1
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Liu Z, Gillis TG, Raman S, Cui Q. A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery. eLife 2024; 12:RP92262. [PMID: 38836839 PMCID: PMC11152574 DOI: 10.7554/elife.92262] [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: 06/06/2024] Open
Abstract
New experimental findings continue to challenge our understanding of protein allostery. Recent deep mutational scanning study showed that allosteric hotspots in the tetracycline repressor (TetR) and its homologous transcriptional factors are broadly distributed rather than spanning well-defined structural pathways as often assumed. Moreover, hotspot mutation-induced allostery loss was rescued by distributed additional mutations in a degenerate fashion. Here, we develop a two-domain thermodynamic model for TetR, which readily rationalizes these intriguing observations. The model accurately captures the in vivo activities of various mutants with changes in physically transparent parameters, allowing the data-based quantification of mutational effects using statistical inference. Our analysis reveals the intrinsic connection of intra- and inter-domain properties for allosteric regulation and illustrate epistatic interactions that are consistent with structural features of the protein. The insights gained from this study into the nature of two-domain allostery are expected to have broader implications for other multi-domain allosteric proteins.
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Affiliation(s)
- Zhuang Liu
- Department of Physics, Boston UniversityBostonUnited States
| | - Thomas G Gillis
- Department of Biochemistry, University of WisconsinMadisonUnited States
| | - Srivatsan Raman
- Department of Biochemistry, University of WisconsinMadisonUnited States
- Department of Chemistry, University of WisconsinMadisonUnited States
- Department of Bacteriology, University of WisconsinMadisonUnited States
| | - Qiang Cui
- Department of Physics, Boston UniversityBostonUnited States
- Department of Chemistry, Boston UniversityBostonUnited States
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2
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Stevanovic M, Teuber Carvalho JP, Bittihn P, Schultz D. Dynamical model of antibiotic responses linking expression of resistance genes to metabolism explains emergence of heterogeneity during drug exposures. Phys Biol 2024; 21:036002. [PMID: 38412523 PMCID: PMC10988634 DOI: 10.1088/1478-3975/ad2d64] [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: 09/14/2023] [Revised: 01/25/2024] [Accepted: 02/27/2024] [Indexed: 02/29/2024]
Abstract
Antibiotic responses in bacteria are highly dynamic and heterogeneous, with sudden exposure of bacterial colonies to high drug doses resulting in the coexistence of recovered and arrested cells. The dynamics of the response is determined by regulatory circuits controlling the expression of resistance genes, which are in turn modulated by the drug's action on cell growth and metabolism. Despite advances in understanding gene regulation at the molecular level, we still lack a framework to describe how feedback mechanisms resulting from the interdependence between expression of resistance and cell metabolism can amplify naturally occurring noise and create heterogeneity at the population level. To understand how this interplay affects cell survival upon exposure, we constructed a mathematical model of the dynamics of antibiotic responses that links metabolism and regulation of gene expression, based on the tetracycline resistancetetoperon inE. coli. We use this model to interpret measurements of growth and expression of resistance in microfluidic experiments, both in single cells and in biofilms. We also implemented a stochastic model of the drug response, to show that exposure to high drug levels results in large variations of recovery times and heterogeneity at the population level. We show that stochasticity is important to determine how nutrient quality affects cell survival during exposure to high drug concentrations. A quantitative description of how microbes respond to antibiotics in dynamical environments is crucial to understand population-level behaviors such as biofilms and pathogenesis.
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Affiliation(s)
- Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - João Pedro Teuber Carvalho
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
| | - Philip Bittihn
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States of America
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3
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Széliová D, Müller S, Zanghellini J. Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate. Commun Biol 2024; 7:196. [PMID: 38368456 PMCID: PMC10874399 DOI: 10.1038/s42003-024-05815-4] [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: 11/05/2023] [Accepted: 01/12/2024] [Indexed: 02/19/2024] Open
Abstract
Ribosomes are key to cellular self-fabrication and limit growth rate. While most enzymes are proteins, ribosomes consist of 1/3 protein and 2/3 ribonucleic acid (RNA) (in E. coli).Here, we develop a mechanistic model of a self-fabricating cell, validated across diverse growth conditions. Through resource balance analysis (RBA), we explore the variation in maximum growth rate with ribosome composition, assuming constant kinetic parameters.Our model highlights the importance of RNA instability. If we neglect it, RNA synthesis is always cheaper than protein synthesis, leading to an RNA-only ribosome at maximum growth rate. Upon accounting for RNA turnover, we find that a mixed ribosome composed of RNA and proteins maximizes growth rate. To account for RNA turnover, we explore two scenarios regarding the activity of RNases. In (a) degradation is proportional to RNA content. In (b) ribosomal proteins cooperatively mitigate RNA instability by protecting it from misfolding and subsequent degradation. In both cases, higher protein content elevates protein synthesis costs and simultaneously lowers RNA turnover expenses, resulting in mixed RNA-protein ribosomes. Only scenario (b) aligns qualitatively with experimental data across varied growth conditions.Our research provides fresh insights into ribosome biogenesis and evolution, paving the way for understanding protein-rich ribosomes in archaea and mitochondria.
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Affiliation(s)
- Diana Széliová
- Department of Analytical Chemistry, University of Vienna, Vienna, 1090, Austria
| | - Stefan Müller
- Faculty of Mathematics, University of Vienna, Vienna, 1090, Austria
| | - Jürgen Zanghellini
- Department of Analytical Chemistry, University of Vienna, Vienna, 1090, Austria.
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4
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Dimitriou NM, Demirag E, Strati K, Mitsis GD. A calibration and uncertainty quantification analysis of classical, fractional and multiscale logistic models of tumour growth. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 243:107920. [PMID: 37976612 DOI: 10.1016/j.cmpb.2023.107920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/27/2023] [Accepted: 11/05/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND AND OBJECTIVE The validation of mathematical models of tumour growth is frequently hampered by the lack of sufficient experimental data, resulting in qualitative rather than quantitative studies. Recent approaches to this problem have attempted to extract information about tumour growth by integrating multiscale experimental measurements, such as longitudinal cell counts and gene expression data. In the present study, we investigated the performance of several mathematical models of tumour growth, including classical logistic, fractional and novel multiscale models, in terms of quantifying in-vitro tumour growth in the presence and absence of therapy. We further examined the effect of genes associated with changes in chemosensitivity in cell death rates. METHODS The multiscale expansion of logistic growth models was performed by coupling gene expression profiles to the cell death rates. State-of-the-art Bayesian inference, likelihood maximisation and uncertainty quantification techniques allowed a thorough evaluation of model performance. RESULTS The results suggest that the classical single-cell population model (SCPM) was the best fit for the untreated and low-dose treatment conditions, while the multiscale model with a cell death rate symmetric with the expression profile of OCT4 (Sym-SCPM) yielded the best fit for the high-dose treatment data. Further identifiability analysis showed that the multiscale model was both structurally and practically identifiable under the condition of known OCT4 expression profiles. CONCLUSIONS Overall, the present study demonstrates that model performance can be improved by incorporating multiscale measurements of tumour growth when high-dose treatment is involved.
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Affiliation(s)
| | - Ece Demirag
- Department of Biological Sciences, University of Cyprus, Nicosia, 2109, Cyprus
| | - Katerina Strati
- Department of Biological Sciences, University of Cyprus, Nicosia, 2109, Cyprus
| | - Georgios D Mitsis
- Department of Bioengineering, McGill University, Montreal, H3A 0E9, QC, Canada.
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5
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Choudhury A, Gachet B, Dixit Z, Faure R, Gill RT, Tenaillon O. Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs. Nat Commun 2023; 14:6319. [PMID: 37813857 PMCID: PMC10562459 DOI: 10.1038/s41467-023-41882-7] [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: 02/23/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023] Open
Abstract
RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple traits involving trade-offs such as growth versus maintenance. Laboratory evolution has revealed that mutations in RNAP subunits, including RpoB, are frequently selected. However, we lack a systems view of how mutations alter the RNAP molecular functions to promote adaptation. We, therefore, measured the fitness of thousands of mutations within a region of rpoB under multiple conditions and genetic backgrounds, to find that adaptive mutations cluster in two modules. Mutations in one module favor growth over maintenance through a partial loss of an interaction associated with faster elongation. Mutations in the other favor maintenance over growth through a destabilized RNAP-DNA complex. The two molecular handles capture the versatile RNAP-mediated adaptations. Combining both interaction losses simultaneously improved maintenance and growth, challenging the idea that growth-maintenance tradeoff resorts only from limited resources, and revealing how compensatory evolution operates within RNAP.
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Affiliation(s)
- Alaksh Choudhury
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Laboratoire Biophysique et Évolution (LBE), UMR Chimie Biologie Innovation 8231, ESPCI Paris, Université PSL, CNRS, 75005, Paris, France.
| | - Benoit Gachet
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
| | - Zoya Dixit
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France
| | - Roland Faure
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France
- Université de Rennes, INRIA RBA, CNRS UMR 6074, Rennes, France
- Service Evolution Biologique et Ecologie, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Ryan T Gill
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado-Boulder, Boulder, CO, 80309-0027, USA
- Novo Nordisk Foundation, Denmark Technical University, 2800 Kgs, Lyngby, Denmark
| | - Olivier Tenaillon
- Université de Paris Cité, INSERM, IAME, UMR 1137, 75018, Paris, France.
- Université de Paris Cité, INSERM, CNRS, Institut Cochin, UMR 1016, 75014, Paris, France.
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6
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Stevanovic M, Carvalho JPT, Bittihn P, Schultz D. Dynamical model of antibiotic responses linking expression of resistance to metabolism explains emergence of heterogeneity during drug exposures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558994. [PMID: 37790326 PMCID: PMC10542528 DOI: 10.1101/2023.09.22.558994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Antibiotic responses in bacteria are highly dynamic and heterogeneous, with sudden exposure of bacterial colonies to high drug doses resulting in the coexistence of recovered and arrested cells. The dynamics of the response is determined by regulatory circuits controlling the expression of resistance genes, which are in turn modulated by the drug's action on cell growth and metabolism. Despite advances in understanding gene regulation at the molecular level, we still lack a framework to describe how feedback mechanisms resulting from the interdependence between expression of resistance and cell metabolism can amplify naturally occurring noise and create heterogeneity at the population level. To understand how this interplay affects cell survival upon exposure, we constructed a mathematical model of the dynamics of antibiotic responses that links metabolism and regulation of gene expression, based on the tetracycline resistance tet operon in E. coli. We use this model to interpret measurements of growth and expression of resistance in microfluidic experiments, both in single cells and in biofilms. We also implemented a stochastic model of the drug response, to show that exposure to high drug levels results in large variations of recovery times and heterogeneity at the population level. We show that stochasticity is important to determine how nutrient quality affects cell survival during exposure to high drug concentrations. A quantitative description of how microbes respond to antibiotics in dynamical environments is crucial to understand population-level behaviors such as biofilms and pathogenesis.
