1
|
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.
Collapse
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
| |
Collapse
|
2
|
Ke CL, Lew SQ, Hsieh Y, Chang SC, Lin CH. Convergent and divergent roles of the glucose-responsive kinase SNF4 in Candida tropicalis. Virulence 2023; 14:2175914. [PMID: 36745535 PMCID: PMC9928470 DOI: 10.1080/21505594.2023.2175914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The sucrose non-fermenting 1 (SNF1) complex is a heterotrimeric protein kinase complex that is an ortholog of the mammalian AMPK complex and is evolutionally conserved in most eukaryotes. This complex contains a catalytic subunit (Snf1), a regulatory subunit (Snf4) and a scaffolding subunit (Sip1/Sip2/Gal73) in budding yeast. Although the function of AMPK has been well studied in Saccharomyces cerevisiae and Candida albicans, the role of AMPK in Candida tropicalis has never been investigated. In this study, we focused on SNF4 in C. tropicalis as this fungus cannot produce a snf1Δ mutant. We demonstrated that C. tropicalis SNF4 shares similar roles in glucose derepression and is necessary for cell wall integrity and virulence. The expression of both SNF1 and SNF4 was significantly induced when glucose was limited. Furthermore, snf4Δ strains exhibited high sensitivity to many surface-perturbing agents because the strains contained lower levels of glucan, chitin and mannan. Interestingly, in contrast to C. albicans sak1Δ and snf4Δ, C. tropicalis snf4Δ exhibited phenotypes for cell aggregation and pseudohypha production. These data indicate that SNF4 performs convergent and divergent roles in C. tropicalis and possibly other unknown roles in the C. tropicalis SNF1-SNF4 AMPK pathway.
Collapse
Affiliation(s)
- Cai-Ling Ke
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Shi Qian Lew
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Yi Hsieh
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Szu-Cheng Chang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Ching-Hsuan Lin
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei, Taiwan,CONTACT Ching-Hsuan Lin
| |
Collapse
|
3
|
Giwa AS, Ali N, Akhter MS. Cellulose Degradation Enzymes in Filamentous Fungi, A Bioprocessing Approach Towards Biorefinery. Mol Biotechnol 2023:10.1007/s12033-023-00900-1. [PMID: 37839042 DOI: 10.1007/s12033-023-00900-1] [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: 03/07/2023] [Accepted: 09/04/2023] [Indexed: 10/17/2023]
Abstract
The economic exploration of renewable energy resources has hot fundamentals among the countries besides dwindling energy resources and increasing public pressure. Cellulose accumulation is a major bio-natural resource from agricultural waste. Cellulases are the most potential enzymes that systematically degrade cellulosic biomass into monomers which could be further processed into several efficient value-added products via chemical and biological reactions including useful biomaterial for human benefits. This could lower the environmental risks problems followed by an energy crisis. Cellulases are mainly synthesized by special fungal genotypes. The strain Trichoderma orientalis could highly express cellulases and was regarded as an ideal strain for further research, as the genetic tools have found compatibility for cellulose breakdown by producing effective cellulose-degrading enzymes. This strain has found a cellulase production of about 35 g/L that needs further studies for advancement. The enzyme activity of strain Trichoderma orientalis needed to be further improved from a molecular level which is one of the important methods. Considering synthetic biological approaches to unveil the genetic tools will boost the knowledge about commercial cellulases bioproduction. Several genetic transformation methods were significantly cited in this study. The transformation approaches that are currently researchers are exploring is transcription regulatory factors that are deeply explained in this study, that are considered essential regulators of gene expression.
Collapse
Affiliation(s)
- Abdulmoseen Segun Giwa
- School of Environment and Civil Engineering, Nanchang Institute of Science and Technology, Nanchang, 330108, China
| | - Nasir Ali
- Institute of Biotechnology Genetic Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan.
| | - Mohammed Salim Akhter
- Department of Chemistry, College of Science, University of Bahrain, Sakheer Campus Bahrain, Zallaq, Bahrain
| |
Collapse
|
4
|
Attfield PV. Crucial aspects of metabolism and cell biology relating to industrial production and processing of Saccharomyces biomass. Crit Rev Biotechnol 2023; 43:920-937. [PMID: 35731243 DOI: 10.1080/07388551.2022.2072268] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/27/2022] [Accepted: 04/21/2022] [Indexed: 12/16/2022]
Abstract
The multitude of applications to which Saccharomyces spp. are put makes these yeasts the most prolific of industrial microorganisms. This review considers biological aspects pertaining to the manufacture of industrial yeast biomass. It is proposed that the production of yeast biomass can be considered in two distinct but interdependent phases. Firstly, there is a cell replication phase that involves reproduction of cells by their transitions through multiple budding and metabolic cycles. Secondly, there needs to be a cell conditioning phase that enables the accrued biomass to withstand the physicochemical challenges associated with downstream processing and storage. The production of yeast biomass is not simply a case of providing sugar, nutrients, and other growth conditions to enable multiple budding cycles to occur. In the latter stages of culturing, it is important that all cells are induced to complete their current budding cycle and subsequently enter into a quiescent state engendering robustness. Both the cell replication and conditioning phases need to be optimized and considered in concert to ensure good biomass production economics, and optimum performance of industrial yeasts in food and fermentation applications. Key features of metabolism and cell biology affecting replication and conditioning of industrial Saccharomyces are presented. Alternatives for growth substrates are discussed, along with the challenges and prospects associated with defining the genetic bases of industrially important phenotypes, and the generation of new yeast strains."I must be cruel only to be kind: Thus bad begins, and worse remains behind." William Shakespeare: Hamlet, Act 3, Scene 4.
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Liu Y, Zhou Z, Wu S, Ni G, Zhang A, Tsimring LS, Hasty J, Hao N. Enhanced cellular longevity arising from environmental fluctuations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547867. [PMID: 37461504 PMCID: PMC10350066 DOI: 10.1101/2023.07.05.547867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Cellular longevity is regulated by both genetic and environmental factors. However, the interactions of these factors in the context of aging remain largely unclear. Here, we formulate a mathematical model for dynamic glucose modulation of a core gene circuit in yeast aging, which not only guided the design of pro-longevity interventions, but also revealed the theoretical principles underlying these interventions. We introduce the dynamical systems theory to capture two general means for promoting longevity - the creation of a stable fixed point in the "healthy" state of the cell and the dynamic stabilization of the system around this healthy state through environmental oscillations. Guided by the model, we investigate how both of these can be experimentally realized by dynamically modulating environmental glucose levels. The results establish a paradigm for theoretically analyzing the trajectories and perturbations of aging that can be generalized to aging processes in diverse cell types and organisms.
Collapse
Affiliation(s)
- Yuting Liu
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhen Zhou
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Songlin Wu
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gavin Ni
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alex Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lev S. Tsimring
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
| | - Jeff Hasty
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Nan Hao
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Synthetic Biology Institute, University of California San Diego, La Jolla, CA 92093, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
7
|
Gong C, Xu D, Sun D, Kang J, Wang W, Xu JR, Zhang X. FgSnt1 of the Set3 HDAC complex plays a key role in mediating the regulation of histone acetylation by the cAMP-PKA pathway in Fusarium graminearum. PLoS Genet 2022; 18:e1010510. [PMID: 36477146 PMCID: PMC9728937 DOI: 10.1371/journal.pgen.1010510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
The cAMP-PKA pathway is critical for regulating growth, differentiation, and pathogenesis in fungal pathogens. In Fusarium graminearum, mutants deleted of PKR regulatory-subunit of PKA had severe defects but often produced spontaneous suppressors. In this study eleven pkr suppressors were found to have mutations in FgSNT1, a component of the Set3C histone deacetylase (HDAC) complex, that result in the truncation of its C-terminal region. Targeted deletion of the C-terminal 98 aa (CT98) in FgSNT1 suppressed the defects of pkr in growth and H4 acetylation. CT98 truncation also increased the interaction of FgSnt1 with Hdf1, a major HDAC in the Set3 complex. The pkr mutant had no detectable expression of the Cpk1 catalytic subunit and PKA activities, which was not suppressed by mutations in FgSNT1. Cpk1 directly interacted with the N-terminal region of FgSnt1 and phosphorylated it at S443, a conserved PKA-phosphorylation site. CT98 of FgSnt1 carrying the S443D mutation interacted with its own N-terminal region. Expression of FgSNT1S443D rescued the defects of pkr in growth and H4 acetylation. Therefore, phosphorylation at S443 and suppressor mutations may relieve self-inhibitory binding of FgSnt1 and increase its interaction with Hdf1 and H4 acetylation, indicating a key role of FgSnt1 in crosstalk between cAMP signaling and Set3 complex.
Collapse
Affiliation(s)
- Chen Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Daiying Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Daiyuan Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jiangang Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Wei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (J-RX); (XZ)
| | - Xue Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- * E-mail: (J-RX); (XZ)
| |
Collapse
|
8
|
Abstract
Most cells live in environments that are permissive for proliferation only a small fraction of the time. Entering quiescence enables cells to survive long periods of nondivision and reenter the cell cycle when signaled to do so. Here, we describe what is known about the molecular basis for quiescence in Saccharomyces cerevisiae, with emphasis on the progress made in the last decade. Quiescence is triggered by depletion of an essential nutrient. It begins well before nutrient exhaustion, and there is extensive crosstalk between signaling pathways to ensure that all proliferation-specific activities are stopped when any one essential nutrient is limiting. Every aspect of gene expression is modified to redirect and conserve resources. Chromatin structure and composition change on a global scale, from histone modifications to three-dimensional chromatin structure. Thousands of proteins and RNAs aggregate, forming unique structures with unique fates, and the cytoplasm transitions to a glass-like state.
