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Kim HJ, Cho SY, Jung SJ, Cho YJ, Roe JH, Kim KD. Non-Mitochondrial Aconitase-2 Mediates the Transcription of Nuclear-Encoded Electron Transport Chain Genes in Fission Yeast. J Microbiol 2024:10.1007/s12275-024-00147-8. [PMID: 38916790 DOI: 10.1007/s12275-024-00147-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 06/26/2024]
Abstract
Aconitase-2 (Aco2) is present in the mitochondria, cytosol, and nucleus of fission yeast. To explore its function beyond the well-known role in the mitochondrial tricarboxylic acid (TCA) cycle, we conducted genome-wide profiling using the aco2ΔNLS mutant, which lacks a nuclear localization signal (NLS). The RNA sequencing (RNA-seq) data showed a general downregulation of electron transport chain (ETC) genes in the aco2ΔNLS mutant, except for those in the complex II, leading to a growth defect in respiratory-prone media. Complementation analysis with non-catalytic Aco2 [aco2ΔNLS + aco2(3CS)], where three cysteines were substituted with serine, restored normal growth and typical ETC gene expression. This suggests that Aco2's catalytic activity is not essential for its role in ETC gene regulation. Our mRNA decay assay indicated that the decrease in ETC gene expression was due to transcriptional regulation rather than changes in mRNA stability. Additionally, we investigated the Php complex's role in ETC gene regulation and found that ETC genes, except those within complex II, were downregulated in php3Δ and php5Δ strains, similar to the aco2ΔNLS mutant. These findings highlight a novel role for nuclear aconitase in ETC gene regulation and suggest a potential connection between the Php complex and Aco2.
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Affiliation(s)
- Ho-Jung Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Soo-Yeon Cho
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Soo-Jin Jung
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Center for RNA Research, Institute for Basic Science, Seoul, 08826, Republic of Korea
| | - Yong-Jun Cho
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jung-Hye Roe
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyoung-Dong Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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2
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Wang Y, Ruan L, Zhu J, Zhang X, Chang ACC, Tomaszewski A, Li R. Metabolic regulation of misfolded protein import into mitochondria. eLife 2024; 12:RP87518. [PMID: 38900507 PMCID: PMC11189628 DOI: 10.7554/elife.87518] [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] [Indexed: 06/21/2024] Open
Abstract
Mitochondria are the cellular energy hub and central target of metabolic regulation. Mitochondria also facilitate proteostasis through pathways such as the 'mitochondria as guardian in cytosol' (MAGIC) whereby cytosolic misfolded proteins (MPs) are imported into and degraded inside mitochondria. In this study, a genome-wide screen in Saccharomyces cerevisiae uncovered that Snf1, the yeast AMP-activated protein kinase (AMPK), inhibits the import of MPs into mitochondria while promoting mitochondrial biogenesis under glucose starvation. We show that this inhibition requires a downstream transcription factor regulating mitochondrial gene expression and is likely to be conferred through substrate competition and mitochondrial import channel selectivity. We further show that Snf1/AMPK activation protects mitochondrial fitness in yeast and human cells under stress induced by MPs such as those associated with neurodegenerative diseases.
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Affiliation(s)
- Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of SingaporeSingaporeSingapore
| | - Xi Zhang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Alexander Chih-Chieh Chang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Alexis Tomaszewski
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
- Mechanobiology Institute and Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins UniversityBaltimoreUnited States
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3
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Alfatah M, Lim JJJ, Zhang Y, Naaz A, Cheng TYN, Yogasundaram S, Faidzinn NA, Lin JJ, Eisenhaber B, Eisenhaber F. Uncharacterized yeast gene YBR238C, an effector of TORC1 signaling in a mitochondrial feedback loop, accelerates cellular aging via HAP4- and RMD9-dependent mechanisms. eLife 2024; 12:RP92178. [PMID: 38713053 PMCID: PMC11076046 DOI: 10.7554/elife.92178] [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] [Indexed: 05/08/2024] Open
Abstract
Uncovering the regulators of cellular aging will unravel the complexity of aging biology and identify potential therapeutic interventions to delay the onset and progress of chronic, aging-related diseases. In this work, we systematically compared genesets involved in regulating the lifespan of Saccharomyces cerevisiae (a powerful model organism to study the cellular aging of humans) and those with expression changes under rapamycin treatment. Among the functionally uncharacterized genes in the overlap set, YBR238C stood out as the only one downregulated by rapamycin and with an increased chronological and replicative lifespan upon deletion. We show that YBR238C and its paralog RMD9 oppositely affect mitochondria and aging. YBR238C deletion increases the cellular lifespan by enhancing mitochondrial function. Its overexpression accelerates cellular aging via mitochondrial dysfunction. We find that the phenotypic effect of YBR238C is largely explained by HAP4- and RMD9-dependent mechanisms. Furthermore, we find that genetic- or chemical-based induction of mitochondrial dysfunction increases TORC1 (Target of Rapamycin Complex 1) activity that, subsequently, accelerates cellular aging. Notably, TORC1 inhibition by rapamycin (or deletion of YBR238C) improves the shortened lifespan under these mitochondrial dysfunction conditions in yeast and human cells. The growth of mutant cells (a proxy of TORC1 activity) with enhanced mitochondrial function is sensitive to rapamycin whereas the growth of defective mitochondrial mutants is largely resistant to rapamycin compared to wild type. Our findings demonstrate a feedback loop between TORC1 and mitochondria (the TORC1-MItochondria-TORC1 (TOMITO) signaling process) that regulates cellular aging processes. Hereby, YBR238C is an effector of TORC1 modulating mitochondrial function.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jolyn Jia Jia Lim
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Yizhong Zhang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Arshia Naaz
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Trishia Yi Ning Cheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Sonia Yogasundaram
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Nashrul Afiq Faidzinn
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jovian Jing Lin
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
- LASA – Lausitz Advanced Scientific Applications gGmbHWeißwasserGermany
- School of Biological Sciences (SBS), Nanyang Technological University (NTU)SingaporeSingapore
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4
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Martinez KP, Gasmi N, Jeronimo C, Klimova N, Robert F, Turcotte B. Yeast zinc cluster transcription factors involved in the switch from fermentation to respiration show interdependency for DNA binding revealing a novel type of DNA recognition. Nucleic Acids Res 2024; 52:2242-2259. [PMID: 38109318 PMCID: PMC10954478 DOI: 10.1093/nar/gkad1185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023] Open
Abstract
In budding yeast, fermentation is the most important pathway for energy production. Under low-glucose conditions, ethanol is used for synthesis of this sugar requiring a shift to respiration. This process is controlled by the transcriptional regulators Cat8, Sip4, Rds2 and Ert1. We characterized Gsm1 (glucose starvation modulator 1), a paralog of Rds2 and Ert1. Genome-wide analysis showed that Gsm1 has a DNA binding profile highly similar to Rds2. Binding of Gsm1 and Rds2 is interdependent at the gluconeogenic gene FBP1. However, Rds2 is required for Gsm1 to bind at other promoters but not the reverse. Gsm1 and Rds2 also bind to DNA independently of each other. Western blot analysis revealed that Rds2 controls expression of Gsm1. In addition, we showed that the DNA binding domains of Gsm1 and Rds2 bind cooperatively in vitro to the FBP1 promoter. In contrast, at the HAP4 gene, Ert1 cooperates with Rds2 for DNA binding. Mutational analysis suggests that Gsm1/Rds2 and Ert1/Rds2 bind to short common DNA stretches, revealing a novel mode of binding for this class of factors. Two-point mutations in a HAP4 site convert it to a Gsm1 binding site. Thus, Rds2 controls binding of Gsm1 at many promoters by two different mechanisms: regulation of Gsm1 levels and increased DNA binding by formation of heterodimers.
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Affiliation(s)
- Karla Páez Martinez
- Department of Medicine, McGill University Health Centre, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| | - Najla Gasmi
- Department of Biochemistry, McGill University, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Natalia Klimova
- Department of Medicine, McGill University Health Centre, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - Bernard Turcotte
- Department of Medicine, McGill University Health Centre, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
- Department of Biochemistry, McGill University, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
- Department of Microbiology and Immunology, McGill University, 1001 Boul. Décarie, Room E02.7212, Montréal, QC H4A 3J1, Canada
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5
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Niphadkar S, Karinje L, Laxman S. The PP2A-like phosphatase Ppg1 mediates assembly of the Far complex to balance gluconeogenic outputs and enables adaptation to glucose depletion. PLoS Genet 2024; 20:e1011202. [PMID: 38452140 PMCID: PMC10950219 DOI: 10.1371/journal.pgen.1011202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/19/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
To sustain growth in changing nutrient conditions, cells reorganize outputs of metabolic networks and appropriately reallocate resources. Signaling by reversible protein phosphorylation can control such metabolic adaptations. In contrast to kinases, the functions of phosphatases that enable metabolic adaptation as glucose depletes are poorly studied. Using a Saccharomyces cerevisiae deletion screen, we identified the PP2A-like phosphatase Ppg1 as required for appropriate carbon allocations towards gluconeogenic outputs-trehalose, glycogen, UDP-glucose, UDP-GlcNAc-after glucose depletion. This Ppg1 function is mediated via regulation of the assembly of the Far complex-a multi-subunit complex that tethers to the ER and mitochondrial outer membranes forming localized signaling hubs. The Far complex assembly is Ppg1 catalytic activity-dependent. Ppg1 regulates the phosphorylation status of multiple ser/thr residues on Far11 to enable the proper assembly of the Far complex. The assembled Far complex is required to maintain gluconeogenic outputs after glucose depletion. Glucose in turn regulates Far complex amounts. This Ppg1-mediated Far complex assembly, and Ppg1-Far complex dependent control of gluconeogenic outputs enables adaptive growth under glucose depletion. Our study illustrates how protein dephosphorylation is required for the assembly of a multi-protein scaffold present in localized cytosolic pools, to thereby alter gluconeogenic flux and enable cells to metabolically adapt to nutrient fluctuations.
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Affiliation(s)
- Shreyas Niphadkar
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lavanya Karinje
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (DBT-inStem) Bangalore, India
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6
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Assalve G, Lunetti P, Zara V, Ferramosca A. Ctp1 and Yhm2: Two Mitochondrial Citrate Transporters to Support Metabolic Flexibility of Saccharomyces cerevisiae. Int J Mol Sci 2024; 25:1870. [PMID: 38339147 PMCID: PMC10855732 DOI: 10.3390/ijms25031870] [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: 12/16/2023] [Revised: 01/28/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Differently from higher eukaryotic cells, in the yeast Saccharomyces cerevisiae there are two mitochondrial carrier proteins involved in the transport of citrate: Ctp1 and Yhm2. Very little is known about the physiological role of these proteins. Wild-type and mutant yeast strains deleted in CTP1 and YHM2 were grown in media supplemented with a fermentable (glucose) or a nonfermentable (ethanol) carbon source. To assess changes in Ctp1 and Yhm2 mRNA expression levels, real-time PCR was performed after total RNA extraction. In the wild-type strain, the metabolic switch from the exponential to the stationary phase is associated with an increase in the expression level of the two citrate transporters. In addition, the results obtained in the mutant strains suggest that the presence of a single citrate transporter can partially compensate for the absence of the other. Ctp1 and Yhm2 differently contribute to fermentative and respiratory metabolism. Moreover, the two mitochondrial carriers represent a link between the Krebs cycle and the glyoxylate cycle, which play a key role in the metabolic adaptation strategies of S. cerevisiae.
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Affiliation(s)
- Graziana Assalve
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Paola Lunetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Vincenzo Zara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
| | - Alessandra Ferramosca
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (G.A.); (P.L.); (V.Z.)
