1
|
Szádeczky-Kardoss I, Szaker H, Verma R, Darkó É, Pettkó-Szandtner A, Silhavy D, Csorba T. Elongation factor TFIIS is essential for heat stress adaptation in plants. Nucleic Acids Res 2022; 50:1927-1950. [PMID: 35100405 PMCID: PMC8886746 DOI: 10.1093/nar/gkac020] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/11/2021] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Elongation factor TFIIS (transcription factor IIS) is structurally and biochemically probably the best characterized elongation cofactor of RNA polymerase II. However, little is known about TFIIS regulation or its roles during stress responses. Here, we show that, although TFIIS seems unnecessary under optimal conditions in Arabidopsis, its absence renders plants supersensitive to heat; tfIIs mutants die even when exposed to sublethal high temperature. TFIIS activity is required for thermal adaptation throughout the whole life cycle of plants, ensuring both survival and reproductive success. By employing a transcriptome analysis, we unravel that the absence of TFIIS makes transcriptional reprogramming sluggish, and affects expression and alternative splicing pattern of hundreds of heat-regulated transcripts. Transcriptome changes indirectly cause proteotoxic stress and deterioration of cellular pathways, including photosynthesis, which finally leads to lethality. Contrary to expectations of being constantly present to support transcription, we show that TFIIS is dynamically regulated. TFIIS accumulation during heat occurs in evolutionary distant species, including the unicellular alga Chlamydomonas reinhardtii, dicot Brassica napus and monocot Hordeum vulgare, suggesting that the vital role of TFIIS in stress adaptation of plants is conserved.
Collapse
Affiliation(s)
- István Szádeczky-Kardoss
- Genetics and Biotechnology Institute, MATE University, Szent-Györgyi A. u. 4, 2100 Gödöllő, Hungary
| | - Henrik Mihály Szaker
- Genetics and Biotechnology Institute, MATE University, Szent-Györgyi A. u. 4, 2100 Gödöllő, Hungary
- Faculty of Natural Sciences, Eötvös Lóránd University, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62., 6726 Szeged, Hungary
| | - Radhika Verma
- Genetics and Biotechnology Institute, MATE University, Szent-Györgyi A. u. 4, 2100 Gödöllő, Hungary
- Doctorate School of Biological Sciences, MATE University, Pater Karoly u. 1, 2100 Gödöllő, Hungary
| | - Éva Darkó
- Agricultural Institute, Centre for Agricultural Research, Brunszvik u. 2., 2462 Martonvásár, Hungary
| | | | - Dániel Silhavy
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62., 6726 Szeged, Hungary
| | - Tibor Csorba
- Genetics and Biotechnology Institute, MATE University, Szent-Györgyi A. u. 4, 2100 Gödöllő, Hungary
| |
Collapse
|
2
|
García-Martínez J, Medina DA, Bellvís P, Sun M, Cramer P, Chávez S, Pérez-Ortín JE. The total mRNA concentration buffering system in yeast is global rather than gene-specific. RNA (NEW YORK, N.Y.) 2021; 27:1281-1290. [PMID: 34272303 PMCID: PMC8456998 DOI: 10.1261/rna.078774.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Gene expression in eukaryotes does not follow a linear process from transcription to translation and mRNA degradation. Instead it follows a circular process in which cytoplasmic mRNA decay crosstalks with nuclear transcription. In many instances, this crosstalk contributes to buffer mRNA at a roughly constant concentration. Whether the mRNA buffering concept operates on the total mRNA concentration or at the gene-specific level, and if the mechanism to do so is a global or a specific one, remain unknown. Here we assessed changes in mRNA concentrations and their synthesis rates along the transcriptome of aneuploid strains of the yeast Saccharomyces cerevisiae We also assessed mRNA concentrations and their synthesis rates in nonsense-mediated decay (NMD) targets in euploid strains. We found that the altered synthesis rates in the genes from the aneuploid chromosome and the changes in their mRNA stabilities were not counterbalanced. In addition, the stability of NMD targets was not specifically compensated by the changes in synthesis rate. We conclude that there is no genetic compensation of NMD mRNA targets in yeast, and total mRNA buffering uses mostly a global system rather than a gene-specific one.
Collapse
Affiliation(s)
- José García-Martínez
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, E46100 Burjassot, Spain
| | - Daniel A Medina
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, E46100 Burjassot, Spain
| | - Pablo Bellvís
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
| | - Mai Sun
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, 37077 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, 37077 Göttingen, Germany
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
- Dirección de Evaluación y Acreditación, Agencia Andaluza del Conocimiento, planta 3ª C.P. 14006 Córdoba, Spain
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, E46100 Burjassot, Spain
| |
Collapse
|
3
|
García-Martínez J, Pérez-Martínez ME, Pérez-Ortín JE, Alepuz P. Recruitment of Xrn1 to stress-induced genes allows efficient transcription by controlling RNA polymerase II backtracking. RNA Biol 2020; 18:1458-1474. [PMID: 33258404 DOI: 10.1080/15476286.2020.1857521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A new paradigm has emerged proposing that the crosstalk between nuclear transcription and cytoplasmic mRNA stability keeps robust mRNA levels in cells under steady-state conditions. A key piece in this crosstalk is the highly conserved 5'-3' RNA exonuclease Xrn1, which degrades most cytoplasmic mRNAs but also associates with nuclear chromatin to activate transcription by not well-understood mechanisms. Here, we investigated the role of Xrn1 in the transcriptional response of Saccharomyces cerevisiae cells to osmotic stress. We show that a lack of Xrn1 results in much lower transcriptional induction of the upregulated genes but in similar high levels of their transcripts because of parallel mRNA stabilization. Unexpectedly, lower transcription in xrn1 occurs with a higher accumulation of RNA polymerase II (RNAPII) at stress-inducible genes, suggesting that this polymerase remains inactive backtracked. Xrn1 seems to be directly implicated in the formation of a competent elongation complex because Xrn1 is recruited to the osmotic stress-upregulated genes in parallel with the RNAPII complex, and both are dependent on the mitogen-activated protein kinase Hog1. Our findings extend the role of Xrn1 in preventing the accumulation of inactive RNAPII at highly induced genes to other situations of rapid and strong transcriptional upregulation.