Collapse
Affiliation(s)
- Linda L Breeden
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA; ,
| |
Collapse
|
9
|
Chatfield-Reed K, Marno Jones K, Shah F, Chua G. Genetic-interaction screens uncover novel biological roles and regulators of transcription factors in fission yeast. G3 GENES|GENOMES|GENETICS 2022; 12:6655692. [PMID: 35924983 PMCID: PMC9434175 DOI: 10.1093/g3journal/jkac194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 12/05/2022]
Abstract
In Schizosaccharomyces pombe, systematic analyses of single transcription factor deletion or overexpression strains have made substantial advances in determining the biological roles and target genes of transcription factors, yet these characteristics are still relatively unknown for over a quarter of them. Moreover, the comprehensive list of proteins that regulate transcription factors remains incomplete. To further characterize Schizosaccharomyces pombe transcription factors, we performed synthetic sick/lethality and synthetic dosage lethality screens by synthetic genetic array. Examination of 2,672 transcription factor double deletion strains revealed a sick/lethality interaction frequency of 1.72%. Phenotypic analysis of these sick/lethality strains revealed potential cell cycle roles for several poorly characterized transcription factors, including SPBC56F2.05, SPCC320.03, and SPAC3C7.04. In addition, we examined synthetic dosage lethality interactions between 14 transcription factors and a miniarray of 279 deletion strains, observing a synthetic dosage lethality frequency of 4.99%, which consisted of known and novel transcription factor regulators. The miniarray contained deletions of genes that encode primarily posttranslational-modifying enzymes to identify putative upstream regulators of the transcription factor query strains. We discovered that ubiquitin ligase Ubr1 and its E2/E3-interacting protein, Mub1, degrade the glucose-responsive transcriptional repressor Scr1. Loss of ubr1+ or mub1+ increased Scr1 protein expression, which resulted in enhanced repression of flocculation through Scr1. The synthetic dosage lethality screen also captured interactions between Scr1 and 2 of its known repressors, Sds23 and Amk2, each affecting flocculation through Scr1 by influencing its nuclear localization. Our study demonstrates that sick/lethality and synthetic dosage lethality screens can be effective in uncovering novel functions and regulators of Schizosaccharomyces pombe transcription factors.
Collapse
Affiliation(s)
- Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Kurtis Marno Jones
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | - Farah Shah
- Department of Biological Sciences, University of Calgary , Calgary, Alberta T2N 1N4, Canada
| | | |
Collapse
|
10
|
Snf1p/Hxk2p/Mig1p pathway regulates hexose transporters transcript levels, affecting the exponential growth and mitochondrial respiration of Saccharomyces cerevisiae. Fungal Genet Biol 2022; 161:103701. [DOI: 10.1016/j.fgb.2022.103701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/12/2022] [Accepted: 04/30/2022] [Indexed: 11/19/2022]
|
11
|
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.
Collapse
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 ()
| |
Collapse
|
12
|
Zinc finger protein LipR represses docosahexaenoic acid and lipid biosynthesis in Schizochytrium sp. Appl Environ Microbiol 2022; 88:e0206321. [PMID: 35108079 DOI: 10.1128/aem.02063-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The heterotrophic marine microalgae Schizochytrium sp. is an important industrial producer of docosahexaenoic acid (DHA). Increased production of DHA and lipids in Schizochytrium sp. have been achieved by standard fermentation optimization and metabolic engineering methods; however, regulatory mechanisms for DHA and lipid biosynthesis remain unknown. In this study, the C2H2 zinc finger protein LipR was identified in Schizochytrium sp. ATCC20888 by transcriptional analysis. Deletion of the lipR gene significantly (p< 0.001) increased production of total lipids and DHA by (respectively) 33% and 48%. LipR repressed DHA and lipid production by directly inhibiting transcription of polyunsaturated fatty acid (PUFA) and fatty acid synthase (FAS) genes (pfa1, pfa2, pfa3, fas). Specific binding of LipR to 9-bp recognition sequence 5'-(C/A)(A/G)CCATCTT-3' in upstream regions of target genes was demonstrated by electrophoretic mobility shift assays (EMSAs) and DNase I footprinting assays. Expression of several key genes (acc, acl, ampD, fabD, mae, zwf, dga1) related to levels of precursors and NADPH, and to triacylglycerol storage rate, were also directly repressed by LipR. Our findings, taken together, indicate that the evolutionarily unique regulator LipR is an essential repressor of DHA and saturated fatty acid biosynthesis in Schizochytrium sp. Importance Regulatory mechanisms for DHA and saturated fatty acid biosynthesis in the heterotrophic marine microalgae Schizochytrium sp. are unclear. We demonstrate here that deletion of the gene (lipR) encoding the C2H2 zinc finger protein LipR promotes DHA and saturated fatty acid production in this genus. LipR acts as a key repressor of such production by binding to 9-bp consensus sequence 5'-(C/A)(A/G)CCATCTT-3' in the upstream regions of polyunsaturated fatty acid and fatty acid synthase genes (pfa1, pfa2, pfa3, fas), and genes related to levels of precursors and NADPH (acc, acl, ampD, fabD, mae, zwf), and to triacylglycerol storage rate (dga1). This is the first demonstration that a regulator inhibits synthesis of DHA and lipids in Schizochytrium sp. by directly controlling transcription of PUFA synthase and fas genes. Manipulation of the lipR gene provides a potential strategy for enhancing accumulation of polyunsaturated fatty acids and lipids in thraustochytrids.
Collapse
|
13
|
Gan Y, Qi X, Lin Y, Guo Y, Zhang Y, Wang Q. A Hierarchical Transcriptional Regulatory Network Required for Long-Term Thermal Stress Tolerance in an Industrial Saccharomyces cerevisiae Strain. Front Bioeng Biotechnol 2022; 9:826238. [PMID: 35118059 PMCID: PMC8804346 DOI: 10.3389/fbioe.2021.826238] [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: 11/30/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
Yeast cells suffer from continuous and long-term thermal stress during high-temperature ethanol fermentation. Understanding the mechanism of yeast thermotolerance is important not only for studying microbial stress biology in basic research but also for developing thermotolerant strains for industrial application. Here, we compared the effects of 23 transcription factor (TF) deletions on high-temperature ethanol fermentation and cell survival after heat shock treatment and identified three core TFs, Sin3p, Srb2p and Mig1p, that are involved in regulating the response to long-term thermotolerance. Further analyses of comparative transcriptome profiling of the core TF deletions and transcription regulatory associations revealed a hierarchical transcriptional regulatory network centered on these three TFs. This global transcriptional regulatory network provided a better understanding of the regulatory mechanism behind long-term thermal stress tolerance as well as potential targets for transcriptome engineering to improve the performance of high-temperature ethanol fermentation by an industrial Saccharomyces cerevisiae strain.
Collapse
Affiliation(s)
- Yuman Gan
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning, China
| | - Xianni Qi
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yuping Lin
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- *Correspondence: Qinhong Wang, ; Yuping Lin,
| | - Yufeng Guo
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Yuanyuan Zhang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Qinhong Wang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, China
- *Correspondence: Qinhong Wang, ; Yuping Lin,
| |
Collapse
|
14
|
The signaling pathways involved in metabolic regulation and stress responses of the yeast-like fungi Aureobasidium spp. Biotechnol Adv 2021; 55:107898. [PMID: 34974157 DOI: 10.1016/j.biotechadv.2021.107898] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 12/22/2022]
Abstract
Aureobasidium spp. can use a wide range of substrates and are widely distributed in different environments, suggesting that they can sense and response to various extracellular signals and be adapted to different environments. It is true that their pullulan, lipid and liamocin biosynthesis and cell growth are regulated by the cAMP-PKA signaling pathway; Polymalate (PMA) and pullulan biosynthesis is controlled by the Ca2+ and TORC1 signaling pathways; the HOG1 signaling pathway determines high osmotic tolerance and high pullulan and liamocin biosynthesis; the Snf1/Mig1 pathway controls glucose repression on pullulan and liamocin biosynthesis; DHN-melanin biosynthesis and stress resistance are regulated by the CWI signaling pathway and TORC1 signaling pathway. In addition, the HSF1 pathway may control cell growth of some novel strains of A. melanogenum at 37 °C. However, the detailed molecular mechanisms of high temperature growth and thermotolerance of some novel strains of A. melanogenum and glucose derepression in A. melanogenum TN3-1 are still unclear.
