl Kochanowski
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland; Life Science Zurich PhD Program on Systems Biology, Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland.
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland
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Gold ND, Gowen CM, Lussier FX, Cautha SC, Mahadevan R, Martin VJJ. Metabolic engineering of a tyrosine-overproducing yeast platform using targeted metabolomics. Microb Cell Fact 2015; 14:73. [PMID: 26016674 PMCID: PMC4458059 DOI: 10.1186/s12934-015-0252-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/06/2015] [Indexed: 11/30/2022] Open
Abstract
Background L-tyrosine is a common precursor for a wide range of valuable secondary metabolites, including benzylisoquinoline alkaloids (BIAs) and many polyketides. An industrially tractable yeast strain optimized for production of L-tyrosine could serve as a platform for the development of BIA and polyketide cell factories. This study applied a targeted metabolomics approach to evaluate metabolic engineering strategies to increase the availability of intracellular L-tyrosine in the yeast Saccharomyces cerevisiae CEN.PK. Our engineering strategies combined localized pathway engineering with global engineering of central metabolism, facilitated by genome-scale steady-state modelling. Results Addition of a tyrosine feedback resistant version of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase Aro4 from S. cerevisiae was combined with overexpression of either a tyrosine feedback resistant yeast chorismate mutase Aro7, the native pentafunctional arom protein Aro1, native prephenate dehydrogenase Tyr1 or cyclohexadienyl dehydrogenase TyrC from Zymomonas mobilis. Loss of aromatic carbon was limited by eliminating phenylpyruvate decarboxylase Aro10. The TAL gene from Rhodobacter sphaeroides was used to produce coumarate as a simple test case of a heterologous by-product of tyrosine. Additionally, multiple strategies for engineering global metabolism to promote tyrosine production were evaluated using metabolic modelling. The T21E mutant of pyruvate kinase Cdc19 was hypothesized to slow the conversion of phosphoenolpyruvate to pyruvate and accumulate the former as precursor to the shikimate pathway. The ZWF1 gene coding for glucose-6-phosphate dehydrogenase was deleted to create an NADPH deficiency designed to force the cell to couple its growth to tyrosine production via overexpressed NADP+-dependent prephenate dehydrogenase Tyr1. Our engineered Zwf1− strain expressing TYRC ARO4FBR and grown in the presence of methionine achieved an intracellular L-tyrosine accumulation up to 520 μmol/g DCW or 192 mM in the cytosol, but sustained flux through this pathway was found to depend on the complete elimination of feedback inhibition and degradation pathways. Conclusions Our targeted metabolomics approach confirmed a likely regulatory site at DAHP synthase and identified another possible cofactor limitation at prephenate dehydrogenase. Additionally, the genome-scale metabolic model identified design strategies that have the potential to improve availability of erythrose 4-phosphate for DAHP synthase and cofactor availability for prephenate dehydrogenase. We evaluated these strategies and provide recommendations for further improvement of aromatic amino acid biosynthesis in S. cerevisiae. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0252-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas D Gold
- Department of Biology and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC, H4B 1R6, Canada.
| | - Christopher M Gowen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada.
| | - Francois-Xavier Lussier
- Department of Biology and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC, H4B 1R6, Canada.
| | - Sarat C Cautha
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada.
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada. .,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
| | - Vincent J J Martin
- Department of Biology and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC, H4B 1R6, Canada.
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Xu YF, Lu W, Rabinowitz JD. Avoiding misannotation of in-source fragmentation products as cellular metabolites in liquid chromatography-mass spectrometry-based metabolomics. Anal Chem 2015; 87:2273-81. [PMID: 25591916 DOI: 10.1021/ac504118y] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) technology allows for rapid quantitation of cellular metabolites, with metabolites identified by mass spectrometry and chromatographic retention time. Recently, with the development of rapid scanning high-resolution high accuracy mass spectrometers and the desire for high throughput screening, minimal or no chromatographic separation has become increasingly popular. When analyzing complex cellular extracts, however, the lack of chromatographic separation could potentially result in misannotation of structurally related metabolites. Here, we show that, even using electrospray ionization, a soft ionization method, in-source fragmentation generates unwanted byproducts of identical mass to common metabolites. For example, nucleotide-triphosphates generate nucleotide-diphosphates, and hexose-phosphates generate triose-phosphates. We evaluated yeast intracellular metabolite extracts and found more than 20 cases of in-source fragments that mimic common metabolites. Accordingly, chromatographic separation is required for accurate quantitation of many common cellular metabolites.