Collapse
Affiliation(s)
- José García-Martínez
- ERI Biotecmed, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain.,Departamento De Genética, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain
| | - María E Pérez-Martínez
- ERI Biotecmed, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain.,Departamento De Bioquímica Y Biología Molecular, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain
| | - José E Pérez-Ortín
- ERI Biotecmed, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain.,Departamento De Bioquímica Y Biología Molecular, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain
| | - Paula Alepuz
- ERI Biotecmed, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain.,Departamento De Bioquímica Y Biología Molecular, Facultad De Ciencias Biológicas, Universitat De València, Burjassot, Spain
| |
Collapse
|
4
|
Begley V, Jordán-Pla A, Peñate X, Garrido-Godino AI, Challal D, Cuevas-Bermúdez A, Mitjavila A, Barucco M, Gutiérrez G, Singh A, Alepuz P, Navarro F, Libri D, Pérez-Ortín JE, Chávez S. Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration. RNA Biol 2020; 18:1310-1323. [PMID: 33138675 DOI: 10.1080/15476286.2020.1845504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
mRNA homoeostasis is favoured by crosstalk between transcription and degradation machineries. Both the Ccr4-Not and the Xrn1-decaysome complexes have been described to influence transcription. While Ccr4-Not has been shown to directly stimulate transcription elongation, the information available on how Xrn1 influences transcription is scarce and contradictory. In this study we have addressed this issue by mapping RNA polymerase II (RNA pol II) at high resolution, using CRAC and BioGRO-seq techniques in Saccharomyces cerevisiae. We found significant effects of Xrn1 perturbation on RNA pol II profiles across the genome. RNA pol II profiles at 5' exhibited significant alterations that were compatible with decreased elongation rates in the absence of Xrn1. Nucleosome mapping detected altered chromatin configuration in the gene bodies. We also detected accumulation of RNA pol II shortly upstream of polyadenylation sites by CRAC, although not by BioGRO-seq, suggesting higher frequency of backtracking before pre-mRNA cleavage. This phenomenon was particularly linked to genes with poorly positioned nucleosomes at this position. Accumulation of RNA pol II at 3' was also detected in other mRNA decay mutants. According to these and other pieces of evidence, Xrn1 seems to influence transcription elongation at least in two ways: by directly favouring elongation rates and by a more general mechanism that connects mRNA decay to late elongation.
Collapse
Affiliation(s)
- Victoria Begley
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. Del Rocío, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València; Burjassot, Valencia, Spain
| | - Xenia Peñate
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. Del Rocío, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Ana I Garrido-Godino
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Drice Challal
- Institut Jacques Monod, Centre National De La Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Abel Cuevas-Bermúdez
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Adrià Mitjavila
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. Del Rocío, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Mara Barucco
- Institut Jacques Monod, Centre National De La Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Gabriel Gutiérrez
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, USA
| | - Paula Alepuz
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València; Burjassot, Valencia, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Domenico Libri
- Institut Jacques Monod, Centre National De La Recherche Scientifique, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València; Burjassot, Valencia, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. Del Rocío, Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| |
Collapse
|
5
|
Martínez-Fernández V, Cuevas-Bermúdez A, Gutiérrez-Santiago F, Garrido-Godino AI, Rodríguez-Galán O, Jordán-Pla A, Lois S, Triviño JC, de la Cruz J, Navarro F. Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2020; 26:1360-1379. [PMID: 32503921 PMCID: PMC7491330 DOI: 10.1261/rna.075507.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/28/2020] [Indexed: 05/08/2023]
Abstract
Understanding the functional connection that occurs for the three nuclear RNA polymerases to synthesize ribosome components during the ribosome biogenesis process has been the focal point of extensive research. To preserve correct homeostasis on the production of ribosomal components, cells might require the existence of proteins that target a common subunit of these RNA polymerases to impact their respective activities. This work describes how the yeast prefoldin-like Bud27 protein, which physically interacts with the Rpb5 common subunit of the three RNA polymerases, is able to modulate the transcription mediated by the RNA polymerase I, likely by influencing transcription elongation, the transcription of the RNA polymerase III, and the processing of ribosomal RNA. Bud27 also regulates both RNA polymerase II-dependent transcription of ribosomal proteins and ribosome biogenesis regulon genes, likely by occupying their DNA ORFs, and the processing of the corresponding mRNAs. With RNA polymerase II, this association occurs in a transcription rate-dependent manner. Our data also indicate that Bud27 inactivation alters the phosphorylation kinetics of ribosomal protein S6, a readout of TORC1 activity. We conclude that Bud27 impacts the homeostasis of the ribosome biogenesis process by regulating the activity of the three RNA polymerases and, in this way, the synthesis of ribosomal components. This quite likely occurs through a functional connection of Bud27 with the TOR signaling pathway.
