1
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Curry E, Muir G, Qu J, Kis Z, Hulley M, Brown A. Engineering an Escherichia coli based in vivo mRNA manufacturing platform. Biotechnol Bioeng 2024; 121:1912-1926. [PMID: 38419526 DOI: 10.1002/bit.28684] [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: 11/03/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
Abstract
Synthetic mRNA is currently produced in standardized in vitro transcription systems. However, this one-size-fits-all approach has associated drawbacks in supply chain shortages, high reagent costs, complex product-related impurity profiles, and limited design options for molecule-specific optimization of product yield and quality. Herein, we describe for the first time development of an in vivo mRNA manufacturing platform, utilizing an Escherichia coli cell chassis. Coordinated mRNA, DNA, cell and media engineering, primarily focussed on disrupting interactions between synthetic mRNA molecules and host cell RNA degradation machinery, increased product yields >40-fold compared to standard "unengineered" E. coli expression systems. Mechanistic dissection of cell factory performance showed that product mRNA accumulation levels approached theoretical limits, accounting for ~30% of intracellular total RNA mass, and that this was achieved via host-cell's reallocating biosynthetic capacity away from endogenous RNA and cell biomass generation activities. We demonstrate that varying sized functional mRNA molecules can be produced in this system and subsequently purified. Accordingly, this study introduces a new mRNA production technology, expanding the solution space available for mRNA manufacturing.
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Affiliation(s)
- Edward Curry
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - George Muir
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Jixin Qu
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Zoltán Kis
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | | | - Adam Brown
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
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2
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Zhou Y, Sun H, Rapiejko AR, Vargas-Blanco DA, Martini MC, Chase MR, Joubran SR, Davis AB, Dainis JP, Kelly JM, Ioerger TR, Roberts LA, Fortune SM, Shell SS. Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of most Mycolicibacterium smegmatis mRNAs. J Biol Chem 2023; 299:105312. [PMID: 37802316 PMCID: PMC10641625 DOI: 10.1016/j.jbc.2023.105312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/29/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023] Open
Abstract
The mechanisms and regulation of RNA degradation in mycobacteria have been subject to increased interest following the identification of interplay between RNA metabolism and drug resistance. Mycobacteria encode multiple ribonucleases predicted to participate in mRNA degradation and/or processing of stable RNAs. RNase E is hypothesized to play a major role in mRNA degradation because of its essentiality in mycobacteria and its role in mRNA degradation in gram-negative bacteria. Here, we defined the impact of RNase E on mRNA degradation rates transcriptome-wide in the nonpathogenic model Mycolicibacterium smegmatis. RNase E played a rate-limiting role in degradation of the transcripts encoded by at least 89% of protein-coding genes, with leadered transcripts often being more affected by RNase E repression than leaderless transcripts. There was an apparent global slowing of transcription in response to knockdown of RNase E, suggesting that M. smegmatis regulates transcription in responses to changes in mRNA degradation. This compensation was incomplete, as the abundance of most transcripts increased upon RNase E knockdown. We assessed the sequence preferences for cleavage by RNase E transcriptome-wide in M. smegmatis and Mycobacterium tuberculosis and found a consistent bias for cleavage in C-rich regions. Purified RNase E had a clear preference for cleavage immediately upstream of cytidines, distinct from the sequence preferences of RNase E in gram-negative bacteria. We furthermore report a high-resolution map of mRNA cleavage sites in M. tuberculosis, which occur primarily within the RNase E-preferred sequence context, confirming that RNase E has a broad impact on the M. tuberculosis transcriptome.
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Affiliation(s)
- Ying Zhou
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Huaming Sun
- Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Abigail R Rapiejko
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Diego A Vargas-Blanco
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Maria Carla Martini
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Michael R Chase
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Samantha R Joubran
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Alexa B Davis
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Joseph P Dainis
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Jessica M Kelly
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Thomas R Ioerger
- Department of Computer Science & Engineering, Texas A&M University, College Station, Texas, USA
| | - Louis A Roberts
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA.
