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Cozma E, Rao M, Dusick M, Genereaux J, Rodriguez-Mias RA, Villén J, Brandl CJ, Berg MD. Anticodon sequence determines the impact of mistranslating tRNA Ala variants. RNA Biol 2023; 20:791-804. [PMID: 37776539 PMCID: PMC10543346 DOI: 10.1080/15476286.2023.2257471] [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] [Accepted: 08/31/2023] [Indexed: 10/02/2023] Open
Abstract
Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNAAla and the anticodon plays no role in charging, tRNAAla variants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNAAla anticodon variants on the growth of Saccharomyces cerevisiae. Overall, 36 tRNAAla anticodon variants decreased growth in single- or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C-rich anticodons resulted in larger growth deficits than A/U-rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNAAla variant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNAAla anticodon variants.
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Affiliation(s)
- Ecaterina Cozma
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Megha Rao
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Madison Dusick
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Christopher J. Brandl
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada
| | - Matthew D. Berg
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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2
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Berg MD, Brandl CJ. Transfer RNAs: diversity in form and function. RNA Biol 2021; 18:316-339. [PMID: 32900285 PMCID: PMC7954030 DOI: 10.1080/15476286.2020.1809197] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/31/2020] [Accepted: 08/08/2020] [Indexed: 12/11/2022] Open
Abstract
As the adaptor that decodes mRNA sequence into protein, the basic aspects of tRNA structure and function are central to all studies of biology. Yet the complexities of their properties and cellular roles go beyond the view of tRNAs as static participants in protein synthesis. Detailed analyses through more than 60 years of study have revealed tRNAs to be a fascinatingly diverse group of molecules in form and function, impacting cell biology, physiology, disease and synthetic biology. This review analyzes tRNA structure, biosynthesis and function, and includes topics that demonstrate their diversity and growing importance.
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Affiliation(s)
- Matthew D. Berg
- Department of Biochemistry, The University of Western Ontario, London, Canada
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3
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Impact of Pus1 Pseudouridine Synthase on Specific Decoding Events in Saccharomyces cerevisiae. Biomolecules 2020; 10:biom10050729. [PMID: 32392804 PMCID: PMC7277083 DOI: 10.3390/biom10050729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022] Open
Abstract
Pus1-dependent pseudouridylation occurs in many tRNAs and at multiple positions, yet the functional impact of this modification is incompletely understood. We analyzed the consequences of PUS1 deletion on the essential decoding of CAG (Gln) codons by tRNAGlnCUG in yeast. Synthetic lethality was observed upon combining the modification defect with destabilized variants of tRNAGlnCUG, pointing to a severe CAG-decoding defect of the hypomodified tRNA. In addition, we demonstrated that misreading of UAG stop codons by a tRNAGlnCUG variant is positively affected by Pus1. Genetic approaches further indicated that mildly elevated temperature decreases the decoding efficiency of CAG and UAG via destabilized tRNAGlnCAG variants. We also determined the misreading of CGC (Arg) codons by tRNAHisGUG, where the CGC decoder tRNAArgICG contains Pus1-dependent pseudouridine, but not the mistranslating tRNAHis. We found that the absence of Pus1 increased CGC misreading by tRNAHis, demonstrating a positive role of the modification in the competition against non-synonymous near-cognate tRNA. Part of the in vivo decoding defects and phenotypes in pus1 mutants and strains carrying destabilized tRNAGlnCAG were suppressible by additional deletion of the rapid tRNA decay (RTD)-relevant MET22, suggesting the involvement of RTD-mediated tRNA destabilization.
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Costa OY, Zerillo MM, Zühlke D, Kielak AM, Pijl A, Riedel K, Kuramae EE. Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses. Microorganisms 2020; 8:E244. [PMID: 32059463 PMCID: PMC7074687 DOI: 10.3390/microorganisms8020244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 01/18/2023] Open
Abstract
The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.
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Affiliation(s)
- Ohana Y.A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Marcelo M. Zerillo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Anna M. Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Strasse 8, 17487 Greifswald, Germany; (D.Z.); (K.R.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands (M.M.Z.); (A.M.K.); (A.P.)
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5
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Prabhakar A, Vadaie N, Krzystek T, Cullen PJ. Proteins That Interact with the Mucin-Type Glycoprotein Msb2p Include a Regulator of the Actin Cytoskeleton. Biochemistry 2019; 58:4842-4856. [PMID: 31710471 DOI: 10.1021/acs.biochem.9b00725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transmembrane mucin-type glycoproteins can regulate signal transduction pathways. In yeast, signaling mucins regulate mitogen-activated protein kinase (MAPK) pathways that induce cell differentiation to filamentous growth (fMAPK pathway) and the response to osmotic stress (HOG pathway). To explore regulatory aspects of signaling mucin function, protein microarrays were used to identify proteins that interact with the cytoplasmic domain of the mucin-like glycoprotein Msb2p. Eighteen proteins were identified that comprised functional categories of metabolism, actin filament capping and depolymerization, aerobic and anaerobic growth, chromatin organization and bud growth, sporulation, ribosome biogenesis, protein modification by iron-sulfur clusters, RNA catabolism, and DNA replication and DNA repair. A subunit of actin capping protein, Cap2p, interacted with the cytoplasmic domain of Msb2p. Cells lacking Cap2p showed altered localization of Msb2p and increased levels of shedding of Msb2p's N-terminal glycosylated domain. Consistent with its role in regulating the actin cytoskeleton, Cap2p was required for enhanced cell polarization during filamentous growth. Our study identifies proteins that connect a signaling mucin to diverse cellular processes and may provide insight into new aspects of mucin function.