Collapse
|
15
|
Mohamed RA, Ren K, Mou YN, Ying SH, Feng MG. Genome-Wide Insight into Profound Effect of Carbon Catabolite Repressor (Cre1) on the Insect-Pathogenic Lifecycle of Beauveriabassiana. J Fungi (Basel) 2021; 7:jof7110895. [PMID: 34829184 PMCID: PMC8622151 DOI: 10.3390/jof7110895] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 11/16/2022] Open
Abstract
Carbon catabolite repression (CCR) is critical for the preferential utilization of glucose derived from environmental carbon sources and regulated by carbon catabolite repressor A (Cre1/CreA) in filamentous fungi. However, a role of Cre1-mediated CCR in insect-pathogenic fungal utilization of host nutrients during normal cuticle infection (NCI) and hemocoel colonization remains explored insufficiently. Here, we report an indispensability of Cre1 for Beauveriabassiana's utilization of nutrients in insect integument and hemocoel. Deletion of cre1 resulted in severe defects in radial growth on various media, hypersensitivity to oxidative stress, abolished pathogenicity via NCI or intrahemocoel injection (cuticle-bypassing infection) but no change in conidial hydrophobicity and adherence to insect cuticle. Markedly reduced biomass accumulation in the Δcre1 cultures was directly causative of severe defect in aerial conidiation and reduced secretion of various cuticle-degrading enzymes. The majority (1117) of 1881 dysregulated genes identified from the Δcre1 versus wild-type cultures were significantly downregulated, leading to substantial repression of many enriched function terms and pathways, particularly those involved in carbon and nitrogen metabolisms, cuticle degradation, antioxidant response, cellular transport and homeostasis, and direct/indirect gene mediation. These findings offer a novel insight into profound effect of Cre1 on the insect-pathogenic lifestyle of B. bassiana.
Collapse
|
16
|
Lettow J, Aref R, Schüller HJ. Transcriptional repressor Gal80 recruits corepressor complex Cyc8-Tup1 to structural genes of the Saccharomyces cerevisiae GAL regulon. Curr Genet 2021; 68:115-124. [PMID: 34622331 PMCID: PMC8801411 DOI: 10.1007/s00294-021-01215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/14/2021] [Accepted: 09/26/2021] [Indexed: 11/30/2022]
Abstract
Under non-inducing conditions (absence of galactose), yeast structural genes of the GAL regulon are repressed by Gal80, preventing interaction of Gal4 bound to UASGAL promoter motifs with general factors of the transcriptional machinery. In this work, we show that Gal80 is also able to interact with histone deacetylase-recruiting corepressor proteins Cyc8 and Tup1, indicating an additional mechanism of gene repression. This is supported by our demonstration that a lexA–Gal80 fusion efficiently mediates repression of a reporter gene with an upstream lexA operator sequence. Corepressor interaction and in vivo gene repression could be mapped to a Gal80 minimal domain of 65 amino acids (aa 81-145). Site-directed mutagenesis of selected residues within this domain showed that a cluster of aromatic-hydrophobic amino acids (YLFV, aa 118-121) is important, although not solely responsible, for gene repression. Using chromatin immunoprecipitation, Cyc8 and Tup1 were shown to be present at the GAL1 promoter in a wild-type strain but not in a gal80 mutant strain under non-inducing (derepressing) growth conditions. Expression of a GAL1–lacZ fusion was elevated in a tup1 mutant (but not in a cyc8 mutant) grown in derepressing medium, indicating that Tup1 may be mainly responsible for this second mechanism of Gal80-dependent gene repression.
Collapse
Affiliation(s)
- Julia Lettow
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Felix-Hausdorff-Str. 8, 17487, Greifswald, Germany
| | - Rasha Aref
- Department of Genetics, Faculty of Agriculture, Ain Shams University, Shoubra El-Khaymah, Cairo, 11241, Egypt
| | - Hans-Joachim Schüller
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Felix-Hausdorff-Str. 8, 17487, Greifswald, Germany.
| |
Collapse
|
17
|
Kurylenko O, Ruchala J, Kruk B, Vasylyshyn R, Szczepaniak J, Dmytruk K, Sibirny A. The role of Mig1, Mig2, Tup1 and Hap4 transcription factors in regulation of xylose and glucose fermentation in the thermotolerant yeast Ogataea polymorpha. FEMS Yeast Res 2021; 21:6275188. [PMID: 33983391 DOI: 10.1093/femsyr/foab029] [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: 11/01/2020] [Accepted: 05/07/2021] [Indexed: 01/20/2023] Open
Abstract
Glucose is a preferred carbon source for most living organisms. The metabolism and regulation of glucose utilization are well studied mostly for Saccharomyces cerevisiae. Xylose is the main pentose sugar released from the lignocellulosic biomass, which has a high potential as a renewable feedstock for bioethanol production. The thermotolerant yeast Ogataea (Hansenula) polymorpha, in contrast to S. cerevisiae, is able to metabolize and ferment not only glucose but also xylose. However, in non-conventional yeasts, the regulation of glucose and xylose metabolism remains poorly understood. In this study, we characterize the role of transcriptional factors Mig1, Mig2, Tup1 and Hap4 in the natural xylose-fermenting yeast O. polymorpha. The deletion of MIG1 had no significant influence on ethanol production either from xylose or glucose, however the deletion of both MIG1 and MIG2 reduced the amount of ethanol produced from these sugars. The deletion of HAP4-A and TUP1 genes resulted in increased ethanol production from xylose. Inversely, the overexpression of HAP4-A and TUP1 genes reduced ethanol production during xylose alcoholic fermentation. Thus, HAP4-A and TUP1 are involved in repression of xylose metabolism and fermentation in yeast O. polymorpha and their deletion could be a viable strategy to improve ethanol production from this pentose.
Collapse
Affiliation(s)
- Olena Kurylenko
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Justyna Ruchala
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine.,Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Barbara Kruk
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Roksolana Vasylyshyn
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Justyna Szczepaniak
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| | - Kostyantyn Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine.,Department of Microbiology and Molecular Genetics, University of Rzeszow, Cwiklinskiej 2D, Building D10, Rzeszow 35-601, Poland
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Carbon Catabolite Repression Governs Diverse Physiological Processes and Development in Aspergillus nidulans. mBio 2021; 13:e0373421. [PMID: 35164551 PMCID: PMC8844935 DOI: 10.1128/mbio.03734-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Carbon catabolite repression (CCR) is a common phenomenon of microorganisms that enable efficient utilization of carbon nutrients, critical for the fitness of microorganisms in the wild and for pathogenic species to cause infection. In most filamentous fungal species, the conserved transcription factor CreA/Cre1 mediates CCR. Previous studies demonstrated a primary function for CreA/Cre1 in carbon metabolism; however, the phenotype of creA/cre1 mutants indicated broader roles. The global function and regulatory mechanism of this wide-domain transcription factor has remained elusive. Here, we applied two powerful genomics methods (transcriptome sequencing and chromatin immunoprecipitation sequencing) to delineate the direct and indirect roles of Aspergillus nidulans CreA across diverse physiological processes, including secondary metabolism, iron homeostasis, oxidative stress response, development, N-glycan biosynthesis, unfolded protein response, and nutrient and ion transport. The results indicate intricate connections between the regulation of carbon metabolism and diverse cellular functions. Moreover, our work also provides key mechanistic insights into CreA regulation and identifies CreA as a master regulator controlling many transcription factors of different regulatory networks. The discoveries for this highly conserved transcriptional regulator in a model fungus have important implications for CCR in related pathogenic and industrial species. IMPORTANCE The ability to scavenge and use a wide range of nutrients for growth is crucial for microorganisms' survival in the wild. Carbon catabolite repression (CCR) is a transcriptional regulatory phenomenon of both bacteria and fungi to coordinate the expression of genes required for preferential utilization of carbon sources. Since carbon metabolism is essential for growth, CCR is central to the fitness of microorganisms. In filamentous fungi, CCR is mediated by the conserved transcription factor CreA/Cre1, whose function in carbon metabolism has been well established. However, the global roles and regulatory mechanism of CreA/Cre1 are poorly defined. This study uncovers the direct and indirect functions of CreA in the model organism Aspergillus nidulans over diverse physiological processes and development and provides mechanistic insights into how CreA controls different regulatory networks. The work also reveals an interesting functional divergence between filamentous fungal and yeast CreA/Cre1 orthologues.