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Affiliation(s)
- Yi-Fan Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University , Princeton, New Jersey 08544, United States
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38
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Pisithkul T, Patel NM, Amador-Noguez D. Post-translational modifications as key regulators of bacterial metabolic fluxes. Curr Opin Microbiol 2015; 24:29-37. [PMID: 25597444 DOI: 10.1016/j.mib.2014.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 12/22/2014] [Accepted: 12/30/2014] [Indexed: 01/05/2023]
Abstract
In order to survive and compete in natural settings, bacteria must excel at quickly adapting their metabolism to fluctuations in nutrient availability and other environmental variables. This necessitates fast-acting post-translational regulatory mechanisms, that is, allostery or covalent modification, to control metabolic flux. While allosteric regulation has long been a well-established strategy for regulating metabolic enzyme activity in bacteria, covalent post-translational modes of regulation, such as phosphorylation or acetylation, have previously been regarded as regulatory mechanisms employed primarily by eukaryotic organisms. Recent findings, however, have shifted this perception and point to a widespread role for covalent posttranslational modification in the regulation of metabolic enzymes and fluxes in bacteria. This review provides an outline of the exciting recent advances in this area.
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Affiliation(s)
- Tippapha Pisithkul
- Cellular and Molecular Biology, University of Wisconsin-Madison, United States; Department of Bacteriology, University of Wisconsin-Madison, United States
| | - Nishaben M Patel
- Department of Bacteriology, University of Wisconsin-Madison, United States
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39
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Glycolysis controls plasma membrane glucose sensors to promote glucose signaling in yeasts. Mol Cell Biol 2014; 35:747-57. [PMID: 25512610 DOI: 10.1128/mcb.00515-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sensing of extracellular glucose is necessary for cells to adapt to glucose variation in their environment. In the respiratory yeast Kluyveromyces lactis, extracellular glucose controls the expression of major glucose permease gene RAG1 through a cascade similar to the Saccharomyces cerevisiae Snf3/Rgt2/Rgt1 glucose signaling pathway. This regulation depends also on intracellular glucose metabolism since we previously showed that glucose induction of the RAG1 gene is abolished in glycolytic mutants. Here we show that glycolysis regulates RAG1 expression through the K. lactis Rgt1 (KlRgt1) glucose signaling pathway by targeting the localization and probably the stability of Rag4, the single Snf3/Rgt2-type glucose sensor of K. lactis. Additionally, the control exerted by glycolysis on glucose signaling seems to be conserved in S. cerevisiae. This retrocontrol might prevent yeasts from unnecessary glucose transport and intracellular glucose accumulation.
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40
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Feng Y, De Franceschi G, Kahraman A, Soste M, Melnik A, Boersema PJ, de Laureto PP, Nikolaev Y, Oliveira AP, Picotti P. Global analysis of protein structural changes in complex proteomes. Nat Biotechnol 2014; 32:1036-44. [PMID: 25218519 DOI: 10.1038/nbt.2999] [Citation(s) in RCA: 244] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 07/25/2014] [Indexed: 01/28/2023]
Abstract
Changes in protein conformation can affect protein function, but methods to probe these structural changes on a global scale in cells have been lacking. To enable large-scale analyses of protein conformational changes directly in their biological matrices, we present a method that couples limited proteolysis with a targeted proteomics workflow. Using our method, we assessed the structural features of more than 1,000 yeast proteins simultaneously and detected altered conformations for ~300 proteins upon a change of nutrients. We find that some branches of carbon metabolism are transcriptionally regulated whereas others are regulated by enzyme conformational changes. We detect structural changes in aggregation-prone proteins and show the functional relevance of one of these proteins to the metabolic switch. This approach enables probing of both subtle and pronounced structural changes of proteins on a large scale.
