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Gaze into the Abyss of Energy Metabolism
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Gaze into the Abyss of Energy Metabolism

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Endocrinology and Metabolism".

Deadline for manuscript submissions: closed (28 February 2024) | Viewed by 6901

Special Issue Editors

Prof. Dr. Takashi Amemiya

E-Mail Website
Guest Editor
Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
Interests: nonlinear dynamics; biological oscillations; cellular metabolism; nonlinear chemical reaction
Dr. Daisuke Watanabe

E-Mail
Guest Editor
Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
Interests: fermentation science; cellular response and adaptation to environmental stimuli; microbial ecosystem

Special Issue Information

Dear Colleagues, 

The year 2022 CE is 100th anniversary since Otto Fritz Meyerhof was awarded the Nobel Prize for Physiology or Medicine for 1922. Of Meyerhof’s many achievements, perhaps the most important is lactic acid production and metabolism in muscle and this was the foundation of the Embden-Meyerhof pathway of glycolysis. Here it should also be mentioned that Otto Heinrich Warburg, who was also a Nobel Prize laureate for Physiology or Medicine for 1931 and known as his discovery of the Warburg effect in cancer cells, influenced Meyerhof to be interested in cell physiology. After the pioneering studies of energy metabolism including glycolysis by Meyerhof, Warburg, and the other many outstanding scientists, much remains to be learned about cellular metabolism and its regulation. Currently, energy metabolism is rewiring and reigning as one of the hot topics in many research fields including biology, biochemistry, biophysics, mathematics, and data sciences as well. Progress in the analytical techniques for metabolites and metabolic enzymes has significantly advanced our understanding of the molecular basis of energy metabolism, which paves the way for biotechnology and medicine. We are particularly interested in molecular and cellular studies in energy metabolism in several cell types including, but not limited to, yeast or other microbial cells, and mammalian cells such as cancer cells, pancreatic betha-cells, adipocytes, myocytes, and brain cells; experimental, theoretical, and modelling studies will be considered for this Special issue. We accept article types such as article, brief report, hypothesis, opinion, perspective, protocol, technical note, and review. 

Prof. Dr. Takashi Amemiya
Dr. Daisuke Watanabe
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • glycolysis
  • mitochondrial function
  • lipid metabolism
  • glutaminolysis
  • ketosis
  • cancers
  • metabolic disease
  • fermentation and metabolic engineering

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Published Papers (3 papers)