- Department of Experimental Medicine, University of Salento, 73100 Lecce, Italy
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7
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Wang JJT, Steenwyk JL, Brem RB. Natural trait variation across Saccharomycotina species. FEMS Yeast Res 2024; 24:foae002. [PMID: 38218591 PMCID: PMC10833146 DOI: 10.1093/femsyr/foae002] [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: 06/27/2023] [Revised: 10/13/2023] [Accepted: 01/12/2024] [Indexed: 01/15/2024] Open
Abstract
Among molecular biologists, the group of fungi called Saccharomycotina is famous for its yeasts. These yeasts in turn are famous for what they have in common-genetic, biochemical, and cell-biological characteristics that serve as models for plants and animals. But behind the apparent homogeneity of Saccharomycotina species lie a wealth of differences. In this review, we discuss traits that vary across the Saccharomycotina subphylum. We describe cases of bright pigmentation; a zoo of cell shapes; metabolic specialties; and species with unique rules of gene regulation. We discuss the genetics of this diversity and why it matters, including insights into basic evolutionary principles with relevance across Eukarya.
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Affiliation(s)
- Johnson J -T Wang
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob L Steenwyk
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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8
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Watanabe D, Kumano M, Sugimoto Y, Takagi H. Spontaneous Attenuation of Alcoholic Fermentation via the Dysfunction of Cyc8p in Saccharomyces cerevisiae. Int J Mol Sci 2023; 25:304. [PMID: 38203474 PMCID: PMC10778621 DOI: 10.3390/ijms25010304] [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: 12/03/2023] [Revised: 12/19/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
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 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.
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Affiliation(s)
- Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Maika Kumano
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan (H.T.)
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayamacho, Ikoma 630-0192, Nara, Japan
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9
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Wang Z, Chen J, Ding J, Han J, Shi L. GlMPC activated by GCN4 regulates secondary metabolism under nitrogen limitation conditions in Ganoderma lucidum. mBio 2023; 14:e0135623. [PMID: 37732773 PMCID: PMC10653791 DOI: 10.1128/mbio.01356-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/26/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Mitochondrial pyruvate carrier (MPC) is a pyruvate transporter that plays a crucial role in regulating the carbon metabolic flow and is considered an essential mechanism for microorganisms to adapt to environmental changes. However, it remains unclear how MPC responds to environmental stress in organisms. General control non-derepressible 4 (GCN4), a key regulator of nitrogen metabolism, plays a pivotal role in the growth and development of fungi. In this study, we report that GCN4 can directly bind to the promoter region and activate the expression of GlMPC, thereby regulating the tricarboxylic acid cycle and secondary metabolism under nitrogen limitation conditions in Ganoderma lucidum. These findings provide significant insights into the regulation of carbon and nitrogen metabolism in fungi, highlighting the critical role of GCN4 in coordinating metabolic adaptation to environmental stresses.
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Affiliation(s)
- Zi Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Juhong Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Juan Ding
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jing Han
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
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10
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Wang Y, Ruan L, Zhu J, Zhang X, Chih-Chieh Chang A, Tomaszewski A, Li R. Metabolic regulation of misfolded protein import into mitochondria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534670. [PMID: 37034811 PMCID: PMC10081186 DOI: 10.1101/2023.03.29.534670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Mitochondria are the cellular energy hub and central target of metabolic regulation. Mitochondria also facilitate proteostasis through pathways such as the 'mitochondria as guardian in cytosol' (MAGIC) whereby cytosolic misfolded proteins (MPs) are imported into and degraded inside mitochondria. In this study, a genome-wide screen in yeast uncovered that Snf1, the yeast AMP-activated protein kinase (AMPK), inhibits the import of MPs into mitochondria while promoting mitochondrial biogenesis under glucose starvation. We show that this inhibition requires a downstream transcription factor regulating mitochondrial gene expression and is likely to be conferred through substrate competition and mitochondrial import channel selectivity. We further show that Snf1/AMPK activation protects mitochondrial fitness in yeast and human cells under stress induced by MPs such as those associated with neurodegenerative diseases.
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Affiliation(s)
- Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine; Baltimore, MD 21287, USA
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
| | - Jin Zhu
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore 117411, Singapore
| | - Xi Zhang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
| | - Alexander Chih-Chieh Chang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Alexis Tomaszewski
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine; Baltimore, MD 21287, USA
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD 21205, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore; Singapore 117411, Singapore
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University; Baltimore, MD 21218, USA
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11
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Horkai D, Hadj-Moussa H, Whale AJ, Houseley J. Dietary change without caloric restriction maintains a youthful profile in ageing yeast. PLoS Biol 2023; 21:e3002245. [PMID: 37643155 PMCID: PMC10464975 DOI: 10.1371/journal.pbio.3002245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 07/12/2023] [Indexed: 08/31/2023] Open
Abstract
Caloric restriction increases lifespan and improves ageing health, but it is unknown whether these outcomes can be separated or achieved through less severe interventions. Here, we show that an unrestricted galactose diet in early life minimises change during replicative ageing in budding yeast, irrespective of diet later in life. Average mother cell division rate is comparable between glucose and galactose diets, and lifespan is shorter on galactose, but markers of senescence and the progressive dysregulation of gene expression observed on glucose are minimal on galactose, showing that these are not intrinsic aspects of replicative ageing but rather associated processes. Respiration on galactose is critical for minimising hallmarks of ageing, and forced respiration during ageing on glucose by overexpression of the mitochondrial biogenesis factor Hap4 also has the same effect though only in a fraction of cells. This fraction maintains Hap4 activity to advanced age with low senescence and a youthful gene expression profile, whereas other cells in the same population lose Hap4 activity, undergo dramatic dysregulation of gene expression and accumulate fragments of chromosome XII (ChrXIIr), which are tightly associated with senescence. Our findings support the existence of two separable ageing trajectories in yeast. We propose that a complete shift to the healthy ageing mode can be achieved in wild-type cells through dietary change in early life without caloric restriction.
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Affiliation(s)
- Dorottya Horkai
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | | | - Alex J. Whale
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
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12
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Robainas-Del-Pino Y, Viader-Salvadó JM, Herrera-Estala AL, Guerrero-Olazarán M. Functional characterization of the Komagataella phaffii 1033 gene promoter and transcriptional terminator. World J Microbiol Biotechnol 2023; 39:246. [PMID: 37420160 DOI: 10.1007/s11274-023-03682-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
The methylotrophic yeast Komagataella phaffii (syn. Pichia pastoris) is a widely used host for extracellularly producing heterologous proteins via an expression cassette integrated into the yeast genome. A strong promoter in the expression cassette is not always the most favorable choice for heterologous protein production, especially if the correct folding of the protein and/or post-translational processing is the limiting step. The transcriptional terminator is another regulatory element in the expression cassette that can modify the expression levels of the heterologous gene. In this work, we identified and functionally characterized the promoter (P1033) and transcriptional terminator (T1033) of a constitutive gene (i.e., the 1033 gene) with a weak non-methanol-dependent transcriptional activity. We constructed two K. phaffii strains with two combinations of the regulatory DNA elements from the 1033 and AOX1 genes (i.e., P1033-TAOX1 and P1033-T1033 pairs) and evaluated the impact of the regulatory element combinations on the transcript levels of the heterologous gene and endogenous 1033 and GAPDH genes in cells grown in glucose or glycerol, and on the extracellular product/biomass yield. The results indicate that the P1033 has a 2-3% transcriptional activity of the GAP promoter and it is tunable by cell growth and the carbon source. The combinations of the regulatory elements rendered different transcriptional activity of the heterologous and endogenous genes that were dependent on the carbon source. The promoter-terminator pair and the carbon source affected the heterologous gene translation and/or protein secretion pathway. Moreover, low heterologous gene-transcript levels along with glycerol cultures increased translation and/or protein secretion.
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Affiliation(s)
- Yanelis Robainas-Del-Pino
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - José María Viader-Salvadó
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
| | - Ana Lucía Herrera-Estala
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico
| | - Martha Guerrero-Olazarán
- Facultad de Ciencias Biológicas, Instituto de Biotecnología, Universidad Autónoma de Nuevo León UANL, Av. Universidad S/N Col. Ciudad Universitaria, 66455, San Nicolás de los Garza, Nuevo León, Mexico.
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13
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Xu Y, Li Z. Alleviating glucose repression and enhancing respiratory capacity to increase itaconic acid production. Synth Syst Biotechnol 2022; 8:129-140. [PMID: 36632527 PMCID: PMC9827039 DOI: 10.1016/j.synbio.2022.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 12/26/2022] Open
Abstract
The Crabtree effect products ethanol and acetic acid can be used for itaconic acid (IA) production in Saccharomyces cerevisiae. However, both the IA synthesis and oxidative phosphorylation pathways were hampered by glucose repression when glucose was used as the substrate. This study aimed to improve IA titer by increasing gene expressions related to glucose derepression without impairing yeast growth on glucose. Engineering the acetyl-CoA synthesis pathway increased the titer of IA to 257 mg/L in a urea-based medium. Instead of entire pathway overexpression, we found that some signaling pathways regulating glucose repression were effective targets to improve IA production and respiratory capacity. As a consequence of the reduced inhibition, IA titer was further increased by knocking out a negative regulator of the mitochondrial retrograde signaling MKS1. SNF1/MIG1 signaling was disturbed by deleting the hexokinase HXK2 or an endoplasmic reticulum membrane protein GSF2. The shaking results showed that XYY286 (BY4741, HO::cadA, Y::Dz.ada, 208a::Mt.acs, Δhxk2, pRS415-cadA, pRS423-aac2) accumulated 535 mg/L IA in 168 h in the YSCGLU medium. qRT-PCR results verified that deletion of MKS1 or HXK2 upregulated the gene expressions of the IA synthesis and respiratory pathways during the growth on glucose.
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Affiliation(s)
- Yaying Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China,Corresponding author. State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
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14
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Liu J, Huang T, Hong W, Peng F, Lu Z, Peng G, Fu X, Liu G, Wang Z, Peng Q, Gong X, Zhou L, Li L, Li B, Xu Z, Lan H. A comprehensive study on ultrasonic deactivation of opportunistic pathogen Saccharomyces cerevisiae in food processing: From transcriptome to phenotype. Lebensm Wiss Technol 2022; 170:114069. [DOI: 10.1016/j.lwt.2022.114069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Junyan Liu
- College of Light Industry and Food Sciences, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, Ministry of Agriculture, Guangzhou, 510225, China
| | - Tengyi Huang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Wei Hong
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fang Peng
- Department of Critical Care Medicine, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zerong Lu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, 510640, China
| | - Gongyong Peng
- State Key Laboratory of Respiratory Diseases, National Clinical Research Center for Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xin Fu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Gongliang Liu
- College of Light Industry and Food Sciences, Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, Academy of Contemporary Agricultural Engineering Innovations, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, Ministry of Agriculture, Guangzhou, 510225, China
| | - Zhi Wang
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Qingmei Peng
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Xiangjun Gong
- School of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Lizhen Zhou
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Lin Li
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, 510640, China
- Research Institute for Food Nutrition and Human Health, Guangzhou, China
| | - Bing Li
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, 510640, China
- Research Institute for Food Nutrition and Human Health, Guangzhou, China
| | - Zhenbo Xu
- Department of Laboratory Medicine, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou, 510640, China
| | - Haifeng Lan
- Department of Orthopaedic Surgery, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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15
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Gupta A, Rangarajan PN. Coordinate regulation of methanol utilization pathway genes of Komagataella phaffii by transcription factors and chromatin modifiers. Front Microbiol 2022; 13:991192. [PMID: 36147846 PMCID: PMC9485576 DOI: 10.3389/fmicb.2022.991192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/10/2022] [Indexed: 11/17/2022] Open
Abstract
The methylotrophic yeast Komagataella phaffii (a.k.a. Pichia pastoris) harbors a methanol utilization (MUT) pathway, enabling it to utilize methanol as the sole source of carbon. The nexus between transcription factors such as Mxr1p and Trm1p and chromatin-modifying enzymes in the regulation of genes of MUT pathway has not been well studied in K. phaffii. Using transcriptomics, we demonstrate that Gcn5, a histone acetyltransferase, and Gal83, one of the beta subunits of nuclear-localized SNF1 (sucrose non-fermenting 1) kinase complex are essential for the transcriptional regulation by the zinc finger transcription factors Mxr1p and Trm1p. We conclude that interactions among Gcn5, Snf1, Mxr1p, and Trm1p play a critical role in the transcriptional regulation of genes of MUT pathway of K. phaffii.