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Affiliation(s)
- Yuehan Feng
- 1] Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland. [2]
| | - Giorgia De Franceschi
- 1] Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland. [2] CRIBI Biotechnology Centre, University of Padua, Padua, Italy. [3]
| | - Abdullah Kahraman
- 1] Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland. [2]
| | - Martin Soste
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Andre Melnik
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Paul J Boersema
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Yaroslav Nikolaev
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ana Paula Oliveira
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
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41
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Barry RM, Bitbol AF, Lorestani A, Charles EJ, Habrian CH, Hansen JM, Li HJ, Baldwin EP, Wingreen NS, Kollman JM, Gitai Z. Large-scale filament formation inhibits the activity of CTP synthetase. eLife 2014; 3:e03638. [PMID: 25030911 PMCID: PMC4126345 DOI: 10.7554/elife.03638] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
CTP Synthetase (CtpS) is a universally conserved and essential metabolic enzyme. While many enzymes form small oligomers, CtpS forms large-scale filamentous structures of unknown function in prokaryotes and eukaryotes. By simultaneously monitoring CtpS polymerization and enzymatic activity, we show that polymerization inhibits activity, and CtpS's product, CTP, induces assembly. To understand how assembly inhibits activity, we used electron microscopy to define the structure of CtpS polymers. This structure suggests that polymerization sterically hinders a conformational change necessary for CtpS activity. Structure-guided mutagenesis and mathematical modeling further indicate that coupling activity to polymerization promotes cooperative catalytic regulation. This previously uncharacterized regulatory mechanism is important for cellular function since a mutant that disrupts CtpS polymerization disrupts E. coli growth and metabolic regulation without reducing CTP levels. We propose that regulation by large-scale polymerization enables ultrasensitive control of enzymatic activity while storing an enzyme subpopulation in a conformationally restricted form that is readily activatable. DOI:http://dx.doi.org/10.7554/eLife.03638.001 Enzymes are proteins that perform reactions that can convert one or more chemicals (the substrates) into others (the products). The rate at which an enzyme produces its product is often carefully regulated. Some molecules slow or stop an enzyme by binding to and blocking the site where its substrates normally bind: its ‘active site’. Other molecules can also bind to sites other than the active site, which can cause the enzyme to become either more or less active. Almost all living things have an enzyme called CTP synthetase that makes one of the building blocks that is used to build DNA and a similar molecule called RNA. This enzyme converts a molecule called uridine triphosphate (or UTP) into another called cytidine triphosphate (CTP): a reaction that is powered by breaking down molecules of adenosine triphosphate (ATP). The amount of CTP synthetase made by a cell is carefully controlled. The enzyme's activity is also regulated by the levels of UTP and CTP, and by another molecule (called GTP) that binds to a site outside of its active site. Four copies of the CTP synthetase protein must work together before this enzyme can turn UTP into CTP. The enzyme also forms much larger aggregates, or polymers; however, it is not clear what causes these polymers to form, or what they do in a cell. Barry et al. have now discovered that CTP synthetase is almost completely inactivated when these polymers are formed. Furthermore, CTP encourages the polymers to form, whilst UTP and ATP cause them to disassemble. Therefore, this enzyme is least active when there is excess product in the cell, and most active when its substrates are plentiful. By determining the three-dimensional structure of a CTP synthetase polymer, Barry et al. reveal that although CTP is bound to the enzymes, their active sites are still freely accessible. However, the enzymes in the polymer appear to be locked into a shape that makes them unable to carry out their function. When Barry et al. then mutated the enzyme so that it was unable to form polymers it was also no longer inactivated in the same way by CTP. Bacterial cells with only these mutant versions of CTP synthetase are unable to properly control their levels of CTP. This suggests that polymer formation is important for regulating this enzyme in response to a build up of its product. Further work is needed to see whether the regulation of CTP synthetase activity by forming polymers is specific to this enzyme or a widespread mechanism that is used to control other enzymes too. DOI:http://dx.doi.org/10.7554/eLife.03638.002
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Affiliation(s)
- Rachael M Barry
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Anne-Florence Bitbol
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Alexander Lorestani
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Emeric J Charles
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - Chris H Habrian
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Jesse M Hansen
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - Hsin-Jung Li
- Department of Molecular Biology, Princeton University, Princeton, United States
| | - Enoch P Baldwin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, United States Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Justin M Kollman
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Canada
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, United States
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42
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Aldridge BB, Rhee KY. Microbial metabolomics: innovation, application, insight. Curr Opin Microbiol 2014; 19:90-96. [PMID: 25016173 DOI: 10.1016/j.mib.2014.06.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 06/09/2014] [Accepted: 06/19/2014] [Indexed: 11/26/2022]
Abstract
Most textbooks depict metabolism as a well understood housekeeping function of cells. However, organisms vary in their metabolic needs according to the specific niches they reside in and selective pressures encountered therein. Recent advances in analytical chemistry have begun to reveal an unexpected diversity in the composition, structure and regulation of metabolic networks. Here, we review key technological developments in the area of metabolism and their impact on our understanding of the fundamental roles of metabolism in cellular physiology.