Collapse
|
20
|
Laidlaw KME, Bisinski DD, Shashkova S, Paine KM, Veillon MA, Leake MC, MacDonald C. A glucose-starvation response governs endocytic trafficking and eisosomal retention of surface cargoes in budding yeast. J Cell Sci 2021; 134:224110. [PMID: 33443082 PMCID: PMC7860119 DOI: 10.1242/jcs.257733] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 12/07/2020] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic cells adapt their metabolism to the extracellular environment. Downregulation of surface cargo proteins in response to nutrient stress reduces the burden of anabolic processes whilst elevating catabolic production in the lysosome. We show that glucose starvation in yeast triggers a transcriptional response that increases internalisation from the plasma membrane. Nuclear export of the Mig1 transcriptional repressor in response to glucose starvation increases levels of the Yap1801 and Yap1802 clathrin adaptors, which is sufficient to increase cargo internalisation. Beyond this, we show that glucose starvation results in Mig1-independent transcriptional upregulation of various eisosomal factors. These factors serve to sequester a portion of nutrient transporters at existing eisosomes, through the presence of Ygr130c and biochemical and biophysical changes in Pil1, allowing cells to persist throughout the starvation period and maximise nutrient uptake upon return to replete conditions. This provides a physiological benefit for cells to rapidly recover from glucose starvation. Collectively, this remodelling of the surface protein landscape during glucose starvation calibrates metabolism to available nutrients.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Kamilla M E Laidlaw
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Daniel D Bisinski
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Sviatlana Shashkova
- York Biomedical Research Institute and Department of Biology, University of York, York, UK.,Department of Physics, University of York, York YO10 5DD, UK
| | - Katherine M Paine
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Malaury A Veillon
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| | - Mark C Leake
- York Biomedical Research Institute and Department of Biology, University of York, York, UK.,Department of Physics, University of York, York YO10 5DD, UK
| | - Chris MacDonald
- York Biomedical Research Institute and Department of Biology, University of York, York, UK
| |
Collapse
|
21
|
Schmidt MC, O'Donnell AF. 'Sugarcoating' 2-deoxyglucose: mechanisms that suppress its toxic effects. Curr Genet 2020; 67:107-114. [PMID: 33136227 PMCID: PMC7886833 DOI: 10.1007/s00294-020-01122-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/06/2020] [Accepted: 10/19/2020] [Indexed: 12/14/2022]
Abstract
Yeast and cancer cells are metabolically similar as they use fermentation of glucose as a primary means of generating energy. Reliance on glucose fermentation makes both of these cell types highly sensitive to the toxic glucose analog, 2-deoxyglucose. Here we review the cellular and metabolic pathways that play a role in 2-deoxyglucose sensitivity and discuss how the modifications to these pathways result in acquisition of 2-deoxyglucose resistance. Insights gained from genetic and proteomic studies in yeast provide new ideas for the design of combinatorial therapies for cancer treatment.
Collapse
Affiliation(s)
- Martin C Schmidt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA.
| | - Allyson F O'Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| |
Collapse
|
22
|
Snf1 AMPK positively regulates ER-phagy via expression control of Atg39 autophagy receptor in yeast ER stress response. PLoS Genet 2020; 16:e1009053. [PMID: 32986716 PMCID: PMC7544123 DOI: 10.1371/journal.pgen.1009053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 10/08/2020] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
Autophagy is a fundamental process responsible for degradation and recycling of intracellular contents. In the budding yeast, non-selective macroautophagy and microautophagy of the endoplasmic reticulum (ER) are caused by ER stress, the circumstance where aberrant proteins accumulate in the ER. The more recent study showed that protein aggregation in the ER initiates ER-selective macroautophagy, referred to as ER-phagy; however, the mechanisms by which ER stress induces ER-phagy have not been fully elucidated. Here, we show that the expression levels of ATG39, encoding an autophagy receptor specific for ER-phagy, are significantly increased under ER-stressed conditions. ATG39 upregulation in ER stress response is mediated by activation of its promoter, which is positively regulated by Snf1 AMP-activated protein kinase (AMPK) and negatively by Mig1 and Mig2 transcriptional repressors. In response to ER stress, Snf1 promotes nuclear export of Mig1 and Mig2. Our results suggest that during ER stress response, Snf1 mediates activation of the ATG39 promoter and consequently facilitates ER-phagy by negatively regulating Mig1 and Mig2.
Collapse
|
23
|
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.
Collapse
|
24
|
Sukwong P, Sunwoo IY, Jeong DY, Kim SR, Jeong GT, Kim SK. Improvement of bioethanol production by Saccharomyces cerevisiae through the deletion of GLK1, MIG1 and MIG2 and overexpression of PGM2 using the red seaweed Gracilaria verrucosa. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.10.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
25
|
Lagree K, Woolford CA, Huang MY, May G, McManus CJ, Solis NV, Filler SG, Mitchell AP. Roles of Candida albicans Mig1 and Mig2 in glucose repression, pathogenicity traits, and SNF1 essentiality. PLoS Genet 2020; 16:e1008582. [PMID: 31961865 PMCID: PMC6994163 DOI: 10.1371/journal.pgen.1008582] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/31/2020] [Accepted: 12/20/2019] [Indexed: 12/16/2022] Open
Abstract
Metabolic adaptation is linked to the ability of the opportunistic pathogen Candida albicans to colonize and cause infection in diverse host tissues. One way that C. albicans controls its metabolism is through the glucose repression pathway, where expression of alternative carbon source utilization genes is repressed in the presence of its preferred carbon source, glucose. Here we carry out genetic and gene expression studies that identify transcription factors Mig1 and Mig2 as mediators of glucose repression in C. albicans. The well-studied Mig1/2 orthologs ScMig1/2 mediate glucose repression in the yeast Saccharomyces cerevisiae; our data argue that C. albicans Mig1/2 function similarly as repressors of alternative carbon source utilization genes. However, Mig1/2 functions have several distinctive features in C. albicans. First, Mig1 and Mig2 have more co-equal roles in gene regulation than their S. cerevisiae orthologs. Second, Mig1 is regulated at the level of protein accumulation, more akin to ScMig2 than ScMig1. Third, Mig1 and Mig2 are together required for a unique aspect of C. albicans biology, the expression of several pathogenicity traits. Such Mig1/2-dependent traits include the abilities to form hyphae and biofilm, tolerance of cell wall inhibitors, and ability to damage macrophage-like cells and human endothelial cells. Finally, Mig1 is required for a puzzling feature of C. albicans biology that is not shared with S. cerevisiae: the essentiality of the Snf1 protein kinase, a central eukaryotic carbon metabolism regulator. Our results integrate Mig1 and Mig2 into the C. albicans glucose repression pathway and illuminate connections among carbon control, pathogenicity, and Snf1 essentiality. All organisms tailor genetic programs to the available nutrients, such as sources of carbon. Here we define two key regulators of the genetic programs for carbon source utilization in the fungal pathogen Candida albicans. The two regulators have many shared roles, yet are partially specialized to control carbon acquisition and metabolism, respectively. In addition, the regulators together control traits associated with pathogenicity, an indication that carbon regulation is integrated into the pathogenicity program. Finally, the regulators help to explain a long-standing riddle—that the central carbon regulator Snf1 is essential for C. albicans viability.
Collapse
Affiliation(s)
- Katherine Lagree
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Carol A. Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Manning Y. Huang
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Gemma May
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - C. Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Norma V. Solis
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Scott G. Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Aaron P. Mitchell
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| |
Collapse
|
26
|
Zhang S, Jiang H, Xue S, Ge N, Sun Y, Chi Z, Liu G, Chi Z. Efficient Conversion of Cane Molasses into Fructooligosaccharides by a Glucose Derepression Mutant of Aureobasidium melanogenum with High β-Fructofuranosidase Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:13665-13672. [PMID: 31686508 DOI: 10.1021/acs.jafc.9b05826] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fructooligosaccharides (FOSs) are excellent food ingredients or feed additives by stimulating probiotics. In this paper, a CREA gene encoding a glucose repressor in the β-fructofuranosidase producer Aureobasidium melanogenum 33 with high-level FOS biosynthesis was disrupted, and glucose repression in disruptant D28 was relieved. The disruptant D28 produced up to 2100 U/mL of β-fructofuranosidase activity, whereas the enzyme activities produced by parent strain 33 and complemented strain C11 were below 600 U/mL. The whole cells of the disruptant D28 was used to convert cane molasses into FOSs, and 0.58 g of FOSs/g of molasses sugar was synthesized from 350 g/L cane molasses sugar within 4 h. Results demonstrated that the industrial waste cane molasses can be efficiently converted into FOSs by the glucose derepression mutant D28 with high β-fructofuranosidase activity. This low-cost and environmentally friendly bioprocess has great potential applications in bioengineering and biotechnology for FOS production.
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Vassiliadis D, Wong KH, Andrianopoulos A, Monahan BJ. A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe. BMC Genomics 2019; 20:251. [PMID: 30922219 PMCID: PMC6440086 DOI: 10.1186/s12864-019-5602-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/12/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Optimal glucose metabolism is central to the growth and development of cells. In microbial eukaryotes, carbon catabolite repression (CCR) mediates the preferential utilization of glucose, primarily by repressing alternate carbon source utilization. In fission yeast, CCR is mediated by transcriptional repressors Scr1 and the Tup/Ssn6 complex, with the Rst2 transcription factor important for activation of gluconeogenesis and sexual differentiation genes upon derepression. Through genetic and genome-wide methods, this study aimed to comprehensively characterize CCR in fission yeast by identifying the genes and biological processes that are regulated by Scr1, Tup/Ssn6 and Rst2, the core CCR machinery. RESULTS The transcriptional response of fission yeast to glucose-sufficient or glucose-deficient growth conditions in wild type and CCR mutant cells was determined by RNA-seq and ChIP-seq. Scr1 was found to regulate genes involved in carbon metabolism, hexose uptake, gluconeogenesis and the TCA cycle. Surprisingly, a role for Scr1 in the suppression of sexual differentiation was also identified, as homothallic scr1 deletion mutants showed ectopic meiosis in carbon and nitrogen rich conditions. ChIP-seq characterised the targets of Tup/Ssn6 and Rst2 identifying regulatory roles within and independent of CCR. Finally, a subset of genes bound by all three factors was identified, implying that regulation of certain loci may be modulated in a competitive fashion between the Scr1, Tup/Ssn6 repressors and the Rst2 activator. CONCLUSIONS By identifying the genes directly and indirectly regulated by Scr1, Tup/Ssn6 and Rst2, this study comprehensively defined the gene regulatory networks of CCR in fission yeast and revealed the transcriptional complexities governing this system.