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10 pages, 1461 KiB  
Article
Spontaneous Attenuation of Alcoholic Fermentation via the Dysfunction of Cyc8p in Saccharomyces cerevisiae
by Daisuke Watanabe, Maika Kumano, Yukiko Sugimoto and Hiroshi Takagi
Int. J. Mol. Sci. 2024, 25(1), 304; https://doi.org/10.3390/ijms25010304 - 25 Dec 2023
Viewed by 1361
Abstract
A cell population characterized by the release of glucose repression and known as [GAR+] emerges spontaneously in the yeast Saccharomyces cerevisiae. This study revealed that the [GAR+] variants exhibit retarded alcoholic fermentation when glucose is the [...] Read more.
A cell population characterized by the release of glucose repression and known as [GAR+] emerges spontaneously in the yeast Saccharomyces cerevisiae. This study revealed that the [GAR+] variants exhibit retarded alcoholic fermentation when glucose is the sole carbon source. To identify the key to the altered glucose response, the gene expression profile of [GAR+] cells was examined. Based on RNA-seq data, the [GAR+] status was linked to impaired function of the Cyc8p–Tup1p complex. Loss of Cyc8p led to a decrease in the initial rate of alcoholic fermentation under glucose-rich conditions via the inactivation of pyruvate decarboxylase, an enzyme unique to alcoholic fermentation. These results suggest that Cyc8p can become inactive to attenuate alcoholic fermentation. These findings may contribute to the elucidation of the mechanism of non-genetic heterogeneity in yeast alcoholic fermentation. Full article
(This article belongs to the Special Issue Gaze into the Abyss of Energy Metabolism)
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14 pages, 1089 KiB  
Article
Improved 2,3-Butanediol Production Rate of Metabolically Engineered Saccharomyces cerevisiae by Deletion of RIM15 and Activation of Pyruvate Consumption Pathway
by Masahiko Sugimura, Taisuke Seike, Nobuyuki Okahashi, Yoshihiro Izumi, Takeshi Bamba, Jun Ishii and Fumio Matsuda
Int. J. Mol. Sci. 2023, 24(22), 16378; https://doi.org/10.3390/ijms242216378 - 15 Nov 2023
Cited by 3 | Viewed by 2152
Abstract
Saccharomyces cerevisiae is a promising host for the bioproduction of higher alcohols, such as 2,3-butanediol (2,3-BDO). Metabolically engineered S. cerevisiae strains that produce 2,3-BDO via glycolysis have been constructed. However, the specific 2,3-BDO production rates of engineered strains must be improved. To identify [...] Read more.
Saccharomyces cerevisiae is a promising host for the bioproduction of higher alcohols, such as 2,3-butanediol (2,3-BDO). Metabolically engineered S. cerevisiae strains that produce 2,3-BDO via glycolysis have been constructed. However, the specific 2,3-BDO production rates of engineered strains must be improved. To identify approaches to improving the 2,3-BDO production rate, we investigated the factors contributing to higher ethanol production rates in certain industrial strains of S. cerevisiae compared to laboratory strains. Sequence analysis of 11 industrial strains revealed the accumulation of many nonsynonymous substitutions in RIM15, a negative regulator of high fermentation capability. Comparative metabolome analysis suggested a positive correlation between the rate of ethanol production and the activity of the pyruvate-consuming pathway. Based on these findings, RIM15 was deleted, and the pyruvate-consuming pathway was activated in YHI030, a metabolically engineered S. cerevisiae strain that produces 2,3-BDO. The titer, specific production rate, and yield of 2,3-BDO in the test tube-scale culture using the YMS106 strain reached 66.4 ± 4.4 mM, 1.17 ± 0.017 mmol (g dry cell weight h)−1, and 0.70 ± 0.03 mol (mol glucose consumed)−1. These values were 2.14-, 2.92-, and 1.81-fold higher than those of the vector control, respectively. These results suggest that bioalcohol production via glycolysis can be enhanced in a metabolically engineered S. cerevisiae strain by deleting RIM15 and activating the pyruvate-consuming pathway. Full article
(This article belongs to the Special Issue Gaze into the Abyss of Energy Metabolism)
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16 pages, 4797 KiB  
Hypothesis
Metabolic Oscillations and Glycolytic Phenotypes of Cancer Cells
by Takashi Amemiya, Kenichi Shibata and Tomohiko Yamaguchi
Int. J. Mol. Sci. 2023, 24(15), 11914; https://doi.org/10.3390/ijms241511914 - 25 Jul 2023
Cited by 8 | Viewed by 2608
Abstract
Cancer cells show several metabolic phenotypes depending on the cancer types and the microenvironments in tumor tissues. The glycolytic phenotype is one of the hallmarks of cancer cells and is considered to be one of the crucial features of malignant cancers. Here, we [...] Read more.
Cancer cells show several metabolic phenotypes depending on the cancer types and the microenvironments in tumor tissues. The glycolytic phenotype is one of the hallmarks of cancer cells and is considered to be one of the crucial features of malignant cancers. Here, we show glycolytic oscillations in the concentrations of metabolites in the glycolytic pathway in two types of cancer cells, HeLa cervical cancer cells and DU145 prostate cancer cells, and in two types of cellular morphologies, spheroids and monolayers. Autofluorescence from nicotinamide adenine dinucleotide (NADH) in cells was used for monitoring the glycolytic oscillations at the single-cell level. The frequencies of NADH oscillations were different among the cellular types and morphologies, indicating that more glycolytic cancer cells tended to exhibit oscillations with higher frequencies than less glycolytic cells. A mathematical model for glycolytic oscillations in cancer cells reproduced the experimental results quantitatively, confirming that the higher frequencies of oscillations were due to the higher activities of glycolytic enzymes. Thus, glycolytic oscillations are expected as a medical indicator to evaluate the malignancy of cancer cells with glycolytic phenotypes. Full article
(This article belongs to the Special Issue Gaze into the Abyss of Energy Metabolism)
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