1
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Yang B, Li C, Ren Y, Wang W, Zhang X, Han X. Construction of the Glycolysis Metabolic Pathway Inside an Artificial Cell for the Synthesis of Amino Acid and Its Reversible Deformation. J Am Chem Soc 2024; 146:21847-21858. [PMID: 39042264 DOI: 10.1021/jacs.4c06227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
The bottom-up construction of artificial cells is beneficial for understanding cell working mechanisms. The glycolysis metabolism mimicry inside artificial cells is challenging. Herein, the glycolytic pathway (Entner-Doudoroff pathway in archaea) is reconstituted inside artificial cells. The glycolytic pathway comprising glucose dehydrogenase (GDH), gluconate dehydratase (GAD), and 2-keto-3-deoxygluconate aldolase (KDGA) converts glucose molecules to pyruvate molecules. Inside artificial cells, pyruvate molecules are further converted into alanine with the help of alanine dehydrogenase (AlaDH) to build a metabolic pathway for synthesizing amino acid. On the other hand, the pyruvate molecules from glycolysis stimulate the living mitochondria to produce ATP inside artificial cells, which further trigger actin monomers to polymerize to form actin filaments. With the addition of methylcellulose inside the artificial cell, the actin filaments form adjacent to the inner lipid bilayer, deforming the artificial cell from a spherical shape to a spindle shape. The spindle-shaped artificial cell reverses to a spherical shape by depolymerizing the actin filament upon laser irradiation. The glycolytic pathway and its further extension to produce amino acids (or ATP) inside artificial cells pave the path to build functional artificial cells with more complicated metabolic pathways.
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Affiliation(s)
- Boyu Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Chao Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Yongshuo Ren
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Weichen Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Xiangxiang Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
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2
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Arunachalam E, Keber FC, Law RC, Kumar CK, Shen Y, Park JO, Wühr M, Needleman DJ. Robustness of mitochondrial biogenesis and respiration explain aerobic glycolysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.601975. [PMID: 39005310 PMCID: PMC11245115 DOI: 10.1101/2024.07.04.601975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
A long-standing observation is that in fast-growing cells, respiration rate declines with increasing growth rate and is compensated by an increase in fermentation, despite respiration being more efficient than fermentation. This apparent preference for fermentation even in the presence of oxygen is known as aerobic glycolysis, and occurs in bacteria, yeast, and cancer cells. Considerable work has focused on understanding the potential benefits that might justify this seemingly wasteful metabolic strategy, but its mechanistic basis remains unclear. Here we show that aerobic glycolysis results from the saturation of mitochondrial respiration and the decoupling of mitochondrial biogenesis from the production of other cellular components. Respiration rate is insensitive to acute perturbations of cellular energetic demands or nutrient supplies, and is explained simply by the amount of mitochondria per cell. Mitochondria accumulate at a nearly constant rate across different growth conditions, resulting in mitochondrial amount being largely determined by cell division time. In contrast, glucose uptake rate is not saturated, and is accurately predicted by the abundances and affinities of glucose transporters. Combining these models of glucose uptake and respiration provides a quantitative, mechanistic explanation for aerobic glycolysis. The robustness of specific respiration rate and mitochondrial biogenesis, paired with the flexibility of other bioenergetic and biosynthetic fluxes, may play a broad role in shaping eukaryotic cell metabolism.
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Affiliation(s)
- Easun Arunachalam
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Felix C. Keber
- Lewis-Sigler Institute for Integrative Genomics
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Richard C. Law
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chirag K. Kumar
- Lewis-Sigler Institute for Integrative Genomics
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yihui Shen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Junyoung O. Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Daniel J. Needleman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
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3
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Liu JJ, Wang J, Chen QY, Chen F, Wang GJ. Photoresponsive Nanoarchitectonics Based on Copper-Porphyrins for Near-Infrared-Enhanced Bacterial Treatment. ACS OMEGA 2024; 9:24513-24519. [PMID: 38882152 PMCID: PMC11170729 DOI: 10.1021/acsomega.4c00496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/15/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024]
Abstract
Antibiotic resistance is one of the biggest challenges that causes incurable diseases and endangers public health. Metal-porphyrin-modified nanoarchitectonics can enhance the bacterial affinity and destruction of cell walls. Herein, a new photoresponsive nanoarchitectonics (BPGa@COF-Cu) was synthesized by doping Ga(III) on the surface of black phosphorus (BP) and subsequently loaded into a Cu(II)-based covalent-organic framework (COF-Cu). The COF-Cu was induced by the coupling reaction of terephthalic chloride with amino-substituted porphyrin derivatives (THPP), followed by the coordination of the Cu(II) ion. The material BPGa@COF-Cu is a nanoball, and the mean radius is ca. 250 nm. The photochemical properties of BPGa@COF-Cu show that it efficiently catalyzes H2O2 into ·OH. BPGa@COF-Cu can also produce both singlet oxygen and heat upon 808 nm irradiation. Further, BPGa@COF-Cu was employed to inhibit bacteria, and the results showed that it can destroy the membrane of bacteria. The MIC (minimal inhibition concentration) of BPGa@COF-Cu against E. coli was 1 μg/mL. All the data suggest that BPGa@COF-Cu is a multiple nanoarchitectonics for bacterial treatment.
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Affiliation(s)
- Jing-Jing Liu
- School of Chemistry and Chemical Engineering, Jiangsu University, Jingkou District, Xuefu Road, Zhenjiang 212013, People's Republic of China
| | - Jun Wang
- School of Chemistry and Chemical Engineering, Jiangsu University, Jingkou District, Xuefu Road, Zhenjiang 212013, People's Republic of China
| | - Qiu-Yun Chen
- School of Chemistry and Chemical Engineering, Jiangsu University, Jingkou District, Xuefu Road, Zhenjiang 212013, People's Republic of China
| | - Feng Chen
- School of Chemistry and Chemical Engineering, Jiangsu University, Jingkou District, Xuefu Road, Zhenjiang 212013, People's Republic of China
| | - Gao-Ji Wang
- School of Chemistry and Chemical Engineering, Jiangsu University, Jingkou District, Xuefu Road, Zhenjiang 212013, People's Republic of China
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4
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Lakhani A, Chen X, Chen LC, Hong M, Khericha M, Chen Y, Chen YY, Park JO. Extracellular domains of CARs reprogramme T cell metabolism without antigen stimulation. Nat Metab 2024; 6:1143-1160. [PMID: 38658805 DOI: 10.1038/s42255-024-01034-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Metabolism is an indispensable part of T cell proliferation, activation and exhaustion, yet the metabolism of chimeric antigen receptor (CAR)-T cells remains incompletely understood. CARs are composed of extracellular domains-often single-chain variable fragments (scFvs)-that determine ligand specificity and intracellular domains that trigger signalling following antigen binding. Here, we show that CARs differing only in the scFv variously reprogramme T cell metabolism. Even without exposure to antigens, some CARs increase proliferation and nutrient uptake in T cells. Using stable isotope tracers and mass spectrometry, we observed basal metabolic fluxes through glycolysis doubling and amino acid uptake overtaking anaplerosis in CAR-T cells harbouring a rituximab scFv, unlike other similar anti-CD20 scFvs. Disparate rituximab and 14G2a-based anti-GD2 CAR-T cells are similarly hypermetabolic and channel excess nutrients to nitrogen overflow metabolism. Modest overflow metabolism of CAR-T cells and metabolic compatibility between cancer cells and CAR-T cells are identified as features of efficacious CAR-T cell therapy.
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Affiliation(s)
- Aliya Lakhani
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ximin Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laurence C Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mihe Hong
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mobina Khericha
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yu Chen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yvonne Y Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, CA, USA
- Parker Institute for Cancer Immunotherapy at UCLA, Los Angeles, CA, USA
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, CA, USA.
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5
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Mori M, Patsalo V, Euler C, Williamson JR, Scott M. Proteome partitioning constraints in long-term laboratory evolution. Nat Commun 2024; 15:4087. [PMID: 38744842 PMCID: PMC11094134 DOI: 10.1038/s41467-024-48447-2] [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: 08/04/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Adaptive laboratory evolution experiments provide a controlled context in which the dynamics of selection and adaptation can be followed in real-time at the single-nucleotide level. And yet this precision introduces hundreds of degrees-of-freedom as genetic changes accrue in parallel lineages over generations. On short timescales, physiological constraints have been leveraged to provide a coarse-grained view of bacterial gene expression characterized by a small set of phenomenological parameters. Here, we ask whether this same framework, operating at a level between genotype and fitness, informs physiological changes that occur on evolutionary timescales. Using a strain adapted to growth in glucose minimal medium, we find that the proteome is substantially remodeled over 40 000 generations. The most striking change is an apparent increase in enzyme efficiency, particularly in the enzymes of lower-glycolysis. We propose that deletion of metabolic flux-sensing regulation early in the adaptation results in increased enzyme saturation and can account for the observed proteome remodeling.
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Affiliation(s)
- Matteo Mori
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
| | - Vadim Patsalo
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Christian Euler
- Department of Chemical Engineering, University of Waterloo, Waterloo, ON, Canada
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Matthew Scott
- Waterloo Centre for Microbial Research and the Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada.
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6
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Shen Y, Dinh HV, Cruz ER, Chen Z, Bartman CR, Xiao T, Call CM, Ryseck RP, Pratas J, Weilandt D, Baron H, Subramanian A, Fatma Z, Wu ZY, Dwaraknath S, Hendry JI, Tran VG, Yang L, Yoshikuni Y, Zhao H, Maranas CD, Wühr M, Rabinowitz JD. Mitochondrial ATP generation is more proteome efficient than glycolysis. Nat Chem Biol 2024:10.1038/s41589-024-01571-y. [PMID: 38448734 DOI: 10.1038/s41589-024-01571-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
Metabolic efficiency profoundly influences organismal fitness. Nonphotosynthetic organisms, from yeast to mammals, derive usable energy primarily through glycolysis and respiration. Although respiration is more energy efficient, some cells favor glycolysis even when oxygen is available (aerobic glycolysis, Warburg effect). A leading explanation is that glycolysis is more efficient in terms of ATP production per unit mass of protein (that is, faster). Through quantitative flux analysis and proteomics, we find, however, that mitochondrial respiration is actually more proteome efficient than aerobic glycolysis. This is shown across yeast strains, T cells, cancer cells, and tissues and tumors in vivo. Instead of aerobic glycolysis being valuable for fast ATP production, it correlates with high glycolytic protein expression, which promotes hypoxic growth. Aerobic glycolytic yeasts do not excel at aerobic growth but outgrow respiratory cells during oxygen limitation. We accordingly propose that aerobic glycolysis emerges from cells maintaining a proteome conducive to both aerobic and hypoxic growth.