Collapse
Affiliation(s)
- Dane Vassiliadis
- Genetics, Genomics & Systems Biology, School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia. .,Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, Australia.
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau, China.,Institute of Translational Medicine, University of Macau, Macau, China
| | - Alex Andrianopoulos
- Genetics, Genomics & Systems Biology, School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Brendon J Monahan
- Genetics, Genomics & Systems Biology, School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia. .,Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, Victoria, Australia. .,Cancer Therapeutics (CTx), Parkville, Victoria, Australia.
| |
Collapse
|
29
|
Welkenhuysen N, Schnitzer B, Österberg L, Cvijovic M. Robustness of Nutrient Signaling Is Maintained by Interconnectivity Between Signal Transduction Pathways. Front Physiol 2019; 9:1964. [PMID: 30719010 PMCID: PMC6348271 DOI: 10.3389/fphys.2018.01964] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/31/2018] [Indexed: 12/16/2022] Open
Abstract
Systems biology approaches provide means to study the interplay between biological processes leading to the mechanistic understanding of the properties of complex biological systems. Here, we developed a vector format rule-based Boolean logic model of the yeast S. cerevisiae cAMP-PKA, Snf1, and the Snf3-Rgt2 pathway to better understand the role of crosstalk on network robustness and function. We identified that phosphatases are the common unknown components of the network and that crosstalk from the cAMP-PKA pathway to other pathways plays a critical role in nutrient sensing events. The model was simulated with known crosstalk combinations and subsequent analysis led to the identification of characteristics and impact of pathway interconnections. Our results revealed that the interconnections between the Snf1 and Snf3-Rgt2 pathway led to increased robustness in these signaling pathways. Overall, our approach contributes to the understanding of the function and importance of crosstalk in nutrient signaling.
Collapse
Affiliation(s)
- Niek Welkenhuysen
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Barbara Schnitzer
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - 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
| | - Marija Cvijovic
- Department of Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden.,Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
30
|
Alipourfard I, Datukishvili N, Bakhtiyari S, Haghani K, Di Renzo L, de Miranda RC, Mikeladze D. MIG1 Glucose Repression in Metabolic Processes of Saccharomyces cerevisiae: Genetics to Metabolic Engineering. Avicenna J Med Biotechnol 2019; 11:215-220. [PMID: 31379993 PMCID: PMC6626512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND Although Saccharomyces cerevisiae has several industrial applications, there are still fundamental problems associated with sequential use of carbon sources. As such, glucose repression effect can direct metabolism of yeast to preferably anaerobic conditions. This leads to higher ethanol production and less efficient production of recombinant products. The general glucose repression system is constituted by MIG1, TUP1 and SSN6 factors. The role of MIG1 is known in glucose repression but the evaluation of effects on aerobic/anaerobic metabolism by deletion of MIG1 and constructing an optimal strain brand remains unclear and an objective to be explored. METHODS To find the impact of MIG1 in induction of glucose-repression, the Mig1 disruptant strain (ΔMIG1) was produced for comparing with its congenic wild-type strain (2805). The analysis approached for changes in the rate of glucose consumption, biomass yield, cell protein contents, ethanol and intermediate metabolites production. The MIG1 disruptant strain exhibited 25% glucose utilization, 12% biomass growth rate and 22% protein content over the wild type. The shift to respiratory pathway has been demonstrated by 122.86 and 40% increase of glycerol and pyruvate production, respectively as oxidative metabolites, while the reduction of fermentative metabolites such as acetate 35.48 and ethanol 24%. RESULTS Results suggest that ΔMIG1 compared to the wild-type strain can significantly present less effects of glucose repression. CONCLUSION The constructed strain has more efficient growth in aerobic cultivations and it can be a potential host for biotechnological recombinant yields and industrial interests.
Collapse
Affiliation(s)
- Iraj Alipourfard
- Institute of Chemical Biology, Faculty of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia,Center of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Nelly Datukishvili
- Institute of Chemical Biology, Faculty of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia
| | - Salar Bakhtiyari
- Department of Clinical Biochemistry, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran,Corresponding authors: Salar Bakhtiyari, Ph.D., Department of Clinical Biochemistry, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran, E-mail:
| | - Karimeh Haghani
- Department of Clinical Biochemistry, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Laura Di Renzo
- Section of Clinical Nutrition and Nutrigenomics, Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Renata Costa de Miranda
- Faculty of Applied Medical-Surgical Sciences, University of Rome Tor Vergata, Rome, Italy,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - David Mikeladze
- Institute of Chemical Biology, Faculty of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia,David Mikeladze, Ph.D., Institute of Chemical Biology, Faculty of Natural Sciences and Engineering, Ilia State University, Tbilisi, Georgia, Tel/Fax: +995 2221703, +98 84 32235745, E-mail:
| |
Collapse
|
31
|
Transcriptome and metabolome analyses reveal global behaviour of a genetically engineered methanol-independent Pichia pastoris strain. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
32
|
Smith JT, White JW, Dungrawala H, Hua H, Schneider BL. Yeast lifespan variation correlates with cell growth and SIR2 expression. PLoS One 2018; 13:e0200275. [PMID: 29979754 PMCID: PMC6034835 DOI: 10.1371/journal.pone.0200275] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/22/2018] [Indexed: 11/19/2022] Open
Abstract
Isogenic wild type yeast cells raised in controlled environments display a significant range of lifespan variation. Recent microfluidic studies suggest that differential growth or gene expression patterns may explain some of the heterogeneity of aging assays. Herein, we sought to complement this work by similarly examining a large set of replicative lifespan data from traditional plate assays. In so doing, we reproduced the finding that short-lived cells tend to arrest at senescence with a budded morphology. Further, we found that wild type cells born unusually small did not have an extended lifespan. However, large birth size and/or high inter-generational growth rates significantly correlated with a reduced lifespan. Finally, we found that SIR2 expression levels correlated with lifespan and intergenerational growth. SIR2 expression was significantly reduced in large cells and increased in small wild type cells. A moderate increase in SIR2 expression correlated with reduced growth, decreased proliferation and increased lifespan in plate aging assays. We conclude that cellular growth rates and SIR2 expression levels may contribute to lifespan variation in individual cells.
Collapse
Affiliation(s)
- Jessica T. Smith
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
| | - Jill W. White
- Center for the Integration of STEM Education & Research, Texas Tech University, Lubbock, TX, United States of America
| | - Huzefa Dungrawala
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Hui Hua
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
| | - Brandt L. Schneider
- Department of Medical Education, Texas Tech University Health Sciences Center, Lubbock, TX, United States of America
| |
Collapse
|
33
|
Talavera D, Kershaw CJ, Costello JL, Castelli LM, Rowe W, Sims PFG, Ashe MP, Grant CM, Pavitt GD, Hubbard SJ. Archetypal transcriptional blocks underpin yeast gene regulation in response to changes in growth conditions. Sci Rep 2018; 8:7949. [PMID: 29785040 PMCID: PMC5962585 DOI: 10.1038/s41598-018-26170-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/01/2018] [Indexed: 01/30/2023] Open
Abstract
The transcriptional responses of yeast cells to diverse stresses typically include gene activation and repression. Specific stress defense, citric acid cycle and oxidative phosphorylation genes are activated, whereas protein synthesis genes are coordinately repressed. This view was achieved from comparative transcriptomic experiments delineating sets of genes whose expression greatly changed with specific stresses. Less attention has been paid to the biological significance of 1) consistent, albeit modest, changes in RNA levels across multiple conditions, and 2) the global gene expression correlations observed when comparing numerous genome-wide studies. To address this, we performed a meta-analysis of 1379 microarray-based experiments in yeast, and identified 1388 blocks of RNAs whose expression changes correlate across multiple and diverse conditions. Many of these blocks represent sets of functionally-related RNAs that act in a coordinated fashion under normal and stress conditions, and map to global cell defense and growth responses. Subsequently, we used the blocks to analyze novel RNA-seq experiments, demonstrating their utility and confirming the conclusions drawn from the meta-analysis. Our results provide a new framework for understanding the biological significance of changes in gene expression: 'archetypal' transcriptional blocks that are regulated in a concerted fashion in response to external stimuli.
