1
|
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.
Collapse
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
| |
Collapse
|
2
|
Darmasaputra GS, van Rijnberk LM, Galli M. Functional consequences of somatic polyploidy in development. Development 2024; 151:dev202392. [PMID: 38415794 PMCID: PMC10946441 DOI: 10.1242/dev.202392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Polyploid cells contain multiple genome copies and arise in many animal tissues as a regulated part of development. However, polyploid cells can also arise due to cell division failure, DNA damage or tissue damage. Although polyploidization is crucial for the integrity and function of many tissues, the cellular and tissue-wide consequences of polyploidy can be very diverse. Nonetheless, many polyploid cell types and tissues share a remarkable similarity in function, providing important information about the possible contribution of polyploidy to cell and tissue function. Here, we review studies on polyploid cells in development, underlining parallel functions between different polyploid cell types, as well as differences between developmentally-programmed and stress-induced polyploidy.
Collapse
Affiliation(s)
- Gabriella S. Darmasaputra
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Lotte M. van Rijnberk
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Matilde Galli
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| |
Collapse
|
3
|
Syddall KL, Fernandez-Martell A, Cartwright JF, Alexandru-Crivac CN, Hodgson A, Racher AJ, Young RJ, James DC. Directed evolution of biomass intensive CHO cells by adaptation to sub-physiological temperature. Metab Eng 2024; 81:53-69. [PMID: 38007176 DOI: 10.1016/j.ymben.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 11/05/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023]
Abstract
We report a simple and effective means to increase the biosynthetic capacity of host CHO cells. Lonza proprietary CHOK1SV® cells were evolved by serial sub-culture for over 150 generations at 32 °C. During this period the specific proliferation rate of hypothermic cells gradually recovered to become comparable to that of cells routinely maintained at 37 °C. Cold-adapted cell populations exhibited (1) a significantly increased volume and biomass content (exemplified by total RNA and protein), (2) increased mitochondrial function, (3) an increased antioxidant capacity, (4) altered central metabolism, (5) increased transient and stable productivity of a model IgG4 monoclonal antibody and Fc-fusion protein, and (6) unaffected recombinant protein N-glycan processing. This phenotypic transformation was associated with significant genome-scale changes in both karyotype and the relative abundance of thousands of cellular mRNAs across numerous functional groups. Taken together, these observations provide evidence of coordinated cellular adaptations to sub-physiological temperature. These data reveal the extreme genomic/functional plasticity of CHO cells, and that directed evolution is a viable genome-scale cell engineering strategy that can be exploited to create host cells with an increased cellular capacity for recombinant protein production.
Collapse
Affiliation(s)
- Katie L Syddall
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, S1 3JD, UK
| | - Alejandro Fernandez-Martell
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, S1 3JD, UK
| | - Joseph F Cartwright
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, S1 3JD, UK
| | - Cristina N Alexandru-Crivac
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, S1 3JD, UK
| | - Adam Hodgson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | | | | | - David C James
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield, S1 3JD, UK.
| |
Collapse
|
4
|
Swaffer MP, Marinov GK, Zheng H, Fuentes Valenzuela L, Tsui CY, Jones AW, Greenwood J, Kundaje A, Greenleaf WJ, Reyes-Lamothe R, Skotheim JM. RNA polymerase II dynamics and mRNA stability feedback scale mRNA amounts with cell size. Cell 2023; 186:5254-5268.e26. [PMID: 37944513 DOI: 10.1016/j.cell.2023.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/16/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023]
Abstract
A fundamental feature of cellular growth is that total protein and RNA amounts increase with cell size to keep concentrations approximately constant. A key component of this is that global transcription rates increase in larger cells. Here, we identify RNA polymerase II (RNAPII) as the limiting factor scaling mRNA transcription with cell size in budding yeast, as transcription is highly sensitive to the dosage of RNAPII but not to other components of the transcriptional machinery. Our experiments support a dynamic equilibrium model where global RNAPII transcription at a given size is set by the mass action recruitment kinetics of unengaged nucleoplasmic RNAPII to the genome. However, this only drives a sub-linear increase in transcription with size, which is then partially compensated for by a decrease in mRNA decay rates as cells enlarge. Thus, limiting RNAPII and feedback on mRNA stability work in concert to scale mRNA amounts with cell size.
Collapse
Affiliation(s)
| | - Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Huan Zheng
- Department of Biology, McGill University, Montreal, QC H3G 0B1, Canada
| | | | - Crystal Yee Tsui
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | | | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|
5
|
Lanz MC, Zhang S, Swaffer MP, Hernández Götz L, McCarty F, Ziv I, Jarosz DF, Elias JE, Skotheim JM. Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562558. [PMID: 37905015 PMCID: PMC10614910 DOI: 10.1101/2023.10.16.562558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how size influences cell physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be biochemically different. Here, we corroborate these results in mouse hepatocytes and extend our analysis using yeast. We find that size-dependent proteome changes are highly conserved and mostly independent of metabolic state. As eukaryotic cells grow larger, the dilution of the genome elicits a starvation-like proteome phenotype, suggesting that growth in large cells is limited by the genome in a manner analogous to a limiting nutrient. We also demonstrate that the proteomes of replicatively-aged yeast are primarily determined by their large size. Overall, our data suggest that genome concentration is a universal determinant of proteome content in growing cells.
Collapse
|
6
|
Seel A, Padovani F, Mayer M, Finster A, Bureik D, Thoma F, Osman C, Klecker T, Schmoller KM. Regulation with cell size ensures mitochondrial DNA homeostasis during cell growth. Nat Struct Mol Biol 2023; 30:1549-1560. [PMID: 37679564 PMCID: PMC10584693 DOI: 10.1038/s41594-023-01091-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/07/2023] [Indexed: 09/09/2023]
Abstract
To maintain stable DNA concentrations, proliferating cells need to coordinate DNA replication with cell growth. For nuclear DNA, eukaryotic cells achieve this by coupling DNA replication to cell-cycle progression, ensuring that DNA is doubled exactly once per cell cycle. By contrast, mitochondrial DNA replication is typically not strictly coupled to the cell cycle, leaving the open question of how cells maintain the correct amount of mitochondrial DNA during cell growth. Here, we show that in budding yeast, mitochondrial DNA copy number increases with cell volume, both in asynchronously cycling populations and during G1 arrest. Our findings suggest that cell-volume-dependent mitochondrial DNA maintenance is achieved through nuclear-encoded limiting factors, including the mitochondrial DNA polymerase Mip1 and the packaging factor Abf2, whose amount increases in proportion to cell volume. By directly linking mitochondrial DNA maintenance to nuclear protein synthesis and thus cell growth, constant mitochondrial DNA concentrations can be robustly maintained without a need for cell-cycle-dependent regulation.
Collapse
Affiliation(s)
- Anika Seel
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Francesco Padovani
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Moritz Mayer
- Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany
| | - Alissa Finster
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Daniela Bureik
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Felix Thoma
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christof Osman
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Till Klecker
- Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany.
| |
Collapse
|
7
|
Devany J, Falk MJ, Holt LJ, Murugan A, Gardel ML. Epithelial tissue confinement inhibits cell growth and leads to volume-reducing divisions. Dev Cell 2023; 58:1462-1476.e8. [PMID: 37339629 PMCID: PMC10528006 DOI: 10.1016/j.devcel.2023.05.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 05/12/2023] [Accepted: 05/26/2023] [Indexed: 06/22/2023]
Abstract
Cell proliferation is a central process in tissue development, homeostasis, and disease, yet how proliferation is regulated in the tissue context remains poorly understood. Here, we introduce a quantitative framework to elucidate how tissue growth dynamics regulate cell proliferation. Using MDCK epithelial monolayers, we show that a limiting rate of tissue expansion creates confinement that suppresses cell growth; however, this confinement does not directly affect the cell cycle. This leads to uncoupling between rates of cell growth and division in epithelia and, thereby, reduces cell volume. Division becomes arrested at a minimal cell volume, which is consistent across diverse epithelia in vivo. Here, the nucleus approaches the minimum volume capable of packaging the genome. Loss of cyclin D1-dependent cell-volume regulation results in an abnormally high nuclear-to-cytoplasmic volume ratio and DNA damage. Overall, we demonstrate how epithelial proliferation is regulated by the interplay between tissue confinement and cell-volume regulation.
Collapse
Affiliation(s)
- John Devany
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA; James Franck Institute, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Martin J Falk
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA; James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Liam J Holt
- Institute for Systems Genetics, New York University, Grossman School of Medicine, New York, NY 10016, USA
| | - Arvind Murugan
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA; James Franck Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Margaret L Gardel
- Department of Physics, The University of Chicago, Chicago, IL 60637, USA; James Franck Institute, The University of Chicago, Chicago, IL 60637, USA; Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
8
|
Miller KE, Vargas-Garcia C, Singh A, Moseley JB. The fission yeast cell size control system integrates pathways measuring cell surface area, volume, and time. Curr Biol 2023; 33:3312-3324.e7. [PMID: 37463585 PMCID: PMC10529673 DOI: 10.1016/j.cub.2023.06.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023]
Abstract
Eukaryotic cells tightly control their size, but the relevant aspect of size is unknown in most cases. Fission yeast divide at a threshold cell surface area (SA) due, in part, to the protein kinase Cdr2. We find that fission yeast cells only divide by SA under a size threshold. Mutants that divide at a larger size shift to volume-based divisions. Diploid cells divide at a larger size than haploid cells do, but they maintain SA-based divisions, and this indicates that the size threshold for changing from surface-area-based to volume-based control is set by ploidy. Within this size control system, we found that the mitotic activator Cdc25 accumulates like a volume-based sizer molecule, whereas the mitotic cyclin Cdc13 accumulates in the nucleus as a timer. We propose an integrated model for cell size control based on multiple signaling pathways that report on distinct aspects of cell size and growth, including cell SA (Cdr2), cell volume (Cdc25), and time (Cdc13). Combined modeling and experiments show how this system can generate both sizer- and adder-like properties.