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Affiliation(s)
- Aditi Prabhakar
- Department of Biological Sciences , State University of New York at Buffalo , Buffalo , New York 14260-1300 , United States
| | - Nadia Vadaie
- Department of Biological Sciences , State University of New York at Buffalo , Buffalo , New York 14260-1300 , United States
| | - Thomas Krzystek
- Department of Biological Sciences , State University of New York at Buffalo , Buffalo , New York 14260-1300 , United States
| | - Paul J Cullen
- Department of Biological Sciences , State University of New York at Buffalo , Buffalo , New York 14260-1300 , United States
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Zelezniak A, Vowinckel J, Capuano F, Messner CB, Demichev V, Polowsky N, Mülleder M, Kamrad S, Klaus B, Keller MA, Ralser M. Machine Learning Predicts the Yeast Metabolome from the Quantitative Proteome of Kinase Knockouts. Cell Syst 2018; 7:269-283.e6. [PMID: 30195436 PMCID: PMC6167078 DOI: 10.1016/j.cels.2018.08.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/29/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023]
Abstract
A challenge in solving the genotype-to-phenotype relationship is to predict a cell’s metabolome, believed to correlate poorly with gene expression. Using comparative quantitative proteomics, we found that differential protein expression in 97 Saccharomyces cerevisiae kinase deletion strains is non-redundant and dominated by abundance changes in metabolic enzymes. Associating differential enzyme expression landscapes to corresponding metabolomes using network models provided reasoning for poor proteome-metabolome correlations; differential protein expression redistributes flux control between many enzymes acting in concert, a mechanism not captured by one-to-one correlation statistics. Mapping these regulatory patterns using machine learning enabled the prediction of metabolite concentrations, as well as identification of candidate genes important for the regulation of metabolism. Overall, our study reveals that a large part of metabolism regulation is explained through coordinated enzyme expression changes. Our quantitative data indicate that this mechanism explains more than half of metabolism regulation and underlies the interdependency between enzyme levels and metabolism, which renders the metabolome a predictable phenotype. The proteome of kinase knockouts is dominated by enzyme abundance changes The enzyme expression profiles of kinase knockouts are non-redundant Metabolism is regulated by many expression changes acting in concert Machine learning accurately predicts the metabolome from enzyme abundance
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Affiliation(s)
- Aleksej Zelezniak
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Biognosys AG, Schlieren, Switzerland
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Christoph B Messner
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK
| | - Vadim Demichev
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Nicole Polowsky
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Michael Mülleder
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Stephan Kamrad
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Bernd Klaus
- Centre for Statistical Data Analysis, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Medical University of Innsbruck, Innsbruck, Austria
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism laboratory, London, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK; Department of Biochemistry, Charité Universitaetsmedizin Berlin, Berlin, Germany.
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7
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Generation of an arginine-tRNA-adapted Saccharomyces cerevisiae strain for effective heterologous protein expression. Curr Genet 2017; 64:589-598. [PMID: 29098364 DOI: 10.1007/s00294-017-0774-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/30/2017] [Accepted: 10/27/2017] [Indexed: 10/18/2022]
Abstract
The tRNA population reflects the codon bias of the organism and affects the translation of heterologous target mRNA molecules. In this study, Saccharomyces cerevisiae strains with modified levels of rare tRNA were engineered, that allowed efficient generation of recombinant proteins with unfavorable codon usage. We established a novel synthetic tRNA expression cassette and verified functional nonsense suppressor tRNAGlnSCUA generation in a stop codon read-through assay with a modified β-galactosidase reporter gene. Correlation between altered tRNA and protein level was shown by survival of copper sensitive S. cerevisiae cells in the presence of copper ions by an increased transcription of tRNAArgCCG molecules, recognizing rare codons in a modified CUP1 gene. Genome integration of tRNA expression cassette led to the generation of arginine-tRNA-adapted S. cerevisiae strains, which showed elevated tRNA levels (tRNAArgCCG, tRNAArgGCG and tRNAArgUCG) pairing to rare codons. The modified strain MNY3 revealed a considerably improved monitoring of protein-protein interaction from Aspergillus fumigatus bait and prey sequences in yeast two-hybrid experiments. In future, this principle to overcome limited recombinant protein expression by tRNA adaption of expression strains instead of codon adaption might provide new designer yeast cells for an efficient protein production and for improved genome-wide protein-protein interaction analyses.
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8
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Klassen R, Schaffrath R. Role of Pseudouridine Formation by Deg1 for Functionality of Two Glutamine Isoacceptor tRNAs. Biomolecules 2017; 7:biom7010008. [PMID: 28134782 PMCID: PMC5372720 DOI: 10.3390/biom7010008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 12/22/2022] Open
Abstract
Loss of Deg1/Pus3 and concomitant elimination of pseudouridine in tRNA at positions 38 and 39 (ψ38/39) was shown to specifically impair the function of tRNAGlnUUG under conditions of temperature-induced down-regulation of wobble uridine thiolation in budding yeast and is linked to intellectual disability in humans. To further characterize the differential importance of the frequent ψ38/39 modification for tRNAs in yeast, we analyzed the in vivo function of non-sense suppressor tRNAs SUP4 and sup70-65 in the absence of the modifier. In the tRNATyrGψA variant SUP4, UAA read-through is enabled due to an anticodon mutation (UψA), whereas sup70-65 is a mutant form of tRNAGlnCUG (SUP70) that mediates UAG decoding due to a mutation of the anticodon-loop closing base pair (G31:C39 to A31:C39). While SUP4 function is unaltered in deg1/pus3 mutants, the ability of sup70-65 to mediate non-sense suppression and to complement a genomic deletion of the essential SUP70 gene is severely compromised. These results and the differential suppression of growth defects in deg1 mutants by multi-copy SUP70 or tQ(UUG) are consistent with the interpretation that ψ38 is most important for tRNAGlnUUG function under heat stress but becomes crucial for tRNAGlnCUG as well when the anticodon loop is destabilized by the sup70-65 mutation. Thus, ψ38/39 may protect the anticodon loop configuration from disturbances by loss of other modifications or base changes.
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Affiliation(s)
- Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany.
| | - Raffael Schaffrath
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, Heinrich-Plett-Str. 40, D-34132 Kassel, Germany.
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9
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Honigberg SM. Similar environments but diverse fates: Responses of budding yeast to nutrient deprivation. MICROBIAL CELL 2016; 3:302-328. [PMID: 27917388 PMCID: PMC5134742 DOI: 10.15698/mic2016.08.516] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diploid budding yeast (Saccharomyces cerevisiae) can adopt one
of several alternative differentiation fates in response to nutrient limitation,
and each of these fates provides distinct biological functions. When different
strain backgrounds are taken into account, these various fates occur in response
to similar environmental cues, are regulated by the same signal transduction
pathways, and share many of the same master regulators. I propose that the
relationships between fate choice, environmental cues and signaling pathways are
not Boolean, but involve graded levels of signals, pathway activation and
master-regulator activity. In the absence of large differences between
environmental cues, small differences in the concentration of cues may be
reinforced by cell-to-cell signals. These signals are particularly essential for
fate determination within communities, such as colonies and biofilms, where fate
choice varies dramatically from one region of the community to another. The lack
of Boolean relationships between cues, signaling pathways, master regulators and
cell fates may allow yeast communities to respond appropriately to the wide
range of environments they encounter in nature.