Collapse
Affiliation(s)
- David Talavera
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| | - Christopher J Kershaw
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Joseph L Costello
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Lydia M Castelli
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, United Kingdom
| | - William Rowe
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.,Department of Chemistry, Loughborough University, Loughborough, United Kingdom
| | - Paul F G Sims
- Manchester Institute of Biotechnology (MIB), The University of Manchester, Manchester, United Kingdom
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Chris M Grant
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Graham D Pavitt
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| | - Simon J Hubbard
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
34
|
Xiao W, Duan X, Lin Y, Cao Q, Li S, Guo Y, Gan Y, Qi X, Zhou Y, Guo L, Qin P, Wang Q, Shui W. Distinct Proteome Remodeling of Industrial Saccharomyces cerevisiae in Response to Prolonged Thermal Stress or Transient Heat Shock. J Proteome Res 2018; 17:1812-1825. [PMID: 29611422 DOI: 10.1021/acs.jproteome.7b00842] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To gain a deep understanding of yeast-cell response to heat stress, multiple laboratory strains have been intensively studied via genome-wide expression analysis for the mechanistic dissection of classical heat-shock response (HSR). However, robust industrial strains of Saccharomyces cerevisiae have hardly been explored in global analysis for elucidation of the mechanism of thermotolerant response (TR) during fermentation. Herein, we employed data-independent acquisition and sequential window acquisition of all theoretical mass spectra based proteomic workflows to characterize proteome remodeling of an industrial strain, ScY01, responding to prolonged thermal stress or transient heat shock. By comparing the proteomic signatures of ScY01 in TR versus HSR as well as the HSR of the industrial strain versus a laboratory strain, our study revealed disparate response mechanisms of ScY01 during thermotolerant growth or under heat shock. In addition, through proteomics data-mining for decoding transcription factor interaction networks followed by validation experiments, we uncovered the functions of two novel transcription factors, Mig1 and Srb2, in enhancing the thermotolerance of the industrial strain. This study has demonstrated that accurate and high-throughput quantitative proteomics not only provides new insights into the molecular basis for complex microbial phenotypes but also pinpoints upstream regulators that can be targeted for improving the desired traits of industrial microorganisms.
Collapse
Affiliation(s)
- Weidi Xiao
- College of Life Sciences , Nankai University , Tianjin 300071 , China
| | - Xiaoxiao Duan
- College of Life Sciences , Nankai University , Tianjin 300071 , China.,Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Yuping Lin
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Qichen Cao
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | | | - Yufeng Guo
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Yuman Gan
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Xianni Qi
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | - Yue Zhou
- Demo Laboratory of Thermofisher Scientific China , Shanghai 200120 , China
| | - Lihai Guo
- AB SCIEX , No. 1 Building, No. 24 Yard, Jiuxianqiao Mid Road , Chaoyang District, Beijing 100015 , China
| | - Peibin Qin
- AB SCIEX , No. 1 Building, No. 24 Yard, Jiuxianqiao Mid Road , Chaoyang District, Beijing 100015 , China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300308 , China
| | | |
Collapse
|
35
|
Maqani N, Fine RD, Shahid M, Li M, Enriquez-Hesles E, Smith JS. Spontaneous mutations in CYC8 and MIG1 suppress the short chronological lifespan of budding yeast lacking SNF1/AMPK. MICROBIAL CELL 2018; 5:233-248. [PMID: 29796388 PMCID: PMC5961917 DOI: 10.15698/mic2018.05.630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronologically aging yeast cells are prone to adaptive regrowth, whereby mutants with a survival advantage spontaneously appear and re-enter the cell cycle in stationary phase cultures. Adaptive regrowth is especially noticeable with short-lived strains, including those defective for SNF1, the homolog of mammalian AMP-activated protein kinase (AMPK). SNF1 becomes active in response to multiple environmental stresses that occur in chronologically aging cells, including glucose depletion and oxidative stress. SNF1 is also required for the extension of chronological lifespan (CLS) by caloric restriction (CR) as defined as limiting glucose at the time of culture inoculation. To identify specific downstream SNF1 targets responsible for CLS extension during CR, we screened for adaptive regrowth mutants that restore chronological longevity to a short-lived snf1∆ parental strain. Whole genome sequencing of the adapted mutants revealed missense mutations in TPR motifs 9 and 10 of the transcriptional co-repressor Cyc8 that specifically mediate repression through the transcriptional repressor Mig1. Another mutation occurred in MIG1 itself, thus implicating the activation of Mig1-repressed genes as a key function of SNF1 in maintaining CLS. Consistent with this conclusion, the cyc8 TPR mutations partially restored growth on alternative carbon sources and significantly extended CLS compared to the snf1∆ parent. Furthermore, cyc8 TPR mutations reactivated multiple Mig1-repressed genes, including the transcription factor gene CAT8, which is responsible for activating genes of the glyoxylate and gluconeogenesis pathways. Deleting CAT8 completely blocked CLS extension by the cyc8 TPR mutations on CLS, identifying these pathways as key Snf1-regulated CLS determinants.
Collapse
Affiliation(s)
- Nazif Maqani
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Ryan D Fine
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Mehreen Shahid
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Mingguang Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908.,Department of Laboratory Medicine, Jilin Medical University, Jilin, 132013, China
| | - Elisa Enriquez-Hesles
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Jeffrey S Smith
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908
| |
Collapse
|
36
|
Osiro KO, Brink DP, Borgström C, Wasserstrom L, Carlquist M, Gorwa-Grauslund MF. Assessing the effect of d-xylose on the sugar signaling pathways of Saccharomyces cerevisiae in strains engineered for xylose transport and assimilation. FEMS Yeast Res 2018; 18:4791530. [DOI: 10.1093/femsyr/fox096] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/27/2017] [Indexed: 01/18/2023] Open
Affiliation(s)
- Karen O Osiro
- Applied Microbiology, Department of Chemistry, Lund University, Kemicentrum, Naturvetarvägen 14, Lund 223 62, Sweden
| | - Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, Kemicentrum, Naturvetarvägen 14, Lund 223 62, Sweden
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, Kemicentrum, Naturvetarvägen 14, Lund 223 62, Sweden
| | - Lisa Wasserstrom
- Applied Microbiology, Department of Chemistry, Lund University, Kemicentrum, Naturvetarvägen 14, Lund 223 62, Sweden
| | - Magnus Carlquist
- Applied Microbiology, Department of Chemistry, Lund University, Kemicentrum, Naturvetarvägen 14, Lund 223 62, Sweden
| | | |
Collapse
|
37
|
Galello F, Pautasso C, Reca S, Cañonero L, Portela P, Moreno S, Rossi S. Transcriptional regulation of the protein kinase a subunits inSaccharomyces cerevisiaeduring fermentative growth. Yeast 2017; 34:495-508. [DOI: 10.1002/yea.3252] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/26/2017] [Accepted: 08/09/2017] [Indexed: 11/08/2022] Open
Affiliation(s)
- Fiorella Galello
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Constanza Pautasso
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Sol Reca
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Luciana Cañonero
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Paula Portela
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Silvia Moreno
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| | - Silvia Rossi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento Química Biológica and CONICET - Universidad de Buenos Aires; Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Buenos Aires Argentina
| |
Collapse
|
38
|
Hovsepian J, Defenouillère Q, Albanèse V, Váchová L, Garcia C, Palková Z, Léon S. Multilevel regulation of an α-arrestin by glucose depletion controls hexose transporter endocytosis. J Cell Biol 2017; 216:1811-1831. [PMID: 28468835 PMCID: PMC5461024 DOI: 10.1083/jcb.201610094] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/03/2017] [Accepted: 03/28/2017] [Indexed: 01/13/2023] Open
Abstract
Changes in nutrient availability trigger massive rearrangements of the yeast plasma membrane proteome. This work shows that the arrestin-related protein Csr2/Art8 is regulated by glucose signaling at multiple levels, allowing control of hexose transporter ubiquitylation and endocytosis upon glucose depletion. Nutrient availability controls the landscape of nutrient transporters present at the plasma membrane, notably by regulating their ubiquitylation and subsequent endocytosis. In yeast, this involves the Nedd4 ubiquitin ligase Rsp5 and arrestin-related trafficking adaptors (ARTs). ARTs are targeted by signaling pathways and warrant that cargo ubiquitylation and endocytosis appropriately respond to nutritional inputs. Here, we show that glucose deprivation regulates the ART protein Csr2/Art8 at multiple levels to trigger high-affinity glucose transporter endocytosis. Csr2 is transcriptionally induced in these conditions through the AMPK orthologue Snf1 and downstream transcriptional repressors. Upon synthesis, Csr2 becomes activated by ubiquitylation. In contrast, glucose replenishment induces CSR2 transcriptional shutdown and switches Csr2 to an inactive, deubiquitylated form. This glucose-induced deubiquitylation of Csr2 correlates with its phospho-dependent association with 14-3-3 proteins and involves protein kinase A. Thus, two glucose signaling pathways converge onto Csr2 to regulate hexose transporter endocytosis by glucose availability. These data illustrate novel mechanisms by which nutrients modulate ART activity and endocytosis.