Collapse
Affiliation(s)
- Kristi E Miller
- Department of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Cesar Vargas-Garcia
- Grupo de Investigación en Sistemas Agropecuarios Sostenibles, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá 250047, Colombia
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
| | - James B Moseley
- Department of Biochemistry and Cell Biology, The Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
| |
Collapse
|
9
|
Biondo M, Singh A, Caselle M, Osella M. Out-of-equilibrium gene expression fluctuations in the presence of extrinsic noise. Phys Biol 2023; 20:10.1088/1478-3975/acea4e. [PMID: 37489881 PMCID: PMC10680095 DOI: 10.1088/1478-3975/acea4e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/25/2023] [Indexed: 07/26/2023]
Abstract
Cell-to-cell variability in protein concentrations is strongly affected by extrinsic noise, especially for highly expressed genes. Extrinsic noise can be due to fluctuations of several possible cellular factors connected to cell physiology and to the level of key enzymes in the expression process. However, how to identify the predominant sources of extrinsic noise in a biological system is still an open question. This work considers a general stochastic model of gene expression with extrinsic noise represented as fluctuations of the different model rates, and focuses on the out-of-equilibrium expression dynamics. Combining analytical calculations with stochastic simulations, we characterize how extrinsic noise shapes the protein variability during gene activation or inactivation, depending on the prevailing source of extrinsic variability, on its intensity and timescale. In particular, we show that qualitatively different noise profiles can be identified depending on which are the fluctuating parameters. This indicates an experimentally accessible way to pinpoint the dominant sources of extrinsic noise using time-coarse experiments.
Collapse
Affiliation(s)
- Marta Biondo
- Department of Physics, University of Turin and INFN, via P. Giuria 1, I-10125 Turin, Italy
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, Department of Biomedical Engineering, Department of Mathematical Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, United States of America
| | - Michele Caselle
- Department of Physics, University of Turin and INFN, via P. Giuria 1, I-10125 Turin, Italy
| | - Matteo Osella
- Department of Physics, University of Turin and INFN, via P. Giuria 1, I-10125 Turin, Italy
| |
Collapse
|
10
|
Weidemann DE, Holehouse J, Singh A, Grima R, Hauf S. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. SCIENCE ADVANCES 2023; 9:eadh5138. [PMID: 37556551 PMCID: PMC10411910 DOI: 10.1126/sciadv.adh5138] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023]
Abstract
Gene expression inherently gives rise to stochastic variation ("noise") in the production of gene products. Minimizing noise is crucial for ensuring reliable cellular functions. However, noise cannot be suppressed below a certain intrinsic limit. For constitutively expressed genes, this limit is typically assumed to be Poissonian noise, wherein the variance in mRNA numbers is equal to their mean. Here, we demonstrate that several cell division genes in fission yeast exhibit mRNA variances significantly below this limit. The reduced variance can be explained by a gene expression model incorporating multiple transcription and mRNA degradation steps. Notably, in this sub-Poissonian regime, distinct from Poissonian or super-Poissonian regimes, cytoplasmic noise is effectively suppressed through a higher mRNA export rate. Our findings redefine the lower limit of eukaryotic gene expression noise and uncover molecular requirements for achieving ultralow noise, which is expected to be important for vital cellular functions.
Collapse
Affiliation(s)
- Douglas E. Weidemann
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - James Holehouse
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87510, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Silke Hauf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| |
Collapse
|
11
|
Ji X, Lin J. Implications of differential size-scaling of cell-cycle regulators on cell size homeostasis. PLoS Comput Biol 2023; 19:e1011336. [PMID: 37506170 PMCID: PMC10411824 DOI: 10.1371/journal.pcbi.1011336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 08/09/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Accurate timing of division and size homeostasis is crucial for cells. A potential mechanism for cells to decide the timing of division is the differential scaling of regulatory protein copy numbers with cell size. However, it remains unclear whether such a mechanism can lead to robust growth and division, and how the scaling behaviors of regulatory proteins influence the cell size distribution. Here we study a mathematical model combining gene expression and cell growth, in which the cell-cycle activators scale superlinearly with cell size while the inhibitors scale sublinearly. The cell divides once the ratio of their concentrations reaches a threshold value. We find that the cell can robustly grow and divide within a finite range of the threshold value with the cell size proportional to the ploidy. In a stochastic version of the model, the cell size at division is uncorrelated with that at birth. Also, the more differential the cell-size scaling of the cell-cycle regulators is, the narrower the cell-size distribution is. Intriguingly, our model with multiple regulators rationalizes the observation that after the deletion of a single regulator, the coefficient of variation of cell size remains roughly the same though the average cell size changes significantly. Our work reveals that the differential scaling of cell-cycle regulators provides a robust mechanism of cell size control.
Collapse
Affiliation(s)
- Xiangrui Ji
- Yuanpei College, Peking University, Beijing, China
| | - Jie Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| |
Collapse
|
12
|
Alonso-Sáez L, Palacio AS, Cabello AM, Robaina-Estévez S, González JM, Garczarek L, López-Urrutia Á. Transcriptional Mechanisms of Thermal Acclimation in Prochlorococcus. mBio 2023:e0342522. [PMID: 37052490 DOI: 10.1128/mbio.03425-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30°C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17°C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones. IMPORTANCE Prochlorococcus is a major marine primary producer with a global impact on atmospheric CO2 fixation. This cyanobacterium is widely distributed across the temperate ocean, but virtually absent at latitudes above 40° for yet unknown reasons. Temperature has been suggested as a major limiting factor, but the exact mechanisms behind Prochlorococcus thermal growth restriction remain unexplored. This study brings us closer to understanding how Prochlorococcus functions under challenging temperature conditions, by focusing on its transcriptional response after long-term acclimation from its optimum to its thermal thresholds. Our results show that the drop in Prochlorococcus growth rate under cold conditions was paralleled by a transcriptional suppression of the photosynthetic machinery during daytime and a loss in the organism's regulatory capacity to maintain circadian expression patterns. Notably, warm temperature induced a marked shrinkage of the organism's cellular transcript inventory, which may also induce regulatory imbalances in the future functioning of this cyanobacterium.
Collapse
Affiliation(s)
- Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Antonio S Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ana M Cabello
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, IEO-CSIC, Gijón, Asturias, Spain
| |
Collapse
|
13
|
Weidemann DE, Singh A, Grima R, Hauf S. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531283. [PMID: 36945401 PMCID: PMC10028819 DOI: 10.1101/2023.03.06.531283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Stochastic variation in gene products ("noise") is an inescapable by-product of gene expression. Noise must be minimized to allow for the reliable execution of cellular functions. However, noise cannot be suppressed beyond an intrinsic lower limit. For constitutively expressed genes, this limit is believed to be Poissonian, meaning that the variance in mRNA numbers cannot be lower than their mean. Here, we show that several cell division genes in fission yeast have mRNA variances significantly below this limit, which cannot be explained by the classical gene expression model for low-noise genes. Our analysis reveals that multiple steps in both transcription and mRNA degradation are essential to explain this sub-Poissonian variance. The sub-Poissonian regime differs qualitatively from previously characterized noise regimes, a hallmark being that cytoplasmic noise is reduced when the mRNA export rate increases. Our study re-defines the lower limit of eukaryotic gene expression noise and identifies molecular requirements for ultra-low noise which are expected to support essential cell functions.
Collapse
Affiliation(s)
- Douglas E Weidemann
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE 19716, USA
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, Scotland, UK
| | - Silke Hauf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USA
| |
Collapse
|
14
|
Terhorst A, Sandikci A, Whittaker CA, Szórádi T, Holt LJ, Neurohr GE, Amon A. The environmental stress response regulates ribosome content in cell cycle-arrested S. cerevisiae. Front Cell Dev Biol 2023; 11:1118766. [PMID: 37123399 PMCID: PMC10130656 DOI: 10.3389/fcell.2023.1118766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/21/2023] [Indexed: 05/02/2023] Open
Abstract
Prolonged cell cycle arrests occur naturally in differentiated cells and in response to various stresses such as nutrient deprivation or treatment with chemotherapeutic agents. Whether and how cells survive prolonged cell cycle arrests is not clear. Here, we used S. cerevisiae to compare physiological cell cycle arrests and genetically induced arrests in G1-, meta- and anaphase. Prolonged cell cycle arrest led to growth attenuation in all studied conditions, coincided with activation of the Environmental Stress Response (ESR) and with a reduced ribosome content as determined by whole ribosome purification and TMT mass spectrometry. Suppression of the ESR through hyperactivation of the Ras/PKA pathway reduced cell viability during prolonged arrests, demonstrating a cytoprotective role of the ESR. Attenuation of cell growth and activation of stress induced signaling pathways also occur in arrested human cell lines, raising the possibility that the response to prolonged cell cycle arrest is conserved.
