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Rothman DL, Moore PB, Shulman RG. The impact of metabolism on the adaptation of organisms to environmental change. Front Cell Dev Biol 2023; 11:1197226. [PMID: 37377740 PMCID: PMC10291235 DOI: 10.3389/fcell.2023.1197226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Since Jacob and Monod's discovery of the lac operon ∼1960, the explanations offered for most metabolic adaptations have been genetic. The focus has been on the adaptive changes in gene expression that occur, which are often referred to as "metabolic reprogramming." The contributions metabolism makes to adaptation have been largely ignored. Here we point out that metabolic adaptations, including the associated changes in gene expression, are highly dependent on the metabolic state of an organism prior to the environmental change to which it is adapting, and on the plasticity of that state. In support of this hypothesis, we examine the paradigmatic example of a genetically driven adaptation, the adaptation of E. coli to growth on lactose, and the paradigmatic example of a metabolic driven adaptation, the Crabtree effect in yeast. Using a framework based on metabolic control analysis, we have reevaluated what is known about both adaptations, and conclude that knowledge of the metabolic properties of these organisms prior to environmental change is critical for understanding not only how they survive long enough to adapt, but also how the ensuing changes in gene expression occur, and their phenotypes post-adaptation. It would be useful if future explanations for metabolic adaptations acknowledged the contributions made to them by metabolism, and described the complex interplay between metabolic systems and genetic systems that make these adaptations possible.
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Affiliation(s)
- Douglas L. Rothman
- Departments of Radiology, Yale University, New Haven, CT, United States
- Biomedical Engineering, Yale University, New Haven, CT, United States
- Yale Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
| | - Peter B. Moore
- Department of Molecular Biology and Biophysics, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Robert G. Shulman
- Yale Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
- Department of Molecular Biology and Biophysics, Yale University, New Haven, CT, United States
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Diankristanti PA, Ng IS. Microbial itaconic acid bioproduction towards sustainable development: Insights, challenges, and prospects. BIORESOURCE TECHNOLOGY 2023:129280. [PMID: 37290713 DOI: 10.1016/j.biortech.2023.129280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Microbial biomanufacturing is a promising approach to produce high-value compounds with low-carbon footprint and significant economic benefits. Among twelve "Top Value-Added Chemicals from Biomass", itaconic acid (IA) stands out as a versatile platform chemical with numerous applications. IA is naturally produced by Aspergillus and Ustilago species through a cascade enzymatic reaction between aconitase (EC 4.2.1.3) and cis-aconitic acid decarboxylase (EC 4.1.1.6). Recently, non-native hosts such as Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Yarrowia lipolytica have been genetically engineered to produce IA through the introduction of key enzymes. This review provides an up-to-date summary of the progress made in IA bioproduction, from native to engineered hosts, covers in vivo and in vitro approaches, and highlights the prospects of combination tactics. Current challenges and recent endeavors are also addressed to envision comprehensive strategies for renewable IA production in the future towards sustainable development goals (SDGs).
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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Rothman DL, Behar KL, Petroff OAC, Shulman RG. The early days of ex vivo 1 H, 13 C, and 31 P nuclear magnetic resonance in the laboratory of Dr. Robert G. Shulman from 1975 to 1995. NMR IN BIOMEDICINE 2023; 36:e4879. [PMID: 36424353 DOI: 10.1002/nbm.4879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
This paper provides a brief description of the early use of ex vivo nuclear magnetic resonance (NMR) studies of tissue and tissue extracts performed in the laboratory of Dr. Robert G. Shulman from 1975 through 1995 at Bell Laboratories, then later at Yale University. During that period, ex vivo NMR provided critical information in support of resonance assignments and the quantitation of concentrations for magnetic resonance spectroscopy studies. The period covered saw rapid advances in magnet technology, starting with studies of microorganisms in vertical bore high-resolution NMR studies, then by 1981 studies of small mammals in a horizontal bore magnet, and then studies of humans in 1984. Ex vivo NMR played a critical role in all these studies. A general strategy developed in the lab for using ex vivo NMR to support in vivo studies is presented, as well as illustrative examples.
