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Griego A, Douché T, Gianetto QG, Matondo M, Manina G. RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness. iScience 2022; 25:104233. [PMID: 35521527 PMCID: PMC9062218 DOI: 10.1016/j.isci.2022.104233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 12/26/2022] Open
Abstract
RNA turnover is a primary source of gene expression variation, in turn promoting cellular adaptation. Mycobacteria leverage reversible mRNA stabilization to endure hostile conditions. Although RNase E is essential for RNA turnover in several species, its role in mycobacterial single-cell physiology and functional phenotypic diversification remains unexplored. Here, by integrating live-single-cell and quantitative-mass-spectrometry approaches, we show that RNase E forms dynamic foci, which are associated with cellular homeostasis and fate, and we discover a versatile molecular interactome. We show a likely interaction between RNase E and the nucleoid-associated protein HupB, which is particularly pronounced during drug treatment and infection, where phenotypic diversity increases. Disruption of RNase E expression affects HupB levels, impairing Mycobacterium tuberculosis growth homeostasis during treatment, intracellular replication, and host spread. Our work lays the foundation for targeting the RNase E and its partner HupB, aiming to undermine M. tuberculosis cellular balance, diversification capacity, and persistence. Single mycobacterial cells exhibit phenotypic variation in RNase E expression RNase E is implicated in the maintenance of mycobacterial cell growth homeostasis RNase E and HupB show a functional interplay in single mycobacterial cells RNase E-HupB disruption impairs Mycobacterium tuberculosis fate under drug and in macrophages
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Arbel-Goren R, Di Patti F, Fanelli D, Stavans J. Noise⁻Seeded Developmental Pattern Formation in Filamentous Cyanobacteria. Life (Basel) 2018; 8:life8040058. [PMID: 30423937 PMCID: PMC6316479 DOI: 10.3390/life8040058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/24/2018] [Accepted: 11/05/2018] [Indexed: 11/16/2022] Open
Abstract
Under nitrogen-poor conditions, multicellular cyanobacteria such as Anabaena sp. PCC 7120 undergo a process of differentiation, forming nearly regular, developmental patterns of individual nitrogen-fixing cells, called heterocysts, interspersed between intervals of vegetative cells that carry out photosynthesis. Developmental pattern formation is mediated by morphogen species that can act as activators and inhibitors, some of which can diffuse along filaments. We survey the limitations of the classical, deterministic Turing mechanism that has been often invoked to explain pattern formation in these systems, and then, focusing on a simpler system governed by birth-death processes, we illustrate pedagogically a recently proposed paradigm that provides a much more robust description of pattern formation: stochastic Turing patterns. We emphasize the essential role that cell-to-cell differences in molecular numbers—caused by inevitable fluctuations in gene expression—play, the so called demographic noise, in seeding the formation of stochastic Turing patterns over a much larger region of parameter space, compared to their deterministic counterparts.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Francesca Di Patti
- Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali, Dip. di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Firenze, Italy.
- Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, via G. Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy.
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse, via G. Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy.
| | - Duccio Fanelli
- Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, via G. Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy.
- Centro Interdipartimentale per lo Studio delle Dinamiche Complesse, via G. Sansone 1, 50019 Sesto Fiorentino, Firenze, Italy.
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Firenze, Italy.
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Valentini M, Gonzalez D, Mavridou DA, Filloux A. Lifestyle transitions and adaptive pathogenesis of Pseudomonas aeruginosa. Curr Opin Microbiol 2017; 41:15-20. [PMID: 29166621 DOI: 10.1016/j.mib.2017.11.006] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/31/2017] [Accepted: 11/04/2017] [Indexed: 02/06/2023]
Abstract
Pseudomonas aeruginosa acute and chronic infections are of great concern to human health, especially in hospital settings. It is currently assumed that P. aeruginosa has two antagonistic pathogenic strategies that parallel two different lifestyles; free-living cells are predominantly cytotoxic and induce an acute inflammatory reaction, while biofilm-forming communities cause refractory chronic infections. Recent findings suggest that the planktonic-to-sessile transition is a complex, reversible and overall dynamic differentiation process. Here, we examine how the Gac/Rsm regulatory cascade, a key player in this lifestyle switch, endows P. aeruginosa with both a permissive lifecycle in nature and flexible virulence strategy during infection.