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16
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Waite KA, Roelofs J. Proteasome granule formation is regulated through mitochondrial respiration and kinase signaling. J Cell Sci 2022; 135:jcs259778. [PMID: 35975718 PMCID: PMC9482347 DOI: 10.1242/jcs.259778] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, proteasomes are enriched in cell nuclei, in which they execute important cellular functions. Nutrient stress can change this localization, indicating that proteasomes respond to the metabolic state of the cell. However, the signals that connect these processes remain poorly understood. Carbon starvation triggers a reversible translocation of proteasomes to cytosolic condensates known as proteasome storage granules. Surprisingly, we observed strongly reduced levels of proteasome granules when cells had active cellular respiration prior to starvation. This suggests that the mitochondrial activity of cells is a determining factor in the response of proteasomes to carbon starvation. Consistent with this, upon inhibition of mitochondrial function, we observed that proteasomes relocalize to granules. These links between proteasomes and metabolism involve specific signaling pathways, as we identified a mitogen-activated protein kinase (MAPK) cascade that is critical to the formation of proteasome granules after respiratory growth but not following glycolytic growth. Furthermore, the yeast homolog of AMP kinase, Snf1, is important for proteasome granule formation induced by mitochondrial inhibitors, but it is dispensable for granule formation following carbon starvation. We propose a model in which mitochondrial activity promotes nuclear localization of the proteasome. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, 3901 Rainbow Blvd., HLSIC 1077, Kansas City, KS 66160-7421, USA
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17
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Chen H, Chai X, Wang Y, Liu J, Zhou G, Wei P, Song Y, Ma L. The multiple effects of REG1 deletion and SNF1 overexpression improved the production of S-adenosyl-L-methionine in Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:174. [PMID: 36030199 PMCID: PMC9419380 DOI: 10.1186/s12934-022-01900-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 08/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Saccharomyces cerevisiae is often used as a cell factory for the production of S-adenosyl-L-methionine (SAM) for diverse pharmaceutical applications. However, SAM production by S. cerevisiae is negatively influenced by glucose repression, which is regulated by a serine/threonine kinase SNF1 complex. Here, a strategy of alleviating glucose repression by deleting REG1 (encodes the regulatory subunit of protein phosphatase 1) and overexpressing SNF1 (encodes the catalytic subunit of the SNF1 complex) was applied to improve SAM production in S. cerevisiae. SAM production, growth conditions, glucose consumption, ethanol accumulation, lifespan, glycolysis and amino acid metabolism were analyzed in the mutant strains. RESULTS The results showed that the multiple effects of REG1 deletion and/or SNF1 overexpression exhibited a great potential for improving the SAM production in yeast. Enhanced the expression levels of genes involved in glucose transport and glycolysis, which improved the glucose utilization and then elevated the levels of glycolytic intermediates. The expression levels of ACS1 (encoding acetyl-CoA synthase I) and ALD6 (encoding aldehyde dehydrogenase), and the activity of alcohol dehydrogenase II (ADH2) were enhanced especially in the presence of excessive glucose levels, which probably promoted the conversion of ethanol in fermentation broth into acetyl-CoA. The gene expressions involved in sulfur-containing amino acids were also enhanced for the precursor amino acid biosynthesis. In addition, the lifespan of yeast was extended by REG1 deletion and/or SNF1 overexpression. As expected, the final SAM yield of the mutant YREG1ΔPSNF1 reached 8.28 g/L in a 10-L fermenter, which was 51.6% higher than the yield of the parent strain S. cerevisiae CGMCC 2842. CONCLUSION This study showed that the multiple effects of REG1 deletion and SNF1 overexpression improved SAM production in S. cerevisiae, providing new insight into the application of the SNF1 complex to abolish glucose repression and redirect carbon flux to nonethanol products in S. cerevisiae.
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Affiliation(s)
- Hailong Chen
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Xiaoqin Chai
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Yan Wang
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Jing Liu
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Guohai Zhou
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Pinghe Wei
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China
| | - Yuhe Song
- Jiangsu Key Laboratory of Chiral Pharmaceuticals Biosynthesis, College of Pharmacy and Chemistry & Chemical Engineering, Taizhou University, 93 Ji Chuan Road, 225300, Taizhou, Jiangsu, People's Republic of China.
| | - Lingman Ma
- School of Life Science and Technology, China Pharmaceutical University, 211198, Nanjing, Jiangsu, People's Republic of China.
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18
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Morata A, Arroyo T, Bañuelos MA, Blanco P, Briones A, Cantoral JM, Castrillo D, Cordero-Bueso G, Del Fresno JM, Escott C, Escribano-Viana R, Fernández-González M, Ferrer S, García M, González C, Gutiérrez AR, Loira I, Malfeito-Ferreira M, Martínez A, Pardo I, Ramírez M, Ruiz-Muñoz M, Santamaría P, Suárez-Lepe JA, Vilela A, Capozzi V. Wine yeast selection in the Iberian Peninsula: Saccharomyces and non- Saccharomyces as drivers of innovation in Spanish and Portuguese wine industries. Crit Rev Food Sci Nutr 2022; 63:10899-10927. [PMID: 35687346 DOI: 10.1080/10408398.2022.2083574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Yeast selection for the wine industry in Spain started in 1950 for the understanding of the microbial ecology, and for the selection of optimal strains to improve the performance of alcoholic fermentation and the overall wine quality. This process has been strongly developed over the last 30 years, firstly on Saccharomyces cerevisiae, and, lately, with intense activity on non-Saccharomyces. Several thousand yeast strains have been isolated, identified and tested to select those with better performance and/or specific technological properties. The present review proposes a global survey of this massive ex-situ preservation of eukaryotic microorganisms, a reservoir of biotechnological solutions for the wine sector, overviewing relevant screenings that led to the selection of strains from 12 genera and 22 species of oenological significance. In the first part, the attention goes to the selection programmes related to relevant wine-producing areas (i.e. Douro, Extremadura, Galicia, La Mancha and Uclés, Ribera del Duero, Rioja, Sherry area, and Valencia). In the second part, the focus shifted on specific non-Saccharomyces genera/species selected from different Spanish and Portuguese regions, exploited to enhance particular attributes of the wines. A fil rouge of the dissertation is the design of tailored biotechnological solutions for wines typical of given geographic areas.
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Affiliation(s)
- A Morata
- EnotecUPM, ETSIAAB, Universidad Politécnica de Madrid, Madrid, Spain
| | - T Arroyo
- Departamento de Investigación Agroalimentaria, IMIDRA, Finca El Encín, Madrid, Spain
| | - M A Bañuelos
- EnotecUPM, ETSIAAB, Universidad Politécnica de Madrid, Madrid, Spain
| | - P Blanco
- Estación de Viticultura e Enoloxía de Galicia (EVEGA-AGACAL), Leiro, Ourense, Spain
| | - A Briones
- Tecnología de alimentos, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - J M Cantoral
- Laboratorio de Microbiología. Dept. de Biomedicina, Biotecnología y Salud Pública. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, Cádiz, Spain
| | - D Castrillo
- Estación de Viticultura e Enoloxía de Galicia (EVEGA-AGACAL), Leiro, Ourense, Spain
| | - G Cordero-Bueso
- Laboratorio de Microbiología. Dept. de Biomedicina, Biotecnología y Salud Pública. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, Cádiz, Spain
| | - J M Del Fresno
- EnotecUPM, ETSIAAB, Universidad Politécnica de Madrid, Madrid, Spain
| | - C Escott
- EnotecUPM, ETSIAAB, Universidad Politécnica de Madrid, Madrid, Spain
| | - R Escribano-Viana
- Finca La Grajera, Instituto de Ciencias de la Vid y el Vino (Universidad de La Rioja, Gobierno de La Rioja, CSIC), Logroño, Spain
| | - M Fernández-González
- Tecnología de alimentos, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Ciudad Real, Spain
| | - S Ferrer
- ENOLAB, Institut de Biotecnologia i Biomedicina (BioTecMed), Universitat de València, Valencia, Spain
| | - M García
- Departamento de Investigación Agroalimentaria, IMIDRA, Finca El Encín, Madrid, Spain
| | - C González
- EnotecUPM, ETSIAAB, Universidad Politécnica de Madrid, Madrid, Spain
| | - A R Gutiérrez
- Finca La Grajera, Instituto de Ciencias de la Vid y el Vino (Universidad de La Rioja, Gobierno de La Rioja, CSIC), Logroño, Spain
| | - I Loira
- EnotecUPM, ETSIAAB, Universidad Politécnica de Madrid, Madrid, Spain
| | - M Malfeito-Ferreira
- Departamento Recursos Naturais Ambiente e Território (DRAT), Linking Landscape Environment Agriculture and Food Research Centre (LEAF), Instituto Superior de Agronomía, Tapada da Ajuda, Lisboa, Portugal
| | - A Martínez
- Departamento de Ciencias Biomédicas, Facultad de Ciencias (Edificio Antiguo Rectorado), Universidad de Extremadura, Badajoz, Spain
| | - I Pardo
- ENOLAB, Institut de Biotecnologia i Biomedicina (BioTecMed), Universitat de València, Valencia, Spain
| | - M Ramírez
- Departamento de Ciencias Biomédicas, Facultad de Ciencias (Edificio Antiguo Rectorado), Universidad de Extremadura, Badajoz, Spain
| | - M Ruiz-Muñoz
- Laboratorio de Microbiología. Dept. de Biomedicina, Biotecnología y Salud Pública. Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Puerto Real, Cádiz, Spain
| | - P Santamaría
- Finca La Grajera, Instituto de Ciencias de la Vid y el Vino (Universidad de La Rioja, Gobierno de La Rioja, CSIC), Logroño, Spain
| | - J A Suárez-Lepe
- EnotecUPM, ETSIAAB, Universidad Politécnica de Madrid, Madrid, Spain
| | - A Vilela
- CQ-VR, Chemistry Research Centre, School of Life and Environmental Sciences (ECVA), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - V Capozzi
- National Research Council (CNR) of Italy, c/o CS-DAT, Institute of Sciences of Food Production, Foggia, Italy
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Laidlaw KME, Paine KM, Bisinski DD, Calder G, Hogg K, Ahmed S, James S, O’Toole PJ, MacDonald C. Endosomal cargo recycling mediated by Gpa1 and phosphatidylinositol 3-kinase is inhibited by glucose starvation. Mol Biol Cell 2022; 33:ar31. [PMID: 35080991 PMCID: PMC9250360 DOI: 10.1091/mbc.e21-04-0163] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Cell surface protein trafficking is regulated in response to nutrient availability, with multiple pathways directing surface membrane proteins to the lysosome for degradation in response to suboptimal extracellular nutrients. Internalized protein and lipid cargoes recycle back to the surface efficiently in glucose-replete conditions, but this trafficking is attenuated following glucose starvation. We find that cells with either reduced or hyperactive phosphatidylinositol 3-kinase (PI3K) activity are defective for endosome to surface recycling. Furthermore, we find that the yeast Gα subunit Gpa1, an endosomal PI3K effector, is required for surface recycling of cargoes. Following glucose starvation, mRNA and protein levels of a distinct Gα subunit Gpa2 are elevated following nuclear translocation of Mig1, which inhibits recycling of various cargoes. As Gpa1 and Gpa2 interact at the surface where Gpa2 concentrates during glucose starvation, we propose that this disrupts PI3K activity required for recycling, potentially diverting Gpa1 to the surface and interfering with its endosomal role in recycling. In support of this model, glucose starvation and overexpression of Gpa2 alter PI3K endosomal phosphoinositide production. Glucose deprivation therefore triggers a survival mechanism to increase retention of surface cargoes in endosomes and promote their lysosomal degradation.
