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Jadhav R, Mach RL, Mach-Aigner AR. Protein secretion and associated stress in industrially employed filamentous fungi. Appl Microbiol Biotechnol 2024; 108:92. [PMID: 38204136 PMCID: PMC10781871 DOI: 10.1007/s00253-023-12985-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024]
Abstract
Application of filamentous fungi for the production of commercial enzymes such as amylase, cellulase, or xylanase is on the rise due to the increasing demand to degrade several complex carbohydrates as raw material for biotechnological processes. Also, protein production by fungi for food and feed gains importance. In any case, the protein production involves both cellular synthesis and secretion outside of the cell. Unfortunately, the secretion of proteins or enzymes can be hampered due to accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) as a result of too high synthesis of enzymes or (heterologous) protein expression. To cope with this ER stress, the cell generates a response known as unfolded protein response (UPR). Even though this mechanism should re-establish the protein homeostasis equivalent to a cell under non-stress conditions, the enzyme expression might still suffer from repression under secretory stress (RESS). Among eukaryotes, Saccharomyces cerevisiae is the only fungus, which is studied quite extensively to unravel the UPR pathway. Several homologs of the proteins involved in this signal transduction cascade are also found in filamentous fungi. Since RESS seems to be absent in S. cerevisiae and was only reported in Trichoderma reesei in the presence of folding and glycosylation inhibitors such as dithiothreitol and tunicamycin, more in-depth study about this mechanism, specifically in filamentous fungi, is the need of the hour. Hence, this review article gives an overview on both, protein secretion and associated stress responses in fungi. KEY POINTS: • Enzymes produced by filamentous fungi are crucial in industrial processes • UPR mechanism is conserved among many fungi, but mediated by different proteins • RESS is not fully understood or studied in industrially relevant filamentous fungi.
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Affiliation(s)
- Reshma Jadhav
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Robert L Mach
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, A-1060, Vienna, Austria.
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2
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McCarthy J. Engineering and standardization of posttranscriptional biocircuitry in Saccharomyces cerevisiae. Integr Biol (Camb) 2021; 13:210-220. [PMID: 34270725 DOI: 10.1093/intbio/zyab013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/14/2022]
Abstract
This short review considers to what extent posttranscriptional steps of gene expression can provide the basis for novel control mechanisms and procedures in synthetic biology and biotechnology. The term biocircuitry is used here to refer to functionally connected components comprising DNA, RNA or proteins. The review begins with an overview of the diversity of devices being developed and then considers the challenges presented by trying to engineer more scaled-up systems. While the engineering of RNA-based and protein-based circuitry poses new challenges, the resulting 'toolsets' of components and novel mechanisms of operation will open up multiple new opportunities for synthetic biology. However, agreed procedures for standardization will need to be placed at the heart of this expanding field if the full potential benefits are to be realized.
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Affiliation(s)
- John McCarthy
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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3
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Muller R, Meacham ZA, Ferguson L, Ingolia NT. CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes. Science 2020; 370:eabb9662. [PMID: 33303588 PMCID: PMC7819735 DOI: 10.1126/science.abb9662] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
To realize the promise of CRISPR-Cas9-based genetics, approaches are needed to quantify a specific, molecular phenotype across genome-wide libraries of genetic perturbations. We addressed this challenge by profiling transcriptional, translational, and posttranslational reporters using CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). Our barcoding approach allowed us to connect an entire library of guides to their individual phenotypic consequences using pooled sequencing. CiBER-seq profiling fully recapitulated the integrated stress response (ISR) pathway in yeast. Genetic perturbations causing uncharged transfer RNA (tRNA) accumulation activated ISR reporter transcription. Notably, tRNA insufficiency also activated the reporter, independent of the uncharged tRNA sensor. By uncovering alternate triggers for ISR activation, we illustrate how precise, comprehensive CiBER-seq profiling provides a powerful and broadly applicable tool for dissecting genetic networks.
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Affiliation(s)
- Ryan Muller
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Zuriah A Meacham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lucas Ferguson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
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4
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Srinivasan R, Walvekar AS, Rashida Z, Seshasayee A, Laxman S. Genome-scale reconstruction of Gcn4/ATF4 networks driving a growth program. PLoS Genet 2020; 16:e1009252. [PMID: 33378328 PMCID: PMC7773203 DOI: 10.1371/journal.pgen.1009252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
Growth and starvation are considered opposite ends of a spectrum. To sustain growth, cells use coordinated gene expression programs and manage biomolecule supply in order to match the demands of metabolism and translation. Global growth programs complement increased ribosomal biogenesis with sufficient carbon metabolism, amino acid and nucleotide biosynthesis. How these resources are collectively managed is a fundamental question. The role of the Gcn4/ATF4 transcription factor has been best studied in contexts where cells encounter amino acid starvation. However, high Gcn4 activity has been observed in contexts of rapid cell proliferation, and the roles of Gcn4 in such growth contexts are unclear. Here, using a methionine-induced growth program in yeast, we show that Gcn4/ATF4 is the fulcrum that maintains metabolic supply in order to sustain translation outputs. By integrating matched transcriptome and ChIP-Seq analysis, we decipher genome-wide direct and indirect roles for Gcn4 in this growth program. Genes that enable metabolic precursor biosynthesis indispensably require Gcn4; contrastingly ribosomal genes are partly repressed by Gcn4. Gcn4 directly binds promoter-regions and transcribes a subset of metabolic genes, particularly driving lysine and arginine biosynthesis. Gcn4 also globally represses lysine and arginine enriched transcripts, which include genes encoding the translation machinery. The Gcn4 dependent lysine and arginine supply thereby maintains the synthesis of the translation machinery. This is required to maintain translation capacity. Gcn4 consequently enables metabolic-precursor supply to bolster protein synthesis, and drive a growth program. Thus, we illustrate how growth and starvation outcomes are both controlled using the same Gcn4 transcriptional outputs that function in distinct contexts.
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Affiliation(s)
- Rajalakshmi Srinivasan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK post, Bangalore, India
| | - Adhish S. Walvekar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK post, Bangalore, India
| | - Zeenat Rashida
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK post, Bangalore, India
| | - Aswin Seshasayee
- National Centre for Biological Sciences–TIFR, GKVK post, Bellary Road, Bangalore, India
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK post, Bangalore, India
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5
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Pan Y, Gao L, Zhang X, Qin Y, Liu G, Qu Y. The Role of Cross-Pathway Control Regulator CpcA in the Growth and Extracellular Enzyme Production of Penicillium oxalicum. Curr Microbiol 2019; 77:49-54. [PMID: 31701162 DOI: 10.1007/s00284-019-01803-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/28/2019] [Indexed: 10/25/2022]
Abstract
CpcA is a conserved transcriptional activator for the cross-pathway control of amino acid biosynthetic genes in filamentous fungi. Previous studies of this regulator mainly revealed its function under amino acid starvation condition, where amino acid biosynthetic inhibitors were added in the culture. In this study, the biological function of CpcA in Penicillium oxalicum was investigated under different cultivation conditions. Disruption of cpcA led to decreased cell growth either in the presence or absence of histidine biosynthetic inhibitor, and the phenotype could be rescued by the addition of exogenous amino acid sources. In addition, CpcA was required for the rapid production of cellulase when cells were cultured on cellulose. Transcript abundance measurement showed that a set of amino acid biosynthetic genes as well as two major cellulase genes were significantly down-regulated in cpcA deletion mutant relative to wild type. Taken together, the results revealed the biological role of CpcA in supporting normal growth and extracellular enzyme production of P. oxalicum under amino acid non-starvation condition.
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Affiliation(s)
- Yunjun Pan
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, 266237, Shandong, People's Republic of China
| | - Liwei Gao
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, 266237, Shandong, People's Republic of China
| | - Xiujun Zhang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, 266237, Shandong, People's Republic of China
| | - Yuqi Qin
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, 266237, Shandong, People's Republic of China.
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, 266237, Shandong, People's Republic of China.
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Qingdao, 266237, Shandong, People's Republic of China
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6
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Sequence-Specific DNA Binding by Noncovalent Peptide-Azocyclodextrin Dimer Complex as a Suitable Model for Conformational Fuzziness. Molecules 2019; 24:molecules24132508. [PMID: 31324018 PMCID: PMC6650922 DOI: 10.3390/molecules24132508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 01/08/2023] Open
Abstract
Transcription factors are proteins lying at the endpoint of signaling pathways that control the complex process of DNA transcription. Typically, they are structurally disordered in the inactive state, but in response to an external stimulus, like a suitable ligand, they change their conformation, thereby activating DNA transcription in a spatiotemporal fashion. The observed disorder or fuzziness is functionally beneficial because it can add adaptability, versatility, and reversibility to the interaction. In this context, mimetics of the basic region of the GCN4 transcription factor (Tf) and their interaction with dsDNA sequences would be suitable models to explore the concept of conformational fuzziness experimentally. Herein, we present the first example of a system that mimics the DNA sequence-specific recognition by the GCN4 Tf through the formation of a non- covalent tetra-component complex: peptide–azoβ-CyD(dimer)–peptide–DNA. The non-covalent complex is constructed on the one hand by a 30 amino acid peptide corresponding to the basic region of GCN4 and functionalized with an adamantane moiety, and on the other hand an allosteric receptor, the azoCyDdimer, that has an azobenzene linker connecting two β-cyclodextrin units. The azoCyDdimer responds to light stimulus, existing as two photo-states: the first thermodynamically stable with an E:Z isomer ratio of 95:5 and the second obtained after irradiation with ultraviolet light, resulting in a photostationary state with a 60:40 E:Z ratio. Through electrophoretic shift assays and circular dichroism spectroscopy, we demonstrate that the E isomer is responsible for dimerization and recognition. The formation of the non-covalent tetra component complex occurs in the presence of the GCN4 cognate dsDNA sequence (′5-..ATGA cg TCAT..-3′) but not with (′5-..ATGA c TCAT..-3′) that differs in only one spacing nucleotide. Thus, we demonstrated that the tetra-component complex is formed in a specific manner that depends on the geometry of the ligand, the peptide length, and the ds DNA sequence. We hypothesized that the mechanism of interaction is sequential, and it can be described by the polymorphism model of static fuzziness. We argue that chemically modified peptides of the GCN4 Tf are suitable minimalist experimental models to investigate conformational fuzziness in protein–DNA interactions.