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Affiliation(s)
- Mirjana Stevanovic
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - João Pedro Teuber Carvalho
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Philip Bittihn
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
- Institute for the Dynamics of Complex Systems, University of Göttingen, Göttingen, Germany
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
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7
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Zhu J, Chu P, Fu X. Unbalanced response to growth variations reshapes the cell fate decision landscape. Nat Chem Biol 2023; 19:1097-1104. [PMID: 36959461 DOI: 10.1038/s41589-023-01302-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/27/2023] [Indexed: 03/25/2023]
Abstract
The global regulation of cell growth rate on gene expression perturbs the performance of gene networks, which would impose complex variations on the cell-fate decision landscape. Here we use a simple synthetic circuit of mutual repression that allows a bistable landscape to examine how such global regulation would affect the stability of phenotypic landscape and the accompanying dynamics of cell-fate determination. We show that the landscape experiences a growth-rate-induced bifurcation between monostability and bistability. Theoretical and experimental analyses reveal that this bifurcating deformation of landscape arises from the unbalanced response of gene expression to growth variations. The path of growth transition across the bifurcation would reshape cell-fate decisions. These results demonstrate the importance of growth regulation on cell-fate determination processes, regardless of specific molecular signaling or regulation.
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Affiliation(s)
- Jingwen Zhu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Pan Chu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiongfei Fu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
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8
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Fan J, El Sayyed H, Pambos OJ, Stracy M, Kyropoulos J, Kapanidis AN. RNA polymerase redistribution supports growth in E. coli strains with a minimal number of rRNA operons. Nucleic Acids Res 2023; 51:8085-8101. [PMID: 37351576 PMCID: PMC10450203 DOI: 10.1093/nar/gkad511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023] Open
Abstract
Bacterial transcription by RNA polymerase (RNAP) is spatially organized. RNAPs transcribing highly expressed genes locate in the nucleoid periphery, and form clusters in rich medium, with several studies linking RNAP clustering and transcription of rRNA (rrn). However, the nature of RNAP clusters and their association with rrn transcription remains unclear. Here we address these questions by using single-molecule tracking to monitor the subcellular distribution of mobile and immobile RNAP in strains with a heavily reduced number of chromosomal rrn operons (Δrrn strains). Strikingly, we find that the fraction of chromosome-associated RNAP (which is mainly engaged in transcription) is robust to deleting five or six of the seven chromosomal rrn operons. Spatial analysis in Δrrn strains showed substantial RNAP redistribution during moderate growth, with clustering increasing at cell endcaps, where the remaining rrn operons reside. These results support a model where RNAPs in Δrrn strains relocate to copies of the remaining rrn operons. In rich medium, Δrrn strains redistribute RNAP to minimize growth defects due to rrn deletions, with very high RNAP densities on rrn genes leading to genomic instability. Our study links RNAP clusters and rrn transcription, and offers insight into how bacteria maintain growth in the presence of only 1-2 rrn operons.
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Affiliation(s)
- Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, China
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
| | - Mathew Stracy
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Jingwen Kyropoulos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin building, University of Oxford, Sherrington Road, Oxford OX1 3QU, UK
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9
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Li R, Rozum JC, Quail MM, Qasim MN, Sindi SS, Nobile CJ, Albert R, Hernday AD. Inferring gene regulatory networks using transcriptional profiles as dynamical attractors. PLoS Comput Biol 2023; 19:e1010991. [PMID: 37607190 PMCID: PMC10473541 DOI: 10.1371/journal.pcbi.1010991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 09/01/2023] [Accepted: 07/19/2023] [Indexed: 08/24/2023] Open
Abstract
Genetic regulatory networks (GRNs) regulate the flow of genetic information from the genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the phenotypic characteristics of cells. Numerous methods exist for profiling mRNA transcript levels and identifying protein-DNA binding interactions at the genome-wide scale. These enable researchers to determine the structure and output of transcriptional regulatory networks, but uncovering the complete structure and regulatory logic of GRNs remains a challenge. The field of GRN inference aims to meet this challenge using computational modeling to derive the structure and logic of GRNs from experimental data and to encode this knowledge in Boolean networks, Bayesian networks, ordinary differential equation (ODE) models, or other modeling frameworks. However, most existing models do not incorporate dynamic transcriptional data since it has historically been less widely available in comparison to "static" transcriptional data. We report the development of an evolutionary algorithm-based ODE modeling approach (named EA) that integrates kinetic transcription data and the theory of attractor matching to infer GRN architecture and regulatory logic. Our method outperformed six leading GRN inference methods, none of which incorporate kinetic transcriptional data, in predicting regulatory connections among TFs when applied to a small-scale engineered synthetic GRN in Saccharomyces cerevisiae. Moreover, we demonstrate the potential of our method to predict unknown transcriptional profiles that would be produced upon genetic perturbation of the GRN governing a two-state cellular phenotypic switch in Candida albicans. We established an iterative refinement strategy to facilitate candidate selection for experimentation; the experimental results in turn provide validation or improvement for the model. In this way, our GRN inference approach can expedite the development of a sophisticated mathematical model that can accurately describe the structure and dynamics of the in vivo GRN.
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Affiliation(s)
- Ruihao Li
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, California, United States of America
| | - Jordan C. Rozum
- Department of Systems Science and Industrial Engineering, Binghamton University (State University of New York), Binghamton, New York, United States of America
| | - Morgan M. Quail
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, California, United States of America
| | - Mohammad N. Qasim
- Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, California, United States of America
| | - Suzanne S. Sindi
- Department of Applied Mathematics, University of California, Merced, Merced, California, United States of America
| | - Clarissa J. Nobile
- Department of Molecular Cell Biology, University of California, Merced, Merced, California, United States of America
- Health Sciences Research Institute, University of California, Merced, Merced, California, United States of America
| | - Réka Albert
- Department of Physics, Pennsylvania State University, University Park, University Park, Pennsylvania, United States of America
- Department of Biology, Pennsylvania State University, University Park, University Park, Pennsylvania, United States of America
| | - Aaron D. Hernday
- Department of Molecular Cell Biology, University of California, Merced, Merced, California, United States of America
- Health Sciences Research Institute, University of California, Merced, Merced, California, United States of America
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10
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Gerber A, van Otterdijk S, Bruggeman FJ, Tutucci E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription 2023; 14:105-126. [PMID: 37050882 PMCID: PMC10807504 DOI: 10.1080/21541264.2023.2199669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.
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Affiliation(s)
- Alan Gerber
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Sander van Otterdijk
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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11
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Morichaud Z, Trapani S, Vishwakarma RK, Chaloin L, Lionne C, Lai-Kee-Him J, Bron P, Brodolin K. Structural basis of the mycobacterial stress-response RNA polymerase auto-inhibition via oligomerization. Nat Commun 2023; 14:484. [PMID: 36717560 PMCID: PMC9886945 DOI: 10.1038/s41467-023-36113-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Self-assembly of macromolecules into higher-order symmetric structures is fundamental for the regulation of biological processes. Higher-order symmetric structure self-assembly by the gene expression machinery, such as bacterial DNA-dependent RNA polymerase (RNAP), has never been reported before. Here, we show that the stress-response σB factor from the human pathogen, Mycobacterium tuberculosis, induces the RNAP holoenzyme oligomerization into a supramolecular complex composed of eight RNAP units. Cryo-electron microscopy revealed a pseudo-symmetric structure of the RNAP octamer in which RNAP protomers are captured in an auto-inhibited state and display an open-clamp conformation. The structure shows that σB is sequestered by the RNAP flap and clamp domains. The transcriptional activator RbpA prevented octamer formation by promoting the initiation-competent RNAP conformation. Our results reveal that a non-conserved region of σ is an allosteric controller of transcription initiation and demonstrate how basal transcription factors can regulate gene expression by modulating the RNAP holoenzyme assembly and hibernation.
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Affiliation(s)
- Zakia Morichaud
- Institut de Recherche en Infectiologie de Montpellier, Univ Montpellier, CNRS, Montpellier, 34293, France
| | - Stefano Trapani
- Centre de Biologie Structurale, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Rishi K Vishwakarma
- Institut de Recherche en Infectiologie de Montpellier, Univ Montpellier, CNRS, Montpellier, 34293, France.,Department of Biochemistry & Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Laurent Chaloin
- Institut de Recherche en Infectiologie de Montpellier, Univ Montpellier, CNRS, Montpellier, 34293, France
| | - Corinne Lionne
- Centre de Biologie Structurale, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Patrick Bron
- Centre de Biologie Structurale, Univ Montpellier, CNRS, INSERM, Montpellier, France.
| | - Konstantin Brodolin
- Institut de Recherche en Infectiologie de Montpellier, Univ Montpellier, CNRS, Montpellier, 34293, France. .,INSERM, Montpellier, France.