Collapse
Affiliation(s)
- Allegra Terhorst
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Arzu Sandikci
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Charles A. Whittaker
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tamás Szórádi
- Institute for Systems Genetics, New York University Langone Health, New York City, NY, United States
| | - Liam J. Holt
- Institute for Systems Genetics, New York University Langone Health, New York City, NY, United States
| | - Gabriel E. Neurohr
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- *Correspondence: Gabriel E. Neurohr,
| | - Angelika Amon
- David H. Koch Institute for Integrative Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States
| |
Collapse
|
15
|
Jia C, Grima R. Coupling gene expression dynamics to cell size dynamics and cell cycle events: Exact and approximate solutions of the extended telegraph model. iScience 2022; 26:105746. [PMID: 36619980 PMCID: PMC9813732 DOI: 10.1016/j.isci.2022.105746] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/02/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The standard model describing the fluctuations of mRNA numbers in single cells is the telegraph model which includes synthesis and degradation of mRNA, and switching of the gene between active and inactive states. While commonly used, this model does not describe how fluctuations are influenced by the cell cycle phase, cellular growth and division, and other crucial aspects of cellular biology. Here, we derive the analytical time-dependent solution of an extended telegraph model that explicitly considers the doubling of gene copy numbers upon DNA replication, dependence of the mRNA synthesis rate on cellular volume, gene dosage compensation, partitioning of molecules during cell division, cell-cycle duration variability, and cell-size control strategies. Based on the time-dependent solution, we obtain the analytical distributions of transcript numbers for lineage and population measurements in steady-state growth and also find a linear relation between the Fano factor of mRNA fluctuations and cell volume fluctuations. We show that generally the lineage and population distributions in steady-state growth cannot be accurately approximated by the steady-state solution of extrinsic noise models, i.e. a telegraph model with parameters drawn from probability distributions. This is because the mRNA lifetime is often not small enough compared to the cell cycle duration to erase the memory of division and replication. Accurate approximations are possible when this memory is weak, e.g. for genes with bursty expression and for which there is sufficient gene dosage compensation when replication occurs.
Collapse
Affiliation(s)
- Chen Jia
- Applied and Computational Mathematics Division, Beijing Computational Science Research Center, Beijing 100193, China
| | - Ramon Grima
- School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK,Corresponding author
| |
Collapse
|
16
|
Balachandra S, Sarkar S, Amodeo AA. The Nuclear-to-Cytoplasmic Ratio: Coupling DNA Content to Cell Size, Cell Cycle, and Biosynthetic Capacity. Annu Rev Genet 2022; 56:165-185. [PMID: 35977407 PMCID: PMC10165727 DOI: 10.1146/annurev-genet-080320-030537] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Though cell size varies between different cells and across species, the nuclear-to-cytoplasmic (N/C) ratio is largely maintained across species and within cell types. A cell maintains a relatively constant N/C ratio by coupling DNA content, nuclear size, and cell size. We explore how cells couple cell division and growth to DNA content. In some cases, cells use DNA as a molecular yardstick to control the availability of cell cycle regulators. In other cases, DNA sets a limit for biosynthetic capacity. Developmentally programmed variations in the N/C ratio for a given cell type suggest that a specific N/C ratio is required to respond to given physiological demands. Recent observations connecting decreased N/C ratios with cellular senescence indicate that maintaining the proper N/C ratio is essential for proper cellular functioning. Together, these findings suggest a causative, not simply correlative, role for the N/C ratio in regulating cell growth and cell cycle progression.
Collapse
Affiliation(s)
- Shruthi Balachandra
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA; ,
| | - Sharanya Sarkar
- Department of Microbiology and Immunology, Dartmouth College, Hanover, New Hampshire, USA;
| | - Amanda A Amodeo
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA; ,
| |
Collapse
|
17
|
Abstract
The most fundamental feature of cellular form is size, which sets the scale of all cell biological processes. Growth, form, and function are all necessarily linked in cell biology, but we often do not understand the underlying molecular mechanisms nor their specific functions. Here, we review progress toward determining the molecular mechanisms that regulate cell size in yeast, animals, and plants, as well as progress toward understanding the function of cell size regulation. It has become increasingly clear that the mechanism of cell size regulation is deeply intertwined with basic mechanisms of biosynthesis, and how biosynthesis can be scaled (or not) in proportion to cell size. Finally, we highlight recent findings causally linking aberrant cell size regulation to cellular senescence and their implications for cancer therapies.
Collapse
Affiliation(s)
- Shicong Xie
- Department of Biology, Stanford University, Stanford, California, USA;
| | - Matthew Swaffer
- Department of Biology, Stanford University, Stanford, California, USA;
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, California, USA;
- Chan Zuckerberg Biohub, San Francisco, California, USA
| |
Collapse
|
18
|
Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis. PLoS Comput Biol 2022; 18:e1010574. [PMID: 36194626 PMCID: PMC9565450 DOI: 10.1371/journal.pcbi.1010574] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/14/2022] [Accepted: 09/14/2022] [Indexed: 11/19/2022] Open
Abstract
Intracellular reaction rates depend on concentrations and hence their levels are often regulated. However classical models of stochastic gene expression lack a cell size description and cannot be used to predict noise in concentrations. Here, we construct a model of gene product dynamics that includes a description of cell growth, cell division, size-dependent gene expression, gene dosage compensation, and size control mechanisms that can vary with the cell cycle phase. We obtain expressions for the approximate distributions and power spectra of concentration fluctuations which lead to insight into the emergence of concentration homeostasis. We find that (i) the conditions necessary to suppress cell division-induced concentration oscillations are difficult to achieve; (ii) mRNA concentration and number distributions can have different number of modes; (iii) two-layer size control strategies such as sizer-timer or adder-timer are ideal because they maintain constant mean concentrations whilst minimising concentration noise; (iv) accurate concentration homeostasis requires a fine tuning of dosage compensation, replication timing, and size-dependent gene expression; (v) deviations from perfect concentration homeostasis show up as deviations of the concentration distribution from a gamma distribution. Some of these predictions are confirmed using data for E. coli, fission yeast, and budding yeast.
Collapse
|
19
|
Zatulovskiy E, Lanz MC, Zhang S, McCarthy F, Elias JE, Skotheim JM. Delineation of proteome changes driven by cell size and growth rate. Front Cell Dev Biol 2022; 10:980721. [PMID: 36133920 PMCID: PMC9483106 DOI: 10.3389/fcell.2022.980721] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/09/2022] [Indexed: 01/10/2023] Open
Abstract
Increasing cell size drives changes to the proteome, which affects cell physiology. As cell size increases, some proteins become more concentrated while others are diluted. As a result, the state of the cell changes continuously with increasing size. In addition to these proteomic changes, large cells have a lower growth rate (protein synthesis rate per unit volume). That both the cell’s proteome and growth rate change with cell size suggests they may be interdependent. To test this, we used quantitative mass spectrometry to measure how the proteome changes in response to the mTOR inhibitor rapamycin, which decreases the cellular growth rate and has only a minimal effect on cell size. We found that large cell size and mTOR inhibition, both of which lower the growth rate of a cell, remodel the proteome in similar ways. This suggests that many of the effects of cell size are mediated by the size-dependent slowdown of the cellular growth rate. For example, the previously reported size-dependent expression of some senescence markers could reflect a cell’s declining growth rate rather than its size per se. In contrast, histones and other chromatin components are diluted in large cells independently of the growth rate, likely so that they remain in proportion with the genome. Finally, size-dependent changes to the cell’s growth rate and proteome composition are still apparent in cells continually exposed to a saturating dose of rapamycin, which indicates that cell size can affect the proteome independently of mTORC1 signaling. Taken together, our results clarify the dependencies between cell size, growth, mTOR activity, and the proteome remodeling that ultimately controls many aspects of cell physiology.
Collapse
Affiliation(s)
| | - Michael C. Lanz
- Department of Biology, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, Stanford, CA, United States
| | - Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA, United States
| | | | | | - Jan M. Skotheim
- Department of Biology, Stanford University, Stanford, CA, United States
- Chan Zuckerberg Biohub, Stanford, CA, United States
- *Correspondence: Jan M. Skotheim,
| |
Collapse
|
20
|
Lanz MC, Zatulovskiy E, Swaffer MP, Zhang L, Ilerten I, Zhang S, You DS, Marinov G, McAlpine P, Elias JE, Skotheim JM. Increasing cell size remodels the proteome and promotes senescence. Mol Cell 2022; 82:3255-3269.e8. [PMID: 35987199 PMCID: PMC9444988 DOI: 10.1016/j.molcel.2022.07.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/06/2022] [Accepted: 07/25/2022] [Indexed: 01/10/2023]
Abstract
Cell size is tightly controlled in healthy tissues, but it is unclear how deviations in cell size affect cell physiology. To address this, we measured how the cell's proteome changes with increasing cell size. Size-dependent protein concentration changes are widespread and predicted by subcellular localization, size-dependent mRNA concentrations, and protein turnover. As proliferating cells grow larger, concentration changes typically associated with cellular senescence are increasingly pronounced, suggesting that large size may be a cause rather than just a consequence of cell senescence. Consistent with this hypothesis, larger cells are prone to replicative, DNA-damage-induced, and CDK4/6i-induced senescence. Size-dependent changes to the proteome, including those associated with senescence, are not observed when an increase in cell size is accompanied by an increase in ploidy. Together, our findings show how cell size could impact many aspects of cell physiology by remodeling the proteome and provide a rationale for cell size control and polyploidization.