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Affiliation(s)
| | | | | | - Grant Calder
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Karen Hogg
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Sophia Ahmed
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Sally James
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Peter J. O’Toole
- Bioscience Technology Facility, Department of Biology, University of York, YO10 5DD York, UK
| | - Chris MacDonald
- York Biomedical Research Institute and Department of Biology and,*Address correspondence to: Chris MacDonald ()
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20
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Liu Q, Chang CE, Wooldredge AC, Fong B, Kennedy BK, Zhou C. Tom70-based transcriptional regulation of mitochondrial biogenesis and aging. eLife 2022; 11:e75658. [PMID: 35234609 PMCID: PMC8926401 DOI: 10.7554/elife.75658] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial biogenesis has two major steps: the transcriptional activation of nuclear genome-encoded mitochondrial proteins and the import of nascent mitochondrial proteins that are synthesized in the cytosol. These nascent mitochondrial proteins are aggregation-prone and can cause cytosolic proteostasis stress. The transcription factor-dependent transcriptional regulations and the TOM-TIM complex-dependent import of nascent mitochondrial proteins have been extensively studied. Yet, little is known regarding how these two steps of mitochondrial biogenesis coordinate with each other to avoid the cytosolic accumulation of these aggregation-prone nascent mitochondrial proteins. Here, we show that in budding yeast, Tom70, a conserved receptor of the TOM complex, moonlights to regulate the transcriptional activity of mitochondrial proteins. Tom70's transcription regulatory role is conserved in Drosophila. The dual roles of Tom70 in both transcription/biogenesis and import of mitochondrial proteins allow the cells to accomplish mitochondrial biogenesis without compromising cytosolic proteostasis. The age-related reduction of Tom70, caused by reduced biogenesis and increased degradation of Tom70, is associated with the loss of mitochondrial membrane potential, mtDNA, and mitochondrial proteins. While loss of Tom70 accelerates aging and age-related mitochondrial defects, overexpressing TOM70 delays these mitochondrial dysfunctions and extends the replicative lifespan. Our results reveal unexpected roles of Tom70 in mitochondrial biogenesis and aging.
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Affiliation(s)
- Qingqing Liu
- Buck Institute for Research on AgingNovatoUnited States
| | | | | | - Benjamin Fong
- Buck Institute for Research on AgingNovatoUnited States
| | - Brian K Kennedy
- Buck Institute for Research on AgingNovatoUnited States
- Healthy Longevity Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
- Singapore Institute of Clinical Sciences, A(∗)STARSingaporeSingapore
| | - Chuankai Zhou
- Buck Institute for Research on AgingNovatoUnited States
- USC Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
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21
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Barba-Aliaga M, Alepuz P. Role of eIF5A in Mitochondrial Function. Int J Mol Sci 2022; 23:1284. [PMID: 35163207 PMCID: PMC8835957 DOI: 10.3390/ijms23031284] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 12/17/2022] Open
Abstract
The eukaryotic translation initiation factor 5A (eIF5A) is an evolutionarily conserved protein that binds ribosomes to facilitate the translation of peptide motifs with consecutive prolines or combinations of prolines with glycine and charged amino acids. It has also been linked to other molecular functions and cellular processes, such as nuclear mRNA export and mRNA decay, proliferation, differentiation, autophagy, and apoptosis. The growing interest in eIF5A relates to its association with the pathogenesis of several diseases, including cancer, viral infection, and diabetes. It has also been proposed as an anti-aging factor: its levels decay in aged cells, whereas increasing levels of active eIF5A result in the rejuvenation of the immune and vascular systems and improved brain cognition. Recent data have linked the role of eIF5A in some pathologies with its function in maintaining healthy mitochondria. The eukaryotic translation initiation factor 5A is upregulated under respiratory metabolism and its deficiency reduces oxygen consumption, ATP production, and the levels of several mitochondrial metabolic enzymes, as well as altering mitochondria dynamics. However, although all the accumulated data strongly link eIF5A to mitochondrial function, the precise molecular role and mechanisms involved are still unknown. In this review, we discuss the findings linking eIF5A and mitochondria, speculate about its role in regulating mitochondrial homeostasis, and highlight its potential as a target in diseases related to energy metabolism.
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Affiliation(s)
- Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, 46100 València, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, 46100 València, Spain
| | - Paula Alepuz
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, 46100 València, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, 46100 València, Spain
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22
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Ata Ö, Ergün BG, Fickers P, Heistinger L, Mattanovich D, Rebnegger C, Gasser B. What makes Komagataella phaffii non-conventional? FEMS Yeast Res 2021; 21:6440159. [PMID: 34849756 PMCID: PMC8709784 DOI: 10.1093/femsyr/foab059] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/23/2021] [Indexed: 12/30/2022] Open
Abstract
The important industrial protein production host Komagataella phaffii (syn Pichia pastoris) is classified as a non-conventional yeast. But what exactly makes K. phaffii non-conventional? In this review, we set out to address the main differences to the 'conventional' yeast Saccharomyces cerevisiae, but also pinpoint differences to other non-conventional yeasts used in biotechnology. Apart from its methylotrophic lifestyle, K. phaffii is a Crabtree-negative yeast species. But even within the methylotrophs, K. phaffii possesses distinct regulatory features such as glycerol-repression of the methanol-utilization pathway or the lack of nitrate assimilation. Rewiring of the transcriptional networks regulating carbon (and nitrogen) source utilization clearly contributes to our understanding of genetic events occurring during evolution of yeast species. The mechanisms of mating-type switching and the triggers of morphogenic phenotypes represent further examples for how K. phaffii is distinguished from the model yeast S. cerevisiae. With respect to heterologous protein production, K. phaffii features high secretory capacity but secretes only low amounts of endogenous proteins. Different to S. cerevisiae, the Golgi apparatus of K. phaffii is stacked like in mammals. While it is tempting to speculate that Golgi architecture is correlated to the high secretion levels or the different N-glycan structures observed in K. phaffii, there is recent evidence against this. We conclude that K. phaffii is a yeast with unique features that has a lot of potential to explore both fundamental research questions and industrial applications.
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Affiliation(s)
- Özge Ata
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Burcu Gündüz Ergün
- UNAM-National Nanotechnology Research Center, Bilkent University, Ankara, Turkey.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Av. de la Faculté 2B, 5030 Gembloux, Belgium
| | - Lina Heistinger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Innovative Immunotherapeutics, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria
| | - Corinna Rebnegger
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Christian Doppler Laboratory for Growth-Decoupled Protein Production in Yeast, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190 Vienna, Austria.,Biotechnology Research Center, Ministry of Agriculture and Forestry, Ankara, Turkey
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23
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Interactions of Both Pathogenic and Nonpathogenic CUG Clade Candida Species with Macrophages Share a Conserved Transcriptional Landscape. mBio 2021; 12:e0331721. [PMID: 34903044 PMCID: PMC8669484 DOI: 10.1128/mbio.03317-21] [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] [Indexed: 01/17/2023] Open
Abstract
Candida species are a leading cause of opportunistic, hospital-associated bloodstream infections with high mortality rates, typically in immunocompromised patients. Several species, including Candida albicans, the most prevalent cause of infection, belong to the monophyletic CUG clade of yeasts. Innate immune cells such as macrophages are crucial for controlling infection, and C. albicans responds to phagocytosis by a coordinated induction of pathways involved in catabolism of nonglucose carbon sources, termed alternative carbon metabolism, which together are essential for virulence. However, the interactions of other CUG clade species with macrophages have not been characterized. Here, we analyzed transcriptional responses to macrophage phagocytosis by six Candida species across a range of virulence and clinical importance. We define a core induced response common to pathogenic and nonpathogenic species alike, heavily weighted to alternative carbon metabolism. One prominent pathogen, Candida parapsilosis, showed species-specific expansion of phagocytosis-responsive genes, particularly metabolite transporters. C. albicans and Candida tropicalis, the other prominent pathogens, also had species-specific responses, but these were largely comprised of functionally uncharacterized genes. Transcriptional analysis of macrophages also demonstrated highly correlated proinflammatory transcriptional responses to different Candida species that were largely independent of fungal viability, suggesting that this response is driven by recognition of conserved cell wall components. This study significantly broadens our understanding of host interactions in CUG clade species, demonstrating that although metabolic plasticity is crucial for virulence in Candida, it alone is not sufficient to confer pathogenicity. Instead, we identify sets of mostly uncharacterized genes that may explain the evolution of pathogenicity.
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Wijnants S, Vreys J, Van Dijck P. Interesting antifungal drug targets in the central metabolism of Candida albicans. Trends Pharmacol Sci 2021; 43:69-79. [PMID: 34756759 DOI: 10.1016/j.tips.2021.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 01/04/2023]
Abstract
To treat infections caused by Candida albicans, azoles, polyenes, and echinocandins are used. However, resistance occurs against all three, so there is an urgent need for new antifungal drugs with a novel mode of action. Recently, it became clear that central metabolism plays an important role in the virulence of C. albicans. Glycolysis is, for example, upregulated during virulence conditions, whereas the glyoxylate cycle is important upon phagocytosis by host immune cells. These findings indicate that C. albicans adapts its metabolism to the environment for maximal virulence. In this review, we provide an overview of the potency of different central metabolic pathways and their key enzymes as potential antifungal drug targets.
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Affiliation(s)
- Stefanie Wijnants
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Jolien Vreys
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
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25
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Hong J, Palme J, Hua B, Springer M. Computational analysis of GAL pathway pinpoints mechanisms underlying natural variation. PLoS Comput Biol 2021; 17:e1008691. [PMID: 34570755 PMCID: PMC8496860 DOI: 10.1371/journal.pcbi.1008691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 10/07/2021] [Accepted: 08/17/2021] [Indexed: 11/19/2022] Open
Abstract
Quantitative traits are measurable phenotypes that show continuous variation over a wide phenotypic range. Enormous effort has recently been put into determining the genetic influences on a variety of quantitative traits with mixed success. We identified a quantitative trait in a tractable model system, the GAL pathway in yeast, which controls the uptake and metabolism of the sugar galactose. GAL pathway activation depends both on galactose concentration and on the concentrations of competing, preferred sugars such as glucose. Natural yeast isolates show substantial variation in the behavior of the pathway. All studied yeast strains exhibit bimodal responses relative to external galactose concentration, i.e. a set of galactose concentrations existed at which both GAL-induced and GAL-repressed subpopulations were observed. However, these concentrations differed in different strains. We built a mechanistic model of the GAL pathway and identified parameters that are plausible candidates for capturing the phenotypic features of a set of strains including standard lab strains, natural variants, and mutants. In silico perturbation of these parameters identified variation in the intracellular galactose sensor, Gal3p, the negative feedback node within the GAL regulatory network, Gal80p, and the hexose transporters, HXT, as the main sources of the bimodal range variation. We were able to switch the phenotype of individual yeast strains in silico by tuning parameters related to these three elements. Determining the basis for these behavioral differences may give insight into how the GAL pathway processes information, and into the evolution of nutrient metabolism preferences in different strains. More generally, our method of identifying the key parameters that explain phenotypic variation in this system should be generally applicable to other quantitative traits. Microbes adopt elaborate strategies for the preferred uptake and use of nutrients to cope with complex and fluctuating environments. As a result, yeast strains originating from different ecological niches show significant variation in the way they induce genes in the galactose metabolism (GAL) pathway in response to nutrient signals. To identify the mechanistic sources of this variation, we built a mathematical model to simulate the dynamics of the galactose metabolic regulation network, and studied how parameters with different biological implications contributed to the natural variation. We found that variations in the behavior of the galactose sensor Gal3p, the negative feedback node Gal80p, and the hexose transporters HXT were critical elements in the GAL pathway response. Tuning single parameters in silico was sufficient to achieve phenotype switching between different yeast strains. Our computational approach should be generally useful to help pinpoint the genetic and molecular bases of natural variation in other systems.