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12
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Understanding the Genome-Wide Transcription Response To Various cAMP Levels in Bacteria Using Phenomenological Models. mSystems 2022; 7:e0090022. [PMID: 36409084 PMCID: PMC9765429 DOI: 10.1128/msystems.00900-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Attempts to understand gene regulation by global transcription factors have largely been limited to expression studies under binary conditions of presence and absence of the transcription factor. Studies addressing genome-wide transcriptional responses to changing transcription factor concentration at high resolution are lacking. Here, we create a data set containing the entire Escherichia coli transcriptome in Luria-Bertani (LB) broth as it responds to 10 different cAMP concentrations spanning the biological range. We use the Hill's model to accurately summarize individual gene responses into three intuitively understandable parameters, Emax, n, and k, reflecting the sensitivity, nonlinearity, and midpoint of the dynamic range. Our data show that most cAMP-regulated genes have an n of >2, with their k values centered around the wild-type concentration of cAMP. Additionally, cAMP receptor protein (CRP) affinity to a promoter is correlated with Emax but not k, hinting that a high-affinity CRP promoter need not ensure transcriptional activation at lower cAMP concentrations and instead affects the magnitude of the response. Finally, genes belonging to different functional classes are tuned to have different k, n, and Emax values. We demonstrate that phenomenological models are a better alternative for studying gene expression trends than classical clustering methods, with the phenomenological constants providing greater insights into how genes are tuned in a regulatory network. IMPORTANCE Different genes may follow different trends in response to various transcription factor concentrations. In this study, we ask two questions: (i) what are the trends that different genes follow in response to changing transcription factor concentrations and (ii) what methods can be used to extract information from the gene trends so obtained. We demonstrate a method to analyze transcription factor concentration-dependent genome-wide expression data using phenomenological models. Conventional clustering methods and principal-component analysis (PCA) can be used to summarize trends in data but have limited interpretability. The use of phenomenological models greatly enhances the interpretability and thus utility of conventional clustering. Transformation of dose-response data into phenomenological constants opens up avenues to ask and answer many different kinds of question. We show that the phenomenological constants obtained from the model fits can be used to generate insights about network topology and allows integration of other experimental data such as chromatin immunoprecipitation sequencing (ChIP-seq) to understand the system in greater detail.
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13
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Vidal G, Vitalis C, Muñoz Silva M, Castillo-Passi C, Yáñez Feliú G, Federici F, Rudge TJ. Accurate characterization of dynamic microbial gene expression and growth rate profiles. Synth Biol (Oxf) 2022; 7:ysac020. [PMID: 36267953 PMCID: PMC9569155 DOI: 10.1093/synbio/ysac020] [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: 12/09/2021] [Revised: 07/16/2022] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic circuits are subject to variability due to cellular and compositional contexts. Cells face changing internal states and environments, the cellular context, to which they sense and respond by changing their gene expression and growth rates. Furthermore, each gene in a genetic circuit operates in a compositional context of genes which may interact with each other and the host cell in complex ways. The context of genetic circuits can, therefore, change gene expression and growth rates, and measuring their dynamics is essential to understanding natural and synthetic regulatory networks that give rise to functional phenotypes. However, reconstruction of microbial gene expression and growth rate profiles from typical noisy measurements of cell populations is difficult due to the effects of noise at low cell densities among other factors. We present here a method for the estimation of dynamic microbial gene expression rates and growth rates from noisy measurement data. Compared to the current state-of-the-art, our method significantly reduced the mean squared error of reconstructions from simulated data of growth and gene expression rates, improving the estimation of timing and magnitude of relevant shapes of profiles. We applied our method to characterize a triple-reporter plasmid library combining multiple transcription units in different compositional and cellular contexts in Escherichia coli. Our analysis reveals cellular and compositional context effects on microbial growth and gene expression rate dynamics and suggests a method for the dynamic ratiometric characterization of constitutive promoters relative to an in vivo reference.
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Affiliation(s)
- Gonzalo Vidal
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
| | - Carolus Vitalis
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Macarena Muñoz Silva
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Castillo-Passi
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- School of Biomedical Engineering and Imaging Sciences, King’s College London, St Thomas’ Hospital, London, UK
- Millennium Institute for Intelligent Healthcare Engineering (iHEALTH), Santiago, Chile
| | - Guillermo Yáñez Feliú
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fernán Federici
- Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID – Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio) & FONDAP Center for Genome Regulation, Santiago, Chile
| | - Timothy J Rudge
- Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle Upon Tyne, UK
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14
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Zhang ZX, Wang YZ, Nong FT, Xu Y, Ye C, Gu Y, Sun XM, Huang H. Developing a dynamic equilibrium system in Escherichia coli to improve the production of recombinant proteins. Appl Microbiol Biotechnol 2022; 106:6125-6137. [PMID: 36056198 DOI: 10.1007/s00253-022-12145-0] [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: 05/04/2022] [Revised: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 11/02/2022]
Abstract
The combination of Escherichia coli BL21 (DE3) and the pET expression system is used extensively for the expression of various recombinant proteins (RPs). However, RP overexpression often introduces a growth burden for the host, especially in the case of toxic proteins. The key to solving this problem is to reduce the host burden associated with protein overproduction, which is often achieved by regulating the expression or activity of T7 RNAP or growth-decoupled systems. However, these strategies mainly relieve or interrupt the robbing of host resources, and do not eliminate other types of host burdens in the production process. In this study, we constructed a production system based on a dynamic equilibrium to precisely relieve the host burden and increase the RP production. The system is composed of three modules, including the overexpression of basic growth-related genes (rRNA, RNAP core enzyme, sigma factors), prediction and overexpression of key proteins using the enzyme-constrained model ec_iECBD_1354, and dynamic regulation of growth-related and key protein expression intensity based on a burden-driven promoter. Using this system, the production of many high-burden proteins, including autolysis protein and E. coli membrane proteins, was increased to varying degrees. Among them, the cytosine transporter protein (CodB) was most significantly improved, with a 4.02-fold higher production compared to the wild strain. This system can effectively reduce the optimizing costs, and is suitable for developing various types of RP expression hosts rapidly. KEY POINTS: • The basic growth-related resources can relieve the host burden from recombinant protein. • The enzyme-constrained model can accurately predict key genes to improve yield. • The expression intensity can be dynamically adjusted with changes in burden.
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Affiliation(s)
- Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Yu-Zhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Fang-Tong Nong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Yan Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
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15
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Ciechonska M, Sturrock M, Grob A, Larrouy-Maumus G, Shahrezaei V, Isalan M. Emergent expression of fitness-conferring genes by phenotypic selection. PNAS NEXUS 2022; 1:pgac069. [PMID: 36741458 PMCID: PMC9896880 DOI: 10.1093/pnasnexus/pgac069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/23/2022] [Indexed: 02/07/2023]
Abstract
Genotypic and phenotypic adaptation is the consequence of ongoing natural selection in populations and is key to predicting and preventing drug resistance. Whereas classic antibiotic persistence is all-or-nothing, here we demonstrate that an antibiotic resistance gene displays linear dose-responsive selection for increased expression in proportion to rising antibiotic concentration in growing Escherichia coli populations. Furthermore, we report the potentially wide-spread nature of this form of emergent gene expression (EGE) by instantaneous phenotypic selection process under bactericidal and bacteriostatic antibiotic treatment, as well as an amino acid synthesis pathway enzyme under a range of auxotrophic conditions. We propose an analogy to Ohm's law in electricity (V = IR), where selection pressure acts similarly to voltage (V), gene expression to current (I), and resistance (R) to cellular machinery constraints and costs. Lastly, mathematical modeling using agent-based models of stochastic gene expression in growing populations and Bayesian model selection reveal that the EGE mechanism requires variability in gene expression within an isogenic population, and a cellular "memory" from positive feedbacks between growth and expression of any fitness-conferring gene. Finally, we discuss the connection of the observed phenomenon to a previously described general fluctuation-response relationship in biology.
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Affiliation(s)
| | | | - Alice Grob
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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16
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Fleurier S, Dapa T, Tenaillon O, Condon C, Matic I. rRNA operon multiplicity as a bacterial genome stability insurance policy. Nucleic Acids Res 2022; 50:12601-12620. [PMID: 35552441 PMCID: PMC9825170 DOI: 10.1093/nar/gkac332] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/12/2022] [Accepted: 04/21/2022] [Indexed: 01/29/2023] Open
Abstract
Quick growth restart after upon encountering favourable environmental conditions is a major fitness contributor in natural environment. It is widely assumed that the time required to restart growth after nutritional upshift is determined by how long it takes for cells to synthesize enough ribosomes to produce the proteins required to reinitiate growth. Here we show that a reduction in the capacity to synthesize ribosomes by reducing number of ribosomal RNA (rRNA) operons (rrn) causes a longer transition from stationary phase to growth of Escherichia coli primarily due to high mortality rates. Cell death results from DNA replication blockage and massive DNA breakage at the sites of the remaining rrn operons that become overloaded with RNA polymerases (RNAPs). Mortality rates and growth restart duration can be reduced by preventing R-loop formation and improving DNA repair capacity. The same molecular mechanisms determine the duration of the recovery phase after ribosome-damaging stresses, such as antibiotics, exposure to bile salts or high temperature. Our study therefore suggests that a major function of rrn operon multiplicity is to ensure that individual rrn operons are not saturated by RNAPs, which can result in catastrophic chromosome replication failure and cell death during adaptation to environmental fluctuations.
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Affiliation(s)
- Sebastien Fleurier
- Department of Infection, Immunity and Inflammation, Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, 75014 Paris, France
| | - Tanja Dapa
- Department of Infection, Immunity and Inflammation, Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, 75014 Paris, France
| | | | - Ciarán Condon
- Institut de Biologie Physico-Chimique, CNRS UMR8261, Université de Paris, 75005 Paris, France
| | - Ivan Matic
- To whom correspondence should be addressed.
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17
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Importance of RpoD- and Non-RpoD-Dependent Expression of Horizontally Acquired Genes in Cupriavidus metallidurans. Microbiol Spectr 2022; 10:e0012122. [PMID: 35311568 PMCID: PMC9045368 DOI: 10.1128/spectrum.00121-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of the metal-resistant, hydrogen-oxidizing bacterium Cupriavidus metallidurans contains a large number of horizontally acquired plasmids and genomic islands that were integrated into its chromosome or chromid. For the C. metallidurans CH34 wild-type strain growing under nonchallenging conditions, 5,763 transcriptional starting sequences (TSSs) were determined. Using a custom-built motif discovery software based on hidden Markov models, patterns upstream of the TSSs were identified. The pattern TTGACA, −35.6 ± 1.6 bp upstream of the TSSs, in combination with a TATAAT sequence 15.8 ± 1.4 bp upstream occurred frequently, especially upstream of the TSSs for 48 housekeeping genes, and these were assigned to promoters used by RNA polymerase containing the main housekeeping sigma factor RpoD. From patterns upstream of the housekeeping genes, a score for RpoD-dependent promoters in C. metallidurans was derived and applied to all 5,763 TSSs. Among these, 2,572 TSSs could be associated with RpoD with high probability, 373 with low probability, and 2,818 with no probability. In a detailed analysis of horizontally acquired genes involved in metal resistance and not involved in this process, the TSSs responsible for the expression of these genes under nonchallenging conditions were assigned to RpoD- or non-RpoD-dependent promoters. RpoD-dependent promoters occurred frequently in horizontally acquired metal resistance and other determinants, which should allow their initial expression in a new host. However, other sigma factors and sense/antisense effects also contribute—maybe to mold in subsequent adaptation steps the assimilated gene into the regulatory network of the cell. IMPORTANCE In their natural environment, bacteria are constantly acquiring genes by horizontal gene transfer. To be of any benefit, these genes should be expressed. We show here that the main housekeeping sigma factor RpoD plays an important role in the expression of horizontally acquired genes in the metal-resistant hydrogen-oxidizing bacterium C. metallidurans. By conservation of the RpoD recognition consensus sequence, a newly arriving gene has a high probability to be expressed in the new host cell. In addition to integrons and genes travelling together with that for their sigma factor, conservation of the RpoD consensus sequence may be an important contributor to the overall evolutionary success of horizontal gene transfer in bacteria. Using C. metallidurans as an example, this publication sheds some light on the fate and function of horizontally acquired genes in bacteria.