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Affiliation(s)
- Saul M Honigberg
- Division of Cell Biology and Biophysics, University of Missouri-Kansas City, 5007 Rockhill Rd, Kansas City MO 64110, USA
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10
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Gorgoni B, Ciandrini L, McFarland MR, Romano MC, Stansfield I. Identification of the mRNA targets of tRNA-specific regulation using genome-wide simulation of translation. Nucleic Acids Res 2016; 44:9231-9244. [PMID: 27407108 PMCID: PMC5100601 DOI: 10.1093/nar/gkw630] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/02/2016] [Indexed: 01/11/2023] Open
Abstract
tRNA gene copy number is a primary determinant of tRNA abundance and therefore the rate at which each tRNA delivers amino acids to the ribosome during translation. Low-abundance tRNAs decode rare codons slowly, but it is unclear which genes might be subject to tRNA-mediated regulation of expression. Here, those mRNA targets were identified via global simulation of translation. In-silico mRNA translation rates were compared for each mRNA in both wild-type and a \documentclass[12pt]{minimal}
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}{}${\rm{tRNA}}_{{\rm{CUG}}}^{{\rm{Gln}}}$\end{document}sup70-65 mutant, which exhibits a pseudohyphal growth phenotype and a 75% slower CAG codon translation rate. Of 4900 CAG-containing mRNAs, 300 showed significantly reduced in silico translation rates in a simulated tRNA mutant. Quantitative immunoassay confirmed that the reduced translation rates of sensitive mRNAs were \documentclass[12pt]{minimal}
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}{}${\rm{tRNA}}_{{\rm{CUG}}}^{{\rm{Gln}}}$\end{document} concentration-dependent. Translation simulations showed that reduced \documentclass[12pt]{minimal}
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}{}${\rm{tRNA}}_{{\rm{CUG}}}^{{\rm{Gln}}}$\end{document} concentrations triggered ribosome queues, which dissipated at reduced translation initiation rates. To validate this prediction experimentally, constitutive gcn2 kinase mutants were used to reduce in vivo translation initiation rates. This repaired the relative translational rate defect of target mRNAs in the sup70-65 background, and ameliorated sup70-65 pseudohyphal growth phenotypes. We thus validate global simulation of translation as a new tool to identify mRNA targets of tRNA-specific gene regulation.
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Affiliation(s)
- Barbara Gorgoni
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Luca Ciandrini
- DIMNP - UMR 5235 & CNRS, Université de Montpellier, 34095 Montpellier, France.,Laboratoire Charles Coulomb UMR5221 & CNRS, Université de Montpellier, 34095 Montpellier, France
| | - Matthew R McFarland
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - M Carmen Romano
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK.,University of Aberdeen, Institute for Complex Systems and Mathematical Biology, King's College, Aberdeen AB24 3UE, UK
| | - Ian Stansfield
- University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
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Petrova A, Kiktev D, Askinazi O, Chabelskaya S, Moskalenko S, Zemlyanko O, Zhouravleva G. The translation termination factor eRF1 (Sup45p) of Saccharomyces cerevisiae is required for pseudohyphal growth and invasion. FEMS Yeast Res 2015; 15:fov033. [PMID: 26054854 DOI: 10.1093/femsyr/fov033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 01/16/2023] Open
Abstract
Mutations in the essential genes SUP45 and SUP35, encoding yeast translation termination factors eRF1 and eRF3, respectively, lead to a wide range of phenotypes and affect various cell processes. In this work, we show that nonsense and missense mutations in the SUP45, but not the SUP35, gene abolish diploid pseudohyphal and haploid invasive growth. Missense mutations that change phosphorylation sites of Sup45 protein do not affect the ability of yeast strains to form pseudohyphae. Deletion of the C-terminal part of eRF1 did not lead to impairment of filamentation. We show a correlation between the filamentation defect and the budding pattern in sup45 strains. Inhibition of translation with specific antibiotics causes a significant reduction in pseudohyphal growth in the wild-type strain, suggesting a strong correlation between translation and the ability for filamentous growth. Partial restoration of pseudohyphal growth by addition of exogenous cAMP assumes that sup45 mutants are defective in the cAMP-dependent pathway that control filament formation.
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Affiliation(s)
- Alexandra Petrova
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Denis Kiktev
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Olga Askinazi
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Svetlana Chabelskaya
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Svetlana Moskalenko
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Olga Zemlyanko
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
| | - Galina Zhouravleva
- Department of Genetics and Biotechnology, St Petersburg State University and St Petersburg Branch Vavilov Institute of General Genetics, Russian Academy of Science, Universitetskaya emb. 7/9, 199034, St Petersburg, Russia
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12
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Han L, Kon Y, Phizicky EM. Functional importance of Ψ38 and Ψ39 in distinct tRNAs, amplified for tRNAGln(UUG) by unexpected temperature sensitivity of the s2U modification in yeast. RNA (NEW YORK, N.Y.) 2015; 21:188-201. [PMID: 25505024 PMCID: PMC4338347 DOI: 10.1261/rna.048173.114] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The numerous modifications of tRNA play central roles in controlling tRNA structure and translation. Modifications in and around the anticodon loop often have critical roles in decoding mRNA and in maintaining its reading frame. Residues U38 and U39 in the anticodon stem-loop are frequently modified to pseudouridine (Ψ) by members of the widely conserved TruA/Pus3 family of pseudouridylases. We investigate here the cause of the temperature sensitivity of pus3Δ mutants of the yeast Saccharomyces cerevisiae and find that, although Ψ38 or Ψ39 is found on at least 19 characterized cytoplasmic tRNA species, the temperature sensitivity is primarily due to poor function of tRNA(Gln(UUG)), which normally has Ψ38. Further investigation reveals that at elevated temperatures there are substantially reduced levels of the s(2)U moiety of mcm(5)s(2)U34 of tRNA(Gln(UUG)) and the other two cytoplasmic species with mcm(5)s(2)U34, that the reduced s(2)U levels occur in the parent strain BY4741 and in the widely used strain W303, and that reduced levels of the s(2)U moiety are detectable in BY4741 at temperatures as low as 33°C. Additional examination of the role of Ψ38,39 provides evidence that Ψ38 is important for function of tRNA(Gln(UUG)) at permissive temperature, and indicates that Ψ39 is important for the function of tRNA(Trp(CCA)) in trm10Δ pus3Δ mutants and of tRNA(Leu(CAA)) as a UAG nonsense suppressor. These results provide evidence for important roles of both Ψ38 and Ψ39 in specific tRNAs, and establish that modification of the wobble position is subject to change under relatively mild growth conditions.