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Affiliation(s)
- Jiayin Hong
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Julius Palme
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Bo Hua
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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26
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Infant T, Deb R, Ghose S, Nagotu S. Post-translational modifications of proteins associated with yeast peroxisome membrane: An essential mode of regulatory mechanism. Genes Cells 2021; 26:843-860. [PMID: 34472666 PMCID: PMC9291962 DOI: 10.1111/gtc.12892] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022]
Abstract
Peroxisomes are single membrane‐bound organelles important for the optimum functioning of eukaryotic cells. Seminal discoveries in the field of peroxisomes are made using yeast as a model. Several proteins required for the biogenesis and function of peroxisomes are identified to date. As with proteins involved in other major cellular pathways, peroxisomal proteins are also subjected to regulatory post‐translational modifications. Identification, characterization and mapping of these modifications to specific amino acid residues on proteins are critical toward understanding their functional significance. Several studies have tried to identify post‐translational modifications of peroxisomal proteins and determine their impact on peroxisome structure and function. In this manuscript, we provide an overview of the various post‐translational modifications that govern the peroxisome dynamics in yeast.
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Affiliation(s)
- Terence Infant
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Rachayeeta Deb
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Suchetana Ghose
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
| | - Shirisha Nagotu
- Organelle Biology and Cellular Ageing Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, India
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27
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Salsaa M, Aziz K, Lazcano P, Schmidtke MW, Tarsio M, Hüttemann M, Reynolds CA, Kane PM, Greenberg ML. Valproate activates the Snf1 kinase in Saccharomyces cerevisiae by decreasing the cytosolic pH. J Biol Chem 2021; 297:101110. [PMID: 34428448 PMCID: PMC8449051 DOI: 10.1016/j.jbc.2021.101110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022] Open
Abstract
Valproate (VPA) is a widely used mood stabilizer, but its therapeutic mechanism of action is not understood. This knowledge gap hinders the development of more effective drugs with fewer side effects. Using the yeast model to elucidate the effects of VPA on cellular metabolism, we determined that the drug upregulated expression of genes normally repressed during logarithmic growth on glucose medium and increased levels of activated (phosphorylated) Snf1 kinase, the major metabolic regulator of these genes. VPA also decreased the cytosolic pH (pHc) and reduced glycolytic production of 2/3-phosphoglycerate. ATP levels and mitochondrial membrane potential were increased, and glucose-mediated extracellular acidification decreased in the presence of the drug, as indicated by a smaller glucose-induced shift in pH, suggesting that the major P-type proton pump Pma1 was inhibited. Interestingly, decreasing the pHc by omeprazole-mediated inhibition of Pma1 led to Snf1 activation. We propose a model whereby VPA lowers the pHc causing a decrease in glycolytic flux. In response, Pma1 is inhibited and Snf1 is activated, resulting in increased expression of normally repressed metabolic genes. These findings suggest a central role for pHc in regulating the metabolic program of yeast cells.
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Affiliation(s)
- Michael Salsaa
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Kerestin Aziz
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Pablo Lazcano
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Michael W Schmidtke
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Maureen Tarsio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, Michigan, USA
| | - Christian A Reynolds
- Department of Emergency Medicine, School of Medicine, Wayne State University, Detroit, Michigan, USA; Department of Biotechnology, University of Rijeka, Rijeka, Croatia
| | - Patricia M Kane
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA.
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28
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Dekker WJC, Ortiz-Merino RA, Kaljouw A, Battjes J, Wiering FW, Mooiman C, Torre PDL, Pronk JT. Engineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth. Metab Eng 2021; 67:347-364. [PMID: 34303845 DOI: 10.1016/j.ymben.2021.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae, these yeasts cannot grow in the absence of oxygen. Responses of K. marxianus and S. cerevisiae to different oxygen-limitation regimes were analyzed in chemostats. Genome and transcriptome analysis, physiological responses to sterol supplementation and sterol-uptake measurements identified absence of a functional sterol-uptake mechanism as a key factor underlying the oxygen requirement of K. marxianus. Heterologous expression of a squalene-tetrahymanol cyclase enabled oxygen-independent synthesis of the sterol surrogate tetrahymanol in K. marxianus. After a brief adaptation under oxygen-limited conditions, tetrahymanol-expressing K. marxianus strains grew anaerobically on glucose at temperatures of up to 45 °C. These results open up new directions in the development of thermotolerant yeast strains for anaerobic industrial applications.
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Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Julius Battjes
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Frank W Wiering
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Pilar de la Torre
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands.
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29
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Plocek V, Fadrhonc K, Maršíková J, Váchová L, Pokorná A, Hlaváček O, Wilkinson D, Palková Z. Mitochondrial Retrograde Signaling Contributes to Metabolic Differentiation in Yeast Colonies. Int J Mol Sci 2021; 22:ijms22115597. [PMID: 34070491 PMCID: PMC8198273 DOI: 10.3390/ijms22115597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/16/2022] Open
Abstract
During development of yeast colonies, various cell subpopulations form, which differ in their properties and specifically localize within the structure. Three branches of mitochondrial retrograde (RTG) signaling play a role in colony development and differentiation, each of them activating the production of specific markers in different cell types. Here, aiming to identify proteins and processes controlled by the RTG pathway, we analyzed proteomes of individual cell subpopulations from colonies of strains, mutated in genes of the RTG pathway. Resulting data, along with microscopic analyses revealed that the RTG pathway predominantly regulates processes in U cells, long-lived cells with unique properties, which are localized in upper colony regions. Rtg proteins therein activate processes leading to amino acid biosynthesis, including transport of metabolic intermediates between compartments, but also repress expression of mitochondrial ribosome components, thus possibly contributing to reduced mitochondrial translation in U cells. The results reveal the RTG pathway's role in activating metabolic processes, important in U cell adaptation to altered nutritional conditions. They also point to the important role of Rtg regulators in repressing mitochondrial activity in U cells.
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Affiliation(s)
- Vítězslav Plocek
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
| | - Kristýna Fadrhonc
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
| | - Jana Maršíková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
| | - Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 14220 Prague, Czech Republic; (L.V.); (A.P.); (O.H.)
| | - Alexandra Pokorná
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 14220 Prague, Czech Republic; (L.V.); (A.P.); (O.H.)
| | - Otakar Hlaváček
- Institute of Microbiology of the Czech Academy of Sciences, BIOCEV, 14220 Prague, Czech Republic; (L.V.); (A.P.); (O.H.)
| | - Derek Wilkinson
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
| | - Zdena Palková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, BIOCEV, 12800 Prague, Czech Republic; (V.P.); (K.F.); (J.M.); (D.W.)
- Correspondence:
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30
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Peterson PP, Liu Z. Identification and Characterization of Rapidly Accumulating sch9Δ Suppressor Mutations in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2021; 11:6254187. [PMID: 33901283 DOI: 10.1093/g3journal/jkab134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/14/2021] [Indexed: 01/30/2023]
Abstract
Nutrient sensing is important for cell growth, aging, and longevity. In Saccharomyces cerevisiae, Sch9, an AGC-family protein kinase, is a major nutrient sensing kinase homologous to mammalian Akt and S6 kinase. Sch9 integrates environmental cues with cell growth by functioning downstream of TORC1 and in parallel with the Ras/PKA pathway. Mutations in SCH9 lead to reduced cell growth in dextrose medium; however, reports on the ability of sch9Δ mutants to utilize non-fermentable carbon sources are inconsistent. Here we show that sch9Δ mutant strains cannot grow on non-fermentable carbon sources and rapidly accumulate suppressor mutations, which reverse growth defects of sch9Δ mutants. sch9Δ induces gene expression of three transcription factors required for utilization of non-fermentable carbon sources, Cat8, Adr1, and Hap4, while sch9Δ suppressor mutations, termed sns1 and sns2, strongly decrease the gene expression of those transcription factors. Despite the genetic suppression interactions, both sch9Δ and sns1 (or sns2) homozygous mutants have severe defects in meiosis. By screening mutants defective in sporulation, we identified additional sch9Δ suppressor mutants with mutations in GPB1, GPB2, and MCK1. Using library complementation and genetic analysis, we identified SNS1 and SNS2 to be IRA2 and IRA1, respectively. Furthermore, we discovered that lifespan extension in sch9Δ mutants is dependent on IRA2 and that PKA inactivation greatly increases basal expression of CAT8, ADR1, and HAP4. Our results demonstrate that sch9Δ leads to complete loss of growth on non-fermentable carbon sources and mutations in MCK1 or genes encoding negative regulators of the Ras/PKA pathway reverse sch9Δ mutant phenotypes.
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Affiliation(s)
- Patricia P Peterson
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Zhengchang Liu
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
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31
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Xiberras J, Klein M, Prosch C, Malubhoy Z, Nevoigt E. Anaplerotic reactions active during growth of Saccharomyces cerevisiae on glycerol. FEMS Yeast Res 2021; 20:5672635. [PMID: 31821485 DOI: 10.1093/femsyr/foz086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/09/2019] [Indexed: 02/01/2023] Open
Abstract
Anaplerotic reactions replenish TCA cycle intermediates during growth. In Saccharomyces cerevisiae, pyruvate carboxylase and the glyoxylate cycle have been experimentally identified to be the main anaplerotic routes during growth on glucose (C6) and ethanol (C2), respectively. The current study investigates the importance of the two isoenzymes of pyruvate carboxylase (PYC1 and PYC2) and one of the key enzymes of the glyoxylate cycle (ICL1) for growth on glycerol (C3) as a sole carbon source. As the wild-type strains of the CEN.PK family are unable to grow in pure synthetic glycerol medium, a reverse engineered derivative showing a maximum specific growth rate of 0.14 h-1 was used as the reference strain. While the deletion of PYC1 reduced the maximum specific growth rate by about 38%, the deletion of PYC2 had no significant impact, neither in the reference strain nor in the pyc1Δ mutant. The deletion of ICL1 only marginally reduced growth of the reference strain but further decreased the growth rate of the pyc1 deletion strain by 20%. Interestingly, the triple deletion (pyc1Δ pyc2Δ icl1Δ) did not show any growth. Therefore, both the pyruvate carboxylase and the glyoxylate cycle are involved in anaplerosis during growth on glycerol.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Celina Prosch
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Zahabiya Malubhoy
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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Österberg L, Domenzain I, Münch J, Nielsen J, Hohmann S, Cvijovic M. A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism. PLoS Comput Biol 2021; 17:e1008891. [PMID: 33836000 PMCID: PMC8059808 DOI: 10.1371/journal.pcbi.1008891] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/21/2021] [Accepted: 03/18/2021] [Indexed: 12/11/2022] Open
Abstract
The interplay between nutrient-induced signaling and metabolism plays an important role in maintaining homeostasis and its malfunction has been implicated in many different human diseases such as obesity, type 2 diabetes, cancer, and neurological disorders. Therefore, unraveling the role of nutrients as signaling molecules and metabolites together with their interconnectivity may provide a deeper understanding of how these conditions occur. Both signaling and metabolism have been extensively studied using various systems biology approaches. However, they are mainly studied individually and in addition, current models lack both the complexity of the dynamics and the effects of the crosstalk in the signaling system. To gain a better understanding of the interconnectivity between nutrient signaling and metabolism in yeast cells, we developed a hybrid model, combining a Boolean module, describing the main pathways of glucose and nitrogen signaling, and an enzyme-constrained model accounting for the central carbon metabolism of Saccharomyces cerevisiae, using a regulatory network as a link. The resulting hybrid model was able to capture a diverse utalization of isoenzymes and to our knowledge outperforms constraint-based models in the prediction of individual enzymes for both respiratory and mixed metabolism. The model showed that during fermentation, enzyme utilization has a major contribution in governing protein allocation, while in low glucose conditions robustness and control are prioritized. In addition, the model was capable of reproducing the regulatory effects that are associated with the Crabtree effect and glucose repression, as well as regulatory effects associated with lifespan increase during caloric restriction. Overall, we show that our hybrid model provides a comprehensive framework for the study of the non-trivial effects of the interplay between signaling and metabolism, suggesting connections between the Snf1 signaling pathways and processes that have been related to chronological lifespan of yeast cells.