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3
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Tomlinson BR, Denham GA, Torres NJ, Brzozowski RS, Allen JL, Jackson JK, Eswara PJ, Shaw LN. Assessing the Role of Cold-Shock Protein C: a Novel Regulator of Acinetobacter baumannii Biofilm Formation and Virulence. Infect Immun 2022; 90:e0037622. [PMID: 36121221 PMCID: PMC9584223 DOI: 10.1128/iai.00376-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii is a formidable opportunistic pathogen that is notoriously difficult to eradicate from hospital settings. This resilience is often attributed to a proclivity for biofilm formation, which facilitates a higher tolerance toward external stress, desiccation, and antimicrobials. Despite this, little is known regarding the mechanisms orchestrating A. baumannii biofilm formation. Here, we performed RNA sequencing (RNA-seq) on biofilm and planktonic populations for the multidrug-resistant isolate AB5075 and identified 438 genes with altered expression. To assess the potential role of genes upregulated within biofilms, we tested the biofilm-forming capacity of their respective mutants from an A. baumannii transposon library. In so doing, we uncovered 24 genes whose disruption led to reduced biofilm formation. One such element, cold shock protein C (cspC), had a highly mucoid colony phenotype, enhanced tolerance to polysaccharide degradation, altered antibiotic tolerance, and diminished adherence to abiotic surfaces. RNA-seq of the cspC mutant revealed 201 genes with altered expression, including the downregulation of pili and fimbria genes and the upregulation of multidrug efflux pumps. Using transcriptional arrest assays, it appears that CspC mediates its effects, at least in part, through RNA chaperone activity, influencing the half-life of several important transcripts. Finally, we show that CspC is required for survival during challenge by the human immune system and is key for A. baumannii dissemination and/or colonization during systemic infection. Collectively, our work identifies a cadre of new biofilm-associated genes within A. baumannii and provides unique insight into the global regulatory network of this emerging human pathogen.
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Affiliation(s)
- Brooke R. Tomlinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Grant A. Denham
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Nathanial J. Torres
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Robert S. Brzozowski
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Jessie L. Allen
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Jessica K. Jackson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Prahathees J. Eswara
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
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4
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Buck LD, Paladino MM, Nagashima K, Brezel ER, Holtzman JS, Urso SJ, Ryno LM. Temperature-Dependent Influence of FliA Overexpression on PHL628 E. coli Biofilm Growth and Composition. Front Cell Infect Microbiol 2022; 11:775270. [PMID: 34976858 PMCID: PMC8718923 DOI: 10.3389/fcimb.2021.775270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Biofilm growth and survival pose a problem in both medical and industrial fields. Bacteria in biofilms are more tolerant to antibiotic treatment due to the inability of antibiotics to permeate to the bottom layers of cells in a biofilm and the creation of altered microenvironments of bacteria deep within the biofilm. Despite the abundance of information we have about E. coli biofilm growth and maturation, we are still learning how manipulating different signaling pathways influences the formation and fitness of biofilm. Understanding the impact of signaling pathways on biofilm formation may narrow the search for novel small molecule inhibitors or activators that affect biofilm production and stability. Here, we study the influence of the minor sigma transcription factor FliA (RpoF, sigma-28), which controls late-stage flagellar assembly and chemotaxis, on biofilm production and composition at various temperatures in the E. coli strain PHL628, which abundantly produces the extracellular structural protein curli. We examined FliA's influence on external cellular structures like curli and flagella and the biomolecular composition of the biofilm's extracellular polymeric substance (EPS) using biochemical assays, immunoblotting, and confocal laser scanning microscopy (CLSM). At 37°C, FliA overexpression results in the dramatic growth of biofilm in polystyrene plates and more modest yet significant biofilm growth on silica slides. We observed no significant differences in curli concentration and carbohydrate concentration in the EPS with FliA overexpression. Still, we did see significant changes in the abundance of EPS protein using CLSM at higher growth temperatures. We also noticed increased flagellin concentration, a major structural protein in flagella, occurred with FliA overexpression, specifically in planktonic cultures. These experiments have aided in narrowing our focus to FliA's role in changing the protein composition of the EPS, which we will examine in future endeavors.
