1
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Holbrook-Smith D, Trouillon J, Sauer U. Metabolomics and Microbial Metabolism: Toward a Systematic Understanding. Annu Rev Biophys 2024; 53:41-64. [PMID: 38109374 DOI: 10.1146/annurev-biophys-030722-021957] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Over the past decades, our understanding of microbial metabolism has increased dramatically. Metabolomics, a family of techniques that are used to measure the quantities of small molecules in biological samples, has been central to these efforts. Advances in analytical chemistry have made it possible to measure the relative and absolute concentrations of more and more compounds with increasing levels of certainty. In this review, we highlight how metabolomics has contributed to understanding microbial metabolism and in what ways it can still be deployed to expand our systematic understanding of metabolism. To that end, we explain how metabolomics was used to (a) characterize network topologies of metabolism and its regulation networks, (b) elucidate the control of metabolic function, and (c) understand the molecular basis of higher-order phenomena. We also discuss areas of inquiry where technological advances should continue to increase the impact of metabolomics, as well as areas where our understanding is bottlenecked by other factors such as the availability of statistical and modeling frameworks that can extract biological meaning from metabolomics data.
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Affiliation(s)
| | - Julian Trouillon
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland;
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2
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Weeramange C, Menjivar C, O'Neil PT, El Qaidi S, Harrison KS, Meinhardt S, Bird CL, Sreenivasan S, Hardwidge PR, Fenton AW, Hefty PS, Bose JL, Swint-Kruse L. Fructose-1-kinase has pleiotropic roles in Escherichia coli. J Biol Chem 2024; 300:107352. [PMID: 38723750 PMCID: PMC11157272 DOI: 10.1016/j.jbc.2024.107352] [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: 01/23/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/21/2024] Open
Abstract
In Escherichia coli, the master transcription regulator catabolite repressor activator (Cra) regulates >100 genes in central metabolism. Cra binding to DNA is allosterically regulated by binding to fructose-1-phosphate (F-1-P), but the only documented source of F-1-P is from the concurrent import and phosphorylation of exogenous fructose. Thus, many have proposed that fructose-1,6-bisphosphate (F-1,6-BP) is also a physiological regulatory ligand. However, the role of F-1,6-BP has been widely debated. Here, we report that the E. coli enzyme fructose-1-kinase (FruK) can carry out its "reverse" reaction under physiological substrate concentrations to generate F-1-P from F-1,6-BP. We further show that FruK directly binds Cra with nanomolar affinity and forms higher order, heterocomplexes. Growth assays with a ΔfruK strain and fruK complementation show that FruK has a broader role in metabolism than fructose catabolism. Since fruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli's central metabolism that occur in response to changing nutrients. These findings might have wide-spread relevance to other γ-proteobacteria, which conserve both Cra and FruK.
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Affiliation(s)
- Chamitha Weeramange
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cindy Menjivar
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Pierce T O'Neil
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Kelly S Harrison
- The Department of Molecular Biosciences, The University of Kansas - Lawrence, Lawrence, Kansas, USA
| | - Sarah Meinhardt
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cole L Bird
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Shwetha Sreenivasan
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Aron W Fenton
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - P Scott Hefty
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Jeffrey L Bose
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Liskin Swint-Kruse
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
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3
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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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4
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Moreno R, Rojo F. What are the signals that control catabolite repression in Pseudomonas? Microb Biotechnol 2024; 17:e14407. [PMID: 38227132 PMCID: PMC10832556 DOI: 10.1111/1751-7915.14407] [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: 11/17/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Metabolically versatile bacteria exhibit a global regulatory response known as carbon catabolite repression (CCR), which prioritizes some carbon sources over others when all are present in sufficient amounts. This optimizes growth by distributing metabolite fluxes, but can restrict yields in biotechnological applications. The molecular mechanisms and preferred substrates for CCR vary between bacterial groups. Escherichia coli prioritizes glucose whereas Pseudomonas sp. prefer certain organic acids or amino acids. A significant issue in understanding (and potentially bypassing) CCR is the lack of information about the signals that trigger this regulatory response. In E. coli, several key compounds act as flux sensors, governing the flow of metabolites through catabolic pathways and preventing imbalances. These flux sensors can also modulate the CCR response. It has been suggested that the order of substrate preference is determined by carbon uptake flux rather than substrate identity. For Pseudomonas, much less information is available, as the signals that induce CCR are poorly understood. This article briefly discusses the available evidence on the signals that trigger CCR and the questions that remain to be answered in Pseudomonas.
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Affiliation(s)
- Renata Moreno
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
| | - Fernando Rojo
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología, CSICMadridSpain
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5
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Weeramange C, Menjivar C, O’Neil PT, El Qaidi S, Harrison KS, Meinhardt S, Bird CL, Sreenivasan S, Hardwidge PR, Fenton AW, Hefty PS, Bose JL, Swint-Kruse L. Fructose-1-kinase has pleiotropic roles in Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571569. [PMID: 38168282 PMCID: PMC10760178 DOI: 10.1101/2023.12.14.571569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
In Escherichia coli, the master transcription regulator Catabolite Repressor Activator (Cra) regulates >100 genes in central metabolism. Cra binding to DNA is allosterically regulated by binding to fructose-1-phosphate (F-1-P), but the only documented source of F-1-P is from the concurrent import and phosphorylation of exogenous fructose. Thus, many have proposed that fructose-1,6-bisphosphate (F-1,6-BP) is also a physiological regulatory ligand. However, the role of F-1,6-BP has been widely debated. Here, we report that the E. coli enzyme fructose-1-kinase (FruK) can carry out its "reverse" reaction under physiological substrate concentrations to generate F-1-P from F-1,6-BP. We further show that FruK directly binds Cra with nanomolar affinity and forms higher order, heterocomplexes. Growth assays with a ΔfruK strain and fruK complementation show that FruK has a broader role in metabolism than fructose catabolism. The ΔfruK strain also alters biofilm formation. Since fruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli central metabolism that occur in response to changing nutrients. These findings might have wide-spread relevance to other γ-proteobacteria, which conserve both Cra and FruK.
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Affiliation(s)
- Chamitha Weeramange
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Cindy Menjivar
- The Department of Microbiology, Molecular Genetics and Immunology, 3901 Rainbow Blvd, MSN 3029, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Pierce T. O’Neil
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Samir El Qaidi
- College of Veterinary Medicine, 1800 Denison Ave, Kansas State University, Manhattan, KS, USA 66506
| | - Kelly S. Harrison
- The Department of Molecular Biosciences, 2034 Haworth Hall, 1200 Sunnyside Avenue, The University of Kansas – Lawrence, Lawrence, Kansas, USA 66045
| | - Sarah Meinhardt
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Cole L. Bird
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Shwetha Sreenivasan
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Philip R. Hardwidge
- College of Veterinary Medicine, 1800 Denison Ave, Kansas State University, Manhattan, KS, USA 66506
| | - Aron W. Fenton
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - P. Scott Hefty
- College of Veterinary Medicine, 1800 Denison Ave, Kansas State University, Manhattan, KS, USA 66506
| | - Jeffrey L. Bose
- The Department of Microbiology, Molecular Genetics and Immunology, 3901 Rainbow Blvd, MSN 3029, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
| | - Liskin Swint-Kruse
- The Department of Biochemistry and Molecular Biology, 3901 Rainbow Blvd, MSN 3030, The University of Kansas Medical Center, Kansas City, Kansas, USA 66160
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6
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Jakowec NA, Finegan M, Finkel SE. Disruption of trehalose periplasmic recycling dysregulates cAMP-CRP signaling in Escherichia coli during stationary phase. J Bacteriol 2023; 205:e0029223. [PMID: 37916804 PMCID: PMC10662143 DOI: 10.1128/jb.00292-23] [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: 09/05/2023] [Accepted: 10/13/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Survival during starvation hinges on the ability to manage intracellular energy reserves and to initiate appropriate metabolic responses to perturbations of such reserves. How Escherichia coli manage carbon storage systems under starvation stress, as well as transpose changes in intracellular metabolite levels into regulatory signals, is not well understood. Endogenous trehalose metabolism may be at the center of these processes, coupling carbon storage with carbon starvation responses. The coupled transport to the periplasm and subsequent hydrolysis of trehalose back to glucose for transport to the cytoplasm may function as a crucial metabolic signaling pathway. Although trehalose has been characterized as a stress protectant in E. coli, the disaccharide also functions as both an energy storage compound and a regulator of carbohydrate metabolism in fungi, plants, and other bacteria. Our research explores the metabolic regulatory properties of trehalose in E. coli and a potential mechanism by which the intracellular carbon pool is interconnected with regulatory circuits, enabling long-term survival.
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Affiliation(s)
- Nicolaus A. Jakowec
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Melissa Finegan
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Steven E. Finkel
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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7
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Sporre E, Karlsen J, Schriever K, Asplund-Samuelsson J, Janasch M, Strandberg L, Karlsson A, Kotol D, Zeckey L, Piazza I, Syrén PO, Edfors F, Hudson EP. Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation. Commun Biol 2023; 6:947. [PMID: 37723200 PMCID: PMC10507043 DOI: 10.1038/s42003-023-05318-8] [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: 01/27/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023] Open
Abstract
Metabolite-level regulation of enzyme activity is important for microbes to cope with environmental shifts. Knowledge of such regulations can also guide strain engineering for biotechnology. Here we apply limited proteolysis-small molecule mapping (LiP-SMap) to identify and compare metabolite-protein interactions in the proteomes of two cyanobacteria and two lithoautotrophic bacteria that fix CO2 using the Calvin cycle. Clustering analysis of the hundreds of detected interactions shows that some metabolites interact in a species-specific manner. We estimate that approximately 35% of interacting metabolites affect enzyme activity in vitro, and the effect is often minor. Using LiP-SMap data as a guide, we find that the Calvin cycle intermediate glyceraldehyde-3-phosphate enhances activity of fructose-1,6/sedoheptulose-1,7-bisphosphatase (F/SBPase) from Synechocystis sp. PCC 6803 and Cupriavidus necator in reducing conditions, suggesting a convergent feed-forward activation of the cycle. In oxidizing conditions, glyceraldehyde-3-phosphate inhibits Synechocystis F/SBPase by promoting enzyme aggregation. In contrast, the glycolytic intermediate glucose-6-phosphate activates F/SBPase from Cupriavidus necator but not F/SBPase from Synechocystis. Thus, metabolite-level regulation of the Calvin cycle is more prevalent than previously appreciated.