Collapse
Affiliation(s)
- Junie Hovsepian
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Quentin Defenouillère
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Véronique Albanèse
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Libuše Váchová
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i. BIOCEV, 252 50 Vestec, Czech Republic.,Faculty of Science, Charles University, BIOCEV, 252 50 Vestec, Czech Republic
| | - Camille Garcia
- Proteomics Facility, Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Zdena Palková
- Faculty of Science, Charles University, BIOCEV, 252 50 Vestec, Czech Republic
| | - Sébastien Léon
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75013 Paris, France
| |
Collapse
|
39
|
León-Ramírez CG, Cabrera-Ponce JL, Martínez-Soto D, Sánchez-Arreguin A, Aréchiga-Carvajal ET, Ruiz-Herrera J. Transcriptomic analysis of basidiocarp development in Ustilago maydis (DC) Cda. Fungal Genet Biol 2017; 101:34-45. [PMID: 28285895 DOI: 10.1016/j.fgb.2017.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 02/07/2017] [Accepted: 02/28/2017] [Indexed: 01/20/2023]
Abstract
Previously, we demonstrated that when Ustilago maydis (DC) Cda., a phytopathogenic basidiomycete and the causal agent of corn smut, is grown in the vicinity of maize embryogenic calli in a medium supplemented with the herbicide Dicamba, it developed gastroid-like basidiocarps. To elucidate the molecular mechanisms involved in the basidiocarp development by the fungus, we proceeded to analyze the transcriptome of the process, identifying a total of 2002 and 1064 differentially expressed genes at two developmental stages, young and mature basidiocarps, respectively. Function of these genes was analyzed with the use of different databases. MIPS analysis revealed that in the stage of young basidiocarp, among the ca. two thousand differentially expressed genes, there were some previously described for basidiocarp development in other fungal species. Additional elements that operated at this stage included, among others, genes encoding the transcription factors FOXO3, MIG3, PRO1, TEC1, copper and MFS transporters, and cytochromes P450. During mature basidiocarp development, important up-regulated genes included those encoding hydrophobins, laccases, and ferric reductase (FRE/NOX). The demonstration that a mapkk mutant was unable to form basidiocarps, indicated the importance of the MAPK signaling pathway in this developmental process.
Collapse
Affiliation(s)
- C G León-Ramírez
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico
| | - J L Cabrera-Ponce
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico.
| | - D Martínez-Soto
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico
| | - A Sánchez-Arreguin
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico; Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, Nuevo León, Mexico
| | - E T Aréchiga-Carvajal
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, Nuevo León, Mexico
| | - J Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del IPN, 36825 Irapuato, Guanajuato, Mexico.
| |
Collapse
|
40
|
Wang QQ, Lu Y, Ren ZY, Chi Z, Liu GL, Chi ZM. CreA is directly involved in pullulan biosynthesis and regulation of Aureobasidium melanogenum P16. Curr Genet 2016; 63:471-485. [DOI: 10.1007/s00294-016-0650-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/06/2016] [Accepted: 09/09/2016] [Indexed: 10/21/2022]
|
41
|
Sugar and Glycerol Transport in Saccharomyces cerevisiae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:125-168. [PMID: 26721273 DOI: 10.1007/978-3-319-25304-6_6] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In Saccharomyces cerevisiae the process of transport of sugar substrates into the cell comprises a complex network of transporters and interacting regulatory mechanisms. Members of the large family of hexose (HXT) transporters display uptake efficiencies consistent with their environmental expression and play physiological roles in addition to feeding the glycolytic pathway. Multiple glucose-inducing and glucose-independent mechanisms serve to regulate expression of the sugar transporters in yeast assuring that expression levels and transporter activity are coordinated with cellular metabolism and energy needs. The expression of sugar transport activity is modulated by other nutritional and environmental factors that may override glucose-generated signals. Transporter expression and activity is regulated transcriptionally, post-transcriptionally and post-translationally. Recent studies have expanded upon this suite of regulatory mechanisms to include transcriptional expression fine tuning mediated by antisense RNA and prion-based regulation of transcription. Much remains to be learned about cell biology from the continued analysis of this dynamic process of substrate acquisition.
Collapse
|
42
|
Sameith K, Amini S, Groot Koerkamp MJA, van Leenen D, Brok M, Brabers N, Lijnzaad P, van Hooff SR, Benschop JJ, Lenstra TL, Apweiler E, van Wageningen S, Snel B, Holstege FCP, Kemmeren P. A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions. BMC Biol 2015; 13:112. [PMID: 26700642 PMCID: PMC4690272 DOI: 10.1186/s12915-015-0222-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/14/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Genetic interactions, or non-additive effects between genes, play a crucial role in many cellular processes and disease. Which mechanisms underlie these genetic interactions has hardly been characterized. Understanding the molecular basis of genetic interactions is crucial in deciphering pathway organization and understanding the relationship between genotype, phenotype and disease. RESULTS To investigate the nature of genetic interactions between gene-specific transcription factors (GSTFs) in Saccharomyces cerevisiae, we systematically analyzed 72 GSTF pairs by gene expression profiling double and single deletion mutants. These pairs were selected through previously published growth-based genetic interactions as well as through similarity in DNA binding properties. The result is a high-resolution atlas of gene expression-based genetic interactions that provides systems-level insight into GSTF epistasis. The atlas confirms known genetic interactions and exposes new ones. Importantly, the data can be used to investigate mechanisms that underlie individual genetic interactions. Two molecular mechanisms are proposed, "buffering by induced dependency" and "alleviation by derepression". CONCLUSIONS These mechanisms indicate how negative genetic interactions can occur between seemingly unrelated parallel pathways and how positive genetic interactions can indirectly expose parallel rather than same-pathway relationships. The focus on GSTFs is important for understanding the transcription regulatory network of yeast as it uncovers details behind many redundancy relationships, some of which are completely new. In addition, the study provides general insight into the complex nature of epistasis and proposes mechanistic models for genetic interactions, the majority of which do not fall into easily recognizable within- or between-pathway relationships.
Collapse
Affiliation(s)
- Katrin Sameith
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Saman Amini
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Marian J A Groot Koerkamp
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Dik van Leenen
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Mariel Brok
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Nathalie Brabers
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Sander R van Hooff
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Joris J Benschop
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Tineke L Lenstra
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Eva Apweiler
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Sake van Wageningen
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Patrick Kemmeren
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands.
| |
Collapse
|
43
|
Moktaduzzaman M, Galafassi S, Capusoni C, Vigentini I, Ling Z, Piškur J, Compagno C. Galactose utilization sheds new light on sugar metabolism in the sequenced strain Dekkera bruxellensis CBS 2499. FEMS Yeast Res 2015; 15:fou009. [PMID: 25673757 DOI: 10.1093/femsyr/fou009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Dekkera bruxellensis and Saccharomyces cerevisiae are considered two phylogenetically distant relatives, but they share several industrial relevant traits such as the ability to produce ethanol under aerobic conditions (Crabtree effect), high tolerance towards ethanol and acids, and ability to grow without oxygen. Beside a huge adaptability, D. bruxellensis exhibits a broader spectrum in utilization of carbon and nitrogen sources in comparison to S. cerevisiae. With the aim to better characterize its carbon source metabolism and regulation, the usage of galactose and the role that glucose plays on sugar metabolism were investigated in D. bruxellensis CBS 2499. The results indicate that in this yeast galactose is a non-fermentable carbon source, in contrast to S. cerevisiae that can ferment it. In particular, its metabolism is affected by the nitrogen source. Interestingly, D. bruxellensis CBS 2499 exhibits the 'short-term Crabtree effect', and the expression of genes involved in galactose utilization and in respiratory metabolism is repressed by glucose, similarly to what occurs in S. cerevisiae.
