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Pérez-Ortín JE, García-Marcelo MJ, Delgado-Román I, Muñoz-Centeno MC, Chávez S. Influence of cell volume on the gene transcription rate. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195008. [PMID: 38246270 DOI: 10.1016/j.bbagrm.2024.195008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Cells vary in volume throughout their life cycle and in many other circumstances, while their genome remains identical. Hence, the RNA production factory must adapt to changing needs, while maintaining the same production lines. This paradox is resolved by different mechanisms in distinct cells and circumstances. RNA polymerases have evolved to cope with the particular circumstances of each case and the different characteristics of the several RNA molecule types, especially their stabilities. Here we review current knowledge on these issues. We focus on the yeast Saccharomyces cerevisiae, where many of the studies have been performed, although we compare and discuss the results obtained in other eukaryotes and propose several ideas and questions to be tested and solved in the future. TAKE AWAY.
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Affiliation(s)
- José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain.
| | - María J García-Marcelo
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Facultad de Biológicas, Universitat de València, C/ Dr. Moliner 50, E46100 Burjassot, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Irene Delgado-Román
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - María C Muñoz-Centeno
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville 41012, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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2
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Ishikawa K. Multilayered regulation of proteome stoichiometry. Curr Genet 2021; 67:883-890. [PMID: 34382105 PMCID: PMC8592966 DOI: 10.1007/s00294-021-01205-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 01/02/2023]
Abstract
Cellular systems depend on multiprotein complexes whose functionalities require defined stoichiometries of subunit proteins. Proper stoichiometry is achieved by controlling the amount of protein synthesis and degradation even in the presence of genetic perturbations caused by changes in gene dosage. As a consequence of increased gene copy number, excess subunits unassembled into the complex are synthesized and rapidly degraded by the ubiquitin–proteasome system. This mechanism, called protein-level dosage compensation, is widely observed not only under such perturbed conditions but also in unperturbed physiological cells. Recent studies have shown that recognition of unassembled subunits and their selective degradation are intricately regulated. This review summarizes the nature, strategies, and increasing complexity of protein-level dosage compensation and discusses possible mechanisms for controlling proteome stoichiometry in multiple layers of biological processes.
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Affiliation(s)
- Koji Ishikawa
- Center for Molecular Biology, ZMBH-DKFZ Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
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3
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Bar-Ziv R, Brodsky S, Chapal M, Barkai N. Transcription Factor Binding to Replicated DNA. Cell Rep 2021; 30:3989-3995.e4. [PMID: 32209462 DOI: 10.1016/j.celrep.2020.02.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/13/2020] [Accepted: 02/27/2020] [Indexed: 11/17/2022] Open
Abstract
Genome replication perturbs the DNA regulatory environment by displacing DNA-bound proteins, replacing nucleosomes, and introducing dosage imbalance between regions replicating at different S-phase stages. Recently, we showed that these effects are integrated to maintain transcription homeostasis: replicated genes increase in dosage, but their expression remains stable due to replication-dependent epigenetic changes that suppress transcription. Here, we examine whether reduced transcription from replicated DNA results from limited accessibility to regulatory factors by measuring the time-resolved binding of RNA polymerase II (Pol II) and specific transcription factors (TFs) to DNA during S phase in budding yeast. We show that the Pol II binding pattern is largely insensitive to DNA dosage, indicating limited binding to replicated DNA. In contrast, binding of three TFs (Reb1, Abf1, and Rap1) to DNA increases with the increasing DNA dosage. We conclude that the replication-specific chromatin environment remains accessible to regulatory factors but suppresses RNA polymerase recruitment.
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Affiliation(s)
- Raz Bar-Ziv
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; The Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94720, USA
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Chapal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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Frenkel N, Jonas F, Carmi M, Yaakov G, Barkai N. Rtt109 slows replication speed by histone N-terminal acetylation. Genome Res 2021; 31:426-435. [PMID: 33563717 PMCID: PMC7919450 DOI: 10.1101/gr.266510.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/28/2020] [Indexed: 01/17/2023]
Abstract
The wrapping of DNA around histone octamers challenges processes that use DNA as their template. In vitro, DNA replication through chromatin depends on histone modifiers, raising the possibility that cells modify histones to optimize fork progression. Rtt109 is an acetyl transferase that acetylates histone H3 before its DNA incorporation on the K56 and N-terminal residues. We previously reported that, in budding yeast, a wave of histone H3 K9 acetylation progresses ∼3–5 kb ahead of the replication fork. Whether this wave contributes to replication dynamics remained unknown. Here, we show that the replication fork velocity increases following deletion of RTT109, the gene encoding the enzyme required for the prereplication H3 acetylation wave. By using histone H3 mutants, we find that Rtt109-dependent N-terminal acetylation regulates fork velocity, whereas K56 acetylation contributes to replication dynamics only when N-terminal acetylation is compromised. We propose that acetylation of newly synthesized histones slows replication by promoting replacement of nucleosomes evicted by the incoming fork, thereby protecting genome integrity.