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7
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Lee YT, Fang YY, Sun YW, Hsu HC, Weng SM, Tseng TL, Lin TH, Shieh JC. THR1 mediates GCN4 and CDC4 to link morphogenesis with nutrient sensing and the stress response in Candida albicans. Int J Mol Med 2018; 42:3193-3208. [PMID: 30320368 PMCID: PMC6202100 DOI: 10.3892/ijmm.2018.3930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/08/2018] [Indexed: 12/31/2022] Open
Abstract
Candida albicans (C. albicans) CDC4 (CaCDC4), encoding the F-box protein for the substrate specificity of the Skp1-cullin-F-box E3 ubiquitin ligase complex, suppresses the yeast-to-filament transition in C. albicans. In our previous study, Thr1 was identified as a CaCdc4-associated protein using affinity purification. THR1 encodes a homoserine kinase, which is involved in the threonine biosynthesis pathway. The present study generated a strain with repressible CaCDC4 expression and continuous THR1 expression. Colony and cell morphology analyses, as well as immunoblotting, revealed that the Thr1 protein was detectable under conditions in which the expression of CaCDC4 was repressed and that the filaments resulting from the repressed expression of CaCDC4 were suppressed by the constitutive expression of THR1 in C. albicans. Additionally, by using the CaSAT1-flipper method, the present study produced null mutants of THR1, GCN4, and CaCDC4. The phenotypic consequences were evaluated by growth curves, spotting assays, microscopic analysis, reverse transcription-polymerase chain reaction and XTT-based biofilm formation ability. The results revealed that fewer cells lacking THR1 entered the stationary phase but had no apparent morphological alteration. It was observed that the expression of THR1 was upregulated concurrently with GCN4 during nutrient depletion and that cells lacking GCN4 rescued the lethality of cells in the absence of THR1 in conditions accumulating homoserine in the threonine biosynthesis pathway. Of note, it was found that cells with either CaCDC4 or THR1 loss were sensitive to oxidative stress and osmotic stress, with those with THR1 loss being more sensitive. In addition, it was observed that cells with loss of either CaCDC4 or THR1 exhibited the ability to increase biofilm formation, with those lacking CaCDC4 exhibiting a greater extent of enhancement. It was concluded that CaCDC4 is important in the coordination of morphogenesis, nutrient sensing, and the stress response through THR1 in C. albicans.
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Affiliation(s)
- Yuan-Ti Lee
- Institute of Medicine and School of Medicine, Chung Shan Medical University, Taichung City 40201, Taiwan, R.O.C
| | - Yi-Ya Fang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan, R.O.C
| | - Yu Wen Sun
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan, R.O.C
| | - Hsiao-Chi Hsu
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan, R.O.C
| | - Shan-Mei Weng
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan, R.O.C
| | - Tzu-Ling Tseng
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan, R.O.C
| | - Ting-Hui Lin
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan, R.O.C
| | - Jia-Ching Shieh
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung City 40201, Taiwan, R.O.C
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8
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Regulation of Sensing, Transportation, and Catabolism of Nitrogen Sources in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 2018; 82:82/1/e00040-17. [PMID: 29436478 DOI: 10.1128/mmbr.00040-17] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nitrogen is one of the most important essential nutrient sources for biogenic activities. Regulation of nitrogen metabolism in microorganisms is complicated and elaborate. For this review, the yeast Saccharomyces cerevisiae was chosen to demonstrate the regulatory mechanism of nitrogen metabolism because of its relative clear genetic background. Current opinions on the regulation processes of nitrogen metabolism in S. cerevisiae, including nitrogen sensing, transport, and catabolism, are systematically reviewed. Two major upstream signaling pathways, the Ssy1-Ptr3-Ssy5 sensor system and the target of rapamycin pathway, which are responsible for sensing extracellular and intracellular nitrogen, respectively, are discussed. The ubiquitination of nitrogen transporters, which is the most general and efficient means for controlling nitrogen transport, is also summarized. The following metabolic step, nitrogen catabolism, is demonstrated at two levels: the transcriptional regulation process related to GATA transcriptional factors and the translational regulation process related to the general amino acid control pathway. The interplay between nitrogen regulation and carbon regulation is also discussed. As a model system, understanding the meticulous process by which nitrogen metabolism is regulated in S. cerevisiae not only could facilitate research on global regulation mechanisms and yeast metabolic engineering but also could provide important insights and inspiration for future studies of other common microorganisms and higher eukaryotic cells.
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9
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Abstract
A large body of evidence indicates that genome annotation pipelines have biased our view of coding sequences because they generally undersample small proteins and peptides. The recent development of genome-wide translation profiling reveals the prevalence of small/short open reading frames (smORFs or sORFs), which are scattered over all classes of transcripts, including both mRNAs and presumptive long noncoding RNAs. Proteomic approaches further confirm an unexpected variety of smORF-encoded peptides (SEPs), representing an overlooked reservoir of bioactive molecules. Indeed, functional studies in a broad range of species from yeast to humans demonstrate that SEPs can harbor key activities for the control of development, differentiation, and physiology. Here we summarize recent advances in the discovery and functional characterization of smORF/SEPs and discuss why these small players can no longer be ignored with regard to genome function.
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Affiliation(s)
- Serge Plaza
- Laboratoire de Recherches en Sciences Végétales, Université de Toulouse, Université Paul Sabatier, 31326 Castanet Tolosan, France; .,CNRS, UMR5546, Laboratoire de Recherches en Sciences Végétales, 31326 Castanet Tolosan, France
| | - Gerben Menschaert
- Department of Mathematical Modeling, Statistics and Bioinformatics, University of Ghent, 9000 Gent, Belgium
| | - François Payre
- Centre de Biologie du Développement, Centre de Biologie Intégrative, Université de Toulouse, CNRS, Université Paul Sabatier, 31062 Toulouse, France;
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10
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Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae. Genetics 2017; 203:65-107. [PMID: 27183566 DOI: 10.1534/genetics.115.186221] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/24/2016] [Indexed: 12/18/2022] Open
Abstract
In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs.
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11
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Bultman KM, Kowalski CH, Cramer RA. Aspergillus fumigatus virulence through the lens of transcription factors. Med Mycol 2016; 55:24-38. [PMID: 27816905 DOI: 10.1093/mmy/myw120] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 08/19/2016] [Accepted: 10/17/2016] [Indexed: 02/07/2023] Open
Abstract
Invasive aspergillosis (IA), most commonly caused by the filamentous fungus Aspergillus fumigatus, occurs in immune compromised individuals. The ability of A. fumigatus to proliferate in a multitude of environments is hypothesized to contribute to its pathogenicity and virulence. Transcription factors (TF) have long been recognized as critical proteins for fungal pathogenicity, as many are known to play important roles in the transcriptional regulation of pathways implicated in virulence. Such pathways include regulation of conidiation and development, adhesion, nutrient acquisition, adaptation to environmental stress, and interactions with the host immune system among others. In both murine and insect models of IA, TF loss of function in A. fumigatus results in cases of hyper- and hypovirulence as determined through host survival, fungal burden, and immune response analyses. Consequently, the study of specific TFs in A. fumigatus has revealed important insights into mechanisms of pathogenicity and virulence. Although in vitro studies have identified virulence-related functions of specific TFs, the full picture of their in vivo functions remain largely enigmatic and an exciting area of current research. Moreover, the vast majority of TFs remain to be characterized and studied in this important human pathogen. Here in this mini-review we provide an overview of selected TFs in A. fumigatus and their contribution to our understanding of this important human pathogen's pathogenicity and virulence.
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Affiliation(s)
- Katherine M Bultman
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Caitlin H Kowalski
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Robert A Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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12
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Ross D, Altmann M. A fast protocol for purification of translating mRNAs. Methods 2016; 107:57-62. [PMID: 27020892 DOI: 10.1016/j.ymeth.2016.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 12/01/2022] Open
Abstract
We present a protocol that enables easy extraction of translating mRNAs by purification of tagged ribosomes and associated mRNAs. By studying three different examples of stress influenced genes, we demonstrate the effectiveness and compare our rapid method to an older protocol (Halbeisen et al., 2009).
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Affiliation(s)
- Daniela Ross
- Institute of Biochemistry and Molecular Medicine (IBMM), Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Michael Altmann
- Institute of Biochemistry and Molecular Medicine (IBMM), Bühlstrasse 28, 3012 Bern, Switzerland.