Collapse
Affiliation(s)
- Verónica Martínez-Fernández
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Abel Cuevas-Bermúdez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Francisco Gutiérrez-Santiago
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Ana I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain
| | - Antonio Jordán-Pla
- ERI Biotecmed, Facultad de Biológicas, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | - Sergio Lois
- Sistemas Genómicos. Ronda de Guglielmo Marconi, 6, 46980 Paterna, Valencia, Spain
| | - Juan C Triviño
- Sistemas Genómicos. Ronda de Guglielmo Marconi, 6, 46980 Paterna, Valencia, Spain
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, E-41013 Seville, Spain
- Departamento de Genética, Universidad de Sevilla, E-41012 Seville, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
- Centro de Estudios Avanzados en Aceite de Oliva y Olivar, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| |
Collapse
|
6
|
Begley V, Corzo D, Jordán-Pla A, Cuevas-Bermúdez A, Miguel-Jiménez LD, Pérez-Aguado D, Machuca-Ostos M, Navarro F, Chávez MJ, Pérez-Ortín JE, Chávez S. The mRNA degradation factor Xrn1 regulates transcription elongation in parallel to Ccr4. Nucleic Acids Res 2019; 47:9524-9541. [PMID: 31392315 PMCID: PMC6765136 DOI: 10.1093/nar/gkz660] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/26/2019] [Accepted: 07/17/2019] [Indexed: 01/05/2023] Open
Abstract
Co-transcriptional imprinting of mRNA by Rpb4 and Rpb7 subunits of RNA polymerase II (RNAPII) and by the Ccr4-Not complex conditions its post-transcriptional fate. In turn, mRNA degradation factors like Xrn1 are able to influence RNAPII-dependent transcription, making a feedback loop that contributes to mRNA homeostasis. In this work, we have used repressible yeast GAL genes to perform accurate measurements of transcription and mRNA degradation in a set of mutants. This genetic analysis uncovered a link from mRNA decay to transcription elongation. We combined this experimental approach with computational multi-agent modelling and tested different possibilities of Xrn1 and Ccr4 action in gene transcription. This double strategy brought us to conclude that both Xrn1-decaysome and Ccr4-Not regulate RNAPII elongation, and that they do it in parallel. We validated this conclusion measuring TFIIS genome-wide recruitment to elongating RNAPII. We found that xrn1Δ and ccr4Δ exhibited very different patterns of TFIIS versus RNAPII occupancy, which confirmed their distinct role in controlling transcription elongation. We also found that the relative influence of Xrn1 and Ccr4 is different in the genes encoding ribosomal proteins as compared to the rest of the genome.
Collapse
Affiliation(s)
- Victoria Begley
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
| | - Daniel Corzo
- Escuela Técnica Superior de Informática, Universidad de Sevilla, Seville 41012, Spain
| | - Antonio Jordán-Pla
- E.R.I. Biotecmed, Universitat de València; Burjassot, Valencia 46100, Spain
| | - Abel Cuevas-Bermúdez
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - Lola de Miguel-Jiménez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
| | - David Pérez-Aguado
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
| | - Mercedes Machuca-Ostos
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
| | - Francisco Navarro
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén 23071, Spain
| | - María José Chávez
- Departamento de Matemática Aplicada I and Instituto de Matemáticas, Universidad de Sevilla, Seville 41012, Spain
| | - José E Pérez-Ortín
- E.R.I. Biotecmed, Universitat de València; Burjassot, Valencia 46100, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain
| |
Collapse
|
7
|
Albert B, Tomassetti S, Gloor Y, Dilg D, Mattarocci S, Kubik S, Hafner L, Shore D. Sfp1 regulates transcriptional networks driving cell growth and division through multiple promoter-binding modes. Genes Dev 2019; 33:288-293. [PMID: 30804227 PMCID: PMC6411004 DOI: 10.1101/gad.322040.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022]
Abstract
In this study, Albert et al. investigated the mechanisms by which the yeast Sfp1 protein coordinates both cell division and growth. They demonstrate that Sfp1 directly controls genes required for ribosome production and many other growth-promoting processes. The yeast Sfp1 protein regulates both cell division and growth but how it coordinates these processes is poorly understood. We demonstrate that Sfp1 directly controls genes required for ribosome production and many other growth-promoting processes. Remarkably, the complete set of Sfp1 target genes is revealed only by a combination of ChIP (chromatin immunoprecipitation) and ChEC (chromatin endogenous cleavage) methods, which uncover two promoter binding modes, one requiring a cofactor and the other a DNA-recognition motif. Glucose-regulated Sfp1 binding at cell cycle “START” genes suggests that Sfp1 controls cell size by coordinating expression of genes implicated in mass accumulation and cell division.
Collapse
Affiliation(s)
- Benjamin Albert
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Susanna Tomassetti
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Yvonne Gloor
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Daniel Dilg
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Stefano Mattarocci
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - Lukas Hafner
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics of Geneva (iGE3), 1211 Geneva 4, Switzerland
| |
Collapse
|
8
|
Widespread Backtracking by RNA Pol II Is a Major Effector of Gene Activation, 5' Pause Release, Termination, and Transcription Elongation Rate. Mol Cell 2018; 73:107-118.e4. [PMID: 30503775 DOI: 10.1016/j.molcel.2018.10.031] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/10/2018] [Accepted: 10/17/2018] [Indexed: 10/27/2022]
Abstract
In addition to phosphodiester bond formation, RNA polymerase II has an RNA endonuclease activity, stimulated by TFIIS, which rescues complexes that have arrested and backtracked. How TFIIS affects transcription under normal conditions is poorly understood. We identified backtracking sites in human cells using a dominant-negative TFIIS (TFIISDN) that inhibits RNA cleavage and stabilizes backtracked complexes. Backtracking is most frequent within 2 kb of start sites, consistent with slow elongation early in transcription, and in 3' flanking regions where termination is enhanced by TFIISDN, suggesting that backtracked pol II is a favorable substrate for termination. Rescue from backtracking by RNA cleavage also promotes escape from 5' pause sites, prevents premature termination of long transcripts, and enhances activation of stress-inducible genes. TFIISDN slowed elongation rates genome-wide by half, suggesting that rescue of backtracked pol II by TFIIS is a major stimulus of elongation under normal conditions.