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Affiliation(s)
- Nelly Frenkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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5
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Yubero P, Poyatos JF. The Impact of Global Transcriptional Regulation on Bacterial Gene Order. iScience 2020; 23:101029. [PMID: 32283521 PMCID: PMC7155222 DOI: 10.1016/j.isci.2020.101029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 12/15/2019] [Accepted: 03/27/2020] [Indexed: 12/04/2022] Open
Abstract
Bacterial gene expression depends on the allocation of limited transcriptional resources provided a particular growth rate and growth condition. Early studies in a few genes suggested this global regulation to generate a unifying hyperbolic expression pattern. Here, we developed a large-scale method that generalizes these experiments to quantify the response to growth of over 700 genes that a priori do not exhibit any specific control. We distinguish a core subset following a promoter-specific hyperbolic response. Within this group, we sort genes with regard to their responsiveness to the global regulatory program to show that those with a particularly sensitive linear response are located near the origin of replication. We then find evidence that this genomic architecture is biologically significant by examining position conservation of E. coli genes in 100 bacteria. The response to the transcriptional resources of the cell results in an additional feature contributing to bacterial genome organization. Cell physiology determines a global transcriptional regulatory program Constitutive genes show a differential response to this global regulation The most responsive constitutive genes are located near the origin of replication Global transcriptional regulation acts as a gene position conservation force
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Affiliation(s)
- Pablo Yubero
- Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain
| | - Juan F Poyatos
- Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain.
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6
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Dessalles R, Fromion V, Robert P. Models of protein production along the cell cycle: An investigation of possible sources of noise. PLoS One 2020; 15:e0226016. [PMID: 31945071 PMCID: PMC6964835 DOI: 10.1371/journal.pone.0226016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 11/18/2019] [Indexed: 01/20/2023] Open
Abstract
In this article, we quantitatively study, through stochastic models, the effects of several intracellular phenomena, such as cell volume growth, cell division, gene replication as well as fluctuations of available RNA polymerases and ribosomes. These phenomena are indeed rarely considered in classic models of protein production and no relative quantitative comparison among them has been performed. The parameters for a large and representative class of proteins are determined using experimental measures. The main important and surprising conclusion of our study is to show that despite the significant fluctuations of free RNA polymerases and free ribosomes, they bring little variability to protein production contrary to what has been previously proposed in the literature. After verifying the robustness of this quite counter-intuitive result, we discuss its possible origin from a theoretical view, and interpret it as the result of a mean-field effect.
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Affiliation(s)
- Renaud Dessalles
- Dept. of Biomathematics, UCLA, Los Angeles, CA, United States of America
| | - Vincent Fromion
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
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7
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Vargas–Garcia CA, Ghusinga KR, Singh A. Cell size control and gene expression homeostasis in single-cells. CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 8:109-116. [PMID: 29862376 PMCID: PMC5978733 DOI: 10.1016/j.coisb.2018.01.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Growth of a cell and its subsequent division into daughters is a fundamental aspect of all cellular living systems. During these processes, how do individual cells correct size aberrations so that they do not grow abnormally large or small? How do cells ensure that the concentration of essential gene products are maintained at desired levels, in spite of dynamic/stochastic changes in cell size during growth and division? Both these questions have fascinated researchers for over a century. We review how advances in singe-cell technologies and measurements are providing unique insights into these questions across organisms from prokaryotes to human cells. More specifically, diverse strategies based on timing of cell-cycle events, regulating growth, and number of daughters are employed to maintain cell size homeostasis. Interestingly, size homeostasis often results in size optimality - proliferation of individual cells in a population is maximized at an optimal cell size. We further discuss how size-dependent expression or gene-replication timing can buffer concentration of a gene product from cell-to-cell size variations within a population. Finally, we speculate on an intriguing hypothesis that specific size control strategies may have evolved as a consequence of gene-product concentration homeostasis.