Collapse
Affiliation(s)
- Michael C Lanz
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, Stanford, CA 94305, USA
| | | | | | | | - Ilayda Ilerten
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Shuyuan Zhang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Dong Shin You
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Georgi Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | | | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
21
|
Burkart V, Kowalski K, Aldag-Niebling D, Beck J, Frick DA, Holler T, Radocaj A, Piep B, Zeug A, Hilfiker-Kleiner D, dos Remedios CG, van der Velden J, Montag J, Kraft T. Transcriptional bursts and heterogeneity among cardiomyocytes in hypertrophic cardiomyopathy. Front Cardiovasc Med 2022; 9:987889. [PMID: 36082122 PMCID: PMC9445301 DOI: 10.3389/fcvm.2022.987889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/02/2022] [Indexed: 12/01/2022] Open
Abstract
Transcriptional bursting is a common expression mode for most genes where independent transcription of alleles leads to different ratios of allelic mRNA from cell to cell. Here we investigated burst-like transcription and its consequences in cardiac tissue from Hypertrophic Cardiomyopathy (HCM) patients with heterozygous mutations in the sarcomeric proteins cardiac myosin binding protein C (cMyBP-C, MYBPC3) and cardiac troponin I (cTnI, TNNI3). Using fluorescence in situ hybridization (RNA-FISH) we found that both, MYBPC3 and TNNI3 are transcribed burst-like. Along with that, we show unequal allelic ratios of TNNI3-mRNA among single cardiomyocytes and unequally distributed wildtype cMyBP-C protein across tissue sections from heterozygous HCM-patients. The mutations led to opposing functional alterations, namely increasing (cMyBP-Cc.927−2A>G) or decreasing (cTnIR145W) calcium sensitivity. Regardless, all patients revealed highly variable calcium-dependent force generation between individual cardiomyocytes, indicating contractile imbalance, which appears widespread in HCM-patients. Altogether, we provide strong evidence that burst-like transcription of sarcomeric genes can lead to an allelic mosaic among neighboring cardiomyocytes at mRNA and protein level. In HCM-patients, this presumably induces the observed contractile imbalance among individual cardiomyocytes and promotes HCM-development.
Collapse
Affiliation(s)
- Valentin Burkart
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
- Valentin Burkart
| | - Kathrin Kowalski
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - David Aldag-Niebling
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Julia Beck
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Dirk Alexander Frick
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Tim Holler
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Ante Radocaj
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Birgit Piep
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| | - Andre Zeug
- Institute for Cellular Neurophysiology, Hannover Medical School, Hannover, Germany
| | | | - Cristobal G. dos Remedios
- Mechanosensory Biophysics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | | | - Judith Montag
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
- *Correspondence: Judith Montag
| | - Theresia Kraft
- Institute for Molecular and Cell Physiology, Hannover Medical School, Hannover, Germany
| |
Collapse
|
22
|
Esposito E, Weidemann DE, Rogers JM, Morton CM, Baybay EK, Chen J, Hauf S. Mitotic checkpoint gene expression is tuned by codon usage bias. EMBO J 2022; 41:e107896. [PMID: 35811551 PMCID: PMC9340482 DOI: 10.15252/embj.2021107896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022] Open
Abstract
The mitotic checkpoint (also called spindle assembly checkpoint, SAC) is a signaling pathway that safeguards proper chromosome segregation. Correct functioning of the SAC depends on adequate protein concentrations and appropriate stoichiometries between SAC proteins. Yet very little is known about the regulation of SAC gene expression. Here, we show in the fission yeast Schizosaccharomyces pombe that a combination of short mRNA half-lives and long protein half-lives supports stable SAC protein levels. For the SAC genes mad2+ and mad3+ , their short mRNA half-lives are caused, in part, by a high frequency of nonoptimal codons. In contrast, mad1+ mRNA has a short half-life despite a higher frequency of optimal codons, and despite the lack of known RNA-destabilizing motifs. Hence, different SAC genes employ different strategies of expression. We further show that Mad1 homodimers form co-translationally, which may necessitate a certain codon usage pattern. Taken together, we propose that the codon usage of SAC genes is fine-tuned to ensure proper SAC function. Our work shines light on gene expression features that promote spindle assembly checkpoint function and suggests that synonymous mutations may weaken the checkpoint.
Collapse
Affiliation(s)
- Eric Esposito
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Douglas E Weidemann
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Jessie M Rogers
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Claire M Morton
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Erod Keaton Baybay
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Jing Chen
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Silke Hauf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.,Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| |
Collapse
|
23
|
García-Ruano D, Venkova L, Jain A, Ryan JC, Balasubramaniam VR, Piel M, Coudreuse D. Fluorescence exclusion: a rapid, accurate and powerful method for measuring yeast cell volume. J Cell Sci 2022; 135:275598. [PMID: 35662333 DOI: 10.1242/jcs.259392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/26/2022] [Indexed: 11/20/2022] Open
Abstract
Cells exist in an astonishing range of volumes across and within species. However, our understanding of cell size control remains limited, due in large part to the challenges associated with accurate determination of cell volume. Much of our comprehension of size regulation derives from yeast models, but even for these morphologically stereotypical cells, assessment of cell volume has mostly relied on proxies and extrapolations from two-dimensional measurements. Recently, the fluorescence exclusion method (FXm) was developed to evaluate the size of mammalian cells, but whether it could be applied to smaller cells remained unknown. Using specifically designed microfluidic chips and an improved data analysis pipeline, we show here that FXm reliably detects subtle differences in the volume of fission yeast cells, even for those with altered shapes. Moreover, it allows for the monitoring of dynamic volume changes at the single-cell level with high time resolution. Collectively, our work highlights how the coupling of FXm with yeast genetics will bring new insights into the complex biology of cell growth.
Collapse
Affiliation(s)
- Daniel García-Ruano
- Institute of Genetics and Development of Rennes, UMR 6290, CNRS - University of Rennes 1, France
| | - Larisa Venkova
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS UMR 144, Paris, France.,Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, Bordeaux, France
| | - Akanksha Jain
- Institute of Genetics and Development of Rennes, UMR 6290, CNRS - University of Rennes 1, France
| | - Joseph C Ryan
- Institute of Genetics and Development of Rennes, UMR 6290, CNRS - University of Rennes 1, France
| | | | - Matthieu Piel
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS UMR 144, Paris, France
| | - Damien Coudreuse
- Institute of Genetics and Development of Rennes, UMR 6290, CNRS - University of Rennes 1, France.,Institute of Biochemistry and Cellular Genetics, CNRS UMR 5095, Bordeaux, France
| |
Collapse
|
24
|
Mechanisms of cellular mRNA transcript homeostasis. Trends Cell Biol 2022; 32:655-668. [PMID: 35660047 DOI: 10.1016/j.tcb.2022.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022]
Abstract
For most genes, mRNA transcript abundance scales with cell size to ensure a constant concentration. Scaling of mRNA synthesis rates with cell size plays an important role, with regulation of the activity and abundance of RNA polymerase II (Pol II) now emerging as a key point of control. However, there is also considerable evidence for feedback mechanisms that kinetically couple the rates of mRNA synthesis, nuclear export, and degradation to allow cells to compensate for changes in one by adjusting the others. Researchers are beginning to integrate results from these different fields to reveal the mechanisms underlying transcript homeostasis. This will be crucial for moving beyond our current understanding of relative gene expression towards an appreciation of how absolute transcript levels are linked to other aspects of the cellular phenotype.
Collapse
|
25
|
Berry S, Müller M, Rai A, Pelkmans L. Feedback from nuclear RNA on transcription promotes robust RNA concentration homeostasis in human cells. Cell Syst 2022; 13:454-470.e15. [PMID: 35613616 DOI: 10.1016/j.cels.2022.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/13/2021] [Accepted: 04/21/2022] [Indexed: 12/18/2022]
Abstract
RNA concentration homeostasis involves coordinating RNA abundance and synthesis rates with cell size. Here, we study this in human cells by combining genome-wide perturbations with quantitative single-cell measurements. Despite relative ease in perturbing RNA synthesis, we find that RNA concentrations generally remain highly constant. Perturbations that would be expected to increase nuclear mRNA levels, including those targeting nuclear mRNA degradation or export, result in downregulation of RNA synthesis. This is associated with reduced abundance of transcription-associated proteins and protein states that are normally coordinated with RNA production in single cells, including RNA polymerase II (RNA Pol II) itself. Acute perturbations, elevation of nuclear mRNA levels, and mathematical modeling indicate that mammalian cells achieve robust mRNA concentration homeostasis by the mRNA-based negative feedback on transcriptional activity in the nucleus. This ultimately acts to coordinate RNA Pol II abundance with nuclear mRNA degradation and export rates and may underpin the scaling of mRNA abundance with cell size.