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Affiliation(s)
- Emil Sporre
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Karlsen
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Karen Schriever
- Department of Fiber and Polymer Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Johannes Asplund-Samuelsson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Markus Janasch
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Biotechnology and Nanomedicine, SINTEF Industry, 7465, Trondheim, Norway
| | - Linnéa Strandberg
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Anna Karlsson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - David Kotol
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Luise Zeckey
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Per-Olof Syrén
- Department of Fiber and Polymer Technology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Elton P Hudson
- Department of Protein Science, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
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8
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Scott M, Hwa T. Shaping bacterial gene expression by physiological and proteome allocation constraints. Nat Rev Microbiol 2023; 21:327-342. [PMID: 36376406 PMCID: PMC10121745 DOI: 10.1038/s41579-022-00818-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2022] [Indexed: 11/16/2022]
Abstract
Networks of molecular regulators are often the primary objects of focus in the study of gene regulation, with the machinery of protein synthesis tacitly relegated to the background. Shifting focus to the constraints imposed by the allocation of protein synthesis flux reveals surprising ways in which the actions of molecular regulators are shaped by physiological demands. Using carbon catabolite repression as a case study, we describe how physiological constraints are sensed through metabolic fluxes and how flux-controlled regulation gives rise to simple empirical relations between protein levels and the rate of cell growth.
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Affiliation(s)
- Matthew Scott
- Department of Applied Mathematics, University of Waterloo, Waterloo, ON, Canada.
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, CA, USA.
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9
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Ortega AD. Real-Time Assessment of Intracellular Metabolites in Single Cells through RNA-Based Sensors. Biomolecules 2023; 13:biom13050765. [PMID: 37238635 DOI: 10.3390/biom13050765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites.
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Affiliation(s)
- Alvaro Darío Ortega
- Department of Cell Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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10
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Bi S, Kargeti M, Colin R, Farke N, Link H, Sourjik V. Dynamic fluctuations in a bacterial metabolic network. Nat Commun 2023; 14:2173. [PMID: 37061520 PMCID: PMC10105761 DOI: 10.1038/s41467-023-37957-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 04/06/2023] [Indexed: 04/17/2023] Open
Abstract
The operation of the central metabolism is typically assumed to be deterministic, but dynamics and high connectivity of the metabolic network make it potentially prone to generating fluctuations. However, time-resolved measurements of metabolite levels in individual cells that are required to characterize such fluctuations remained a challenge, particularly in small bacterial cells. Here we use single-cell metabolite measurements based on Förster resonance energy transfer, combined with computer simulations, to explore the real-time dynamics of the metabolic network of Escherichia coli. We observe that steplike exposure of starved E. coli to glycolytic carbon sources elicits large periodic fluctuations in the intracellular concentration of pyruvate in individual cells. These fluctuations are consistent with predicted oscillatory dynamics of E. coli metabolic network, and they are primarily controlled by biochemical reactions around the pyruvate node. Our results further indicate that fluctuations in glycolysis propagate to other cellular processes, possibly leading to temporal heterogeneity of cellular states within a population.
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Affiliation(s)
- Shuangyu Bi
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Manika Kargeti
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
| | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany
| | - Niklas Farke
- University of Tübingen, D-72076, Tübingen, Germany
| | - Hannes Link
- University of Tübingen, D-72076, Tübingen, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), D-35043, Marburg, Germany.
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11
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Zhu Y, Gao H, Zhang J, Zhao J, Qi Q, Wang Q. De novo design of the global transcriptional factor Cra-regulated promoters enables highly sensitive glycolysis flux biosensor for dynamic metabolic control. Microb Biotechnol 2023; 16:605-617. [PMID: 36541030 PMCID: PMC9948231 DOI: 10.1111/1751-7915.14166] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 10/09/2022] [Accepted: 10/19/2022] [Indexed: 12/24/2022] Open
Abstract
Glycolytic flux is a fundamental index in microbial cell factories. A glycolytic flux biosensor that can monitor glucose metabolism efficiency is a promising strategy in rewiring metabolic flux to balance growth and biosynthesis. A key design feature of the glycolytic flux biosensors is the interaction between the global transcriptional factor Cra and its regulated promoters. However, overexpression and mutation of Cra has unpredictable effects on global metabolism in Escherichia coli. Therefore, new orthogonal biosensor design strategies should be developed to circumvent metabolic issues. In this report, the promoters in glycolytic flux biosensor were replaced with synthetic promoters of varying strengths or phage-derived promoters, and the Cra DNA-binding sites were deployed into promoters at different positions and distances to yield biosensors. The de nova biosensors that depended on Cra could sense Fructose-1,6-diphosphate (FBP) with broad dynamic ranges and low basal leakage. Then the negative-response biosensors were applied to fine-tune the target ATP synthesis gene, leading to the desired increase in pyruvate production (the highest 9.66 g/L) and cell growth. Moreover, the membrane synthesis gene plsC was also dynamically activated by the positive-response biosensor, leading to effective accumulation of lycopene in the cell membrane and a 50-fold increase in lycopene titre (100.3 mg/L) when compared with the control strain, demonstrating the effective and broader usages of our biosensors.
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Affiliation(s)
- Yuan Zhu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaxiao Gao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jian Zhang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jingyu Zhao
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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12
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El-Mansi M. Control of central metabolism’s architecture in Escherichia coli: An overview. Microbiol Res 2023; 266:127224. [DOI: 10.1016/j.micres.2022.127224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
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13
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Monitoring glycolytic dynamics in single cells using a fluorescent biosensor for fructose 1,6-bisphosphate. Proc Natl Acad Sci U S A 2022; 119:e2204407119. [PMID: 35881794 PMCID: PMC9351453 DOI: 10.1073/pnas.2204407119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cellular metabolism is regulated over space and time to ensure that energy production is efficiently matched with consumption. Fluorescent biosensors are useful tools for studying metabolism as they enable real-time detection of metabolite abundance with single-cell resolution. For monitoring glycolysis, the intermediate fructose 1,6-bisphosphate (FBP) is a particularly informative signal as its concentration is strongly correlated with flux through the whole pathway. Using GFP insertion into the ligand-binding domain of the Bacillus subtilis transcriptional regulator CggR, we developed a fluorescent biosensor for FBP termed HYlight. We demonstrate that HYlight can reliably report the real-time dynamics of glycolysis in living cells and tissues, driven by various metabolic or pharmacological perturbations, alone or in combination with other physiologically relevant signals. Using this sensor, we uncovered previously unknown aspects of β-cell glycolytic heterogeneity and dynamics.
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14
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Fan X, Walther A. 1D Colloidal chains: recent progress from formation to emergent properties and applications. Chem Soc Rev 2022; 51:4023-4074. [PMID: 35502721 DOI: 10.1039/d2cs00112h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrating nanoscale building blocks of low dimensionality (0D; i.e., spheres) into higher dimensional structures endows them and their corresponding materials with emergent properties non-existent or only weakly existent in the individual building blocks. Constructing 1D chains, 2D arrays and 3D superlattices using nanoparticles and colloids therefore continues to be one of the grand goals in colloid and nanomaterial science. Amongst these higher order structures, 1D colloidal chains are of particular interest, as they possess unique anisotropic properties. In recent years, the most relevant advances in 1D colloidal chain research have been made in novel synthetic methodologies and applications. In this review, we first address a comprehensive description of the research progress concerning various synthetic strategies developed to construct 1D colloidal chains. Following this, we highlight the amplified and emergent properties of the resulting materials, originating from the assembly of the individual building blocks and their collective behavior, and discuss relevant applications in advanced materials. In the discussion of synthetic strategies, properties, and applications, particular attention will be paid to overarching concepts, fresh trends, and potential areas of future research. We believe that this comprehensive review will be a driver to guide the interdisciplinary field of 1D colloidal chains, where nanomaterial synthesis, self-assembly, physical property studies, and material applications meet, to a higher level, and open up new research opportunities at the interface of classical disciplines.
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Affiliation(s)
- Xinlong Fan
- Institute for Macromolecular Chemistry, Albert-Ludwigs-University Freiburg, Stefan-Meier-Str. 31, 79104, Freiburg, Germany.
| | - Andreas Walther
- A3BMS Lab, Department of Chemistry, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
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15
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Losa J, Leupold S, Alonso-Martinez D, Vainikka P, Thallmair S, Tych KM, Marrink SJ, Heinemann M. Perspective: a stirring role for metabolism in cells. Mol Syst Biol 2022; 18:e10822. [PMID: 35362256 PMCID: PMC8972047 DOI: 10.15252/msb.202110822] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022] Open
Abstract
Based on recent findings indicating that metabolism might be governed by a limit on the rate at which cells can dissipate Gibbs energy, in this Perspective, we propose a new mechanism of how metabolic activity could globally regulate biomolecular processes in a cell. Specifically, we postulate that Gibbs energy released in metabolic reactions is used to perform work, allowing enzymes to self‐propel or to break free from supramolecular structures. This catalysis‐induced enzyme movement will result in increased intracellular motion, which in turn can compromise biomolecular functions. Once the increased intracellular motion has a detrimental effect on regulatory mechanisms, this will establish a feedback mechanism on metabolic activity, and result in the observed thermodynamic limit. While this proposed explanation for the identified upper rate limit on cellular Gibbs energy dissipation rate awaits experimental validation, it offers an intriguing perspective of how metabolic activity can globally affect biomolecular functions and will hopefully spark new research.