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Affiliation(s)
- Luke D Buck
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH, United States
| | - Maddison M Paladino
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH, United States
| | - Kyogo Nagashima
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH, United States
| | - Emma R Brezel
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH, United States
| | - Joshua S Holtzman
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH, United States
| | - Sarel J Urso
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH, United States
| | - Lisa M Ryno
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH, United States
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5
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Roux C, Etienne TA, Hajnsdorf E, Ropers D, Carpousis AJ, Cocaign-Bousquet M, Girbal L. The essential role of mRNA degradation in understanding and engineering E. coli metabolism. Biotechnol Adv 2021; 54:107805. [PMID: 34302931 DOI: 10.1016/j.biotechadv.2021.107805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/28/2021] [Accepted: 07/14/2021] [Indexed: 11/17/2022]
Abstract
Metabolic engineering strategies are crucial for the development of bacterial cell factories with improved performance. Until now, optimal metabolic networks have been designed based on systems biology approaches integrating large-scale data on the steady-state concentrations of mRNA, protein and metabolites, sometimes with dynamic data on fluxes, but rarely with any information on mRNA degradation. In this review, we compile growing evidence that mRNA degradation is a key regulatory level in E. coli that metabolic engineering strategies should take into account. We first discuss how mRNA degradation interacts with transcription and translation, two other gene expression processes, to balance transcription regulation and remove poorly translated mRNAs. The many reciprocal interactions between mRNA degradation and metabolism are also highlighted: metabolic activity can be controlled by changes in mRNA degradation and in return, the activity of the mRNA degradation machinery is controlled by metabolic factors. The mathematical models of the crosstalk between mRNA degradation dynamics and other cellular processes are presented and discussed with a view towards novel mRNA degradation-based metabolic engineering strategies. We show finally that mRNA degradation-based strategies have already successfully been applied to improve heterologous protein synthesis. Overall, this review underlines how important mRNA degradation is in regulating E. coli metabolism and identifies mRNA degradation as a key target for innovative metabolic engineering strategies in biotechnology.
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Affiliation(s)
- Charlotte Roux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | - Thibault A Etienne
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; Univ. Grenoble Alpes, Inria, 38000 Grenoble, France.
| | - Eliane Hajnsdorf
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | | | - A J Carpousis
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France; LMGM, Université de Toulouse, CNRS, UPS, CBI, 31062 Toulouse, France.
| | | | - Laurence Girbal
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France.
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6
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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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7
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Forés-Martos J, Forte A, García-Martínez J, Pérez-Ortín JE. A Trans-Omics Comparison Reveals Common Gene Expression Strategies in Four Model Organisms and Exposes Similarities and Differences between Them. Cells 2021; 10:334. [PMID: 33562654 PMCID: PMC7914595 DOI: 10.3390/cells10020334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/01/2022] Open
Abstract
The ultimate goal of gene expression regulation is on the protein level. However, because the amounts of mRNAs and proteins are controlled by their synthesis and degradation rates, the cellular amount of a given protein can be attained by following different strategies. By studying omics data for six expression variables (mRNA and protein amounts, plus their synthesis and decay rates), we previously demonstrated the existence of common expression strategies (CESs) for functionally related genes in the yeast Saccharomyces cerevisiae. Here we extend that study to two other eukaryotes: the yeast Schizosaccharomyces pombe and cultured human HeLa cells. We also use genomic data from the model prokaryote Escherichia coli as an external reference. We show that six-variable profiles (6VPs) can be constructed for every gene and that these 6VPs are similar for genes with similar functions in all the studied organisms. The differences in 6VPs between organisms can be used to establish their phylogenetic relationships. The analysis of the correlations among the six variables supports the hypothesis that most gene expression control occurs in actively growing organisms at the transcription rate level, and that translation plays a minor role. We propose that living organisms use CESs for the genes acting on the same physiological pathways, especially for those belonging to stable macromolecular complexes, but CESs have been modeled by evolution to adapt to the specific life circumstances of each organism.