Collapse
Affiliation(s)
- Md Moktaduzzaman
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
| | - Silvia Galafassi
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
| | - Claudia Capusoni
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
| | - Ileana Vigentini
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
| | - Zhihao Ling
- Department of Biology, Lund University, Box 117, 221 00 Lund, Sweden
| | - Jure Piškur
- Department of Biology, Lund University, Box 117, 221 00 Lund, Sweden
| | - Concetta Compagno
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Via G. Celoria 2, 20133, Italy
| |
Collapse
|
44
|
The interaction of induction and repression mechanisms in the regulation of galacturonic acid-induced genes in Aspergillus niger. Fungal Genet Biol 2015; 82:32-42. [DOI: 10.1016/j.fgb.2015.06.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 06/04/2015] [Accepted: 06/08/2015] [Indexed: 02/05/2023]
|
45
|
Shashkova S, Welkenhuysen N, Hohmann S. Molecular communication: crosstalk between the Snf1 and other signaling pathways. FEMS Yeast Res 2015; 15:fov026. [DOI: 10.1093/femsyr/fov026] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2015] [Indexed: 02/02/2023] Open
|
46
|
Yao Y, Tsuchiyama S, Yang C, Bulteau AL, He C, Robison B, Tsuchiya M, Miller D, Briones V, Tar K, Potrero A, Friguet B, Kennedy BK, Schmidt M. Proteasomes, Sir2, and Hxk2 form an interconnected aging network that impinges on the AMPK/Snf1-regulated transcriptional repressor Mig1. PLoS Genet 2015; 11:e1004968. [PMID: 25629410 PMCID: PMC4309596 DOI: 10.1371/journal.pgen.1004968] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/19/2014] [Indexed: 01/20/2023] Open
Abstract
Elevated proteasome activity extends lifespan in model organisms such as yeast, worms and flies. This pro-longevity effect might be mediated by improved protein homeostasis, as this protease is an integral module of the protein homeostasis network. Proteasomes also regulate cellular processes through temporal and spatial degradation of signaling pathway components. Here we demonstrate that the regulatory function of the proteasome plays an essential role in aging cells and that the beneficial impact of elevated proteasome capacity on lifespan partially originates from deregulation of the AMPK signaling pathway. Proteasome-mediated lifespan extension activity was carbon-source dependent and cells with enhancement proteasome function exhibited increased respiratory activity and oxidative stress response. These findings suggested that the pro-aging impact of proteasome upregulation might be related to changes in the metabolic state through a premature induction of respiration. Deletion of yeast AMPK, SNF1, or its activator SNF4 abrogated proteasome-mediated lifespan extension, supporting this hypothesis as the AMPK pathway regulates metabolism. We found that the premature induction of respiration in cells with increased proteasome activity originates from enhanced turnover of Mig1, an AMPK/Snf1 regulated transcriptional repressor that prevents the induction of genes required for respiration. Increasing proteasome activity also resulted in partial relocation of Mig1 from the nucleus to the mitochondria. Collectively, the results argue for a model in which elevated proteasome activity leads to the uncoupling of Snf1-mediated Mig1 regulation, resulting in a premature activation of respiration and thus the induction of a mitohormetic response, beneficial to lifespan. In addition, we observed incorrect Mig1 localization in two other long-lived yeast aging models: cells that overexpress SIR2 or deleted for the Mig1-regulator HXK2. Finally, compromised proteasome function blocks lifespan extension in both strains. Thus, our findings suggest that proteasomes, Sir2, Snf1 and Hxk2 form an interconnected aging network that controls metabolism through coordinated regulation of Mig1. Advanced cellular age is associated with decreased efficiency of the proteostasis network. The proteasome, a protease in the cytoplasm and nuclei of eukaryotic cells, is an important component of this network. Recent studies demonstrate that increased proteasome capacity has a positive impact on longevity. The underlying mechanisms, however, have not been fully identified. Here we report that proteasomes are involved in regulating the AMP-activated kinase (AMPK) pathway and thus participate in correct metabolic adaptation. We find that Mig1, a transcriptional repressor downstream of yeast AMPK, Snf1, is a proteasome target and a negative regulator of lifespan. Increased proteasome activity results in enhanced turnover and incorrect localization of Mig1. The reduced Mig1 levels result in the induction of respiration and upregulation of the oxidative stress response. Premature Mig1 inactivation is also observed in two additional long-lived strains that overexpress SIR2 or are deleted for HXK2 and lifespan extension in both strains requires correct proteasome function. Our results uncover an interconnected network comprised of the proteasome, Sir2 and AMPK/Hxk2 signaling that impacts longevity through regulation of Mig1 and modulates respiratory metabolism. Mechanistic information on the cross-communication between these pathways is expected to facilitate the identification of novel pro-aging interventions.
Collapse
Affiliation(s)
- Yanhua Yao
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | | | - Ciyu Yang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | | | - Chong He
- Buck Institute, Novato, California, United States of America
| | - Brett Robison
- Buck Institute, Novato, California, United States of America
| | | | - Delana Miller
- Buck Institute, Novato, California, United States of America
| | - Valeria Briones
- Buck Institute, Novato, California, United States of America
| | - Krisztina Tar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Anahi Potrero
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
| | - Bertrand Friguet
- Laboratoire de Biologie Cellulaire du Vieillissement, UR4-IFR83, Université Pierre et Marie Curie-Paris 6, Paris, France
| | - Brian K. Kennedy
- Buck Institute, Novato, California, United States of America
- * E-mail: (MS); (BKK)
| | - Marion Schmidt
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, New York, United States of America
- * E-mail: (MS); (BKK)
| |
Collapse
|
47
|
Protein acetylation and acetyl coenzyme a metabolism in budding yeast. EUKARYOTIC CELL 2014; 13:1472-83. [PMID: 25326522 DOI: 10.1128/ec.00189-14] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cells sense and appropriately respond to the physical conditions and availability of nutrients in their environment. This sensing of the environment and consequent cellular responses are orchestrated by a multitude of signaling pathways and typically involve changes in transcription and metabolism. Recent discoveries suggest that the signaling and transcription machineries are regulated by signals which are derived from metabolism and reflect the metabolic state of the cell. Acetyl coenzyme A (CoA) is a key metabolite that links metabolism with signaling, chromatin structure, and transcription. Acetyl-CoA is produced by glycolysis as well as other catabolic pathways and used as a substrate for the citric acid cycle and as a precursor in synthesis of fatty acids and steroids and in other anabolic pathways. This central position in metabolism endows acetyl-CoA with an important regulatory role. Acetyl-CoA serves as a substrate for lysine acetyltransferases (KATs), which catalyze the transfer of acetyl groups to the epsilon-amino groups of lysines in histones and many other proteins. Fluctuations in the concentration of acetyl-CoA, reflecting the metabolic state of the cell, are translated into dynamic protein acetylations that regulate a variety of cell functions, including transcription, replication, DNA repair, cell cycle progression, and aging. This review highlights the synthesis and homeostasis of acetyl-CoA and the regulation of transcriptional and signaling machineries in yeast by acetylation.
Collapse
|
48
|
Coregulated expression of the Na+/phosphate Pho89 transporter and Ena1 Na+-ATPase allows their functional coupling under high-pH stress. Mol Cell Biol 2014; 34:4420-35. [PMID: 25266663 DOI: 10.1128/mcb.01089-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The yeast Saccharomyces cerevisiae has two main high-affinity inorganic phosphate (Pi) transporters, Pho84 and Pho89, that are functionally relevant at acidic/neutral pH and alkaline pH, respectively. Upon Pi starvation, PHO84 and PHO89 are induced by the activation of the PHO regulon by the binding of the Pho4 transcription factor to specific promoter sequences. We show that PHO89 and PHO84 are induced by alkalinization of the medium with different kinetics and that the network controlling Pho89 expression in response to alkaline pH differs from that of other members of the PHO regulon. In addition to Pho4, the PHO89 promoter is regulated by the transcriptional activator Crz1 through the calcium-activated phosphatase calcineurin, and it is under the control of several repressors (Mig2, Nrg1, and Nrg2) coordinately regulated by the Snf1 protein kinase and the Rim101 transcription factor. This network mimics the one regulating expression of the Na(+)-ATPase gene ENA1, encoding a major determinant for Na(+) detoxification. Our data highlight a scenario in which the activities of Pho89 and Ena1 are functionally coordinated to sustain growth in an alkaline environment.
Collapse
|
49
|
Lee KE, Ahn JY, Kim JM, Hwang CS. Synthetic lethal screen of NAA20, a catalytic subunit gene of NatB N-terminal acetylase in Saccharomyces cerevisiae. J Microbiol 2014; 52:842-8. [PMID: 25163837 DOI: 10.1007/s12275-014-3694-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 06/30/2014] [Accepted: 07/24/2014] [Indexed: 01/08/2023]
Abstract
The Saccharomyces cerevisiae NatB N-terminal acetylase contains a catalytic subunit Naa20 and an auxiliary subunit Naa25. To elucidate the cellular functions of the NatB, we utilized the Synthetic Genetic Array to screen for genes that are essential for cell growth in the absence of NAA20. The genome-wide synthetic lethal screen of NAA20 identified genes encoding for serine/threonine protein kinase Vps15, 1,3-beta-glucanosyltransferase Gas5, and a catabolic repression regulator Mig3. The present study suggests that the catalytic activity of the NatB N-terminal aceytase is involved in vacuolar protein sorting and cell wall maintenance.
Collapse
Affiliation(s)
- Kang-Eun Lee
- Department of Life Sciences, Pohang University of Science and Technology, Gyeongbuk, 790-784, Republic of Korea
| | | | | | | |
Collapse
|
50
|
Ye T, Bendrioua L, Carmena D, García-Salcedo R, Dahl P, Carling D, Hohmann S. The mammalian AMP-activated protein kinase complex mediates glucose regulation of gene expression in the yeast Saccharomyces cerevisiae. FEBS Lett 2014; 588:2070-7. [PMID: 24815694 DOI: 10.1016/j.febslet.2014.04.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 04/21/2014] [Accepted: 04/24/2014] [Indexed: 11/24/2022]
Abstract
The AMP-activated protein kinase (AMPK) controls energy homeostasis in eukaryotic cells. Here we expressed hetero-trimeric mammalian AMPK complexes in a Saccharomyces cerevisiae mutant lacking all five genes encoding yeast AMPK/SNF1 components. Certain mammalian complexes complemented the growth defect of the yeast mutant on non-fermentable carbon sources. Phosphorylation of the AMPK α1-subunit was glucose-regulated, albeit not by the Glc7-Reg1/2 phosphatase, which performs this function on yeast AMPK/SNF1. AMPK could take over SNF1 function in glucose derepression. While indirectly acting anti-diabetic drugs had no effect on AMPK in yeast, compound 991 stimulated α1-subunit phosphorylation. Our results demonstrate a remarkable functional conservation of AMPK and that glucose regulation of AMPK may not be mediated by regulatory features of a specific phosphatase.
Collapse
Affiliation(s)
- Tian Ye
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden
| | - Loubna Bendrioua
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden
| | - David Carmena
- MRC Clinical Sciences Centre, Cellular Stress Group, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Raúl García-Salcedo
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden
| | - Peter Dahl
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden
| | - David Carling
- MRC Clinical Sciences Centre, Cellular Stress Group, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Stefan Hohmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, S-40530 Göteborg, Sweden.
| |
Collapse
|