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Affiliation(s)
- José Losa
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Simeon Leupold
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Diego Alonso-Martinez
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Petteri Vainikka
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Sebastian Thallmair
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Katarzyna M Tych
- Chemical Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Siewert J Marrink
- Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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16
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Smith K, Shen F, Lee HJ, Chandrasekaran S. Metabolic signatures of regulation by phosphorylation and acetylation. iScience 2022; 25:103730. [PMID: 35072016 PMCID: PMC8762462 DOI: 10.1016/j.isci.2021.103730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/15/2021] [Accepted: 12/30/2021] [Indexed: 10/31/2022] Open
Abstract
Acetylation and phosphorylation are highly conserved posttranslational modifications (PTMs) that regulate cellular metabolism, yet how metabolic control is shared between these PTMs is unknown. Here we analyze transcriptome, proteome, acetylome, and phosphoproteome datasets in E. coli, S. cerevisiae, and mammalian cells across diverse conditions using CAROM, a new approach that uses genome-scale metabolic networks and machine learning to classify targets of PTMs. We built a single machine learning model that predicted targets of each PTM in a condition across all three organisms based on reaction attributes (AUC>0.8). Our model predicted phosphorylated enzymes during a mammalian cell-cycle, which we validate using phosphoproteomics. Interpreting the machine learning model using game theory uncovered enzyme properties including network connectivity, essentiality, and condition-specific factors such as maximum flux that differentiate targets of phosphorylation from acetylation. The conserved and predictable partitioning of metabolic regulation identified here between these PTMs may enable rational rewiring of regulatory circuits.
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Affiliation(s)
- Kirk Smith
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fangzhou Shen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ho Joon Lee
- Department of Genetics, Yale University, New Haven, CT 06510, USA.,Yale Center for Genome Analysis, Yale University, New Haven, CT 06510, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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17
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Euler C, Mahadevan R. On the design principles of metabolic flux sensing. Biophys J 2022; 121:237-247. [PMID: 34951981 PMCID: PMC8790210 DOI: 10.1016/j.bpj.2021.12.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/01/2021] [Accepted: 12/16/2021] [Indexed: 01/21/2023] Open
Abstract
Metabolism is precisely coordinated, with the goal of balancing fluxes to maintain robust growth. However, coordinating fluxes requires information about rates, which can only be inferred through concentrations. While flux-sensitive metabolites have been reported, the design principles underlying such sensing have not been clearly elucidated. Here we use kinetic modeling to show that substrate concentrations of thermodynamically constrained reactions reflect upstream flux and therefore carry information about rates. Then we use untargeted multi-omic data from Escherichia coli and Saccharomyces cerevisiae to show that the concentrations of some metabolites in central carbon metabolism reflect fluxes as a result of thermodynamic constraints. We then establish, using 37 real concentration-flux relationships across both organisms, that in vivo ΔG∘≥-4 kJ/mol is the threshold above which substrates are likely to be sensitive to upstream flux(es).
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Affiliation(s)
- Christian Euler
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada; Institute for Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada.
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18
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Miyazawa H, Snaebjornsson MT, Prior N, Kafkia E, Hammarén HM, Tsuchida-Straeten N, Patil KR, Beck M, Aulehla A. Glycolytic flux-signaling controls mouse embryo mesoderm development. eLife 2022; 11:83299. [PMID: 36469462 PMCID: PMC9771359 DOI: 10.7554/elife.83299] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/06/2022] [Indexed: 12/12/2022] Open
Abstract
How cellular metabolic state impacts cellular programs is a fundamental, unresolved question. Here, we investigated how glycolytic flux impacts embryonic development, using presomitic mesoderm (PSM) patterning as the experimental model. First, we identified fructose 1,6-bisphosphate (FBP) as an in vivo sentinel metabolite that mirrors glycolytic flux within PSM cells of post-implantation mouse embryos. We found that medium-supplementation with FBP, but not with other glycolytic metabolites, such as fructose 6-phosphate and 3-phosphoglycerate, impaired mesoderm segmentation. To genetically manipulate glycolytic flux and FBP levels, we generated a mouse model enabling the conditional overexpression of dominant active, cytoplasmic PFKFB3 (cytoPFKFB3). Overexpression of cytoPFKFB3 indeed led to increased glycolytic flux/FBP levels and caused an impairment of mesoderm segmentation, paralleled by the downregulation of Wnt-signaling, reminiscent of the effects seen upon FBP-supplementation. To probe for mechanisms underlying glycolytic flux-signaling, we performed subcellular proteome analysis and revealed that cytoPFKFB3 overexpression altered subcellular localization of certain proteins, including glycolytic enzymes, in PSM cells. Specifically, we revealed that FBP supplementation caused depletion of Pfkl and Aldoa from the nuclear-soluble fraction. Combined, we propose that FBP functions as a flux-signaling metabolite connecting glycolysis and PSM patterning, potentially through modulating subcellular protein localization.
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Affiliation(s)
- Hidenobu Miyazawa
- Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | | | - Nicole Prior
- Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Eleni Kafkia
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Henrik M Hammarén
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | | | - Kiran R Patil
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Martin Beck
- Structural and Computational Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
| | - Alexander Aulehla
- Developmental Biology Unit, European Molecular Biology LaboratoryHeidelbergGermany
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19
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Schink SJ, Christodoulou D, Mukherjee A, Athaide E, Brunner V, Fuhrer T, Bradshaw GA, Sauer U, Basan M. Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing. Mol Syst Biol 2022; 18:e10704. [PMID: 34994048 PMCID: PMC8738977 DOI: 10.15252/msb.202110704] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 11/29/2022] Open
Abstract
Central carbon metabolism is highly conserved across microbial species, but can catalyze very different pathways depending on the organism and their ecological niche. Here, we study the dynamic reorganization of central metabolism after switches between the two major opposing pathway configurations of central carbon metabolism, glycolysis, and gluconeogenesis in Escherichia coli, Pseudomonas aeruginosa, and Pseudomonas putida. We combined growth dynamics and dynamic changes in intracellular metabolite levels with a coarse-grained model that integrates fluxes, regulation, protein synthesis, and growth and uncovered fundamental limitations of the regulatory network: After nutrient shifts, metabolite concentrations collapse to their equilibrium, rendering the cell unable to sense which direction the flux is supposed to flow through the metabolic network. The cell can partially alleviate this by picking a preferred direction of regulation at the expense of increasing lag times in the opposite direction. Moreover, decreasing both lag times simultaneously comes at the cost of reduced growth rate or higher futile cycling between metabolic enzymes. These three trade-offs can explain why microorganisms specialize for either glycolytic or gluconeogenic substrates and can help elucidate the complex growth patterns exhibited by different microbial species.
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Affiliation(s)
| | - Dimitris Christodoulou
- Systems Biology DepartmentHarvard Medical SchoolBostonMAUSA
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Avik Mukherjee
- Systems Biology DepartmentHarvard Medical SchoolBostonMAUSA
- Applied Mathematics DepartmentHarvard CollegeCambridgeMAUSA
| | - Edward Athaide
- Applied Mathematics DepartmentHarvard CollegeCambridgeMAUSA
| | - Viktoria Brunner
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Gary Andrew Bradshaw
- Laboratory of Systems PharmacologyHarvard Program in Therapeutic ScienceHarvard Medical SchoolBostonMAUSA
| | - Uwe Sauer
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Markus Basan
- Systems Biology DepartmentHarvard Medical SchoolBostonMAUSA
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20
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Shimizu K, Matsuoka Y. Feedback regulation and coordination of the main metabolism for bacterial growth and metabolic engineering for amino acid fermentation. Biotechnol Adv 2021; 55:107887. [PMID: 34921951 DOI: 10.1016/j.biotechadv.2021.107887] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/28/2022]
Abstract
Living organisms such as bacteria are often exposed to continuous changes in the nutrient availability in nature. Therefore, bacteria must constantly monitor the environmental condition, and adjust the metabolism quickly adapting to the change in the growth condition. For this, bacteria must orchestrate (coordinate and integrate) the complex and dynamically changing information on the environmental condition. In particular, the central carbon metabolism (CCM), monomer synthesis, and macromolecular synthesis must be coordinately regulated for the efficient growth. It is a grand challenge in bioscience, biotechnology, and synthetic biology to understand how living organisms coordinate the metabolic regulation systems. Here, we consider the integrated sensing of carbon sources by the phosphotransferase system (PTS), and the feed-forward/feedback regulation systems incorporated in the CCM in relation to the pool sizes of flux-sensing metabolites and αketoacids. We also consider the metabolic regulation of amino acid biosynthesis (as well as purine and pyrimidine biosyntheses) paying attention to the feedback control systems consisting of (fast) enzyme level regulation with (slow) transcriptional regulation. The metabolic engineering for the efficient amino acid production by bacteria such as Escherichia coli and Corynebacterium glutamicum is also discussed (in relation to the regulation mechanisms). The amino acid synthesis is important for determining the rate of ribosome biosynthesis. Thus, the growth rate control (growth law) is further discussed on the relationship between (p)ppGpp level and the ribosomal protein synthesis.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Department of Fisheries Distribution and Management, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan
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21
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Boecker S, Slaviero G, Schramm T, Szymanski W, Steuer R, Link H, Klamt S. Deciphering the physiological response of Escherichia coli under high ATP demand. Mol Syst Biol 2021; 17:e10504. [PMID: 34928538 PMCID: PMC8686765 DOI: 10.15252/msb.202110504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 11/20/2022] Open
Abstract
One long-standing question in microbiology is how microbes buffer perturbations in energy metabolism. In this study, we systematically analyzed the impact of different levels of ATP demand in Escherichia coli under various conditions (aerobic and anaerobic, with and without cell growth). One key finding is that, under all conditions tested, the glucose uptake increases with rising ATP demand, but only to a critical level beyond which it drops markedly, even below wild-type levels. Focusing on anaerobic growth and using metabolomics and proteomics data in combination with a kinetic model, we show that this biphasic behavior is induced by the dual dependency of the phosphofructokinase on ATP (substrate) and ADP (allosteric activator). This mechanism buffers increased ATP demands by a higher glycolytic flux but, as shown herein, it collapses under very low ATP concentrations. Model analysis also revealed two major rate-controlling steps in the glycolysis under high ATP demand, which could be confirmed experimentally. Our results provide new insights on fundamental mechanisms of bacterial energy metabolism and guide the rational engineering of highly productive cell factories.
