101
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Wong-Ng J, Celani A, Vergassola M. Exploring the function of bacterial chemotaxis. Curr Opin Microbiol 2018; 45:16-21. [DOI: 10.1016/j.mib.2018.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/10/2018] [Indexed: 10/18/2022]
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102
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Lu H, Cao W, Liu X, Sui Y, Ouyang L, Xia J, Huang M, Zhuang Y, Zhang S, Noorman H, Chu J. Multi-omics integrative analysis with genome-scale metabolic model simulation reveals global cellular adaptation of Aspergillus niger under industrial enzyme production condition. Sci Rep 2018; 8:14404. [PMID: 30258063 PMCID: PMC6158188 DOI: 10.1038/s41598-018-32341-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/31/2018] [Indexed: 11/29/2022] Open
Abstract
Oxygen limitation is regarded as a useful strategy to improve enzyme production by mycelial fungus like Aspergillus niger. However, the intracellular metabolic response of A. niger to oxygen limitation is still obscure. To address this, the metabolism of A. niger was studied using multi-omics integrated analysis based on the latest GEMs (genome-scale metabolic model), including metabolomics, fluxomics and transcriptomics. Upon sharp reduction of the oxygen supply, A. niger metabolism shifted to higher redox level status, as well as lower energy supply, down-regulation of genes for fatty acid synthesis and a rapid decrease of the specific growth rate. The gene expression of the glyoxylate bypass was activated, which was consistent with flux analysis using the A. niger GEMs iHL1210. The increasing flux of the glyoxylate bypass was assumed to reduce the NADH formation from TCA cycle and benefit maintenance of the cellular redox balance under hypoxic conditions. In addition, the relative fluxes of the EMP pathway were increased, which possibly relieved the energy demand for cell metabolism. The above multi-omics integrative analysis provided new insights on metabolic regulatory mechanisms of A. niger associated with enzyme production under oxygen-limited condition, which will benefit systematic design and optimization of the A. niger microbial cell factory.
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Affiliation(s)
- Hongzhong Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Weiqiang Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Xiaoyun Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yufei Sui
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yingping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Henk Noorman
- DSM Biotechnology Center, P.O. Box 1, 2600MA, Delft, The Netherlands
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
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103
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Bley Folly B, Ortega AD, Hubmann G, Bonsing-Vedelaar S, Wijma HJ, van der Meulen P, Milias-Argeitis A, Heinemann M. Assessment of the interaction between the flux-signaling metabolite fructose-1,6-bisphosphate and the bacterial transcription factors CggR and Cra. Mol Microbiol 2018; 109:278-290. [DOI: 10.1111/mmi.14008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Brenda Bley Folly
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Alvaro D. Ortega
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
- Department of Cell Biology, Faculty of Biology; Complutense University of Madrid; José Antonio Nováis 12 28040 Madrid Spain
| | - Georg Hubmann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Silke Bonsing-Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Hein J. Wijma
- Biotechnology, Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Pieter van der Meulen
- Stratingh Institute for Chemistry; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Andreas Milias-Argeitis
- 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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104
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105
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Costello Z, Martin HG. A machine learning approach to predict metabolic pathway dynamics from time-series multiomics data. NPJ Syst Biol Appl 2018; 4:19. [PMID: 29872542 PMCID: PMC5974308 DOI: 10.1038/s41540-018-0054-3] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/11/2018] [Accepted: 04/20/2018] [Indexed: 02/01/2023] Open
Abstract
New synthetic biology capabilities hold the promise of dramatically improving our ability to engineer biological systems. However, a fundamental hurdle in realizing this potential is our inability to accurately predict biological behavior after modifying the corresponding genotype. Kinetic models have traditionally been used to predict pathway dynamics in bioengineered systems, but they take significant time to develop, and rely heavily on domain expertise. Here, we show that the combination of machine learning and abundant multiomics data (proteomics and metabolomics) can be used to effectively predict pathway dynamics in an automated fashion. The new method outperforms a classical kinetic model, and produces qualitative and quantitative predictions that can be used to productively guide bioengineering efforts. This method systematically leverages arbitrary amounts of new data to improve predictions, and does not assume any particular interactions, but rather implicitly chooses the most predictive ones.
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Affiliation(s)
- Zak Costello
- 1Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA.,DOE Agile Biofoundry, Emeryville, CA USA.,3DOE Joint BioEnergy Institute, Emeryville, CA USA
| | - Hector Garcia Martin
- 1Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA.,DOE Agile Biofoundry, Emeryville, CA USA.,3DOE Joint BioEnergy Institute, Emeryville, CA USA.,4BCAM, Basque Center for Applied Mathematics, Bilbao, Spain
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106
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Reznik E, Christodoulou D, Goldford JE, Briars E, Sauer U, Segrè D, Noor E. Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity. Cell Rep 2018; 20:2666-2677. [PMID: 28903046 DOI: 10.1016/j.celrep.2017.08.066] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/05/2017] [Accepted: 08/19/2017] [Indexed: 12/21/2022] Open
Abstract
Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurements and the SMRN to make inferences on the sensitivity of enzymes to their regulators. Generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis.
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Affiliation(s)
- Ed Reznik
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Dimitris Christodoulou
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland
| | | | - Emma Briars
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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107
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Cinquemani E, Laroute V, Cocaign-Bousquet M, de Jong H, Ropers D. Estimation of time-varying growth, uptake and excretion rates from dynamic metabolomics data. Bioinformatics 2018; 33:i301-i310. [PMID: 28881984 PMCID: PMC5870603 DOI: 10.1093/bioinformatics/btx250] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Motivation Technological advances in metabolomics have made it possible to monitor the concentration of extracellular metabolites over time. From these data, it is possible to compute the rates of uptake and excretion of the metabolites by a growing cell population, providing precious information on the functioning of intracellular metabolism. The computation of the rate of these exchange reactions, however, is difficult to achieve in practice for a number of reasons, notably noisy measurements, correlations between the concentration profiles of the different extracellular metabolites, and discontinuties in the profiles due to sudden changes in metabolic regime. Results We present a method for precisely estimating time-varying uptake and excretion rates from time-series measurements of extracellular metabolite concentrations, specifically addressing all of the above issues. The estimation problem is formulated in a regularized Bayesian framework and solved by a combination of extended Kalman filtering and smoothing. The method is shown to improve upon methods based on spline smoothing of the data. Moreover, when applied to two actual datasets, the method recovers known features of overflow metabolism in Escherichia coli and Lactococcus lactis, and provides evidence for acetate uptake by L. lactis after glucose exhaustion. The results raise interesting perspectives for further work on rate estimation from measurements of intracellular metabolites. Availability and implementation The Matlab code for the estimation method is available for download at https://team.inria.fr/ibis/rate-estimation-software/, together with the datasets. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Valérie Laroute
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | | | - Hidde de Jong
- Inria, Centre de Recherche Grenoble - Rhône-Alpes, Montbonnot, France
| | - Delphine Ropers
- Inria, Centre de Recherche Grenoble - Rhône-Alpes, Montbonnot, France
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108
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McCloskey D, Xu J, Schrübbers L, Christensen HB, Herrgård MJ. RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli. Metab Eng 2018; 47:383-392. [PMID: 29702276 DOI: 10.1016/j.ymben.2018.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 11/20/2022]
Abstract
Fast metabolite quantification methods are required for high throughput screening of microbial strains obtained by combinatorial or evolutionary engineering approaches. In this study, a rapid RIP-LC-MS/MS (RapidRIP) method for high-throughput quantitative metabolomics was developed and validated that was capable of quantifying 102 metabolites from central, amino acid, energy, nucleotide, and cofactor metabolism in less than 5 minutes. The method was shown to have comparable sensitivity and resolving capability as compared to a full length RIP-LC-MS/MS method (FullRIP). The RapidRIP method was used to quantify the metabolome of seven industrial strains of E. coli revealing significant differences in glycolytic, pentose phosphate, TCA cycle, amino acid, and energy and cofactor metabolites were found. These differences translated to statistically and biologically significant differences in thermodynamics of biochemical reactions between strains that could have implications when choosing a host for bioprocessing.