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Affiliation(s)
- Cesar A. Vargas–Garcia
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
| | - Khem Raj Ghusinga
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, USA
- Department of Mathematical Sciences, University of Delaware, Newark, DE, USA
- Center for Applications of Mathematics in Medicine, University of Delaware, Newark, DE, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
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Abstract
For a subset of genes in our genome a change in gene dosage, by duplication or deletion, causes a phenotypic effect. These dosage-sensitive genes may confer an advantage upon copy number change, but more typically they are associated with disease, including heart disease, cancers and neuropsychiatric disorders. This gene copy number sensitivity creates characteristic evolutionary constraints that can serve as a diagnostic to identify dosage-sensitive genes. Though the link between copy number change and disease is well-established, the mechanism of pathogenicity is usually opaque. We propose that gene expression level may provide a common basis for the pathogenic effects of many copy number variants.
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Affiliation(s)
- Alan M Rice
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland.
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9
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Luo H, Xi Y, Li W, Li J, Li Y, Dong S, Peng L, Liu Y, Yu W. Cell identity bookmarking through heterogeneous chromatin landscape maintenance during the cell cycle. Hum Mol Genet 2017; 26:4231-4243. [DOI: 10.1093/hmg/ddx312] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/02/2017] [Indexed: 12/29/2022] Open
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van Boxtel C, van Heerden JH, Nordholt N, Schmidt P, Bruggeman FJ. Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments. J R Soc Interface 2017; 14:20170141. [PMID: 28701503 PMCID: PMC5550968 DOI: 10.1098/rsif.2017.0141] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/16/2017] [Indexed: 01/08/2023] Open
Abstract
Natural selection has shaped the strategies for survival and growth of microorganisms. The success of microorganisms depends not only on slow evolutionary tuning but also on the ability to adapt to unpredictable changes in their environment. In principle, adaptive strategies range from purely deterministic mechanisms to those that exploit the randomness intrinsic to many cellular and molecular processes. Depending on the environment and selective pressures, particular strategies can lie somewhere along this continuum. In recent years, non-genetic cell-to-cell differences have received a lot of attention, not least because of their potential impact on the ability of microbial populations to survive in dynamic environments. Using several examples, we describe the origins of spontaneous and induced mechanisms of phenotypic adaptation. We identify some of the commonalities of these examples and consider the potential role of chance and constraints in microbial phenotypic adaptation.
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Affiliation(s)
- Coco van Boxtel
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Johan H van Heerden
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Niclas Nordholt
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Phillipp Schmidt
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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11
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Paijmans J, Lubensky DK, Rein Ten Wolde P. Robustness of synthetic oscillators in growing and dividing cells. Phys Rev E 2017; 95:052403. [PMID: 28618495 DOI: 10.1103/physreve.95.052403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Indexed: 06/07/2023]
Abstract
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. Elowitz and Leibler [Nature (London) 403, 335 (2000)NATUAS0028-083610.1038/35002125] showed that by rational design of the reaction network, and using existing biological components, they could create a network that exhibits periodic gene expression, dubbed the repressilator. More recently, Stricker et al. [Nature (London) 456, 516 (2008)NATUAS0028-083610.1038/nature07389] presented another synthetic oscillator, called the dual-feedback oscillator, which is more stable. Detailed studies have been carried out to determine how the stability of these oscillators is affected by the intrinsic noise of the interactions between the components and the stochastic expression of their genes. However, as all biological oscillators reside in growing and dividing cells, an important question is how these oscillators are perturbed by the cell cycle. In previous work we showed that the periodic doubling of the gene copy numbers due to DNA replication can couple not only natural, circadian oscillators to the cell cycle [Paijmans et al., Proc. Natl. Acad. Sci. (USA) 113, 4063 (2016)PNASA60027-842410.1073/pnas.1507291113], but also these synthetic oscillators. Here we expand this study. We find that the strength of the locking between oscillators depends not only on the positions of the genes on the chromosome, but also on the noise in the timing of gene replication: noise tends to weaken the coupling. Yet, even in the limit of high levels of noise in the replication times of the genes, both synthetic oscillators show clear signatures of locking to the cell cycle. This work enhances our understanding of the design of robust biological oscillators inside growing and diving cells.
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Affiliation(s)
- Joris Paijmans
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - David K Lubensky
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109-1040, USA
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