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Affiliation(s)
- Linnea Österberg
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Julia Münch
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- BioInnovation Institute, Copenhagen, Denmark
| | - Stefan Hohmann
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
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Zhao Y, Li J, Su R, Liu Y, Wang J, Deng Y. Effect of magnesium ions on glucaric acid production in the engineered Saccharomyces cerevisiae. J Biotechnol 2021; 332:61-71. [PMID: 33812897 DOI: 10.1016/j.jbiotec.2021.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 03/16/2021] [Accepted: 03/25/2021] [Indexed: 11/27/2022]
Abstract
Glucaric acid has been successfully produced in Escherichia coli and fungus. Here, we first analyzed the effects of different metal ions on glucaric acid production in the engineered Saccharomyces cerevisiae Bga-3 strain harboring the glucaric acid synthesis pathway. We found that magnesium ions could promote the growth rate of yeast cells, and thus, increase the glucaric acid production by elevating the glucose and myo-inositol utilization of Bga-3 strain. RNA-Seq transcriptome analysis results showed that the upregulation of genes involved in the gluconeogenesis pathway, as well as the downregulation of genes associated with the glycolysis pathway and pentose phosphate pathway in response to MgCl2 were all benefit for the enhancement of the glucose-6-phosphate flux, which was the precursor for myo-inositol and glucaric acid. In addition, we found that MgCl2 could also increase the activity of MIOX4, which was also crucial for glucaric acid synthesis. At last, a final glucaric acid titer of 10.6 g/L, the highest reported titer, was achieved in the fed-batch fermentation using a 5-L bioreactor by adding 100 mM MgCl2. Our findings will provide a new way of promoting the production of other chemicals in the engineered yeast cells.
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Affiliation(s)
- Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jie Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Ruifang Su
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yingli Liu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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Two homologs of the Cat8 transcription factor are involved in the regulation of ethanol utilization in Komagataella phaffii. Curr Genet 2021; 67:641-661. [PMID: 33725138 PMCID: PMC8254726 DOI: 10.1007/s00294-021-01165-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/26/2022]
Abstract
The transcription factors Cat8 and Sip4 were described in Saccharomyces cerevisiae and Kluyveromyces lactis to have very similar DNA binding domains and to be necessary for derepression of a variety of genes under non-fermentative growth conditions via binding to the carbon source responsive elements (CSREs). The methylotrophic yeast Komagataella phaffii (syn Pichia pastoris) has two transcription factors (TFs), which are putative homologs of Cat8 based on sequence similarity, termed Cat8-1 and Cat8-2. It is yet unclear in which cellular processes they are involved and if one of them is actually the homolog of Sip4. To study the roles of the Cat8 homologs in K. phaffii, overexpression or deletion strains were generated for the two TFs. The ability of these mutant strains to grow on different carbon sources was tested, and transcript levels of selected genes from the carbon metabolism were quantified. Our experiments showed that the TFs are required for the growth of K. phaffii on C2 carbon sources, but not on glucose, glycerol or methanol. K. phaffii deleted for Cat8-1 showed impaired growth on acetate, while both Cat8-1 and Cat8-2 are involved in the growth of K. phaffii on ethanol. Correspondingly, both TFs are participating in the activation of ADH2, ALD4 and ACS1, three genes encoding enzymes important for the assimilation of ethanol. Different from S. cerevisiae and K. lactis, Cat8-1 is not regulating the transcription of the putative Sip4-family member Cat8-2 in K. phaffii. Furthermore, Cat8-1 is necessary for the activation of genes from the glyoxylate cycle, whereas Cat8-2 is necessary for the activation of genes from the carnitine shuttle. Neither Cat8-1 nor Cat8-2 are required for the activation of gluconeogenesis genes. Finally, the CAT8-2 gene is repressed by the Mig1-2 transcription factor on glucose and autorepressed by the Cat8-2 protein on all tested carbon sources. Our study identified the involvement of K. phaffii Cat8-1 and Cat8-2 in C2-metabolism, and highlighted similarities and differences to their homologs in other yeast species.
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Amino acid starvation inhibits autophagy in lipid droplet-deficient cells through mitochondrial dysfunction. Biochem J 2021; 477:3613-3623. [PMID: 32886124 DOI: 10.1042/bcj20200551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022]
Abstract
Lipid droplets are ubiquitous organelles in eukaryotes that act as storage sites for neutral lipids. Under normal growth conditions, they are not required in the yeast Saccharomyces cerevisiae. However, recent works have shown that lipid droplets are required for autophagy to proceed in response to nitrogen starvation and that they play an essential role in maintaining ER homeostasis. Autophagy is a major catabolic pathway that helps degradation and recycling of potentially harmful proteins and organelles. It can be pharmacologically induced by rapamycin even in the absence of lipid droplets. Here, we show that amino acid starvation is responsible for autophagy failure in lipid droplet-deficient yeast. It not only fails to induce autophagy but also inhibits rapamycin-induced autophagy. The general amino acid control pathway is not involved in this paradoxical effect of amino acid shortage. We correlate the autophagy failure with mitochondria aggregation and we show that amino acid starvation-induced autophagy is restored in lipid droplet-deficient yeast by increasing mitochondrial biomass physiologically (respiration) or genetically (REG1 deletion). Our results establish a new functional link between lipid droplets, ER and mitochondria during nitrogen starvation-induced autophagy.
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The activity of yeast Apn2 AP endonuclease at uracil-derived AP sites is dependent on the major carbon source. Curr Genet 2021; 67:283-294. [PMID: 33386486 DOI: 10.1007/s00294-020-01141-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/16/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
Yeast Apn2 is an AP endonuclease and DNA 3'-diesterase that belongs to the Exo III family with homology to the E. coli exonuclease III, Schizosaccharomyces pombe eth1, and human AP endonucleases APEX1 and APEX2. In the absence of Apn1, the major AP endonuclease in yeast, Apn2 can cleave the DNA backbone at an AP lesion initiating the base excision repair pathway. To study the role and relative contribution of Apn2, we took advantage of a reporter system that was previously used to delineate how uracil-derived AP sites are repaired. At this reporter, disruption of the Apn1-initiated base excision repair pathway led to a significant elevation of A:T to C:G transversions. Here we show that such highly elevated A:T to C:G transversion mutations associated with uracil residues in DNA are abolished when apn1∆ yeast cells are grown in glucose as the primary carbon source. We also show that the disruption of Apn2, either by the complete gene deletion or by the mutation of a catalytic residue, results in a similarly reduced rate of the uracil-associated mutations. Overall, our results indicate that Apn2 activity is regulated by the glucose repression pathway in yeast.
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Watanabe K, Perez CMT, Kitahori T, Hata K, Aoi M, Takahashi H, Sakuma T, Okamura Y, Nakashimada Y, Yamamoto T, Matsuyama K, Mayuzumi S, Aki T. Improvement of fatty acid productivity of thraustochytrid, Aurantiochytrium sp. by genome editing. J Biosci Bioeng 2020; 131:373-380. [PMID: 33386277 DOI: 10.1016/j.jbiosc.2020.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 01/12/2023]
Abstract
Thraustochytrid strains belonging to the genus Aurantiochytrium accumulate significant amounts of lipids including polyunsaturated fatty acids and carotenoids and, therefore, are expected to be used for industrial production of various valuable materials. Although various efforts such as chemical mutagenesis and homologous gene recombination have been made to improve lipid productivity of Aurantiochytrium species, low specificity and efficiency in the conventional methods hinder the research progress. Here, we attempted to apply a genome editing technology, the CRISPR-Cas9 system as an alternative molecular breeding technique for Aurantiochytrium species to accelerate the metabolic engineering. The efficiency of specific gene knock-in by the homologous recombination increased more than 10-folds by combining the CRISPR-Cas9 system. As a result of disrupting the genes associated with β-oxidation of fatty acids by the improved method, the genome edited strains with higher fatty acid productivity were isolated, demonstrating for the first time that the CRISPR-Cas9 system was effective for molecular breeding of the strains in the genus Aurantiochytrium to improve lipid productivity.
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Affiliation(s)
- Kenshi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Charose Marie Ting Perez
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Tomoki Kitahori
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Kosuke Hata
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Masato Aoi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Hirokazu Takahashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Tetsushi Sakuma
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Yoshiko Okamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Takashi Yamamoto
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | | | - Shinzo Mayuzumi
- Idemitsu Kosan Co., Ltd., 1280 Kami-izumi, Sodegaura, Chiba 299-0293, Japan
| | - Tsunehiro Aki
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
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Barba-Aliaga M, Villarroel-Vicente C, Stanciu A, Corman A, Martínez-Pastor MT, Alepuz P. Yeast Translation Elongation Factor eIF5A Expression Is Regulated by Nutrient Availability through Different Signalling Pathways. Int J Mol Sci 2020; 22:E219. [PMID: 33379337 PMCID: PMC7794953 DOI: 10.3390/ijms22010219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 12/15/2022] Open
Abstract
Translation elongation factor eIF5A binds to ribosomes to promote peptide bonds between problematic amino acids for the reaction like prolines. eIF5A is highly conserved and essential in eukaryotes, which usually contain two similar but differentially expressed paralogue genes. The human eIF5A-1 isoform is abundant and implicated in some cancer types; the eIF5A-2 isoform is absent in most cells but becomes overexpressed in many metastatic cancers. Several reports have connected eIF5A and mitochondria because it co-purifies with the organelle or its inhibition reduces respiration and mitochondrial enzyme levels. However, the mechanisms of eIF5A mitochondrial function, and whether eIF5A expression is regulated by the mitochondrial metabolism, are unknown. We analysed the expression of yeast eIF5A isoforms Tif51A and Tif51B under several metabolic conditions and in mutants. The depletion of Tif51A, but not Tif51B, compromised yeast growth under respiration and reduced oxygen consumption. Tif51A expression followed dual positive regulation: by high glucose through TORC1 signalling, like other translation factors, to promote growth and by low glucose or non-fermentative carbon sources through Snf1 and heme-dependent transcription factor Hap1 to promote respiration. Upon iron depletion, Tif51A was down-regulated and Tif51B up-regulated. Both were Hap1-dependent. Our results demonstrate eIF5A expression regulation by cellular metabolic status.
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Affiliation(s)
- Marina Barba-Aliaga
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Carlos Villarroel-Vicente
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Alice Stanciu
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Alba Corman
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - María Teresa Martínez-Pastor
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Paula Alepuz
- Instituto Biotecmed, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain; (M.B.-A.); (C.V.-V.); (A.S.); (A.C.)
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
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Karayel O, Michaelis AC, Mann M, Schulman BA, Langlois CR. DIA-based systems biology approach unveils E3 ubiquitin ligase-dependent responses to a metabolic shift. Proc Natl Acad Sci U S A 2020; 117:32806-32815. [PMID: 33288721 PMCID: PMC7768684 DOI: 10.1073/pnas.2020197117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a powerful model system for systems-wide biology screens and large-scale proteomics methods. Nearly complete proteomics coverage has been achieved owing to advances in mass spectrometry. However, it remains challenging to scale this technology for rapid and high-throughput analysis of the yeast proteome to investigate biological pathways on a global scale. Here we describe a systems biology workflow employing plate-based sample preparation and rapid, single-run, data-independent mass spectrometry analysis (DIA). Our approach is straightforward, easy to implement, and enables quantitative profiling and comparisons of hundreds of nearly complete yeast proteomes in only a few days. We evaluate its capability by characterizing changes in the yeast proteome in response to environmental perturbations, identifying distinct responses to each of them and providing a comprehensive resource of these responses. Apart from rapidly recapitulating previously observed responses, we characterized carbon source-dependent regulation of the GID E3 ligase, an important regulator of cellular metabolism during the switch between gluconeogenic and glycolytic growth conditions. This unveiled regulatory targets of the GID ligase during a metabolic switch. Our comprehensive yeast system readout pinpointed effects of a single deletion or point mutation in the GID complex on the global proteome, allowing the identification and validation of targets of the GID E3 ligase. Moreover, this approach allowed the identification of targets from multiple cellular pathways that display distinct patterns of regulation. Although developed in yeast, rapid whole-proteome-based readouts can serve as comprehensive systems-level assays in all cellular systems.