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Affiliation(s)
- Yihui Shen
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Hoang V Dinh
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Edward R Cruz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Zihong Chen
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA
| | - Caroline R Bartman
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA
| | - Tianxia Xiao
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Catherine M Call
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Rolf-Peter Ryseck
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Jimmy Pratas
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Daniel Weilandt
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Heide Baron
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Arjuna Subramanian
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Zia Fatma
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zong-Yen Wu
- US Department of Energy Joint Genome Institute and Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sudharsan Dwaraknath
- US Department of Energy Joint Genome Institute and Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John I Hendry
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Vinh G Tran
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Lifeng Yang
- Department of Chemistry, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute and Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton, NJ, USA.
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7
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Law RC, Nurwono G, Park JO. A parallel glycolysis provides a selective advantage through rapid growth acceleration. Nat Chem Biol 2024; 20:314-322. [PMID: 37537378 PMCID: PMC10987256 DOI: 10.1038/s41589-023-01395-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Glycolysis is a universal metabolic process that breaks down glucose to produce adenosine triphosphate (ATP) and biomass precursors. The Entner-Doudoroff (ED) pathway is a glycolytic pathway that parallels textbook glycolysis but yields half as much ATP. Accordingly, in organisms that possess both glycolytic pathways (for example, Escherichia coli), its raison d'être remains a mystery. In this study, we found that the ED pathway provides a selective advantage during growth acceleration. Upon carbon and nitrogen upshifts, E. coli accelerates growth faster with than without the ED pathway. Concurrent isotope tracing reveals that the ED pathway flux increases faster than that of textbook glycolysis. We attribute the fast response time of the ED pathway to its strong thermodynamic driving force and streamlining of glucose import. Intermittent nutrient supply manifests the evolutionary advantage of the parallel glycolysis; thus, the dynamic nature of an ostensibly redundant pathway's role in promoting rapid adaptation constitutes a metabolic design principle.
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Affiliation(s)
- Richard C Law
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Glenn Nurwono
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
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8
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Zhang Z, Chu R, Wei W, Song W, Ye C, Chen X, Wu J, Liu L, Gao C. Systems engineering of Escherichia coli for high-level glutarate production from glucose. Nat Commun 2024; 15:1032. [PMID: 38310110 PMCID: PMC10838341 DOI: 10.1038/s41467-024-45448-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 01/24/2024] [Indexed: 02/05/2024] Open
Abstract
Glutarate is a key monomer in polyester and polyamide production. The low efficiency of the current biosynthetic pathways hampers its production by microbial cell factories. Herein, through metabolic simulation, a lysine-overproducing E. coli strain Lys5 is engineered, achieving titer, yield, and productivity of 195.9 g/L, 0.67 g/g glucose, and 5.4 g/L·h, respectively. Subsequently, the pathway involving aromatic aldehyde synthase, monoamine oxidase, and aldehyde dehydrogenase (AMA pathway) is introduced into E. coli Lys5 to produce glutarate from glucose. To enhance the pathway's efficiency, rational mutagenesis on the aldehyde dehydrogenase is performed, resulting in the development of variant Mu5 with a 50-fold increase in catalytic efficiency. Finally, a glutarate tolerance gene cbpA is identified and genomically overexpressed to enhance glutarate productivity. With enzyme expression optimization, the glutarate titer, yield, and productivity of E. coli AMA06 reach 88.4 g/L, 0.42 g/g glucose, and 1.8 g/L·h, respectively. These findings hold implications for improving glutarate biosynthesis efficiency in microbial cell factories.
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Affiliation(s)
- Zhilan Zhang
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Ruyin Chu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Wanqing Wei
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210000, China
| | - Xiulai Chen
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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9
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Jackson BT, Finley LWS. Metabolic regulation of the hallmarks of stem cell biology. Cell Stem Cell 2024; 31:161-180. [PMID: 38306993 PMCID: PMC10842269 DOI: 10.1016/j.stem.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Stem cells perform many different functions, each of which requires specific metabolic adaptations. Over the past decades, studies of pluripotent and tissue stem cells have uncovered a range of metabolic preferences and strategies that correlate with or exert control over specific cell states. This review aims to describe the common themes that emerge from the study of stem cell metabolism: (1) metabolic pathways supporting stem cell proliferation, (2) metabolic pathways maintaining stem cell quiescence, (3) metabolic control of cellular stress responses and cell death, (4) metabolic regulation of stem cell identity, and (5) metabolic requirements of the stem cell niche.
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Affiliation(s)
- Benjamin T Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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Kelly E, Petersen LH, Huggett D, Hala D. Reaction thermodynamics as a constraint on piscine steroidogenesis flux distributions. Comp Biochem Physiol A Mol Integr Physiol 2024; 287:111533. [PMID: 37844836 DOI: 10.1016/j.cbpa.2023.111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
While a considerable amount is known of the dynamics of piscine steroidogenesis during reproduction, the influence of thermodynamics constraints on its control has not been studied. In this manuscript, Gibbs free energy change of reactions was calculated for piscine steroidogenesis using the in silico eQuilibrator thermodynamics calculator. The analysis identified cytochrome P450 (cyp450) oxidoreductase reactions to have more negative Gibbs free energy changes relative to hydroxysteroid (HSD) and transferase reactions. In addition, a more favorable Gibbs free energy change was predicted for the Δ5 (cyp450 catalyzed) vs. Δ4 (HSD catalyzed) steroidogenesis branch-point, which converts pregnenolone to 17α-hydroxypregnenolone or progesterone respectively. Comparison of in silico predictions with in vivo experimentally measured flux across the Δ5 vs. Δ4 branch-point showed higher flux through the thermodynamically more favorable Δ5 pathway in reproducing or spawning vs. non-spawning fathead minnows (Pimephales promelas). However, the exposure of fish to endocrine stressors such as hypoxia or the synthetic estrogen 17α-ethinylestradiol (EE2), resulted in increased flux through both Δ5 and Δ4 pathways, indicating an adaptive response to increase steroidogenic redundancy. The correspondence of elevated flux through the Δ5 branch-point in spawning fish indicated the use of a thermodynamically favorable pathway to optimize steroid hormone productions during reproduction. We hypothesize that such selective use of a thermodynamically favorable steroidogenesis pathway may conserve reduced equivalents or transcriptional costs for investment to other biosynthetic or catabolic reactions to support reproduction. If generalizable, such an approach can provide novel insights into the structural principles and regulation of steroidogenesis or other metabolic pathways.
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Affiliation(s)
- E Kelly
- Binghamton University, 4400 Vestal Parkway E, Binghamton, NY, USA; Department of Marine Biology, Texas A&M University at Galveston, TX, USA
| | - L H Petersen
- Department of Marine Biology, Texas A&M University at Galveston, TX, USA
| | - D Huggett
- University of North Texas, Denton, TX, USA
| | - D Hala
- Department of Marine Biology, Texas A&M University at Galveston, TX, USA.
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11
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Callaghan MM, Thusoo E, Sharma BD, Getahun F, Stevenson DM, Maranas C, Olson DG, Lynd LR, Amador-Noguez D. Deuterated water as a substrate-agnostic isotope tracer for investigating reversibility and thermodynamics of reactions in central carbon metabolism. Metab Eng 2023; 80:254-266. [PMID: 37923005 DOI: 10.1016/j.ymben.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/16/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
Stable isotope tracers are a powerful tool for the quantitative analysis of microbial metabolism, enabling pathway elucidation, metabolic flux quantification, and assessment of reaction and pathway thermodynamics. 13C and 2H metabolic flux analysis commonly relies on isotopically labeled carbon substrates, such as glucose. However, the use of 2H-labeled nutrient substrates faces limitations due to their high cost and limited availability in comparison to 13C-tracers. Furthermore, isotope tracer studies in industrially relevant bacteria that metabolize complex substrates such as cellulose, hemicellulose, or lignocellulosic biomass, are challenging given the difficulty in obtaining these as isotopically labeled substrates. In this study, we examine the potential of deuterated water (2H2O) as an affordable, substrate-neutral isotope tracer for studying central carbon metabolism. We apply 2H2O labeling to investigate the reversibility of glycolytic reactions across three industrially relevant bacterial species -C. thermocellum, Z. mobilis, and E. coli-harboring distinct glycolytic pathways with unique thermodynamics. We demonstrate that 2H2O labeling recapitulates previous reversibility and thermodynamic findings obtained with established 13C and 2H labeled nutrient substrates. Furthermore, we exemplify the utility of this 2H2O labeling approach by applying it to high-substrate C. thermocellum fermentations -a setting in which the use of conventional tracers is impractical-thereby identifying the glycolytic enzyme phosphofructokinase as a major bottleneck during high-substrate fermentations and unveiling critical insights that will steer future engineering efforts to enhance ethanol production in this cellulolytic organism. This study demonstrates the utility of deuterated water as a substrate-agnostic isotope tracer for examining flux and reversibility of central carbon metabolic reactions, which yields biological insights comparable to those obtained using costly 2H-labeled nutrient substrates.
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Affiliation(s)
- Melanie M Callaghan
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Eashant Thusoo
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Bishal D Sharma
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Fitsum Getahun
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - David M Stevenson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Costas Maranas
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Daniel G Olson
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Lee R Lynd
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Daniel Amador-Noguez
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.