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18
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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.
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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.
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19
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Wenholz DS, Miller M, Dawson C, Bhadbhade M, Black DS, Griffith R, Dinh H, Cain A, Lewis P, Kumar N. Inhibitors of bacterial RNA polymerase transcription complex. Bioorg Chem 2021; 118:105481. [PMID: 34801947 DOI: 10.1016/j.bioorg.2021.105481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 01/28/2023]
Abstract
A series of hybrid compounds that incorporated anthranilic acid with activated 1H-indoles through a glyoxylamide linker were designed to target bacterial RNA polymerase holoenzyme formation using computational docking. Synthesis, in vitro transcription inhibition assays, and biological testing of the hybrids identified a range of potent anti-transcription inhibitors with activity against a range of pathogenic bacteria with MICs as low as 3.1 μM. A structure activity relationship study identified the key structural components necessary for inhibition of both bacterial growth and transcription. Correlation of in vitro transcription inhibition activity with in vivo mechanism of action was established using fluorescence microscopy and resistance passaging using Gram-positive bacteria showed no resistance development over 30 days. Furthermore, no toxicity was observed from the compounds in a wax moth larvae model, establishing a platform for the development of a series of new antibacterial drugs with an established mode of action.
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Affiliation(s)
- Daniel S Wenholz
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia
| | - Michael Miller
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Catherine Dawson
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Mohan Bhadbhade
- Mark Wainwright Analytical Centre, UNSW Sydney, NSW 2052, Australia
| | - David StC Black
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia
| | - Renate Griffith
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia
| | - Hue Dinh
- Department of Biological Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Amy Cain
- Department of Biological Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Peter Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; School of Chemistry and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Naresh Kumar
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia.
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20
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Ropers D, Couté Y, Faure L, Ferré S, Labourdette D, Shabani A, Trouilh L, Vasseur P, Corre G, Ferro M, Teste MA, Geiselmann J, de Jong H. Multiomics Study of Bacterial Growth Arrest in a Synthetic Biology Application. ACS Synth Biol 2021; 10:2910-2926. [PMID: 34739215 DOI: 10.1021/acssynbio.1c00115] [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: 11/29/2022]
Abstract
We investigated the scalability of a previously developed growth switch based on external control of RNA polymerase expression. Our results indicate that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. A multiomics quantification of the physiology of the cells shows that, apart from acetate production, few metabolic side effects occur. However, a number of specific responses to growth slow-down and growth arrest are launched at the transcriptional level. These notably include the downregulation of genes involved in growth-associated processes, such as amino acid and nucleotide metabolism and translation. Interestingly, the transcriptional responses are buffered at the proteome level, probably due to the strong decrease of the total mRNA concentration after the diminution of transcriptional activity and the absence of growth dilution of proteins. Growth arrest thus reduces the opportunities for dynamically adjusting the proteome composition, which poses constraints on the design of biotechnological production processes but may also avoid the initiation of deleterious stress responses.
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Affiliation(s)
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | | | - Sabrina Ferré
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Delphine Labourdette
- GeT-Biopuces, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Arieta Shabani
- Université Grenoble Alpes, Inria, 38000 Grenoble, France
| | - Lidwine Trouilh
- GeT-Biopuces, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | | | | | - Myriam Ferro
- Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, 38000 Grenoble, France
| | - Marie-Ange Teste
- GeT-Biopuces, TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Johannes Geiselmann
- Université Grenoble Alpes, Inria, 38000 Grenoble, France
- Université Grenoble Alpes, CNRS, LIPhy, 38000 Grenoble, France
| | - Hidde de Jong
- Université Grenoble Alpes, Inria, 38000 Grenoble, France
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21
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Chakraborty P, Ghosh S. Emergent correlations in gene expression dynamics as footprints of resource competition. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:131. [PMID: 34694511 DOI: 10.1140/epje/s10189-021-00122-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Genetic circuits need a cellular environment to operate in, which naturally couples the circuit function with the overall functionality of gene regulatory network. To execute their functions, all gene circuits draw resources in the form of RNA polymerases, ribosomes, and tRNAs. Recent experiments pointed out that the role of resource competition on synthetic circuit outputs could be immense. However, the effect of complexity of the circuit architecture on resource sharing dynamics is yet unexplored. In this paper, we employ mathematical modelling and in-silico experiments to identify the sources of resource trade-off and to quantify its impact on the function of a genetic circuit, keeping our focus on regulation of immediate downstream proteins, which are often used as protein read-outs. We show that estimating gene expression dynamics from readings of downstream protein data might be unreliable when the resource is limited and ribosome affinities are asymmetric. We focus on the impact of mRNA copy number and ribosome binding site (RBS) strength on the nonlinear isocline that emerges with two regimes, prominently separated by a tipping point, and study how correlation and competition dominate each other depending on various circuit parameters. Focusing further on genetic toggle circuit, we have identified major effects of resource competition in this model motif and quantified the observations. The observations are testable in wet-lab experiments, as all the parameters chosen are experimentally relevant.
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Affiliation(s)
- Priya Chakraborty
- Department of Physics, National Institute of Technology, Durgapur, 713209, India
| | - Sayantari Ghosh
- Department of Physics, National Institute of Technology, Durgapur, 713209, India.
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22
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Yubero P, Poyatos JF. Dissecting the Fitness Costs of Complex Mutations. Mol Biol Evol 2021; 38:4520-4531. [PMID: 34175930 PMCID: PMC8476139 DOI: 10.1093/molbev/msab193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The fitness cost of complex pleiotropic mutations is generally difficult to assess. On the one hand, it is necessary to identify which molecular properties are directly altered by the mutation. On the other, this alteration modifies the activity of many genetic targets with uncertain consequences. Here, we examine the possibility of addressing these challenges by identifying unique predictors of these costs. To this aim, we consider mutations in the RNA polymerase (RNAP) in Escherichia coli as a model of complex mutations. Changes in RNAP modify the global program of transcriptional regulation, with many consequences. Among others is the difficulty to decouple the direct effect of the mutation from the response of the whole system to such mutation. A problem that we solve quantitatively with data of a set of constitutive genes, those on which the global program acts most directly. We provide a statistical framework that incorporates the direct effects and other molecular variables linked to this program as predictors, which leads to the identification that some genes are more suitable to determine costs than others. Therefore, we not only identified which molecular properties best anticipate fitness, but we also present the paradoxical result that, despite pleiotropy, specific genes serve as more solid predictors. These results have connotations for the understanding of the architecture of robustness in biological systems.
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Affiliation(s)
- Pablo Yubero
- Logic of Genomic Systems Laboratory, CNB-CSIC, Madrid, Spain
| | - Juan F Poyatos
- Logic of Genomic Systems Laboratory, CNB-CSIC, Madrid, Spain
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23
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Belliveau NM, Chure G, Hueschen CL, Garcia HG, Kondev J, Fisher DS, Theriot JA, Phillips R. Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. Cell Syst 2021; 12:924-944.e2. [PMID: 34214468 PMCID: PMC8460600 DOI: 10.1016/j.cels.2021.06.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/12/2021] [Accepted: 06/04/2021] [Indexed: 12/11/2022]
Abstract
Despite abundant measurements of bacterial growth rate, cell size, and protein content, we lack a rigorous understanding of what sets the scale of these quantities and when protein abundances should (or should not) depend on growth rate. Here, we estimate the basic requirements and physical constraints on steady-state growth by considering key processes in cellular physiology across a collection of Escherichia coli proteomic data covering ≈4,000 proteins and 36 growth rates. Our analysis suggests that cells are predominantly tuned for the task of cell doubling across a continuum of growth rates; specific processes do not limit growth rate or dictate cell size. We present a model of proteomic regulation as a function of nutrient supply that reconciles observed interdependences between protein synthesis, cell size, and growth rate and propose that a theoretical inability to parallelize ribosomal synthesis places a firm limit on the achievable growth rate. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Nathan M Belliveau
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Griffin Chure
- Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina L Hueschen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Hernan G Garcia
- Department of Molecular Cell Biology and Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Daniel S Fisher
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Julie A Theriot
- Department of Biology, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA.
| | - Rob Phillips
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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24
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Forquet R, Pineau M, Nasser W, Reverchon S, Meyer S. Role of the Discriminator Sequence in the Supercoiling Sensitivity of Bacterial Promoters. mSystems 2021; 6:e0097821. [PMID: 34427530 PMCID: PMC8422995 DOI: 10.1128/msystems.00978-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022] Open
Abstract
DNA supercoiling acts as a global transcriptional regulator that contributes to the rapid transcriptional response of bacteria to many environmental changes. Although a large fraction of promoters from phylogenetically distant species respond to superhelical variations, the sequence or structural determinants of this behavior remain elusive. Here, we focus on the sequence of the "discriminator" element that was shown to modulate this response in several promoters. We develop a quantitative thermodynamic model of this regulatory effect, focusing on open complex formation during transcription initiation independently from promoter-specific regulatory proteins. We analyze previous and new expression data and show that the model predictions quantitatively match the in vitro and in vivo supercoiling response of selected promoters with mutated discriminator sequences. We then test the universality of this mechanism by a statistical analysis of promoter sequences from transcriptomes of phylogenetically distant bacteria under conditions of supercoiling variations (i) by gyrase inhibitors, (ii) by environmental stresses, or (iii) inherited in the longest-running evolution experiment. In all cases, we identify a robust and significant sequence signature in the discriminator region, suggesting that supercoiling-modulated promoter opening underpins a ubiquitous regulatory mechanism in the prokaryotic kingdom based on the fundamental mechanical properties of DNA and its basal interaction with RNA polymerase. IMPORTANCE In this study, we highlight the role of the discriminator as a global sensor of supercoiling variations and propose the first quantitative regulatory model of this principle, based on the specific step of promoter opening during transcription initiation. It defines the predictive rule by which DNA supercoiling quantitatively modulates the expression rate of bacterial promoters, depending on the G/C content of their discriminator and independently from promoter-specific regulatory proteins. This basal mechanism affects a wide range of species, which is tested by an extensive analysis of global high-throughput expression data. Altogether, ours results confirm and provide a quantitative framework for the long-proposed notion that the discriminator sequence is a significant determinant of promoter supercoiling sensitivity, underpinning the ubiquitous regulatory action of DNA supercoiling on the core transcriptional machinery, in particular in response to quick environmental changes.