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Affiliation(s)
- Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Julia Xu
- Department of Bioengineering, University of California - San Diego, La Jolla, CA 92093, USA
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Hanne B Christensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark.
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109
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Abstract
The succession from aerobic and facultative anaerobic bacteria to obligate anaerobes in the infant gut along with the differences between the compositions of the mucosally adherent vs. luminal microbiota suggests that the gut microbes consume oxygen, which diffuses into the lumen from the intestinal tissue, maintaining the lumen in a deeply anaerobic state. Remarkably, measurements of luminal oxygen levels show nearly identical pO2 (partial pressure of oxygen) profiles in conventional and germ-free mice, pointing to the existence of oxygen consumption mechanisms other than microbial respiration. In vitro experiments confirmed that the luminal contents of germ-free mice are able to chemically consume oxygen (e.g., via lipid oxidation reactions), although at rates significantly lower than those observed in the case of conventionally housed mice. For conventional mice, we also show that the taxonomic composition of the gut microbiota adherent to the gut mucosa and in the lumen throughout the length of the gut correlates with oxygen levels. At the same time, an increase in the biomass of the gut microbiota provides an explanation for the reduction of luminal oxygen in the distal vs. proximal gut. These results demonstrate how oxygen from the mammalian host is used by the gut microbiota, while both the microbes and the oxidative chemical reactions regulate luminal oxygen levels, shaping the composition of the microbial community throughout different regions of the gut.
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110
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Campbell K, Herrera-Dominguez L, Correia-Melo C, Zelezniak A, Ralser M. Biochemical principles enabling metabolic cooperativity and phenotypic heterogeneity at the single cell level. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2017.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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111
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Tummler K, Klipp E. The discrepancy between data for and expectations on metabolic models: How to match experiments and computational efforts to arrive at quantitative predictions? ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2017.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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112
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Zaitsu K, Hayashi Y, Murata T, Yokota K, Ohara T, Kusano M, Tsuchihashi H, Ishikawa T, Ishii A, Ogata K, Tanihata H. In Vivo Real-Time Monitoring System Using Probe Electrospray Ionization/Tandem Mass Spectrometry for Metabolites in Mouse Brain. Anal Chem 2018. [DOI: 10.1021/acs.analchem.7b05291] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Kei Zaitsu
- In Vivo Real-time Omics Laboratory, Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yumi Hayashi
- In Vivo Real-time Omics Laboratory, Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Department of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya, 461-8673, Japan
| | - Tasuku Murata
- Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Kazumi Yokota
- Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Tomomi Ohara
- In Vivo Real-time Omics Laboratory, Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Maiko Kusano
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hitoshi Tsuchihashi
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tetsuya Ishikawa
- Department of Radiological and Medical Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya, 461-8673, Japan
| | - Akira Ishii
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Koretsugu Ogata
- Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto, 604-8511, Japan
| | - Hiroshi Tanihata
- Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto, 604-8511, Japan
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113
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Nontargeted Metabolomics Reveals the Multilevel Response to Antibiotic Perturbations. Cell Rep 2018; 19:1214-1228. [PMID: 28494870 DOI: 10.1016/j.celrep.2017.04.002] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/27/2016] [Accepted: 03/31/2017] [Indexed: 11/21/2022] Open
Abstract
Microbes have shown a remarkable ability in evading the killing actions of antimicrobial agents, such that treatment of bacterial infections represents once more an urgent global challenge. Understanding the initial bacterial response to antimicrobials may reveal intrinsic tolerance mechanisms to antibiotics and suggest alternative and less conventional therapeutic strategies. Here, we used mass spectrometry-based metabolomics to monitor the immediate metabolic response of Escherichia coli to a variety of antibiotic perturbations. We show that rapid metabolic changes can reflect drug mechanisms of action and reveal the active role of metabolism in mediating the first stress response to antimicrobials. We uncovered a role for ammonium imbalance in aggravating chloramphenicol toxicity and the essential function of deoxythymidine 5'-diphosphate (dTDP)-rhamnose synthesis for the immediate transcriptional upregulation of GyrA in response to quinolone antibiotics. Our results suggest bacterial metabolism as an attractive target to interfere with the early bacterial response to antibiotic treatments and reduce the probability for survival and eventual evolution of antibiotic resistance.
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114
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Mahoney DE, Hiebert JB, Thimmesch A, Pierce JT, Vacek JL, Clancy RL, Sauer AJ, Pierce JD. Understanding D-Ribose and Mitochondrial Function. ACTA ACUST UNITED AC 2018; 6:1-5. [PMID: 29780691 PMCID: PMC5959283 DOI: 10.7575/aiac.abcmed.v.6n.1p.1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mitochondria are important organelles referred to as cellular powerhouses for their unique properties of cellular energy production. With many pathologic conditions and aging, mitochondrial function declines, and there is a reduction in the production of adenosine triphosphate. The energy carrying molecule generated by cellular respiration and by pentose phosphate pathway, an alternative pathway of glucose metabolism. D-ribose is a naturally occurring monosaccharide found in the cells and particularly in the mitochondria is essential in energy production. Without sufficient energy, cells cannot maintain integrity and function. Supplemental D-ribose has been shown to improve cellular processes when there is mitochondrial dysfunction. When individuals take supplemental D-ribose, it can bypass part of the pentose pathway to produce D-ribose-5-phosphate for the production of energy. In this article, we review how energy is produced by cellular respiration, the pentose pathway, and the use of supplemental D-ribose.
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Affiliation(s)
- Diane E Mahoney
- University of Kansas Medical Center, School of Nursing, Kansas, US
| | - John B Hiebert
- University of Kansas Medical Center, School of Nursing, Kansas, US
| | - Amanda Thimmesch
- University of Kansas Medical Center, School of Nursing, Kansas, US
| | - John T Pierce
- University of Kansas Medical Center, School of Nursing, Kansas, US
| | | | - Richard L Clancy
- University of Kansas Medical Center, School of Nursing, Kansas, US
| | - Andrew J Sauer
- Center for Advanced Heart Failure and Heart Transplantation, Kansas, US
| | - Janet D Pierce
- University of Kansas Medical Center, School of Nursing, Kansas, US
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115
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Qiu Z, Wu X, Zhang J, Huang C. High-Temperature Induced Changes of Extracellular Metabolites in Pleurotus ostreatus and Their Positive Effects on the Growth of Trichoderma asperellum. Front Microbiol 2018; 9:10. [PMID: 29403462 PMCID: PMC5780403 DOI: 10.3389/fmicb.2018.00010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/05/2018] [Indexed: 12/30/2022] Open
Abstract
Pleurotus ostreatus is a widely cultivated edible fungus in China. Green mold disease of P. ostreatus which can seriously affect yield is a common disease during cultivation. It occurs mostly after P. ostreatus mycelia have been subjected to high temperatures. However, little information is available on the relationship between high temperature and green mold disease. The aim of this study is to prove that extracellular metabolites of P. ostreatus affected by high temperature can promote the growth of Trichoderma asperellum. After P. ostreatus mycelia was subjected to high temperature, the extracellular fluid of P. ostreatus showed a higher promoting effect on mycelial growth and conidial germination of T. asperellum. The thiobarbituric acid reactive substance (TBARS) content reached the maximum after 48 h at 36°C. A comprehensive metabolite profiling strategy involving gas chromatography-mass spectrometry (GC/MS) combined with liquid chromatography-mass spectrometry (LC/MS) was used to analyze the changes of extracellular metabolites in response to high temperature. A total of 141 differential metabolites were identified, including 84.4% up-regulated and 15.6% down-regulated. Exogenous metabolites whose concentrations were increased after high temperature were randomly selected, and nearly all of them were able to promote the mycelial growth and conidial germination of T. asperellum. The combination of all selected exogenous metabolites also has the promotion effects on the mycelial growth and conidial germination of T. asperellum in a given concentration range in vitro. Overall, these results provide a first view that high temperature affects the extracellular metabolites of P. ostreatus, and the extensive change in metabolites promotes T. asperellum growth.