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13
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Tan SZ, Manchester S, Prather KLJ. Controlling Central Carbon Metabolism for Improved Pathway Yields in Saccharomyces cerevisiae. ACS Synth Biol 2016; 5:116-24. [PMID: 26544022 DOI: 10.1021/acssynbio.5b00164] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Engineering control of metabolic pathways is important to improving product titers and yields. Traditional methods such as overexpressing pathway enzymes and deleting competing ones are restricted by the interdependence of metabolic reactions and the finite nature of cellular resources. Here, we developed a metabolite valve that controls glycolytic flux through central carbon metabolism in Saccharomyces cerevisiae. In a Hexokinase 2 and Glucokinase 1 deleted strain (hxk2Δglk1Δ), glucose flux was diverted away from glycolysis and into a model pathway, gluconate, by controlling the transcription of Hexokinase 1 with the tetracycline transactivator protein (tTA). A maximum 10-fold decrease in hexokinase activity resulted in a 50-fold increase in gluconate yields, from 0.7% to 36% mol/mol of glucose. The reduction in glucose flux resulted in a significant decrease in ethanol byproduction that extended to semianaerobic conditions, as shown in the production of isobutanol. This proof-of-concept is one of the first demonstrations in S. cerevisiae of dynamic redirection of glucose from glycolysis and into a heterologous pathway.
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Affiliation(s)
- Sue Zanne Tan
- Department of Chemical Engineering, ‡MIT Center for Integrative Synthetic
Biology, §Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Shawn Manchester
- Department of Chemical Engineering, ‡MIT Center for Integrative Synthetic
Biology, §Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kristala L. J. Prather
- Department of Chemical Engineering, ‡MIT Center for Integrative Synthetic
Biology, §Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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14
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Zeigler RD, Cohen BA. Discrimination between thermodynamic models of cis-regulation using transcription factor occupancy data. Nucleic Acids Res 2013; 42:2224-34. [PMID: 24288374 PMCID: PMC3936720 DOI: 10.1093/nar/gkt1230] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many studies have identified binding preferences for transcription factors (TFs), but few have yielded predictive models of how combinations of transcription factor binding sites generate specific levels of gene expression. Synthetic promoters have emerged as powerful tools for generating quantitative data to parameterize models of combinatorial cis-regulation. We sought to improve the accuracy of such models by quantifying the occupancy of TFs on synthetic promoters in vivo and incorporating these data into statistical thermodynamic models of cis-regulation. Using chromatin immunoprecipitation-seq, we measured the occupancy of Gcn4 and Cbf1 in synthetic promoter libraries composed of binding sites for Gcn4, Cbf1, Met31/Met32 and Nrg1. We measured the occupancy of these two TFs and the expression levels of all promoters in two growth conditions. Models parameterized using only expression data predicted expression but failed to identify several interactions between TFs. In contrast, models parameterized with occupancy and expression data predicted expression data, and also revealed Gcn4 self-cooperativity and a negative interaction between Gcn4 and Nrg1. Occupancy data also allowed us to distinguish between competing regulatory mechanisms for the factor Gcn4. Our framework for combining occupancy and expression data produces predictive models that better reflect the mechanisms underlying combinatorial cis-regulation of gene expression.
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Affiliation(s)
- Robert D Zeigler
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, MO 63108, USA
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15
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Timpner C, Braus-Stromeyer SA, Tran VT, Braus GH. The Cpc1 regulator of the cross-pathway control of amino acid biosynthesis is required for pathogenicity of the vascular pathogen Verticillium longisporum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1312-1324. [PMID: 23883358 DOI: 10.1094/mpmi-06-13-0181-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The plant-pathogenic fungus Verticillium longisporum is a causal agent of early senescence and ripening in cruciferous crops like Brassica napus. Verticillium wilts have become serious agricultural threats in recent decades. Verticillium species infect host plants through the roots and colonize xylem vessels of the host plant. The xylem fluid provides an environment with limited carbon sources and unbalanced amino acid supply, which requires V. longisporum to induce the cross-pathway control of amino acid biosynthesis. RNA-mediated gene silencing reduced the expression of the two CPC1 isogenes (VlCPC1-1 and VlCPC1-2) of the allodiploid V. longisporum up to 85%. VlCPC1 encodes the conserved transcription factor of the cross-pathway control. The silenced mutants were highly sensitive to amino-acid starvation, and the infected plants showed significantly fewer symptoms such as stunting or early senescence in oilseed rape plant infection assays. Consistently, deletion of single CPC1 of the haploid V. dahliae resulted in strains that are sensitive to amino-acid starvation and cause strongly reduced symptoms in the plant-host tomato (Solanum lycopersicum). The allodiploid V. longisporum and the haploid V. dahliae are the first phytopathogenic fungi that were shown to require CPC1 for infection and colonization of their respective host plants, oilseed rape and tomato.
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16
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Mutual cross talk between the regulators Hac1 of the unfolded protein response and Gcn4 of the general amino acid control of Saccharomyces cerevisiae. EUKARYOTIC CELL 2013; 12:1142-54. [PMID: 23794510 DOI: 10.1128/ec.00123-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Hac1 is the activator of the cellular response to the accumulation of unfolded proteins in the endoplasmic reticulum. Hac1 function requires the activity of Gcn4, which mainly acts as a regulator of the general amino acid control network providing Saccharomyces cerevisiae cells with amino acids. Here, we demonstrate novel functions of Hac1 and describe a mutual connection between Hac1 and Gcn4. Hac1 is required for induction of Gcn4-responsive promoter elements in haploid as well as diploid cells and therefore participates in the cellular amino acid supply. Furthermore, Hac1 and Gcn4 mutually influence their mRNA expression levels. Hac1 is also involved in FLO11 expression and adhesion upon amino acid starvation. Hac1 and Gcn4 act through the same promoter regions of the FLO11 flocculin. The results indicate an indirect effect of both transcription factors on FLO11 expression. Our data suggest a complex mutual cross talk between the Hac1- and Gcn4-controlled networks.
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17
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Kazemi Seresht A, Cruz AL, de Hulster E, Hebly M, Palmqvist EA, van Gulik W, Daran JM, Pronk J, Olsson L. Long-term adaptation of Saccharomyces cerevisiae to the burden of recombinant insulin production. Biotechnol Bioeng 2013; 110:2749-63. [PMID: 23568816 DOI: 10.1002/bit.24927] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/19/2013] [Accepted: 03/28/2013] [Indexed: 12/28/2022]
Abstract
High-level production of heterologous proteins is likely to impose a metabolic burden on the host cell and can thus affect various aspects of cellular physiology. A data-driven approach was applied to study the secretory production of a human insulin analog precursor (IAP) in Saccharomyces cerevisiae during prolonged cultivation (80 generations) in glucose-limited aerobic chemostat cultures. Physiological characterization of the recombinant cells involved a comparison with cultures of a congenic reference strain that did not produce IAP, and time-course analysis of both strains aimed at identifying the metabolic adaptation of the cells towards the burden of IAP production. All cultures were examined at high cell density conditions (30 g/L dry weight) to increase the industrial relevance of the results. The burden of heterologous protein production in the recombinant strain was explored by global transcriptome analysis and targeted metabolome analysis, including the analysis of intracellular amino acid pools, glycolytic metabolites, and TCA intermediates. The cellular re-arrangements towards IAP production were categorized in direct responses, for example, enhanced metabolism of amino acids as precursors for the formation of IAP, as well as indirect responses, for example, changes in the central carbon metabolism. As part of the long-term adaptation, a metabolic re-modeling of the IAP-expressing strain was observed, indicating an augmented negative selection pressure on glycolytic overcapacity, and the emergence of mitochondrial dysfunction. The evoked metabolic re-modeling of the cells led to less optimal conditions with respect to the expression and processing of the target protein and thus decreased the cellular expression capacity for the secretory production of IAP during prolonged cultivation.
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Affiliation(s)
- Ali Kazemi Seresht
- Industrial Biotechnology, Department of Chemical and Biological Engineering, Chalmers University of Technology, Kemivaegen 10, 41296, Gothenburg, Sweden
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18
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Tan BSN, Lonic A, Morris MB, Rathjen PD, Rathjen J. The amino acid transporter SNAT2 mediates l-proline-induced differentiation of ES cells. Am J Physiol Cell Physiol 2011; 300:C1270-9. [DOI: 10.1152/ajpcell.00235.2010] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
There is an increasing appreciation that amino acids can act as signaling molecules in the regulation of cellular processes through modulation of intracellular cell signaling pathways. In culture, embryonic stem (ES) cells can be differentiated to a second, pluripotent cell population, early primitive ectoderm-like cells in response to biological activities within the conditioned medium MEDII. The amino acid l-proline has been identified as a component of MEDII required for ES cell differentiation. Here, we define the primary l-proline transporter on ES and early primitive ectoderm-like cells as sodium-coupled neutral amino acid transporter 2 (SNAT2). SNAT2 uptake of l-proline can be inhibited by the addition of millimolar concentrations of other substrates. The addition of excess amino acids was used to regulate the uptake of l-proline by ES cells, and the effect on differentiation was analyzed. The ability of SNAT2 substrates, but not other amino acids, to prevent changes in morphology, gene expression, and differentiation kinetics suggested that l-proline uptake through SNAT2 was required for ES cell differentiation. These data reveal an unexpected role for amino acid uptake and the amino acid transporter SNAT2 in regulation of pluripotent cells in culture and provides a number of specific, inexpensive, and nontoxic culture additives with the potential to improve the quality of ES cell culture.