Collapse
|
9
|
Gutiérrez G, Millán-Zambrano G, Medina DA, Jordán-Pla A, Pérez-Ortín JE, Peñate X, Chávez S. Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning. Epigenetics Chromatin 2017; 10:58. [PMID: 29212533 PMCID: PMC5719526 DOI: 10.1186/s13072-017-0165-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase). Maps based on these exhaustively digested samples miss any MNase-sensitive nucleosomes caused by transcription. In contrast, partial digestion approaches preserve such nucleosomes, but introduce noise due to MNase sequence preferences. A systematic way of correcting this bias for massively parallel sequencing experiments is still missing. RESULTS To investigate the contribution of TFIIS to the chromatin landscape, we developed a refined nucleosome-mapping method in Saccharomyces cerevisiae. Based on partial MNase digestion and a sequence-bias correction derived from naked DNA cleavage, the refined method efficiently mapped nucleosomes in promoter regions rich in MNase-sensitive structures. The naked DNA correction was also important for mapping gene body nucleosomes, particularly in those genes whose core promoters contain a canonical TATA element. With this improved method, we analyzed the global nucleosomal changes caused by lack of TFIIS. We detected a general increase in nucleosomal fuzziness and more restricted changes in nucleosome occupancy, which concentrated in some gene categories. The TATA-containing genes were preferentially associated with decreased occupancy in gene bodies, whereas the TATA-like genes did so with increased fuzziness. The detected chromatin alterations correlated with functional defects in nascent transcription, as revealed by genomic run-on experiments. CONCLUSIONS The combination of partial MNase digestion and naked DNA correction of the sequence bias is a precise nucleosomal mapping method that does not exclude MNase-sensitive nucleosomes. This method is useful for detecting subtle alterations in nucleosome positioning produced by lack of TFIIS. Their analysis revealed that TFIIS generally contributed to nucleosome positioning in both gene promoters and bodies. The independent effect of lack of TFIIS on nucleosome occupancy and fuzziness supports the existence of alternative chromatin dynamics during transcription elongation.
Collapse
Affiliation(s)
| | - Gonzalo Millán-Zambrano
- Departamento de Genética, Universidad de Sevilla, Seville, Spain.,Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain.,The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Daniel A Medina
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain.,Department of Chemical and Bioprocess Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Antonio Jordán-Pla
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Valencia, Spain
| | - Xenia Peñate
- Departamento de Genética, Universidad de Sevilla, Seville, Spain. .,Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain.
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla, Seville, Spain. .,Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain.
| |
Collapse
|
10
|
Gómez-Herreros F, Margaritis T, Rodríguez-Galán O, Pelechano V, Begley V, Millán-Zambrano G, Morillo-Huesca M, Muñoz-Centeno MC, Pérez-Ortín JE, de la Cruz J, Holstege FCP, Chávez S. The ribosome assembly gene network is controlled by the feedback regulation of transcription elongation. Nucleic Acids Res 2017. [PMID: 28637236 PMCID: PMC5737610 DOI: 10.1093/nar/gkx529] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosome assembly requires the concerted expression of hundreds of genes, which are transcribed by all three nuclear RNA polymerases. Transcription elongation involves dynamic interactions between RNA polymerases and chromatin. We performed a synthetic lethal screening in Saccharomyces cerevisiae with a conditional allele of SPT6, which encodes one of the factors that facilitates this process. Some of these synthetic mutants corresponded to factors that facilitate pre-rRNA processing and ribosome biogenesis. We found that the in vivo depletion of one of these factors, Arb1, activated transcription elongation in the set of genes involved directly in ribosome assembly. Under these depletion conditions, Spt6 was physically targeted to the up-regulated genes, where it helped maintain their chromatin integrity and the synthesis of properly stable mRNAs. The mRNA profiles of a large set of ribosome biogenesis mutants confirmed the existence of a feedback regulatory network among ribosome assembly genes. The transcriptional response in this network depended on both the specific malfunction and the role of the regulated gene. In accordance with our screening, Spt6 positively contributed to the optimal operation of this global network. On the whole, this work uncovers a feedback control of ribosome biogenesis by fine-tuning transcription elongation in ribosome assembly factor-coding genes.
Collapse
Affiliation(s)
- Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Thanasis Margaritis
- Molecular Cancer Research, University Medical Center Utrecht, & Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Vicent Pelechano
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed. Facultad de Biológicas, Universitat de València. Burjassot, Spain.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Victoria Begley
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Gonzalo Millán-Zambrano
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Macarena Morillo-Huesca
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Mari Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed. Facultad de Biológicas, Universitat de València. Burjassot, Spain
| | - Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Center Utrecht, & Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| |
Collapse
|
11
|
de la Cruz J, Gómez-Herreros F, Rodríguez-Galán O, Begley V, de la Cruz Muñoz-Centeno M, Chávez S. Feedback regulation of ribosome assembly. Curr Genet 2017; 64:393-404. [PMID: 29022131 DOI: 10.1007/s00294-017-0764-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/06/2017] [Accepted: 10/07/2017] [Indexed: 12/12/2022]
Abstract
Ribosome biogenesis is a crucial process for growth and constitutes the major consumer of cellular resources. This pathway is subjected to very stringent regulation to ensure correct ribosome manufacture with a wide variety of environmental and metabolic changes, and intracellular insults. Here we summarise our current knowledge on the regulation of ribosome biogenesis in Saccharomyces cerevisiae by particularly focusing on the feedback mechanisms that maintain ribosome homeostasis. Ribosome biogenesis in yeast is controlled mainly at the level of the production of both pre-rRNAs and ribosomal proteins through the transcriptional and post-transcriptional control of the TORC1 and protein kinase A signalling pathways. Pre-rRNA processing can occur before or after the 35S pre-rRNA transcript is completed; the switch between these two alternatives is regulated by growth conditions. The expression of both ribosomal proteins and the large family of transacting factors involved in ribosome biogenesis is co-regulated. Recently, it has been shown that the synthesis of rRNA and ribosomal proteins, but not of trans-factors, is coupled. Thus the so-called CURI complex sequesters specific transcription factor Ifh1 to repress ribosomal protein genes when rRNA transcription is impaired. We recently found that an analogue system should operate to control the expression of transacting factor genes in response to actual ribosome assembly performance. Regulation of ribosome biogenesis manages situations of imbalanced ribosome production or misassembled ribosomal precursors and subunits, which have been closely linked to distinct human diseases.