Collapse
Affiliation(s)
- Scott Berry
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - Micha Müller
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Arpan Rai
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
26
|
Population balance modelling captures host cell protein dynamics in CHO cell cultures. PLoS One 2022; 17:e0265886. [PMID: 35320326 PMCID: PMC8959726 DOI: 10.1371/journal.pone.0265886] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/09/2022] [Indexed: 11/19/2022] Open
Abstract
Monoclonal antibodies (mAbs) have been extensively studied for their wide therapeutic and research applications. Increases in mAb titre has been achieved mainly by cell culture media/feed improvement and cell line engineering to increase cell density and specific mAb productivity. However, this improvement has shifted the bottleneck to downstream purification steps. The higher accumulation of the main cell-derived impurities, host cell proteins (HCPs), in the supernatant can negatively affect product integrity and immunogenicity in addition to increasing the cost of capture and polishing steps. Mathematical modelling of bioprocess dynamics is a valuable tool to improve industrial production at fast rate and low cost. Herein, a single stage volume-based population balance model (PBM) has been built to capture Chinese hamster ovary (CHO) cell behaviour in fed-batch bioreactors. Using cell volume as the internal variable, the model captures the dynamics of mAb and HCP accumulation extracellularly under physiological and mild hypothermic culture conditions. Model-based analysis and orthogonal measurements of lactate dehydrogenase activity and double-stranded DNA concentration in the supernatant show that a significant proportion of HCPs found in the extracellular matrix is secreted by viable cells. The PBM then served as a platform for generating operating strategies that optimise antibody titre and increase cost-efficiency while minimising impurity levels.
Collapse
|
27
|
Zhivkoplias EK, Vavulov O, Hillerton T, Sonnhammer ELL. Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops. Front Genet 2022; 13:815692. [PMID: 35222536 PMCID: PMC8872634 DOI: 10.3389/fgene.2022.815692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/13/2022] [Indexed: 11/13/2022] Open
Abstract
The regulatory relationships between genes and proteins in a cell form a gene regulatory network (GRN) that controls the cellular response to changes in the environment. A number of inference methods to reverse engineer the original GRN from large-scale expression data have recently been developed. However, the absence of ground-truth GRNs when evaluating the performance makes realistic simulations of GRNs necessary. One aspect of this is that local network motif analysis of real GRNs indicates that the feed-forward loop (FFL) is significantly enriched. To simulate this properly, we developed a novel motif-based preferential attachment algorithm, FFLatt, which outperformed the popular GeneNetWeaver network generation tool in reproducing the FFL motif occurrence observed in literature-based biological GRNs. It also preserves important topological properties such as scale-free topology, sparsity, and average in/out-degree per node. We conclude that FFLatt is well-suited as a network generation module for a benchmarking framework with the aim to provide fair and robust performance evaluation of GRN inference methods.
Collapse
Affiliation(s)
- Erik K. Zhivkoplias
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Oleg Vavulov
- Bioinformatics Institute, St. Petersburg, Russia
| | - Thomas Hillerton
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Erik L. L. Sonnhammer
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
- *Correspondence: Erik L. L. Sonnhammer,
| |
Collapse
|
28
|
Swaffer MP, Kim J, Chandler-Brown D, Langhinrichs M, Marinov GK, Greenleaf WJ, Kundaje A, Schmoller KM, Skotheim JM. Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size. Mol Cell 2021; 81:4861-4875.e7. [PMID: 34731644 PMCID: PMC8642314 DOI: 10.1016/j.molcel.2021.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/01/2021] [Accepted: 10/11/2021] [Indexed: 10/19/2022]
Abstract
Biosynthesis scales with cell size such that protein concentrations generally remain constant as cells grow. As an exception, synthesis of the cell-cycle inhibitor Whi5 "sub-scales" with cell size so that its concentration is lower in larger cells to promote cell-cycle entry. Here, we find that transcriptional control uncouples Whi5 synthesis from cell size, and we identify histones as the major class of sub-scaling transcripts besides WHI5 by screening for similar genes. Histone synthesis is thereby matched to genome content rather than cell size. Such sub-scaling proteins are challenged by asymmetric cell division because proteins are typically partitioned in proportion to newborn cell volume. To avoid this fate, Whi5 uses chromatin-binding to partition similar protein amounts to each newborn cell regardless of cell size. Disrupting both Whi5 synthesis and chromatin-based partitioning weakens G1 size control. Thus, specific transcriptional and partitioning mechanisms determine protein sub-scaling to control cell size.
Collapse
Affiliation(s)
| | - Jacob Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kurt M Schmoller
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
29
|
Wang Q, Lin J. Heterogeneous recruitment abilities to RNA polymerases generate nonlinear scaling of gene expression with cell volume. Nat Commun 2021; 12:6852. [PMID: 34824198 PMCID: PMC8617254 DOI: 10.1038/s41467-021-26952-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 10/27/2021] [Indexed: 11/09/2022] Open
Abstract
While most genes' expression levels are proportional to cell volumes, some genes exhibit nonlinear scaling between their expression levels and cell volume. Therefore, their mRNA and protein concentrations change as the cell volume increases, which often have crucial biological functions such as cell-cycle regulation. However, the biophysical mechanism underlying the nonlinear scaling between gene expression and cell volume is still unclear. In this work, we show that the nonlinear scaling is a direct consequence of the heterogeneous recruitment abilities of promoters to RNA polymerases based on a gene expression model at the whole-cell level. Those genes with weaker (stronger) recruitment abilities than the average ability spontaneously exhibit superlinear (sublinear) scaling with cell volume. Analysis of the promoter sequences and the nonlinear scaling of Saccharomyces cerevisiae's mRNA levels shows that motifs associated with transcription regulation are indeed enriched in genes exhibiting nonlinear scaling, in concert with our model.
Collapse
Affiliation(s)
- Qirun Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jie Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| |
Collapse
|
30
|
Carrier M, Šimončičová E, St-Pierre MK, McKee C, Tremblay MÈ. Psychological Stress as a Risk Factor for Accelerated Cellular Aging and Cognitive Decline: The Involvement of Microglia-Neuron Crosstalk. Front Mol Neurosci 2021; 14:749737. [PMID: 34803607 PMCID: PMC8599581 DOI: 10.3389/fnmol.2021.749737] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022] Open
Abstract
The relationship between the central nervous system (CNS) and microglia is lifelong. Microglia originate in the embryonic yolk sac during development and populate the CNS before the blood-brain barrier forms. In the CNS, they constitute a self-renewing population. Although they represent up to 10% of all brain cells, we are only beginning to understand how much brain homeostasis relies on their physiological functions. Often compared to a double-edged sword, microglia hold the potential to exert neuroprotective roles that can also exacerbate neurodegeneration once compromised. Microglia can promote synaptic growth in addition to eliminating synapses that are less active. Synaptic loss, which is considered one of the best pathological correlates of cognitive decline, is a distinctive feature of major depressive disorder (MDD) and cognitive aging. Long-term psychological stress accelerates cellular aging and predisposes to various diseases, including MDD, and cognitive decline. Among the underlying mechanisms, stress-induced neuroinflammation alters microglial interactions with the surrounding parenchymal cells and exacerbates oxidative burden and cellular damage, hence inducing changes in microglia and neurons typical of cognitive aging. Focusing on microglial interactions with neurons and their synapses, this review discusses the disrupted communication between these cells, notably involving fractalkine signaling and the triggering receptor expressed on myeloid cells (TREM). Overall, chronic stress emerges as a key player in cellular aging by altering the microglial sensome, notably via fractalkine signaling deficiency. To study cellular aging, novel positron emission tomography radiotracers for TREM and the purinergic family of receptors show interest for human study.
Collapse
Affiliation(s)
- Micaël Carrier
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada.,Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Eva Šimončičová
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Marie-Kim St-Pierre
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Department of Molecular Medicine, Université Laval, Québec City, QC, Canada
| | - Chloe McKee
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Marie-Ève Tremblay
- Axe Neurosciences, Centre de Recherche du CHU de Québec, Université Laval, Québec City, QC, Canada.,Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Department of Molecular Medicine, Université Laval, Québec City, QC, Canada.,Neurology and Neurosurgery Department, McGill University, Montreal, QC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
31
|
Diaz-Muñoz MD, Osma-Garcia IC. The RNA regulatory programs that govern lymphocyte development and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1683. [PMID: 34327847 DOI: 10.1002/wrna.1683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/25/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022]
Abstract
Lymphocytes require of constant and dynamic changes in their transcriptome for timely activation and production of effector molecules to combat external pathogens. Synthesis and translation of messenger (m)RNAs into these effector proteins is controlled both quantitatively and qualitatively by RNA binding proteins (RBPs). RBP-dependent regulation of RNA editing, subcellular location, stability, and translation shapes immune cell development and immunity. Extensive evidences have now been gathered from few model RBPs, HuR, PTBP1, ZFP36, and Roquin. However, recently developed methodologies for global characterization of protein:RNA interactions suggest the existence of complex RNA regulatory networks in which RBPs co-ordinately regulate the fate of sets of RNAs controlling cellular pathways and functions. In turn, RNA can also act as scaffolding of functionally related proteins modulating their activation and function. Here we review current knowledge about how RBP-dependent regulation of RNA shapes our immune system and discuss about the existence of a hidden immune cell epitranscriptome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Manuel D Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
| | - Ines C Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
| |
Collapse
|
32
|
Claude KL, Bureik D, Chatzitheodoridou D, Adarska P, Singh A, Schmoller KM. Transcription coordinates histone amounts and genome content. Nat Commun 2021; 12:4202. [PMID: 34244507 PMCID: PMC8270936 DOI: 10.1038/s41467-021-24451-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
Biochemical reactions typically depend on the concentrations of the molecules involved, and cell survival therefore critically depends on the concentration of proteins. To maintain constant protein concentrations during cell growth, global mRNA and protein synthesis rates are tightly linked to cell volume. While such regulation is appropriate for most proteins, certain cellular structures do not scale with cell volume. The most striking example of this is the genomic DNA, which doubles during the cell cycle and increases with ploidy, but is independent of cell volume. Here, we show that the amount of histone proteins is coupled to the DNA content, even though mRNA and protein synthesis globally increase with cell volume. As a consequence, and in contrast to the global trend, histone concentrations decrease with cell volume but increase with ploidy. We find that this distinct coordination of histone homeostasis and genome content is already achieved at the transcript level, and is an intrinsic property of histone promoters that does not require direct feedback mechanisms. Mathematical modeling and histone promoter truncations reveal a simple and generalizable mechanism to control the cell volume- and ploidy-dependence of a given gene through the balance of the initiation and elongation rates.