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Affiliation(s)
- Martina Valentini
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom.
| | - Diego Gonzalez
- Département de Microbiologie Fondamentale, Université de Lausanne, CH-1015 Lausanne, Switzerland
| | - Despoina Ai Mavridou
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Microbiology and Infection, Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom.
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Ramanouskaya TV, Grinev VV. The determinants of alternative RNA splicing in human cells. Mol Genet Genomics 2017; 292:1175-1195. [PMID: 28707092 DOI: 10.1007/s00438-017-1350-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022]
Abstract
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.
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Jaquet V, Hsu C, Becskei A. Measurement of bistability in a multidimensional parameter space. Integr Biol (Camb) 2017; 9:167-177. [PMID: 28134382 DOI: 10.1039/c6ib00242k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bistability plays an important role to generate two stable states for alternative cell fates, or to promote cellular diversity and cell cycle oscillations. Positive feedback loops are necessary for the existence of bistability and ultrasensitive reactions in the loops broaden the parameter range of bistability. The broader parameter range a system's bistability covers, the more robust the two states are. It is challenging to determine the bistable range of a parameter because noise and transient processes induce transitions between the two states. We found that a threshold of transition rates coincides with the bistability boundaries determined by the open-loop approach. With this threshold, we estimated the boundaries for various synthetic single-gene positive feedback loops in yeast in a two dimensional parameter space: the inducer concentration and promoter dynamic range. While the bistable range of inducer concentration was influenced by many factors, the promoter dynamic range was more informative. The narrowest promoter dynamic range at which bistability can emerge revealed whether the full potential of an ultrasensitive reaction, such as dimerization, is exploited in the feedback loop. The convenient control of basal expression to adjust the promoter dynamic range permits a practical and reliable comparison of robustness of related positive feedback loops.
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Affiliation(s)
- Vincent Jaquet
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland.
| | - Chieh Hsu
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland. and School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - Attila Becskei
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland.
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Arbel-Goren R, Tal A, Parasar B, Dym A, Costantino N, Muñoz-García J, Court DL, Stavans J. Transcript degradation and noise of small RNA-controlled genes in a switch activated network in Escherichia coli. Nucleic Acids Res 2016; 44:6707-20. [PMID: 27085802 PMCID: PMC5001584 DOI: 10.1093/nar/gkw273] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/05/2016] [Indexed: 12/20/2022] Open
Abstract
Post-transcriptional regulatory processes may change transcript levels and affect cell-to-cell variability or noise. We study small-RNA downregulation to elucidate its effects on noise in the iron homeostasis network of Escherichia coli. In this network, the small-RNA RyhB undergoes stoichiometric degradation with the transcripts of target genes in response to iron stress. Using single-molecule fluorescence in situ hybridization, we measured transcript numbers of the RyhB-regulated genes sodB and fumA in individual cells as a function of iron deprivation. We observed a monotonic increase of noise with iron stress but no evidence of theoretically predicted, enhanced stoichiometric fluctuations in transcript numbers, nor of bistable behavior in transcript distributions. Direct detection of RyhB in individual cells shows that its noise is much smaller than that of these two targets, when RyhB production is significant. A generalized two-state model of bursty transcription that neglects RyhB fluctuations describes quantitatively the dependence of noise and transcript distributions on iron deprivation, enabling extraction of in vivo RyhB-mediated transcript degradation rates. The transcripts’ threshold-linear behavior indicates that the effective in vivo interaction strength between RyhB and its two target transcripts is comparable. Strikingly, the bacterial cell response exhibits Fur-dependent, switch-like activation instead of a graded response to iron deprivation.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Asaf Tal