Collapse
Affiliation(s)
- Jesús de la Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
| | - Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Olga Rodríguez-Galán
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Victoria Begley
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - María de la Cruz Muñoz-Centeno
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain.,Departamento de Genética, Universidad de Sevilla, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC, Universidad de Sevilla, Seville, Spain. .,Departamento de Genética, Universidad de Sevilla, Seville, Spain.
| |
Collapse
|
12
|
Di Santo R, Aboulhouda S, Weinberg DE. The fail-safe mechanism of post-transcriptional silencing of unspliced HAC1 mRNA. eLife 2016; 5. [PMID: 27692069 PMCID: PMC5114014 DOI: 10.7554/elife.20069] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/30/2016] [Indexed: 12/11/2022] Open
Abstract
HAC1 encodes a transcription factor that is the central effector of the unfolded protein response (UPR) in budding yeast. When the UPR is inactive, HAC1 mRNA is stored as an unspliced isoform in the cytoplasm and no Hac1 protein is detectable. Intron removal is both necessary and sufficient to relieve the post-transcriptional silencing of HAC1 mRNA, yet the precise mechanism by which the intron prevents Hac1 protein accumulation has remained elusive. Here, we show that a combination of inhibited translation initiation and accelerated protein degradation—both dependent on the intron—prevents the accumulation of Hac1 protein when the UPR is inactive. Functionally, both components of this fail-safe silencing mechanism are required to prevent ectopic production of Hac1 protein and concomitant activation of the UPR. Our results provide a mechanistic understanding of HAC1 regulation and reveal a novel strategy for complete post-transcriptional silencing of a cytoplasmic mRNA. DOI:http://dx.doi.org/10.7554/eLife.20069.001 Molecular machines called ribosomes read the genetic instructions in an mRNA molecule and then translate them to make proteins. However, cells do not translate all of the template mRNAs that they have available into proteins; instead they have a number of ways to block the process to control when certain proteins are made. In budding yeast, the mRNA that codes for a protein called Hac1 is always present in the cell but the protein is normally not detected. The Hac1 protein is responsible for helping the cell deal with certain types of stress, so it only accumulates when the cell is experiencing such stresses. The mRNA that encodes Hac1 (referred to as HAC1 mRNA) contains a sequence called an intron. These sequences are normally cut out of mRNAs before they are read by the ribosome. However, the intron in the HAC1 mRNA is unusual, because it is only removed when cells are subjected to stress. The rest of the time, this intron serves to block the production of Hac1 through a poorly understood mechanism. Now, Di Santo et al. show the HAC1 mRNA uses two strategies to keep itself fully repressed—both of which involve its intron. One strategy relies on a structure formed in the HAC1 mRNA that prevents ribosomes from starting translation in the first place. However, this block is occasionally bypassed, causing some Hac1 protein to be produced when it should not be. To deal with this, the Hac1 protein that is produced contains a short protein sequence, encoded by the intron, that targets this unneeded protein for degradation. These two strategies together comprise a “fail-safe” mechanism to completely repress the HAC1 mRNA. Following on from these findings, it will be important to determine whether other mRNAs – both in budding yeast and in other species including humans – use a similar fail-safe strategy to block proteins from being made when they should not be. DOI:http://dx.doi.org/10.7554/eLife.20069.002
Collapse
Affiliation(s)
- Rachael Di Santo
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Soufiane Aboulhouda
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - David E Weinberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,Sandler Faculty Fellows Program, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
13
|
Gupta I, Villanyi Z, Kassem S, Hughes C, Panasenko OO, Steinmetz LM, Collart MA. Translational Capacity of a Cell Is Determined during Transcription Elongation via the Ccr4-Not Complex. Cell Rep 2016; 15:1782-94. [PMID: 27184853 DOI: 10.1016/j.celrep.2016.04.055] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 02/08/2016] [Accepted: 04/04/2016] [Indexed: 11/29/2022] Open
Abstract
The current understanding of gene expression considers transcription and translation to be independent processes. Challenging this notion, we found that translation efficiency is determined during transcription elongation through the imprinting of mRNAs with Not1, the central scaffold of the Ccr4-Not complex. We determined that another subunit of the complex, Not5, defines Not1 binding to specific mRNAs, particularly those produced from ribosomal protein genes. This imprinting mechanism specifically regulates ribosomal protein gene expression, which in turn determines the translational capacity of cells. We validate our model by SILAC and polysome profiling experiments. As a proof of concept, we demonstrate that enhanced translation compensates for transcriptional elongation stress. Taken together, our data indicate that in addition to defining mRNA stability, components of the Ccr4-Not imprinting complex regulate RNA translatability, thus ensuring global gene expression homeostasis.
Collapse
Affiliation(s)
- Ishaan Gupta
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Zoltan Villanyi
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, Institute of Genetics and Genomics, University of Geneva, 1211 Geneva 4, Switzerland
| | - Sari Kassem
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, Institute of Genetics and Genomics, University of Geneva, 1211 Geneva 4, Switzerland
| | - Christopher Hughes
- Genome Sciences Center, British Columbia Cancer Research Agency, Vancouver, BC V5Z 1L3, Canada
| | - Olesya O Panasenko
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, Institute of Genetics and Genomics, University of Geneva, 1211 Geneva 4, Switzerland
| | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, Institute of Genetics and Genomics, University of Geneva, 1211 Geneva 4, Switzerland.
| |
Collapse
|
14
|
García-Martínez J, Delgado-Ramos L, Ayala G, Pelechano V, Medina DA, Carrasco F, González R, Andrés-León E, Steinmetz L, Warringer J, Chávez S, Pérez-Ortín JE. The cellular growth rate controls overall mRNA turnover, and modulates either transcription or degradation rates of particular gene regulons. Nucleic Acids Res 2015; 44:3643-58. [PMID: 26717982 PMCID: PMC4856968 DOI: 10.1093/nar/gkv1512] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/16/2015] [Indexed: 01/02/2023] Open
Abstract
We analyzed 80 different genomic experiments, and found a positive correlation between both RNA polymerase II transcription and mRNA degradation with growth rates in yeast. Thus, in spite of the marked variation in mRNA turnover, the total mRNA concentration remained approximately constant. Some genes, however, regulated their mRNA concentration by uncoupling mRNA stability from the transcription rate. Ribosome-related genes modulated their transcription rates to increase mRNA levels under fast growth. In contrast, mitochondria-related and stress-induced genes lowered mRNA levels by reducing mRNA stability or the transcription rate, respectively. We also detected these regulations within the heterogeneity of a wild-type cell population growing in optimal conditions. The transcriptomic analysis of sorted microcolonies confirmed that the growth rate dictates alternative expression programs by modulating transcription and mRNA decay. The regulation of overall mRNA turnover keeps a constant ratio between mRNA decay and the dilution of [mRNA] caused by cellular growth. This regulation minimizes the indiscriminate transmission of mRNAs from mother to daughter cells, and favors the response capacity of the latter to physiological signals and environmental changes. We also conclude that, by uncoupling mRNA synthesis from decay, cells control the mRNA abundance of those gene regulons that characterize fast and slow growth.