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Affiliation(s)
- Raphaël Forquet
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
| | - Maïwenn Pineau
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
| | - William Nasser
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
| | - Sylvie Reverchon
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
| | - Sam Meyer
- Université de Lyon, INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, MAP, Lyon, France
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25
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Kremling A. A counting-strategy together with a spatial structured model describes RNA polymerase and ribosome availability in Escherichia coli. Metab Eng 2021; 67:145-152. [PMID: 34174424 DOI: 10.1016/j.ymben.2021.06.006] [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: 09/23/2020] [Revised: 05/06/2021] [Accepted: 06/21/2021] [Indexed: 11/30/2022]
Abstract
The allocation of resources during bacterial growth is strongly related to the availability of ribosomes and RNA polymerase molecules. Here, coarse-grained models offer a promising start due to their simple structure and the limited number of kinetic parameters. Based on published data sets for proteome and mRNA data in Escherichia coli, and together with mass balance equations describing gene expression, we are able to calculate the number of active molecules (that is, the number of ribosomes that are currently translating nascent and mature mRNA, as well as the number of RNA polymerase molecules on the DNA). This information is a prerequisite for meaningful coarse-grained models. In our approach, the cellular compartment is structured into a cytosolic region and a nucleoid region, and the processes of transcription and translation are assigned accordingly. The theoretical study reveals a quadratic relationship between the number of active ribosomes and the growth rate μ. While the overall available number of ribosomes follows the linear "bacterial growth law", the approach allows us to determine the growth limit for the chosen experimental environment (minimal medium, only one C source). The new approach is in good agreement with published experimental data, and, with a simple rule of thumb can be applied to other cellular systems.
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Affiliation(s)
- Andreas Kremling
- Systems Biotechnology, Technical University of Munich, Boltzmannstr. 15, Garching b, München, Germany.
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26
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Zhao P, Tian P. Biosynthesis pathways and strategies for improving 3-hydroxypropionic acid production in bacteria. World J Microbiol Biotechnol 2021; 37:117. [PMID: 34128152 DOI: 10.1007/s11274-021-03091-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/08/2021] [Indexed: 12/01/2022]
Abstract
3-Hydroxypropionic acid (3-HP) represents an economically important platform compound from which a panel of bulk chemicals can be derived. Compared with petroleum-dependent chemical synthesis, bioproduction of 3-HP has attracted more attention due to utilization of renewable biomass. This review outlines bacterial production of 3-HP, covering aspects of host strains (e.g., Escherichia coli and Klebsiella pneumoniae), metabolic pathways, key enzymes, and hurdles hindering high-level production. Inspired by the state-of-the-art advances in metabolic engineering and synthetic biology, we come up with protocols to overcome the hurdles constraining 3-HP production. The protocols range from rewiring of metabolic networks, alleviation of metabolite toxicity, to dynamic control of cell size and density. Especially, this review highlights the substantial contribution of microbial growth to 3-HP production, as we recognize the synchronization between cell growth and 3-HP formation. Accordingly, we summarize the following growth-promoting strategies: (i) optimization of fermentation conditions; (ii) construction of gene circuits to alleviate feedback inhibition; (iii) recruitment of RNA polymerases to overexpress key enzymes which in turn boost cell growth and 3-HP production. Lastly, we propose metabolic engineering approaches to simplify downstream separation and purification. Overall, this review aims to portray a picture of bacterial production of 3-HP.
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Affiliation(s)
- Peng Zhao
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Pingfang Tian
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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27
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Yong C, Gyorgy A. Stability and Robustness of Unbalanced Genetic Toggle Switches in the Presence of Scarce Resources. Life (Basel) 2021; 11:271. [PMID: 33805212 PMCID: PMC8064337 DOI: 10.3390/life11040271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/24/2022] Open
Abstract
While the vision of synthetic biology is to create complex genetic systems in a rational fashion, system-level behaviors are often perplexing due to the context-dependent dynamics of modules. One major source of context-dependence emerges due to the limited availability of shared resources, coupling the behavior of disconnected components. Motivated by the ubiquitous role of toggle switches in genetic circuits ranging from controlling cell fate differentiation to optimizing cellular performance, here we reveal how their fundamental dynamic properties are affected by competition for scarce resources. Combining a mechanistic model with nullcline-based stability analysis and potential landscape-based robustness analysis, we uncover not only the detrimental impacts of resource competition, but also how the unbalancedness of the switch further exacerbates them. While in general both of these factors undermine the performance of the switch (by pushing the dynamics toward monostability and increased sensitivity to noise), we also demonstrate that some of the unwanted effects can be alleviated by strategically optimized resource competition. Our results provide explicit guidelines for the context-aware rational design of toggle switches to mitigate our reliance on lengthy and expensive trial-and-error processes, and can be seamlessly integrated into the computer-aided synthesis of complex genetic systems.
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Affiliation(s)
- Chentao Yong
- Department of Chemical and Biological Engineering, New York University, New York, NY 10003, USA;
| | - Andras Gyorgy
- Department of Electrical and Computer Engineering, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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28
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The Context-Dependent Influence of Promoter Sequence Motifs on Transcription Initiation Kinetics and Regulation. J Bacteriol 2021; 203:JB.00512-20. [PMID: 33139481 DOI: 10.1128/jb.00512-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The fitness of an individual bacterial cell is highly dependent upon the temporal tuning of gene expression levels when subjected to different environmental cues. Kinetic regulation of transcription initiation is a key step in modulating the levels of transcribed genes to promote bacterial survival. The initiation phase encompasses the binding of RNA polymerase (RNAP) to promoter DNA and a series of coupled protein-DNA conformational changes prior to entry into processive elongation. The time required to complete the initiation phase can vary by orders of magnitude and is ultimately dictated by the DNA sequence of the promoter. In this review, we aim to provide the required background to understand how promoter sequence motifs may affect initiation kinetics during promoter recognition and binding, subsequent conformational changes which lead to DNA opening around the transcription start site, and promoter escape. By calculating the steady-state flux of RNA production as a function of these effects, we illustrate that the presence/absence of a consensus promoter motif cannot be used in isolation to make conclusions regarding promoter strength. Instead, the entire series of linked, sequence-dependent structural transitions must be considered holistically. Finally, we describe how individual transcription factors take advantage of the broad distribution of sequence-dependent basal kinetics to either increase or decrease RNA flux.
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29
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Yu R, Vorontsov E, Sihlbom C, Nielsen J. Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast. eLife 2021; 10:e65722. [PMID: 33720010 PMCID: PMC8016476 DOI: 10.7554/elife.65722] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/13/2021] [Indexed: 12/18/2022] Open
Abstract
In addition to controlled expression of genes by specific regulatory circuits, the abundance of proteins and transcripts can also be influenced by physiological states of the cell such as growth rate and metabolism. Here we examine the control of gene expression by growth rate and metabolism, by analyzing a multi-omics dataset consisting of absolute-quantitative abundances of the transcriptome, proteome, and amino acids in 22 steady-state yeast cultures. We find that transcription and translation are coordinately controlled by the cell growth rate via RNA polymerase II and ribosome abundance, but they are independently controlled by nitrogen metabolism via amino acid and nucleotide availabilities. Genes in central carbon metabolism, however, are distinctly regulated and do not respond to the cell growth rate or nitrogen metabolism as all other genes. Understanding these effects allows the confounding factors of growth rate and metabolism to be accounted for in gene expression profiling studies.
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Affiliation(s)
- Rosemary Yu
- Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburgSweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of TechnologyGothenburgSweden
| | - Egor Vorontsov
- Proteomics Core Facility, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy, University of GothenburgGothenburgSweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburgSweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of TechnologyGothenburgSweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of DenmarkLyngbyDenmark
- BioInnovation InstituteCopenhagenDenmark
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30
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Sudzinová P, Kambová M, Ramaniuk O, Benda M, Šanderová H, Krásný L. Effects of DNA Topology on Transcription from rRNA Promoters in Bacillus subtilis. Microorganisms 2021; 9:microorganisms9010087. [PMID: 33401387 PMCID: PMC7824091 DOI: 10.3390/microorganisms9010087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 01/24/2023] Open
Abstract
The expression of rRNA is one of the most energetically demanding cellular processes and, as such, it must be stringently controlled. Here, we report that DNA topology, i.e., the level of DNA supercoiling, plays a role in the regulation of Bacillus subtilis σA-dependent rRNA promoters in a growth phase-dependent manner. The more negative DNA supercoiling in exponential phase stimulates transcription from rRNA promoters, and DNA relaxation in stationary phase contributes to cessation of their activity. Novobiocin treatment of B. subtilis cells relaxes DNA and decreases rRNA promoter activity despite an increase in the GTP level, a known positive regulator of B. subtilis rRNA promoters. Comparative analyses of steps during transcription initiation then reveal differences between rRNA promoters and a control promoter, Pveg, whose activity is less affected by changes in supercoiling. Additional data then show that DNA relaxation decreases transcription also from promoters dependent on alternative sigma factors σB, σD, σE, σF, and σH with the exception of σN where the trend is the opposite. To summarize, this study identifies DNA topology as a factor important (i) for the expression of rRNA in B. subtilis in response to nutrient availability in the environment, and (ii) for transcription activities of B. subtilis RNAP holoenzymes containing alternative sigma factors.
