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Metur SP, Klionsky DJ. Nutrient-dependent signaling pathways that control autophagy in yeast. FEBS Lett 2024; 598:32-47. [PMID: 37758520 PMCID: PMC10841420 DOI: 10.1002/1873-3468.14741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
Macroautophagy/autophagy is a highly conserved catabolic process vital for cellular stress responses and maintaining equilibrium within the cell. Malfunctioning autophagy has been implicated in the pathogenesis of various diseases, including certain neurodegenerative disorders, diabetes, metabolic diseases, and cancer. Cells face diverse metabolic challenges, such as limitations in nitrogen, carbon, and minerals such as phosphate and iron, necessitating the integration of complex metabolic information. Cells utilize a signal transduction network of sensors, transducers, and effectors to coordinate the execution of the autophagic response, concomitant with the severity of the nutrient-starvation condition. This review presents the current mechanistic understanding of how cells regulate the initiation of autophagy through various nutrient-dependent signaling pathways. Emphasizing findings from studies in yeast, we explore the emerging principles that underlie the nutrient-dependent regulation of autophagy, significantly shaping stress-induced autophagy responses under various metabolic stress conditions.
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Affiliation(s)
- Shree Padma Metur
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Department of Molecular, Cellular and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
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2
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Papapetridis I, Verhoeven MD, Wiersma SJ, Goudriaan M, van Maris AJA, Pronk JT. Laboratory evolution for forced glucose-xylose co-consumption enables identification of mutations that improve mixed-sugar fermentation by xylose-fermenting Saccharomyces cerevisiae. FEMS Yeast Res 2018; 18:4996351. [PMID: 29771304 PMCID: PMC6001886 DOI: 10.1093/femsyr/foy056] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/14/2018] [Indexed: 01/18/2023] Open
Abstract
Simultaneous fermentation of glucose and xylose can contribute to improved productivity and robustness of yeast-based processes for bioethanol production from lignocellulosic hydrolysates. This study explores a novel laboratory evolution strategy for identifying mutations that contribute to simultaneous utilisation of these sugars in batch cultures of Saccharomyces cerevisiae. To force simultaneous utilisation of xylose and glucose, the genes encoding glucose-6-phosphate isomerase (PGI1) and ribulose-5-phosphate epimerase (RPE1) were deleted in a xylose-isomerase-based xylose-fermenting strain with a modified oxidative pentose-phosphate pathway. Laboratory evolution of this strain in serial batch cultures on glucose-xylose mixtures yielded mutants that rapidly co-consumed the two sugars. Whole-genome sequencing of evolved strains identified mutations in HXK2, RSP5 and GAL83, whose introduction into a non-evolved xylose-fermenting S. cerevisiae strain improved co-consumption of xylose and glucose under aerobic and anaerobic conditions. Combined deletion of HXK2 and introduction of a GAL83G673T allele yielded a strain with a 2.5-fold higher xylose and glucose co-consumption ratio than its xylose-fermenting parental strain. These two modifications decreased the time required for full sugar conversion in anaerobic bioreactor batch cultures, grown on 20 g L-1 glucose and 10 g L-1 xylose, by over 24 h. This study demonstrates that laboratory evolution and genome resequencing of microbial strains engineered for forced co-consumption is a powerful approach for studying and improving simultaneous conversion of mixed substrates.