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Affiliation(s)
- Douglas L Rothman
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Biomedical Engineering, Yale University School of Medicine, New Haven, Connecticut, USA
- Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kevin L Behar
- Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ognen A C Petroff
- Department of Neurology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Robert G Shulman
- Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, Connecticut, USA
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Choueiry F, Barham A, Zhu J. Analyses of lung cancer-derived volatiles in exhaled breath and in vitro models. Exp Biol Med (Maywood) 2022; 247:1179-1190. [PMID: 35410512 PMCID: PMC9335511 DOI: 10.1177/15353702221082634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Lung cancer is one of the leading causes of cancer incidence and cancer-related deaths in the world. Early diagnosis of pulmonary tumors results in improved survival compared to diagnosis with more advanced disease, yet early disease is not reliably indicated by symptoms. Despite of the improved testing and monitoring techniques for lung cancer in the past decades, most diagnostic tests, such as sputum cytology or tissue biopsies, are invasive and risky, rendering them unfeasible for large population screening. The non-invasive analysis of exhaled breath has gained attentions as an innovative screening method to measure chemical alterations within the human volatilome profile as a result of oncogenesis. More importantly, volatile organic compounds (VOCs) have been correlated to the pathophysiology of disease since the source of volatile compounds relies mostly on endogenous metabolic processes that are altered as a result of disease onset. Therefore, studying VOCs emitted from human breath may assist lung cancer diagnosis, treatment monitoring, and other surveillance of this devastating disease. In this mini review, we evaluated recent human studies that have attempted to identify lung cancer-derived volatiles in exhaled breath of patients. We also examined reported volatiles in cell cultures of lung cancer to better understand the origins of cancer-associated VOCs. We highlight the metabolic processes of lung cancer that could be responsible for the endogenous synthesis of these VOCs and pinpoint the protein-encoding genes involved in these pathways. Finally, we highlight the potential value of a breath test in lung cancer and propose prominent areas for future research required for the incorporation of VOCs-based testing into clinical settings.
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Affiliation(s)
- Fouad Choueiry
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210-1132, USA
| | - Addison Barham
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210-1132, USA
| | - Jiangjiang Zhu
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210-1132, USA,James Comprehensive Cancer Center, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA,Jiangjiang Zhu.
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Calhoun S, Kamel B, Bell TA, Kruse CP, Riley R, Singan V, Kunde Y, Gleasner CD, Chovatia M, Sandor L, Daum C, Treen D, Bowen BP, Louie KB, Northen TR, Starkenburg SR, Grigoriev IV. Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Love A, Wagner GP. Co-option of stress mechanisms in the origin of evolutionary novelties. Evolution 2021; 76:394-413. [PMID: 34962651 PMCID: PMC9303342 DOI: 10.1111/evo.14421] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 10/19/2021] [Accepted: 10/24/2021] [Indexed: 11/30/2022]
Abstract
It is widely accepted that stressful conditions can facilitate evolutionary change. The mechanisms elucidated thus far accomplish this with a generic increase in heritable variation that facilitates more rapid adaptive evolution, often via plastic modifications of existing characters. Through scrutiny of different meanings of stress in biological research, and an explicit recognition that stressors must be characterized relative to their effect on capacities for maintaining functional integrity, we distinguish between: (1) previously identified stress‐responsive mechanisms that facilitate evolution by maintaining an adaptive fit with the environment, and (2) the co‐option of stress‐responsive mechanisms that are specific to stressors leading to the origin of novelties via compensation. Unlike standard accounts of gene co‐option that identify component sources of evolutionary change, our model documents the cost‐benefit trade‐offs and thereby explains how one mechanism—an immediate response to acute stress—is transformed evolutionarily into another—routine protection from recurring stressors. We illustrate our argument with examples from cell type origination as well as processes and structures at higher levels of organization. These examples suggest a general principle of evolutionary origination based on the capacity to switch between regulatory states related to reproduction and proliferation versus survival and differentiation.