Collapse
Affiliation(s)
- José García-Martínez
- Departamento de Genética, Facultad de Ciencias Biológicas, Universitat de València. C/ Dr. Moliner 50. E46100, Burjassot, Spain ERI Biotecmed, Facultad de Ciencias Biológicas, Universitat de Valencia. C/ Dr. Moliner 50. E46100, Burjassot, Spain
| | - Lidia Delgado-Ramos
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, C/ Antonio Maura Montaner, E41013 Sevilla Departamento de Genética, Universidad de Sevilla, Avenida de la Reina Mercedes s/n, E41012, Spain
| | - Guillermo Ayala
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universitat de València. C/ Dr. Moliner 50. E46100, Burjassot, Spain
| | - Vicent Pelechano
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel A Medina
- ERI Biotecmed, Facultad de Ciencias Biológicas, Universitat de Valencia. C/ Dr. Moliner 50. E46100, Burjassot, Spain Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de Valencia. C/ Dr. Moliner 50. E46100, Burjassot, Spain
| | - Fany Carrasco
- ERI Biotecmed, Facultad de Ciencias Biológicas, Universitat de Valencia. C/ Dr. Moliner 50. E46100, Burjassot, Spain Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de Valencia. C/ Dr. Moliner 50. E46100, Burjassot, Spain
| | - Ramón González
- Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja), Finca La Grajera LO-20 Salida 13, Autovía del Camino de Santiago, E26007 Logroño, Spain
| | - Eduardo Andrés-León
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, C/ Antonio Maura Montaner, E41013 Sevilla
| | - Lars Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany Stanford University School of Medicine, Department of Genetics, Stanford, CA 94305, USA Stanford Genome Technology Center, 3165 Porter Dr. Palo Alto, CA 94305, USA
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9 c, 40530 Göteborg, Sweden
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, C/ Antonio Maura Montaner, E41013 Sevilla Departamento de Genética, Universidad de Sevilla, Avenida de la Reina Mercedes s/n, E41012, Spain
| | - José E Pérez-Ortín
- ERI Biotecmed, Facultad de Ciencias Biológicas, Universitat de Valencia. C/ Dr. Moliner 50. E46100, Burjassot, Spain Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de Valencia. C/ Dr. Moliner 50. E46100, Burjassot, Spain
| |
Collapse
|
15
|
Protein Composition of Infectious Spores Reveals Novel Sexual Development and Germination Factors in Cryptococcus. PLoS Genet 2015; 11:e1005490. [PMID: 26313153 PMCID: PMC4551743 DOI: 10.1371/journal.pgen.1005490] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 08/07/2015] [Indexed: 11/19/2022] Open
Abstract
Spores are an essential cell type required for long-term survival across diverse organisms in the tree of life and are a hallmark of fungal reproduction, persistence, and dispersal. Among human fungal pathogens, spores are presumed infectious particles, but relatively little is known about this robust cell type. Here we used the meningitis-causing fungus Cryptococcus neoformans to determine the roles of spore-resident proteins in spore biology. Using highly sensitive nanoscale liquid chromatography/mass spectrometry, we compared the proteomes of spores and vegetative cells (yeast) and identified eighteen proteins specifically enriched in spores. The genes encoding these proteins were deleted, and the resulting strains were evaluated for discernable phenotypes. We hypothesized that spore-enriched proteins would be preferentially involved in spore-specific processes such as dormancy, stress resistance, and germination. Surprisingly, however, the majority of the mutants harbored defects in sexual development, the process by which spores are formed. One mutant in the cohort was defective in the spore-specific process of germination, showing a delay specifically in the initiation of vegetative growth. Thus, by using this in-depth proteomics approach as a screening tool for cell type-specific proteins and combining it with molecular genetics, we successfully identified the first germination factor in C. neoformans. We also identified numerous proteins with previously unknown functions in both sexual development and spore composition. Our findings provide the first insights into the basic protein components of infectious spores and reveal unexpected molecular connections between infectious particle production and spore composition in a pathogenic eukaryote.
Collapse
|
16
|
Abstract
A veritable explosion of primary research papers within the past 10 years focuses on nucleolar and ribosomal stress, and for good reason: with ribosome biosynthesis consuming ~80% of a cell’s energy, nearly all metabolic and signaling pathways lead ultimately to or from the nucleolus. We begin by describing p53 activation upon nucleolar stress resulting in cell cycle arrest or apoptosis. The significance of this mechanism cannot be understated, as oncologists are now inducing nucleolar stress strategically in cancer cells as a potential anti-cancer therapy. We also summarize the human ribosomopathies, syndromes in which ribosome biogenesis or function are impaired leading to birth defects or bone narrow failures; the perplexing problem in the ribosomopathies is why only certain cells are affected despite the fact that the causative mutation is systemic. We then describe p53-independent nucleolar stress, first in yeast which lacks p53, and then in other model metazoans that lack MDM2, the critical E3 ubiquitin ligase that normally inactivates p53. Do these presumably ancient p53-independent nucleolar stress pathways remain latent in human cells? If they still exist, can we use them to target >50% of known human cancers that lack functional p53?