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Affiliation(s)
- Simon Boecker
- Analysis and Redesign of Biological NetworksMax Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | - Giulia Slaviero
- Analysis and Redesign of Biological NetworksMax Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
| | - Thorben Schramm
- Dynamic Control of Metabolic NetworksMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Witold Szymanski
- Core Facility for Mass Spectrometry and ProteomicsMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
| | - Ralf Steuer
- Institute for BiologyHumboldt‐University of BerlinBerlinGermany
| | - Hannes Link
- Dynamic Control of Metabolic NetworksMax Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Steffen Klamt
- Analysis and Redesign of Biological NetworksMax Planck Institute for Dynamics of Complex Technical SystemsMagdeburgGermany
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22
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Zhu Y, Li Y, Xu Y, Zhang J, Ma L, Qi Q, Wang Q. Development of bifunctional biosensors for sensing and dynamic control of glycolysis flux in metabolic engineering. Metab Eng 2021; 68:142-151. [PMID: 34610458 DOI: 10.1016/j.ymben.2021.09.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 11/30/2022]
Abstract
Glycolysis is the primary metabolic pathway in all living organisms. Maintaining the balance of glycolysis flux and biosynthetic pathways is the crucial matter involved in the microbial cell factory. Few regulation systems can address the issue of metabolic flux imbalance in glycolysis. Here, we designed and constructed a bifunctional glycolysis flux biosensor that can dynamically regulate glycolysis flux for overproduction of desired biochemicals. A series of positive-and negative-response biosensors were created and modified for varied thresholds and dynamic ranges. These engineered glycolysis flux biosensors were verified to be able to characterize in vivo fructose-1,6-diphosphate concentration. Subsequently, the biosensors were applied for fine-tuning glycolysis flux to effectively balance the biosynthesis of two chemicals: mevalonate and N-acetylglucosamine. A glycolysis flux-dynamically controlled Escherichia coli strain achieved a 111.3 g/L mevalonate titer in a 1L fermenter.
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Affiliation(s)
- Yuan Zhu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Ying Li
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Ya Xu
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Jian Zhang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Linlin Ma
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China
| | - Qingsheng Qi
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China; CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China.
| | - Qian Wang
- National Glycoengineering Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, PR China.
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23
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Okano H, Hermsen R, Hwa T. Hierarchical and simultaneous utilization of carbon substrates: mechanistic insights, physiological roles, and ecological consequences. Curr Opin Microbiol 2021; 63:172-178. [PMID: 34365153 PMCID: PMC9744632 DOI: 10.1016/j.mib.2021.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/03/2021] [Accepted: 07/11/2021] [Indexed: 12/14/2022]
Abstract
Bacteria grown on a mixture of carbon substrates exhibit two utilization patterns: hierarchical utilization (HU) and simultaneous utilization (SU). How and why cells adopt these different behaviors remains poorly understood despite decades of research. Recent studies address various open questions from multiple viewpoints. From a mechanistic perspective, it was found that flux sensors play a central role in the regulation of substrate utilization, accounting for the known dependences on single-substrate growth rates, substrate concentrations, and the point where the substrate enters central metabolism. From a physiological perspective, several recent studies suggested HU or SU as growth-optimizing strategies through efficient allocation of essential proteome resources. However, other studies demonstrate that a significant fraction of the proteome is dedicated to functions apparently unnecessary for growth, casting doubt on explanations based on slight efficiency gains. From an ecological perspective, recent theoretical studies suggest that HU can help increase species diversity in bacterial communities.
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Affiliation(s)
- Hiroyuki Okano
- Department of Physics, University of California at San Diego, La Jolla, CA, USA,corresponding authors: H. Okano () and R. Hermsen ()
| | - Rutger Hermsen
- Theoretical Biology Group, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands,corresponding authors: H. Okano () and R. Hermsen ()
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, CA, USA
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24
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Deatherage DE, Barrick JE. High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing. Cell Syst 2021; 12:1187-1200.e4. [PMID: 34536379 DOI: 10.1016/j.cels.2021.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 07/14/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Understanding how cells are likely to evolve can guide medical interventions and bioengineering efforts that must contend with unwanted mutations. The adaptome of a cell-the neighborhood of genetic changes that are most likely to drive adaptation in a given environment-can be mapped by tracking rare beneficial variants during the early stages of clonal evolution. We used multiplex adaptome capture sequencing (mAdCap-seq), a procedure that combines unique molecular identifiers and hybridization-based enrichment, to characterize mutations in eight Escherichia coli genes known to be under selection in a laboratory environment. We tracked 301 mutations at frequencies as low as 0.01% and inferred the fitness effects of 240 of these mutations. There were distinct molecular signatures of selection on protein structure and function for the three genes with the most beneficial mutations. Our results demonstrate how mAdCap-seq can be used to deeply profile a targeted portion of a cell's adaptome.
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Affiliation(s)
- Daniel E Deatherage
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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25
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Weber J, Li Z, Rinas U. Recombinant protein production provoked accumulation of ATP, fructose-1,6-bisphosphate and pyruvate in E. coli K12 strain TG1. Microb Cell Fact 2021; 20:169. [PMID: 34446023 PMCID: PMC8394631 DOI: 10.1186/s12934-021-01661-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/16/2021] [Indexed: 12/03/2022] Open
Abstract
Background Recently it was shown that production of recombinant proteins in E. coli BL21(DE3) using pET based expression vectors leads to metabolic stress comparable to a carbon overfeeding response. Opposite to original expectations generation of energy as well as catabolic provision of precursor metabolites were excluded as limiting factors for growth and protein production. On the contrary, accumulation of ATP and precursor metabolites revealed their ample formation but insufficient withdrawal as a result of protein production mediated constraints in anabolic pathways. Thus, not limitation but excess of energy and precursor metabolites were identified as being connected to the protein production associated metabolic burden. Results Here we show that the protein production associated accumulation of energy and catabolic precursor metabolites is not unique to E. coli BL21(DE3) but also occurs in E. coli K12. Most notably, it was demonstrated that the IPTG-induced production of hFGF-2 using a tac-promoter based expression vector in the E. coli K12 strain TG1 was leading to persistent accumulation of key regulatory molecules such as ATP, fructose-1,6-bisphosphate and pyruvate. Conclusions Excessive energy generation, respectively, accumulation of ATP during recombinant protein production is not unique to the BL21(DE3)/T7 promoter based expression system but also observed in the E. coli K12 strain TG1 using another promoter/vector combination. These findings confirm that energy is not a limiting factor for recombinant protein production. Moreover, the data also show that an accelerated glycolytic pathway flux aggravates the protein production associated “metabolic burden”. Under conditions of compromised anabolic capacities cells are not able to reorganize their metabolic enzyme repertoire as required for reduced carbon processing.
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Affiliation(s)
- Jan Weber
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Zhaopeng Li
- Technical Chemistry-Life Science, Leibniz University of Hannover, Hannover, Germany
| | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany. .,Technical Chemistry-Life Science, Leibniz University of Hannover, Hannover, Germany.
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26
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Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli. Nat Commun 2021; 12:4929. [PMID: 34389727 PMCID: PMC8363753 DOI: 10.1038/s41467-021-25142-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 07/21/2021] [Indexed: 01/24/2023] Open
Abstract
Synthetic metabolic pathways are a burden for engineered bacteria, but the underlying mechanisms often remain elusive. Here we show that the misregulated activity of the transcription factor Cra is responsible for the growth burden of glycerol overproducing E. coli. Glycerol production decreases the concentration of fructose-1,6-bisphoshate (FBP), which then activates Cra resulting in the downregulation of glycolytic enzymes and upregulation of gluconeogenesis enzymes. Because cells grow on glucose, the improper activation of gluconeogenesis and the concomitant inhibition of glycolysis likely impairs growth at higher induction of the glycerol pathway. We solve this misregulation by engineering a Cra-binding site in the promoter controlling the expression of the rate limiting enzyme of the glycerol pathway to maintain FBP levels sufficiently high. We show the broad applicability of this approach by engineering Cra-dependent regulation into a set of constitutive and inducible promoters, and use one of them to overproduce carotenoids in E. coli. Synthetic pathways represent a metabolic burden on host cells. Here the authors engineer Cra-binding sites to prevent misregulation in glycerol and carotenoid overproducing E. coli strains.