Collapse
Affiliation(s)
- Kora-Lee Claude
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Daniela Bureik
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | - Petia Adarska
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Abhyudai Singh
- Department of Electrical & Computer Engineering, University of Delaware, Newark, DE, USA
| | - Kurt M Schmoller
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Neuherberg, Germany.
| |
Collapse
|
33
|
Prasad V, Millay DP. Skeletal muscle fibers count on nuclear numbers for growth. Semin Cell Dev Biol 2021; 119:3-10. [PMID: 33972174 DOI: 10.1016/j.semcdb.2021.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/30/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
Abstract
Skeletal muscle cells are noteworthy for their syncytial nature, with each myofiber accumulating hundreds or thousands of nuclei derived from resident muscle stem cells (MuSCs). These nuclei are accrued through cell fusion, which is controlled by the two essential fusogens Myomaker and Myomerger that are transiently expressed within the myogenic lineage. While the absolute requirement of fusion for muscle development has been known for decades, the underlying need for the magnitude of multinucleation in muscle remains mysterious. Possible advantages of multinucleation include the potential it affords for transcriptional diversity within these massive cells, and as a means of increasing DNA content to support optimal cell size and function. In this article, we review recent advances that elucidate the relationship between myonuclear numbers and establishment of myofiber size, and discuss how this new information refines our understanding of the concept of myonuclear domains (MND), the cytoplasmic volumes that each resident myonucleus can support. Finally, we explore the potential consequences and costs of multinucleation and its impacts on myonuclear transcriptional reserve capacity, growth potential, myofiber size regulation, and muscle adaptability. We anticipate this report will not only serve to highlight the latest advances in the basic biology of syncytial muscle cells but also provide information to help design the next generation of therapeutic strategies to maintain muscle mass and function.
Collapse
Affiliation(s)
- Vikram Prasad
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Douglas P Millay
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
| |
Collapse
|
34
|
Barba-Aliaga M, Alepuz P, Pérez-Ortín JE. Eukaryotic RNA Polymerases: The Many Ways to Transcribe a Gene. Front Mol Biosci 2021; 8:663209. [PMID: 33968992 PMCID: PMC8097091 DOI: 10.3389/fmolb.2021.663209] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/09/2021] [Indexed: 01/04/2023] Open
Abstract
In eukaryotic cells, three nuclear RNA polymerases (RNA pols) carry out the transcription from DNA to RNA, and they all seem to have evolved from a single enzyme present in the common ancestor with archaea. The multiplicity of eukaryotic RNA pols allows each one to remain specialized in the synthesis of a subset of transcripts, which are different in the function, length, cell abundance, diversity, and promoter organization of the corresponding genes. We hypothesize that this specialization of RNA pols has conditioned the evolution of the regulatory mechanisms used to transcribe each gene subset to cope with environmental changes. We herein present the example of the homeostatic regulation of transcript levels versus changes in cell volume. We propose that the diversity and instability of messenger RNAs, transcribed by RNA polymerase II, have conditioned the appearance of regulatory mechanisms based on different gene promoter strength and mRNA stability. However, for the regulation of ribosomal RNA levels, which are very stable and transcribed mainly by RNA polymerase I from only one promoter, different mechanisms act based on gene copy variation, and a much simpler regulation of the synthesis rate.
Collapse
Affiliation(s)
- Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, València, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, València, Spain
| | - Paula Alepuz
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, València, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, València, Spain
| | - José E Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, València, Spain.,Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universitat de València, València, Spain
| |
Collapse
|
35
|
Pérez-Ortín JE, Mena A, Barba-Aliaga M, Singh A, Chávez S, García-Martínez J. Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast. PLoS Genet 2021; 17:e1009520. [PMID: 33826644 PMCID: PMC8055003 DOI: 10.1371/journal.pgen.1009520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/19/2021] [Accepted: 03/25/2021] [Indexed: 01/20/2023] Open
Abstract
The adjustment of transcription and translation rates to the changing needs of cells is of utmost importance for their fitness and survival. We have previously shown that the global transcription rate for RNA polymerase II in budding yeast Saccharomyces cerevisiae is regulated in relation to cell volume. Total mRNA concentration is constant with cell volume since global RNApol II-dependent nascent transcription rate (nTR) also keeps constant but mRNA stability increases with cell size. In this paper, we focus on the case of rRNA and RNA polymerase I. Contrarily to that found for RNA pol II, we detected that RNA polymerase I nTR increases proportionally to genome copies and cell size in polyploid cells. In haploid mutant cells with larger cell sizes, the rDNA repeat copy number rises. By combining mathematical modeling and experimental work with the large-size cln3 strain, we observed that the increasing repeat copy number is based on a feedback mechanism in which Sir2 histone deacetylase homeostatically controls the amplification of rDNA repeats in a volume-dependent manner. This amplification is paralleled with an increase in rRNA nTR, which indicates a control of the RNA pol I synthesis rate by cell volume. Synthesis rates of biological macromolecules should be strictly regulated and adjusted to the changing conditions of cells. The change in volume is one of the commonest variables along individual cell life and also when comparing different cell types. We previously found that cells with asymmetric division, such as budding yeasts, use a compensatory change in the global RNA polymerase II synthesis rate and mRNA decay rate to maintain mRNA homeostasis. In the present study, we address the same issue for the RNA polymerase that makes rRNAs, which are essential components of ribosomes and the most abundant RNAs in the cell. We found that the copy number of the gene encoding 35S rRNA, transcribed by RNA polymerase I, changes proportionally to the cell volume in budding yeast via a feedback mechanism based on the Sir2 histone deacetylase, which guarantees that yeast cells have the appropriate RNA polymerase I synthesis rate required for rRNA homeostasis.
Collapse
Affiliation(s)
- José E. Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
- * E-mail: (JEP-O); (JG-M)
| | - Adriana Mena
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
| | - Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, United States of America
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla. Campus Hospital Universitario Virgen del Rocío, Seville, Spain
| | - José García-Martínez
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
- * E-mail: (JEP-O); (JG-M)
| |
Collapse
|
36
|
Kohram M, Vashistha H, Leibler S, Xue B, Salman H. Bacterial Growth Control Mechanisms Inferred from Multivariate Statistical Analysis of Single-Cell Measurements. Curr Biol 2021; 31:955-964.e4. [PMID: 33357764 DOI: 10.1016/j.cub.2020.11.063] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/12/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022]
Abstract
Analysis of single-cell measurements of bacterial growth and division often relied on testing preconceived models of cell size control mechanisms. Such an approach could limit the scope of data analysis and prevent us from uncovering new information. Here, we take an "agnostic" approach by applying regression methods to multiple simultaneously measured cellular variables, which allow us to infer dependencies among those variables from their apparent correlations. Besides previously observed correlations attributed to particular cell size control mechanisms, we identify dependencies that point to potentially new mechanisms. In particular, cells born smaller than their sisters tend to grow faster and make up for the size difference acquired during division. We also find that sister cells are correlated beyond what single-cell, size-control models predict. These trends are consistently found in repeat experiments, although the dependencies vary quantitatively. Such variation highlights the sensitivity of cell growth to environmental variations and the limitation of currently used experimental setups.
Collapse
Affiliation(s)
- Maryam Kohram
- Department of Physics and Astronomy, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Harsh Vashistha
- Department of Physics and Astronomy, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Stanislas Leibler
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA; Laboratory of Living Matter and Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA
| | - BingKan Xue
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA; Laboratory of Living Matter and Center for Studies in Physics and Biology, The Rockefeller University, New York, NY 10065, USA.
| | - Hanna Salman
- Department of Physics and Astronomy, Kenneth P. Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| |
Collapse
|
37
|
Picard K, St-Pierre MK, Vecchiarelli HA, Bordeleau M, Tremblay MÈ. Neuroendocrine, neuroinflammatory and pathological outcomes of chronic stress: A story of microglial remodeling. Neurochem Int 2021; 145:104987. [PMID: 33587954 DOI: 10.1016/j.neuint.2021.104987] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 02/07/2023]
Abstract
Microglia, the resident macrophage cells of the central nervous system (CNS), are involved in a myriad of processes required to maintain CNS homeostasis. These cells are dynamic and can adapt their phenotype and functions to the physiological needs of the organism. Microglia rapidly respond to changes occurring in their microenvironment, such as the ones taking place during stress. While stress can be beneficial for the organism to adapt to a situation, it can become highly detrimental when it turns chronic. Microglial response to prolonged stress may lead to an alteration of their beneficial physiological functions, becoming either maladaptive or pro-inflammatory. In this review, we aim to summarize the effects of chronic stress exerted on microglia through the neuroendocrine system and inflammation at adulthood. We also discuss how these effects of chronic stress could contribute to microglial involvement in neuropsychiatric and sleep disorders, as well as neurodegenerative diseases.