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Affiliation(s)
- Bree B Aldridge
- Department of Microbiology & Molecular Biology, Tufts University School of Medicine, Boston, MA 02111, USA; Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Kyu Y Rhee
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA; Department of Microbiology & Immunology, Weill Cornell Medical College, New York, NY 10065, USA.
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43
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Abstract
Beyond fuelling cellular activities with building blocks and energy, metabolism also integrates environmental conditions into intracellular signals. The underlying regulatory network is complex and multifaceted: it ranges from slow interactions, such as changing gene expression, to rapid ones, such as the modulation of protein activity via post-translational modification or the allosteric binding of small molecules. In this Review, we outline the coordination of common metabolic tasks, including nutrient uptake, central metabolism, the generation of energy, the supply of amino acids and protein synthesis. Increasingly, a set of key metabolites is recognized to control individual regulatory circuits, which carry out specific functions of information input and regulatory output. Such a modular view of microbial metabolism facilitates an intuitive understanding of the molecular mechanisms that underlie cellular decision making.
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44
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Saad S, Peter M, Dechant R. In scarcity and abundance: metabolic signals regulating cell growth. Physiology (Bethesda) 2014; 28:298-309. [PMID: 23997189 DOI: 10.1152/physiol.00005.2013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Although nutrient availability is a major driver of cell growth, and continuous adaptation to nutrient supply is critical for the development and survival of all organisms, the molecular mechanisms of nutrient sensing are only beginning to emerge. Here, we highlight recent advances in the field of nutrient sensing and discuss arising principles governing how metabolism might regulate growth-promoting pathways. In addition, we discuss signaling functions of metabolic enzymes not directly related to their metabolic activity.
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Affiliation(s)
- Shady Saad
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
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45
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Kliegman JI, Fiedler D, Ryan CJ, Xu YF, Su XY, Thomas D, Caccese MC, Cheng A, Shales M, Rabinowitz JD, Krogan NJ, Shokat KM. Chemical genetics of rapamycin-insensitive TORC2 in S. cerevisiae. Cell Rep 2013; 5:1725-36. [PMID: 24360963 PMCID: PMC4007695 DOI: 10.1016/j.celrep.2013.11.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 07/10/2013] [Accepted: 11/22/2013] [Indexed: 11/28/2022] Open
Abstract
Current approaches for identifying synergistic targets use cell culture models to see if the combined effect of clinically available drugs is better than predicted by their individual efficacy. New techniques are needed to systematically and rationally identify targets and pathways that may be synergistic targets. Here, we created a tool to screen and identify molecular targets that may synergize with new inhibitors of target of rapamycin (TOR), a conserved protein that is a major integrator of cell proliferation signals in the nutrient-signaling pathway. Although clinical results from TOR complex 1 (TORC1)-specific inhibition using rapamycin analogs have been disappointing, trials using inhibitors that also target TORC2 have been promising. To understand this increased therapeutic efficacy and to discover secondary targets for combination therapy, we engineered Tor2 in S. cerevisiae to accept an orthogonal inhibitor. We used this tool to create a chemical epistasis miniarray profile (ChE-MAP) by measuring interactions between the chemically inhibited Tor2 kinase and a diverse library of deletion mutants. The ChE-MAP identified known TOR components and distinguished between TORC1- and TORC2-dependent functions. The results showed a TORC2-specific interaction with the pentose phosphate pathway, a previously unappreciated TORC2 function that suggests a role for the complex in balancing the high energy demand required for ribosome biogenesis.