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27
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El-Mansi M, Phue JN, Shiloach J. Expression of the ace operon in Escherichia coli is triggered in response to growth rate-dependent flux-signal of ATP. FEMS Microbiol Lett 2021; 368:6070649. [PMID: 33417680 DOI: 10.1093/femsle/fnaa221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/31/2020] [Indexed: 01/06/2023] Open
Abstract
The signal that triggers the expression of the ace operon and, in turn, the transition of central metabolism's architecture from acetogenic to gluconeogenic in Escherichia coli remains elusive despite extensive research both in vivo and in vitro. Here, with the aid of flux analysis together with measurements of the enzymic activity of isocitrate lyase (ICL) and its aceA-messenger ribonucleuc acid (mRNA) transcripts, we provide credible evidence suggesting that the expression of the ace operon in E. coli is triggered in response to growth rate-dependent threshold flux-signal of adenosine triphosphate (ATP). Flux analysis revealed that the shortfall in ATP supply observed as the growth rate ($\mu $) diminishes from µmax to ≤ 0.43h-1 ($ \pm 0.02;n4)\ $is partially redressed by up-regulating flux through succinyl CoA synthetase. Unlike glycerol and glucose, pyruvate cannot feed directly into the two glycolytic ATP-generating reactions catalyzed by phosphoglycerokinase and pyruvate kinase. On the other hand, glycerol, which upon its conversion to D-glyceraldehyde, feeds into the phosphorylation and dephosphorylation parts of glycolysis including the substrate-level phosphorylation-ATP generating reactions, thus preventing ATP flux from dropping to the critical threshold signal required to trigger the acetate-diauxic switch until glycerol is fully consumed. The mRNA transcriptional patterns of key gluconeogenic enzymes, namely, ackA, acetate kinase; pta, phosphotransacetylase; acs, acetyl CoA synthetase and aceA, ICL, suggest that the pyruvate phenotype is better equipped than the glycerol phenotype for the switch from acetogenic to gluconeogenic metabolism.
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Affiliation(s)
- Mansi El-Mansi
- Bio-Ed, Scotland UK, 17/7 Watson Crescent, Edinburgh EGH11 1HA, Scotland, UK.,University of Africa, Toru-Orua, Department of Biotechnology, Faculty of Science, Sagbama L.G.A. Bayelsa State, Nigeria
| | - Je-Nie Phue
- Biotechnology Lab, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 14A, Room 173, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Joseph Shiloach
- Biotechnology Lab, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 14A, Room 173, 9000 Rockville Pike, Bethesda, MD 20892, USA
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Fuentes DAF, Manfredi P, Jenal U, Zampieri M. Pareto optimality between growth-rate and lag-time couples metabolic noise to phenotypic heterogeneity in Escherichia coli. Nat Commun 2021; 12:3204. [PMID: 34050162 PMCID: PMC8163773 DOI: 10.1038/s41467-021-23522-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/04/2021] [Indexed: 02/04/2023] Open
Abstract
Despite mounting evidence that in clonal bacterial populations, phenotypic variability originates from stochasticity in gene expression, little is known about noise-shaping evolutionary forces and how expression noise translates to phenotypic differences. Here we developed a high-throughput assay that uses a redox-sensitive dye to couple growth of thousands of bacterial colonies to their respiratory activity and show that in Escherichia coli, noisy regulation of lower glycolysis and citric acid cycle is responsible for large variations in respiratory metabolism. We found that these variations are Pareto optimal to maximization of growth rate and minimization of lag time, two objectives competing between fermentative and respiratory metabolism. Metabolome-based analysis revealed the role of respiratory metabolism in preventing the accumulation of toxic intermediates of branched chain amino acid biosynthesis, thereby supporting early onset of cell growth after carbon starvation. We propose that optimal metabolic tradeoffs play a key role in shaping and preserving phenotypic heterogeneity and adaptation to fluctuating environments.
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Affiliation(s)
| | | | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Mattia Zampieri
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland.
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29
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Fan X, Walther A. pH Feedback Lifecycles Programmed by Enzymatic Logic Gates Using Common Foods as Fuels. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202017003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xinlong Fan
- Institute for Macromolecular Chemistry University of Freiburg Stefan-Meier-Str. 31 79104 Freiburg Germany
| | - Andreas Walther
- Institute for Macromolecular Chemistry University of Freiburg Stefan-Meier-Str. 31 79104 Freiburg Germany
- A3BMS Lab Department of Chemistry University of Mainz Duesbergweg 10–14 55128 Mainz Germany
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30
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Fan X, Walther A. pH Feedback Lifecycles Programmed by Enzymatic Logic Gates Using Common Foods as Fuels. Angew Chem Int Ed Engl 2021; 60:11398-11405. [PMID: 33682231 PMCID: PMC8252529 DOI: 10.1002/anie.202017003] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/22/2021] [Indexed: 12/12/2022]
Abstract
Artificial temporal signaling systems, which mimic living out-of-equilibrium conditions, have made large progress. However, systems programmed by enzymatic reaction networks in multicomponent and unknown environments, and using biocompatible components remain a challenge. Herein, we demonstrate an approach to program temporal pH signals by enzymatic logic gates. They are realized by an enzymatic disaccharide-to-monosaccharide-to-sugar acid reaction cascade catalyzed by two metabolic chains: invertase-glucose oxidase and β-galactosidase-glucose oxidase, respectively. Lifetimes of the transient pH signal can be programmed from less than 15 min to more than 1 day. We study enzymatic kinetics of the reaction cascades and reveal the underlying regulatory mechanisms. Operating with all-food grade chemicals and coupling to self-regulating hydrogel, our system is quite robust to work in a complicated medium with unknown components and in a biocompatible fashion.
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Affiliation(s)
- Xinlong Fan
- Institute for Macromolecular ChemistryUniversity of FreiburgStefan-Meier-Str. 3179104FreiburgGermany
| | - Andreas Walther
- Institute for Macromolecular ChemistryUniversity of FreiburgStefan-Meier-Str. 3179104FreiburgGermany
- ABMS LabDepartment of ChemistryUniversity of MainzDuesbergweg 10–1455128MainzGermany
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31
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Ortega AD, Takhaveev V, Vedelaar SR, Long Y, Mestre-Farràs N, Incarnato D, Ersoy F, Olsen LF, Mayer G, Heinemann M. A synthetic RNA-based biosensor for fructose-1,6-bisphosphate that reports glycolytic flux. Cell Chem Biol 2021; 28:1554-1568.e8. [PMID: 33915105 DOI: 10.1016/j.chembiol.2021.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/25/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022]
Abstract
RNA-based sensors for intracellular metabolites are a promising solution to the emerging issue of metabolic heterogeneity. However, their development, i.e., the conversion of an aptamer into an in vivo-functional intracellular metabolite sensor, still harbors challenges. Here, we accomplished this for the glycolytic flux-signaling metabolite, fructose-1,6-bisphosphate (FBP). Starting from in vitro selection of an aptamer, we constructed device libraries with a hammerhead ribozyme as actuator. Using high-throughput screening in yeast with fluorescence-activated cell sorting (FACS), next-generation sequencing, and genetic-environmental perturbations to modulate the intracellular FBP levels, we identified a sensor that generates ratiometric fluorescent readout. An abrogated response in sensor mutants and occurrence of two sensor conformations-revealed by RNA structural probing-indicated in vivo riboswitching activity. Microscopy showed that the sensor can differentiate cells with different glycolytic fluxes within yeast populations, opening research avenues into metabolic heterogeneity. We demonstrate the possibility to generate RNA-based sensors for intracellular metabolites for which no natural metabolite-binding RNA element exits.
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Affiliation(s)
- Alvaro Darío Ortega
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands; Department of Cell Biology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Vakil Takhaveev
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Silke Roelie Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Yi Long
- LIMES Institute, University of Bonn, 53121 Bonn, Germany; Institute of Biochemistry and Molecular Biology, University of Southern Denmark, DK5230 Odense M, Denmark
| | - Neus Mestre-Farràs
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | - Danny Incarnato
- Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands
| | | | - Lars Folke Olsen
- Institute of Biochemistry and Molecular Biology, University of Southern Denmark, DK5230 Odense M, Denmark
| | - Günter Mayer
- LIMES Institute, University of Bonn, 53121 Bonn, Germany; Center of Aptamer Research & Development, University of Bonn, 53121 Bonn, Germany
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands.
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32
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Kochanowski K, Okano H, Patsalo V, Williamson J, Sauer U, Hwa T. Global coordination of metabolic pathways in Escherichia coli by active and passive regulation. Mol Syst Biol 2021; 17:e10064. [PMID: 33852189 PMCID: PMC8045939 DOI: 10.15252/msb.202010064] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 12/15/2022] Open
Abstract
Microorganisms adjust metabolic activity to cope with diverse environments. While many studies have provided insights into how individual pathways are regulated, the mechanisms that give rise to coordinated metabolic responses are poorly understood. Here, we identify the regulatory mechanisms that coordinate catabolism and anabolism in Escherichia coli. Integrating protein, metabolite, and flux changes in genetically implemented catabolic or anabolic limitations, we show that combined global and local mechanisms coordinate the response to metabolic limitations. To allocate proteomic resources between catabolism and anabolism, E. coli uses a simple global gene regulatory program. Surprisingly, this program is largely implemented by a single transcription factor, Crp, which directly activates the expression of catabolic enzymes and indirectly reduces the expression of anabolic enzymes by passively sequestering cellular resources needed for their synthesis. However, metabolic fluxes are not controlled by this regulatory program alone; instead, fluxes are adjusted mostly through passive changes in the local metabolite concentrations. These mechanisms constitute a simple but effective global regulatory program that coarsely partitions resources between different parts of metabolism while ensuring robust coordination of individual metabolic reactions.