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Affiliation(s)
- Lu Han
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Yoshiko Kon
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Eric M Phizicky
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
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13
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Nitrogen starvation and TorC1 inhibition differentially affect nuclear localization of the Gln3 and Gat1 transcription factors through the rare glutamine tRNACUG in Saccharomyces cerevisiae. Genetics 2014; 199:455-74. [PMID: 25527290 DOI: 10.1534/genetics.114.173831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A leucine, leucyl-tRNA synthetase-dependent pathway activates TorC1 kinase and its downstream stimulation of protein synthesis, a major nitrogen consumer. We previously demonstrated, however, that control of Gln3, a transcription activator of catabolic genes whose products generate the nitrogenous precursors for protein synthesis, is not subject to leucine-dependent TorC1 activation. This led us to conclude that excess nitrogen-dependent down-regulation of Gln3 occurs via a second mechanism that is independent of leucine-dependent TorC1 activation. A major site of Gln3 and Gat1 (another GATA-binding transcription activator) control occurs at their access to the nucleus. In excess nitrogen, Gln3 and Gat1 are sequestered in the cytoplasm in a Ure2-dependent manner. They become nuclear and activate transcription when nitrogen becomes limiting. Long-term nitrogen starvation and treatment of cells with the glutamine synthetase inhibitor methionine sulfoximine (Msx) also elicit nuclear Gln3 localization. The sensitivity of Gln3 localization to glutamine and inhibition of glutamine synthesis prompted us to investigate the effects of a glutamine tRNA mutation (sup70-65) on nitrogen-responsive control of Gln3 and Gat1. We found that nuclear Gln3 localization elicited by short- and long-term nitrogen starvation; growth in a poor, derepressive medium; Msx or rapamycin treatment; or ure2Δ mutation is abolished in a sup70-65 mutant. However, nuclear Gat1 localization, which also exhibits a glutamine tRNACUG requirement for its response to short-term nitrogen starvation or growth in proline medium or a ure2Δ mutation, does not require tRNACUG for its response to rapamycin. Also, in contrast with Gln3, Gat1 localization does not respond to long-term nitrogen starvation. These observations demonstrate the existence of a specific nitrogen-responsive component participating in the control of Gln3 and Gat1 localization and their downstream production of nitrogenous precursors. This component is highly sensitive to the function of the rare glutamine tRNACUG, which cannot be replaced by the predominant glutamine tRNACAA. Our observations also demonstrate distinct mechanistic differences between the responses of Gln3 and Gat1 to rapamycin inhibition of TorC1 and nitrogen starvation.
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14
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Controlling translation elongation efficiency: tRNA regulation of ribosome flux on the mRNA. Biochem Soc Trans 2014; 42:160-5. [DOI: 10.1042/bst20130132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Gene expression can be regulated by a wide variety of mechanisms. One example concerns the growing body of evidence that the protein-production rate can be regulated at the level of translation elongation by controlling ribosome flux across the mRNA. Variations in the abundance of tRNA molecules cause different rates of translation of their counterpart codons. This, in turn, produces a variable landscape of translational rate across each and every mRNA, with the dynamic formation and deformation of ribosomal queues being regulated by both tRNA availability and the rates of translation initiation and termination. In the present article, a range of examples of tRNA control of gene expression are reviewed, and the use of mathematical modelling to develop a predictive understanding of the consequences of that regulation is discussed and explained. These findings encourage a view that predicting the protein-synthesis rate of each mRNA requires a holistic understanding of how each stage of translation, including elongation, contributes to the overall protein-production rate.
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15
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Berchowitz LE, Gajadhar AS, van Werven FJ, De Rosa AA, Samoylova ML, Brar GA, Xu Y, Xiao C, Futcher B, Weissman JS, White FM, Amon A. A developmentally regulated translational control pathway establishes the meiotic chromosome segregation pattern. Genes Dev 2013; 27:2147-63. [PMID: 24115771 PMCID: PMC3850098 DOI: 10.1101/gad.224253.113] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/03/2013] [Indexed: 11/25/2022]
Abstract
Production of haploid gametes from diploid progenitor cells is mediated by a specialized cell division, meiosis, where two divisions, meiosis I and II, follow a single S phase. Errors in progression from meiosis I to meiosis II lead to aneuploid and polyploid gametes, but the regulatory mechanisms controlling this transition are poorly understood. Here, we demonstrate that the conserved kinase Ime2 regulates the timing and order of the meiotic divisions by controlling translation. Ime2 coordinates translational activation of a cluster of genes at the meiosis I-meiosis II transition, including the critical determinant of the meiotic chromosome segregation pattern CLB3. We further show that Ime2 mediates translational control through the meiosis-specific RNA-binding protein Rim4. Rim4 inhibits translation of CLB3 during meiosis I by interacting with the 5' untranslated region (UTR) of CLB3. At the onset of meiosis II, Ime2 kinase activity rises and triggers a decrease in Rim4 protein levels, thereby alleviating translational repression. Our results elucidate a novel developmentally regulated translational control pathway that establishes the meiotic chromosome segregation pattern.
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Affiliation(s)
- Luke E. Berchowitz
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute
| | - Aaron S. Gajadhar
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Folkert J. van Werven
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute
| | - Alexandra A. De Rosa
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute
| | - Mariya L. Samoylova
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute
| | - Gloria A. Brar
- Howard Hughes Medical Institute
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94158, USA
- California Institute for Quantitative Biosciences, San Francisco, California 94158, USA
| | - Yifeng Xu
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Che Xiao
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Bruce Futcher
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Jonathan S. Weissman
- Howard Hughes Medical Institute
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94158, USA
- California Institute for Quantitative Biosciences, San Francisco, California 94158, USA
| | - Forest M. White
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Angelika Amon
- Koch Institute for Integrative Cancer Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute
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16
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Kemp AJ, Betney R, Ciandrini L, Schwenger ACM, Romano MC, Stansfield I. A yeast tRNA mutant that causes pseudohyphal growth exhibits reduced rates of CAG codon translation. Mol Microbiol 2012; 87:284-300. [PMID: 23146061 PMCID: PMC3664417 DOI: 10.1111/mmi.12096] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2012] [Indexed: 11/27/2022]
Abstract
In Saccharomyces cerevisiae, the SUP70 gene encodes the CAG-decoding tRNA(Gln)(CUG). A mutant allele, sup70-65, induces pseudohyphal growth on rich medium, an inappropriate nitrogen starvation response. This mutant tRNA is also a UAG nonsense suppressor via first base wobble. To investigate the basis of the pseudohyphal phenotype, 10 novel sup70 UAG suppressor alleles were identified, defining positions in the tRNA(Gln)(CUG) anticodon stem that restrict first base wobble. However, none conferred pseudohyphal growth, showing altered CUG anticodon presentation cannot itself induce pseudohyphal growth. Northern blot analysis revealed the sup70-65 tRNA(Gln)(CUG) is unstable, inefficiently charged, and 80% reduced in its effective concentration. A stochastic model simulation of translation predicted compromised expression of CAG-rich ORFs in the tRNA(Gln)(CUG)-depleted sup70-65 mutant. This prediction was validated by demonstrating that luciferase expression in the mutant was 60% reduced by introducing multiple tandem CAG (but not CAA) codons into this ORF. In addition, the sup70-65 pseudohyphal phenotype was partly complemented by overexpressing CAA-decoding tRNA(Gln)(UUG), an inefficient wobble-decoder of CAG. We thus show that introducing codons decoded by a rare tRNA near the 5' end of an ORF can reduce eukaryote translational expression, and that the mutant tRNA(CUG)(Gln) constitutive pseudohyphal differentiation phenotype correlates strongly with reduced CAG decoding efficiency.