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Affiliation(s)
| | - Ana Lonic
- School of Molecular and Biomedical Science, University of Adelaide, South Australia; and
- Australian Stem Cell Centre, Monash University, Clayton, Victoria, Australia
| | - Michael B. Morris
- School of Molecular and Biomedical Science, University of Adelaide, South Australia; and
- Australian Stem Cell Centre, Monash University, Clayton, Victoria, Australia
| | - Peter D. Rathjen
- Department of Zoology, University of Melbourne, Melbourne, Victoria
- School of Molecular and Biomedical Science, University of Adelaide, South Australia; and
- Australian Stem Cell Centre, Monash University, Clayton, Victoria, Australia
| | - Joy Rathjen
- Department of Zoology, University of Melbourne, Melbourne, Victoria
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19
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Zhang F, Hinnebusch AG. An upstream ORF with non-AUG start codon is translated in vivo but dispensable for translational control of GCN4 mRNA. Nucleic Acids Res 2011; 39:3128-40. [PMID: 21227927 PMCID: PMC3082883 DOI: 10.1093/nar/gkq1251] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genome-wide analysis of ribosome locations in mRNAs of Saccharomyces cerevisiae has revealed the translation of upstream open reading frames that initiate with near-cognate start codons in many transcripts. Two such non-translation initiation codon (AUG)-initiated upstream open reading frames (uORFs) (nAuORFs 1 and 2) occur in GCN4 mRNA upstream of the four AUG-initiated uORFs (uORFs 1–4) that regulate GCN4 translation. We verified that nAuORF2 is translated in vivo by demonstrating β-galactosidase production from lacZ coding sequences fused to nAuORF2, in a manner abolished by replacing its non-AUG initiation codon (AUA) start codon with the non-cognate triplet AAA, whereas translation of nAuORF1 was not detected. Importantly, replacing the near-cognate start codons of both nAuORFs with non-cognate triplets had little or no effect on the repression of GCN4 translation in non-starved cells, nor on its derepression in response to histidine limitation, nutritional shift-down or treatment with rapamycin, hydrogen peroxide or methyl methanesulfonate. Additionally, we found no evidence that initiation from the AUA codon of nAuORF2 is substantially elevated, or dependent on Gcn2, the sole eIF2α kinase of yeast, in histidine-deprived cells. Thus, although nAuORF2 is translated in vivo, it appears that this event is not stimulated by eIF2α phosphorylation nor significantly influences GCN4 translational induction under various starvation or stress conditions.
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Affiliation(s)
- Fan Zhang
- Laboratory of Gene Regulation and Development, Eunice K Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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20
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A feedback circuit between transcriptional activation and self-destruction of Gcn4 separates its metabolic and morphogenic response in diploid yeasts. J Mol Biol 2010; 405:909-25. [PMID: 21111745 DOI: 10.1016/j.jmb.2010.11.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Revised: 11/06/2010] [Accepted: 11/16/2010] [Indexed: 11/20/2022]
Abstract
The basic zipper Gcn4 protein activates transcription in the yeast Saccharomyces cerevisiae in response to amino acid starvation. This includes numerous metabolic genes of amino acid or purine biosynthesis and the developmental cell-surface flocculin gene FLO11, which is required for diploid pseudohyphae formation and for adhesion upon nutrient starvation. We separated the metabolic from the developmental response by screening for GCN4 alleles that allow growth during amino acid starvation but are impaired in adhesion and are unable to form pseudohyphae. The identified Gcn4(L267S) variant carries an amino acid substitution in the third of the four conserved leucines of the zipper dimerization domain. This mutation abolished FLO11 expression and results in reduced but sufficient transcriptional activity for amino acid biosynthetic genes. The Leu267Ser substitution impairs Gcn4 homodimer formation and is a significantly more stable protein than the wild-type protein. A helix-breaker substitution in Leu253 results in a transcriptionally inactive but highly stable protein variant. This is due to a feedback circuit between transcriptional activity of Gcn4 and its own stability, which depends on the Gcn4-controlled cyclin PCL5. Gcn4(L253G) reduces the expression of Pcl5 and therefore reduces its own degradation. This self-controlled buffer system to restrict transcriptional activity results in a reciprocal correlation between Gcn4 transcriptional activity and protein stability.
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21
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Retrotransposon expression in ethanol-stressed Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2010; 87:1447-54. [PMID: 20393705 DOI: 10.1007/s00253-010-2562-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 03/08/2010] [Accepted: 03/14/2010] [Indexed: 10/19/2022]
Abstract
There are five retrotransposon families in Saccharomyces cerevisiae, three (Ty1, Ty2, and Ty3) of which are known to be transcriptionally active. Early investigations reported yeast retrotransposons to be stress-induced; however, microarray-based studies do not report retrotransposition-related Gene Ontology (GO) categories in the ethanol stress response of S. cerevisiae. In this study, microarray technology was used to investigate the ethanol stress response of S. cerevisiae W303-1A, and the highest stress-induced GO categories, based on z-score, were found to be retrotransposition-related, namely, Retrotransposition Nucleocapsid and Transposition, RNA-Mediated. Further investigation, involving reanalysis of previously published results on the stress response of S. cerevisiae, identified the absence of annotation for retrotransposon genes and associated GO categories and their omission during the printing of spotted arrays as two reasons why these categories in previous gene expression studies on the ethanol stress response of yeast were not reported.
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22
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Homoserine toxicity in Saccharomyces cerevisiae and Candida albicans homoserine kinase (thr1Delta) mutants. EUKARYOTIC CELL 2010; 9:717-28. [PMID: 20305002 DOI: 10.1128/ec.00044-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In addition to threonine auxotrophy, mutation of the Saccharomyces cerevisiae threonine biosynthetic genes THR1 (encoding homoserine kinase) and THR4 (encoding threonine synthase) results in a plethora of other phenotypes. We investigated the basis for these other phenotypes and found that they are dependent on the toxic biosynthetic intermediate homoserine. Moreover, homoserine is also toxic for Candida albicans thr1Delta mutants. Since increasing levels of threonine, but not other amino acids, overcome the homoserine toxicity of thr1Delta mutants, homoserine may act as a toxic threonine analog. Homoserine-mediated lethality of thr1Delta mutants is blocked by cycloheximide, consistent with a role for protein synthesis in this lethality. We identified various proteasome and ubiquitin pathway components that either when mutated or present in high copy numbers suppressed the thr1Delta mutant homoserine toxicity. Since the doa4Delta and proteasome mutants identified have reduced ubiquitin- and/or proteasome-mediated proteolysis, the degradation of a particular protein or subset of proteins likely contributes to homoserine toxicity.
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23
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Staschke KA, Dey S, Zaborske JM, Palam LR, McClintick JN, Pan T, Edenberg HJ, Wek RC. Integration of general amino acid control and target of rapamycin (TOR) regulatory pathways in nitrogen assimilation in yeast. J Biol Chem 2010; 285:16893-911. [PMID: 20233714 DOI: 10.1074/jbc.m110.121947] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Two important nutrient-sensing and regulatory pathways, the general amino acid control (GAAC) and the target of rapamycin (TOR), participate in the control of yeast growth and metabolism during changes in nutrient availability. Amino acid starvation activates the GAAC through Gcn2p phosphorylation of translation factor eIF2 and preferential translation of GCN4, a transcription activator. TOR senses nitrogen availability and regulates transcription factors such as Gln3p. We used microarray analyses to address the integration of the GAAC and TOR pathways in directing the yeast transcriptome during amino acid starvation and rapamycin treatment. We found that GAAC is a major effector of the TOR pathway, with Gcn4p and Gln3p each inducing a similar number of genes during rapamycin treatment. Although Gcn4p activates a common core of 57 genes, the GAAC directs significant variations in the transcriptome during different stresses. In addition to inducing amino acid biosynthetic genes, Gcn4p in conjunction with Gln3p activates genes required for the assimilation of secondary nitrogen sources such as gamma-aminobutyric acid (GABA). Gcn2p activation upon shifting to secondary nitrogen sources is suggested to occur by means of a dual mechanism. First, Gcn2p is induced by the release of TOR repression through a mechanism involving Sit4p protein phosphatase. Second, this eIF2 kinase is activated by select uncharged tRNAs, which were shown to accumulate during the shift to the GABA medium. This study highlights the mechanisms by which the GAAC and TOR pathways are integrated to recognize changing nitrogen availability and direct the transcriptome for optimal growth adaptation.