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12
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Lu W, Park NR, TeSlaa T, Jankowski CS, Samarah L, McReynolds M, Xing X, Schembri J, Woolf MT, Rabinowitz JD, Davidson SM. Acidic Methanol Treatment Facilitates Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging of Energy Metabolism. Anal Chem 2023; 95:14879-14888. [PMID: 37756255 PMCID: PMC10568533 DOI: 10.1021/acs.analchem.3c01875] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/15/2023] [Indexed: 09/29/2023]
Abstract
Detection of small molecule metabolites (SMM), particularly those involved in energy metabolism using MALDI-mass spectrometry imaging (MSI), is challenging due to factors including ion suppression from other analytes present (e.g., proteins and lipids). One potential solution to enhance SMM detection is to remove analytes that cause ion suppression from tissue sections before matrix deposition through solvent washes. Here, we systematically investigated solvent treatment conditions to improve SMM signal and preserve metabolite localization. Washing with acidic methanol significantly enhances the detection of phosphate-containing metabolites involved in energy metabolism. The improved detection is due to removing lipids and highly polar metabolites that cause ion suppression and denaturing proteins that release bound phosphate-containing metabolites. Stable isotope infusions of [13C6]nicotinamide coupled to MALDI-MSI ("Iso-imaging") in the kidney reveal patterns that indicate blood vessels, medulla, outer stripe, and cortex. We also observed different ATP:ADP raw signals across mouse kidney regions, consistent with regional differences in glucose metabolism favoring either gluconeogenesis or glycolysis. In mouse muscle, Iso-imaging using [13C6]glucose shows high glycolytic flux from infused circulating glucose in type 1 and 2a fibers (soleus) and relatively lower glycolytic flux in type 2b fiber type (gastrocnemius). Thus, improved detection of phosphate-containing metabolites due to acidic methanol treatment combined with isotope tracing provides an improved way to probe energy metabolism with spatial resolution in vivo.
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Affiliation(s)
- Wenyun Lu
- 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
| | - Noel R. Park
- Lewis
Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Tara TeSlaa
- Department
of Molecular and Medical Pharmacology, University
of California Los Angeles, Los Angeles, California 90095, United States
| | - Connor S.R. Jankowski
- Lewis
Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Laith Samarah
- Lewis
Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Melanie McReynolds
- Department
of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Xi Xing
- 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
| | - Jessica Schembri
- Lewis
Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
| | - Morgan T. Woolf
- Department
of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Joshua D. Rabinowitz
- Lewis
Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Rutgers
Cancer Institute of New Jersey (CINJ), Rutgers
University, New Brunswick, New Jersey 08901, United States
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Ludwig
Institute for Cancer Research, Princeton
University, Princeton, New Jersey 08544, United States
| | - Shawn M. Davidson
- Lewis
Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, United States
- Rutgers
Cancer Institute of New Jersey (CINJ), Rutgers
University, New Brunswick, New Jersey 08901, United States
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13
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Wang J, Chen F, Chen QY, Wang GJ. Europium- and Black Phosphorus-Functionalized Porphyrin as an l-Arginine Sensor and l-Arginine-Activated PDT/PTT Agent for Bacterial Treatment. ACS APPLIED MATERIALS & INTERFACES 2023; 15:41861-41869. [PMID: 37610772 DOI: 10.1021/acsami.3c07354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The attenuation of bacterial metabolism provides an adjunct to the treatment of bacterial infections. To develop a bacterial eradication agent, a bioactivatable material (BP@Eu-TCPP) was designed and synthesized by coordination and reduction of europium(III) with thin-layer black phosphorus (BP) and tetrakis (4-carboxyphenyl) porphyrin (TCPP). The existence of the P-Eu bond and Eu2+ 3d5/2 in X-ray photoelectron spectroscopy confirmed the successful synthesis of BP@Eu-TCPP. This material showed high fluorescence sensitivity to l-Arginine (l-Arg) and the main binding ratio of BP@Eu-TCPP to l-Arg was ca. 1:2 or 1:3, with the limit of detection of 4.0 μM. The material also showed good photothermal properties and stability, with a photothermal conversion efficiency of 37.3%. Although metal coordination has blocked the generation of 1O2, the addition of l-Arg to BP@Eu-TCPP can restore 1O2 generation upon red light-emitting diode (LED) light irradiation due to the formation of water-soluble Arg-TCPP species. Additionally, BP@Eu-TCPP was enabled to change the bacterial membrane and interfered with the bacterial iron absorption that effectively contributes to bacterial eradication. Such BP@Eu-TCPP is promised to be a novel material for the detection of l-Arg and l-Arg-activated photodynamic therapy.
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Affiliation(s)
- Jun Wang
- School of the Environment and Safety Engineering, School of Chemistry and Chemical Engineering, Jiangsu University, Xuefu Road, Jingkou District, Zhenjiang 212013, People's Republic of China
| | - Feng Chen
- School of the Environment and Safety Engineering, School of Chemistry and Chemical Engineering, Jiangsu University, Xuefu Road, Jingkou District, Zhenjiang 212013, People's Republic of China
| | - Qiu-Yun Chen
- School of the Environment and Safety Engineering, School of Chemistry and Chemical Engineering, Jiangsu University, Xuefu Road, Jingkou District, Zhenjiang 212013, People's Republic of China
| | - Gao-Ji Wang
- School of the Environment and Safety Engineering, School of Chemistry and Chemical Engineering, Jiangsu University, Xuefu Road, Jingkou District, Zhenjiang 212013, People's Republic of China
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14
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Ooka H, Chiba Y, Nakamura R. Thermodynamic principle to enhance enzymatic activity using the substrate affinity. Nat Commun 2023; 14:4860. [PMID: 37620340 PMCID: PMC10449852 DOI: 10.1038/s41467-023-40471-y] [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: 08/02/2022] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Understanding how to tune enzymatic activity is important not only for biotechnological applications, but also to elucidate the basic principles guiding the design and optimization of biological systems in nature. So far, the Michaelis-Menten equation has provided a fundamental framework of enzymatic activity. However, there is still no concrete guideline on how the parameters should be optimized towards higher activity. Here, we demonstrate that tuning the Michaelis-Menten constant ([Formula: see text]) to the substrate concentration ([Formula: see text]) enhances enzymatic activity. This guideline ([Formula: see text]) was obtained mathematically by assuming that thermodynamically favorable reactions have higher rate constants, and that the total driving force is fixed. Due to the generality of these thermodynamic considerations, we propose [Formula: see text] as a general concept to enhance enzymatic activity. Our bioinformatic analysis reveals that the [Formula: see text] and in vivo substrate concentrations are consistent across a dataset of approximately 1000 enzymes, suggesting that even natural selection follows the principle [Formula: see text].
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Affiliation(s)
- Hideshi Ooka
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Yoko Chiba
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Faculty of Life and Environmental Science, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, 2-12-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
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15
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Sannelli F, Jensen PR, Meier S. In-Cell NMR Approach for Real-Time Exploration of Pathway Versatility: Substrate Mixtures in Nonengineered Yeast. Anal Chem 2023; 95:7262-7270. [PMID: 37097609 DOI: 10.1021/acs.analchem.3c00225] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
The central carbon metabolism of microbes will likely be used in future sustainable bioproduction. A sufficiently deep understanding of central metabolism would advance the control of activity and selectivity in whole-cell catalysis. Opposite to the more obvious effects of adding catalysts through genetic engineering, the modulation of cellular chemistry through effectors and substrate mixtures remains less clear. NMR spectroscopy is uniquely suited for in-cell tracking to advance mechanistic insight and to optimize pathway usage. Using a comprehensive and self-consistent library of chemical shifts, hyperpolarized NMR, and conventional NMR, we probe the versatility of cellular pathways to changes in substrate composition. Conditions for glucose influx into a minor pathway to an industrial precursor (2,3-butanediol) can thus be designed. Changes to intracellular pH can be followed concurrently, while mechanistic details for the minor pathway can be derived using an intermediate-trapping strategy. Overflow at the pyruvate level can be induced in nonengineered yeast with suitably mixed carbon sources (here glucose with auxiliary pyruvate), thus increasing glucose conversion to 2,3-butanediol by more than 600-fold. Such versatility suggests that a reassessment of canonical metabolism may be warranted using in-cell spectroscopy.
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Affiliation(s)
- Francesca Sannelli
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kgs Lyngby, Denmark
| | - Pernille Rose Jensen
- Department of Health Technology, Technical University of Denmark, Elektrovej 349, 2800 Kgs Lyngby, Denmark
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kgs Lyngby, Denmark
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16
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Abstract
The uptake and metabolism of nutrients support fundamental cellular process from bioenergetics to biomass production and cell fate regulation. While many studies of cell metabolism focus on cancer cells, the principles of metabolism elucidated in cancer cells apply to a wide range of mammalian cells. The goal of this review is to discuss how the field of cancer metabolism provides a framework for revealing principles of cell metabolism and for dissecting the metabolic networks that allow cells to meet their specific demands. Understanding context-specific metabolic preferences and liabilities will unlock new approaches to target cancer cells to improve patient care.
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Affiliation(s)
- Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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17
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Increasing the Thermodynamic Driving Force of the Phosphofructokinase Reaction in
Clostridium thermocellum. Appl Environ Microbiol 2022; 88:e0125822. [PMID: 36286488 PMCID: PMC9680637 DOI: 10.1128/aem.01258-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability to control the distribution of thermodynamic driving force throughout a metabolic pathway is likely to be an important tool for metabolic engineering. The phosphofructokinase reaction is a key enzyme in Embden-Mayerhof-Parnas glycolysis and therefore improving the thermodynamic driving force of this reaction in
C. thermocellum
is believed to enable higher product titers.