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Affiliation(s)
- Alain J Kemp
- Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
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17
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Abstract
Filamentous growth is a nutrient-regulated growth response that occurs in many fungal species. In pathogens, filamentous growth is critical for host-cell attachment, invasion into tissues, and virulence. The budding yeast Saccharomyces cerevisiae undergoes filamentous growth, which provides a genetically tractable system to study the molecular basis of the response. Filamentous growth is regulated by evolutionarily conserved signaling pathways. One of these pathways is a mitogen activated protein kinase (MAPK) pathway. A remarkable feature of the filamentous growth MAPK pathway is that it is composed of factors that also function in other pathways. An intriguing challenge therefore has been to understand how pathways that share components establish and maintain their identity. Other canonical signaling pathways-rat sarcoma/protein kinase A (RAS/PKA), sucrose nonfermentable (SNF), and target of rapamycin (TOR)-also regulate filamentous growth, which raises the question of how signals from multiple pathways become integrated into a coordinated response. Together, these pathways regulate cell differentiation to the filamentous type, which is characterized by changes in cell adhesion, cell polarity, and cell shape. How these changes are accomplished is also discussed. High-throughput genomics approaches have recently uncovered new connections to filamentous growth regulation. These connections suggest that filamentous growth is a more complex and globally regulated behavior than is currently appreciated, which may help to pave the way for future investigations into this eukaryotic cell differentiation behavior.
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18
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Miklos I, Ludanyi K, Sipiczki M. The pleiotropic cell separation mutation spl1-1 is a nucleotide substitution in the internal promoter of the proline tRNACGG gene of Schizosaccharomyces pombe. Curr Genet 2009; 55:511-20. [PMID: 19636559 DOI: 10.1007/s00294-009-0262-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 07/06/2009] [Accepted: 07/09/2009] [Indexed: 11/25/2022]
Abstract
spl1-1 was originally identified as a spontaneous mutation genetically interacting with sep1-1 and cdc4-8 in producing multinucleate syncytia. This study shows that it is allelic with the proline-tRNA(CGG) gene SPATRNAPRO.02. Its nucleotide sequence contains a C-->T substitution in the region corresponding to the B-box of the putative intragenic promoter and the TpsiC loop of the mature tRNA. The substitution drastically reduces the transcription efficiency of the gene and pleiotropically affects numerous cellular processes. spl1-1 cells are temperature sensitive, osmosensitive, bend at higher temperatures, have extended G2 phase and are defective in cell separation (septum cleavage). The proline-tRNA(TGG) gene SPATRNAPRO.01 can partially suppress the spl1-1 mutation when introduced into the cells on a multicopy plasmid. The effect of a mutation in a tRNA gene on cell separation brings a new element into the complexity of the regulation of cell division and its co-ordination with other cellular processes in Schizosaccharomyces pombe.
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Affiliation(s)
- Ida Miklos
- Department of Genetics and Applied Microbiology, University of Debrecen, P.O. Box 56, 4010, Debrecen, Hungary
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19
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The tRNA modification complex elongator regulates the Cdc42-dependent mitogen-activated protein kinase pathway that controls filamentous growth in yeast. EUKARYOTIC CELL 2009; 8:1362-72. [PMID: 19633267 DOI: 10.1128/ec.00015-09] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Signal transduction pathways control multiple aspects of cellular behavior, including global changes to the cell cycle, cell polarity, and gene expression, which can result in the formation of a new cell type. In the budding yeast Saccharomyces cerevisiae, the mitogen-activated protein kinase (MAPK) pathway that controls filamentous growth induces a dimorphic foraging response under nutrient-limiting conditions. How nutritional cues feed into MAPK activation remains an open question. Here we report a functional connection between the elongator tRNA modification complex (ELP genes) and activity of the filamentous growth pathway. Elongator was required for filamentous growth pathway signaling, and elp mutants were defective for invasive growth, cell polarization, and MAPK-dependent mat formation. Genetic suppression analysis showed that elongator functions at the level of Msb2p, the signaling mucin that operates at the head of the pathway, which led to the finding that elongator regulates the starvation-dependent expression of the MSB2 gene. The Elp complex was not required for activation of related pathways (pheromone response or high osmolarity glycerol response) that share components with the filamentous growth pathway. Because protein translation provides a rough metric of cellular nutritional status, elongator may convey nutritional information to the filamentous growth pathway at the level of MSB2 expression.
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20
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Abstract
Yeast cells sense the amount and quality of external nutrients through multiple interconnected signaling networks, which allow them to adjust their metabolism, transcriptional profile and developmental program to adapt readily and appropriately to changing nutritional states. We present our current understanding of the nutritional sensing networks yeast cells rely on for perceiving the nutritional landscape, with particular emphasis on those sensitive to carbon and nitrogen sources. We describe the means by which these networks inform the cell's decision among the different developmental programs available to them-growth, quiescence, filamentous development, or meiosis/sporulation. We conclude that the highly interconnected signaling networks provide the cell with a highly nuanced view of the environment and that the cell can interpret that information through a sophisticated calculus to achieve optimum responses to any nutritional condition.
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Affiliation(s)
- Shadia Zaman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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21
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Barberio C, Bianchi L, Pinzauti F, Lodi T, Ferrero I, Polsinelli M, Casalone E. Induction and characterization of morphologic mutants in a natural Saccharomyces cerevisiae strain. Can J Microbiol 2007; 53:223-30. [PMID: 17496970 DOI: 10.1139/w06-132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Saccharomyces cerevisiae is a good model with which to study the effects of morphologic differentiation on the ecological behaviour of fungi. In this work, 33 morphologic mutants of a natural strain of S. cerevisiae, obtained with UV mutagenesis, were selected for their streak shape and cell shape on rich medium. Two of them, showing both high sporulation proficiency and constitutive pseudohyphal growth, were analysed from a genetic and physiologic point of view. Each mutant carries a recessive monogenic mutation, and the two mutations reside in unlinked genes. Flocculation ability and responsiveness to different stimuli distinguished the two mutants. Growth at 37 degrees C affected the cell but not the colony morphology, suggesting that these two phenotypes are regulated differently. The effect of ethidium bromide, which affects mitochondrial DNA replication, suggested a possible "retrograde action" of mitochondria in pseudohyphal growth.