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Affiliation(s)
- Zhiheng Qiu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Xiangli Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Jinxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
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116
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Chiu SWY, Cheng HW, Chen ZX, Wang HH, Lai MY, Wang JK, Wang YL. Quantification of biomolecules responsible for biomarkers in the surface-enhanced Raman spectra of bacteria using liquid chromatography-mass spectrometry. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp07103e] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biomarkers in SERS spectra of bacteria originate from bacterial purine metabolites, whose quantification indicates their continuous release in a stressful water environment.
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Affiliation(s)
- Shirley Wen-Yu Chiu
- Institute of Atomic and Molecular Sciences, Academia Sinica
- Taipei 10617
- Taiwan
- Department of Chemistry, National Tsing Hua University
- Hsinchu 30013
| | - Ho-Wen Cheng
- Institute of Atomic and Molecular Sciences, Academia Sinica
- Taipei 10617
- Taiwan
| | - Zhi-Xin Chen
- Institute of Atomic and Molecular Sciences, Academia Sinica
- Taipei 10617
- Taiwan
| | - Huai-Hsien Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica
- Taipei 10617
- Taiwan
| | - Ming-Yu Lai
- Institute of Atomic and Molecular Sciences, Academia Sinica
- Taipei 10617
- Taiwan
| | - Juen-Kai Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica
- Taipei 10617
- Taiwan
- Center for Condensed Matter Sciences, National Taiwan University
- Taipei 10617
| | - Yuh-Lin Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica
- Taipei 10617
- Taiwan
- Department of Physics, National Taiwan University
- Taipei 10617
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117
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Miniature Fluidic Microtissue Culturing Device for Rapid Biological Detection. INTEGRATED ANALYTICAL SYSTEMS 2018. [DOI: 10.1007/978-3-319-64747-0_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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118
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Hunter WG, Kelly JP, McGarrah RW, Kraus WE, Shah SH. Metabolic Dysfunction in Heart Failure: Diagnostic, Prognostic, and Pathophysiologic Insights From Metabolomic Profiling. Curr Heart Fail Rep 2017; 13:119-31. [PMID: 27216948 DOI: 10.1007/s11897-016-0289-5] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolic impairment is an intrinsic component of heart failure (HF) pathophysiology. Although initially conceived as a myocardial defect, metabolic dysfunction is now recognized as a systemic process with complex interplay between the myocardium and peripheral tissues and organs. Specifically, HF-associated metabolic dysfunction includes alterations in substrate utilization, insulin resistance, defects in energy production, and imbalanced anabolic-catabolic signaling leading to cachexia. Each of these metabolic abnormalities is associated with significant morbidity and mortality in patients with HF; however, their detection and therapeutic management remains challenging. Given the difficulty in obtaining human cardiac tissue for research purposes, peripheral blood metabolomic profiling, a well-established approach for characterizing small-molecule metabolite intermediates from canonical biochemical pathways, may be a useful technology for dissecting biomarkers and mechanisms of metabolic impairment in HF. In this review, metabolic abnormalities in HF will be discussed with particular emphasis on the application of metabolomic profiling to detecting, risk stratifying, and identifying novel targets for metabolic therapy in this heterogeneous population.
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Affiliation(s)
- Wynn G Hunter
- Duke University School of Medicine, 300 North Duke Street, Durham, NC, 27701, USA
| | - Jacob P Kelly
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Durham, NC, USA
| | - Robert W McGarrah
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Durham, NC, USA
| | - William E Kraus
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Durham, NC, USA
| | - Svati H Shah
- Duke University School of Medicine, 300 North Duke Street, Durham, NC, 27701, USA.
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Duke Clinical Research Institute, Durham, NC, USA.
- Duke Molecular Physiology Institute, Durham, NC, USA.
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119
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Gonzalez JE, Bennett RK, Papoutsakis ET, Antoniewicz MR. Methanol assimilation in Escherichia coli is improved by co-utilization of threonine and deletion of leucine-responsive regulatory protein. Metab Eng 2017; 45:67-74. [PMID: 29203222 DOI: 10.1016/j.ymben.2017.11.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/25/2017] [Accepted: 11/29/2017] [Indexed: 12/19/2022]
Abstract
Methane, the main component of natural gas, can be used to produce methanol which can be further converted to other valuable products. There is increasing interest in using biological systems for the production of fuels and chemicals from methanol, termed methylotrophy. In this work, we have examined methanol assimilation metabolism in a synthetic methylotrophic E. coli strain. Specifically, we applied 13C-tracers and evaluated 25 different co-substrates for methanol assimilation, including amino acids, sugars and organic acids. In particular, co-utilization of threonine significantly enhanced methylotrophy. Through our investigations, we proposed specific metabolic pathways that, when activated, correlated with increased methanol assimilation. These pathways are normally repressed by the leucine-responsive regulatory protein (lrp), a global regulator of metabolism associated with the feast-or-famine response in E. coli. By deleting lrp, we were able to further enhance the methylotrophic ability of our synthetic strain, as demonstrated through increased incorporation of 13C carbon from 13C-methanol into biomass.
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Affiliation(s)
- Jacqueline E Gonzalez
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - E Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA.
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120
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Microdosing, isotopic labeling, radiotracers and metabolomics: relevance in drug discovery, development and safety. Bioanalysis 2017; 9:1913-1933. [PMID: 29171759 DOI: 10.4155/bio-2017-0137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This review discusses the use of stable (13C, 2D) or radioactive isotopes (14C, 11C, 18F, 131I, 64Cu, 68Ga) incorporated into the molecular structure of new drug entities for the purpose of pharmacokinetic or -dynamic studies. Metabolite in safety testing requires the administration of pharmacologically active doses. In such studies, radiotracers find application mainly in preclinical animal investigations, whereby LC-MS/MS is used to identify metabolite structure and drug-related effects. In contrast, first-in-human metabolite studies have to be carried out at nonpharmacological doses not exceeding 100 μg (microdose), which is generally too low for metabolite detection by LC-MS/MS. This short-coming can be overcome by specific radio- or isotopic labeling of the drug of interest and measurements using accelerator mass spectroscopy, single-photon emission computed tomography and positron emission tomography. Such combined radioisotope-based approaches permit Phase 0, first-in-human metabolite study.
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121
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Gao C, Wang S, Hu G, Guo L, Chen X, Xu P, Liu L. Engineering Escherichia coli for malate production by integrating modular pathway characterization with CRISPRi-guided multiplexed metabolic tuning. Biotechnol Bioeng 2017; 115:661-672. [PMID: 29105733 DOI: 10.1002/bit.26486] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/13/2017] [Accepted: 10/29/2017] [Indexed: 12/21/2022]
Abstract
The application of rational design in reallocating metabolic flux to overproduce desired chemicals is always restricted by the native regulatory network. Here, we demonstrated that in vitro modular pathway optimization combined with in vivo multiplexed combinatorial engineering enables effective characterization of the bottleneck of a complex biosynthetic cascade and improves the output of the engineered pathway. As a proof of concept, we systematically identified the rate-limiting step of a five-gene malate biosynthetic pathway by combinatorially tuning the enzyme loads of a reconstituted biocatalytic reaction in a cell-free system. Using multiplexed CRISPR interference, we subsequently eliminated the metabolic constraints by rationally assigning an optimal gene expression pattern for each pathway module. The present engineered strain Escherichia coli B0013-47 exhibited a 2.3-fold increase in malate titer compared with that of the parental strain, with a yield of 0.85 mol/mol glucose in shake-flask culture and titer of 269 mM (36 g/L) in fed-batch cultivation. The strategy reported herein represents a powerful method for improving the efficiency of multi-gene pathways and advancing the success of metabolic engineering.