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18
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Janasch M, Crang N, Asplund-Samuelsson J, Sporre E, Bruch M, Gynnå A, Jahn M, Hudson EP. Thermodynamic limitations of PHB production from formate and fructose in Cupriavidus necator. Metab Eng 2022; 73:256-269. [PMID: 35987434 DOI: 10.1016/j.ymben.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/10/2022] [Accepted: 08/06/2022] [Indexed: 11/30/2022]
Abstract
The chemolithotroph Cupriavidus necator H16 is known as a natural producer of the bioplastic-polymer PHB, as well as for its metabolic versatility to utilize different substrates, including formate as the sole carbon and energy source. Depending on the entry point of the substrate, this versatility requires adjustment of the thermodynamic landscape to maintain sufficiently high driving forces for biological processes. Here we employed a model of the core metabolism of C. necator H16 to analyze the thermodynamic driving forces and PHB yields from formate for different metabolic engineering strategies. For this, we enumerated elementary flux modes (EFMs) of the network and evaluated their PHB yields as well as thermodynamics via Max-min driving force (MDF) analysis and random sampling of driving forces. A heterologous ATP:citrate lyase reaction was predicted to increase driving force for producing acetyl-CoA. A heterologous phosphoketolase reaction was predicted to increase maximal PHB yields as well as driving forces. These enzymes were then verified experimentally to enhance PHB titers between 60 and 300% in select conditions. The EFM analysis also revealed that PHB production from formate may be limited by low driving forces through citrate lyase and aconitase, as well as cofactor balancing, and identified additional reactions associated with low and high PHB yield. Proteomics analysis of the engineered strains confirmed an increased abundance of aconitase and cofactor balancing. The findings of this study aid in understanding metabolic adaptation. Furthermore, the outlined approach will be useful in designing metabolic engineering strategies in other non-model bacteria.
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Affiliation(s)
- Markus Janasch
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden.
| | - Nick Crang
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden.
| | - Johannes Asplund-Samuelsson
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Emil Sporre
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Manuel Bruch
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Arvid Gynnå
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Michael Jahn
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden
| | - Elton P Hudson
- Science for Life Laboratory, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, P-Box 1031, 171 21, Solna, Sweden.
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19
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King E, Cui Y, Aspacio D, Nicklen F, Zhang L, Maxel S, Luo R, Siegel JB, Aitchison E, Li H. Engineering Embden-Meyerhof-Parnas Glycolysis to Generate Noncanonical Reducing Power. ACS Catal 2022; 12:8582-8592. [PMID: 37622090 PMCID: PMC10449333 DOI: 10.1021/acscatal.2c01837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncanonical cofactors such as nicotinamide mononucleotide (NMN+) supplant the electron-transfer functionality of the natural cofactors, NAD(P)+, at a lower cost in cell-free biomanufacturing and enable orthogonal electron delivery in whole-cell metabolic engineering. Here, we redesign the high-flux Embden-Meyerhof-Parnas (EMP) glycolytic pathway to generate NMN+-based reducing power, by engineering Streptococcus mutans glyceraldehyde-3-phosphate dehydrogenase (Sm GapN) to utilize NMN+. Through iterative rounds of rational design, we discover the variant GapN Penta (P179K-F153S-S330R-I234E-G210Q) with high NMN+-dependent activity and GapN Ortho (P179K-F153S-S330R-I234E-G214E) with ~3.4 × 106-fold switch in cofactor specificity from its native cofactor NADP+ to NMN+. GapN Ortho is further demonstrated to function in Escherichia coli only in the presence of NMN+, enabling orthogonal control of glucose utilization. Molecular dynamics simulation and residue network connectivity analysis indicate that mutations altering cofactor specificity must be coordinated to maintain the appropriate degree of backbone flexibility to position the catalytic cysteine. These results provide a strategy to guide future designs of NMN+-dependent enzymes and establish the initial steps toward an orthogonal EMP pathway with biomanufacturing potential.
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Affiliation(s)
- Edward King
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Youtian Cui
- Genome Center, University of California, Davis, Davis, California 95616, United States
| | - Derek Aspacio
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Frances Nicklen
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Linyue Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Sarah Maxel
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, Department of Chemical and Biomolecular Engineering, and Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Justin B Siegel
- Department of Chemistry, Genome Center, and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
| | - Erick Aitchison
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Han Li
- Department of Chemical and Biomolecular Engineering and Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697-3900, United States
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20
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Autoregulation of H +/lactate efflux prevents monocarboxylate transport (MCT) inhibitors from reducing glycolytic lactic acid production. Br J Cancer 2022; 127:1365-1377. [PMID: 35840734 PMCID: PMC9519749 DOI: 10.1038/s41416-022-01910-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 12/02/2022] Open
Abstract
Background Pharmacological inhibition of membrane transporters is expected to reduce the flow of solutes, unless flux is restored (i.e., autoregulated) through a compensatory increase in the transmembrane driving force. Drugs acting on monocarboxylate transporters (MCTs) have been developed to disrupt glycolytic metabolism, but autoregulation would render such interventions ineffective. We evaluated whether small-molecule MCT inhibitors reduce cellular H+/lactate production. Methods Cellular assays measured the relationship between MCT activity (expressed as membrane H+/lactate permeability; PHLac) and lactic acid production (inferred from H+ and lactate excretion; JHLac) in a panel of pancreatic ductal adenocarcinoma (PDAC) cells spanning a range of glycolytic phenotype. Results MCT activity did not correlate with lactic acid production, indicating that it is not set by membrane permeability properties. MCT inhibitors did not proportionately reduce JHLac because of a compensatory increase in the transmembrane [lactate] driving force. JHLac was largely insensitive to [lactate], therefore its cytoplasmic build-up upon MCT inhibition does not hinder glycolytic production. Extracellular acidity, an MCT inhibitor, reduced JHLac but this was via cytoplasmic acidification blocking glycolytic enzymes. Conclusions We provide mathematically verified evidence that pharmacological and physiological modulators of MCTs cannot proportionately reduce lactic acid production because of the stabilising effect of autoregulation on overall flux.
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21
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Saydaliev HB, Chin L. Role of green financing and financial inclusion to develop the cleaner environment for macroeconomic stability: Inter-temporal analysis of ASEAN economies. ECONOMIC CHANGE AND RESTRUCTURING 2022. [PMCID: PMC9244391 DOI: 10.1007/s10644-022-09419-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/26/2022] [Indexed: 08/24/2023]
Abstract
The research objective is to assess the role of green financing and financial inclusion in developing a cleaner environment for macroeconomic stability in ASEAN economies. The study attempted to estimate the climate mitigation factor associated with a more sanitary environment between 2012 and 2019. Panel data analysis using the augmented Dicky–Fuller test, Phillip–Perron, and fully modified standard most minor square test provides long-term findings in panel data analysis. In addition, the vector error correction technique was also applied to infer study results. The findings indicate that climate change mitigation indicators have a significant impact on the gross domestic product of ASEAN economies. According to the data, a one percent rise in the green finance index results in a 0.321 percent increase in the amount of pollution removed from the environment. According to the research findings, environmental pollution must be decreased, and energy sources must be switched to more creative and ecologically friendly alternatives. Using study findings, several policy recommendations are offered and suggested for stakeholders for implementation. As per our best understanding, effective implementation of study findings and suggestions maximum chances are developing a cleaner environment and boosting macroeconomic stability in the ASEAN context.
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Affiliation(s)
- Hayot Berk Saydaliev
- Business School, Suleyman Demirel University, Kaskelen, Almaty, Kazakhstan 040900
- Research Fellow, Mathematical Methods in Economics, Tashkent State University of Economics, Tashkent, Uzbekistan 100003
| | - Lee Chin
- School of Business and Economics, Universiti Putra Malaysia, 43400 Serdang, Malaysia
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22
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Geraci I, Autour A, Pietruschka G, Shiian A, Borisova M, Mayer C, Ryckelynck M, Mayer G. Fluorogenic RNA-Based Biosensor to Sense the Glycolytic Flux in Mammalian Cells. ACS Chem Biol 2022; 17:1164-1173. [PMID: 35427113 DOI: 10.1021/acschembio.2c00100] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The visualization of metabolic flux in real time requires sensor molecules that transduce variations of metabolite concentrations into an appropriate output signal. In this regard, fluorogenic RNA-based biosensors are promising molecular tools as they fluoresce only upon binding to another molecule. However, to date no such sensor is available that enables the direct observation of key metabolites in mammalian cells. Toward this direction, we selected and characterized an RNA light-up sensor designed to respond to fructose 1,6-bisphosphate and applied it to probe glycolytic flux variation in mammal cells.
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Affiliation(s)
- Ignazio Geraci
- Life and Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Alexis Autour
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, 67084 Strasbourg, France
| | - Georg Pietruschka
- Life and Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Aleksandra Shiian
- Life and Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
| | - Marina Borisova
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions/Glycobiology, Eberhard Karls University of Tübingen, 72076 Tübingen, Germany
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, 67084 Strasbourg, France
| | - Günter Mayer
- Life and Medical Sciences Institute (LIMES), University of Bonn, Gerhard-Domagk-Str.1, 53121 Bonn, Germany
- Center of Aptamer Research & Development, University of Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany
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23
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Wu Y, Judge MT, Edison AS, Arnold J. Uncovering in vivo biochemical patterns from time-series metabolic dynamics. PLoS One 2022; 17:e0268394. [PMID: 35550643 PMCID: PMC9098013 DOI: 10.1371/journal.pone.0268394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/28/2022] [Indexed: 11/19/2022] Open
Abstract
System biology relies on holistic biomolecule measurements, and untangling biochemical networks requires time-series metabolomics profiling. With current metabolomic approaches, time-series measurements can be taken for hundreds of metabolic features, which decode underlying metabolic regulation. Such a metabolomic dataset is untargeted with most features unannotated and inaccessible to statistical analysis and computational modeling. The high dimensionality of the metabolic space also causes mechanistic modeling to be rather cumbersome computationally. We implemented a faster exploratory workflow to visualize and extract chemical and biochemical dependencies. Time-series metabolic features (about 300 for each dataset) were extracted by Ridge Tracking-based Extract (RTExtract) on measurements from continuous in vivo monitoring of metabolism by NMR (CIVM-NMR) in Neurospora crassa under different conditions. The metabolic profiles were then smoothed and projected into lower dimensions, enabling a comparison of metabolic trends in the cultures. Next, we expanded incomplete metabolite annotation using a correlation network. Lastly, we uncovered meaningful metabolic clusters by estimating dependencies between smoothed metabolic profiles. We thus sidestepped the processes of time-consuming mechanistic modeling, difficult global optimization, and labor-intensive annotation. Multiple clusters guided insights into central energy metabolism and membrane synthesis. Dense connections with glucose 1-phosphate indicated its central position in metabolism in N. crassa. Our approach was benchmarked on simulated random network dynamics and provides a novel exploratory approach to analyzing high-dimensional metabolic dynamics.