Collapse
Affiliation(s)
- Allison James
- a Department of Biological Sciences; Louisiana State University; Baton Rouge, LA USA
| | | | | | | | | |
Collapse
|
17
|
Jordán-Pla A, Gupta I, de Miguel-Jiménez L, Steinmetz LM, Chávez S, Pelechano V, Pérez-Ortín JE. Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle. Nucleic Acids Res 2014; 43:787-802. [PMID: 25550430 PMCID: PMC4333398 DOI: 10.1093/nar/gku1349] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The particular behaviour of eukaryotic RNA polymerases along different gene regions and amongst distinct gene functional groups is not totally understood. To cast light onto the alternative active or backtracking states of RNA polymerase II, we have quantitatively mapped active RNA polymerases at a high resolution following a new biotin-based genomic run-on (BioGRO) technique. Compared with conventional profiling with chromatin immunoprecipitation, the analysis of the BioGRO profiles in Saccharomyces cerevisiae shows that RNA polymerase II has unique activity profiles at both gene ends, which are highly dependent on positioned nucleosomes. This is the first demonstration of the in vivo influence of positioned nucleosomes on transcription elongation. The particular features at the 5' end and around the polyadenylation site indicate that this polymerase undergoes extensive specific-activity regulation in the initial and final transcription elongation phases. The genes encoding for ribosomal proteins show distinctive features at both ends. BioGRO also provides the first nascentome analysis for RNA polymerase III, which indicates that transcription of tRNA genes is poorly regulated at the individual copy level. The present study provides a novel perspective of the transcription cycle that incorporates inactivation/reactivation as an important aspect of RNA polymerase dynamics.
Collapse
Affiliation(s)
- Antonio Jordán-Pla
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| | - Ishaan Gupta
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Lola de Miguel-Jiménez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany Stanford University School of Medicine, Department of Genetics, Stanford, CA 94305, USA Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Virgen del Rocío-CSIC-Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, 41013 Seville, Spain
| | - Vicent Pelechano
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and ERI Biotecmed, Facultad de Biológicas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain
| |
Collapse
|
18
|
Delgado-Ramos L, Marcos AT, Ramos-Guelfo MS, Sánchez-Barrionuevo L, Smet F, Chávez S, Cánovas D. Flow cytometry of microencapsulated colonies for genetics analysis of filamentous fungi. G3 (BETHESDA, MD.) 2014; 4:2271-8. [PMID: 25239104 PMCID: PMC4232552 DOI: 10.1534/g3.114.014357] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 09/13/2014] [Indexed: 11/18/2022]
Abstract
The analysis of filamentous fungi by flow cytometry has been impossible to date due to their filamentous nature and size. In this work, we have developed a method that combines single-spore microencapsulation and large-particle flow cytometry as a powerful alternative for the genetic analysis of filamentous fungi. Individual spores were embedded in monodisperse alginate microparticles and incubated in the appropriate conditions. Growth could be monitored by light or fluorescent microscopy and Complex Object Parametric Analyzer and Sorter large-particle flow cytometry. Microencapsulated Trichoderma and Aspergillus spores could germinate and grow inside the alginate capsules. Growth tests revealed that auxotrophic mutants required the appropriate nutrients and that pyrithiamine and glufosinate halted fungal growth of sensitive but not resistant strains. We used an Aspergillus nidulans, thermosensitive mutant in the cell-cycle regulator gene nimX(CDK1) as proof-of-concept to the detection and identification of genetic phenotypes. Sorting of the microparticles containing the clonal fungal mycelia proved the power of this method to perform positive and/or negative selection during genetic screenings.
Collapse
Affiliation(s)
- Lidia Delgado-Ramos
- Departamento de Genética, Hospital Universitario Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain
| | - Ana T Marcos
- Departamento de Genética, Hospital Universitario Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain
| | - María S Ramos-Guelfo
- Departamento de Genética, Hospital Universitario Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain
| | - Leyre Sánchez-Barrionuevo
- Departamento de Genética, Hospital Universitario Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain
| | | | - Sebastián Chávez
- Departamento de Genética, Hospital Universitario Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain
| | - David Cánovas
- Departamento de Genética, Hospital Universitario Virgen del Rocío-CSIC-Universidad de Sevilla, Seville, Spain
| |
Collapse
|
19
|
Millán-Zambrano G, Rodríguez-Gil A, Peñate X, de Miguel-Jiménez L, Morillo-Huesca M, Krogan N, Chávez S. The prefoldin complex regulates chromatin dynamics during transcription elongation. PLoS Genet 2013; 9:e1003776. [PMID: 24068951 PMCID: PMC3777993 DOI: 10.1371/journal.pgen.1003776] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 07/23/2013] [Indexed: 12/13/2022] Open
Abstract
Transcriptional elongation requires the concerted action of several factors that allow RNA polymerase II to advance through chromatin in a highly processive manner. In order to identify novel elongation factors, we performed systematic yeast genetic screening based on the GLAM (Gene Length-dependent Accumulation of mRNA) assay, which is used to detect defects in the expression of long transcription units. Apart from well-known transcription elongation factors, we identified mutants in the prefoldin complex subunits, which were among those that caused the most dramatic phenotype. We found that prefoldin, so far involved in the cytoplasmic co-translational assembly of protein complexes, is also present in the nucleus and that a subset of its subunits are recruited to chromatin in a transcription-dependent manner. Prefoldin influences RNA polymerase II the elongation rate in vivo and plays an especially important role in the transcription elongation of long genes and those whose promoter regions contain a canonical TATA box. Finally, we found a specific functional link between prefoldin and histone dynamics after nucleosome remodeling, which is consistent with the extensive network of genetic interactions between this factor and the machinery regulating chromatin function. This study establishes the involvement of prefoldin in transcription elongation, and supports a role for this complex in cotranscriptional histone eviction. Transcription is the biological process that allows genes to be copied into RNA; the molecule that can be read by the cell in order to fabricate its structural components, proteins. Transcription is carried out by RNA polymerases, but these molecular machines need auxiliary factors to guide them through the genome and to help them during the RNA synthesis process. We searched for novel auxiliary factors using a genetic procedure and found a set of potential novel transcriptional players. Among them, we encountered a highly unexpected result: a factor, called prefoldin, so far exclusively involved in the folding of proteins during their fabrication. We confirmed that prefoldin binds transcribed genes and plays an important role during gene transcription. We also further investigated this transcriptional role and found that prefoldin is important for unpacking genes, thus facilitating the advance of the RNA polymerases along them.