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Affiliation(s)
- Claudia Barberio
- Department of Animal Biology and Genetics, University of Florence, via Romana 17, I-50125 Firenze, Italy
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22
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Ibrahimo S, Holmes LEA, Ashe MP. Regulation of translation initiation by the yeast eIF4E binding proteins is required for the pseudohyphal response. Yeast 2007; 23:1075-88. [PMID: 17083129 DOI: 10.1002/yea.1415] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The eukaryotic translation initiation factor eIF4E is responsible for the recognition of the mRNA cap structure and, as such, plays a key role in the selection of mRNAs for translation. The interaction of eIF4E with the 'multi-adaptor' eIF4G (and thus recruitment of ribosomes to mRNA) can be regulated via competitive binding of 4E-binding proteins (4E-BPs). 4E-BPs have broad functions in cell growth, proliferation and development. We have found that disruption of the genes for either of the yeast 4E-BPs (Eap1p or Caf20p) leads to an inhibition of pseudohyphal growth in the resulting diploid yeast strain following nitrogen limitation. Specific 4E-binding domain mutations destroy the capacity of each 4E-BP gene to complement the non-pseudohyphal phenotype, suggesting that a translational function for the 4E-BPs is important for pseudohyphal growth. In addition, neither of the 4E-BP deletion strains is deficient in global or stress-regulated protein synthesis. However, our evidence reveals that the two 4E-BPs are functionally distinct with regard to pseudohyphal growth. Therefore, this work supports a model where the yeast 4E-BPs are acting on specific mRNAs to facilitate a defined proliferative response to environmental stress in yeast.
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Affiliation(s)
- Salma Ibrahimo
- Faculty of Life Sciences, The University of Manchester, The Michael Smith Building, Oxford Road, Manchester, UK
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23
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Holtzman T, Meimoun A, Kornitzer D. Synthetic Genetic Interaction Between the Ubiquitin-Conjugating Enzyme Cdc34 and a tRNA Mutant. Isr J Chem 2006. [DOI: 10.1560/688a-xh1u-xnuy-23kr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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24
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Rossi B, Manasse S, Serrani F, Berardi E. Hansenula polymorpha NMR2 and NMR4, two new loci involved in nitrogen metabolite repression. FEMS Yeast Res 2005; 5:1009-17. [PMID: 16214423 DOI: 10.1016/j.femsyr.2005.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2005] [Revised: 08/02/2005] [Accepted: 08/24/2005] [Indexed: 11/18/2022] Open
Abstract
In the yeast Hansenula polymorpha (Pichia angusta) nitrate assimilation is tightly regulated and subject to a dual control: nitrogen metabolite repression (NMR), triggered by reduced nitrogen compounds, and induction, elicited by nitrate itself. In a previous paper [Serrani, F., Rossi, B. and Berardi, E (2001) Nitrogen metabolite repression in Hansenula polymorpha: the nmrl-l mutation. Curr. Genet. 40, 243-250], we identified five loci (NMR1-NMR5) involved in NMR, and characterised one of them (NMR1), which likely identifies a regulatory factor. Here, we describe two more mutants, namely nmr2-1 and nmr4-1. The first one possibly identifies a regulatory factor involved in nitrogen metabolite repression by various nitrogen sources alternative to ammonium. The second one, apparently involved in ammonium assimilation, probably has sensor functions.
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Affiliation(s)
- Beatrice Rossi
- Laboratorio di Genetica Microbica, DiSA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
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25
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Tork S, Hatin I, Rousset JP, Fabret C. The major 5' determinant in stop codon read-through involves two adjacent adenines. Nucleic Acids Res 2004; 32:415-21. [PMID: 14736996 PMCID: PMC373328 DOI: 10.1093/nar/gkh201] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aim of this approach was to identify the major determinants, located at the 5' end of the stop codon, that modulate translational read-through in Saccharomyces cerevisiae. We developed a library of oligonucleotides degenerate at the six positions immediately upstream of the termination codon, cloned in the ADE2 reporter gene. Variations at these positions modulated translational read-through efficiency approximately 16-fold. The major effect was imposed by the two nucleotides immediately upstream of the stop codon. We showed that this effect was neither mediated by the last amino acid residues present in the polypeptide chain nor by the tRNA present in the ribosomal P site. We propose that the mRNA structure, depending on the nucleotides in the P site, is the main 5' determinant of read-through efficiency.
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MESH Headings
- Adenine Nucleotides/genetics
- Base Composition
- Base Sequence
- Binding Sites
- Codon, Terminator/genetics
- Gene Library
- Genes, Fungal/genetics
- Genes, Reporter/genetics
- Nucleic Acid Conformation
- Oligoribonucleotides/chemistry
- Oligoribonucleotides/genetics
- Oligoribonucleotides/metabolism
- Peptide Chain Elongation, Translational/genetics
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Regulatory Sequences, Ribonucleic Acid/genetics
- Ribosomes/genetics
- Ribosomes/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae Proteins/genetics
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Affiliation(s)
- Sanaa Tork
- CNRS UMR 8621, Institut de Génétique et Microbiologie, Université Paris-Sud, 91405 Orsay Cedex, France
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26
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Gagiano M, Bauer FF, Pretorius IS. The sensing of nutritional status and the relationship to filamentous growth in Saccharomyces cerevisiae. FEMS Yeast Res 2002; 2:433-70. [PMID: 12702263 DOI: 10.1111/j.1567-1364.2002.tb00114.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Heterotrophic organisms rely on the ingestion of organic molecules or nutrients from the environment to sustain energy and biomass production. Non-motile, unicellular organisms have a limited ability to store nutrients or to take evasive action, and are therefore most directly dependent on the availability of nutrients in their immediate surrounding. Such organisms have evolved numerous developmental options in order to adapt to and to survive the permanently changing nutritional status of the environment. The phenotypical, physiological and molecular nature of nutrient-induced cellular adaptations has been most extensively studied in the yeast Saccharomyces cerevisiae. These studies have revealed a network of sensing mechanisms and of signalling pathways that generate and transmit the information on the nutritional status of the environment to the cellular machinery that implements specific developmental programmes. This review integrates our current knowledge on nutrient sensing and signalling in S. cerevisiae, and suggests how an integrated signalling network may lead to the establishment of a specific developmental programme, namely pseudohyphal differentiation and invasive growth.