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Affiliation(s)
- Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - André C Michaelis
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Christine R Langlois
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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Zhao EM, Lalwani MA, Lovelett RJ, García-Echauri SA, Hoffman SM, Gonzalez CL, Toettcher JE, Kevrekidis IG, Avalos JL. Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering. ACS Synth Biol 2020; 9:3254-3266. [PMID: 33232598 PMCID: PMC10399620 DOI: 10.1021/acssynbio.0c00305] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The use of optogenetics in metabolic engineering for light-controlled microbial chemical production raises the prospect of utilizing control and optimization techniques routinely deployed in traditional chemical manufacturing. However, such mechanisms require well-characterized, customizable tools that respond fast enough to be used as real-time inputs during fermentations. Here, we present OptoINVRT7, a new rapid optogenetic inverter circuit to control gene expression in Saccharomyces cerevisiae. The circuit induces gene expression in only 0.6 h after switching cells from light to darkness, which is at least 6 times faster than previous OptoINVRT optogenetic circuits used for chemical production. In addition, we introduce an engineered inducible GAL1 promoter (PGAL1-S), which is stronger than any constitutive or inducible promoter commonly used in yeast. Combining OptoINVRT7 with PGAL1-S achieves strong and light-tunable levels of gene expression with as much as 132.9 ± 22.6-fold induction in darkness. The high performance of this new optogenetic circuit in controlling metabolic enzymes boosts production of lactic acid and isobutanol by more than 50% and 15%, respectively. The strength and controllability of OptoINVRT7 and PGAL1-S open the door to applying process control tools to engineered metabolisms to improve robustness and yields in microbial fermentations for chemical production.
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Affiliation(s)
- Evan M. Zhao
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Makoto A. Lalwani
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Robert J. Lovelett
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, 221 Maryland
Hall, Johns Hopkins University, 2400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Sergio A. García-Echauri
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Shannon M. Hoffman
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Christopher L. Gonzalez
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Jared E. Toettcher
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Ioannis G. Kevrekidis
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, 221 Maryland
Hall, Johns Hopkins University, 2400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, 86 Olden Street, Princeton, New Jersey 08544, United States
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Hong J, Hua B, Springer M, Tang C. Computational study on ratio-sensing in yeast galactose utilization pathway. PLoS Comput Biol 2020; 16:e1007960. [PMID: 33275601 PMCID: PMC7744065 DOI: 10.1371/journal.pcbi.1007960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 12/16/2020] [Accepted: 10/16/2020] [Indexed: 01/02/2023] Open
Abstract
Metabolic networks undergo gene expression regulation in response to external nutrient signals. In microbes, the synthesis of enzymes that are used to transport and catabolize less preferred carbon sources is repressed in the presence of a preferred carbon source. For most microbes, glucose is a preferred carbon source, and it has long been believed that as long as glucose is present in the environment, the expression of genes related to the metabolism of alternative carbon sources is shut down, due to catabolite repression. However, recent studies have shown that the induction of the galactose (GAL) metabolic network does not solely depend on the exhaustion of glucose. Instead, the GAL genes respond to the external concentration ratio of galactose to glucose, a phenomenon of unknown mechanism that we termed ratio-sensing. Using mathematical modeling, we found that ratio-sensing is a general phenomenon that can arise from competition between two carbon sources for shared transporters, between transcription factors for binding to communal regulatory sequences of the target genes, or a combination of the aforementioned two levels of competition. We analyzed how the parameters describing the competitive interaction influenced ratio-sensing behaviors in each scenario and found that the concatenation of both layers of signal integration could expand the dynamical range of ratio-sensing. Finally, we investigated the influence of circuit topology on ratio-sensing and found that incorporating negative auto-regulation and/or coherent feedforward loop motifs to the basic signal integration unit could tune the sensitivity of the response to the external nutrient signals. Our study not only deepened our understanding of how ratio-sensing is achieved in yeast GAL metabolic regulation, but also elucidated design principles for ratio-sensing signal processing that can be used in other biological settings, such as being introduced into circuit designs for synthetic biology applications. Microbes make sophisticated choices about the uptake and metabolism of nutrients depending on the variety of nutrient choices available to them in their environment. In the well-studied yeast galactose utilization network, a recent study has shown that galactose metabolic genes respond to the external concentration ratio of galactose to glucose. Using computational models, we showed that this type of phenomenon could arise from a competition between galactose and glucose for transporters, a competition between transcription factors for promoters, or a combination of these two mechanisms. We further revealed the controlling parameters that determined the system sensitivity towards competing input signals and that determined the concentration ratio required to induce the metabolic network in each scenario. Combining competition inhibition at both the transporter level and the transcriptional level can enlarge the ratio-sensing regime, resulting a robust signal integration module. We suspect that modules of this kind may be common in many areas of biology.
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Affiliation(s)
- Jiayin Hong
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bo Hua
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Springer
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chao Tang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,School of Physics, Peking University, Beijing, China
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Longanesi L, Bouxin FP, Fan J, Auta H, Gammons R, Abeln F, Budarin VL, Clark JH, Chuck CJ. Scaled-Up Microwave-Assisted Pretreatment and Continuous Fermentation to Produce Yeast Lipids from Brewery Wastes. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c03463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca Longanesi
- Department of Chemical Engineering, University of Bath, Bath BA2 7AY, U.K
| | - Florent P. Bouxin
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Jiajun Fan
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Hadiza Auta
- Department of Chemical Engineering, University of Bath, Bath BA2 7AY, U.K
| | - Richard Gammons
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Felix Abeln
- Department of Chemical Engineering, University of Bath, Bath BA2 7AY, U.K
| | - Vitaliy L. Budarin
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - James H. Clark
- Green Chemistry Centre of Excellence, Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
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Transcriptional Rewiring, Adaptation, and the Role of Gene Duplication in the Metabolism of Ethanol of Saccharomyces cerevisiae. mSystems 2020; 5:5/4/e00416-20. [PMID: 32788405 PMCID: PMC7426151 DOI: 10.1128/msystems.00416-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ethanol is the main by-product of yeast sugar fermentation that affects microbial growth parameters, being considered a dual molecule, a nutrient and a stressor. Previous works demonstrated that the budding yeast arose after an ancient hybridization process resulted in a tier of duplicated genes within its genome, many of them with implications in this ethanol "produce-accumulate-consume" strategy. The evolutionary link between ethanol production, consumption, and tolerance versus ploidy and stability of the hybrids is an ongoing debatable issue. The implication of ancestral duplicates in this metabolic rewiring, and how these duplicates differ transcriptionally, remains unsolved. Here, we study the transcriptomic adaptive signatures to ethanol as a nonfermentative carbon source to sustain clonal yeast growth by experimental evolution, emphasizing the role of duplicated genes in the adaptive process. As expected, ethanol was able to sustain growth but at a lower rate than glucose. Our results demonstrate that in asexual populations a complete transcriptomic rewiring was produced, strikingly by downregulation of duplicated genes, mainly whole-genome duplicates, whereas small-scale duplicates exhibited significant transcriptional divergence between copies. Overall, this study contributes to the understanding of evolution after gene duplication, linking transcriptional divergence with duplicates' fate in a multigene trait as ethanol tolerance.IMPORTANCE Gene duplication events have been related with increasing biological complexity through the tree of life, but also with illnesses, including cancer. Early evolutionary theories indicated that duplicated genes could explore alternative functions due to relaxation of selective constraints in one of the copies, as the other remains as ancestral-function backup. In unicellular eukaryotes like yeasts, it has been demonstrated that the fate and persistence of duplicates depend on duplication mechanism (whole-genome or small-scale events), shaping their actual genomes. Although it has been shown that small-scale duplicates tend to innovate and whole-genome duplicates specialize in ancestral functions, the implication of duplicates' transcriptional plasticity and transcriptional divergence on environmental and metabolic responses remains largely obscure. Here, by experimental adaptive evolution, we show that Saccharomyces cerevisiae is able to respond to metabolic stress (ethanol as nonfermentative carbon source) due to the persistence of duplicated genes. These duplicates respond by transcriptional rewiring, depending on their transcriptional background. Our results shed light on the mechanisms that determine the role of duplicates, and on their evolvability.
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Zhang X, Xu C, Liu Y, Wang J, Zhao Y, Deng Y. Enhancement of glucaric acid production in Saccharomyces cerevisiae by expressing Vitreoscilla hemoglobin. Biotechnol Lett 2020; 42:2169-2178. [PMID: 32691185 DOI: 10.1007/s10529-020-02966-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 07/11/2020] [Indexed: 10/23/2022]
Abstract
OBJECTIVE To enhance the glucaric acid (GA) production in Saccharomyces cerevisiae, the Vitreoscilla hemoglobin was employed to reinforce cellular oxygen supplement. Additionally, the pH-free fermentation strategy was engaged to lower the cost brought by base feeding during the acid-accumulated and long-period glucaric acid production. RESULTS Recombinant yeast Bga-4 was constructed harboring Vitreoscilla hemoglobin on the basis of previous Bga-3. Higher glucose uptake rate, growth rate, and ethanol reuse rate were achieved in Bga-4 in shake-flask fermentation than those in Bga-3. Furthermore, the fed-batch fermentation in a 5-L bioreactor was performed without pH control, resulting in a final glucaric acid titer of 6.38 g/L. CONCLUSIONS Both the GA titer and biomass were enhanced along with the efficiency of ethanol re-utilization in the presence of VHb. Moreover, the absence of base feeding for long-period fermentation reduced production cost, which is meaningful for industrial applications.
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Affiliation(s)
- Xi Zhang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China
| | - Chi Xu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China
| | - YingLi Liu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, People's Republic of China
| | - Jing Wang
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.,China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing, 100048, People's Republic of China
| | - YunYing Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China. .,Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, People's Republic of China.
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45
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Transcriptional regulatory proteins in central carbon metabolism of Pichia pastoris and Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2020; 104:7273-7311. [PMID: 32651601 DOI: 10.1007/s00253-020-10680-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 01/21/2023]
Abstract
System-wide interactions in living cells and discovery of the diverse roles of transcriptional regulatory proteins that are mediator proteins with catalytic domains and regulatory subunits and transcription factors in the cellular pathways have become crucial for understanding the cellular response to environmental conditions. This review provides information for future metabolic engineering strategies through analyses on the highly interconnected regulatory networks in Saccharomyces cerevisiae and Pichia pastoris and identifying their components. We discuss the current knowledge on the carbon catabolite repression (CCR) mechanism, interconnecting regulatory system of the central metabolic pathways that regulate cell metabolism based on nutrient availability in the industrial yeasts. The regulatory proteins and their functions in the CCR signalling pathways in both yeasts are presented and discussed. We highlight the importance of metabolic signalling networks by signifying ways on how effective engineering strategies can be designed for generating novel regulatory circuits, furthermore to activate pathways that reconfigure the network architecture. We summarize the evidence that engineering of multilayer regulation is needed for directed evolution of the cellular network by putting the transcriptional control into a new perspective for the regulation of central carbon metabolism of the industrial yeasts; furthermore, we suggest research directions that may help to enhance production of recombinant products in the widely used, creatively engineered, but relatively less studied P. pastoris through de novo metabolic engineering strategies based on the discovery of components of signalling pathways in CCR metabolism. KEY POINTS: • Transcriptional regulation and control is the key phenomenon in the cellular processes. • Designing de novo metabolic engineering strategies depends on the discovery of signalling pathways in CCR metabolism. • Crosstalk between pathways occurs through essential parts of transcriptional machinery connected to specific catalytic domains. • In S. cerevisiae, a major part of CCR metabolism is controlled through Snf1 kinase, Glc7 phosphatase, and Srb10 kinase. • In P. pastoris, signalling pathways in CCR metabolism have not yet been clearly known yet. • Cellular regulations on the transcription of promoters are controlled with carbon sources.