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Affiliation(s)
- Yue Wu
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Michael T. Judge
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Arthur S. Edison
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States of America
- * E-mail: (ASE); (JA)
| | - Jonathan Arnold
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Department of Statistics, University of Georgia, Athens, GA, United States of America
- Department of Physics and Astronomy, University of Georgia, Athens, GA, United States of America
- * E-mail: (ASE); (JA)
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24
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Developmental energetics: Energy expenditure, budgets and metabolism during animal embryogenesis. Semin Cell Dev Biol 2022; 138:83-93. [PMID: 35317962 DOI: 10.1016/j.semcdb.2022.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/07/2022] [Accepted: 03/05/2022] [Indexed: 11/22/2022]
Abstract
Developing embryos are metabolically active, open systems that constantly exchange matter and energy with their environment. They function out of thermodynamic equilibrium and continuously use metabolic pathways to obtain energy from maternal nutrients, in order to fulfill the energetic requirements of growth and development. While an increasing number of studies highlight the role of metabolism in different developmental contexts, the physicochemical basis of embryogenesis, or how cellular processes use energy and matter to act together and transform a zygote into an adult organism, remains unknown. As we obtain a better understanding of metabolism, and benefit from current technology development, it is a promising time to revisit the energetic cost of development and how energetic principles may govern embryogenesis. Here, we review recent advances in methodology to measure and infer energetic parameters in developing embryos. We highlight a potential common pattern in embryonic energy expenditure and metabolic strategy across animal embryogenesis, and discuss challenges and open questions in developmental energetics.
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25
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Yang X, Li J, Lai JL, Zhang Y, Luo XG. Adsorption and enrichment of U in a cellulase-producing Trichoderma sp. and its physiological response mechanism. CHEMOSPHERE 2022; 287:132173. [PMID: 34509764 DOI: 10.1016/j.chemosphere.2021.132173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/21/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
The cellulase produced by Trichoderma sp. was characterized by investigating the adsorption and enrichment of U and the physiological response to U exposure. The effects of U exposure (0 and 400 μM) on the growth, morphological characteristics, cellulase production, U adsorption, and U enrichment capacity of the Trichoderma strain were assessed. The effects of U exposure on the basic metabolism of this fungus were also analyzed by non-targeted metabolomics. Exposure to U (400 μM) for 24 h resulted in OD600 turbidity of 0.278, and activities of carboxymethyl cellulase (CMC), filter paper enzyme (FPA), and β-glucosidase of 12834 U·mL-1, 9285 U·mL-1, and 12574 U·mL-1, respectively. The measurement of the background α and β radioactivity showed an α activity concentration of 3.35 × 106 Bq·kg-1 in the fungus, a β activity concentration of 6.28 × 105 Bq·kg-1, and a U enrichment rate of 70.4 ± 4.5%. GC-MS metabolomics analysis identified a total of 319 metabolites (34 up-regulated and 30 down-regulated), which mainly caused the metabolic imbalance of organic acids and derivatives. The alanine, aspartate, and glutamate metabolic pathways were the most significantly enriched. Trichoderma sp. therefore has a strong ability to tolerate/accumulate U and continues to produce cellulase under U (400 μM) exposure. However, U interferes with the basic metabolism of this fungus.
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Affiliation(s)
- Xu Yang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Jie Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Jin-Long Lai
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China; Engineering Research Center of Biomass Materials, Ministry of Education of SWUST, Mianyang, 621010, China.
| | - Yu Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.
| | - Xue-Gang Luo
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
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26
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Khana DB, Callaghan MM, Amador-Noguez D. Novel computational and experimental approaches for investigating the thermodynamics of metabolic networks. Curr Opin Microbiol 2021; 66:21-31. [PMID: 34974376 DOI: 10.1016/j.mib.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 11/18/2022]
Abstract
Thermodynamic analysis of metabolic networks has emerged as a useful new tool for pathway design and metabolic engineering. Understanding the relationship between the thermodynamic driving force of biochemical reactions and metabolic flux has generated new insights regarding the design principles of microbial carbon metabolism. This review summarizes the various lessons that can be obtained from the thermodynamic analysis of metabolic pathways, illustrates concepts of computational thermodynamic tools, and highlights recent applications of thermodynamic analysis to pathway design in industrially relevant microbes.
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Affiliation(s)
- Daven B Khana
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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27
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Functional analysis of H +-pumping membrane-bound pyrophosphatase, ADP-glucose synthase, and pyruvate phosphate dikinase as pyrophosphate sources in Clostridium thermocellum. Appl Environ Microbiol 2021; 88:e0185721. [PMID: 34936842 PMCID: PMC8863071 DOI: 10.1128/aem.01857-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The atypical glycolysis of Clostridium thermocellum is characterized by the use of pyrophosphate (PPi) as phosphoryl donor for phosphofructokinase (Pfk) and pyruvate phosphate dikinase (Ppdk) reactions. Previously, biosynthetic PPi was calculated to be stoichiometrically insufficient to drive glycolysis. This study investigates the role of a H+-pumping membrane-bound pyrophosphatase, glycogen cycling, a predicted Ppdk-malate shunt cycle and acetate cycling in generating PPi. Knockout studies and enzyme assays confirmed that clo1313_0823 encodes a membrane-bound pyrophosphatase. Additionally, clo1313_0717-0718 was confirmed to encode ADP-glucose synthase by knockouts, glycogen measurements in C. thermocellum and heterologous expression in E. coli. Unexpectedly, individually-targeted gene deletions of the four putative PPi sources did not have a significant phenotypic effect. Although combinatorial deletion of all four putative PPi sources reduced the growth rate by 22% (0.30±0.01 h-1) and the biomass yield by 38% (0.18±0.00 gbiomass gsubstrate-1), this change was much smaller than what would be expected for stoichiometrically essential PPi-supplying mechanisms. Growth-arrested cells of the quadruple knockout readily fermented cellobiose indicating that the unknown PPi-supplying mechanisms are independent of biosynthesis. An alternative hypothesis that ATP-dependent Pfk activity circumvents a need for PPi altogether, was falsified by enzyme assays, heterologous expression of candidate genes and whole-genome sequencing. As a secondary outcome, enzymatic assays confirmed functional annotation of clo1313_1832 as ATP- and GTP-dependent fructokinase. These results indicate that the four investigated PPi sources individually and combined play no significant PPi-supplying role and the true source(s) of PPi, or alternative phosphorylating mechanisms, that drive glycolysis in C. thermocellum remain(s) elusive. IMPORTANCE Increased understanding of the central metabolism of C. thermocellum is important from a fundamental as well as from a sustainability and industrial perspective. In addition to showing that H+-pumping membrane-bound PPase, glycogen cycling, a Ppdk-malate shunt cycle, and acetate cycling are not significant sources of PPi supply, this study adds functional annotation of four genes and availability of an updated PPi stoichiometry from biosynthesis to the scientific domain. Together, this aids future metabolic engineering attempts aimed to improve C. thermocellum as a cell factory for sustainable and efficient production of ethanol from lignocellulosic material through consolidated bioprocessing with minimal pretreatment. Getting closer to elucidating the elusive source of PPi, or alternative phosphorylating mechanisms, for the atypical glycolysis is itself of fundamental importance. Additionally, the findings of this study directly contribute to investigations into trade-offs between thermodynamic driving force versus energy yield of PPi- and ATP-dependent glycolysis.
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28
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Martien JI, Trujillo EA, Jacobson TB, Tatli M, Hebert AS, Stevenson DM, Coon JJ, Amador-Noguez D. Metabolic Remodeling during Nitrogen Fixation in Zymomonas mobilis. mSystems 2021; 6:e0098721. [PMID: 34783580 PMCID: PMC8594446 DOI: 10.1128/msystems.00987-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/06/2021] [Indexed: 11/20/2022] Open
Abstract
Zymomonas mobilis is an ethanologenic bacterium currently being developed for production of advanced biofuels. Recent studies have shown that Z. mobilis can fix dinitrogen gas (N2) as a sole nitrogen source. During N2 fixation, Z. mobilis exhibits increased biomass-specific rates of ethanol production. In order to better understand the physiology of Z. mobilis during N2 fixation and during changes in ammonium (NH4+) availability, we performed liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomics and shotgun proteomics under three regimes of nitrogen availability: continuous N2 fixation, gradual NH4+ depletion, and acute NH4+ addition to N2-fixing cells. We report dynamic changes in abundance of proteins and metabolites related to nitrogen fixation, motility, ammonium assimilation, amino acid biosynthesis, nucleotide biosynthesis, isoprenoid biosynthesis, and Entner-Doudoroff (ED) glycolysis, providing insight into the regulatory mechanisms that control these processes in Z. mobilis. Our analysis identified potential physiological mechanisms that may contribute to increased specific ethanol production during N2 fixation, including decreased activity of biosynthetic pathways, increased protein abundance of alcohol dehydrogenase (ADHI), and increased thermodynamic favorability of the ED pathway. Of particular relevance to advanced biofuel production, we found that intermediates in the methylerythritol phosphate (MEP) pathway for isoprenoid biosynthesis were depleted during N2 fixation, coinciding with decreased protein abundance of deoxyxylulose 5-phosphate synthase (DXS), the first enzyme in the pathway. This implies that DXS protein abundance serves as a native control point in regulating MEP pathway activity in Z. mobilis. The results of this study will inform metabolic engineering to further develop Z. mobilis as a platform organism for biofuel production. IMPORTANCE Biofuels and bioproducts have the potential to serve as environmentally sustainable replacements for petroleum-derived fuels and commodity molecules. Advanced fuels such as higher alcohols and isoprenoids are more suitable gasoline replacements than bioethanol. Developing microbial systems to generate advanced biofuels requires metabolic engineering to reroute carbon away from ethanol and other native products and toward desired pathways, such as the MEP pathway for isoprenoid biosynthesis. However, rational engineering of microbial metabolism relies on understanding metabolic control points, in terms of both enzyme activity and thermodynamic favorability. In Z. mobilis, the factors that control glycolytic rates, ethanol production, and isoprenoid production are still not fully understood. In this study, we performed metabolomic, proteomic, and thermodynamic analysis of Z. mobilis during N2 fixation. This analysis identified key changes in metabolite levels, enzyme abundance, and glycolytic thermodynamic favorability that occurred during changes in NH4+ availability, helping to inform future efforts in metabolic engineering.