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Affiliation(s)
| | | | - Sanne J Wiersma
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maaike Goudriaan
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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Hsp90 Maintains Proteostasis of the Galactose Utilization Pathway To Prevent Cell Lethality. Mol Cell Biol 2016; 36:1412-24. [PMID: 26951197 DOI: 10.1128/mcb.01064-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/26/2016] [Indexed: 12/15/2022] Open
Abstract
Hsp90 is a molecular chaperone that aids in the folding of its metastable client proteins. Past studies have shown that it can exert a strong impact on some cellular pathways by controlling key regulators. However, it is unknown whether several components of a single pathway are collectively regulated by Hsp90. Here, we observe that Hsp90 influences the protein abundance of multiple Gal proteins and the efficiency of galactose utilization even after the galactose utilization pathway (GAL pathway) is fully induced. The effect of Hsp90 on Gal proteins is not at the transcriptional level. Moreover, Gal1 is found to physically interact with Hsp90, and its stability is reduced in low-Hsp90 cells. When Hsp90 is compromised, several Gal proteins form protein aggregates that colocalize with the disaggregase Hsp104. These results suggest that Gal1 and other Gal proteins are probably the clients of Hsp90. An unbalanced GAL pathway has been known to cause fatal growth arrest due to accumulation of toxic galactose metabolic intermediates. It is likely that Hsp90 chaperones multiple Gal proteins to maintain proteostasis and prevent cell lethality especially in a fluctuating environment.
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Metabolic Impacts of Using Nitrogen and Copper-Regulated Promoters to Regulate Gene Expression in Neurospora crassa. G3-GENES GENOMES GENETICS 2015; 5:1899-908. [PMID: 26194204 PMCID: PMC4555226 DOI: 10.1534/g3.115.020073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The filamentous fungus Neurospora crassa is a long-studied eukaryotic microbial system amenable to heterologous expression of native and foreign proteins. However, relatively few highly tunable promoters have been developed for this species. In this study, we compare the tcu-1 and nit-6 promoters for controlled expression of a GFP reporter gene in N. crassa. Although the copper-regulated tcu-1 has been previously characterized, this is the first investigation exploring nitrogen-controlled nit-6 for expression of heterologous genes in N. crassa. We determined that fragments corresponding to 1.5-kb fragments upstream of the tcu-1 and nit-6 open reading frames are needed for optimal repression and expression of GFP mRNA and protein. nit-6 was repressed using concentrations of glutamine from 2 to 20 mM and induced in medium containing 0.5–20 mM nitrate as the nitrogen source. Highest levels of expression were achieved within 3 hr of induction for each promoter and GFP mRNA could not be detected within 1 hr after transfer to repressing conditions using the nit-6 promoter. We also performed metabolic profiling experiments using proton NMR to identify changes in metabolite levels under inducing and repressing conditions for each promoter. The results demonstrate that conditions used to regulate tcu-1 do not significantly change the primary metabolome and that the differences between inducing and repressing conditions for nit-6 can be accounted for by growth under nitrate or glutamine as a nitrogen source. Our findings demonstrate that nit-6 is a tunable promoter that joins tcu-1 as a choice for regulation of gene expression in N. crassa.
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Franco-Duarte R, Bigey F, Carreto L, Mendes I, Dequin S, Santos MAS, Pais C, Schuller D. Intrastrain genomic and phenotypic variability of the commercialSaccharomyces cerevisiaestrain Zymaflore VL1 reveals microevolutionary adaptation to vineyard environments. FEMS Yeast Res 2015; 15:fov063. [DOI: 10.1093/femsyr/fov063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2015] [Indexed: 11/13/2022] Open
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6
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Clapp P, Capper AB, Taussig R. Genetic selection of regulatory mutants of mammalian adenylyl cyclases. Methods Enzymol 2002; 345:241-51. [PMID: 11665608 DOI: 10.1016/s0076-6879(02)45020-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Initial steps in the identification of the Gs alpha-binding site present in mammalian adenylyl cyclases can be achieved with the use of the yeast genetic system described. It must be stressed that this system serves as a means to identify mutants that are candidates; biochemical analysis of these mutants is a next and necessary step in the confirmation of these phenotypes. The system described can be readily adapted for the isolation of additional classes of mammalian adenylyl cyclase mutants including mutants with altered regulation toward forskolin, catalytic abnormalities, or enhanced sensitivities toward activators. In addition, this system can be employed for the isolation of constitutively active adenylyl cyclase mutants, or by coexpressing other adenylyl cyclase isoforms and their known regulators, mutations in the binding sites for these molecules can be elucidated.