Collapse
Affiliation(s)
- Gonzalo Millán-Zambrano
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Alfonso Rodríguez-Gil
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Xenia Peñate
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Lola de Miguel-Jiménez
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Macarena Morillo-Huesca
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Sebastián Chávez
- Departmento de Genética, Universidad de Sevilla, and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
- * E-mail:
| |
Collapse
|
20
|
Gómez-Herreros F, Rodríguez-Galán O, Morillo-Huesca M, Maya D, Arista-Romero M, de la Cruz J, Chávez S, Muñoz-Centeno MC. Balanced production of ribosome components is required for proper G1/S transition in Saccharomyces cerevisiae. J Biol Chem 2013; 288:31689-700. [PMID: 24043628 DOI: 10.1074/jbc.m113.500488] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Cell cycle regulation is a very accurate process that ensures cell viability and the genomic integrity of daughter cells. A fundamental part of this regulation consists in the arrest of the cycle at particular points to ensure the completion of a previous event, to repair cellular damage, or to avoid progression in potentially risky situations. In this work, we demonstrate that a reduction in nucleotide levels or the depletion of RNA polymerase I or III subunits generates a cell cycle delay at the G1/S transition in Saccharomyces cerevisiae. This delay is concomitant with an imbalance between ribosomal RNAs and proteins which, among others, provokes an accumulation of free ribosomal protein L5. Consistently with a direct impact of free L5 on the G1/S transition, rrs1 mutants, which weaken the assembly of L5 and L11 on pre-60S ribosomal particles, enhance both the G1/S delay and the accumulation of free ribosomal protein L5. We propose the existence of a surveillance mechanism that couples the balanced production of yeast ribosomal components and cell cycle progression through the accumulation of free ribosomal proteins. This regulatory pathway resembles the p53-dependent nucleolar-stress checkpoint response described in human cells, which indicates that this is a general control strategy extended throughout eukaryotes.
Collapse
Affiliation(s)
- Fernando Gómez-Herreros
- From the Departamento de Genética, Universidad de Sevilla and Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41012 Sevilla, Spain
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Haimovich G, Medina DA, Causse SZ, Garber M, Millán-Zambrano G, Barkai O, Chávez S, Pérez-Ortín JE, Darzacq X, Choder M. Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Cell 2013; 153:1000-11. [PMID: 23706738 DOI: 10.1016/j.cell.2013.05.012] [Citation(s) in RCA: 250] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 01/03/2013] [Accepted: 05/07/2013] [Indexed: 01/14/2023]
Abstract
Maintaining proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. We demonstrate that most yeast mRNAs are degraded by the cytoplasmic 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway because defects in various decaysome components lead to transcription downregulation. Moreover, these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation. In the nucleus, they associate with chromatin-preferentially ∼30 bp upstream of transcription start-sites-and directly stimulate transcription initiation and elongation. The nuclear role of the decaysome in transcription is linked to its cytoplasmic role in mRNA decay; linkage, in turn, seems to depend on proper shuttling of its components. The gene expression process is therefore circular, whereby the hitherto first and last stages are interconnected.
Collapse
Affiliation(s)
- Gal Haimovich
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Correct assembly of RNA polymerase II depends on the foot domain and is required for multiple steps of transcription in Saccharomyces cerevisiae. Mol Cell Biol 2013; 33:3611-26. [PMID: 23836886 DOI: 10.1128/mcb.00262-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recent papers have provided insight into the cytoplasmic assembly of RNA polymerase II (RNA pol II) and its transport to the nucleus. However, little is known about the mechanisms governing its nuclear assembly, stability, degradation, and recycling. We demonstrate that the foot of RNA pol II is crucial for the assembly and stability of the complex, by ensuring the correct association of Rpb1 with Rpb6 and of the dimer Rpb4-Rpb7 (Rpb4/7). Mutations at the foot affect the assembly and stability of the enzyme, a defect that is offset by RPB6 overexpression, in coordination with Rpb1 degradation by an Asr1-independent mechanism. Correct assembly is a prerequisite for the proper maintenance of several transcription steps. In fact, assembly defects alter transcriptional activity and the amount of enzyme associated with the genes, affect C-terminal domain (CTD) phosphorylation, interfere with the mRNA-capping machinery, and possibly increase the amount of stalled RNA pol II. In addition, our data show that TATA-binding protein (TBP) occupancy does not correlate with RNA pol II occupancy or transcriptional activity, suggesting a functional relationship between assembly, Mediator, and preinitiation complex (PIC) stability. Finally, our data help clarify the mechanisms governing the assembly and stability of RNA pol II.
Collapse
|
23
|
Kaplan CD. Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:39-54. [PMID: 23022618 DOI: 10.1016/j.bbagrm.2012.09.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/18/2012] [Accepted: 09/20/2012] [Indexed: 01/12/2023]
Abstract
Transcription by RNA polymerase II (Pol II), and all RNA polymerases for that matter, may be understood as comprising two cycles. The first cycle relates to the basic mechanism of the transcription process wherein Pol II must select the appropriate nucleoside triphosphate (NTP) substrate complementary to the DNA template, catalyze phosphodiester bond formation, and translocate to the next position on the DNA template. Performing this cycle in an iterative fashion allows the synthesis of RNA chains that can be over one million nucleotides in length in some larger eukaryotes. Overlaid upon this enzymatic cycle, transcription may be divided into another cycle of three phases: initiation, elongation, and termination. Each of these phases has a large number of associated transcription factors that function to promote or regulate the gene expression process. Complicating matters, each phase of the latter transcription cycle are coincident with cotranscriptional RNA processing events. Additionally, transcription takes place within a highly dynamic and regulated chromatin environment. This chromatin environment is radically impacted by active transcription and associated chromatin modifications and remodeling, while also functioning as a major platform for Pol II regulation. This review will focus on our basic knowledge of the Pol II transcription mechanism, and how altered Pol II activity impacts gene expression in vivo in the model eukaryote Saccharomyces cerevisiae. This article is part of a Special Issue entitled: RNA Polymerase II Transcript Elongation.
Collapse
Affiliation(s)
- Craig D Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
| |
Collapse
|