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Affiliation(s)
- Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Shihui Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Peng Xu
- Chemical Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
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122
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de Jong H, Casagranda S, Giordano N, Cinquemani E, Ropers D, Geiselmann J, Gouzé JL. Mathematical modelling of microbes: metabolism, gene expression and growth. J R Soc Interface 2017; 14:20170502. [PMID: 29187637 PMCID: PMC5721159 DOI: 10.1098/rsif.2017.0502] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/31/2017] [Indexed: 11/12/2022] Open
Abstract
The growth of microorganisms involves the conversion of nutrients in the environment into biomass, mostly proteins and other macromolecules. This conversion is accomplished by networks of biochemical reactions cutting across cellular functions, such as metabolism, gene expression, transport and signalling. Mathematical modelling is a powerful tool for gaining an understanding of the functioning of this large and complex system and the role played by individual constituents and mechanisms. This requires models of microbial growth that provide an integrated view of the reaction networks and bridge the scale from individual reactions to the growth of a population. In this review, we derive a general framework for the kinetic modelling of microbial growth from basic hypotheses about the underlying reaction systems. Moreover, we show that several families of approximate models presented in the literature, notably flux balance models and coarse-grained whole-cell models, can be derived with the help of additional simplifying hypotheses. This perspective clearly brings out how apparently quite different modelling approaches are related on a deeper level, and suggests directions for further research.
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Affiliation(s)
| | - Stefano Casagranda
- University Côte d'Azur, Inria, INRA, CNRS, UPMC University Paris 06, BIOCORE team, Sophia-Antipolis, France
| | - Nils Giordano
- University Grenoble-Alpes, Inria, Grenoble, France
- University Grenoble-Alpes, CNRS, LIPhy, Grenoble, France
| | | | | | - Johannes Geiselmann
- University Grenoble-Alpes, Inria, Grenoble, France
- University Grenoble-Alpes, CNRS, LIPhy, Grenoble, France
| | - Jean-Luc Gouzé
- University Côte d'Azur, Inria, INRA, CNRS, UPMC University Paris 06, BIOCORE team, Sophia-Antipolis, France
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123
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Navas-Carrillo D, Rodriguez JM, Montoro-García S, Orenes-Piñero E. High-resolution proteomics and metabolomics in thyroid cancer: Deciphering novel biomarkers. Crit Rev Clin Lab Sci 2017; 54:446-457. [DOI: 10.1080/10408363.2017.1394266] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Diana Navas-Carrillo
- Department of Surgery, Hospital de la Vega Lorenzo Guirao, University of Murcia, Murcia, Spain
| | - José Manuel Rodriguez
- Department of Surgery, Hospital Universitario Virgen de la Arrixaca, University of Murcia, Murcia, Spain
| | | | - Esteban Orenes-Piñero
- Proteomic Unit, Instituto Murciano de Investigación Biosanitaria Virgen de la Arrixaca (IMIB-Arrixaca), Universidad de Murcia, Murcia, Spain
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124
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Abstract
While yeast is one of the most studied organisms, its intricate biology remains to be fully mapped and understood. This is especially the case when it comes to capture rapid, in vivo fluctuations of metabolite levels. Secondary electrospray ionization-high resolution mass spectrometry SESI-HRMS is introduced here as a sensitive and noninvasive analytical technique for online monitoring of microbial metabolic activity. The power of this technique is exemplarily shown for baker’s yeast fermentation, for which the time-resolved abundance of about 300 metabolites is demonstrated. The results suggest that a large number of metabolites produced by yeast from glucose neither are reported in the literature nor are their biochemical origins deciphered. With the technique demonstrated here, researchers interested in distant disciplines such as yeast physiology and food quality will gain new insights into the biochemical capability of this simple eukaryote.
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125
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A global resource allocation strategy governs growth transition kinetics of Escherichia coli. Nature 2017; 551:119-123. [PMID: 29072300 DOI: 10.1038/nature24299] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 09/20/2017] [Indexed: 12/24/2022]
Abstract
A grand challenge of systems biology is to predict the kinetic responses of living systems to perturbations starting from the underlying molecular interactions. Changes in the nutrient environment have long been used to study regulation and adaptation phenomena in microorganisms and they remain a topic of active investigation. Although much is known about the molecular interactions that govern the regulation of key metabolic processes in response to applied perturbations, they are insufficiently quantified for predictive bottom-up modelling. Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models from steady-state growth into the kinetic regime. Using only qualitative knowledge of the underlying regulatory processes and imposing the condition of flux balance, we derive a quantitative model of bacterial growth transitions that is independent of inaccessible kinetic parameters. The resulting flux-controlled regulation model accurately predicts the time course of gene expression and biomass accumulation in response to carbon upshifts and downshifts (for example, diauxic shifts) without adjustable parameters. As predicted by the model and validated by quantitative proteomics, cells exhibit suboptimal recovery kinetics in response to nutrient shifts owing to a rigid strategy of protein synthesis allocation, which is not directed towards alleviating specific metabolic bottlenecks. Our approach does not rely on kinetic parameters, and therefore points to a theoretical framework for describing a broad range of such kinetic processes without detailed knowledge of the underlying biochemical reactions.
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126
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Pinu FR, Villas-Boas SG, Aggio R. Analysis of Intracellular Metabolites from Microorganisms: Quenching and Extraction Protocols. Metabolites 2017; 7:E53. [PMID: 29065530 PMCID: PMC5746733 DOI: 10.3390/metabo7040053] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/11/2017] [Accepted: 10/21/2017] [Indexed: 11/17/2022] Open
Abstract
Sample preparation is one of the most important steps in metabolome analysis. The challenges of determining microbial metabolome have been well discussed within the research community and many improvements have already been achieved in last decade. The analysis of intracellular metabolites is particularly challenging. Environmental perturbations may considerably affect microbial metabolism, which results in intracellular metabolites being rapidly degraded or metabolized by enzymatic reactions. Therefore, quenching or the complete stop of cell metabolism is a pre-requisite for accurate intracellular metabolite analysis. After quenching, metabolites need to be extracted from the intracellular compartment. The choice of the most suitable metabolite extraction method/s is another crucial step. The literature indicates that specific classes of metabolites are better extracted by different extraction protocols. In this review, we discuss the technical aspects and advancements of quenching and extraction of intracellular metabolite analysis from microbial cells.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand.
| | - Silas G Villas-Boas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand.
| | - Raphael Aggio
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L693BX, UK.