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Affiliation(s)
- Karl Kochanowski
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Life Science Zurich PhD Program on Systems BiologyZurichSwitzerland
| | - Hiroyuki Okano
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
| | - Vadim Patsalo
- Department of Integrative Structural and Computational Biology, and The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCAUSA
| | - James Williamson
- Department of Integrative Structural and Computational Biology, and The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCAUSA
| | - Uwe Sauer
- Institute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Terence Hwa
- Department of PhysicsUniversity of California at San DiegoLa JollaCAUSA
- Institute for Theoretical ScienceETH ZurichZurichSwitzerland
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33
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The Entner-Doudoroff Pathway Is an Essential Metabolic Route for Methylotuvimicrobium buryatense 5GB1C. Appl Environ Microbiol 2021; 87:AEM.02481-20. [PMID: 33218997 DOI: 10.1128/aem.02481-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/11/2020] [Indexed: 11/20/2022] Open
Abstract
Methylotuvimicrobium buryatense 5GB1C, a fast-growing gammaproteobacterial methanotroph, is equipped with two glycolytic pathways, the Entner-Doudoroff (ED) pathway and the Embden-Meyerhof-Parnas (EMP) pathway. Metabolic flux analysis and 13C-labeling experiments have shown the EMP pathway is the principal glycolytic route in M. buryatense 5GB1C, while the ED pathway appears to be metabolically and energetically insignificant. However, it has not been possible to obtain a null mutant in the edd-eda genes encoding the two unique enzymatic reactions in the ED pathway, suggesting the ED pathway may be essential for M. buryatense 5GB1C growth. In this study, the inducible P BAD promoter was used to manipulate gene expression of edd-eda, and in addition, the expression of these two genes was separated from that of a downstream gltA gene. The resulting strain shows arabinose-dependent growth that correlates with ED pathway activity, with normal growth achieved in the presence of ∼0.1 g/liter arabinose. Flux balance analysis shows that M. buryatense 5GB1C with a strong ED pathway has a reduced energy budget, thereby limiting the mutant growth at a high concentration of arabinose. Collectively, our study demonstrates that the ED pathway is essential for M. buryatense 5GB1C. However, no known mechanism can directly explain the essentiality of the ED pathway, and thus, it may have a yet unknown regulatory role required for sustaining a healthy and functional metabolism in this bacterium.IMPORTANCE The gammaproteobacterial methanotrophs possess a unique central metabolic architecture where methane and other reduced C1 carbon sources are assimilated through the ribulose monophosphate cycle. Although efforts have been made to better understand methanotrophic metabolism in these bacteria via experimental and computational approaches, many questions remain unanswered. One of these is the essentiality of the ED pathway for M. buryatense 5GB1C, as current results appear contradictory. By creating a construct with edd-eda and gltA genes controlled by P BAD and P J23101 , respectively, we demonstrated the essentiality of the ED pathway for this obligate methanotroph. It is also demonstrated that these genetic tools are applicable to M. buryatense 5GB1C and that expression of the target genes can be tightly controlled across an extensive range. Our study adds to the expanding knowledge of methanotrophic metabolism and practical approaches to genetic manipulation for obligate methanotrophs.
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Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell 2020; 184:545-559.e22. [PMID: 33357446 PMCID: PMC7836100 DOI: 10.1016/j.cell.2020.12.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/21/2020] [Accepted: 12/11/2020] [Indexed: 02/02/2023]
Abstract
Biological processes are regulated by intermolecular interactions and chemical modifications that do not affect protein levels, thus escaping detection in classical proteomic screens. We demonstrate here that a global protein structural readout based on limited proteolysis-mass spectrometry (LiP-MS) detects many such functional alterations, simultaneously and in situ, in bacteria undergoing nutrient adaptation and in yeast responding to acute stress. The structural readout, visualized as structural barcodes, captured enzyme activity changes, phosphorylation, protein aggregation, and complex formation, with the resolution of individual regulated functional sites such as binding and active sites. Comparison with prior knowledge, including other ‘omics data, showed that LiP-MS detects many known functional alterations within well-studied pathways. It suggested distinct metabolite-protein interactions and enabled identification of a fructose-1,6-bisphosphate-based regulatory mechanism of glucose uptake in E. coli. The structural readout dramatically increases classical proteomics coverage, generates mechanistic hypotheses, and paves the way for in situ structural systems biology. Dynamic structural proteomic screens detect functional changes at high resolution Detect enzyme activity, phosphorylation, and molecular interactions in situ Generate new molecular hypotheses and increase functional proteomics coverage Enabled discovery of a regulatory mechanism of glucose uptake in E. coli
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35
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Opening a Novel Biosynthetic Pathway to Dihydroxyacetone and Glycerol in Escherichia coli Mutants through Expression of a Gene Variant ( fsaAA129S) for Fructose 6-Phosphate Aldolase. Int J Mol Sci 2020; 21:ijms21249625. [PMID: 33348713 PMCID: PMC7767278 DOI: 10.3390/ijms21249625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/05/2020] [Accepted: 12/15/2020] [Indexed: 01/19/2023] Open
Abstract
Phosphofructokinase (PFK) plays a pivotal role in glycolysis. By deletion of the genes pfkA, pfkB (encoding the two PFK isoenzymes), and zwf (glucose 6-phosphate dehydrogenase) in Escherichia coli K-12, a mutant strain (GL3) with a complete block in glucose catabolism was created. Introduction of plasmid-borne copies of the fsaA wild type gene (encoding E. coli fructose 6-phosphate aldolase, FSAA) did not allow a bypass by splitting fructose 6-phosphate (F6P) into dihydroxyacetone (DHA) and glyceraldehyde 3-phosphate (G3P). Although FSAA enzyme activity was detected, growth on glucose was not reestablished. A mutant allele encoding for FSAA with an amino acid exchange (Ala129Ser) which showed increased catalytic efficiency for F6P, allowed growth on glucose with a µ of about 0.12 h−1. A GL3 derivative with a chromosomally integrated copy of fsaAA129S (GL4) grew with 0.05 h−1 on glucose. A mutant strain from GL4 where dhaKLM genes were deleted (GL5) excreted DHA. By deletion of the gene glpK (glycerol kinase) and overexpression of gldA (of glycerol dehydrogenase), a strain (GL7) was created which showed glycerol formation (21.8 mM; yield approximately 70% of the theoretically maximal value) as main end product when grown on glucose. A new-to-nature pathway from glucose to glycerol was created.
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36
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Titrating bacterial growth and chemical biosynthesis for efficient N-acetylglucosamine and N-acetylneuraminic acid bioproduction. Nat Commun 2020; 11:5078. [PMID: 33033266 PMCID: PMC7544899 DOI: 10.1038/s41467-020-18960-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/21/2020] [Indexed: 12/27/2022] Open
Abstract
Metabolic engineering facilitates chemical biosynthesis by rewiring cellular resources to produce target compounds. However, an imbalance between cell growth and bioproduction often reduces production efficiency. Genetic code expansion (GCE)-based orthogonal translation systems incorporating non-canonical amino acids (ncAAs) into proteins by reassigning non-canonical codons to ncAAs qualify for balancing cellular metabolism. Here, GCE-based cell growth and biosynthesis balance engineering (GCE-CGBBE) is developed, which is based on titrating expression of cell growth and metabolic flux determinant genes by constructing ncAA-dependent expression patterns. We demonstrate GCE-CGBBE in genome-recoded Escherichia coli Δ321AM by precisely balancing glycolysis and N-acetylglucosamine production, resulting in a 4.54-fold increase in titer. GCE-CGBBE is further expanded to non-genome-recoded Bacillus subtilis to balance growth and N-acetylneuraminic acid bioproduction by titrating essential gene expression, yielding a 2.34-fold increase in titer. Moreover, the development of ncAA-dependent essential gene expression regulation shows efficient biocontainment of engineered B. subtilis to avoid unintended proliferation in nature. An imbalance between cell growth and bioproduction of engineered microbes often reduces production efficiency. Here, the authors report genetic code expansion-based cell growth and biosynthesis balance engineering to achieve high levels production of N-acetylglucosamine in E. coli and N-acetylneuraminic acid in B. subtilis.
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37
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Schmutzer M, Wagner A. Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments. PLoS Comput Biol 2020; 16:e1007727. [PMID: 33104710 PMCID: PMC7644098 DOI: 10.1371/journal.pcbi.1007727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 11/05/2020] [Accepted: 09/15/2020] [Indexed: 02/03/2023] Open
Abstract
Nongenetic phenotypic variation can either speed up or slow down adaptive evolution. We show that it can speed up evolution in environments where available carbon and energy sources change over time. To this end, we use an experimentally validated model of Escherichia coli growth on two alternative carbon sources, glucose and acetate. On the superior carbon source (glucose), all cells achieve high growth rates, while on the inferior carbon source (acetate) only a small fraction of the population manages to initiate growth. Consequently, populations experience a bottleneck when the environment changes from the superior to the inferior carbon source. Growth on the inferior carbon source depends on a circuit under the control of a transcription factor that is repressed in the presence of the superior carbon source. We show that noise in the expression of this transcription factor can increase the probability that cells start growing on the inferior carbon source. In doing so, it can decrease the severity of the bottleneck and increase mean population fitness whenever this fitness is low. A modest amount of noise can also enhance the fitness effects of a beneficial allele that increases the fraction of a population initiating growth on acetate. Additionally, noise can protect this allele from extinction, accelerate its spread, and increase its likelihood of going to fixation. Central to the adaptation-enhancing principle we identify is the ability of noise to mitigate population bottlenecks, particularly in environments that fluctuate periodically. Because such bottlenecks are frequent in fluctuating environments, and because periodically fluctuating environments themselves are common, this principle may apply to a broad range of environments and organisms.