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Affiliation(s)
- Kirk A Staschke
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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24
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Metabolic control of antifungal drug resistance. Fungal Genet Biol 2010; 47:81-93. [DOI: 10.1016/j.fgb.2009.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 07/01/2009] [Accepted: 07/06/2009] [Indexed: 11/16/2022]
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25
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Shigematsu M, Ogawa T, Kido A, Kitamoto HK, Hidaka M, Masaki H. Cellular and transcriptional responses of yeast to the cleavage of cytosolic tRNAs induced by colicin D. Yeast 2009; 26:663-73. [PMID: 19877125 DOI: 10.1002/yea.1725] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
MESH Headings
- Base Sequence
- Cell Proliferation
- Cytosol/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Nucleic Acid Conformation
- Oligonucleotide Array Sequence Analysis
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Peptide Fragments/metabolism
- Pheromones/metabolism
- Plasmids/genetics
- Protein Structure, Tertiary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Transfer, Arg/chemistry
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Arg/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/metabolism
- Signal Transduction
- Transcription, Genetic
- Transformation, Genetic
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Affiliation(s)
- Megumi Shigematsu
- Department of Biotechnology, University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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26
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Silencing of Vlaro2 for chorismate synthase revealed that the phytopathogen Verticillium longisporum induces the cross-pathway control in the xylem. Appl Microbiol Biotechnol 2009; 85:1961-76. [PMID: 19826808 PMCID: PMC2811248 DOI: 10.1007/s00253-009-2269-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2009] [Revised: 09/20/2009] [Accepted: 09/20/2009] [Indexed: 11/18/2022]
Abstract
The first leaky auxotrophic mutant for aromatic amino acids of the near-diploid fungal plant pathogen Verticillium longisporum (VL) has been generated. VL enters its host Brassica napus through the roots and colonizes the xylem vessels. The xylem contains little nutrients including low concentrations of amino acids. We isolated the gene Vlaro2 encoding chorismate synthase by complementation of the corresponding yeast mutant strain. Chorismate synthase produces the first branch point intermediate of aromatic amino acid biosynthesis. A novel RNA-mediated gene silencing method reduced gene expression of both isogenes by 80% and resulted in a bradytrophic mutant, which is a leaky auxotroph due to impaired expression of chorismate synthase. In contrast to the wild type, silencing resulted in increased expression of the cross-pathway regulatory gene VlcpcA (similar to cpcA/GCN4) during saprotrophic life. The mutant fungus is still able to infect the host plant B. napus and the model Arabidopsis thaliana with reduced efficiency. VlcpcA expression is increased in planta in the mutant and the wild-type fungus. We assume that xylem colonization requires induction of the cross-pathway control, presumably because the fungus has to overcome imbalanced amino acid supply in the xylem.
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27
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Tsoi BM, Beckhouse AG, Gelling CL, Raftery MJ, Chiu J, Tsoi AM, Lauterbach L, Rogers PJ, Higgins VJ, Dawes IW. Essential role of one-carbon metabolism and Gcn4p and Bas1p transcriptional regulators during adaptation to anaerobic growth of Saccharomyces cerevisiae. J Biol Chem 2009; 284:11205-15. [PMID: 19224916 DOI: 10.1074/jbc.m809225200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The transcriptional activator Gcn4p is considered the master regulator of amino acid metabolism in Saccharomyces cerevisiae and is required for the transcriptional response to amino acid starvation. Here it is shown that Gcn4p plays a previously undescribed role in regulating adaptation to anaerobic growth. A gcn4 mutant exhibited a highly extended lag phase after a shift to anaerobiosis that was the result of l-serine depletion. In addition, the one-carbon metabolism and purine biosynthesis transcriptional regulator Bas1p were strictly required for anaerobic growth on minimal medium, and this was similarly due to l-serine limitation in bas1 mutants. The induction of one-carbon metabolism during anaerobiosis is needed to increase the supply of l-serine from the glycine and threonine pathways. Using a number of experimental approaches, we demonstrate that these transcription regulators play vital roles in regulating l-serine biosynthesis in the face of increased demand during adaptation to anaerobiosis. This increased l-serine requirement is most likely due to anaerobic remodeling of the cell wall, involving de novo synthesis of a large number of very serine-rich mannoproteins and an increase in the total serine content of the cell wall. During anaerobic starvation for l-serine, this essential amino acid is preferentially directed to the cell wall, indicating the existence of a regulatory mechanism to balance competing cellular demands.
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Affiliation(s)
- Bonny M Tsoi
- School of Biomedical and Health Sciences, University of Western Sydney, Penrith, New South Wales DC 1791, Australia
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28
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Yang HT, Hsu CP, Hwang MJ. An analytical rate expression for the kinetics of gene transcription mediated by dimeric transcription factors. J Biochem 2007; 142:135-44. [PMID: 17652330 DOI: 10.1093/jb/mvm151] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To model gene transcription kinetics, empirical fitting with the Hill function or S-system is often used. In this study, we derived an analytical expression for gene transcription rates in a manner similar to that developed for enzyme kinetics to describe the kinetics of gene transcription mediated by dimeric transcription factors (TFs) such as Gcn4p, a Saccharomyces cerevisiae master gene regulator. We showed that the analytical rate expression and its parameters estimated from several sets of experimental data could accurately reproduce the experimentally measured promoter-binding activity of Gcn4p. Furthermore, the analytical rate expression allowed us to derive analytically, rather than fit empirically, the parameters of the Hill function and S-system for use in modelling transcription kinetics. We found that a plot of gene transcription rate against Gcn4p concentration gave a sigmoidal dose-response curve with a positive co-operativity Hill coefficient (approximately 1.25), in accordance with previous experimental findings on the promoter binding of dimeric TFs. The characteristics of the dose-response curve around the estimated cellular Gcn4p concentration suggest that transcription regulation is efficiently controlled under physiological conditions. This work is a useful initial step towards analytically modelling and simulating complicated gene transcription networks.
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Affiliation(s)
- Hsih-Te Yang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
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29
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Whitaker RD, Walt DR. Fiber-based single cell analysis of reporter gene expression in yeast two-hybrid systems. Anal Biochem 2007; 360:63-74. [PMID: 17113561 DOI: 10.1016/j.ab.2006.10.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/09/2006] [Accepted: 10/10/2006] [Indexed: 11/23/2022]
Abstract
Yeast two-hybrid (Y2H) systems conventionally are used when screening for protein-protein interactions. A recurring problem with Y2H systems is the high prevalence of both false positives and false negatives. Distinguishing between real results and artifacts to characterize a protein-protein interaction properly can often be time-consuming and laborious. In this article, we report a new method for statistically evaluating single cell reporter gene transcriptional activation and expression in yeast two-hybrid systems. The system is based on statistical analysis of many yeast cells contained in a fiber-optic array, allowing for thorough characterization of reporter gene expression at different stringency levels.
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30
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Lemmens K, Dhollander T, De Bie T, Monsieurs P, Engelen K, Smets B, Winderickx J, De Moor B, Marchal K. Inferring transcriptional modules from ChIP-chip, motif and microarray data. Genome Biol 2006; 7:R37. [PMID: 16677396 PMCID: PMC1779513 DOI: 10.1186/gb-2006-7-5-r37] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 12/21/2005] [Accepted: 04/10/2006] [Indexed: 12/29/2022] Open
Abstract
'ReMoDiscovery' is an intuitive algorithm to correlate regulatory programs with regulators and corresponding motifs to a set of co-expressed genes. It exploits in a concurrent way three independent data sources: ChIP-chip data, motif information and gene expression profiles. When compared to published module discovery algorithms, ReMoDiscovery is fast and easily tunable. We evaluated our method on yeast data, where it was shown to generate biologically meaningful findings and allowed the prediction of potential novel roles of transcriptional regulators.
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Affiliation(s)
- Karen Lemmens
- BIOI@SCD, Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
| | - Thomas Dhollander
- BIOI@SCD, Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
| | - Tijl De Bie
- Research Group on Quantitative Psychology, Department of Psychology, KU Leuven, Tiensestraat, B-3000 Leuven, Belgium
| | - Pieter Monsieurs
- BIOI@SCD, Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
| | - Kristof Engelen
- BIOI@SCD, Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
| | - Bart Smets
- Molecular Physiology of Plants and Micro-organisms Section, Biology Department, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
| | - Joris Winderickx
- Molecular Physiology of Plants and Micro-organisms Section, Biology Department, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
| | - Bart De Moor
- BIOI@SCD, Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
| | - Kathleen Marchal
- BIOI@SCD, Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
- CMPG, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg, B-3001 Heverlee, Belgium
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31
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Arvas M, Pakula T, Lanthaler K, Saloheimo M, Valkonen M, Suortti T, Robson G, Penttilä M. Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae. BMC Genomics 2006; 7:32. [PMID: 16504068 PMCID: PMC1397821 DOI: 10.1186/1471-2164-7-32] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Accepted: 02/22/2006] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Secretion stress is caused by compromised folding, modification or transport of proteins in the secretory pathway. In fungi, induction of genes in response to secretion stress is mediated mainly by the unfolded protein response (UPR) pathway. This study aims at uncovering transcriptional responses occurring in the filamentous fungi Trichoderma reesei exposed to secretion stress and comparing these to those found in the yeast Saccharomyces cerevisiae. RESULTS Chemostat cultures of T. reesei expressing human tissue plasminogen activator (tPA) and batch bioreactor cultures treated with dithiothreitol (DTT) to prevent correct protein folding were analysed with cDNA subtraction and cDNA-amplified fragment length polymorphism (AFLP) experiments. ESTs corresponding to 457 unique genes putatively induced under secretion stress were isolated and the expression pattern of 60 genes was confirmed by Northern analysis. Expression of these genes was also studied in a strain over-expressing inositol-requiring enzyme 1 (IREI) protein, a sensor for the UPR pathway. To compare the data with that of S. cerevisiae, published transcriptome profiling data on various stress responses in S. cerevisiae was reanalysed. The genes up-regulated in response to secretion stress included a large number of secretion related genes in both organisms. In addition, analysis of T. reesei revealed up regulation of the cpc1 transcription factor gene and nucleosomal genes. The induction of the cpcA and histone gene H4 were shown to be induced also in cultures of Aspergillus nidulans treated with DTT. CONCLUSION Analysis of the genes induced under secretion stress has revealed novel features in the stress response in T. reesei and in filamentous fungi. We have demonstrated that in addition to the previously rather well characterised induction of genes for many ER proteins or secretion related proteins also other types of responses exist.