Collapse
Affiliation(s)
- Katherine Picard
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Division of Medical Sciences, University of Victoria, Victoria, BC, Canada; Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Marie-Kim St-Pierre
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Division of Medical Sciences, University of Victoria, Victoria, BC, Canada; Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | | | - Maude Bordeleau
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Marie-Ève Tremblay
- Axe Neurosciences, Centre de recherche du CHU de Québec-Université Laval, Québec, QC, Canada; Division of Medical Sciences, University of Victoria, Victoria, BC, Canada; Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada; Neurology and Neurosurgery Department, McGill University, Montréal, QC, Canada; Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada.
| |
Collapse
|
38
|
Cramer AAW, Prasad V, Eftestøl E, Song T, Hansson KA, Dugdale HF, Sadayappan S, Ochala J, Gundersen K, Millay DP. Nuclear numbers in syncytial muscle fibers promote size but limit the development of larger myonuclear domains. Nat Commun 2020; 11:6287. [PMID: 33293533 PMCID: PMC7722938 DOI: 10.1038/s41467-020-20058-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 10/30/2020] [Indexed: 12/11/2022] Open
Abstract
Mammalian cells exhibit remarkable diversity in cell size, but the factors that regulate establishment and maintenance of these sizes remain poorly understood. This is especially true for skeletal muscle, comprised of syncytial myofibers that each accrue hundreds of nuclei during development. Here, we directly explore the assumed causal relationship between multinucleation and establishment of normal size through titration of myonuclear numbers during mouse neonatal development. Three independent mouse models, where myonuclear numbers were reduced by 75, 55, or 25%, led to the discovery that myonuclei possess a reserve capacity to support larger functional cytoplasmic volumes in developing myofibers. Surprisingly, the results revealed an inverse relationship between nuclei numbers and reserve capacity. We propose that as myonuclear numbers increase, the range of transcriptional return on a per nuclear basis in myofibers diminishes, which accounts for both the absolute reliance developing myofibers have on nuclear accrual to establish size, and the limits of adaptability in adult skeletal muscle.
Collapse
Affiliation(s)
- Alyssa A W Cramer
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Vikram Prasad
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Einar Eftestøl
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Taejeong Song
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Kenth-Arne Hansson
- Department of Biosciences, University of Oslo, Oslo, Norway
- Center for Integrative Neuroplasticity (CINPLA), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Hannah F Dugdale
- Center of Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sakthivel Sadayappan
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Julien Ochala
- Center of Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
- Randall Center for Cell and Molecular Biophysics, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, Guy's Campus, King's College London, London, UK
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Douglas P Millay
- Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
| |
Collapse
|
39
|
Chen Y, Futcher B. Scaling gene expression for cell size control and senescence in Saccharomyces cerevisiae. Curr Genet 2020; 67:41-47. [PMID: 33151380 PMCID: PMC7886820 DOI: 10.1007/s00294-020-01098-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/08/2020] [Accepted: 07/15/2020] [Indexed: 11/29/2022]
Abstract
Cells divide with appropriate frequency by coupling division to growth—that is, cells divide only when they have grown sufficiently large. This process is poorly understood, but has been studied using cell size mutants. In principle, mutations affecting cell size could affect the mean size (“set-point” mutants), or they could affect the variability of sizes (“homeostasis” mutants). In practice, almost all known size mutants affect set-point, with little effect on size homeostasis. One model for size-dependent division depends on a size-dependent gene expression program: Activators of cell division are over-expressed at larger and larger sizes, while inhibitors are under-expressed. At sufficiently large size, activators overcome inhibitors, and the cell divides. Amounts of activators and inhibitors determine the set-point, but the gene expression program (the rate at which expression changes with cell size) determines the breadth of the size distribution (homeostasis). In this model, set-point mutants identify cell cycle activators and inhibitors, while homeostasis mutants identify regulators that couple expression of activators and inhibitors to size. We consider recent results suggesting that increased cell size causes senescence, and suggest that at very large sizes, an excess of DNA binding proteins leads to size induced senescence.
Collapse
Affiliation(s)
- Yuping Chen
- Department of Chemical and Systems Biology, Stanford Medicine, Stanford, CA, 94305-5174, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, 11794-5222, USA.
| |
Collapse
|
40
|
Landis JB, Kurti A, Lawhorn AJ, Litt A, McCarthy EW. Differential Gene Expression with an Emphasis on Floral Organ Size Differences in Natural and Synthetic Polyploids of Nicotiana tabacum (Solanaceae). Genes (Basel) 2020; 11:E1097. [PMID: 32961813 PMCID: PMC7563459 DOI: 10.3390/genes11091097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
Abstract
Floral organ size, especially the size of the corolla, plays an important role in plant reproduction by facilitating pollination efficiency. Previous studies have outlined a hypothesized organ size pathway. However, the expression and function of many of the genes in the pathway have only been investigated in model diploid species; therefore, it is unknown how these genes interact in polyploid species. Although correlations between ploidy and cell size have been shown in many systems, it is unclear whether there is a difference in cell size between naturally occurring and synthetic polyploids. To address these questions comparing floral organ size and cell size across ploidy, we use natural and synthetic polyploids of Nicotiana tabacum (Solanaceae) as well as their known diploid progenitors. We employ a comparative transcriptomics approach to perform analyses of differential gene expression, focusing on candidate genes that may be involved in floral organ size, both across developmental stages and across accessions. We see differential expression of several known floral organ candidate genes including ARF2, BIG BROTHER, and GASA/GAST1. Results from linear models show that ploidy, cell width, and cell number positively influence corolla tube circumference; however, the effect of cell width varies by ploidy, and diploids have a significantly steeper slope than both natural and synthetic polyploids. These results demonstrate that polyploids have wider cells and that polyploidy significantly increases corolla tube circumference.
Collapse
Affiliation(s)
- Jacob B. Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
| | - Amelda Kurti
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
| | - Amber J. Lawhorn
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
| | - Amy Litt
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
| | - Elizabeth W. McCarthy
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
- Department of Biology, SUNY Cortland, Cortland, NY 13045, USA
| |
Collapse
|
41
|
Gu Y, Oliferenko S. The principles of cellular geometry scaling. Curr Opin Cell Biol 2020; 68:20-27. [PMID: 32950004 DOI: 10.1016/j.ceb.2020.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 01/11/2023]
Abstract
Cellular dimensions profoundly influence cellular physiology. For unicellular organisms, this has direct bearing on their ecology and evolution. The morphology of a cell is governed by scaling rules. As it grows, the ratio of its surface area to volume is expected to decrease. Similarly, if environmental conditions force proliferating cells to settle on different size optima, cells of the same type may exhibit size-dependent variation in cellular processes. In fungi, algae and plants where cells are surrounded by a rigid wall, division at smaller size often produces immediate changes in geometry, decreasing cell fitness. Here, we discuss how cells interpret their size, buffer against changes in shape and, if necessary, scale their polarity to maintain optimal shape at different cell volumes.
Collapse
Affiliation(s)
- Ying Gu
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK
| | - Snezhana Oliferenko
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK; Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, SE1 1UL, UK.
| |
Collapse
|
42
|
Gene Transcription as a Limiting Factor in Protein Production and Cell Growth. G3-GENES GENOMES GENETICS 2020; 10:3229-3242. [PMID: 32694199 PMCID: PMC7466996 DOI: 10.1534/g3.120.401303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cell growth is driven by the synthesis of proteins, genes, and other cellular components. Defining processes that limit biosynthesis rates is fundamental for understanding the determinants of cell physiology. Here, we analyze the consequences of engineering cells to express extremely high levels of mCherry proteins, as a tool to define limiting processes that fail to adapt upon increasing biosynthetic demands. Protein-burdened cells were transcriptionally and phenotypically similar to mutants of the Mediator, a transcription coactivator complex. However, our binding data suggest that the Mediator was not depleted from endogenous promoters. Burdened cells showed an overall increase in the abundance of the majority of endogenous transcripts, except for highly expressed genes. Our results, supported by mathematical modeling, suggest that wild-type cells transcribe highly expressed genes at the maximal possible rate, as defined by the transcription machinery’s physical properties. We discuss the possible cellular benefit of maximal transcription rates to allow a coordinated optimization of cell size and cell growth.