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Affiliation(s)
- Peter Clapp
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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7
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Hardie DG, Carling D, Carlson M. The AMP-activated/SNF1 protein kinase subfamily: metabolic sensors of the eukaryotic cell? Annu Rev Biochem 1998; 67:821-55. [PMID: 9759505 DOI: 10.1146/annurev.biochem.67.1.821] [Citation(s) in RCA: 1111] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Mammalian AMP-activated protein kinase and yeast SNF1 protein kinase are the central components of kinase cascades that are highly conserved between animals, fungi, and plants. The AMP-activated protein kinase cascade acts as a metabolic sensor or "fuel gauge" that monitors cellular AMP and ATP levels because it is activated by increases in the AMP:ATP ratio. Once activated, the enzyme switches off ATP-consuming anabolic pathways and switches on ATP-producing catabolic pathways, such as fatty acid oxidation. The SNF1 complex in yeast is activated in response to the stress of glucose deprivation. In this case the intracellular signal or signals have not been identified; however, SNF1 activation is associated with depletion of ATP and elevation of AMP. The SNF1 complex acts primarily by inducing expression of genes required for catabolic pathways that generate glucose, probably by triggering phosphorylation of transcription factors. SNF1-related protein kinases in higher plants are likely to be involved in the response of plant cells to environmental and/or nutritional stress.
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Affiliation(s)
- D G Hardie
- Biochemistry Department, University, Dundee, Scotland, United Kingdom.
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Zimmermann G, Zhou D, Taussig R. Mutations uncover a role for two magnesium ions in the catalytic mechanism of adenylyl cyclase. J Biol Chem 1998; 273:19650-5. [PMID: 9677392 DOI: 10.1074/jbc.273.31.19650] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The recent determination of the crystal structure of adenylyl cyclase has elucidated many structural features that determine the regulatory properties of the enzyme. In addition, the characterization of adenylyl cyclase by mutagenic techniques and the identification of the binding site for P-site inhibitors have led to modeling studies that describe the ATP-binding site. Despite these advances, the catalytic mechanism of adenylyl cyclase remains uncertain, especially with respect to the role that magnesium ions may play in this process. We have identified four mutant mammalian adenylyl cyclases defective in their metal dependence, allowing us to further characterize the function of metal ions in the catalytic mechanism of this enzyme. The wild-type adenylyl cyclase shows a biphasic Mg2+ dose-response curve in which the high-affinity component displays cooperativity (Hill coefficient of 1.4). Two mutations (C441R and Y442H) reduce the affinity of the adenylyl cyclase for Mg2+ dramatically without affecting the binding of MgATP, suggesting that there is a metal requirement in addition to the ATP-bound Mg2+. The results of this study thus demonstrate multiple metal requirements of adenylyl cyclase and support the existence of a Mg2+ ion essential for catalysis and distinct from the ATP-bound ion. We propose that adenylyl cyclase employs a catalytic mechanism analogous to that of DNA polymerase, in which two key magnesium ions facilitate the nucleophilic attack of the 3'-hydroxyl group and the subsequent elimination of pyrophosphate.
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Affiliation(s)
- G Zimmermann
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-0636, USA
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9
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Huang D, Chun KT, Goebl MG, Roach PJ. Genetic interactions between REG1/HEX2 and GLC7, the gene encoding the protein phosphatase type 1 catalytic subunit in Saccharomyces cerevisiae. Genetics 1996; 143:119-27. [PMID: 8722767 PMCID: PMC1207245 DOI: 10.1093/genetics/143.1.119] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mutations in GLC7, the gene encoding the type 1 protein phosphatase catalytic subunit, cause a variety of abberrant phenotypes in yeast, such as impaired glycogen synthesis and relief of glucose repression of the expression of some genes. Loss of function of the REG1/HEX2 gene, necessary for glucose repression of several genes, was found to suppress the glycogen-deficient phenotype of the glc7-1 allele. Deletion of REG1 in a wild-type background led to overaccumulation of glycogen as well as slow growth and an enlarged cell size. However, loss of REG1 did not suppress other phenotypes associated with GLC7 mutations, such as inability to sporulate or, in cells bearing the glc7Y-170 allele, lack of growth at 14 degrees. The effect of REG1 deletion on glycogen accumulation is not simply due to derepression of glucose-repressed genes, although it does require the presence of SNF1, which encodes a protein kinase essential for expression of glucose-repressed genes and for glycogen accumulation. We propose that REG1 has a role in controlling glycogen accumulation.