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127
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Diether M, Sauer U. Towards detecting regulatory protein–metabolite interactions. Curr Opin Microbiol 2017; 39:16-23. [DOI: 10.1016/j.mib.2017.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/21/2017] [Accepted: 07/27/2017] [Indexed: 01/20/2023]
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128
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Schmitz AC, Hartline CJ, Zhang F. Engineering Microbial Metabolite Dynamics and Heterogeneity. Biotechnol J 2017; 12. [PMID: 28901715 DOI: 10.1002/biot.201700422] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/06/2017] [Indexed: 11/09/2022]
Abstract
As yields for biological chemical production in microorganisms approach their theoretical maximum, metabolic engineering requires new tools, and approaches for improvements beyond what traditional strategies can achieve. Engineering metabolite dynamics and metabolite heterogeneity is necessary to achieve further improvements in product titers, productivities, and yields. Metabolite dynamics, the ensemble change in metabolite concentration over time, arise from the need for microbes to adapt their metabolism in response to the extracellular environment and are important for controlling growth and productivity in industrial fermentations. Metabolite heterogeneity, the cell-to-cell variation in a metabolite concentration in an isoclonal population, has a significant impact on ensemble productivity. Recent advances in single cell analysis enable a more complete understanding of the processes driving metabolite heterogeneity and reveal metabolic engineering targets. The authors present an overview of the mechanistic origins of metabolite dynamics and heterogeneity, why they are important, their potential effects in chemical production processes, and tools and strategies for engineering metabolite dynamics and heterogeneity. The authors emphasize that the ability to control metabolite dynamics and heterogeneity will bring new avenues of engineering to increase productivity of microbial strains.
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Affiliation(s)
- Alexander C Schmitz
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Christopher J Hartline
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, USA.,Division of Biological and Biomedical Sciences, and Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, USA
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129
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Krejci A, Tennessen JM. Metabolism in time and space – exploring the frontier of developmental biology. Development 2017; 144:3193-3198. [DOI: 10.1242/dev.150573] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the fact that metabolic studies played a prominent role in the early history of developmental biology research, the field of developmental metabolism was largely ignored following the advent of modern molecular biology. Metabolism, however, has recently re-emerged as a focal point of biomedical studies and, as a result, developmental biologists are once again exploring the chemical and energetic forces that shape growth, development and maturation. In May 2017, a diverse group of scientists assembled at the EMBO/EMBL Symposium ‘Metabolism in Time and Space’ to discuss how metabolism influences cellular and developmental processes. The speakers not only described how metabolic flux adapts to the energetic needs of a developing organism, but also emphasized that metabolism can directly regulate developmental progression. Overall, and as we review here, this interdisciplinary meeting provided a valuable forum to explore the interface between developmental biology and metabolism.
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Affiliation(s)
- Alena Krejci
- University of South Bohemia, Faculty of Science, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
- Biology Centre, Institute of Entomology, Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Jason M. Tennessen
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
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130
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Gehrke S, Reisz JA, Nemkov T, Hansen KC, D’Alessandro A. Characterization of rapid extraction protocols for high-throughput metabolomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1445-1452. [PMID: 28586533 PMCID: PMC5547002 DOI: 10.1002/rcm.7916] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE In the last five years, high-throughput metabolomics has significantly advanced scientific research and holds the potential to promote strides in the fields of clinical metabolomics and personalized medicine. While innovations in the field of flow-injection mass spectrometry and three-minute metabolomics methods now allow investigators to process hundreds to thousands of samples per day, time-sensitive clinical applications, particularly in the emergency department, are limited by a lack of rapid extraction methods. METHODS Here we characterized the efficacy of fast liquid-liquid extractions for characterization of hydrophilic compounds through ultra-high-pressure liquid chromatography/mass spectrometry. Internal stable-isotope-labeled standards were used to quantitatively characterize markers of energy and oxidative metabolism in human whole blood, plasma and red blood cells - three common matrices of clinical relevance. RESULTS For all the tested matrices, vortexing time (4-60 min) did not significantly affect extraction yields for the tested hydrophilic metabolites. Coefficients of variations <<20% for all tested compounds, except for the redox-sensitive metabolite cystine (accumulating over time). Internal standards and second extractions confirmed recoveries >80% for all tested metabolites, except for basic amino acids and polyamines, which showed reproducible yields ranging from 50 to 75%. Global profiling and absolute quantitation of 24 metabolites revealed similarities between the plasma and red blood cell metabolomes. CONCLUSIONS Rapid extraction (~4 min) of hydrophilic compounds is a viable and potentially automatable strategy to perform quantitative analysis of whole blood, plasma and red blood cells for research or clinical applications.
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Affiliation(s)
- Sarah Gehrke
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
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131
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Time-Resolved Pharmacological Studies using Automated, On-line Monitoring of Five Parallel Suspension Cultures. Sci Rep 2017; 7:10337. [PMID: 28871151 PMCID: PMC5583285 DOI: 10.1038/s41598-017-10472-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 08/10/2017] [Indexed: 12/16/2022] Open
Abstract
Early stage pharmacological studies rely on in vitro methodologies for screening and testing compounds. Conventional assays based on endpoint measurements provide limited information because the lack in temporal resolution may not determine the pharmacological effect at its maximum. We developed an on-line, automated system for near real-time monitoring of extracellular content from five parallel suspension cultures, combining cell density measurements with a high-resolution separations every 12 minutes for 4 days. Selector and switching valves provide the fluidic control required to sample from one culture during the analysis of the previous sample from another culture, a time-saving measure that is fundamental to the throughput of the presented system. The system was applied to study the metabolic effects of the drugs rotenone, β-lapachone and clioquinol using lactate as metabolic indicator. For each drug, 96 assays were executed on the extracellular matrix at three concentrations with two controls in parallel, consuming only 5.78 mL of media from each culture over four days, less than 60 μL per analysis. The automated system provides high sample throughput, good temporal resolution and low sample consumption combined with a rugged analytical method with adequate sensitivity, providing a promising new platform for pharmacological and biotechnological studies.
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132
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Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD. Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu Rev Biochem 2017; 86:277-304. [PMID: 28654323 DOI: 10.1146/annurev-biochem-061516-044952] [Citation(s) in RCA: 261] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolites are the small biological molecules involved in energy conversion and biosynthesis. Studying metabolism is inherently challenging due to metabolites' reactivity, structural diversity, and broad concentration range. Herein, we review the common pitfalls encountered in metabolomics and provide concrete guidelines for obtaining accurate metabolite measurements, focusing on water-soluble primary metabolites. We show how seemingly straightforward sample preparation methods can introduce systematic errors (e.g., owing to interconversion among metabolites) and how proper selection of quenching solvent (e.g., acidic acetonitrile:methanol:water) can mitigate such problems. We discuss the specific strengths, pitfalls, and best practices for each common analytical platform: liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and enzyme assays. Together this information provides a pragmatic knowledge base for carrying out biologically informative metabolite measurements.
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Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Xiaoyang Su
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Matthias S Klein
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, California 95616.,Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
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133
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Kuehne A, Mayr U, Sévin DC, Claassen M, Zamboni N. Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data. PLoS Comput Biol 2017; 13:e1005577. [PMID: 28598965 PMCID: PMC5482507 DOI: 10.1371/journal.pcbi.1005577] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 06/23/2017] [Accepted: 05/16/2017] [Indexed: 12/30/2022] Open
Abstract
In recent years, the number of large-scale metabolomics studies on various cellular processes in different organisms has increased drastically. However, it remains a major challenge to perform a systematic identification of mechanistic regulatory events that mediate the observed changes in metabolite levels, due to complex interdependencies within metabolic networks. We present the metabolic network segmentation (MNS) algorithm, a probabilistic graphical modeling approach that enables genome-scale, automated prediction of regulated metabolic reactions from differential or serial metabolomics data. The algorithm sections the metabolic network into modules of metabolites with consistent changes. Metabolic reactions that connect different modules are the most likely sites of metabolic regulation. In contrast to most state-of-the-art methods, the MNS algorithm is independent of arbitrary pathway definitions, and its probabilistic nature facilitates assessments of noisy and incomplete measurements. With serial (i.e., time-resolved) data, the MNS algorithm also indicates the sequential order of metabolic regulation. We demonstrated the power and flexibility of the MNS algorithm with three, realistic case studies with bacterial and human cells. Thus, this approach enables the identification of mechanistic regulatory events from large-scale metabolomics data, and contributes to the understanding of metabolic processes and their interplay with cellular signaling and regulation processes. Reciprocal crosstalk between metabolism and cellular signaling pathways plays a crucial role in cellular decision-making. In recent years, this premise has motivated several metabolomics studies that aimed to gain a mechanistic understanding of metabolic phenotypes. However, due to complex interactions within metabolic networks, it remains a challenge to infer mechanisms that underlie metabolome changes. We present the metabolic network segmentation approach, a novel method that aimed to identify the sites and sequential order of metabolic regulatory events, based merely on steady state or dynamic metabolomics data. This method employs probabilistic graphical models to partition the entire metabolic network into modules with correlated metabolites. It identifies fractures between modules (i.e., reactions that connect non-correlated metabolites) as sites of regulation. We performed validation and benchmark analyses in hundreds of E. coli knockout mutants deficient in enzymes and transcription factors. Moreover, we verified the capability of our method for identifying the sequential order of metabolic regulatory events by testing it on fibroblasts exposed to oxidative stress. Our metabolic network segmentation algorithm is widely applicable, and thus, it will enhance our mechanistic understanding of metabolic phenotypes and their connections to cellular signaling and regulatory processes.