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31
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Zhang Q, Zhang Z, Shi H. Cell Size Is Coordinated with Cell Cycle by Regulating Initiator Protein DnaA in E. coli. Biophys J 2020; 119:2537-2557. [PMID: 33189684 DOI: 10.1016/j.bpj.2020.10.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/22/2020] [Accepted: 10/16/2020] [Indexed: 10/23/2022] Open
Abstract
Sixty years ago, bacterial cell size was found to be an exponential function of growth rate. Fifty years ago, a more general relationship was proposed, in which cell mass was equal to the initiation mass multiplied by 2 to the power of the ratio of the total time of C and D periods to the doubling time. This relationship has recently been experimentally confirmed by perturbing doubling time, C period, D period, or initiation mass. However, the underlying molecular mechanism remains unclear. Here, we developed a theoretical model for initiator protein DnaA mediating DNA replication initiation in Escherichia coli. We introduced an initiation probability function for competitive binding of DnaA-ATP and DnaA-ADP at oriC. We established a kinetic description of regulatory processes (e.g., expression regulation, titration, inactivation, and reactivation) of DnaA. Cell size as a spatial constraint also participates in the regulation of DnaA. By simulating DnaA kinetics, we obtained a regular DnaA oscillation coordinated with cell cycle and a converged cell size that matches replication initiation frequency to the growth rate. The relationship between the simulated cell size and growth rate, C period, D period, or initiation mass reproduces experimental results. The model also predicts how DnaA number and initiation mass vary with perturbation parameters, comparable with experimental data. The results suggest that 1) when growth rate, C period, or D period changes, the regulation of DnaA determines the invariance of initiation mass; 2) ppGpp inhibition of replication initiation may be important for the growth rate independence of initiation mass because three possible mechanisms therein produce different DnaA dynamics, which is experimentally verifiable; and 3) perturbation of some DnaA regulatory process causes a changing initiation mass or even an abnormal cell cycle. This study may provide clues for concerted control of cell size and cell cycle in synthetic biology.
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Affiliation(s)
- Qing Zhang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China.
| | - Zhichao Zhang
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China
| | - Hualin Shi
- CAS Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China.
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32
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Wlodarski M, Mancini L, Raciti B, Sclavi B, Lagomarsino MC, Cicuta P. Cytosolic Crowding Drives the Dynamics of Both Genome and Cytosol in Escherichia coli Challenged with Sub-lethal Antibiotic Treatments. iScience 2020; 23:101560. [PMID: 33083729 PMCID: PMC7522891 DOI: 10.1016/j.isci.2020.101560] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/22/2020] [Accepted: 09/10/2020] [Indexed: 11/28/2022] Open
Abstract
In contrast to their molecular mode of action, the system-level effect of antibiotics on cells is only beginning to be quantified. Molecular crowding is expected to be a relevant global regulator, which we explore here through the dynamic response phenotypes in Escherichia coli, at single-cell resolution, under sub-lethal regimes of different classes of clinically relevant antibiotics, acting at very different levels in the cell. We measure chromosomal mobility through tracking of fast (<15 s timescale) fluctuations of fluorescently tagged chromosomal loci, and we probe the fluidity of the cytoplasm by tracking cytosolic aggregates. Measuring cellular density, we show how the overall levels of macromolecular crowding affect both quantities, regardless of antibiotic-specific effects. The dominant trend is a strong correlation between the effects in different parts of the chromosome and between the chromosome and cytosol, supporting the concept of an overall global role of molecular crowding in cellular physiology.
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Affiliation(s)
- Michal Wlodarski
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Dipartimento di Fisica and I.N.F.N., Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy
| | - Leonardo Mancini
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Bianca Raciti
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Bianca Sclavi
- Laboratory of Biology and Applied Pharmacology (UMR 8113 CNRS), École Normale Supérieure, Paris-Saclay, France
| | | | - Pietro Cicuta
- IFOM Foundation FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
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33
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Espah Borujeni A, Zhang J, Doosthosseini H, Nielsen AAK, Voigt CA. Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage. Nat Commun 2020; 11:5001. [PMID: 33020480 PMCID: PMC7536230 DOI: 10.1038/s41467-020-18630-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
To perform their computational function, genetic circuits change states through a symphony of genetic parts that turn regulator expression on and off. Debugging is frustrated by an inability to characterize parts in the context of the circuit and identify the origins of failures. Here, we take snapshots of a large genetic circuit in different states: RNA-seq is used to visualize circuit function as a changing pattern of RNA polymerase (RNAP) flux along the DNA. Together with ribosome profiling, all 54 genetic parts (promoters, ribozymes, RBSs, terminators) are parameterized and used to inform a mathematical model that can predict circuit performance, dynamics, and robustness. The circuit behaves as designed; however, it is riddled with genetic errors, including cryptic sense/antisense promoters and translation, attenuation, incorrect start codons, and a failed gate. While not impacting the expected Boolean logic, they reduce the prediction accuracy and could lead to failures when the parts are used in other designs. Finally, the cellular power (RNAP and ribosome usage) required to maintain a circuit state is calculated. This work demonstrates the use of a small number of measurements to fully parameterize a regulatory circuit and quantify its impact on host.
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Affiliation(s)
- Amin Espah Borujeni
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jing Zhang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hamid Doosthosseini
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alec A K Nielsen
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Christopher A Voigt
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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34
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Abstract
Exposure of bacteria to sublethal concentrations of antibiotics can lead to bacterial adaptation and survival at higher doses of inhibitors, which in turn can lead to the emergence of antibiotic resistance. The presence of sublethal concentrations of antibiotics targeting translation results in an increase in the amount of ribosomes per cell but nonetheless a decrease in the cells’ growth rate. In this work, we have found that inhibition of ribosome activity can result in a decrease in the amount of free RNA polymerase available for transcription, thus limiting the protein expression rate via a different pathway than what was expected. This result can be explained by our observation that long genes, such as those coding for RNA polymerase subunits, have a higher probability of premature translation termination in the presence of ribosome inhibitors, while expression of short ribosomal genes is affected less, consistent with their increased concentration. In bacterial cells, inhibition of ribosomes by sublethal concentrations of antibiotics leads to a decrease in the growth rate despite an increase in ribosome content. The limitation of ribosomal activity results in an increase in the level of expression from ribosomal promoters; this can deplete the pool of RNA polymerase (RNAP) that is available for the expression of nonribosomal genes. However, the magnitude of this effect remains to be quantified. Here, we use the change in the activity of constitutive promoters with different affinities for RNAP to quantify the change in the concentration of free RNAP. The data are consistent with a significant decrease in the amount of RNAP available for transcription of both ribosomal and nonribosomal genes. Results obtained with different reporter genes reveal an mRNA length dependence on the amount of full-length translated protein, consistent with the decrease in ribosome processivity affecting more strongly the translation of longer genes. The genes coding for the β and β' subunits of RNAP are among the longest genes in the Escherichia coli genome, while the genes coding for ribosomal proteins are among the shortest genes. This can explain the observed decrease in transcription capacity that favors the expression of genes whose promoters have a high affinity for RNAP, such as ribosomal promoters. IMPORTANCE Exposure of bacteria to sublethal concentrations of antibiotics can lead to bacterial adaptation and survival at higher doses of inhibitors, which in turn can lead to the emergence of antibiotic resistance. The presence of sublethal concentrations of antibiotics targeting translation results in an increase in the amount of ribosomes per cell but nonetheless a decrease in the cells’ growth rate. In this work, we have found that inhibition of ribosome activity can result in a decrease in the amount of free RNA polymerase available for transcription, thus limiting the protein expression rate via a different pathway than what was expected. This result can be explained by our observation that long genes, such as those coding for RNA polymerase subunits, have a higher probability of premature translation termination in the presence of ribosome inhibitors, while expression of short ribosomal genes is affected less, consistent with their increased concentration.
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35
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Control of ribosome synthesis in bacteria: the important role of rRNA chain elongation rate. SCIENCE CHINA-LIFE SCIENCES 2020; 64:795-802. [DOI: 10.1007/s11427-020-1742-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/26/2020] [Indexed: 10/23/2022]
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36
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Ali MZ, Parisutham V, Choubey S, Brewster RC. Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif. eLife 2020; 9:56517. [PMID: 32808926 PMCID: PMC7505660 DOI: 10.7554/elife.56517] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/07/2020] [Indexed: 12/20/2022] Open
Abstract
Predicting gene expression from DNA sequence remains a major goal in the field of gene regulation. A challenge to this goal is the connectivity of the network, whose role in altering gene expression remains unclear. Here, we study a common autoregulatory network motif, the negative single-input module, to explore the regulatory properties inherited from the motif. Using stochastic simulations and a synthetic biology approach in E. coli, we find that the TF gene and its target genes have inherent asymmetry in regulation, even when their promoters are identical; the TF gene being more repressed than its targets. The magnitude of asymmetry depends on network features such as network size and TF-binding affinities. Intriguingly, asymmetry disappears when the growth rate is too fast or too slow and is most significant for typical growth conditions. These results highlight the importance of accounting for network architecture in quantitative models of gene expression.
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Affiliation(s)
- Md Zulfikar Ali
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Vinuselvi Parisutham
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Sandeep Choubey
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Robert C Brewster
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
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37
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Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation. Proc Natl Acad Sci U S A 2020; 117:18540-18549. [PMID: 32675239 PMCID: PMC7414142 DOI: 10.1073/pnas.2005019117] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacterial cells are small and were long thought to have little to no internal structure. However, advances in microscopy have revealed that bacteria do indeed contain subcellular compartments. But how these compartments form has remained a mystery. Recent progress in larger, more complex eukaryotic cells has identified a novel mechanism for intracellular organization known as liquid–liquid phase separation. This process causes certain types of molecules to concentrate within distinct compartments inside the cell. Here, we demonstrate that the same process also occurs in bacteria. This work, together with a growing body of literature, suggests that liquid–liquid phase separation is a common mechanism for intracellular organization in both eukaryotic and prokaryotic cells. Once described as mere “bags of enzymes,” bacterial cells are in fact highly organized, with many macromolecules exhibiting nonuniform localization patterns. Yet the physical and biochemical mechanisms that govern this spatial heterogeneity remain largely unknown. Here, we identify liquid–liquid phase separation (LLPS) as a mechanism for organizing clusters of RNA polymerase (RNAP) in Escherichia coli. Using fluorescence imaging, we show that RNAP quickly transitions from a dispersed to clustered localization pattern as cells enter log phase in nutrient-rich media. RNAP clusters are sensitive to hexanediol, a chemical that dissolves liquid-like compartments in eukaryotic cells. In addition, we find that the transcription antitermination factor NusA forms droplets in vitro and in vivo, suggesting that it may nucleate RNAP clusters. Finally, we use single-molecule tracking to characterize the dynamics of cluster components. Our results indicate that RNAP and NusA molecules move inside clusters, with mobilities faster than a DNA locus but slower than bulk diffusion through the nucleoid. We conclude that RNAP clusters are biomolecular condensates that assemble through LLPS. This work provides direct evidence for LLPS in bacteria and demonstrates that this process can serve as a mechanism for intracellular organization in prokaryotes and eukaryotes alike.