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Affiliation(s)
- Julia I. Martien
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Edna A. Trujillo
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Tyler B. Jacobson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Mehmet Tatli
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Alexander S. Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - David M. Stevenson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
| | - Joshua J. Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Daniel Amador-Noguez
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin, USA
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29
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Linnan B, Yanzhe W, Ling Z, Yuyuan L, Sijia C, Xinmiao X, Fengqin L, Xiaoxia W. In situ Metabolomics of Metabolic Reprogramming Involved in a Mouse Model of Type 2 Diabetic Kidney Disease. Front Physiol 2021; 12:779683. [PMID: 34916961 PMCID: PMC8670437 DOI: 10.3389/fphys.2021.779683] [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: 09/19/2021] [Accepted: 11/10/2021] [Indexed: 01/03/2023] Open
Abstract
The in situ metabolic profiling of the kidney is crucial to investigate the complex metabolic reprogramming underlying diabetic kidney disease (DKD) and to allow exploration of potential metabolic targets to improve kidney function. However, as the kidney is a highly heterogeneous organ, traditional metabolomic methods based on bulk analysis that produce an averaged measurement are inadequate. Herein, we employed an in situ metabolomics approach to discover alternations of DKD-associated metabolites and metabolic pathways. A series of histology-specific metabolic disturbances were discovered in situ using airflow-assisted desorption electrospray ionization mass spectrometry imaging (AFADESI-MSI). In combination with integrated metabolomics analysis, five dysfunctional metabolic pathways were identified and located in the kidneys of type-2 DKD mice simultaneously for the first time, including taurine metabolism, arginine and proline metabolism, histidine metabolism, biosynthesis of unsaturated fatty acids, and fatty acid degradation pathways. As crucial nodes of metabolic pathways, five dysregulated rate-limiting enzymes related to altered metabolic pathways were further identified. These findings reveal alternations from metabolites to enzymes at the molecular level in the progression of DKD and provide insights into DKD-associated metabolic reprogramming.
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Affiliation(s)
- Bai Linnan
- Department of Nephrology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wang Yanzhe
- Department of Nephrology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhang Ling
- Department of Nephrology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liu Yuyuan
- Department of Nephrology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Sijia
- Department of Nephrology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xie Xinmiao
- Department of Nephrology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Fengqin
- Department of Nephrology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wang Xiaoxia
- Department of Nephrology, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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30
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Molecular mechanism of glycolytic flux control intrinsic to human phosphoglycerate kinase. Proc Natl Acad Sci U S A 2021; 118:2112986118. [PMID: 34893542 DOI: 10.1073/pnas.2112986118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 01/17/2023] Open
Abstract
Glycolysis plays a fundamental role in energy production and metabolic homeostasis. The intracellular [adenosine triphosphate]/[adenosine diphosphate] ([ATP]/[ADP]) ratio controls glycolytic flux; however, the regulatory mechanism underlying reactions catalyzed by individual glycolytic enzymes enabling flux adaptation remains incompletely understood. Phosphoglycerate kinase (PGK) catalyzes the reversible phosphotransfer reaction, which directly produces ATP in a near-equilibrium step of glycolysis. Despite extensive studies on the transcriptional regulation of PGK expression, the mechanism in response to changes in the [ATP]/[ADP] ratio remains obscure. Here, we report a protein-level regulation of human PGK (hPGK) by utilizing the switching ligand-binding cooperativities between adenine nucleotides and 3-phosphoglycerate (3PG). This was revealed by nuclear magnetic resonance (NMR) spectroscopy at physiological salt concentrations. MgADP and 3PG bind to hPGK with negative cooperativity, whereas MgAMPPNP (a nonhydrolyzable ATP analog) and 3PG bind to hPGK with positive cooperativity. These opposite cooperativities enable a shift between different ligand-bound states depending on the intracellular [ATP]/[ADP] ratio. Based on these findings, we present an atomic-scale description of the reaction scheme for hPGK under physiological conditions. Our results indicate that hPGK intrinsically modulates its function via ligand-binding cooperativities that are finely tuned to respond to changes in the [ATP]/[ADP] ratio. The alteration of ligand-binding cooperativities could be one of the self-regulatory mechanisms for enzymes in bidirectional pathways, which enables rapid adaptation to changes in the intracellular environment.
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31
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Beber ME, Gollub MG, Mozaffari D, Shebek KM, Flamholz AI, Milo R, Noor E. eQuilibrator 3.0: a database solution for thermodynamic constant estimation. Nucleic Acids Res 2021; 50:D603-D609. [PMID: 34850162 PMCID: PMC8728285 DOI: 10.1093/nar/gkab1106] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 11/29/2022] Open
Abstract
eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based interface. While the website now counts around 1,000 distinct monthly users, its design could not accommodate larger compound databases and it lacked a scalable Application Programming Interface (API) for integration into other tools developed by the systems biology community. Here, we report on the recent updates to the database as well as the addition of a new Python-based interface to eQuilibrator that adds many new features such as a 100-fold larger compound database, the ability to add novel compounds, improvements in speed and memory use, and correction for Mg2+ ion concentrations. Moreover, the new interface can compute the covariance matrix of the uncertainty between estimates, for which we show the advantages and describe the application in metabolic modelling. We foresee that these improvements will make thermodynamic modelling more accessible and facilitate the integration of eQuilibrator into other software platforms.
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Affiliation(s)
- Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark.,Unseen Biometrics ApS, Fruebjergvej 3, 2100 København Ø, Denmark
| | - Mattia G Gollub
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zürich, Basel 4058, Switzerland
| | - Dana Mozaffari
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zürich, Basel 4058, Switzerland.,Institute of Chemical Sciences and Engineering, EPFL, Lausanne 1015, Switzerland
| | - Kevin M Shebek
- Department of Chemical and Biological Engineering, Chemistry of Life Processes Institute, and Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Avi I Flamholz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Herzl 234, Rehovot 7610001, Israel
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Herzl 234, Rehovot 7610001, Israel
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32
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Jensen PR, Sannelli F, Stauning LT, Meier S. Enhanced 13C NMR detects extended reaction networks in living cells. Chem Commun (Camb) 2021; 57:10572-10575. [PMID: 34558573 DOI: 10.1039/d1cc03838a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Insights into intracellular chemistry have remained sparse, but would be impactful for the advancement of biomedicine and bioproduction. A suitable 13C NMR approach provides improvements in sensitivity that make extended reaction networks and assay time windows, previously inaccessible cell densities and relative flux measurements accessible in living cells.
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Affiliation(s)
- Pernille Rose Jensen
- Department of Health Technology Technical University of Denmark Elektrovej, 349 2800-Kgs. Lyngby, Denmark.
| | - Francesca Sannelli
- Department of Chemistry Technical University of Denmark Kemitorvet, Bygning 207, 2800 Kgs. Lyngby, Denmark.
| | - Ludvig Tving Stauning
- Department of Health Technology Technical University of Denmark Elektrovej, 349 2800-Kgs. Lyngby, Denmark. .,Department of Chemistry Technical University of Denmark Kemitorvet, Bygning 207, 2800 Kgs. Lyngby, Denmark.
| | - Sebastian Meier
- Department of Chemistry Technical University of Denmark Kemitorvet, Bygning 207, 2800 Kgs. Lyngby, Denmark.
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33
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Radic Shechter K, Kafkia E, Zirngibl K, Gawrzak S, Alladin A, Machado D, Lüchtenborg C, Sévin DC, Brügger B, Patil KR, Jechlinger M. Metabolic memory underlying minimal residual disease in breast cancer. Mol Syst Biol 2021; 17:e10141. [PMID: 34694069 PMCID: PMC8543468 DOI: 10.15252/msb.202010141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 01/11/2023] Open
Abstract
Tumor relapse from treatment-resistant cells (minimal residual disease, MRD) underlies most breast cancer-related deaths. Yet, the molecular characteristics defining their malignancy have largely remained elusive. Here, we integrated multi-omics data from a tractable organoid system with a metabolic modeling approach to uncover the metabolic and regulatory idiosyncrasies of the MRD. We find that the resistant cells, despite their non-proliferative phenotype and the absence of oncogenic signaling, feature increased glycolysis and activity of certain urea cycle enzyme reminiscent of the tumor. This metabolic distinctiveness was also evident in a mouse model and in transcriptomic data from patients following neo-adjuvant therapy. We further identified a marked similarity in DNA methylation profiles between tumor and residual cells. Taken together, our data reveal a metabolic and epigenetic memory of the treatment-resistant cells. We further demonstrate that the memorized elevated glycolysis in MRD is crucial for their survival and can be targeted using a small-molecule inhibitor without impacting normal cells. The metabolic aberrances of MRD thus offer new therapeutic opportunities for post-treatment care to prevent breast tumor recurrence.