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Affiliation(s)
- D Huang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis 46202-5122, USA
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10
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Woods A, Cheung PC, Smith FC, Davison MD, Scott J, Beri RK, Carling D. Characterization of AMP-activated protein kinase beta and gamma subunits. Assembly of the heterotrimeric complex in vitro. J Biol Chem 1996; 271:10282-90. [PMID: 8626596 DOI: 10.1074/jbc.271.17.10282] [Citation(s) in RCA: 181] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
There is growing evidence that mammalian AMP-activated protein kinase (AMPK) plays a role in protecting cells from stresses that cause ATP depletion by switching off ATP-consuming biosynthetic pathways. The active form of AMPK from rat liver exists as a heterotrimeric complex and we have previously shown that the catalytic subunit is structurally and functionally related to the SNF1 protein kinase from Saccharomyces cerevisiae. Here we describe the isolation and characterization of the two other polypeptides, termed AMPKbeta and AMPKgamma, that together with the catalytic subunit (AMPKalpha) form the active kinase complex in mammalian liver. Sequence analysis of cDNA clones encoding these subunits reveals that they are related to yeast proteins that interact with SNF1, providing further evidence that the regulation and function of AMPK and SNF1 have been conserved throughout evolution. The amino acid sequence of the beta subunit is most closely related to SIP2 (35% identity), while the amino acid sequence of the gamma subunit is 35% identical with SNF4. We show that both AMPKbeta and AMPKgamma mRNA and protein are expressed widely in rat tissues. We show that AMPKbeta interacts with both AMPKalpha and AMPKgamma in vitro, whereas AMPKalpha does not interact with AMPKgamma under the same conditions. These results suggest that AMPKbeta mediates the association of the heterotrimeric AMPK complex in vitro, and will facilitate future studies aimed at investigating the regulation of AMPK in vivo.
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Affiliation(s)
- A Woods
- Medical Research Council Clinical Sciences Centre, Department of Molecular Medicine, Royal Postgraduate Medical School, DuCane Road, London W12 0NN, United Kingdom
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11
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Goffrini P, Ficarelli A, Donnini C, Lodi T, Puglisi PP, Ferrero I. FOG1 and FOG2 genes, required for the transcriptional activation of glucose-repressible genes of Kluyveromyces lactis, are homologous to GAL83 and SNF1 of saccharomyces cerevisiae. Curr Genet 1996; 29:316-26. [PMID: 8598052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The fog1 and fog2 mutants of the yeast Kluyveromyces lactis were identified by inability to grow on a number of both fermentable and non-fermentable carbon sources. Genetic and physiological evidences suggest a role for FOG1 and FOG2 in the regulation of glucose-repressible gene expression in response to a glucose limitation. The regulatory effect appears to be at the transcriptional level, at least for beta-galactosidase. Both genes have been cloned by complementation and sequenced. FOG1 is a unique gene homologous to GAL83, SIP1 and SIP2, a family of regulatory genes affecting glucose repression of the GAL system in Saccharomyces cerevisiae. However, major differences exist between fog1 and gal83 mutants. FOG2 is structurally and functionally homologous to SNF1 of S. cerevisiae and shares with SNF1 a role also in sporulation.