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Affiliation(s)
- Michael Schmutzer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Santa Fe Institute, Santa Fe, New Mexico, USA
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38
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Kimkes TEP, Heinemann M. How bacteria recognise and respond to surface contact. FEMS Microbiol Rev 2020; 44:106-122. [PMID: 31769807 PMCID: PMC7053574 DOI: 10.1093/femsre/fuz029] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/23/2019] [Indexed: 12/27/2022] Open
Abstract
Bacterial biofilms can cause medical problems and issues in technical systems. While a large body of knowledge exists on the phenotypes of planktonic and of sessile cells in mature biofilms, our understanding of what happens when bacteria change from the planktonic to the sessile state is still very incomplete. Fundamental questions are unanswered: for instance, how do bacteria sense that they are in contact with a surface, and what are the very initial cellular responses to surface contact. Here, we review the current knowledge on the signals that bacteria could perceive once they attach to a surface, the signal transduction systems that could be involved in sensing the surface contact and the cellular responses that are triggered as a consequence to surface contact ultimately leading to biofilm formation. Finally, as the main obstacle in investigating the initial responses to surface contact has been the difficulty to experimentally study the dynamic response of single cells upon surface attachment, we also review recent experimental approaches that could be employed to study bacterial surface sensing, which ultimately could lead to an improved understanding of how biofilm formation could be prevented.
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Affiliation(s)
- Tom E P Kimkes
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
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39
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Birkeland ES, Koch LM, Dechant R. Another Consequence of the Warburg Effect? Metabolic Regulation of Na +/H + Exchangers May Link Aerobic Glycolysis to Cell Growth. Front Oncol 2020; 10:1561. [PMID: 32974190 PMCID: PMC7462004 DOI: 10.3389/fonc.2020.01561] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022] Open
Abstract
To adjust cell growth and proliferation to changing environmental conditions or developmental requirements, cells have evolved a remarkable network of signaling cascades that integrates cues from cellular metabolism, growth factor availability and a large variety of stresses. In these networks, cellular information flow is mostly mediated by posttranslational modifications, most notably phosphorylation, or signaling molecules such as GTPases. Yet, a large body of evidence also implicates cytosolic pH (pHc) as a highly conserved cellular signal driving cell growth and proliferation, suggesting that pH-dependent protonation of specific proteins also regulates cellular signaling. In mammalian cells, pHc is regulated by growth factor derived signals and responds to metabolic cues in response to glucose stimulation. Importantly, high pHc has also been identified as a hall mark of cancer, but mechanisms of pH regulation in cancer are only poorly understood. Here, we discuss potential mechanisms of pH regulation with emphasis on metabolic signals regulating pHc by Na+/H+-exchangers. We hypothesize that elevated NHE activity and pHc in cancer are a direct consequence of the metabolic adaptations in tumor cells including enhanced aerobic glycolysis, generally referred to as the Warburg effect. This hypothesis not only provides an explanation for the growth advantage conferred by a switch to aerobic glycolysis beyond providing precursors for accumulation of biomass, but also suggests that treatments targeting pH regulation as a potential anti-cancer therapy may effectively target the result of altered tumor cell metabolism.
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Affiliation(s)
- Eivind Salmorin Birkeland
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zurich, Switzerland.,Life Science Zurich, Ph.D. Program for Molecular Life Sciences, Zurich, Switzerland
| | - Lisa Maria Koch
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zurich, Switzerland.,Life Science Zurich, Ph.D. Program for Molecular Life Sciences, Zurich, Switzerland
| | - Reinhard Dechant
- Institute of Biochemistry, Department of Biology, ETH Zürich, Zurich, Switzerland
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40
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Flux controlling technology for central carbon metabolism for efficient microbial bio-production. Curr Opin Biotechnol 2020; 64:169-174. [PMID: 32485613 DOI: 10.1016/j.copbio.2020.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/27/2020] [Accepted: 04/20/2020] [Indexed: 11/22/2022]
Abstract
Syntheses of many commodities that are produced using microorganisms require cofactors such as ATP and NAD(P)H. Thus, optimization of the flux distribution in central carbon metabolism, which plays a key role in cofactor regeneration, is critical for enhancing the production of the target compounds. Since the intracellular and extracellular conditions change over time in the fermentation process, dynamic control of the metabolic system for maintaining the cellular state appropriately is necessary. Here, we review techniques for detecting the intracellular metabolic state with fluorescent sensors and controlling the flux of central carbon metabolism with optogenetic tools, as well as present a prospect of bio-production processes for fine-tuning the flux distribution.
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41
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Nochino N, Toya Y, Shimizu H. Transcription Factor ArcA is a Flux Sensor for the Oxygen Consumption Rate in Escherichia coli. Biotechnol J 2020; 15:e1900353. [PMID: 32383263 DOI: 10.1002/biot.201900353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/30/2020] [Indexed: 12/24/2022]
Abstract
Oxygen supply is one of the major factors determining the metabolic state in microorganisms, and it affects the productivity of various compounds during bioproduction. In Escherichia coli (E. coli), the expression levels of numerous metabolic genes are regulated by transcription factors in response to changes in environmental oxygen conditions. Even at a same dissolved oxygen concentration, the amount of available oxygen changes depending on the oxygen transfer coefficient. However, it is not known whether E. coli is able to sense differences in the oxygen consumption rate. Therefore, the present study, is focused on the role of the transcription factor ArcA in the oxygen response of E. coli and investigated the relationship between ArcA activity and the oxygen consumption rate. To evaluate the activity of ArcA, a sensor plasmid expressing fluorescent protein under the control of the icd promoter, which is regulated by ArcA, is designed. E. coli containing the sensor plasmid is grown in continuous cultures with different oxygen supplies under different dilution rates. Although there is no correlation between ArcA activity and dissolved oxygen concentration, a strong negative correlation between ArcA activity and the specific oxygen consumption rate (R2 > 0.93) is observed.
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Affiliation(s)
- Naoya Nochino
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
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42
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Wang G, Haringa C, Tang W, Noorman H, Chu J, Zhuang Y, Zhang S. Coupled metabolic-hydrodynamic modeling enabling rational scale-up of industrial bioprocesses. Biotechnol Bioeng 2019; 117:844-867. [PMID: 31814101 DOI: 10.1002/bit.27243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/28/2019] [Accepted: 11/30/2019] [Indexed: 12/13/2022]
Abstract
Metabolomics aims to address what and how regulatory mechanisms are coordinated to achieve flux optimality, different metabolic objectives as well as appropriate adaptations to dynamic nutrient availability. Recent decades have witnessed that the integration of metabolomics and fluxomics within the goal of synthetic biology has arrived at generating the desired bioproducts with improved bioconversion efficiency. Absolute metabolite quantification by isotope dilution mass spectrometry represents a functional readout of cellular biochemistry and contributes to the establishment of metabolic (structured) models required in systems metabolic engineering. In industrial practices, population heterogeneity arising from fluctuating nutrient availability frequently leads to performance losses, that is reduced commercial metrics (titer, rate, and yield). Hence, the development of more stable producers and more predictable bioprocesses can benefit from a quantitative understanding of spatial and temporal cell-to-cell heterogeneity within industrial bioprocesses. Quantitative metabolomics analysis and metabolic modeling applied in computational fluid dynamics (CFD)-assisted scale-down simulators that mimic industrial heterogeneity such as fluctuations in nutrients, dissolved gases, and other stresses can procure informative clues for coping with issues during bioprocessing scale-up. In previous studies, only limited insights into the hydrodynamic conditions inside the industrial-scale bioreactor have been obtained, which makes case-by-case scale-up far from straightforward. Tracking the flow paths of cells circulating in large-scale bioreactors is a highly valuable tool for evaluating cellular performance in production tanks. The "lifelines" or "trajectories" of cells in industrial-scale bioreactors can be captured using Euler-Lagrange CFD simulation. This novel methodology can be further coupled with metabolic (structured) models to provide not only a statistical analysis of cell lifelines triggered by the environmental fluctuations but also a global assessment of the metabolic response to heterogeneity inside an industrial bioreactor. For the future, the industrial design should be dependent on the computational framework, and this integration work will allow bioprocess scale-up to the industrial scale with an end in mind.
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Affiliation(s)
- Guan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Cees Haringa
- Transport Phenomena, Chemical Engineering Department, Delft University of Technology, Delft, The Netherlands.,DSM Biotechnology Center, Delft, The Netherlands
| | - Wenjun Tang
- DSM Biotechnology Center, Delft, The Netherlands
| | - Henk Noorman
- DSM Biotechnology Center, Delft, The Netherlands.,Bioprocess Engineering, Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, People's Republic of China
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43
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Regulation underlying hierarchical and simultaneous utilization of carbon substrates by flux sensors in Escherichia coli. Nat Microbiol 2019; 5:206-215. [PMID: 31819215 PMCID: PMC6925339 DOI: 10.1038/s41564-019-0610-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/16/2019] [Indexed: 12/24/2022]
Abstract
Many microbes exhibit nutrient preferences, exemplified by the “hierarchical” consumption of certain carbon substrates. Here we systematically investigate under which physiological conditions hierarchical substrate utilization occurs and its mechanisms of implementation. We show utilization hierarchy of Escherichia coli to be ordered by the carbon-uptake flux rather than the identity of the substrates. A detailed study of glycerol uptake finds that it is fully suppressed if the uptake flux of another glycolytic substrate exceeds a threshold, set to the influx obtained when grown on glycerol alone. Below this threshold, limited glycerol uptake is “supplemented” such that the total carbon uptake is maintained at the threshold. This behavior results from total-flux feedback mediated by cAMP-Crp signaling, but also requires inhibition by regulator fructose-1,6-bisphosphate, which senses the upper glycolytic flux and ensures that glycerol uptake defers to other glycolytic substrates but not to gluconeogenic ones. A quantitative model reproduces all observed utilization patterns including those of key mutants. The proposed mechanism relies on differential regulation of uptake enzymes and requires a specific operon organization. This organization is found conserved across related species for several uptake systems, suggesting the deployment of similar mechanisms for hierarchical substrate utilization by a spectrum of microbes.