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Affiliation(s)
- Andreas Kuehne
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,PhD Program Systems Biology, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Urs Mayr
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Daniel C Sévin
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland.,PhD Program Systems Biology, Life Science Zurich Graduate School, Zurich, Switzerland
| | | | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Switzerland
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134
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NEMKOV T, HANSEN KC, D’ALESSANDRO A. A three-minute method for high-throughput quantitative metabolomics and quantitative tracing experiments of central carbon and nitrogen pathways. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:663-673. [PMID: 28195377 PMCID: PMC5364945 DOI: 10.1002/rcm.7834] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 02/02/2017] [Accepted: 02/02/2017] [Indexed: 05/07/2023]
Abstract
RATIONALE The implementation of mass spectrometry (MS)-based metabolomics is advancing many areas of biomedical research. The time associated with traditional chromatographic methods for resolving metabolites prior to mass analysis has limited the potential to perform large-scale, highly powered metabolomics studies and clinical applications. METHODS Here we describe a three-minute method for the rapid profiling of central metabolic pathways through UHPLC/MS, tracing experiments in vitro and in vivo, and targeted quantification of compounds of interest using spiked in heavy labeled standards. RESULTS This method has shown to be linear, reproducible, selective, sensitive, and robust for the semi-targeted analysis of central carbon and nitrogen metabolism. Isotopically labeled internal standards are used for absolute quantitation of steady-state metabolite levels and de novo synthesized metabolites in tracing studies. We further propose exploratory applications to biofluids, cell and tissue extracts derived from relevant biomedical/clinical samples. CONCLUSIONS While limited to the analysis of central carbon and nitrogen metabolism, this method enables the analysis of hundreds of samples per day derived from diverse biological matrices. This approach makes it possible to analyze samples from large patient populations for translational research, personalized medicine, and clinical metabolomics applications. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Travis NEMKOV
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, 80045 Aurora, CO, USA
| | - Kirk C. HANSEN
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, 80045 Aurora, CO, USA
| | - Angelo D’ALESSANDRO
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, 80045 Aurora, CO, USA
- Corresponding author: Angelo D’Alessandro, PhD, Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, 12801 East 17th Ave., 80045 Aurora, CO, Phone # 303 724-8495,
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Abstract
Metabolism is highly complex and involves thousands of different connected reactions; it is therefore necessary to use mathematical models for holistic studies. The use of mathematical models in biology is referred to as systems biology. In this review, the principles of systems biology are described, and two different types of mathematical models used for studying metabolism are discussed: kinetic models and genome-scale metabolic models. The use of different omics technologies, including transcriptomics, proteomics, metabolomics, and fluxomics, for studying metabolism is presented. Finally, the application of systems biology for analyzing global regulatory structures, engineering the metabolism of cell factories, and analyzing human diseases is discussed.
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Affiliation(s)
- Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41128 Gothenburg, Sweden; .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark.,Science for Life Laboratory, Royal Institute of Technology, SE17121 Stockholm, Sweden
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136
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Metabolomics: A Primer. Trends Biochem Sci 2017; 42:274-284. [PMID: 28196646 DOI: 10.1016/j.tibs.2017.01.004] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/13/2016] [Accepted: 01/12/2017] [Indexed: 02/08/2023]
Abstract
Metabolomics generates a profile of small molecules that are derived from cellular metabolism and can directly reflect the outcome of complex networks of biochemical reactions, thus providing insights into multiple aspects of cellular physiology. Technological advances have enabled rapid and increasingly expansive data acquisition with samples as small as single cells; however, substantial challenges in the field remain. In this primer we provide an overview of metabolomics, especially mass spectrometry (MS)-based metabolomics, which uses liquid chromatography (LC) for separation, and discuss its utilities and limitations. We identify and discuss several areas at the frontier of metabolomics. Our goal is to give the reader a sense of what might be accomplished when conducting a metabolomics experiment, now and in the near future.
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137
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Guder JC, Schramm T, Sander T, Link H. Time-Optimized Isotope Ratio LC–MS/MS for High-Throughput Quantification of Primary Metabolites. Anal Chem 2017; 89:1624-1631. [DOI: 10.1021/acs.analchem.6b03731] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Christopher Guder
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Thorben Schramm
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Timur Sander
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
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138
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Zampieri M, Sekar K, Zamboni N, Sauer U. Frontiers of high-throughput metabolomics. Curr Opin Chem Biol 2017; 36:15-23. [PMID: 28064089 DOI: 10.1016/j.cbpa.2016.12.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/30/2016] [Accepted: 12/05/2016] [Indexed: 02/06/2023]
Abstract
Large scale metabolomics studies are increasingly used to investigate genetically different individuals and time-dependent responses to environmental stimuli. New mass spectrometric approaches with at least an order of magnitude more rapid analysis of small molecules within the cell's metabolome are now paving the way towards true high-throughput metabolomics, opening new opportunities in systems biology, functional genomics, drug discovery, and personalized medicine. Here we discuss the impact and advantages of the progress made in profiling large cohorts and dynamic systems with high temporal resolution and automated sampling. In both areas, high-throughput metabolomics is gaining traction because it can generate hypotheses on molecular mechanisms and metabolic regulation. We conclude with the current status of the less mature single cell analyses where high-throughput analytics will be indispensable to resolve metabolic heterogeneity in populations and compartmentalization of metabolites.
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Affiliation(s)
- Mattia Zampieri
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland
| | - Karthik Sekar
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, CH-8093 Zurich, Switzerland.
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139
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Ortmayr K, Charwat V, Kasper C, Hann S, Koellensperger G. Uncertainty budgeting in fold change determination and implications for non-targeted metabolomics studies in model systems. Analyst 2017; 142:80-90. [DOI: 10.1039/c6an01342b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Uncertainty budgeting provides error intervals for fold change values and complements significance testing in non-targeted metabolomics.