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Affiliation(s)
- Mikko Arvas
- VTT Biotechnology, Tietotie 2, Espoo, PL 1500, 02044 VTT, Finland
| | - Tiina Pakula
- VTT Biotechnology, Tietotie 2, Espoo, PL 1500, 02044 VTT, Finland
| | - Karin Lanthaler
- School of Biological Sciences, University of Manchester, 1800 Stopford Building, Oxford Road, Manchester M13 9 PT, UK
| | - Markku Saloheimo
- VTT Biotechnology, Tietotie 2, Espoo, PL 1500, 02044 VTT, Finland
| | - Mari Valkonen
- VTT Biotechnology, Tietotie 2, Espoo, PL 1500, 02044 VTT, Finland
| | - Tapani Suortti
- VTT Biotechnology, Tietotie 2, Espoo, PL 1500, 02044 VTT, Finland
| | - Geoff Robson
- School of Biological Sciences, University of Manchester, 1800 Stopford Building, Oxford Road, Manchester M13 9 PT, UK
| | - Merja Penttilä
- VTT Biotechnology, Tietotie 2, Espoo, PL 1500, 02044 VTT, Finland
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32
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Abstract
Cells reprogram gene expression in response to environmental changes by mobilizing transcriptional activators. The activator protein Gcn4 of the yeast Saccharomyces cerevisiae is regulated by an intricate translational control mechanism, which is the primary focus of this review, and also by the modulation of its stability in response to nutrient availability. Translation of GCN4 mRNA is derepressed in amino acid-deprived cells, leading to transcriptional induction of nearly all genes encoding amino acid biosynthetic enzymes. The trans-acting proteins that control GCN4 translation have general functions in the initiation of protein synthesis, or regulate the activities of initiation factors, so that the molecular events that induce GCN4 translation also reduce the rate of general protein synthesis. This dual regulatory response enables cells to limit their consumption of amino acids while diverting resources into amino acid biosynthesis in nutrient-poor environments. Remarkably, mammalian cells use the same strategy to downregulate protein synthesis while inducing transcriptional activators of stress-response genes under various stressful conditions, including amino acid starvation.
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Affiliation(s)
- Alan G Hinnebusch
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, Bethesda, Maryland 20892, USA.
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Tournu H, Tripathi G, Bertram G, Macaskill S, Mavor A, Walker L, Odds FC, Gow NAR, Brown AJP. Global role of the protein kinase Gcn2 in the human pathogen Candida albicans. EUKARYOTIC CELL 2005; 4:1687-96. [PMID: 16215176 PMCID: PMC1265895 DOI: 10.1128/ec.4.10.1687-1696.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The pathogen Candida albicans responds to amino acid starvation by activating pseudohyphal development and the expression of amino acid biosynthetic genes (GCN response). In Saccharomyces cerevisiae, the GCN response is dependent on Gcn2, which regulates the translation of the transcription factor Gcn4. Therefore, we examined the role of Gcn2 in C. albicans by using molecular, cellular, and genomic approaches. We show that C. albicans GCN2 encodes an eIF2alpha kinase, like its S. cerevisiae homologue. However, GCN4 appears to be regulated mainly at the transcriptional level in C. albicans. Furthermore, the inactivation of C. albicans Gcn2 only partially attenuates growth under amino acid starvation conditions and resistance to the histidine analogue 3-aminotriazole. Our comparison of the Gcn4 and Gcn2 regulons by transcript profiling reinforces the view that Gcn2 contributes to, but is not essential for, the activation of general amino acid control in C. albicans.
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Affiliation(s)
- Hélène Tournu
- Aberdeen Fungal Group, School of Medical Sciences, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
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Smirnova JB, Selley JN, Sanchez-Cabo F, Carroll K, Eddy AA, McCarthy JEG, Hubbard SJ, Pavitt GD, Grant CM, Ashe MP. Global gene expression profiling reveals widespread yet distinctive translational responses to different eukaryotic translation initiation factor 2B-targeting stress pathways. Mol Cell Biol 2005; 25:9340-9. [PMID: 16227585 PMCID: PMC1265828 DOI: 10.1128/mcb.25.21.9340-9349.2005] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Global inhibition of protein synthesis is a hallmark of many cellular stress conditions. Even though specific mRNAs defy this (e.g., yeast GCN4 and mammalian ATF4), the extent and variation of such resistance remain uncertain. In this study, we have identified yeast mRNAs that are translationally maintained following either amino acid depletion or fusel alcohol addition. Both stresses inhibit eukaryotic translation initiation factor 2B, but via different mechanisms. Using microarray analysis of polysome and monosome mRNA pools, we demonstrate that these stress conditions elicit widespread yet distinct translational reprogramming, identifying a fundamental role for translational control in the adaptation to environmental stress. These studies also highlight the complex interplay that exists between different stages in the gene expression pathway to allow specific preordained programs of proteome remodeling. For example, many ribosome biogenesis genes are coregulated at the transcriptional and translational levels following amino acid starvation. The transcriptional regulation of these genes has recently been connected to the regulation of cellular proliferation, and on the basis of our results, the translational control of these mRNAs should be factored into this equation.
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Affiliation(s)
- Julia B Smirnova
- Faculty of Life Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester M13 9PT, United Kingdom
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35
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Lipford JR, Smith GT, Chi Y, Deshaies RJ. A putative stimulatory role for activator turnover in gene expression. Nature 2005; 438:113-6. [PMID: 16267558 DOI: 10.1038/nature04098] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Accepted: 08/03/2005] [Indexed: 11/09/2022]
Abstract
The ubiquitin-proteasome system (UPS) promotes the destruction of target proteins by attaching to them a ubiquitin chain that is recognized by the 26S proteasome. The UPS influences most cellular processes, and its targets include transcriptional activators that are primary determinants of gene expression. Emerging evidence indicates that non-proteolytic functions of the UPS might stimulate transcriptional activity. Here we show that the proteolysis of some transcriptional activators by the UPS can stimulate their function. We focused on the role of UPS-dependent proteolysis in the function of inducible transcriptional activators in yeast, and found that inhibition of the proteasome reduced transcription of the targets of the activators Gcn4, Gal4 and Ino2/4. In addition, mutations in SCF(Cdc4), the ubiquitin ligase for Gcn4 (ref. 5), or mutations in ubiquitin that prevent degradation, also impaired the transcription of Gcn4 targets. These transcriptional defects were manifested despite the enhanced abundance of Gcn4 on cognate promoters. Proteasome inhibition also decreased the association of RNA polymerase II with Gcn4, Gal4 and Ino2/4 targets, as did mutations in SCF(Cdc4) for Gcn4 targets. Expression of a stable phospho-site mutant of Gcn4 (ref. 7) or disruption of the kinases that target Gcn4 for turnover alleviated the sensitivity of Gcn4 activity to defects in the UPS.
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Affiliation(s)
- J Russell Lipford
- Howard Hughes Medical Institute, Division of Biology, MC 156-29, California Institute of Technology, 1200 E. California Boulevard, Pasadena, California 91125, USA
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36
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Krappmann S, Braus GH. Nitrogen metabolism of Aspergillus and its role in pathogenicity. Med Mycol 2005; 43 Suppl 1:S31-40. [PMID: 16110790 DOI: 10.1080/13693780400024271] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Aspergilli represent unique pathogens. Based on their saprophytic life style they are able to colonize a variety of ecological niches, among them the immunocompromised individual. Distinct fungal attributes that play a role in pathogenicity of aspergilli have been described, and primary metabolism indisputably has to be taken into account for contributing to the virulence potential of this fungal genus. Here we present an overview of studies that focus on this aspect of nutritional versatility. In the predominant pathogenic representative Aspergillus fumigatus regulation of nitrogen utilization and sensing of nitrogen sources have been scrutinized with respect to pathogenicity. The impact of distinct metabolic pathways on virulence capacities could be evaluated by inspection of auxotrophic mutant strains. Among them, para-aminobenzoic acid-requiring mutants revealed that this biosynthetic route is strictly required for pathogenicity. For amino acid anabolism only lysine biosynthesis has been investigated in this regard. Fungal amino acid biosynthesis is generally subject to strict regulation mediated by the Cross-Pathway Control system, a conserved regulatory circuit evolved to counteract conditions of nutritional stress. A clear influence of the system on pathogenicity could be observed by targeting its transcriptional activator CpcA. However, additional metabolic characteristics as well as regulatory instruments that compensate environmental challenges need to be addressed in future research with the aim to assess the significance of fungal primary metabolism for pathogenicity of aspergillus species.
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Affiliation(s)
- S Krappmann
- Institute of Microbiology & Genetics, Department of Molecular Microbiology and Genetics, Georg-August-University, Göttingen, Germany.
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37
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Kilberg MS, Pan YX, Chen H, Leung-Pineda V. Nutritional control of gene expression: how mammalian cells respond to amino acid limitation. Annu Rev Nutr 2005; 25:59-85. [PMID: 16011459 PMCID: PMC3600373 DOI: 10.1146/annurev.nutr.24.012003.132145] [Citation(s) in RCA: 206] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The amino acid response (AAR) pathway in mammalian cells is designed to detect and respond to amino acid deficiency. Limiting any essential amino acid initiates this signaling cascade, which leads to increased translation of a "master regulator," activating transcription factor (ATF) 4, and ultimately, to regulation of many steps along the pathway of DNA to RNA to protein. These regulated events include chromatin remodeling, RNA splicing, nuclear RNA export, mRNA stabilization, and translational control. Proteins that are increased in their expression as targets of the AAR pathway include membrane transporters, transcription factors from the basic region/leucine zipper (bZIP) superfamily, growth factors, and metabolic enzymes. Significant progress has been achieved in understanding the molecular mechanisms by which amino acids control the synthesis and turnover of mRNA and protein. Beyond gaining additional knowledge of these important regulatory pathways, further characterization of how these processes contribute to the pathology of various disease states represents an interesting aspect of future research in molecular nutrition.