Collapse
|
43
|
Song Q, Ando A, Jiang N, Ikeda Y, Chen ZJ. Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes. Genome Biol 2020; 21:178. [PMID: 32698836 PMCID: PMC7375004 DOI: 10.1186/s13059-020-02094-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/06/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Polyploidy provides new genetic material that facilitates evolutionary novelty, species adaptation, and crop domestication. Polyploidy often leads to an increase in cell or organism size, which may affect transcript abundance or transcriptome size, but the relationship between polyploidy and transcriptome changes remains poorly understood. Plant cells often undergo endoreduplication, confounding the polyploid effect. RESULTS To mitigate these effects, we select female gametic cells that are developmentally stable and void of endoreduplication. Using single-cell RNA sequencing (scRNA-seq) in Arabidopsis thaliana tetraploid lines and isogenic diploids, we show that transcriptome abundance doubles in the egg cell and increases approximately 1.6-fold in the central cell, consistent with cell size changes. In the central cell of tetraploid plants, DEMETER (DME) is upregulated, which can activate PRC2 family members FIS2 and MEA, and may suppress the expression of other genes. Upregulation of cell size regulators in tetraploids, including TOR and OSR2, may increase the size of reproductive cells. In diploids, the order of transcriptome abundance is central cell, synergid cell, and egg cell, consistent with their cell size variation. Remarkably, we uncover new sets of female gametophytic cell-specific transcripts with predicted biological roles; the most abundant transcripts encode families of cysteine-rich peptides, implying roles in cell-cell recognition during double fertilization. CONCLUSIONS Transcriptome in single cells doubles in tetraploid plants compared to diploid, while the degree of change and relationship to the cell size depends on cell types. These scRNA-seq resources are free of cross-contamination and are uniquely valuable for advancing plant hybridization, reproductive biology, and polyploid genomics.
Collapse
Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Atsumi Ando
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA
| | - Ning Jiang
- Department of Biomedical Engineering, The University of Texas at Austin, 1 University Station C0800, Austin, TX, 78712, USA
| | - Yoko Ikeda
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Okayama, 710-0046, Japan
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, 1 University Station A5000, Austin, TX, 78712, USA.
| |
Collapse
|
44
|
Zatulovskiy E, Skotheim JM. On the Molecular Mechanisms Regulating Animal Cell Size Homeostasis. Trends Genet 2020; 36:360-372. [PMID: 32294416 PMCID: PMC7162994 DOI: 10.1016/j.tig.2020.01.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 12/19/2022]
Abstract
Cell size is fundamental to cell physiology because it sets the scale of intracellular geometry, organelles, and biosynthetic processes. In animal cells, size homeostasis is controlled through two phenomenologically distinct mechanisms. First, size-dependent cell cycle progression ensures that smaller cells delay cell cycle progression to accumulate more biomass than larger cells prior to cell division. Second, size-dependent cell growth ensures that larger and smaller cells grow slower per unit mass than more optimally sized cells. This decade has seen dramatic progress in single-cell technologies establishing the diverse phenomena of cell size control in animal cells. Here, we review this recent progress and suggest pathways forward to determine the underlying molecular mechanisms.
Collapse
Affiliation(s)
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
45
|
Chen Y, Zhao G, Zahumensky J, Honey S, Futcher B. Differential Scaling of Gene Expression with Cell Size May Explain Size Control in Budding Yeast. Mol Cell 2020; 78:359-370.e6. [PMID: 32246903 DOI: 10.1016/j.molcel.2020.03.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 12/14/2019] [Accepted: 03/10/2020] [Indexed: 01/25/2023]
Abstract
Yeast cells must grow to a critical size before committing to division. It is unknown how size is measured. We find that as cells grow, mRNAs for some cell-cycle activators scale faster than size, increasing in concentration, while mRNAs for some inhibitors scale slower than size, decreasing in concentration. Size-scaled gene expression could cause an increasing ratio of activators to inhibitors with size, triggering cell-cycle entry. Consistent with this, expression of the CLN2 activator from the promoter of the WHI5 inhibitor, or vice versa, interfered with cell size homeostasis, yielding a broader distribution of cell sizes. We suggest that size homeostasis comes from differential scaling of gene expression with size. Differential regulation of gene expression as a function of cell size could affect many cellular processes.
Collapse
Affiliation(s)
- Yuping Chen
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Gang Zhao
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Jakub Zahumensky
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, Prague 142 20, Czech Republic
| | - Sangeet Honey
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA.
| |
Collapse
|
46
|
Size-Dependent Increase in RNA Polymerase II Initiation Rates Mediates Gene Expression Scaling with Cell Size. Curr Biol 2020; 30:1217-1230.e7. [DOI: 10.1016/j.cub.2020.01.053] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/01/2019] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
|
47
|
Abstract
The hallmark of most cardiac diseases is the progressive loss of cardiomyocytes. In the perinatal period, cardiomyocytes still proliferate, and the heart shows the capacity to regenerate upon injury. In the adult heart, however, the actual rate of cardiomyocyte renewal is too low to efficiently counteract substantial cell loss caused by cardiac injury. In mammals, cardiac growth by cell number expansion changes to growth by cardiomyocyte enlargement soon after birth, coinciding with a period in which most cardiomyocytes increase their DNA content by multinucleation and nuclear polyploidization. Although cardiomyocyte hypertrophy is often associated with these processes, whether polyploidy is a prerequisite or a consequence of hypertrophic growth is unclear. Both the benefits of cardiomyocyte enlargement over proliferative growth of the heart and the physiological role of polyploidy in cardiomyocytes are enigmatic. Interestingly, hearts in animal species with substantial cardiac regenerative capacity dominantly comprise diploid cardiomyocytes, raising the hypothesis that cardiomyocyte polyploidy poses a barrier for cardiomyocyte proliferation and subsequent heart regeneration. On the contrary, there is also evidence for self-duplication of multinucleated myocytes, suggesting a more complex picture of polyploidy in heart regeneration. Polyploidy is not restricted to the heart but also occurs in other cell types in the body. In this review, we explore the biological relevance of polyploidy in different species and tissues to acquire insight into its specific role in cardiomyocytes. Furthermore, we speculate about the physiological role of polyploidy in cardiomyocytes and how this might relate to renewal and regeneration.
Collapse
Affiliation(s)
- Wouter Derks
- From the Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany (W.D., O.B.)
| | - Olaf Bergmann
- From the Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany (W.D., O.B.).,Karolinska Institutet, Cell and Molecular Biology, Stockholm, Sweden (O.B.)
| |
Collapse
|
48
|
Relevance and Regulation of Cell Density. Trends Cell Biol 2020; 30:213-225. [PMID: 31980346 DOI: 10.1016/j.tcb.2019.12.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 01/05/2023]
Abstract
Cell density shows very little variation within a given cell type. For example, in humans variability in cell density among cells of a given cell type is 100 times smaller than variation in cell mass. This tight control indicates that maintenance of a cell type-specific cell density is important for cell function. Indeed, pathological conditions such as cellular senescence are accompanied by changes in cell density. Despite the apparent importance of cell-type-specific density, we know little about how cell density affects cell function, how it is controlled, and how it sometimes changes as part of a developmental process or in response to changes in the environment. The recent development of new technologies to accurately measure the cell density of single cells in suspension and in tissues is likely to provide answers to these important questions.
Collapse
|
49
|
Abstract
The genetic control of the characteristic cell sizes of different species and tissues is a long-standing enigma. Plants are convenient for studying this question in a multicellular context, as their cells do not move and are easily tracked and measured from organ initiation in the meristems to subsequent morphogenesis and differentiation. In this article, we discuss cell size control in plants compared with other organisms. As seen from yeast cells to mammalian cells, size homeostasis is maintained cell autonomously in the shoot meristem. In developing organs, vacuolization contributes to cell size heterogeneity and may resolve conflicts between growth control at the cellular and organ levels. Molecular mechanisms for cell size control have implications for how cell size responds to changes in ploidy, which are particularly important in plant development and evolution. We also discuss comparatively the functional consequences of cell size and their potential repercussions at higher scales, including genome evolution.
Collapse
Affiliation(s)
- Marco D'Ario
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Robert Sablowski
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| |
Collapse
|
50
|
Berenson DF, Zatulovskiy E, Xie S, Skotheim JM. Constitutive expression of a fluorescent protein reports the size of live human cells. Mol Biol Cell 2019; 30:2985-2995. [PMID: 31599704 PMCID: PMC6857566 DOI: 10.1091/mbc.e19-03-0171] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 09/20/2019] [Accepted: 10/01/2019] [Indexed: 11/11/2022] Open
Abstract
Cell size is important for cell physiology because it sets the geometric scale of organelles and biosynthesis. A number of methods exist to measure different aspects of cell size, but each has significant drawbacks. Here, we present an alternative method to measure the size of single human cells using a nuclear localized fluorescent protein expressed from a constitutive promoter. We validate this method by comparing it to several established cell size measurement strategies, including flow cytometry optical scatter, total protein dyes, and quantitative phase microscopy. We directly compare our fluorescent protein measurement with the commonly used measurement of nuclear volume and show that our measurements are more robust and less dependent on image segmentation. We apply our method to examine how cell size impacts the cell division cycle and reaffirm that there is a negative correlation between size at cell birth and G1 duration. Importantly, combining our size reporter with fluorescent labeling of a different protein in a different color channel allows measurement of concentration dynamics using simple wide-field fluorescence imaging. Thus, we expect our method will be of use to researchers interested in how dynamically changing protein concentrations control cell fates.
Collapse
Affiliation(s)
| | | | - Shicong Xie
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Jan M. Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305
| |
Collapse
|