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Affiliation(s)
- Jaume Forés-Martos
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - Anabel Forte
- Departamento de Estadística e Investigación Operativa, Facultad de Matemáticas, Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - José García-Martínez
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
| | - José E. Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, C/Dr. Moliner 50, E46100 Burjassot, Spain;
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8
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Etienne TA, Cocaign-Bousquet M, Ropers D. Competitive effects in bacterial mRNA decay. J Theor Biol 2020; 504:110333. [PMID: 32615126 DOI: 10.1016/j.jtbi.2020.110333] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 12/15/2022]
Abstract
In living organisms, the same enzyme catalyses the degradation of thousands of different mRNAs, but the possible influence of competing substrates has been largely ignored so far. We develop a simple mechanistic model of the coupled degradation of all cell mRNAs using the total quasi-steady-state approximation of the Michaelis-Menten framework. Numerical simulations of the model using carefully chosen parameters and analyses of rate sensitivity coefficients show how substrate competition alters mRNA decay. The model predictions reproduce and explain a number of experimental observations on mRNA decay following transcription arrest, such as delays before the onset of degradation, the occurrence of variable degradation profiles with increased non linearities and the negative correlation between mRNA half-life and concentration. The competition acts at different levels, through the initial concentration of cell mRNAs and by modifying the enzyme affinity for its targets. The consequence is a global slow down of mRNA decay due to enzyme titration and the amplification of its apparent affinity. Competition happens to stabilize weakly affine mRNAs and to destabilize the most affine ones. We believe that this mechanistic model is an interesting alternative to the exponential models commonly used for the determination of mRNA half-lives. It allows analysing regulatory mechanisms of mRNA degradation and its predictions are directly comparable to experimental data.
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Affiliation(s)
- Thibault A Etienne
- TBI, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France; Univ. Grenoble Alpes, Inria, 38000 Grenoble, France
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9
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Vargas-Blanco DA, Shell SS. Regulation of mRNA Stability During Bacterial Stress Responses. Front Microbiol 2020; 11:2111. [PMID: 33013770 PMCID: PMC7509114 DOI: 10.3389/fmicb.2020.02111] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
Bacteria have a remarkable ability to sense environmental changes, swiftly regulating their transcriptional and posttranscriptional machinery as a response. Under conditions that cause growth to slow or stop, bacteria typically stabilize their transcriptomes in what has been shown to be a conserved stress response. In recent years, diverse studies have elucidated many of the mechanisms underlying mRNA degradation, yet an understanding of the regulation of mRNA degradation under stress conditions remains elusive. In this review we discuss the diverse mechanisms that have been shown to affect mRNA stability in bacteria. While many of these mechanisms are transcript-specific, they provide insight into possible mechanisms of global mRNA stabilization. To that end, we have compiled information on how mRNA fate is affected by RNA secondary structures; interaction with ribosomes, RNA binding proteins, and small RNAs; RNA base modifications; the chemical nature of 5' ends; activity and concentration of RNases and other degradation proteins; mRNA and RNase localization; and the stringent response. We also provide an analysis of reported relationships between mRNA abundance and mRNA stability, and discuss the importance of stress-associated mRNA stabilization as a potential target for therapeutic development.
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Affiliation(s)
- Diego A Vargas-Blanco
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States.,Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
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10
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Stochastic models coupling gene expression and partitioning in cell division in Escherichia coli. Biosystems 2020; 193-194:104154. [PMID: 32353481 DOI: 10.1016/j.biosystems.2020.104154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 04/03/2020] [Accepted: 04/16/2020] [Indexed: 12/18/2022]
Abstract
Regulation of future RNA and protein numbers is a key process by which cells continuously best fit the environment. In bacteria, RNA and proteins exist in small numbers and their regulatory processes are stochastic. Consequently, there is cell-to-cell variability in these numbers, even between sister cells. Traditionally, the two most studied sources of this variability are gene expression and RNA and protein degradation, with evidence suggesting that the latter is subject to little regulation, when compared to the former. However, time-lapse microscopy and single molecule fluorescent tagging have produced evidence that cell division can also be a significant source of variability due to asymmetries in the partitioning of RNA and proteins. Relevantly, the impact of this noise differs from noise in production and degradation since, unlike these, it is not continuous. Rather, it occurs at specific time points, at which moment it can introduce major fluctuations. Several models have now been proposed that integrate noise from cell division, in addition to noise in gene expression, to mimic the dynamics of RNA and protein numbers of cell lineages. This is expected to be particularly relevant in genetic circuits, where significant fluctuations in one component protein, at specific time moments, are expected to perturb near-equilibrium states of the circuits, which can have long-lasting consequences. Here we review stochastic models coupling these processes in Escherichia coli, from single genes to small circuits.