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38
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Kostinski S, Reuveni S. Ribosome Composition Maximizes Cellular Growth Rates in E. coli. PHYSICAL REVIEW LETTERS 2020; 125:028103. [PMID: 32701325 DOI: 10.1103/physrevlett.125.028103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
Bacterial ribosomes are composed of one-third protein and two-thirds RNA by mass. The predominance of RNA is often attributed to a primordial RNA world, but why exactly two-thirds remains a long-standing mystery. Here we present a quantitative analysis, based on the kinetics of ribosome self-replication, demonstrating that the 1∶2 protein-to-RNA mass ratio uniquely maximizes cellular growth rates in E. coli. A previously unrecognized growth law, and an invariant of bacterial growth, also follow from our analysis. The growth law reveals that the ratio between the number of ribosomes and the number of polymerases making ribosomal RNA is proportional to the cellular doubling time. The invariant is conserved across growth conditions and specifies how key microscopic parameters in the cell, such as transcription and translation rates, are coupled to cellular physiology. Quantitative predictions from the growth law and invariant are shown to be in excellent agreement with E. coli data despite having no fitting parameters. Our analysis can be readily extended to other bacteria once data become available.
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Affiliation(s)
- Sarah Kostinski
- School of Chemistry, Center for the Physics & Chemistry of Living Systems, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Shlomi Reuveni
- School of Chemistry, Center for the Physics & Chemistry of Living Systems, Tel Aviv University, 6997801 Tel Aviv, Israel
- Sackler Center for Computational Molecular & Materials Science, Ratner Institute for Single Molecule Chemistry, Tel Aviv University, 6997801 Tel Aviv, Israel
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39
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Zhang R, Li J, Melendez-Alvarez J, Chen X, Sochor P, Goetz H, Zhang Q, Ding T, Wang X, Tian XJ. Topology-dependent interference of synthetic gene circuit function by growth feedback. Nat Chem Biol 2020; 16:695-701. [PMID: 32251409 PMCID: PMC7246135 DOI: 10.1038/s41589-020-0509-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 02/28/2020] [Indexed: 11/21/2022]
Abstract
Growth-mediated feedback between synthetic gene circuits and host organisms leads to diverse emerged behaviors, including growth bistability and enhanced ultrasensitivity. However, the range of possible impacts of growth feedback on gene circuits remains underexplored. Here, we mathematically and experimentally demonstrated that growth feedback affects the functions of memory circuits in a network topology-dependent way. Specifically, the memory of the self-activation switch is quickly lost due to the growth-mediated dilution of the circuit products. Decoupling of growth feedback reveals its memory, manifested by its hysteresis property across a broad range of inducer concentration. On the contrary, the toggle switch is more refractory to growth-mediated dilution and can retrieve its memory after the fast-growth phase. The underlying principle lies in the different dependence of active and repressive regulations in these circuits on the growth-mediated dilution. Our results unveil the topology-dependent mechanism on how growth-mediated feedback influences the behaviors of gene circuits.
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Affiliation(s)
- Rong Zhang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Jiao Li
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.,Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
| | - Juan Melendez-Alvarez
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Xingwen Chen
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Patrick Sochor
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Hanah Goetz
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Qi Zhang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiao Wang
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.
| | - Xiao-Jun Tian
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA.
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40
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A model for the interplay between plastic tradeoffs and evolution in changing environments. Proc Natl Acad Sci U S A 2020; 117:8934-8940. [PMID: 32245811 DOI: 10.1073/pnas.1915537117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Performance tradeoffs are ubiquitous in both ecological and evolutionary modeling, yet they are usually postulated and built into fitness and ecological landscapes. However, tradeoffs depend on genetic background and evolutionary history and can themselves evolve. We present a simple model capable of capturing the key feedback loop: evolutionary history shapes tradeoff strength, which, in turn, shapes evolutionary future. One consequence of this feedback is that genomes with identical fitness can have different evolutionary properties shaped by prior environmental exposure. Another is that, generically, the best adaptations to one environment may evolve in another. Our simple framework bridges the gap between the phenotypic Fisher's Geometric Model and the genotypic properties, such as modularity and evolvability, and can serve as a rich playground for investigating evolution in multiple or changing environments.
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41
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Yubero P, Poyatos JF. The Impact of Global Transcriptional Regulation on Bacterial Gene Order. iScience 2020; 23:101029. [PMID: 32283521 PMCID: PMC7155222 DOI: 10.1016/j.isci.2020.101029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 12/15/2019] [Accepted: 03/27/2020] [Indexed: 12/04/2022] Open
Abstract
Bacterial gene expression depends on the allocation of limited transcriptional resources provided a particular growth rate and growth condition. Early studies in a few genes suggested this global regulation to generate a unifying hyperbolic expression pattern. Here, we developed a large-scale method that generalizes these experiments to quantify the response to growth of over 700 genes that a priori do not exhibit any specific control. We distinguish a core subset following a promoter-specific hyperbolic response. Within this group, we sort genes with regard to their responsiveness to the global regulatory program to show that those with a particularly sensitive linear response are located near the origin of replication. We then find evidence that this genomic architecture is biologically significant by examining position conservation of E. coli genes in 100 bacteria. The response to the transcriptional resources of the cell results in an additional feature contributing to bacterial genome organization. Cell physiology determines a global transcriptional regulatory program Constitutive genes show a differential response to this global regulation The most responsive constitutive genes are located near the origin of replication Global transcriptional regulation acts as a gene position conservation force
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Affiliation(s)
- Pablo Yubero
- Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain
| | - Juan F Poyatos
- Logic of Genomic Systems Laboratory, CNB - CSIC, Madrid 28049, Spain.
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42
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Planson AG, Sauveplane V, Dervyn E, Jules M. Bacterial growth physiology and RNA metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194502. [PMID: 32044462 DOI: 10.1016/j.bbagrm.2020.194502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/17/2020] [Accepted: 02/06/2020] [Indexed: 12/31/2022]
Abstract
Bacteria are sophisticated systems with high capacity and flexibility to adapt to various environmental conditions. Each prokaryote however possesses a defined metabolic network, which sets its overall metabolic capacity, and therefore the maximal growth rate that can be reached. To achieve optimal growth, bacteria adopt various molecular strategies to optimally adjust gene expression and optimize resource allocation according to the nutrient availability. The resulting physiological changes are often accompanied by changes in the growth rate, and by global regulation of gene expression. The growth-rate-dependent variation of the abundances in the cellular machineries, together with condition-specific regulatory mechanisms, affect RNA metabolism and fate and pose a challenge for rational gene expression reengineering of synthetic circuits. This article is part of a Special Issue entitled: RNA and gene control in bacteria, edited by Dr. M. Guillier and F. Repoila.
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Affiliation(s)
- Anne-Gaëlle Planson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Vincent Sauveplane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Etienne Dervyn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Matthieu Jules
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
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43
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Dessalles R, Fromion V, Robert P. Models of protein production along the cell cycle: An investigation of possible sources of noise. PLoS One 2020; 15:e0226016. [PMID: 31945071 PMCID: PMC6964835 DOI: 10.1371/journal.pone.0226016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 11/18/2019] [Indexed: 01/20/2023] Open
Abstract
In this article, we quantitatively study, through stochastic models, the effects of several intracellular phenomena, such as cell volume growth, cell division, gene replication as well as fluctuations of available RNA polymerases and ribosomes. These phenomena are indeed rarely considered in classic models of protein production and no relative quantitative comparison among them has been performed. The parameters for a large and representative class of proteins are determined using experimental measures. The main important and surprising conclusion of our study is to show that despite the significant fluctuations of free RNA polymerases and free ribosomes, they bring little variability to protein production contrary to what has been previously proposed in the literature. After verifying the robustness of this quite counter-intuitive result, we discuss its possible origin from a theoretical view, and interpret it as the result of a mean-field effect.
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Affiliation(s)
- Renaud Dessalles
- Dept. of Biomathematics, UCLA, Los Angeles, CA, United States of America
| | - Vincent Fromion
- MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
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44
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Ledezma-Tejeida D, Altamirano-Pacheco L, Fajardo V, Collado-Vides J. Limits to a classic paradigm: most transcription factors in E. coli regulate genes involved in multiple biological processes. Nucleic Acids Res 2020; 47:6656-6667. [PMID: 31194874 PMCID: PMC6649764 DOI: 10.1093/nar/gkz525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/29/2019] [Accepted: 06/04/2019] [Indexed: 01/12/2023] Open
Abstract
Transcription factors (TFs) are important drivers of cellular decision-making. When bacteria encounter a change in the environment, TFs alter the expression of a defined set of genes in order to adequately respond. It is commonly assumed that genes regulated by the same TF are involved in the same biological process. Examples of this are methods that rely on coregulation to infer function of not-yet-annotated genes. We have previously shown that only 21% of TFs involved in metabolism regulate functionally homogeneous genes, based on the proximity of the gene products’ catalyzed reactions in the metabolic network. Here, we provide more evidence to support the claim that a 1-TF/1-process relationship is not a general property. We show that the observed functional heterogeneity of regulons is not a result of the quality of the annotation of regulatory interactions, nor the absence of protein–metabolite interactions, and that it is also present when function is defined by Gene Ontology terms. Furthermore, the observed functional heterogeneity is different from the one expected by chance, supporting the notion that it is a biological property. To further explore the relationship between transcriptional regulation and metabolism, we analyzed five other types of regulatory groups and identified complex regulons (i.e. genes regulated by the same combination of TFs) as the most functionally homogeneous, and this is supported by coexpression data. Whether higher levels of related functions exist beyond metabolism and current functional annotations remains an open question.