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Affiliation(s)
- P Goffrini
- Istituto di Genetica, Università di Parma, Viale delle Scienze, Italy
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12
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FOG1 andFOG2 genes, required for the transcriptional activation of glucose-repressible genes ofKluyveromyces lactis, are homologous toGAL83 andSNF1 ofSaccharomyces cerevisiae. Curr Genet 1996. [DOI: 10.1007/bf02208612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Long RM, Hopper JE. Genetic and carbon source regulation of phosphorylation of Sip1p, a Snf1p-associated protein involved in carbon response in Saccharomyces cerevisiae. Yeast 1995; 11:233-46. [PMID: 7785324 DOI: 10.1002/yea.320110306] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The SIP1 gene of Saccharomyces cerevisiae is a carbon-catabolite-specific negative regulator of GAL gene transcription and acts as a multicopy suppressor of growth defects associated with impaired Snf1p protein kinase activity. The Sip1 protein is known to undergo phosphorylation when associated in vitro with the Snf1 protein kinase. We have carried out in vivo studies of the genetic and carbon control of Sip1p phosphorylation. Metabolic labeling reveals phosphorylation of Sip1p under both carbon catabolite-repressing and non-repressing conditions and in both SNF1 wild-type and snf1-deletion cells. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis immunoblot assay, we detect apparent changes in Sip1p phosphorylation states in response to changes in carbon source. At least one dephosphorylation of Sip1p occurs with a shift from non-repressing carbon source to repressing carbon source. The MIG1 gene, acting through SNF1-dependent and SNF1-independent pathways, is required for some Sip1p phosphorylations. REG1 appears to be required for at least one dephosphorylation of Sip1p, whereas SSN6 appears to be required for at least one phosphorylation of Sip1p. These results reveal new complexities in carbon response signaling, and may reflect the involvement of the Sip1 protein in the same complex as the Mig1 and Ssn6 proteins.
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Affiliation(s)
- R M Long
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey 17033, USA
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Affiliation(s)
- J M Gancedo
- Instituto de Investigaciones Biomédicas del C.S.I.C., Facultad de Medicina UAM, Spain
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15
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Abstract
This review briefly surveys the literature on the nature, regulation, genetics, and molecular biology of the major energy-yielding pathways in yeasts, with emphasis on Saccharomyces cerevisiae. While sugar metabolism has received the lion's share of attention from workers in this field because of its bearing on the production of ethanol and other metabolites, more attention is now being paid to ethanol metabolism and the regulation of aerobic metabolism by fermentable and nonfermentable substrates. The utility of yeast as a highly manipulable organism and the discovery that yeast metabolic pathways are subject to the same types of control as those of higher cells open up many opportunities in such diverse areas as molecular evolution and cancer research.
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Affiliation(s)
- C Wills
- Department of Biology, University of California, San Diego, La Jolla
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17
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Abstract
We describe yeast transcriptional activators encoded by E. coli genomic DNA fragments fused to the coding sequence of the DNA-binding portion of GAL4. All of the new activating sequences that we have analyzed, like those of GAL4 and GCN4, are acidic; most of these sequences show no obvious sequence homology when compared with the identified activating regions of GAL4 and GCN4 or among themselves. We also describe a fusion protein that contains no yeast protein sequence but activates transcription in yeast.
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Affiliation(s)
- J Ma
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138
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Abstract
In wild-type yeast the action of the transcriptional activator GAL4 is inhibited by GAL80, and galactose relieves this inhibition. We show that deletion mutants of GAL4 lacking 30 amino acids of the carboxyl terminus activate transcription constitutively, whereas other deletion mutants bearing the carboxy-terminal 30 amino acids are inhibited by GAL80. Moreover, GAL4 fragments bearing these 30 amino acids, when expressed from a strong promoter on multicopy plasmids, free the endogenous GAL4 from inhibition by GAL80. These and other results suggest that GAL80 recognizes the carboxy-terminal 30 amino acids of GAL4, forming a complex that, though bound to DNA, does not activate transcription.