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Bibudha Parasar
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alvah Dym
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nina Costantino
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Javier Muñoz-García
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel Departamento de Matemáticas and GISC, Universidad Carlos III de Madrid, Av. de la Universidad 30, 28911 Leganés, Madrid, Spain
| | - Donald L Court
- Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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Dragin N, Bismuth J, Cizeron-Clairac G, Biferi MG, Berthault C, Serraf A, Nottin R, Klatzmann D, Cumano A, Barkats M, Le Panse R, Berrih-Aknin S. Estrogen-mediated downregulation of AIRE influences sexual dimorphism in autoimmune diseases. J Clin Invest 2016; 126:1525-37. [PMID: 26999605 PMCID: PMC4811157 DOI: 10.1172/jci81894] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 01/21/2016] [Indexed: 01/01/2023] Open
Abstract
Autoimmune diseases affect 5% to 8% of the population, and females are more susceptible to these diseases than males. Here, we analyzed human thymic transcriptome and revealed sex-associated differences in the expression of tissue-specific antigens that are controlled by the autoimmune regulator (AIRE), a key factor in central tolerance. We hypothesized that the level of AIRE is linked to sexual dimorphism susceptibility to autoimmune diseases. In human and mouse thymus, females expressed less AIRE (mRNA and protein) than males after puberty. These results were confirmed in purified murine thymic epithelial cells (TECs). We also demonstrated that AIRE expression is related to sexual hormones, as male castration decreased AIRE thymic expression and estrogen receptor α-deficient mice did not show a sex disparity for AIRE expression. Moreover, estrogen treatment resulted in downregulation of AIRE expression in cultured human TECs, human thymic tissue grafted to immunodeficient mice, and murine fetal thymus organ cultures. AIRE levels in human thymus grafted in immunodeficient mice depended upon the sex of the recipient. Estrogen also upregulated the number of methylated CpG sites in the AIRE promoter. Together, our results indicate that in females, estrogen induces epigenetic changes in the AIRE gene, leading to reduced AIRE expression under a threshold that increases female susceptibility to autoimmune diseases.
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Affiliation(s)
- Nadine Dragin
- Sorbonne Universités, UPMC University of Paris 06, Paris, France
- INSERM U974, Paris, France
- CNRS FRE 3617, Paris, France
- AIM, Institute of Myology, Paris, France
| | - Jacky Bismuth
- Sorbonne Universités, UPMC University of Paris 06, Paris, France
- INSERM U974, Paris, France
- CNRS FRE 3617, Paris, France
- AIM, Institute of Myology, Paris, France
| | | | - Maria Grazia Biferi
- Sorbonne Universités, UPMC University of Paris 06, Paris, France
- INSERM U974, Paris, France
- CNRS FRE 3617, Paris, France
- AIM, Institute of Myology, Paris, France
| | - Claire Berthault
- INSERM U668, Unit for Lymphopoiesis, Immunology Department, Pasteur Institute, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Alain Serraf
- Hôpital Marie Lannelongue, Le Plessis–Robinson, France
| | - Rémi Nottin
- Hôpital Marie Lannelongue, Le Plessis–Robinson, France
| | - David Klatzmann
- Assistance Publique – Hôpitaux de Paris (AP-HP), Pitié-Salpêtrière Hospital, Biotherapy, Paris, France
| | - Ana Cumano
- INSERM U668, Unit for Lymphopoiesis, Immunology Department, Pasteur Institute, Paris, France
| | - Martine Barkats
- Sorbonne Universités, UPMC University of Paris 06, Paris, France
- INSERM U974, Paris, France
- CNRS FRE 3617, Paris, France
- AIM, Institute of Myology, Paris, France
| | - Rozen Le Panse
- Sorbonne Universités, UPMC University of Paris 06, Paris, France
- INSERM U974, Paris, France
- CNRS FRE 3617, Paris, France
- AIM, Institute of Myology, Paris, France
| | - Sonia Berrih-Aknin
- Sorbonne Universités, UPMC University of Paris 06, Paris, France
- INSERM U974, Paris, France
- CNRS FRE 3617, Paris, France
- AIM, Institute of Myology, Paris, France
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