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Affiliation(s)
- Marco Gagiano
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, South Africa
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27
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Palecek SP, Parikh AS, Kron SJ. Sensing, signalling and integrating physical processes during Saccharomyces cerevisiae invasive and filamentous growth. MICROBIOLOGY (READING, ENGLAND) 2002; 148:893-907. [PMID: 11932437 DOI: 10.1099/00221287-148-4-893] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Sean P Palecek
- Department of Chemical Engineering, University of Wisconsin - Madison, Madison, WI 53706, USA1
| | - Archita S Parikh
- Center for Molecular Oncology2 and Department of Molecular Genetics and Cell Biology3, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen J Kron
- Center for Molecular Oncology2 and Department of Molecular Genetics and Cell Biology3, The University of Chicago, Chicago, IL 60637, USA
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28
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Sipiczki M, Grallert A, Zilahi E, Miklós I, Sziljágyi Z. Multifunctional cytokinesis genes in Schizosaccharomyces pombe. ACTA BIOLOGICA HUNGARICA 2002; 52:315-23. [PMID: 11426866 DOI: 10.1556/abiol.52.2001.2-3.16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The proper division of cells is essential for the production of viable daughter cells. In plants and fungi, the dividing cell produces a cross-wall or septum that bisects the cytoplasm. For separation of the daughter cells, the septum has to be cleaved. To study the regulation of this process, we isolated mutants defective in septum cleavage. The mutants showed highly pleiotropic phenotypes and defined 17 novel genes. The deduced amino acid sequences of the products of the cloned genes exhibited homologies to various transcription regulators of other organisms. The homologies and the pleiotropic effects of the mutations on sexual development, stress response, mitotic stability, septum initiation and septum placement indicated that these genes affect cell separation indirectly, through multifunctional regulatory modules.
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Affiliation(s)
- M Sipiczki
- Department of Genetics, University of Debrecen, Hungary.
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29
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Grosshans H, Lecointe F, Grosjean H, Hurt E, Simos G. Pus1p-dependent tRNA pseudouridinylation becomes essential when tRNA biogenesis is compromised in yeast. J Biol Chem 2001; 276:46333-9. [PMID: 11571299 DOI: 10.1074/jbc.m107141200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yeast Pus1p catalyzes the formation of pseudouridine (psi) at specific sites of several tRNAs, but its function is not essential for cell viability. We show here that Pus1p becomes essential when another tRNA:pseudouridine synthase, Pus4p, or the essential minor tRNA for glutamine are mutated. Strikingly, this mutant tRNA, which carries a mismatch in the T psi C arm, displays a nuclear export defect. Furthermore, nuclear export of at least one wild-type tRNA species becomes defective in the absence of Pus1p. Our data, thus, show that the modifications formed by Pus1p are essential when other aspects of tRNA biogenesis or function are compromised and suggest that impairment of nuclear tRNA export in the absence of Pus1p might contribute to this phenotype.
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Affiliation(s)
- H Grosshans
- Biochemie-Zentrum Heidelberg, D-69120 Heidelberg, Germany
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30
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Cutler NS, Pan X, Heitman J, Cardenas ME. The TOR signal transduction cascade controls cellular differentiation in response to nutrients. Mol Biol Cell 2001; 12:4103-13. [PMID: 11739804 PMCID: PMC60779 DOI: 10.1091/mbc.12.12.4103] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2001] [Revised: 09/10/2001] [Accepted: 09/10/2001] [Indexed: 01/05/2023] Open
Abstract
Rapamycin binds and inhibits the Tor protein kinases, which function in a nutrient-sensing signal transduction pathway that has been conserved from the yeast Saccharomyces cerevisiae to humans. In yeast cells, the Tor pathway has been implicated in regulating cellular responses to nutrients, including proliferation, translation, transcription, autophagy, and ribosome biogenesis. We report here that rapamycin inhibits pseudohyphal filamentous differentiation of S. cerevisiae in response to nitrogen limitation. Overexpression of Tap42, a protein phosphatase regulatory subunit, restored pseudohyphal growth in cells exposed to rapamycin. The tap42-11 mutation compromised pseudohyphal differentiation and rendered it resistant to rapamycin. Cells lacking the Tap42-regulated protein phosphatase Sit4 exhibited a pseudohyphal growth defect and were markedly hypersensitive to rapamycin. Mutations in other Tap42-regulated phosphatases had no effect on pseudohyphal differentiation. Our findings support a model in which pseudohyphal differentiation is controlled by a nutrient-sensing pathway involving the Tor protein kinases and the Tap42-Sit4 protein phosphatase. Activation of the MAP kinase or cAMP pathways, or mutation of the Sok2 repressor, restored filamentation in rapamycin treated cells, supporting models in which the Tor pathway acts in parallel with these known pathways. Filamentous differentiation of diverse fungi was also blocked by rapamycin, demonstrating that the Tor signaling cascade plays a conserved role in regulating filamentous differentiation in response to nutrients.
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Affiliation(s)
- N S Cutler
- Department of Genetics, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
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Morozov IY, Galbis-Martinez M, Jones MG, Caddick MX. Characterization of nitrogen metabolite signalling in Aspergillus via the regulated degradation of areA mRNA. Mol Microbiol 2001; 42:269-77. [PMID: 11679084 DOI: 10.1046/j.1365-2958.2001.02636.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AreA is the principal transcription factor involved in determining nitrogen utilization in Aspergillus nidulans. NH4+ and Gln are utilized preferentially but in their absence, AreA acts to facilitate the expression of genes involved in metabolizing alternative nitrogen sources. It is crucial to the function of AreA that its expression is tightly modulated by the quality and availability of nitrogen sources. One signalling mechanism involves regulated degradation of the areA transcript in response to NH4+ and Gln, which provides the first direct means of monitoring nitrogen signalling in this fungus. Here we assess the specificity of the transcript degradation response, determining that it responds qualitatively to a variety of additional nitrogen sources including Asn. Furthermore, the response to Gln and NH4+ requires the same discrete region of the areA 3'-UTR but both NH4+ and Asn need to be metabolized to Gln before they are effective as a signal. However, NH4+ signalling is independent of AreA activity, unlike Gln and Asn signalling. A mutation in the structural gene for NADP-linked glutamate dehydrogenase, gdhA, which disrupts metabolism of NH4+ to Glu, is additive with mutations in two distinct regions of areA that disrupt the previously identified signalling mechanisms. The triple mutant is both strongly derepressed and expresses very high levels of nitrate reductase activity. These data suggest nitrogen metabolism in A. nidulans is in part regulated in response to the intracellular levels of Gln via the regulated degradation of areA mRNA, but the intracellular Gln level is not the sole determinant of nitrogen metabolite repression.