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Affiliation(s)
- Daniela Ledezma-Tejeida
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.,Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Luis Altamirano-Pacheco
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Vicente Fajardo
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
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45
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Rybkin I, Gorin D, Sukhorukov G, Lapanje A. Thickness of Polyelectrolyte Layers of Separately Confined Bacteria Alters Key Physiological Parameters on a Single Cell Level. Front Bioeng Biotechnol 2019; 7:378. [PMID: 31867314 PMCID: PMC6904277 DOI: 10.3389/fbioe.2019.00378] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/14/2019] [Indexed: 12/18/2022] Open
Abstract
Confinement of bacterial cells in a matrix or in capsules is an integral part of many biotechnological applications. Here, the well-known layer-by-layer method of deposition of a polyelectrolyte film a few nanometers in thickness to confine separated bacterial cells in permeable and physically durable shells has been examined. Due to the physical properties of such a confinement, we found that this method enables investigation of effects of physical barriers against mass gain and cell division. Using the method of time-lapse confocal microscopy, we observed a prolonged lag phase, dependent on the number of polyelectrolyte layers. In the confinement, both the GFP fluorescent signal from the leaking T7 promoter and the cell size were increased by factors of more than five and two, respectively. This creates a paradigm shift that enables use of mechanical entrapment for control of bacterial cell physiology and opens possibilities of controlling the division rate as well as gene expression. These effects can be attributed to the perturbation of the sensing of the cell size, which results in disproportional synthesis of a cell envelope impinging the intracellular material and compels cells to grow rapidly. In addition, the charged surface of cells enables prolonged intercellular physical interaction and results in spherically shaped microcolonies.
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Affiliation(s)
- Iaroslav Rybkin
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia.,Remote Controlled Theranostic Systems Lab, Institute of Nanostructures and Biosystems, Saratov State University, Saratov, Russia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia.,Department of Reactive Transport, Helmholtz Zentrum Dresden Rossendorf, Institute of Resource Ecology, Leipzig, Germany
| | - Dmitry Gorin
- Remote Controlled Theranostic Systems Lab, Institute of Nanostructures and Biosystems, Saratov State University, Saratov, Russia.,Center for Photonics and Quantum Materials, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Gleb Sukhorukov
- Remote Controlled Theranostic Systems Lab, Institute of Nanostructures and Biosystems, Saratov State University, Saratov, Russia.,School of Engineering and Materials Science, Queen Mary University of London, London, United Kingdom
| | - Aleš Lapanje
- Department of Environmental Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
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46
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Li X, Chen L, Wang X, Tian P. Physiological investigations of the influences of byproduct pathways on 3-hydroxypropionic acid production in Klebsiella pneumoniae. J Basic Microbiol 2019; 59:1195-1207. [PMID: 31617952 DOI: 10.1002/jobm.201800640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 08/20/2019] [Accepted: 09/29/2019] [Indexed: 01/03/2023]
Abstract
Klebsiella pneumoniae can naturally synthesize 3-hydroxypropionic acid (3-HP), 1,3-propanediol (1,3-PD), and 2,3-butanediol (2,3-BD) from glycerol. However, biosynthesis of these industrially important chemicals is constrained by troublesome byproducts. To clarify the influences of byproducts on 3-HP production, in this study, a total of eight byproduct-producing enzyme genes including pmd, poxB, frdB, fumC, dhaT, ilvH, adhP, and pflB were individually deleted from the K. pneumoniae genome. The resultant eight mutants presented different levels of metabolites. In 24-h shake-flask cultivation, the adhP- and pflB-deletion mutants produced 0.41 and 0.44 g/L 3-HP, respectively. Notably, the adhP and pflB double deletion mutant K. pneumoniaeΔadhPΔpflB produced 1.58 g/L 3-HP in 24-h shake-flask cultivation. When K. pneumoniaeΔadhPΔpflB was harnessed as a host strain to overexpress PuuC, a native aldehyde dehydrogenase (ALDH) catalyzing 3-hydroxypropionaldehyde (3-HPA) to 3-HP, the resulting recombinant strain K. pneumoniaeΔadhPΔpflB(pTAC-puuC) (pTAC-puuC is PuuC expression vector) generated 66.91 g/L 3-HP with a cumulative yield of 70.84% on glycerol in 60-h bioreactor cultivation. Additionally, this strain showed 2.3-, 5.1-, and 0.67-fold decrease in the concentrations of 1,3-PD, 2,3-BD, and acetic acid compared with the reference strain K. pneumoniae(pTAC-puuC). These results indicated that the byproducts exerted differential impacts on the production of 3-HP, 1,3-PD, and 2,3-BD. Although combinatorial elimination of byproduct pathways could reprogram glycerol flux, the enzyme 1,3-propanediol oxidoreductase (DhaT) that catalyzes 3-HPA to 1,3-PD and the enzymes ALDHs, especially, PuuC are most pivotal for 3-HP production. This study provides a deep understanding of how byproducts affect the production of 3-HP, 1,3-PD, and 2,3-BD in K. pneumoniae.
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Affiliation(s)
- Xiaohan Li
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Liuni Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiuling Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Pingfang Tian
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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47
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Brandão HB, Paul P, van den Berg AA, Rudner DZ, Wang X, Mirny LA. RNA polymerases as moving barriers to condensin loop extrusion. Proc Natl Acad Sci U S A 2019; 116:20489-20499. [PMID: 31548377 PMCID: PMC6789630 DOI: 10.1073/pnas.1907009116] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with ongoing transcription. How transcription interferes with the condensin loop-extrusion process is largely unexplored, but recent experiments have shown that sites of high transcription may directionally affect condensin loop extrusion. We quantitatively investigate different mechanisms of interaction between condensin and elongating RNA polymerases (RNAPs) and find that RNAPs are likely steric barriers that can push and interact with condensins. Supported by chromosome conformation capture and chromatin immunoprecipitation for cells after transcription inhibition and RNAP degradation, we argue that translocating condensins must bypass transcribing RNAPs within ∼1 to 2 s of an encounter at rRNA genes and within ∼10 s at protein-coding genes. Thus, while individual RNAPs have little effect on the progress of loop extrusion, long, highly transcribed operons can significantly impede the extrusion process. Our data and quantitative models further suggest that bacterial condensin loop extrusion occurs by 2 independent, uncoupled motor activities; the motors translocate on DNA in opposing directions and function together to enlarge chromosomal loops, each independently bypassing steric barriers in their path. Our study provides a quantitative link between transcription and 3D genome organization and proposes a mechanism of interactions between SMC complexes and elongating transcription machinery relevant from bacteria to higher eukaryotes.
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Affiliation(s)
- Hugo B Brandão
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138
| | - Payel Paul
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Aafke A van den Berg
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47405;
| | - Leonid A Mirny
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138;
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
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48
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Kim J, Darlington A, Salvador M, Utrilla J, Jiménez JI. Trade-offs between gene expression, growth and phenotypic diversity in microbial populations. Curr Opin Biotechnol 2019; 62:29-37. [PMID: 31580950 PMCID: PMC7208540 DOI: 10.1016/j.copbio.2019.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022]
Abstract
Limitations in molecular resources for gene expression influence bacterial physiology. Bacteria optimise trade-offs between resource allocation and growth. Resource allocation plays a role in the emergence of phenotypic heterogeneity. Trade-offs between bet-hedging and growth can be harnessed in biotechnology.
Bacterial cells have a limited number of resources that can be allocated for gene expression. The intracellular competition for these resources has an impact on the cell physiology. Bacteria have evolved mechanisms to optimize resource allocation in a variety of scenarios, showing a trade-off between the resources used to maximise growth (e.g. ribosome synthesis) and the rest of cellular functions. Limitations in gene expression also play a role in generating phenotypic diversity, which is advantageous in fluctuating environments, at the expenses of decreasing growth rates. Our current understanding of these trade-offs can be exploited for biotechnological applications benefiting from the selective manipulation of the allocation of resources.
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Affiliation(s)
- Juhyun Kim
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | | | - Manuel Salvador
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | - José Utrilla
- Centre for Genomic Sciences, Universidad Nacional Autónoma de México, Campus Morelos, Av. Universidad s/n Col. Chamilpa 62210, Cuernavaca, Mexico
| | - José I Jiménez
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom.
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49
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WellInverter: a web application for the analysis of fluorescent reporter gene data. BMC Bioinformatics 2019; 20:309. [PMID: 31185910 PMCID: PMC6558888 DOI: 10.1186/s12859-019-2920-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022] Open
Abstract
Background Fluorescent reporter genes have become widely used for monitoring gene expression in living cells. When a microbial strain carrying a reporter gene is grown in a microplate reader, the fluorescence and the absorbance (optical density) of the culture can be automatically measured every few minutes in a highly parallelized way. The extraction of useful information from the resulting large amounts of data is not easy to achieve, because the fluorescence and absorbance measurements are only indirectly related to promoter activities and protein concentrations, requiring mathematical models of the expression of reporter genes for their interpretation. Although the principles of the analysis of reporter gene data are well-established today, there is a lack of general-purpose bioinformatics tools based on generic measurement models and sound inference procedures. This has motivated the development of WellInverter, a web application based on well-known methods for regularized linear inversion. Results We present a new version of WellInverter that considerably improves the performance and usability of the original application. In particular, we have put in place a parallel computing architecture with a load balancer to distribute analysis queries over several back-end servers, we have completely redesigned the graphical user interface to better support the different analysis steps, and we have developed a plug-in system for the parsing of data files produced by microplate readers from different manufacturers. We illustrate the functioning of WellInverter by analyzing data of the expression of a fluorescent reporter gene controlled by a phage promoter in growing Escherichia coli populations. We show that the expression pattern in different growth media, supporting different growth rates, corresponds to the pattern expected for a constitutive gene. Conclusions The new version of WellInverter is a robust, easy-to-use and scalable web application, which has been deployed on two publicly accessible web servers and which can also be installed locally. A demo version of the application with two sample datasets is available on-line. Electronic supplementary material The online version of this article (10.1186/s12859-019-2920-4) contains supplementary material, which is available to authorized users.
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50
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Exploiting tandem repetitive promoters for high-level production of 3-hydroxypropionic acid. Appl Microbiol Biotechnol 2019; 103:4017-4031. [DOI: 10.1007/s00253-019-09772-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
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