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Baker SM, Johnston SA, Hopper JE, Jaehning JA. Transcription of multiple copies of the yeast GAL7 gene is limited by specific factors in addition to GAL4. MOLECULAR & GENERAL GENETICS : MGG 1987; 208:127-34. [PMID: 3302604 DOI: 10.1007/bf00330433] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
High levels of the GAL7 gene in the yeast cell appear to titrate regulatory factors and to impair transcription of related sequences. To investigate the role that the GAL regulatory factors GAL4 and GAL80 have in this process we have compared the accumulation of mRNA transcribed from single-copy (plasmid-borne GAL7 and chromosomal GAL10) and high-copy (plasmid-borne GAL7) genes in several GAL regulatory mutants. Our results show that functional GAL4 gene product is required for induction of transcription from the single- and high-copy genes. In a strain containing the GAL4 gene fused to the high expression ADH1 promoter, glucose can replace galactose to induce high levels of transcription of GAL7 and GAL10 genes, although the kinetics of accumulation induced by the two sugars are distinctly different. In the presence of high levels of GAL4, maximum accumulation of mRNA from single and high copy genes is elevated two-fold; disruption of the gal80 gene in combination with high levels of GAL4 results in a further two-fold increase in transcription. In this genetic background, galactose-induced transcription of the high copy GAL7 gene results in a greater than 50-fold increase in the levels of GAL7 mRNA, representing 30%-50% of the total cellular mRNA. Our results are consistent with a cooperative effect of saturation of multiple GAL4 DNA binding sites and with a limiting factor, in addition to GAL4, that is required for transcription of the GAL genes.
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20
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Abstract
We describe the activities of a wide array of deletion mutants of GAL4, a yeast transcriptional activator. We identify two short regions of GAL4, each of which activates transcription when fused to the DNA-binding region of the molecule. Very large portions of GAL4 are not required for gene activation.
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Hanes SD, Koren R, Bostian KA. Control of cell growth and division in Saccharomyces cerevisiae. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1986; 21:153-223. [PMID: 3530635 DOI: 10.3109/10409238609113611] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Considerable advances have been made in recent years in our understanding of the biochemistry of protein and nucleic acid synthesis and, particularly, the molecular biology of gene expression in eukaryotes. The yeast Saccharomyces cerevisiae, and to a lesser extent Schizosaccharomyces pombe, has had a preeminent role as a focus for these studies, principally because of the facility with which these organisms can be experimentally manipulated biochemically and genetically. This review will be designed to critically examine and integrate recent advances in several vital areas of regulatory control of enzyme synthesis in yeast: structure and organization of DNA, transcriptional regulation, post-transcriptional modification, control of translation, post-translational modification and secretion, and cell-cycle modulation. It will attempt to emphasize and illustrate, where detailed information is available, principal underlying molecular mechanisms, and it will attempt to make relevant comparisons of this material to inferred and demonstrated facets of regulatory control of enzyme and protein synthesis in higher eukaryotes.
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23
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Abstract
We present the nucleotide sequence of a 1599-base pair (bp) DNA fragment containing the entire GAL7 gene that encodes galactose-1-phosphate uridyltransferase of Saccharomyces cerevisiae. The deduced peptide was composed of 364 amino acid residues. The expected molecular weight was 42,005 daltons, which agreed with the observed value for the purified enzyme. The 3'-end of the GAL7 transcript mapped at a position 82 bp downstream from the UAA termination codon by the S1 nuclease protection experiment. We constructed a GAL7'-lac'Z fusion on various types of yeast plasmid vectors. The fused gene on any type of vector was induced by galactose and repressed by glucose as for the GAL7 gene on the chromosome. The response of GAL7'-lac'Z fusion to gal4 delta and gal80 delta regulatory mutations was also similar to the response of the chromosomal GAL7 gene. By using various deletions in the 5'-flanking region of the gene fusion, we delimited the sequence essential for galactose controlled expression with a 180 bp-fragment of DNA lying 92 bp upstream of the transcription initiation site.
