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Murata Y, Hirayama R, Miura N, Kataoka M. Large-scale preparation of yeast strains expressing condensates derived from a glycolytic enzyme via controlled dissolved oxygen levels under hypoxia. Lett Appl Microbiol 2023; 76:ovad095. [PMID: 37587018 DOI: 10.1093/lambio/ovad095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Under hypoxia, Saccharomyces cerevisiae forms cytoplasmic condensates composed of proteins, including glycolytic enzymes, that are thought to regulate cellular metabolism. However, the hypoxic conditions required for condensate formation remain unclear. In this study, we developed a 300-mL-scale culture method to produce condensate-forming cells by precisely controlling the dissolved oxygen (DO) level in the media. Using enolase as a model, a foci formation rate of more than 50% was achieved at ∼0.1% DO, and the results showed that the DO level affected the foci formation rate. The foci formation rates of the previously reported foci-deficient strains and strains with single amino acid substitutions in the endogenous enolase were examined, and the effect of these amino acid substitutions on glucose consumption and ethanol and glycerol production under hypoxia was evaluated. The results of this study contribute to the investigation of the mechanisms that regulate biomacromolecular condensates under hypoxia.
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Affiliation(s)
- Yuki Murata
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
| | - Reina Hirayama
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
| | - Natsuko Miura
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Japan
| | - Michihiko Kataoka
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai 599-8531, Japan
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai 599-8531, Japan
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Utsumi R, Murata Y, Ito-Harashima S, Akai M, Miura N, Kuroda K, Ueda M, Kataoka M. Foci-forming regions of pyruvate kinase and enolase at the molecular surface incorporate proteins into yeast cytoplasmic metabolic enzymes transiently assembling (META) bodies. PLoS One 2023; 18:e0283002. [PMID: 37053166 PMCID: PMC10101385 DOI: 10.1371/journal.pone.0283002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/28/2023] [Indexed: 04/14/2023] Open
Abstract
Spatial reorganization of metabolic enzymes to form the "metabolic enzymes transiently assembling (META) body" is increasingly recognized as a mechanism contributing to regulation of cellular metabolism in response to environmental changes. A number of META body-forming enzymes, including enolase (Eno2p) and phosphofructokinase, have been shown to contain condensate-forming regions. However, whether all META body-forming enzymes have condensate-forming regions or whether enzymes have multiple condensate-forming regions remains unknown. The condensate-forming regions of META body-forming enzymes have potential utility in the creation of artificial intracellular enzyme assemblies. In the present study, the whole sequence of yeast pyruvate kinase (Cdc19p) was searched for condensate-forming regions. Four peptide fragments comprising 27-42 amino acids were found to form condensates. Together with the fragment previously identified from Eno2p, these peptide regions were collectively termed "META body-forming sequences (METAfos)." METAfos-tagged yeast alcohol dehydrogenase (Adh1p) was found to co-localize with META bodies formed by endogenous Cdc19p under hypoxic conditions. The effect of Adh1p co-localization with META bodies on cell metabolism was further evaluated. Expression of Adh1p fused with a METAfos-tag increased production of ethanol compared to acetic acid, indicating that spatial reorganization of metabolic enzymes affects cell metabolism. These results contribute to understanding of the mechanisms and biological roles of META body formation.
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Affiliation(s)
- Ryotaro Utsumi
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Yuki Murata
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
| | - Sayoko Ito-Harashima
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Japan
| | - Misaki Akai
- School of Applied Life Sciences, College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai, Japan
| | - Natsuko Miura
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Japan
- School of Applied Life Sciences, College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai, Japan
- Research Institute for LAC-SYS (RILACS), Osaka Metropolitan University, Sakai, Japan
| | - Kouichi Kuroda
- Department of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Department of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Michihiko Kataoka
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan
- Department of Applied Biological Chemistry, Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Japan
- School of Applied Life Sciences, College of Life, Environment, and Advanced Sciences, Osaka Prefecture University, Sakai, Japan
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Acedos MG, de la Torre I, Santos VE, García-Ochoa F, García JL, Galán B. Modulating redox metabolism to improve isobutanol production in Shimwellia blattae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:8. [PMID: 33407735 PMCID: PMC7789792 DOI: 10.1186/s13068-020-01862-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 12/17/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Isobutanol is a candidate to replace gasoline from fossil resources. This higher alcohol can be produced from sugars using genetically modified microorganisms. Shimwellia blattae (p424IbPSO) is a robust strain resistant to high concentration of isobutanol that can achieve a high production rate of this alcohol. Nevertheless, this strain, like most strains developed for isobutanol production, has some limitations in its metabolic pathway. Isobutanol production under anaerobic conditions leads to a depletion of NADPH, which is necessary for two enzymes in the metabolic pathway. In this work, two independent approaches have been studied to mitigate the co-substrates imbalance: (i) using a NADH-dependent alcohol dehydrogenase to reduce the NADPH dependence of the pathway and (ii) using a transhydrogenase to increase NADPH level. RESULTS The addition of the NADH-dependent alcohol dehydrogenase from Lactococcus lactis (AdhA) to S. blattae (p424IbPSO) resulted in a 19.3% higher isobutanol production. The recombinant strain S. blattae (p424IbPSO, pIZpntAB) harboring the PntAB transhydrogenase produced 39.0% more isobutanol than the original strain, reaching 5.98 g L-1 of isobutanol. In both strains, we observed a significant decrease in the yields of by-products such as lactic acid or ethanol. CONCLUSIONS The isobutanol biosynthesis pathway in S. blattae (p424IbPSO) uses the endogenous NADPH-dependent alcohol dehydrogenase YqhD to complete the pathway. The addition of NADH-dependent AdhA leads to a reduction in the consumption of NADPH that is a bottleneck of the pathway. The higher consumption of NADH by AdhA reduces the availability of NADH required for the transformation of pyruvate into lactic acid and ethanol. On the other hand, the expression of PntAB from E. coli increases the availability of NADPH for IlvC and YqhD and at the same time reduces the availability of NADH and thus, the production of lactic acid and ethanol. In this work it is shown how the expression of AdhA and PntAB enzymes in Shimwellia blattae increases yield from 11.9% to 14.4% and 16.4%, respectively.