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Affiliation(s)
- Alan Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN, USA
| | - Günter P Wagner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT-06520.,Yale Systems Biology Institute, West Haven, CT-06516.,Department of Evolutionary Biology, University of Vienna, Austria
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Lee HM, Ren J, Yu MS, Kim H, Kim WY, Shen J, Yoo SM, Eyun SI, Na D. Construction of a tunable promoter library to optimize gene expression in Methylomonas sp. DH-1, a methanotroph, and its application to cadaverine production. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:228. [PMID: 34863247 PMCID: PMC8645107 DOI: 10.1186/s13068-021-02077-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/16/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND As methane is 84 times more potent than carbon dioxide in exacerbating the greenhouse effect, there is an increasing interest in the utilization of methanotrophic bacteria that can convert harmful methane into various value-added compounds. A recently isolated methanotroph, Methylomonas sp. DH-1, is a promising biofactory platform because of its relatively fast growth. However, the lack of genetic engineering tools hampers its wide use in the bioindustry. RESULTS Through three different approaches, we constructed a tunable promoter library comprising 33 promoters that can be used for the metabolic engineering of Methylomonas sp. DH-1. The library had an expression level of 0.24-410% when compared with the strength of the lac promoter. For practical application of the promoter library, we fine-tuned the expressions of cadA and cadB genes, required for cadaverine synthesis and export, respectively. The strain with PrpmB-cadA and PDnaA-cadB produced the highest cadaverine titre (18.12 ± 1.06 mg/L) in Methylomonas sp. DH-1, which was up to 2.8-fold higher than that obtained from a non-optimized strain. In addition, cell growth and lysine (a precursor of cadaverine) production assays suggested that gene expression optimization through transcription tuning can afford a balance between the growth and precursor supply. CONCLUSIONS The tunable promoter library provides standard and tunable components for gene expression, thereby facilitating the use of methanotrophs, specifically Methylomonas sp. DH-1, as a sustainable cell factory.
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Affiliation(s)
- Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Myeong-Sang Yu
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Hyunjoo Kim
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Woo Young Kim
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Junhao Shen
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seung Min Yoo
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, 84 Heukseok-ro Dongjak-gu, Seoul, 06974, Republic of Korea.
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Rothman DL, Shulman RG. Two transition states of the glycogen shunt and two steady states of gene expression support metabolic flexibility and the Warburg effect in cancer. Neoplasia 2021; 23:879-886. [PMID: 34303218 PMCID: PMC8322124 DOI: 10.1016/j.neo.2021.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/08/2021] [Indexed: 11/12/2022] Open
Abstract
Previously we suggested that the early Warburg effect can be explained by the use by cancer cells the glycogen shunt during a rapid increase in glucose concentration. In analogy to the Crabtree effect in yeast, the shunt plays a critical role in maintaining homeostasis of glycolytic intermediate levels during these transitions. We extend this analysis here, and propose that the recently appreciated flexibility of cancer cell glucose and glycogen metabolism involves 4 metabolic states that we recently identified in metabolic control analysis studies of yeast. Under stable conditions of low glucose and normal O2 yeast, and by analogy cancer, cells are in the Respiration State in which through gene expression for oxidizing non glucose substrates. When their environment changes to high glucose with reduced O2 levels, such as occur in tumors, they transition to the Glycolysis State due to gene expression of new glycolytic enzyme isoforms such as PKM2. These isoforms optimize metabolism to sustain the Warburg effect. When the changes in glucose and O2 levels are rapid there may be insufficient time for gene expression to adapt. The metabolic flexibility conferred by 2 states of the glycogen shunt allow the cells to survive these transitions. The model explains experimental observations in cancer such as the function of the glycogen shunt and the frequent expression of PKM2 in cells undergoing the Warburg Effect. A surprising conclusion is that the function of PKM2 is to maintain glycolytic intermediate homeostasis rather than controlling the glycolytic flux. The glycogen shunt may also have an important role in cancer metabolic reprogramming by allowing cancer cells to survive large glucose and oxygen changes during the selection of mutations that lead to the Warburg phenotype
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Affiliation(s)
- Douglas L Rothman
- Departments of Radiology and Biomedical Engineering, Yale University School of Medicine, New Haven CT; Magnetic Resonance Research Center, Yale University School of Medicine, New Haven CT.
| | - Robert G Shulman
- Magnetic Resonance Research Center, Yale University School of Medicine, New Haven CT
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