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Wāng Y, Wang R, Wáng Y, Li Y, Yang RH, Gong M, Shang JJ, Zhang JS, Mao WJ, Zou G, Bao DP. Diverse function and regulation of CmSnf1 in entomopathogenic fungus Cordyceps militaris. Fungal Genet Biol 2020; 142:103415. [PMID: 32497577 DOI: 10.1016/j.fgb.2020.103415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
SNF1/AMPK protein kinases play important roles in fungal development and activation of catabolite-repressed genes. In this study, we characterized the role of SNF1 ortholog in Cordyceps militaris (CmSnf1). The vegetative growth of a CmSnf1 deletion mutant was (ΔCmSnf1) reduced by 42.2% with arabinose as a sole carbon source. Most strikingly, the ΔCmSnf1 produced only a few conidia and exhibited delayed conidial germination. We found that CmSnf1 was necessary for mycelium to penetrate the insect cuticle to form the fruiting body on silkworm pupae, consistent with the down-regulation of chitinase- and protease-encoding genes in ΔCmSnf1. However, cordycepin content increased by more than 7 times in culture supernatants. Correspondingly, the relative expression levels of cordycepin gene cluster members were also elevated. In particular, the expression of cns4 associated with cordycepin transfer was up-regulated >10-fold. Furthermore, transcriptional analysis showed that CmSnf1 regulated the expression of genes involved in cell autophagy and oxidative stress tolerance. We speculated that under environmental stress, both the ATG and SNF1 pathways might collaborate to sustain adverse environments. Our study provides an initial framework to probe the diverse function and regulation of CmSnf1 in C. militaris, which will shed more light on the direction of molecular improvement of medicinal fungi.
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Affiliation(s)
- Ying Wāng
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China
| | - Rong Wang
- Plant Immunity Center, Haixia Institute of Science and Technology, Fujian Agriculture and Foresty University, Fujian 350002, PR China
| | - Ying Wáng
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China
| | - Yan Li
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China
| | - Rui-Heng Yang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China
| | - Ming Gong
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China
| | - Jun-Jun Shang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China
| | - Jin-Song Zhang
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China
| | - Wen-Jun Mao
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China
| | - Gen Zou
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China.
| | - Da-Peng Bao
- National Engineering Research Centre of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, PR China.
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Songdech P, Ruchala J, Semkiv MV, Jensen LT, Sibirny A, Ratanakhanokchai K, Soontorngun N. Overexpression of Transcription Factor ZNF1 of Glycolysis Improves Bioethanol Productivity under High Glucose Concentration and Enhances Acetic Acid Tolerance of Saccharomyces cerevisiae. Biotechnol J 2020; 15:e1900492. [PMID: 32196937 DOI: 10.1002/biot.201900492] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/01/2020] [Indexed: 12/28/2022]
Abstract
Saccharomyces cerevisiae offers an attractive platform for synthesis of biofuels and biochemical; however, robust strains that can withstand high substrate concentration and fermentation conditions are required. To improve the yield and productivity of bioethanol, modification of glucose metabolism and cellular stress adaptation is investigated. Specifically, the role of Znf1 transcription factor in metabolic regulation of glucose is characterized. Here, Znf1 is first shown to activate key genes in glycolysis, pyruvate metabolism, and alcoholic fermentation when glucose is provided as the sole carbon source. Under conditions of high glucose (20 g L-1 ), overexpression of ZNF1 accelerated glucose consumption with only 0.67-0.80% of glucose remaining after 24 or 36 h of fermentation. Importantly, ZNF1 overexpression increases ethanol concentrations by 14-24% and achieves a maximum ethanol concentration of 76.12-88.60 g L-1 . Ethanol productivity is increased 3.17-3.69 in strains overexpressing ZNF1 compared to 2.42-3.35 and 2.94-3.50 for the znf1Δ and wild-type strains, respectively. Moreover, strains overexpressing ZNF1 also display enhanced tolerance to osmotic and weak-acid stresses, important trait in alcoholic fermentation. Overexpresssion of key transcriptional activators of genes in glycolysis and stress responses appears to be an effective strategy to improve bioethanol productivity and enhance strain robustness.
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Affiliation(s)
- Pattanan Songdech
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Justyna Ruchala
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, 35-601, Poland
| | - Marta V Semkiv
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Lviv, 79005, Ukraine
| | - Laran T Jensen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Andriy Sibirny
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Lviv, 79005, Ukraine
| | - Khanok Ratanakhanokchai
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Nitnipa Soontorngun
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
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48
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Zhou XL, Ouyang Z, Zhang XL, Wei YQ, Tang SX, Tan ZL, Wang CJ, He ZX, Teklebrhan T, Han XF. Effects of a high-dose Saccharomyces cerevisiae inoculum alone or in combination with Lactobacillus plantarum on the nutritional composition and fermentation traits of maize silage. ANIMAL PRODUCTION SCIENCE 2020. [DOI: 10.1071/an18701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
The inoculation of silage with Saccharomyces cerevisiae to deliver viable yeast cells is a novel concept.
Aims
The effects of a high-dose S. cerevisiae inoculum alone or combined with Lactobacillus plantarum on the nutritional composition, fermentation traits and aerobic stability of maize silage were studied after 30, 60 and 90 days of storage.
Methods
Whole-crop maize (309.3 g dry matter (DM)/kg as fed) was subjected to one of three treatments: deionised water (untreated control); S. cerevisiae at an estimated concentration of 108 CFU/g fresh forage (S); or S. cerevisiae at an estimated concentration of 108 CFU/g and L. plantarum at an estimated concentration of 105 CFU/g of fresh forage (SL).
Key results
Compared with the control, the S and SL groups showed increases (P < 0.001) in average pH (3.98 in S and 4.01 in SL vs 3.65 in the control), crude protein (85 g/kg DM in S and 80 g/kg DM in SL vs 63 g/kg DM in the control) and ammonia nitrogen/total nitrogen (122.2 g/kg in S and 163.9 g/kg in SL vs 52.9 g/kg in the control) but a lower (P < 0.001) average concentration of water-soluble carbohydrate (0.9 g/kg DM in S and 0.7 g/kg DM in SL vs 2.3 g/kg DM in the control). The levels of neutral detergent fibre and acid detergent fibre were greater (P < 0.001) in S silage than in the control and SL silages, and the hemicellulose level was lower (P = 0.004) in the SL group than the control and S groups. Starch and aerobic stability were unaffected by treatment, and the average lactate and ethanol concentrations were higher (P < 0.001) in the S (53.7 g lactate/kg DM and 28.7 g ethanol/kg DM) and SL (56.9 g lactate/kg DM and 21.4 g ethanol/kg DM) groups than the control (40.1 g lactate/kg DM and 5.3 g ethanol/kg DM) over 90 days of ensiling.
Conclusions
Overall, a high-dose inoculum of S. cerevisiae alone or combined with L. plantarum affected the nutritional composition and fermentation traits of maize silage.
Implications
The inoculation of maize silage with a high dose of S. cerevisiae needs to be performed with caution.
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Espinosa MI, Williams TC, Pretorius IS, Paulsen IT. Benchmarking two Saccharomyces cerevisiae laboratory strains for growth and transcriptional response to methanol. Synth Syst Biotechnol 2019; 4:180-188. [PMID: 31667368 PMCID: PMC6807065 DOI: 10.1016/j.synbio.2019.10.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/27/2019] [Accepted: 10/03/2019] [Indexed: 11/21/2022] Open
Abstract
One-carbon compounds, such as methanol, are becoming potential alternatives to sugars as feedstocks for the biological production of chemicals, fuels, foods, and pharmaceuticals. Efficient biological production often requires extensive genetic manipulation of a microbial host strain, making well-characterised and genetically-tractable model organisms like the yeast Saccharomyces cerevisiae attractive targets for the engineering of methylotrophic metabolism. S. cerevisiae strains S288C and CEN.PK are the two best-characterised and most widely used hosts for yeast synthetic biology and metabolic engineering, yet they have unpredictable metabolic phenotypes related to their many genomic differences. We therefore sought to benchmark these two strains as potential hosts for engineered methylotrophic metabolism by comparing their growth and transcriptomic responses to methanol. CEN.PK had improved growth in the presence of methanol relative to the S288C derivative BY4741. The CEN.PK transcriptome also had a specific and relevant response to methanol that was either absent or less pronounced in the BY4741 strain. This response included up-regulation of genes associated with mitochondrial and peroxisomal metabolism, alcohol and formate dehydrogenation, glutathione metabolism, and the global transcriptional regulator of metabolism MIG3. Over-expression of MIG3 enabled improved growth in the presence of methanol, suggesting that MIG3 is a mediator of the superior CEN.PK strain growth. CEN.PK was therefore identified as a superior strain for the future development of synthetic methylotrophy in S. cerevisiae.
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Affiliation(s)
- Monica I. Espinosa
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, 2601, Australia
| | - Thomas C. Williams
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, NSW, Australia
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT, 2601, Australia
| | - Isak S. Pretorius
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, NSW, Australia
| | - Ian T. Paulsen
- ARC Centre of Excellence in Synthetic Biology, Department of Molecular Sciences, Macquarie University, NSW, Australia
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50
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Vengayil V, Rashida Z, Laxman S. The E3 ubiquitin ligase Pib1 regulates effective gluconeogenic shutdown upon glucose availability. J Biol Chem 2019; 294:17209-17223. [PMID: 31604822 PMCID: PMC6873170 DOI: 10.1074/jbc.ra119.009822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/27/2019] [Indexed: 12/31/2022] Open
Abstract
Cells use multiple mechanisms to regulate their metabolic states in response to changes in their nutrient environment. One example is the response of cells to glucose. In Saccharomyces cerevisiae growing in glucose-depleted medium, the re-availability of glucose leads to the down-regulation of gluconeogenesis and the activation of glycolysis, leading to "glucose repression." However, our knowledge of the mechanisms mediating the glucose-dependent down-regulation of the gluconeogenic transcription factors is limited. Using the major gluconeogenic transcription factor Rds2 as a candidate, we identify here a novel role for the E3 ubiquitin ligase Pib1 in regulating the stability and degradation of Rds2. Glucose addition to cells growing under glucose limitation results in a rapid ubiquitination of Rds2, followed by its proteasomal degradation. Through in vivo and in vitro experiments, we establish Pib1 as the ubiquitin E3 ligase that regulates Rds2 ubiquitination and stability. Notably, this Pib1-mediated Rds2 ubiquitination, followed by proteasomal degradation, is specific to the presence of glucose. This Pib1-mediated ubiquitination of Rds2 depends on the phosphorylation state of Rds2, suggesting a cross-talk between ubiquitination and phosphorylation to achieve a metabolic state change. Using stable isotope-based metabolic flux experiments, we find that the loss of Pib1 results in an imbalanced gluconeogenic state, regardless of glucose availability. Pib1 is required for complete glucose repression and enables cells to optimally grow in competitive environments when glucose again becomes available. Our results reveal the existence of a Pib1-mediated regulatory program that mediates glucose repression when glucose availability is restored.
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Affiliation(s)
- Vineeth Vengayil
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK Post, Bellary Road, Bangalore 560065, India
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