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Affiliation(s)
- Karin Ortmayr
- Institute of Analytical Chemistry
- University of Vienna
- Faculty of Chemistry
- 1090 Vienna
- Austria
| | - Verena Charwat
- Department of Biotechnology
- University of Natural Resources and Life Sciences (BOKU) Vienna
- 1190 Vienna
- Austria
| | - Cornelia Kasper
- Department of Biotechnology
- University of Natural Resources and Life Sciences (BOKU) Vienna
- 1190 Vienna
- Austria
| | - Stephan Hann
- Department of Chemistry
- University of Natural Resources and Life Sciences (BOKU) Vienna
- 1190 Vienna
- Austria
| | - Gunda Koellensperger
- Institute of Analytical Chemistry
- University of Vienna
- Faculty of Chemistry
- 1090 Vienna
- Austria
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140
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Metabolomics: Definitions and Significance in Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:3-17. [DOI: 10.1007/978-3-319-47656-8_1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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141
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Khomenko I, Stefanini I, Cappellin L, Cappelletti V, Franceschi P, Cavalieri D, Märk TD, Biasioli F. Non-invasive real time monitoring of yeast volatilome by PTR-ToF-MS. Metabolomics 2017; 13:118. [PMID: 28932179 PMCID: PMC5579147 DOI: 10.1007/s11306-017-1259-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/23/2017] [Indexed: 11/09/2022]
Abstract
INTRODUCTION Producing a wide range of volatile secondary metabolites Saccharomyces cerevisiae influences wine, beer, and bread sensory quality and hence selection of strains based on their volatilome becomes pivotal. A rapid on-line method for volatilome assessing of strains growing on standard solid media is still missing. OBJECTIVES Methodologically, the aim of this study was to demonstrate the automatic, real-time, direct, and non-invasive monitoring of yeast volatilome in order to rapidly produce a robust large data set encompassing measurements relative to many strains, replicates and time points. The fundamental scope was to differentiate volatilomes of genetically similar strains of oenological relevance during the whole growing process. METHOD Six different S. cerevisiae strains (four meiotic segregants of a natural strain and two laboratory strains) inoculated onto a solid medium have been monitored on-line by Proton Transfer Reaction-Time-of-Flight-Mass Spectrometry for 11 days every 4 h (3540 time points). FastGC PTR-ToF-MS was performed during the stationary phase on the 5th day. RESULTS More than 300 peaks have been extracted from the average spectra associated to each time point, 70 have been tentatively identified. Univariate and multivariate analyses have been performed on the data matrix (3640 measurements × 70 peaks) highlighting the volatilome evolution and strain-specific features. Laboratory strains with opposite mating type, and meiotic segregants of the same natural strain showed significantly different profiles. CONCLUSIONS The described set-up allows the on-line high-throughput screening of yeast volatilome of S. cerevisiae strains and the identification of strain specific features and new metabolic pathways, discriminating also genetically similar strains, thus revealing a novel method for strain phenotyping, identification, and quality control.
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Affiliation(s)
- Iuliia Khomenko
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige, TN Italy
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Technikerstr. 25, Innsbruck, Austria
| | - Irene Stefanini
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige, TN Italy
- Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry, CV4 7AJ UK
| | - Luca Cappellin
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige, TN Italy
| | - Valentina Cappelletti
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige, TN Italy
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Pietro Franceschi
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige, TN Italy
| | - Duccio Cavalieri
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige, TN Italy
- Biology Department, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, FI Italy
| | - Tilmann D. Märk
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Technikerstr. 25, Innsbruck, Austria
| | - Franco Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all’Adige, TN Italy
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142
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Dai X, Zhu M, Warren M, Balakrishnan R, Patsalo V, Okano H, Williamson JR, Fredrick K, Wang YP, Hwa T. Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth. Nat Microbiol 2016; 2:16231. [PMID: 27941827 PMCID: PMC5346290 DOI: 10.1038/nmicrobiol.2016.231] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 10/17/2016] [Indexed: 01/13/2023]
Abstract
Bacteria growing under different conditions experience a broad range of demand on the rate of protein synthesis, which profoundly affects cellular resource allocation. During fast growth, protein synthesis has long been known to be modulated by adjusting the ribosome content, with the vast majority of ribosomes engaged at a near-maximal rate of elongation. Here, we systematically characterize protein synthesis by Escherichia coli, focusing on slow-growth conditions. We establish that the translational elongation rate decreases as growth slows, exhibiting a Michaelis-Menten dependence on the abundance of the cellular translational apparatus. However, an appreciable elongation rate is maintained even towards zero growth, including the stationary phase. This maintenance, critical for timely protein synthesis in harsh environments, is accompanied by a drastic reduction in the fraction of active ribosomes. Interestingly, well-known antibiotics such as chloramphenicol also cause a substantial reduction in the pool of active ribosomes, instead of slowing down translational elongation as commonly thought.
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Affiliation(s)
- Xiongfeng Dai
- Department of Physics, University of California at San Diego, La Jolla CA 92093-0374
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Manlu Zhu
- Department of Physics, University of California at San Diego, La Jolla CA 92093-0374
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Mya Warren
- Department of Physics, University of California at San Diego, La Jolla CA 92093-0374
| | - Rohan Balakrishnan
- Department of Physics, University of California at San Diego, La Jolla CA 92093-0374
- Department of Microbiology and Ohio State Biochemistry Program, the Ohio State University, Columbus OH 43210
| | - Vadim Patsalo
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Hiroyuki Okano
- Department of Physics, University of California at San Diego, La Jolla CA 92093-0374
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Kurt Fredrick
- Department of Microbiology and Ohio State Biochemistry Program, the Ohio State University, Columbus OH 43210
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla CA 92093-0374
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143
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Olson DG, Hörl M, Fuhrer T, Cui J, Zhou J, Maloney MI, Amador-Noguez D, Tian L, Sauer U, Lynd LR. Glycolysis without pyruvate kinase in Clostridium thermocellum. Metab Eng 2016; 39:169-180. [PMID: 27914869 DOI: 10.1016/j.ymben.2016.11.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/21/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023]
Abstract
The metabolism of Clostridium thermocellum is notable in that it assimilates sugar via the EMP pathway but does not possess a pyruvate kinase enzyme. In the wild type organism, there are three proposed pathways for conversion of phosphoenolpyruvate (PEP) to pyruvate, which differ in their cofactor usage. One path uses pyruvate phosphate dikinase (PPDK), another pathway uses the combined activities of PEP carboxykinase (PEPCK) and oxaloacetate decarboxylase (ODC). Yet another pathway, the malate shunt, uses the combined activities of PEPCK, malate dehydrogenase and malic enzyme. First we showed that there is no flux through the ODC pathway by enzyme assay. Flux through the remaining two pathways (PPDK and malate shunt) was determined by dynamic 13C labeling. In the wild-type strain, the malate shunt accounts for about 33±2% of the flux to pyruvate, with the remainder via the PPDK pathway. Deletion of the ppdk gene resulted in a redirection of all pyruvate flux through the malate shunt. This provides the first direct evidence of the in-vivo function of the malate shunt.
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Affiliation(s)
- Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
| | - Manuel Hörl
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Jingxuan Cui
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jilai Zhou
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Marybeth I Maloney
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Liang Tian
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA.
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144
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Recent advances in high-throughput 13C-fluxomics. Curr Opin Biotechnol 2016; 43:104-109. [PMID: 27838571 DOI: 10.1016/j.copbio.2016.10.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Abstract
The rise of high throughput (HT) strain engineering tools accompanying the area of synthetic biology is supporting the generation of a large number of microbial cell factories. A current bottleneck in process development is our limited capacity to rapidly analyze the metabolic state of the engineered strains, and in particular their intracellular fluxes. HT 13C-fluxomics workflows have not yet become commonplace, despite the existence of several HT tools at each of the required stages. This includes cultivation and sampling systems, analytics for isotopic analysis, and software for data processing and flux calculation. Here, we review recent advances in the field and highlight bottlenecks that must be overcome to allow the emergence of true HT 13C-fluxomics workflows.