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Affiliation(s)
- M S Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0245, USA.
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38
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Zhang Z, Dietrich FS. Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae. Curr Genet 2005; 48:77-87. [PMID: 16012843 DOI: 10.1007/s00294-005-0001-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Revised: 05/23/2005] [Accepted: 05/30/2005] [Indexed: 01/17/2023]
Abstract
We have taken advantage of recently sequenced hemiascomycete fungal genomes to computationally identify additional genes potentially regulated by upstream open reading frames (uORFs). Our approach is based on the observation that the structure, including the uORFs, of the post-transcriptionally uORF regulated Saccharomyces cerevisiae genes GCN4 and CPA1 is conserved in related species. Thirty-eight candidate genes for which uORFs were found in multiple species were identified and tested. We determined by 5' RACE that 15 of these 38 genes are transcribed. Most of these 15 genes have only a single uORF in their 5' UTR, and the length of these uORFs range from 3 to 24 codons. We cloned seven full-length UTR sequences into a luciferase (LUC) reporter system. Luciferase activity and mRNA level were compared between the wild-type UTR construct and a construct where the uORF start codon was mutated. The translational efficiency index (TEI) of each construct was calculated to test the possible regulatory function on translational level. We hypothesize that uORFs in the UTR of RPC11, TPK1, FOL1, WSC3, and MKK1 may have translational regulatory roles while uORFs in the 5' UTR of ECM7 and IMD4 have little effect on translation under the conditions tested.
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Affiliation(s)
- Zhihong Zhang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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39
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Arava Y, Boas FE, Brown PO, Herschlag D. Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res 2005; 33:2421-32. [PMID: 15860778 PMCID: PMC1087779 DOI: 10.1093/nar/gki331] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Translation of an mRNA is generally divided into three stages: initiation, elongation and termination. The relative rates of these steps determine both the number and position of ribosomes along the mRNA, but traditional velocity sedimentation assays for the translational status of mRNA determine only the number of bound ribosomes. We developed a procedure, termed Ribosome Density Mapping (RDM), that uses site-specific cleavage of polysomal mRNA followed by separation on a sucrose gradient and northern analysis, to determine the number of ribosomes associated with specified portions of a particular mRNA. This procedure allows us to test models for translation and its control, and to examine properties of individual steps of translation in vivo. We tested specific predictions from the current model for translational control of GCN4 expression in yeast and found that ribosomes were differentially associated with the uORFs elements and coding region under different growth conditions, consistent with this model. We also mapped ribosome density along the ORF of several mRNAs, to probe basic kinetic properties of translational steps in yeast. We found no detectable decline in ribosome density between the 5′ and 3′ ends of the ORFs, suggesting that the average processivity of elongation is very high. Conversely, there was no queue of ribosomes at the termination site, suggesting that termination is not very slow relative to elongation and initiation. Finally, the RDM results suggest that less frequent initiation of translation on mRNAs with longer ORFs is responsible for the inverse correlation between ORF length and ribosomal density that we observed in a global analysis of translation. These results provide new insights into eukaryotic translation in vivo.
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Affiliation(s)
| | - F. Edward Boas
- Department of Biochemistry, Stanford UniversityStanford, CA 94305-5307, USA
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford UniversityStanford, CA 94305-5307, USA
- To whom correspondence should be addressed. Tel: +1 650 723 9442; Fax: +1 650 723 6783;
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40
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Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA. Transcriptional regulatory code of a eukaryotic genome. Nature 2004; 431:99-104. [PMID: 15343339 PMCID: PMC3006441 DOI: 10.1038/nature02800] [Citation(s) in RCA: 1554] [Impact Index Per Article: 77.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Accepted: 07/01/2004] [Indexed: 11/09/2022]
Abstract
DNA-binding transcriptional regulators interpret the genome's regulatory code by binding to specific sequences to induce or repress gene expression. Comparative genomics has recently been used to identify potential cis-regulatory sequences within the yeast genome on the basis of phylogenetic conservation, but this information alone does not reveal if or when transcriptional regulators occupy these binding sites. We have constructed an initial map of yeast's transcriptional regulatory code by identifying the sequence elements that are bound by regulators under various conditions and that are conserved among Saccharomyces species. The organization of regulatory elements in promoters and the environment-dependent use of these elements by regulators are discussed. We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators.
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Affiliation(s)
- Christopher T Harbison
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
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41
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Patil CK, Li H, Walter P. Gcn4p and novel upstream activating sequences regulate targets of the unfolded protein response. PLoS Biol 2004; 2:E246. [PMID: 15314660 PMCID: PMC509306 DOI: 10.1371/journal.pbio.0020246] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Accepted: 05/17/2004] [Indexed: 01/23/2023] Open
Abstract
Eukaryotic cells respond to accumulation of unfolded proteins in the endoplasmic reticulum (ER) by activating the unfolded protein response (UPR), a signal transduction pathway that communicates between the ER and the nucleus. In yeast, a large set of UPR target genes has been experimentally determined, but the previously characterized unfolded protein response element (UPRE), an upstream activating sequence (UAS) found in the promoter of the UPR target gene KAR2, cannot account for the transcriptional regulation of most genes in this set. To address this puzzle, we analyzed the promoters of UPR target genes computationally, identifying as candidate UASs short sequences that are statistically overrepresented. We tested the most promising of these candidate UASs for biological activity, and identified two novel UPREs, which are necessary and sufficient for UPR activation of promoters. A genetic screen for activators of the novel motifs revealed that the transcription factor Gcn4p plays an essential and previously unrecognized role in the UPR: Gcn4p and its activator Gcn2p are required for induction of a majority of UPR target genes during ER stress. Both Hac1p and Gcn4p bind target gene promoters to stimulate transcriptional induction. Regulation of Gcn4p levels in response to changing physiological conditions may function as an additional means to modulate the UPR. The discovery of a role for Gcn4p in the yeast UPR reveals an additional level of complexity and demonstrates a surprising conservation of the signaling circuit between yeast and metazoan cells. The yeast unfolded protein response activates a large set of target genes, but a characterized element found in the promoter of one target, KAR2, cannot account for most targets. Using computational and experimental methods, the authors identify additional elements, as well a role for GCN4p in the response
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Affiliation(s)
- Christopher K Patil
- 1Howard Hughes Medical Institute, Chevy ChaseMaryland, United States of America
- 2Department of Biochemistry and Biophysics, University of CaliforniaSan Francisco, California, United States of America
| | - Hao Li
- 2Department of Biochemistry and Biophysics, University of CaliforniaSan Francisco, California, United States of America
- 3California Institute for Quantitative Biomedical Research, San FranciscoCaliforniaUnited States of America
| | - Peter Walter
- 1Howard Hughes Medical Institute, Chevy ChaseMaryland, United States of America
- 2Department of Biochemistry and Biophysics, University of CaliforniaSan Francisco, California, United States of America
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42
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Krappmann S, Bignell EM, Reichard U, Rogers T, Haynes K, Braus GH. The Aspergillus fumigatus transcriptional activator CpcA contributes significantly to the virulence of this fungal pathogen. Mol Microbiol 2004; 52:785-99. [PMID: 15101984 DOI: 10.1111/j.1365-2958.2004.04015.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have cloned and characterized the Aspergillus fumigatus cpcA gene encoding the transcriptional activator of the cross-pathway control system of amino acid biosynthesis. cpcA encodes a functional orthologue of Saccharomyces cerevisiae Gcn4p. The coding sequence of the 2.2 kb transcript is preceded by two short upstream open reading frames, the larger one being well conserved among Aspergilli. Deletion strains in which either the coding sequence or the entire locus are replaced by a bifunctional dominant marker are impaired in their cross-pathway control response upon amino acid starvation, as demonstrated by analyses of selected reporter genes and specific enzymatic activities. In a murine model of pulmonary aspergillosis, cpcAdelta strains display attenuated virulence. Pathogenicity is restored to wild-type levels in strains with reconstitution of the genomic locus. Competitive mixed infection experiments additionally demonstrate that cpcAdelta strains are less able to survive in vivo than their wild-type progenitor. Our data suggest that specific stress conditions are encountered by A. fumigatus within the mammalian host and that the fungal cross-pathway control system plays a significant role in pulmonary aspergillosis.
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Affiliation(s)
- Sven Krappmann
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
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43
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Holmes LEA, Campbell SG, De Long SK, Sachs AB, Ashe MP. Loss of translational control in yeast compromised for the major mRNA decay pathway. Mol Cell Biol 2004; 24:2998-3010. [PMID: 15024087 PMCID: PMC371117 DOI: 10.1128/mcb.24.7.2998-3010.2004] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The cytoplasmic fate of mRNAs is dictated by the relative activities of the intimately connected mRNA decay and translation initiation pathways. In this study, we have found that yeast strains compromised for stages downstream of deadenylation in the major mRNA decay pathway are incapable of inhibiting global translation initiation in response to stress. In the past, the paradigm of the eIF2alpha kinase-dependent amino acid starvation pathway in yeast has been used to evaluate this highly conserved stress response in all eukaryotic cells. Using a similar approach we have found that even though the mRNA decay mutants maintain high levels of general translation, they exhibit many of the hallmarks of amino acid starvation, including increased eIF2alpha phosphorylation and activated GCN4 mRNA translation. Therefore, these mutants appear translationally oblivious to decreased ternary complex abundance, and we propose that this is due to higher rates of mRNA recruitment to the 40S ribosomal subunit.
