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Millard P, Enjalbert B, Uttenweiler-Joseph S, Portais JC, Létisse F. Control and regulation of acetate overflow in Escherichia coli. eLife 2021; 10:63661. [PMID: 33720011 PMCID: PMC8021400 DOI: 10.7554/elife.63661] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 03/12/2021] [Indexed: 12/21/2022] Open
Abstract
Overflow metabolism refers to the production of seemingly wasteful by-products by cells during growth on glucose even when oxygen is abundant. Two theories have been proposed to explain acetate overflow in Escherichia coli – global control of the central metabolism and local control of the acetate pathway – but neither accounts for all observations. Here, we develop a kinetic model of E. coli metabolism that quantitatively accounts for observed behaviours and successfully predicts the response of E. coli to new perturbations. We reconcile these theories and clarify the origin, control, and regulation of the acetate flux. We also find that, in turns, acetate regulates glucose metabolism by coordinating the expression of glycolytic and TCA genes. Acetate should not be considered a wasteful end-product since it is also a co-substrate and a global regulator of glucose metabolism in E. coli. This has broad implications for our understanding of overflow metabolism.
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Affiliation(s)
- Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Brice Enjalbert
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Jean-Charles Portais
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.,RESTORE, Université de Toulouse, INSERM U1031, CNRS 5070, Université Toulouse III - Paul Sabatier, EFS, Toulouse, France
| | - Fabien Létisse
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.,Université Toulouse III - Paul Sabatier, Toulouse, France
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2
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Morales-Polanco F, Bates C, Lui J, Casson J, Solari CA, Pizzinga M, Forte G, Griffin C, Garner KEL, Burt HE, Dixon HL, Hubbard S, Portela P, Ashe MP. Core Fermentation (CoFe) granules focus coordinated glycolytic mRNA localization and translation to fuel glucose fermentation. iScience 2021; 24:102069. [PMID: 33554071 PMCID: PMC7859310 DOI: 10.1016/j.isci.2021.102069] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/16/2020] [Accepted: 01/12/2021] [Indexed: 12/24/2022] Open
Abstract
Glycolysis is a fundamental metabolic pathway for glucose catabolism across biology, and glycolytic enzymes are among the most abundant proteins in cells. Their expression at such levels provides a particular challenge. Here we demonstrate that the glycolytic mRNAs are localized to granules in yeast and human cells. Detailed live cell and smFISH studies in yeast show that the mRNAs are actively translated in granules, and this translation appears critical for the localization. Furthermore, this arrangement is likely to facilitate the higher level organization and control of the glycolytic pathway. Indeed, the degree of fermentation required by cells is intrinsically connected to the extent of mRNA localization to granules. On this basis, we term these granules, core fermentation (CoFe) granules; they appear to represent translation factories, allowing high-level coordinated enzyme synthesis for a critical metabolic pathway.