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Affiliation(s)
- Joseph I Kliegman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Dorothea Fiedler
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Colm J Ryan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158, USA; School of Computer Science and Informatics, University College Dublin, Dublin 4, Ireland
| | - Yi-Fan Xu
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Xiao-Yang Su
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - David Thomas
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Max C Caccese
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA
| | - Ada Cheng
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158, USA
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158, USA
| | | | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158, USA; J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, San Francisco, CA 94158, USA.
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Xu YF, Létisse F, Absalan F, Lu W, Kuznetsova E, Brown G, Caudy AA, Yakunin AF, Broach JR, Rabinowitz JD. Nucleotide degradation and ribose salvage in yeast. Mol Syst Biol 2013; 9:665. [PMID: 23670538 PMCID: PMC4039369 DOI: 10.1038/msb.2013.21] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/08/2013] [Indexed: 12/30/2022] Open
Abstract
Nucleotide degradation is a universal metabolic capability. Here we combine metabolomics, genetics and biochemistry to characterize the yeast pathway. Nutrient starvation, via PKA, AMPK/SNF1, and TOR, triggers autophagic breakdown of ribosomes into nucleotides. A protein not previously associated with nucleotide degradation, Phm8, converts nucleotide monophosphates into nucleosides. Downstream steps, which involve the purine nucleoside phosphorylase, Pnp1, and pyrimidine nucleoside hydrolase, Urh1, funnel ribose into the nonoxidative pentose phosphate pathway. During carbon starvation, the ribose-derived carbon accumulates as sedoheptulose-7-phosphate, whose consumption by transaldolase is impaired due to depletion of transaldolase's other substrate, glyceraldehyde-3-phosphate. Oxidative stress increases glyceraldehyde-3-phosphate, resulting in rapid consumption of sedoheptulose-7-phosphate to make NADPH for antioxidant defense. Ablation of Phm8 or double deletion of Pnp1 and Urh1 prevent effective nucleotide salvage, resulting in metabolite depletion and impaired survival of starving yeast. Thus, ribose salvage provides means of surviving nutrient starvation and oxidative stress.
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Affiliation(s)
- Yi-Fan Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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Oliveira AP, Ludwig C, Picotti P, Kogadeeva M, Aebersold R, Sauer U. Regulation of yeast central metabolism by enzyme phosphorylation. Mol Syst Biol 2013; 8:623. [PMID: 23149688 PMCID: PMC3531909 DOI: 10.1038/msb.2012.55] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 10/05/2012] [Indexed: 02/03/2023] Open
Abstract
As a frequent post-translational modification, protein phosphorylation regulates many cellular processes. Although several hundred phosphorylation sites have been mapped to metabolic enzymes in Saccharomyces cerevisiae, functionality was demonstrated for few of them. Here, we describe a novel approach to identify in vivo functionality of enzyme phosphorylation by combining flux analysis with proteomics and phosphoproteomics. Focusing on the network of 204 enzymes that constitute the yeast central carbon and amino-acid metabolism, we combined protein and phosphoprotein levels to identify 35 enzymes that change their degree of phosphorylation during growth under five conditions. Correlations between previously determined intracellular fluxes and phosphoprotein abundances provided first functional evidence for five novel phosphoregulated enzymes in this network, adding to nine known phosphoenzymes. For the pyruvate dehydrogenase complex E1 α subunit Pda1 and the newly identified phosphoregulated glycerol-3-phosphate dehydrogenase Gpd1 and phosphofructose-1-kinase complex β subunit Pfk2, we then validated functionality of specific phosphosites through absolute peptide quantification by targeted mass spectrometry, metabolomics and physiological flux analysis in mutants with genetically removed phosphosites. These results demonstrate the role of phosphorylation in controlling the metabolic flux realised by these three enzymes.
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Affiliation(s)
- Ana Paula Oliveira
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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