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44
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Monteiro F, Hubmann G, Takhaveev V, Vedelaar SR, Norder J, Hekelaar J, Saldida J, Litsios A, Wijma HJ, Schmidt A, Heinemann M. Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor. Mol Syst Biol 2019; 15:e9071. [PMID: 31885198 PMCID: PMC6920703 DOI: 10.15252/msb.20199071] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022] Open
Abstract
Metabolic heterogeneity between individual cells of a population harbors significant challenges for fundamental and applied research. Identifying metabolic heterogeneity and investigating its emergence require tools to zoom into metabolism of individual cells. While methods exist to measure metabolite levels in single cells, we lack capability to measure metabolic flux, i.e., the ultimate functional output of metabolic activity, on the single-cell level. Here, combining promoter engineering, computational protein design, biochemical methods, proteomics, and metabolomics, we developed a biosensor to measure glycolytic flux in single yeast cells. Therefore, drawing on the robust cell-intrinsic correlation between glycolytic flux and levels of fructose-1,6-bisphosphate (FBP), we transplanted the B. subtilis FBP-binding transcription factor CggR into yeast. With the developed biosensor, we robustly identified cell subpopulations with different FBP levels in mixed cultures, when subjected to flow cytometry and microscopy. Employing microfluidics, we were also able to assess the temporal FBP/glycolytic flux dynamics during the cell cycle. We anticipate that our biosensor will become a valuable tool to identify and study metabolic heterogeneity in cell populations.
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Affiliation(s)
- Francisca Monteiro
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Present address:
cE3c‐Centre for Ecology, Evolution and Environmental ChangesFaculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Georg Hubmann
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
- Present address:
Laboratory of Molecular Cell BiologyDepartment of BiologyInstitute of Botany and MicrobiologyKU Leuven, & Center for Microbiology, VIBHeverlee, FlandersBelgium
| | - Vakil Takhaveev
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Silke R Vedelaar
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Justin Norder
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Johan Hekelaar
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Joana Saldida
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Athanasios Litsios
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Hein J Wijma
- Biotechnology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | | | - Matthias Heinemann
- Molecular Systems BiologyGroningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
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45
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Gasperotti A, Brameyer S, Fabiani F, Jung K. Phenotypic heterogeneity of microbial populations under nutrient limitation. Curr Opin Biotechnol 2019; 62:160-167. [PMID: 31698311 DOI: 10.1016/j.copbio.2019.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022]
Abstract
Phenotypic heterogeneity is a phenomenon in which genetically identical individuals have different characteristics. This behavior can also be found in bacteria, even if they grow as monospecies in well-mixed environments such as bioreactors. Here it is discussed how phenotypic heterogeneity is generated by internal factors and how it is promoted under nutrient-limited growth conditions. A better understanding of the molecular levels that control phenotypic heterogeneity could improve biotechnological production processes.
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Affiliation(s)
- Ana Gasperotti
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Florian Fabiani
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-Universität München, 82152 Martinsried, Germany.
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46
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Chen X, Tao L, Ru Y, Weng S, Chen Z, Wang J, Guo L, Lin Z, Pan W, Qiu B. Antibacterial mechanism of Tetrastigma hemsleyanum Diels et Gilg's polysaccharides by metabolomics based on HPLC/MS. Int J Biol Macromol 2019; 140:206-215. [DOI: 10.1016/j.ijbiomac.2019.08.097] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/02/2019] [Accepted: 08/10/2019] [Indexed: 12/27/2022]
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47
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Valle A, Cantero D, Bolívar J. Metabolic engineering for the optimization of hydrogen production in Escherichia coli: A review. Biotechnol Adv 2019; 37:616-633. [DOI: 10.1016/j.biotechadv.2019.03.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/29/2022]
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48
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El-Mansi M. Contrasting effects of isocitrate dehydrogenase deletion on fluxes through enzymes of central metabolism in Escherichia coli. FEMS Microbiol Lett 2019; 366:5556941. [DOI: 10.1093/femsle/fnz187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/29/2019] [Indexed: 12/15/2022] Open
Abstract
ABSTRACTFlux analysis is central to understanding cellular metabolism and successful manipulation of metabolic fluxes in microbial cell-factories. Isocitrate dehydrogenase (ICDH) deletion conferred contrasting effects on fluxes through substrate-level phosphorylation (SLP) reactions. While significantly increasing flux through pyruvate kinase, it diminishes flux through succinyl CoA synthetase and upregulates phosphotransacetylase (PTA) and acetate kinase (AK). In addition to acetate, the ICDH-less strain excretes pyruvate, citrate and isocitrate. While efflux to acetate excretion by the Escherichia coli parental strain and its ICDH-less derivative is a reflection of high throughput of glycolytic intermediates, excretion of pyruvate is a reflection of high throughput via pyruvate kinase. On the other hand, citrate and isocitrate excretion is a reflection of truncating the Krebs cycle at the level of ICDH. Furthermore, another striking finding is the inability of the ICDH-less cultures to utilize acetate as a source of carbon despite the availability of an adequate supply of extracellular glutamate (for biosynthesis) and elevated levels of AK and PTA (for acetate uptake). This striking observation is now explicable in the light of the newly proposed hypothesis that the expression of the ace operon enzymes is controlled in response to a minimum threshold signal (ATP), which could not be achieved in the ICDH-less strain.
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Affiliation(s)
- Mansi El-Mansi
- Elizade University, Ilara Mokin, Ondo State, Nigeria
- University of Africa (UAT), Bayelsa State, Nigeria
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49
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Shimizu K, Matsuoka Y. Redox rebalance against genetic perturbations and modulation of central carbon metabolism by the oxidative stress regulation. Biotechnol Adv 2019; 37:107441. [PMID: 31472206 DOI: 10.1016/j.biotechadv.2019.107441] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/04/2019] [Accepted: 08/23/2019] [Indexed: 12/11/2022]
Abstract
The micro-aerophilic organisms and aerobes as well as yeast and higher organisms have evolved to gain energy through respiration (via oxidative phosphorylation), thereby enabling them to grow much faster than anaerobes. However, during respiration, reactive oxygen species (ROSs) are inherently (inevitably) generated, and threaten the cell's survival. Therefore, living organisms (or cells) must furnish the potent defense systems to keep such ROSs at harmless level, where the cofactor balance plays crucial roles. Namely, NADH is the source of energy generation (catabolism) in the respiratory chain reactions, through which ROSs are generated, while NADPH plays important roles not only for the cell synthesis (anabolism) but also for detoxifying ROSs. Therefore, the cell must rebalance the redox ratio by modulating the fluxes of the central carbon metabolism (CCM) by regulating the multi-level regulation machinery upon genetic perturbations and the change in the growth conditions. Here, we discuss about how aerobes accomplish such cofactor homeostasis against redox perturbations. In particular, we consider how single-gene mutants (including pgi, pfk, zwf, gnd and pyk mutants) modulate their metabolisms in relation to cofactor rebalance (and also by adaptive laboratory evolution). We also discuss about how the overproduction of NADPH (by the pathway gene mutation) can be utilized for the efficient production of useful value-added chemicals such as medicinal compounds, polyhydroxyalkanoates, and amino acids, all of which require NADPH in their synthetic pathways. We then discuss about the metabolic responses against oxidative stress, where αketoacids play important roles not only for the coordination between catabolism and anabolism, but also for detoxifying ROSs by non-enzymatic reactions, as well as for reducing the production of ROSs by repressing the activities of the TCA cycle and respiration (via carbon catabolite repression). Thus, we discuss about the mechanisms (basic strategies) that modulate the metabolism from respiration to respiro-fermentative metabolism causing overflow, based on the role of Pyk activity, affecting the NADPH production at the oxidative pentose phosphate (PP) pathway, and the roles of αketoacids for the change in the source of energy generation from the oxidative phosphorylation to the substrate level phosphorylation.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio university, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan.
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50
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Zampieri M, Hörl M, Hotz F, Müller NF, Sauer U. Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli. Nat Commun 2019; 10:3354. [PMID: 31350417 PMCID: PMC6659692 DOI: 10.1038/s41467-019-11331-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 07/05/2019] [Indexed: 02/06/2023] Open
Abstract
How microbes dynamically coordinate uptake and simultaneous utilization of nutrients in complex nutritional ecosystems is still an open question. Here, we develop a constraint-based modeling approach that exploits non-targeted exo-metabolomics data to unravel adaptive decision-making processes in dynamic nutritional environments. We thereby investigate metabolic adaptation of Escherichia coli to continuously changing conditions during batch growth in complex medium. Unexpectedly, model-based analysis of time resolved exo-metabolome data revealed that fastest growth coincides with preferred catabolism of amino acids, which, in turn, reduces glucose uptake and increases acetate overflow. We show that high intracellular levels of the amino acid degradation metabolites pyruvate and oxaloacetate can directly inhibit the phosphotransferase system (PTS), and reveal their functional role in mediating regulatory decisions for uptake and catabolism of alternative carbon sources. Overall, the proposed methodology expands the spectrum of possible applications of flux balance analysis to decipher metabolic adaptation mechanisms in naturally occurring habitats and diverse organisms.
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Affiliation(s)
- Mattia Zampieri
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland.
| | - Manuel Hörl
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland
| | - Florian Hotz
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland
| | - Nicola F Müller
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, 8093, Switzerland.
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