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Affiliation(s)
- L E A Holmes
- Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester M60 1QD, United Kingdom
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44
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Takaku H, Mutoh E, Sagehashi Y, Fukuda R, Horiuchi H, Ochi K, Takagi M, Ohta A. A Gcn4p homolog is essential for the induction of a ribosomal protein L41 variant responsible for cycloheximide resistance in the yeast Candida maltosa. J Biol Chem 2004; 279:23030-7. [PMID: 15039451 DOI: 10.1074/jbc.m400888200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cycloheximide (CYH) resistance in the yeast Candida maltosa is based on the inducible expression of genes encoding a variant of ribosomal protein L41-Q, with glutamine at position 56 instead of the proline found in normal L41. The promoter of L41-Q2a, one of the L41-Q gene alleles encoding L41-Q, has an element similar to the Gcn4p-responsive element of Saccharomyces cerevisiae. In a previous study, this element was shown to be essential for the induction of L41-Q by CYH. In the present study, a C. maltosa GCN4 homolog, C-GCN4, was cloned. It had a long 5'-leader region with three upstream open reading frames. Enhanced expression of the C-GCN4 reporter fusion gene upon the addition of 3-aminotriazole or by mutations in start codons of all three upstream open reading frames indicates that C-GCN4 expression is under translation repression as was seen with GCN4. The C-GCN4-depleted mutant was unable to grow in a nutrient medium containing CYH and did not express L41-Q genes. Recombinant C-Gcn4p bound to the consensus DNA element for Gcn4p, 5'-(G/A)TGACTCAT-3', located upstream of L41-Q2a. Thus, C-Gcn4p, which likely functions in the general control of amino acid biosynthesis, is essential for the expression of L41-Q genes.
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Affiliation(s)
- Hiroaki Takaku
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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45
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Braus GH, Grundmann O, Brückner S, Mösch HU. Amino acid starvation and Gcn4p regulate adhesive growth and FLO11 gene expression in Saccharomyces cerevisiae. Mol Biol Cell 2003; 14:4272-84. [PMID: 14517335 PMCID: PMC207018 DOI: 10.1091/mbc.e03-01-0042] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2003] [Revised: 05/22/2003] [Accepted: 05/27/2003] [Indexed: 11/11/2022] Open
Abstract
In baker's yeast Saccharomyces cerevisiae, cell-cell and cell-surface adhesion are required for haploid invasive growth and diploid pseudohyphal development. These morphogenetic events are induced by starvation for glucose or nitrogen and require the cell surface protein Flo11p. We show that amino acid starvation is a nutritional signal that activates adhesive growth and expression of FLO11 in both haploid and diploid strains in the presence of glucose and ammonium, known suppressors of adhesion. Starvation-induced adhesive growth requires Flo11p and is under control of Gcn2p and Gcn4p, elements of the general amino acid control system. Tpk2p and Flo8p, elements of the cAMP pathway, are also required for activation but not Ste12p and Tec1p, known targets of the mitogen-activated protein kinase cascade. Promoter analysis of FLO11 identifies one upstream activation sequence (UASR) and one repression site (URS) that confer regulation by amino acid starvation. Gcn4p is not required for regulation of the UASR by amino acid starvation, but seems to be indirectly required to overcome the negative effects of the URS on FLO11 transcription. In addition, Gcn4p controls expression of FLO11 by affecting two basal upstream activation sequences (UASB). In summary, our study suggests that amino acid starvation is a nutritional signal that triggers a Gcn4p-controlled signaling pathway, which relieves repression of FLO11 gene expression and induces adhesive growth.
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Affiliation(s)
- Gerhard H Braus
- Institute for Microbiology and Genetics, Georg-August-University, D-37077 Göttingen, Germany.
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46
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Irniger S, Braus GH. Controlling transcription by destruction: the regulation of yeast Gcn4p stability. Curr Genet 2003; 44:8-18. [PMID: 14508604 DOI: 10.1007/s00294-003-0422-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2003] [Revised: 06/17/2003] [Accepted: 06/18/2003] [Indexed: 11/30/2022]
Abstract
The Gcn4 protein, a member of the AP-1 family of transcription factors, is involved in the expression of more than 500 genes in the budding yeast Saccharomyces cerevisiae. A key role of Gcn4p is the increased expression of many amino acid biosynthesis genes in response to amino acid starvation. The accumulation of this transcription activator is mainly induced by efficient translation of the GCN4 ORF and by stabilisation of the Gcn4 protein. Under normal growth conditions, Gcn4p is a highly unstable protein, thereby resembling many eukaryotic transcription factors, including mammalian Jun and Myc proteins. Gcn4p is degraded by ubiquitin-dependent proteolysis mediated by the Skp1/cullin/F-box (SCF) ubiquitin ligase, which recognises specifically phosphorylated substrates. Two cyclin-dependent protein kinases, Pho85p and Srb10p, have crucial functions in regulating Gcn4p phosphorylation and degradation. The past few years have revealed many novel insights into these regulatory processes. Here, we summarise current knowledge about the factors and mechanisms regulating Gcn4p stability.
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Affiliation(s)
- Stefan Irniger
- Institute of Microbiology and Genetics, Georg-August-University, Grisebachstrasse 8, 37077 Göttingen, Germany
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Abstract
The mechanism by which gene regulatory proteins gain access to their DNA target sites is not known. In vitro, binding is inherently cooperative between arbitrary DNA binding proteins whose target sites are located within the same nucleosome. We refer to such competition-based cooperativity as collaborative competition. Here we show that arbitrarily chosen foreign DNA binding proteins, LexA and Tet repressor, cooperate with an adjacently binding endogenous activator protein, Gcn4, to coactivate expression of chromosomal reporter genes in Saccharomyces cerevisiae. Coactivation requires that the cooperating target sites be within a nucleosome-length distance; it leads to increased occupancy by Gcn4 at its binding site; and it requires both Gcn5 and Swi/Snf which, at an endogenous Gcn4-dependent promoter, act subsequent to Gcn4 binding. These results imply that collaborative competition contributes to gene regulation in vivo. They further imply that, even in the presence of the cell's full wild-type complement of chromatin remodeling factors, competition of regulatory proteins with histone octamer for access to regulatory target sites remains a quantitative determinant of gene expression levels. We speculate that initial target site recognition and binding may occur via spontaneous nucleosomal site exposure, with remodeling factor action required downstream to lock in higher levels of regulatory protein occupancy.
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Affiliation(s)
- Joanna A Miller
- Department of Biochemistry, Molecular Biology and Cellular Biology, Northwestern University, Evanston, Illinois 60208-3500, USA
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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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Winderickx J, Holsbeeks I, Lagatie O, Giots F, Thevelein J, de Winde H. From feast to famine; adaptation to nutrient availability in yeast. ACTA ACUST UNITED AC 2002. [DOI: 10.1007/3-540-45611-2_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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50
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Tripathi G, Wiltshire C, Macaskill S, Tournu H, Budge S, Brown AJ. Gcn4 co-ordinates morphogenetic and metabolic responses to amino acid starvation in Candida albicans. EMBO J 2002; 21:5448-56. [PMID: 12374745 PMCID: PMC129063 DOI: 10.1093/emboj/cdf507] [Citation(s) in RCA: 153] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2001] [Revised: 07/31/2002] [Accepted: 08/05/2002] [Indexed: 11/13/2022] Open
Abstract
Candida albicans is a major fungal pathogen of humans. It regulates its morphology in response to various environmental signals, but many of these signals are poorly defined. We show that amino acid starvation induces filamentous growth in C.albicans. Also, starvation for a single amino acid (histidine) induces CaHIS4, CaHIS7, CaARO4, CaLYS1 and CaLYS2 gene expression in a manner reminiscent of the GCN response in Saccharomyces cerevisiae. These morphogenetic and GCN-like responses are both dependent upon CaGcn4, which is a functional homologue of S.cerevisiae Gcn4. Like ScGcn4, CaGcn4 activates the transcription of amino acid biosynthetic genes via the GCRE element, and CaGcn4 confers resistance to the histidine analogue, 3-aminotriazole. CaGcn4 interacts with the Ras-cAMP pathway to promote filamentous growth, but the GCN-like response is not dependent upon morphogenetic signalling. CaGcn4 acts as a global regulator in C.albicans, co-ordinating both metabolic and morphogenetic responses to amino acid starvation.
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Affiliation(s)
- Gyanendra Tripathi
- Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
Present address: The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Present address: CRC Beatson Laboratories, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK Corresponding author e-mail:
| | - Carolyn Wiltshire
- Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
Present address: The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Present address: CRC Beatson Laboratories, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK Corresponding author e-mail:
| | | | | | | | - Alistair J.P. Brown
- Department of Molecular and Cell Biology, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
Present address: The Babraham Institute, Babraham, Cambridge CB2 4AT, UK Present address: CRC Beatson Laboratories, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK Corresponding author e-mail:
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