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Affiliation(s)
- I Y Morozov
- Plant Science and Fungal Molecular Biology Research Group, School of Biological Sciences, Donnan Labs, The University of Liverpool, Liverpool L69 7ZD, UK
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Parsons R, Sunley RJ. Nitrogen nutrition and the role of root-shoot nitrogen signalling particularly in symbiotic systems. JOURNAL OF EXPERIMENTAL BOTANY 2001; 52:435-443. [PMID: 11326050 DOI: 10.1093/jexbot/52.suppl_1.435] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
To obtain and concentrate reduced N from the environment, plants have evolved a diverse array of adaptations to utilize soil, biotic and atmospheric N. In symbiotic N(2)-fixing systems the potential for oversupply exists and regulation of activity to match demand is crucial. N status in plants is likely to be most strongly sensed in the shoot and signals translocated to the roots may involve phloem transported amino compounds or very low concentrations of specific signal molecules. The mechanism for sensing N status in plant cells is not understood at the molecular level although it may be expected to be similar in all plants. Mechanisms for the regulation of symbiotic N(2) fixation may be very different in the different symbiotic types. Rhizobia, Frankia and cyanobacteria are all symbiotic with different species of plants and the provision of O(2), carbohydrate or other nutrients may control symbiotic activity to varying extents in the different symbioses.
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Affiliation(s)
- R Parsons
- University of Dundee, Dundee DD1 4HN, Scotland, UK.
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Parsons R, Sunley RJ. Nitrogen nutrition and the role of root-shoot nitrogen signalling particularly in symbiotic systems. JOURNAL OF EXPERIMENTAL BOTANY 2001; 52:435-443. [PMID: 11326050 DOI: 10.1093/jxb/52.suppl_1.435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
To obtain and concentrate reduced N from the environment, plants have evolved a diverse array of adaptations to utilize soil, biotic and atmospheric N. In symbiotic N(2)-fixing systems the potential for oversupply exists and regulation of activity to match demand is crucial. N status in plants is likely to be most strongly sensed in the shoot and signals translocated to the roots may involve phloem transported amino compounds or very low concentrations of specific signal molecules. The mechanism for sensing N status in plant cells is not understood at the molecular level although it may be expected to be similar in all plants. Mechanisms for the regulation of symbiotic N(2) fixation may be very different in the different symbiotic types. Rhizobia, Frankia and cyanobacteria are all symbiotic with different species of plants and the provision of O(2), carbohydrate or other nutrients may control symbiotic activity to varying extents in the different symbioses.
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Affiliation(s)
- R Parsons
- University of Dundee, Dundee DD1 4HN, Scotland, UK.
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Abstract
Pseudohyphal growth in both haploid and diploid strains of Saccharomyces cerevisiae reflects concerted changes in different cellular processes: budding pattern, cell elongation and cell adhesion. These changes are triggered by environmental signals and are controlled by several pathways which act in parallel. Nitrogen deprivation, and possibly other stresses, activate a MAP kinase cascade which has the transcription factor Ste12 as its final target. A cAMP-dependent pathway, in which the protein kinase Tpk2 plays a specific role, is also required for the morphogenetic switch. Both pathways contribute to modulate the expression of the MUC1/FLO11 gene which encodes a cell-surface flocculin required for pseudohyphal and invasive growth. The MAP kinase cascade could also control the activity of the cyclin/Cdc28 complexes which affect both the budding pattern of yeast and cell elongation. A further protein which stimulates filamentous growth in S. cerevisiae is Phd1; although its mode of action is unknown, it may be regulated by a cAMP-dependent protein kinase, as occurs with the homologous protein Efg1 from Candida albicans, which is required for the formation of true hyphae. Morphogenesis in different yeast genera share common elements, but there are also important differences. Although a complete picture cannot yet be drawn, partial models may be proposed for the interaction of the regulatory pathways, both in the case of S. cerevisiae and in that of C. albicans.
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Affiliation(s)
- J M Gancedo
- Instituto de Investigaciones Biomédicas 'Alberto Sols', CSIC-UAM, Arturo Duperier 4, 28029 Madrid, Spain.
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Abstract
Prior studies have shown that S. cerevisiae rim4 mutations cause reduced expression of a sporulation-specific reporter gene and sporulation. We report here that RIM4 (ORF YHL024W) is a putative RNA-binding protein of the RRM class that is expressed at elevated levels early in meiosis. Mutations in the two RRMs reduce or abolish sporulation and, in some cases, cause reduced Rim4p expression. RIM4 is required for expression of early and middle sporulation-specific genes. Unlike other meiotic regulatory genes, RIM4 is required for full gene activation through both the Ime1p and Ime2p pathways. The rim4Delta defect in activation by Ime2p is suppressed by a hyperactive Ime2p derivative. These observations argue that Rim4p may act upstream of Ime2p, perhaps in a nutritional sensing pathway.
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Affiliation(s)
- M Soushko
- Department of Microbiology, Columbia University, New York, NY 10032, USA
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Wrobel C, Schmidt EV, Polymenis M. CDC64 encodes cytoplasmic alanyl-tRNA synthetase, Ala1p, of Saccharomyces cerevisiae. J Bacteriol 1999; 181:7618-20. [PMID: 10601222 PMCID: PMC94222 DOI: 10.1128/jb.181.24.7618-7620.1999] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cdc64-1 mutation causes G(1) arrest in Saccharomyces cerevisiae corresponding to a type II Start phenotype. We report that CDC64 encodes Ala1p, an alanyl-tRNA synthetase. Thus, cdc64-1 might affect charging of tRNA(Ala) and thereby initiation of cell division.
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Affiliation(s)
- C Wrobel
- MGH Cancer Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
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Beeser AE, Cooper TG. Control of nitrogen catabolite repression is not affected by the tRNAGln-CUU mutation, which results in constitutive pseudohyphal growth of Saccharomyces cerevisiae. J Bacteriol 1999; 181:2472-6. [PMID: 10198011 PMCID: PMC93673 DOI: 10.1128/jb.181.8.2472-2476.1999] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae responds to nitrogen availability in several ways. (i) The cell is able to distinguish good nitrogen sources from poor ones through a process designated nitrogen catabolite repression (NCR). Good and poor nitrogen sources do not demonstrably affect the cell cycle other than to influence the cell's doubling time. (ii) Nitrogen starvation promotes the initiation of sporulation and pseudohyphal growth. (iii) Nitrogen starvation strongly affects the cell cycle; nitrogen-starved cells arrest in G1. A specific allele of the SUP70/CDC65 tRNAGln gene (sup70-65) has been reported to be defective in nitrogen signaling associated with pseudohyphal formation, sporulation, and NCR. Our data confirm that pseudohyphal growth occurs gratuitously in sup70-65 mutants cultured in nitrogen-rich medium at 30 degrees C. However, we find neither any defect in NCR in the sup70-65 mutant nor any alteration in the control of YVH1 expression, which has been previously shown to be specifically induced by nitrogen starvation.
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Affiliation(s)
- A E Beeser
- Department of Microbiology and Immunology, University of Tennessee, Memphis, Tennessee 38163, USA
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