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Affiliation(s)
- Fabian Morales-Polanco
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Christian Bates
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Jennifer Lui
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Joseph Casson
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Clara A Solari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Mariavittoria Pizzinga
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Gabriela Forte
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Claire Griffin
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Kirsten E L Garner
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Harriet E Burt
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Hannah L Dixon
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Simon Hubbard
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Paula Portela
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, IQUIBICEN-CONICET, Buenos Aires, Argentina
| | - Mark P Ashe
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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Noh MH, Cha S, Kim M, Jung GY. Recent Advances in Microbial Cell Growth Regulation Strategies for Metabolic Engineering. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0511-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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4
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Lane S, Xu H, Oh EJ, Kim H, Lesmana A, Jeong D, Zhang G, Tsai CS, Jin YS, Kim SR. Glucose repression can be alleviated by reducing glucose phosphorylation rate in Saccharomyces cerevisiae. Sci Rep 2018; 8:2613. [PMID: 29422502 PMCID: PMC5805702 DOI: 10.1038/s41598-018-20804-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/19/2018] [Indexed: 01/06/2023] Open
Abstract
Microorganisms commonly exhibit preferential glucose consumption and diauxic growth when cultured in mixtures of glucose and other sugars. Although various genetic perturbations have alleviated the effects of glucose repression on consumption of specific sugars, a broadly applicable mechanism remains unknown. Here, we report that a reduction in the rate of glucose phosphorylation alleviates the effects of glucose repression in Saccharomyces cerevisiae. Through adaptive evolution under a mixture of xylose and the glucose analog 2-deoxyglucose, we isolated a mutant strain capable of simultaneously consuming glucose and xylose. Genome sequencing of the evolved mutant followed by CRISPR/Cas9-based reverse engineering revealed that mutations in the glucose phosphorylating enzymes (Hxk1, Hxk2, Glk1) were sufficient to confer simultaneous glucose and xylose utilization. We then found that varying hexokinase expression with an inducible promoter led to the simultaneous utilization of glucose and xylose. Interestingly, no mutations in sugar transporters occurred during the evolution, and no specific transporter played an indispensable role in simultaneous sugar utilization. Additionally, we demonstrated that slowing glucose consumption also enabled simultaneous utilization of glucose and galactose. These results suggest that the rate of intracellular glucose phosphorylation is a decisive factor for metabolic regulations of mixed sugars.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Haiqing Xu
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Eun Joong Oh
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Heejin Kim
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anastashia Lesmana
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Guochang Zhang
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ching-Sung Tsai
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. .,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea. .,Institute of Agricultural Science & Technology, Kyungpook National University, Daegu, Republic of Korea.
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Current state and perspectives in hydrogen production by Escherichia coli: roles of hydrogenases in glucose or glycerol metabolism. Appl Microbiol Biotechnol 2018; 102:2041-2050. [DOI: 10.1007/s00253-018-8752-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/28/2017] [Accepted: 12/29/2017] [Indexed: 01/07/2023]
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Steps towards 'drop-in' biofuels: focusing on metabolic pathways. Curr Opin Biotechnol 2017; 53:26-32. [PMID: 29207330 DOI: 10.1016/j.copbio.2017.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
The past decade has witnessed rapid advance in microbial production of 'drop-in' biofuels from renewable resources. Various biosynthetic pathways have been constructed to produce biofuels with diverse structures, and multiple metabolic engineering strategies have been developed to increase biofuel titers, yields, productivities and system robustness. In this review, we intend to give a brief but comprehensive overview of the most recent progresses on four essential pathways leading to 'drop-in' biofuel production, with an emphasis on the metabolic pathway efficiencies and biofuel structures. Furthermore, we also provide an insightful discussion on optimization strategies to improve the robustness of the microbial platforms for biofuel production.
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Zhang Y, Liu D, Chen Z. Production of C2-C4 diols from renewable bioresources: new metabolic pathways and metabolic engineering strategies. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:299. [PMID: 29255482 PMCID: PMC5727944 DOI: 10.1186/s13068-017-0992-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/05/2017] [Indexed: 05/17/2023]
Abstract
C2-C4 diols classically derived from fossil resource are very important bulk chemicals which have been used in a wide range of areas, including solvents, fuels, polymers, cosmetics, and pharmaceuticals. Production of C2-C4 diols from renewable resources has received significant interest in consideration of the reducing fossil resource and the increasing environmental issues. While bioproduction of certain diols like 1,3-propanediol has been commercialized in recent years, biosynthesis of many other important C2-C4 diol isomers is highly challenging due to the lack of natural synthesis pathways. Recent advances in synthetic biology have enabled the de novo design of completely new pathways to non-natural molecules from renewable feedstocks. In this study, we review recent advances in bioproduction of C2-C4 diols, focusing on new metabolic pathways and metabolic engineering strategies being developed. We also discuss the challenges and future trends toward the development of economically competitive processes for bio-based diol production.
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Affiliation(s)
- Ye Zhang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
| | - Dehua Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
- Center of Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
| | - Zhen Chen
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084 China
- Key Lab of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084 China
- Tsinghua Innovation Center in Dongguan, Dongguan, 523808 China
- Center of Synthetic and Systems Biology, Tsinghua University, Beijing, 100084 China
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