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Affiliation(s)
- Miguel G Acedos
- Chemical and Materials Engineering Department, Chemical Sciences School, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Isabel de la Torre
- Chemical and Materials Engineering Department, Chemical Sciences School, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Victoria E Santos
- Chemical and Materials Engineering Department, Chemical Sciences School, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Félix García-Ochoa
- Chemical and Materials Engineering Department, Chemical Sciences School, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - José L García
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Beatriz Galán
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain.
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Tian J, Zhu L, Wang W, Zhang L, Li Z, Zhao Q, Xing K, Feng Z, Peng X. Genomic Analysis of Microbulbifer sp. Strain A4B-17 and the Characterization of Its Metabolic Pathways for 4-Hydroxybenzoic Acid Synthesis. Front Microbiol 2019; 9:3115. [PMID: 30619190 PMCID: PMC6305291 DOI: 10.3389/fmicb.2018.03115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 12/03/2018] [Indexed: 11/21/2022] Open
Abstract
The marine bacterium Microbulbifer sp. A4B-17 produces secondary metabolites such as 4-hydroxybenzoic acid (4HBA) and esters of 4HBA (parabens). 4HBA is a useful material in the synthesis of the liquid crystal. Parabens are man-made compounds that have been extensively used since the 1920s in the cosmetic, pharmaceutical, and food industries for their effective antimicrobial activity. In this study, we completed the sequencing and annotation of the A4B-17 strain genome and found all genes for glucose utilization and 4HBA biosynthesis. Strain A4B-17 uses the Embden-Meyerhof-Parnas (EMP), hexose monophosphate (HMP), and Entner-Doudoroff (ED) pathways to utilize glucose. Other sugars such as fructose, sucrose, xylose, arabinose, galactose, mannitol, and glycerol supported cell growth and 4HBA synthesis. Reverse transcriptional analysis confirmed that the key genes involved in the glucose metabolism were functional. Paraben concentrations were proportionally increased by adding alcohols to the culture medium, indicating that strain A4B-17 synthesizes the 4HBA and the alcohols separately and an esterification reaction between them is responsible for the paraben synthesis. A gene that codes for a carboxylesterase was proposed to catalyze this reaction. The temperature and NaCl concentration for optimal growth were determined to be 35°C and 22.8 g/L.
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Affiliation(s)
- Jun Tian
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Li Zhu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Wenjun Wang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Liping Zhang
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhi Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Qingyu Zhao
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Ke Xing
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zhaozhong Feng
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xue Peng
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
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Rodriguez A, Wojtusik M, Masca F, Santos VE, Garcia-Ochoa F. Kinetic modeling of 1,3-propanediol production from raw glycerol by Shimwellia blattae : Influence of the initial substrate concentration. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.09.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Matsubara M, Urano N, Yamada S, Narutaki A, Fujii M, Kataoka M. Fermentative production of 1-propanol from d-glucose, l-rhamnose and glycerol using recombinant Escherichia coli. J Biosci Bioeng 2016; 122:421-6. [DOI: 10.1016/j.jbiosc.2016.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 03/10/2016] [Accepted: 03/17/2016] [Indexed: 10/22/2022]
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Spakowicz DJ, Strobel SA. Biosynthesis of hydrocarbons and volatile organic compounds by fungi: bioengineering potential. Appl Microbiol Biotechnol 2015; 99:4943-51. [PMID: 25957494 DOI: 10.1007/s00253-015-6641-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/22/2015] [Accepted: 04/29/2015] [Indexed: 01/05/2023]
Abstract
Recent advances in the biological production of fuels have relied on the optimization of pathways involving genes from diverse organisms. Several recent articles have highlighted the potential to expand the pool of useful genes by looking to filamentous fungi. This review highlights the enzymes and organisms used for the production of a variety of fuel types and commodity chemicals with a focus on the usefulness and promise of those from filamentous fungi.
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Affiliation(s)
- Daniel J Spakowicz
- Department of Molecular Biophysics and Biochemistry, Yale University, 260/266 Whitney Avenue, PO Box 208114, New Haven, CT, 06520-8114, USA
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