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Affiliation(s)
| | - Eleni Kafkia
- European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- The Medical Research Council Toxicology UnitUniversity of CambridgeCambridgeUK
| | - Katharina Zirngibl
- European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- The Medical Research Council Toxicology UnitUniversity of CambridgeCambridgeUK
| | - Sylwia Gawrzak
- European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Present address:
Cellzome GmbHFunctional GenomicsGlaxoSmithKlineHeidelbergGermany
| | - Ashna Alladin
- European Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Daniel Machado
- European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- Present address:
Norwegian University of Science and TechnologyTrondheimNorway
| | | | - Daniel C Sévin
- Cellzome GmbHFunctional GenomicsGlaxoSmithKlineHeidelbergGermany
| | - Britta Brügger
- Biochemie‐Zentrum der Universität Heidelberg (BZH)HeidelbergGermany
| | - Kiran R Patil
- European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- The Medical Research Council Toxicology UnitUniversity of CambridgeCambridgeUK
| | - Martin Jechlinger
- European Molecular Biology Laboratory (EMBL)HeidelbergGermany
- MOLIT Institute gGmbHHeilbronnGermany
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34
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Schmidt CA, Fisher-Wellman KH, Neufer PD. From OCR and ECAR to energy: Perspectives on the design and interpretation of bioenergetics studies. J Biol Chem 2021; 297:101140. [PMID: 34461088 PMCID: PMC8479256 DOI: 10.1016/j.jbc.2021.101140] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Biological energy transduction underlies all physiological phenomena in cells. The metabolic systems that support energy transduction have been of great interest due to their association with numerous pathologies including diabetes, cancer, rare genetic diseases, and aberrant cell death. Commercially available bioenergetics technologies (e.g., extracellular flux analysis, high-resolution respirometry, fluorescent dye kits, etc.) have made practical assessment of metabolic parameters widely accessible. This has facilitated an explosion in the number of studies exploring, in particular, the biological implications of oxygen consumption rate (OCR) and substrate level phosphorylation via glycolysis (i.e., via extracellular acidification rate (ECAR)). Though these technologies have demonstrated substantial utility and broad applicability to cell biology research, they are also susceptible to historical assumptions, experimental limitations, and other caveats that have led to premature and/or erroneous interpretations. This review enumerates various important considerations for designing and interpreting cellular and mitochondrial bioenergetics experiments, some common challenges and pitfalls in data interpretation, and some potential "next steps" to be taken that can address these highlighted challenges.
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Affiliation(s)
- Cameron A Schmidt
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina, USA; Departments of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Kelsey H Fisher-Wellman
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina, USA; Departments of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA.
| | - P Darrell Neufer
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina, USA; Departments of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA; Departments of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA.
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35
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Jacobson TB, Callaghan MM, Amador-Noguez D. Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism. Annu Rev Microbiol 2021; 75:515-539. [PMID: 34348026 DOI: 10.1146/annurev-micro-060621-043448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Tyler B Jacobson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Melanie M Callaghan
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA; , , .,Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.,Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Gawthrop PJ, Pan M, Crampin EJ. Modular dynamic biomolecular modelling with bond graphs: the unification of stoichiometry, thermodynamics, kinetics and data. J R Soc Interface 2021; 18:20210478. [PMID: 34428949 PMCID: PMC8385351 DOI: 10.1098/rsif.2021.0478] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/02/2021] [Indexed: 12/14/2022] Open
Abstract
Renewed interest in dynamic simulation models of biomolecular systems has arisen from advances in genome-wide measurement and applications of such models in biotechnology and synthetic biology. In particular, genome-scale models of cellular metabolism beyond the steady state are required in order to represent transient and dynamic regulatory properties of the system. Development of such whole-cell models requires new modelling approaches. Here, we propose the energy-based bond graph methodology, which integrates stoichiometric models with thermodynamic principles and kinetic modelling. We demonstrate how the bond graph approach intrinsically enforces thermodynamic constraints, provides a modular approach to modelling, and gives a basis for estimation of model parameters leading to dynamic models of biomolecular systems. The approach is illustrated using a well-established stoichiometric model of Escherichia coli and published experimental data.
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Affiliation(s)
- Peter J. Gawthrop
- Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Victoria 3010, Australia
| | - Michael Pan
- Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Victoria 3010, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemical and Biomedical Engineering, University of Melbourne, Victoria 3010, Australia
| | - Edmund J. Crampin
- Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Victoria 3010, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, School of Chemical and Biomedical Engineering, University of Melbourne, Victoria 3010, Australia
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37
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Liu N, Stephanopoulos G. Metabolic Engineering Perspectives. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch1] [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]
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38
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Physical bioenergetics: Energy fluxes, budgets, and constraints in cells. Proc Natl Acad Sci U S A 2021; 118:2026786118. [PMID: 34140336 DOI: 10.1073/pnas.2026786118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What are the constraints and limits energy flows impose on cellular processes? Do cells operate near these limits, and if so how do energetic constraints impact cellular functions? Physics has provided many tools to study nonequilibrium systems and to define physical limits, but applying these tools to cell biology remains a challenge. Physical bioenergetics, which resides at the interface of nonequilibrium physics, energy metabolism, and cell biology, seeks to understand how much energy cells are using, how they partition this energy between different cellular processes, and the associated energetic constraints. Here we review recent advances and discuss open questions and challenges in physical bioenergetics.
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Abstract
Living systems formed and evolved under constraints that govern their interactions with the inorganic world. These interactions are definable using basic physico-chemical principles. Here, we formulate a comprehensive set of ten governing abiotic constraints that define possible quantitative metabolomes. We apply these constraints to a metabolic network of Escherichia coli that represents 90% of its metabolome. We show that the quantitative metabolomes allowed by the abiotic constraints are consistent with metabolomic and isotope-labeling data. We find that: (i) abiotic constraints drive the evolution of high-affinity phosphate transporters; (ii) Charge-, hydrogen- and magnesium-related constraints underlie transcriptional regulatory responses to osmotic stress; and (iii) hydrogen-ion and charge imbalance underlie transcriptional regulatory responses to acid stress. Thus, quantifying the constraints that the inorganic world imposes on living systems provides insights into their key characteristics, helps understand the outcomes of evolutionary adaptation, and should be considered as a fundamental part of theoretical biology and for understanding the constraints on evolution.
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Cobbold SA, V Tutor M, Frasse P, McHugh E, Karnthaler M, Creek DJ, Odom John A, Tilley L, Ralph SA, McConville MJ. Non-canonical metabolic pathways in the malaria parasite detected by isotope-tracing metabolomics. Mol Syst Biol 2021; 17:e10023. [PMID: 33821563 PMCID: PMC8022201 DOI: 10.15252/msb.202010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/26/2022] Open
Abstract
The malaria parasite, Plasmodium falciparum, proliferates rapidly in human erythrocytes by actively scavenging multiple carbon sources and essential nutrients from its host cell. However, a global overview of the metabolic capacity of intraerythrocytic stages is missing. Using multiplex 13 C-labelling coupled with untargeted mass spectrometry and unsupervised isotopologue grouping, we have generated a draft metabolome of P. falciparum and its host erythrocyte consisting of 911 and 577 metabolites, respectively, corresponding to 41% of metabolites and over 70% of the metabolic reaction predicted from the parasite genome. An additional 89 metabolites and 92 reactions were identified that were not predicted from genomic reconstructions, with the largest group being associated with metabolite damage-repair systems. Validation of the draft metabolome revealed four previously uncharacterised enzymes which impact isoprenoid biosynthesis, lipid homeostasis and mitochondrial metabolism and are necessary for parasite development and proliferation. This study defines the metabolic fate of multiple carbon sources in P. falciparum, and highlights the activity of metabolite repair pathways in these rapidly growing parasite stages, opening new avenues for drug discovery.
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Affiliation(s)
- Simon A Cobbold
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Madel V Tutor
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Philip Frasse
- Department of MedicineWashington University School of MedicineSt. LouisMOUSA
| | - Emma McHugh
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Markus Karnthaler
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Darren J Creek
- Monash Institute of Pharmaceutical SciencesMonash UniversityParkvilleVic.Australia
| | - Audrey Odom John
- The Children’s Hospital of PhiladelphiaUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Leann Tilley
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
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Österberg L, Domenzain I, Münch J, Nielsen J, Hohmann S, Cvijovic M. A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. PLoS Comput Biol 2021; 17:e1008891. [PMID: 33836000 PMCID: PMC8059808 DOI: 10.1371/journal.pcbi.1008891] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/21/2021] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
The interplay between nutrient-induced signaling and metabolism plays an important role in maintaining homeostasis and its malfunction has been implicated in many different human diseases such as obesity, type 2 diabetes, cancer, and neurological disorders. Therefore, unraveling the role of nutrients as signaling molecules and metabolites together with their interconnectivity may provide a deeper understanding of how these conditions occur. Both signaling and metabolism have been extensively studied using various systems biology approaches. However, they are mainly studied individually and in addition, current models lack both the complexity of the dynamics and the effects of the crosstalk in the signaling system. To gain a better understanding of the interconnectivity between nutrient signaling and metabolism in yeast cells, we developed a hybrid model, combining a Boolean module, describing the main pathways of glucose and nitrogen signaling, and an enzyme-constrained model accounting for the central carbon metabolism of Saccharomyces cerevisiae, using a regulatory network as a link. The resulting hybrid model was able to capture a diverse utalization of isoenzymes and to our knowledge outperforms constraint-based models in the prediction of individual enzymes for both respiratory and mixed metabolism. The model showed that during fermentation, enzyme utilization has a major contribution in governing protein allocation, while in low glucose conditions robustness and control are prioritized. In addition, the model was capable of reproducing the regulatory effects that are associated with the Crabtree effect and glucose repression, as well as regulatory effects associated with lifespan increase during caloric restriction. Overall, we show that our hybrid model provides a comprehensive framework for the study of the non-trivial effects of the interplay between signaling and metabolism, suggesting connections between the Snf1 signaling pathways and processes that have been related to chronological lifespan of yeast cells.
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Affiliation(s)
- Linnea Österberg
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Julia Münch
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- BioInnovation Institute, Copenhagen, Denmark
| | - Stefan Hohmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
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Fritts RK, McCully AL, McKinlay JB. Extracellular Metabolism Sets the Table for Microbial Cross-Feeding. Microbiol Mol Biol Rev 2021; 85:e00135-20. [PMID: 33441489 PMCID: PMC7849352 DOI: 10.1128/mmbr.00135-20] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transfer of nutrients between cells, or cross-feeding, is a ubiquitous feature of microbial communities with emergent properties that influence our health and orchestrate global biogeochemical cycles. Cross-feeding inevitably involves the externalization of molecules. Some of these molecules directly serve as cross-fed nutrients, while others can facilitate cross-feeding. Altogether, externalized molecules that promote cross-feeding are diverse in structure, ranging from small molecules to macromolecules. The functions of these molecules are equally diverse, encompassing waste products, enzymes, toxins, signaling molecules, biofilm components, and nutrients of high value to most microbes, including the producer cell. As diverse as the externalized and transferred molecules are the cross-feeding relationships that can be derived from them. Many cross-feeding relationships can be summarized as cooperative but are also subject to exploitation. Even those relationships that appear to be cooperative exhibit some level of competition between partners. In this review, we summarize the major types of actively secreted, passively excreted, and directly transferred molecules that either form the basis of cross-feeding relationships or facilitate them. Drawing on examples from both natural and synthetic communities, we explore how the interplay between microbial physiology, environmental parameters, and the diverse functional attributes of extracellular molecules can influence cross-feeding dynamics. Though microbial cross-feeding interactions represent a burgeoning field of interest, we may have only begun to scratch the surface.