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Affiliation(s)
- M Tajima
- Laboratory of Molecular Genetics, Keio University School of Medicine, Tokyo, Japan
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24
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Abstract
We show by the following series of experiments that the yeast positive regulatory protein GAL4 binds to four sites in the upstream activating sequence UASG to activate transcription of the adjacent GAL1 and GAL10 genes. GAL4 protein expressed in E. coli protected guanine residues in UASG from methylation by dimethyl sulfate. The same set of protections was seen in vivo in yeast and depended on the GAL4+ allele. This protection pattern is consistent with the idea that GAL4 protein binds to four related 17 bp sequences, each of which displays approximate 2-fold rotational symmetry. A single near-consensus synthetic 17 bp oligonucleotide, installed in front of the yeast GAL1 or CYC1 transcription units, conferred a high level of galactose inducibility upon these genes. Further experiments suggest that one mechanism of glucose repression is inhibition of the binding of GAL4 protein to DNA.
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Yocum RR, Johnston M. Molecular cloning of the GAL80 gene from Saccharomyces cerevisiae and characterization of a gal80 deletion. Gene X 1984; 32:75-82. [PMID: 6397403 DOI: 10.1016/0378-1119(84)90034-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
An integrated GAL1-lacZ fusion provided a useful phenotypic marker for the gal80- regulatory mutation in Saccharomyces cerevisiae. On minimal glucose plates containing a beta-galactosidase indicator, a GAL80 strain containing the fusion gave white colonies, whereas a gal80- strain gave blue colonies. This color difference was used to isolate the GAL80 gene from a plasmid bank by complementation of the gal80- mutant. The putative GAL80 gene was located on a 2.6-kb HindIII-SalI fragment and has been subcloned into an integrating vector. Genetic analysis showed that the clone integrated at the GAL80 locus. A deletion that covered the entire GAL80 region was constructed in vitro and transplaced into the yeast genome to give an isogenic pair of GAL80 and gal80 deletion strains. Glucose repression of a GAL1-lacZ fusion was normal in the gal80 deletion strain, implying that the GAL80 gene product is not involved in glucose repression.
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26
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Abstract
In Saccharomyces, the enzymes used to convert galactose to glucose are specified by three coordinately expressed, tightly linked genes, GAL7, GAL10, and GAL1. These genes are induced by galactose and are controlled by the positive regulator gene gal4 and the negative regulator gene gal80. GAL81 mutations, which are known to alter the gal4 protein, produce a constitutive phenotype. We have cloned fragments of Saccharomyces carlsbergensis DNA that span 26.3 kilobases surrounding the three clustered GAL genes. About 5 kilobases of the sequence was determined, which includes the entire GAL1 gene, the two intercistronic regions, and portions of the coding sequences of GAL10 and GAL7. Some amino acid homology between the GAL1 gene product, galactokinase, and the Escherichia coli galactokinase was detected. By using various Saccharomyces DNA fragments, the accumulation of GAL1 and GAL10 RNA in yeast cells after induction with galactose was studied. Our results, using wild-type, gal4-, gal80-, and GAL81-1- yeast cells, support the hypothesis that control is exerted at the transcriptional level.