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145
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Metabolic pathways in T cell activation and lineage differentiation. Semin Immunol 2016; 28:514-524. [PMID: 27825556 DOI: 10.1016/j.smim.2016.10.009] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/07/2016] [Accepted: 10/14/2016] [Indexed: 12/13/2022]
Abstract
Recent advances in the field of immunometabolism support the concept that fundamental processes in T cell biology, such as TCR-mediated activation and T helper lineage differentiation, are closely linked to changes in the cellular metabolic programs. Although the major task of the intermediate metabolism is to provide the cell with a constant supply of energy and molecular precursors for the production of biomolecules, the dynamic regulation of metabolic pathways also plays an active role in shaping T cell responses. Key metabolic processes such as glycolysis, fatty acid and mitochondrial metabolism are now recognized as crucial players in T cell activation and differentiation, and their modulation can differentially affect the development of T helper cell lineages. In this review, we describe the diverse metabolic processes that T cells engage during their life cycle from naïve towards effector and memory T cells. We consider in particular how the cellular metabolism may actively support the function of T cells in their different states. Moreover, we discuss how molecular regulators such as mTOR or AMPK link environmental changes to adaptations in the cellular metabolism and elucidate the consequences on T cell differentiation and function.
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146
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Geiger R, Rieckmann J, Wolf T, Basso C, Feng Y, Fuhrer T, Kogadeeva M, Picotti P, Meissner F, Mann M, Zamboni N, Sallusto F, Lanzavecchia A. L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity. Cell 2016; 167. [PMID: 27745970 PMCID: PMC5075284 DOI: 10.1016/j.cell.2016.09.031 10.1016/j.cell.2016.09.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Metabolic activity is intimately linked to T cell fate and function. Using high-resolution mass spectrometry, we generated dynamic metabolome and proteome profiles of human primary naive T cells following activation. We discovered critical changes in the arginine metabolism that led to a drop in intracellular L-arginine concentration. Elevating L-arginine levels induced global metabolic changes including a shift from glycolysis to oxidative phosphorylation in activated T cells and promoted the generation of central memory-like cells endowed with higher survival capacity and, in a mouse model, anti-tumor activity. Proteome-wide probing of structural alterations, validated by the analysis of knockout T cell clones, identified three transcriptional regulators (BAZ1B, PSIP1, and TSN) that sensed L-arginine levels and promoted T cell survival. Thus, intracellular L-arginine concentrations directly impact the metabolic fitness and survival capacity of T cells that are crucial for anti-tumor responses.
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Affiliation(s)
- Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland,Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland,Corresponding author
| | - Jan C. Rieckmann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Tobias Wolf
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland,Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland
| | - Camilla Basso
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Yuehan Feng
- Institute of Biochemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Maria Kogadeeva
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Paola Picotti
- Institute of Biochemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Felix Meissner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland,Center of Medical Immunology, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona 6500, Switzerland,Institute of Microbiology, ETH Zurich, Zurich 8093, Switzerland,Corresponding author
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147
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L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity. Cell 2016; 167:829-842.e13. [PMID: 27745970 PMCID: PMC5075284 DOI: 10.1016/j.cell.2016.09.031] [Citation(s) in RCA: 984] [Impact Index Per Article: 123.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/18/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022]
Abstract
Metabolic activity is intimately linked to T cell fate and function. Using high-resolution mass spectrometry, we generated dynamic metabolome and proteome profiles of human primary naive T cells following activation. We discovered critical changes in the arginine metabolism that led to a drop in intracellular L-arginine concentration. Elevating L-arginine levels induced global metabolic changes including a shift from glycolysis to oxidative phosphorylation in activated T cells and promoted the generation of central memory-like cells endowed with higher survival capacity and, in a mouse model, anti-tumor activity. Proteome-wide probing of structural alterations, validated by the analysis of knockout T cell clones, identified three transcriptional regulators (BAZ1B, PSIP1, and TSN) that sensed L-arginine levels and promoted T cell survival. Thus, intracellular L-arginine concentrations directly impact the metabolic fitness and survival capacity of T cells that are crucial for anti-tumor responses. Dataset on dynamic metabolome/proteome profiles of activated human naive T cells Intracellular L-arginine levels regulate several metabolic pathways in T cells T cells with increased L-arginine display enhanced survival and anti-tumor activity LiP-MS identified proteins that are structurally modified by high L-arginine levels
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148
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Yang YT, Wang CY. Review of Microfluidic Photobioreactor Technology for Metabolic Engineering and Synthetic Biology of Cyanobacteria and Microalgae. MICROMACHINES 2016; 7:mi7100185. [PMID: 30404358 PMCID: PMC6190437 DOI: 10.3390/mi7100185] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/16/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022]
Abstract
One goal of metabolic engineering and synthetic biology for cyanobacteria and microalgae is to engineer strains that can optimally produce biofuels and commodity chemicals. However, the current workflow is slow and labor intensive with respect to assembly of genetic parts and characterization of production yields because of the slow growth rates of these organisms. Here, we review recent progress in the microfluidic photobioreactors and identify opportunities and unmet needs in metabolic engineering and synthetic biology. Because of the unprecedented experimental resolution down to the single cell level, long-term real-time monitoring capability, and high throughput with low cost, microfluidic photobioreactor technology will be an indispensible tool to speed up the development process, advance fundamental knowledge, and realize the full potential of metabolic engineering and synthetic biology for cyanobacteria and microalgae.
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Affiliation(s)
- Ya-Tang Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Chun Ying Wang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
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149
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Abstract
BACKGROUND The term 'metabolome' was introduced to the scientific literature in September 1998. AIM AND KEY SCIENTIFIC CONCEPTS OF THE REVIEW To mark its 18-year-old 'coming of age', two of the co-authors of that paper review the genesis of metabolomics, whence it has come and where it may be going.
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Affiliation(s)
- Douglas B. Kell
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131, Princess St, Manchester, M1 7DN UK
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
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150
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Nydegger U, Lung T, Risch L, Risch M, Medina Escobar P, Bodmer T. Inflammation Thread Runs across Medical Laboratory Specialities. Mediators Inflamm 2016; 2016:4121837. [PMID: 27493451 PMCID: PMC4963559 DOI: 10.1155/2016/4121837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/31/2016] [Indexed: 12/16/2022] Open
Abstract
We work on the assumption that four major specialities or sectors of medical laboratory assays, comprising clinical chemistry, haematology, immunology, and microbiology, embraced by genome sequencing techniques, are routinely in use. Medical laboratory markers for inflammation serve as model: they are allotted to most fields of medical lab assays including genomics. Incessant coding of assays aligns each of them in the long lists of big data. As exemplified with the complement gene family, containing C2, C3, C8A, C8B, CFH, CFI, and ITGB2, heritability patterns/risk factors associated with diseases with genetic glitch of complement components are unfolding. The C4 component serum levels depend on sufficient vitamin D whilst low vitamin D is inversely related to IgG1, IgA, and C3 linking vitamin sufficiency to innate immunity. Whole genome sequencing of microbial organisms may distinguish virulent from nonvirulent and antibiotic resistant from nonresistant varieties of the same species and thus can be listed in personal big data banks including microbiological pathology; the big data warehouse continues to grow.
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Affiliation(s)
- Urs Nydegger
- Labormedizinisches Zentrum Dr. Risch and Kantonsspital Graubünden, 7000 Chur, Switzerland
| | - Thomas Lung
- Labormedizinisches Zentrum Dr. Risch and Kantonsspital Graubünden, 7000 Chur, Switzerland
| | - Lorenz Risch
- Labormedizinisches Zentrum Dr. Risch and Kantonsspital Graubünden, 7000 Chur, Switzerland
| | - Martin Risch
- Labormedizinisches Zentrum Dr. Risch and Kantonsspital Graubünden, 7000 Chur, Switzerland
| | - Pedro Medina Escobar
- Labormedizinisches Zentrum Dr. Risch and Kantonsspital Graubünden, 7000 Chur, Switzerland
| | - Thomas Bodmer
- Labormedizinisches Zentrum Dr. Risch and Kantonsspital Graubünden, 7000 Chur, Switzerland
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