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Affiliation(s)
- Ryan K Fritts
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - James B McKinlay
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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Benzarti M, Delbrouck C, Neises L, Kiweler N, Meiser J. Metabolic Potential of Cancer Cells in Context of the Metastatic Cascade. Cells 2020; 9:E2035. [PMID: 32899554 PMCID: PMC7563895 DOI: 10.3390/cells9092035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
The metastatic cascade is a highly plastic and dynamic process dominated by cellular heterogeneity and varying metabolic requirements. During this cascade, the three major metabolic pillars, namely biosynthesis, RedOx balance, and bioenergetics, have variable importance. Biosynthesis has superior significance during the proliferation-dominated steps of primary tumour growth and secondary macrometastasis formation and only minor relevance during the growth-independent processes of invasion and dissemination. Consequently, RedOx homeostasis and bioenergetics emerge as conceivable metabolic key determinants in cancer cells that disseminate from the primary tumour. Within this review, we summarise our current understanding on how cancer cells adjust their metabolism in the context of different microenvironments along the metastatic cascade. With the example of one-carbon metabolism, we establish a conceptual view on how the same metabolic pathway can be exploited in different ways depending on the current cellular needs during metastatic progression.
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Affiliation(s)
- Mohaned Benzarti
- Cancer Metabolism Group, Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg; (M.B.); (C.D.); (L.N.); (N.K.)
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg
| | - Catherine Delbrouck
- Cancer Metabolism Group, Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg; (M.B.); (C.D.); (L.N.); (N.K.)
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg
| | - Laura Neises
- Cancer Metabolism Group, Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg; (M.B.); (C.D.); (L.N.); (N.K.)
| | - Nicole Kiweler
- Cancer Metabolism Group, Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg; (M.B.); (C.D.); (L.N.); (N.K.)
| | - Johannes Meiser
- Cancer Metabolism Group, Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg; (M.B.); (C.D.); (L.N.); (N.K.)
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MR1-Restricted T Cells in Cancer Immunotherapy. Cancers (Basel) 2020; 12:cancers12082145. [PMID: 32756356 PMCID: PMC7464881 DOI: 10.3390/cancers12082145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/20/2020] [Accepted: 07/29/2020] [Indexed: 01/09/2023] Open
Abstract
Major histocompatibility complex class I-related (MR1) was first identified as a cell membrane protein involved in the development and expansion of a unique set of T cells expressing an invariant T-cell receptor (TCR) α-chain. These cells were initially discovered in mucosal tissues, such as the intestinal mucosa, so they are called mucosal-associated invariant T (MAIT) cells. MR1 senses the presence of intermediate metabolites of riboflavin and folic acid synthesis that have been chemically modified by the side-products of glycolysis, glyoxal or methylglyoxal. These modified metabolites form complexes with MR1 and translocate from the endoplasmic reticulum to the plasma membrane where MAIT cells’ TCRs recognize them. Recent publications report that atypical MR1-restricted cytotoxic T cells, differing from MAIT cells in TCR usage, antigen, and transcription factor profile, recognize an as yet unknown cancer-specific metabolite presented by MR1 in cancer cells. This metabolite may represent another class of neoantigens, beyond the neo-peptides arising from altered tumor proteins. In an MR1-dependent manner, these MR1-restricted T cells, while sparing noncancerous cells, kill many cancer cell lines and attenuate cell-line-derived and patient-derived xenograft tumors. As MR1 is monomorphic and expressed in a wide range of cancer tissues, these findings raise the possibility of universal pan-cancer immunotherapies that are dependent on cancer metabolites.
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Zhang C, Wang Y, Ma J, Zhang Q, Wang F, Liu X, Xia T. Black phosphorus for fighting antibiotic-resistant bacteria: What is known and what is missing. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 721:137740. [PMID: 32163736 DOI: 10.1016/j.scitotenv.2020.137740] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
Recently, two-dimensional black phosphorus (BP) nanomaterial has captured much attention due to its superb physiochemical and electronic properties and various promising biomedical applications. However, relatively few studies have explored its antimicrobial properties, particularly for targeting antibiotic-resistant pathogens. A comprehensive understanding of the bactericidal mechanisms of BP is essential for application of this material as an antimicrobial. This review discusses the physicochemical and electronic properties of BP that are relevant for antimicrobial applications, especially the unique characteristics that may play a role in overcoming drug resistance. The literature is discussed in the context of what is known and what information is missing. We also highlight the differences and advantages of BP over other two-dimensional nanomaterials (i.e., graphene oxide and molybdenum disulfide) for bactericidal activity. Finally, we analyze existing challenges and note topics that require future investigation to overcome current inadequacies, aiming to assist the safe development of BP-based nanotechnology for pathogen control.
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Affiliation(s)
- Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100875, China.
| | - Yating Wang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Junjie Ma
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Qiurong Zhang
- College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Fang Wang
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Xinhui Liu
- School of Environment, Beijing Normal University, Beijing 100875, China
| | - Tian Xia
- Division of Nanomedicine, Department of Medicine, California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
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Xu J, Martien J, Gilbertson C, Ma J, Amador-Noguez D, Park JO. Metabolic flux analysis and fluxomics-driven determination of reaction free energy using multiple isotopes. Curr Opin Biotechnol 2020; 64:151-160. [PMID: 32304936 DOI: 10.1016/j.copbio.2020.02.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/08/2020] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
Metabolite concentrations, fluxes, and free energies constitute the basis for understanding and controlling metabolism. Mass spectrometry and stable isotopes are integral tools in quantifying these metabolic features. For absolute metabolite concentration and flux measurement, 13C internal standards and tracers have been the gold standard. In contrast, no established methods exist for comprehensive thermodynamic quantitation under physiological environments. Recently, using high-resolution mass spectrometry and multi-isotope tracing, flux quantitation has been increasingly adopted in broader metabolism. The improved flux quantitation led to determination of Gibbs free energy of reaction (ΔG) in central carbon metabolism using a relationship between reaction reversibility and thermodynamic driving force. Here we highlight recent advances in multi-isotope tracing for metabolic flux and free energy analysis.
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Affiliation(s)
- Jimmy Xu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Julia Martien
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cole Gilbertson
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Junyu Ma
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers. mSystems 2020; 5:5/2/e00736-19. [PMID: 32184362 PMCID: PMC7380578 DOI: 10.1128/msystems.00736-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers. Clostridium thermocellum and Thermoanaerobacterium saccharolyticum are thermophilic anaerobic bacteria with complementary metabolic capabilities that utilize distinct glycolytic pathways for the conversion of cellulosic sugars to biofuels. We integrated quantitative metabolomics with 2H and 13C metabolic flux analysis to investigate the in vivo reversibility and thermodynamics of the central metabolic networks of these two microbes. We found that the glycolytic pathway in C. thermocellum operates remarkably close to thermodynamic equilibrium, with an overall drop in Gibbs free energy 5-fold lower than that of T. saccharolyticum or anaerobically grown Escherichia coli. The limited thermodynamic driving force of glycolysis in C. thermocellum could be attributed in large part to the small free energy of the phosphofructokinase reaction producing fructose bisphosphate. The ethanol fermentation pathway was also substantially more reversible in C. thermocellum than in T. saccharolyticum. These observations help explain the comparatively low ethanol titers of C. thermocellum and suggest engineering interventions that can be used to increase its ethanol productivity and glycolytic rate. In addition to thermodynamic analysis, we used our isotope tracer data to reconstruct the T. saccharolyticum central metabolic network, revealing exclusive use of the Embden-Meyerhof-Parnas (EMP) pathway for glycolysis, a bifurcated tricarboxylic acid (TCA) cycle, and a sedoheptulose bisphosphate bypass active within the pentose phosphate pathway. IMPORTANCE Thermodynamics constitutes a key determinant of flux and enzyme efficiency in metabolic networks. Here, we provide new insights into the divergent thermodynamics of the glycolytic pathways of C. thermocellum and T. saccharolyticum, two industrially relevant thermophilic bacteria whose metabolism still is not well understood. We report that while the glycolytic pathway in T. saccharolyticum is as thermodynamically favorable as that found in model organisms, such as E. coli or Saccharomyces cerevisiae, the glycolytic pathway of C. thermocellum operates near equilibrium. The use of a near-equilibrium glycolytic pathway, with potentially increased ATP yield, by this cellulolytic microbe may represent an evolutionary adaptation to growth on cellulose, but it has the drawback of being highly susceptible to product feedback inhibition. The results of this study will facilitate future engineering of high-performance strains capable of transforming cellulosic biomass to biofuels at high yields and titers.
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49
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McKinlay JB, Cook GM, Hards K. Microbial energy management-A product of three broad tradeoffs. Adv Microb Physiol 2020; 77:139-185. [PMID: 34756210 DOI: 10.1016/bs.ampbs.2020.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Wherever thermodynamics allows, microbial life has evolved to transform and harness energy. Microbial life thus abounds in the most unexpected places, enabled by profound metabolic diversity. Within this diversity, energy is transformed primarily through variations on a few core mechanisms. Energy is further managed by the physiological processes of cell growth and maintenance that use energy. Some aspects of microbial physiology are streamlined for energetic efficiency while other aspects seem suboptimal or even wasteful. We propose that the energy that a microbe harnesses and devotes to growth and maintenance is a product of three broad tradeoffs: (i) economic, trading enzyme synthesis or operational cost for functional benefit, (ii) environmental, trading optimization for a single environment for adaptability to multiple environments, and (iii) thermodynamic, trading energetic yield for forward metabolic flux. Consideration of these tradeoffs allows one to reconcile features of microbial physiology that seem to opposingly promote either energetic efficiency or waste.
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Affiliation(s)
- James B McKinlay
- Department of Biology, Indiana University, Bloomington, IN, United States.
| | - Gregory M Cook
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Kiel Hards
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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