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Benga G, Holmes RP. Interactions between components in biological membranes and their implications for membrane function. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1984; 43:195-257. [PMID: 6087406 DOI: 10.1016/0079-6107(84)90014-2] [Citation(s) in RCA: 122] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Matsumoto K, Uno I, Ishikawa T, Oshima Y. Cyclic AMP may not be involved in catabolite repression in Saccharomyces cerevisiae: evidence from mutants unable to synthesize it. J Bacteriol 1983; 156:898-900. [PMID: 6313623 PMCID: PMC217909 DOI: 10.1128/jb.156.2.898-900.1983] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Yeast cells with a nonsense adenylate cyclase mutation, cyr1-3, required cyclic AMP for growth. This phenotype was suppressed by the byc1 mutation; however, cyr1-3 bcy1 cells produced no detectable level of adenylate cyclase or cyclic AMP. On induction, the bcy1 and cyr1-3 bcy1 mutant cells produced the same levels of galactokinase and alpha-D-glucosidase as did the wild-type cells and fourfold-higher levels of invertase. Since galactokinase synthesis was severely repressed by glucose in the constitutive GAL81 mutants, irrespective of the cyr1-3 bcy1 genotype, cyclic AMP may not be involved in catabolite repression.
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Matsumoto K, Yoshimatsu T, Oshima Y. Recessive mutations conferring resistance to carbon catabolite repression of galactokinase synthesis in Saccharomyces cerevisiae. J Bacteriol 1983; 153:1405-14. [PMID: 6337998 PMCID: PMC221791 DOI: 10.1128/jb.153.3.1405-1414.1983] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A total of 37 recessive mutations showing enhanced resistance to the glucose repression of galactokinase synthesis have been isolated by a selection procedure with a GAL81 gal7 double mutant. These mutations were grouped into three different complementation classes. One class, reg1, contains mutants arising from mutations at a site close to, but complementing, the gal3 locus. The reg1 mutant also showed resistance to the glucose repression of invertase synthesis but not to that of alpha-D-glucosidase. The two other classes were identified as arising from recessive mutations at the GAL82 locus and the GAL83 locus, respectively, at which various dominant mutations were isolated previously. When in a constitutive background due to the GAL81 or gal80 mutation, the GAL82 and GAL83 mutations did not show a mutually additive effect on the resistance to glucose repression of galactokinase synthesis, while the reg1 and GAL82 (or GAL83) mutations did. Based upon the specific behavior of cells with various genotypes for the above genes in response to the concentration of galactose and glucose in the medium, we propose a model involving three independent circuits for glucose signals in the regulation of the structural genes for the galactose pathway enzymes.
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Matsumoto K, Uno I, Toh-E A, Ishikawa T, Oshima Y. Cyclic AMP may not be involved in catabolite repression in Saccharomyes cerevisiae: evidence from mutants capable of utilizing it as an adenine source. J Bacteriol 1982; 150:277-85. [PMID: 6277865 PMCID: PMC220110 DOI: 10.1128/jb.150.1.277-285.1982] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mutants able to utilize 5'-AMP or cyclic AMP as the adenine source were isolated from an ade6 ade10 double mutant by ethyl methane sulfonate mutagenesis. A single amp1 mutation, primarily selected on 5'-AMP medium, confers the phenotype for utilization of exogenous 5'-AMP as the adenine source. From the ade6 ade10 amp1 triple mutant, a mutant able to utilize cyclic AMP was isolated, and the mutant phenotype was proven to be due to the simultaneous occurrence of triple mutations designated as cam1, cam2, and cam3. The cam3 mutation, but not cam1 or cam2, also confers the phenotype for utilizing 5'-AMP, the same phenotype as the amp1 mutation. All of these mutations are recessive to the respective wild-type counterparts. Cells having the ade6 ade10 amp1 cam1 cam2 cam3 genotype showed significant ability to take up exogenous cyclic AMP, whereas no differences were observed in cyclic AMP phosphodiesterase activity in comparison with that of the original strains used in the mutant isolation. Since glucose severely repressed galactokinase synthesis in the constitutive GAL81 mutant having the ade6 ade10 amp1 cam1 cam2 cam3 genotype, irrespective of the presence or absence of cyclic AMP in the medium, it was suggested that cyclic AMP is not involved in the mechanism of catabolite repression in Saccharomyces cerevisiae. It does, however, have a stimulative effect on the galactokinase synthesis in the GAL81 mutant in the absence of glucose.
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