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11
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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: 13] [Impact Index Per Article: 3.3] [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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12
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Loos MS, Ramakrishnan R, Vranken W, Tsirigotaki A, Tsare EP, Zorzini V, Geyter JD, Yuan B, Tsamardinos I, Klappa M, Schymkowitz J, Rousseau F, Karamanou S, Economou A. Structural Basis of the Subcellular Topology Landscape of Escherichia coli. Front Microbiol 2019; 10:1670. [PMID: 31404336 PMCID: PMC6677119 DOI: 10.3389/fmicb.2019.01670] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022] Open
Abstract
Cellular proteomes are distributed in multiple compartments: on DNA, ribosomes, on and inside membranes, or they become secreted. Structural properties that allow polypeptides to occupy subcellular niches, particularly to after crossing membranes, remain unclear. We compared intrinsic and extrinsic features in cytoplasmic and secreted polypeptides of the Escherichia coli K-12 proteome. Structural features between the cytoplasmome and secretome are sharply distinct, such that a signal peptide-agnostic machine learning tool distinguishes cytoplasmic from secreted proteins with 95.5% success. Cytoplasmic polypeptides are enriched in aliphatic, aromatic, charged and hydrophobic residues, unique folds and higher early folding propensities. Secretory polypeptides are enriched in polar/small amino acids, β folds, have higher backbone dynamics, higher disorder and contact order and are more often intrinsically disordered. These non-random distributions and experimental evidence imply that evolutionary pressure selected enhanced secretome flexibility, slow folding and looser structures, placing the secretome in a distinct protein class. These adaptations protect the secretome from premature folding during its cytoplasmic transit, optimize its lipid bilayer crossing and allowed it to acquire cell envelope specific chemistries. The latter may favor promiscuous multi-ligand binding, sensing of stress and cell envelope structure changes. In conclusion, enhanced flexibility, slow folding, looser structures and unique folds differentiate the secretome from the cytoplasmome. These findings have wide implications on the structural diversity and evolution of modern proteomes and the protein folding problem.
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Affiliation(s)
- Maria S Loos
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Reshmi Ramakrishnan
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.,VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, Free University of Brussels, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel and Center for Structural Biology, Brussels, Belgium
| | - Alexandra Tsirigotaki
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Evrydiki-Pandora Tsare
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas, Patras, Greece
| | - Valentina Zorzini
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jozefien De Geyter
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Biao Yuan
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Ioannis Tsamardinos
- Gnosis Data Analysis PC, Heraklion, Greece.,Department of Computer Science, University of Crete, Heraklion, Greece
| | - Maria Klappa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas, Patras, Greece
| | - Joost Schymkowitz
- VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.,Gnosis Data Analysis PC, Heraklion, Greece
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Chemical and Metabolic Controls on Dihydroxyacetone Metabolism Lead to Suboptimal Growth of Escherichia coli. Appl Environ Microbiol 2019; 85:AEM.00768-19. [PMID: 31126940 PMCID: PMC6643234 DOI: 10.1128/aem.00768-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/11/2019] [Indexed: 12/26/2022] Open
Abstract
DHA is an attractive triose molecule with a wide range of applications, notably in cosmetics and the food and pharmaceutical industries. DHA is found in many species, from microorganisms to humans, and can be used by Escherichia coli as a growth substrate. However, knowledge about the mechanisms and regulation of this process is currently lacking, motivating our investigation of DHA metabolism in E. coli. We show that under aerobic conditions, E. coli growth on DHA is far from optimal and is hindered by chemical, hierarchical, and possibly allosteric constraints. We show that optimal growth on DHA can be restored by releasing the hierarchical constraint. These results improve our understanding of DHA metabolism and are likely to help unlock biotechnological applications involving DHA as an intermediate, such as the bioconversion of glycerol or C1 substrates into value-added chemicals. In this work, we shed light on the metabolism of dihydroxyacetone (DHA), a versatile, ubiquitous, and important intermediate for various chemicals in industry, by analyzing its metabolism at the system level in Escherichia coli. Using constraint-based modeling, we show that the growth of E. coli on DHA is suboptimal and identify the potential causes. Nuclear magnetic resonance analysis shows that DHA is degraded nonenzymatically into substrates known to be unfavorable to high growth rates. Transcriptomic analysis reveals that DHA promotes genes involved in biofilm formation, which may reduce the bacterial growth rate. Functional analysis of the genes involved in DHA metabolism proves that under the aerobic conditions used in this study, DHA is mainly assimilated via the dihydroxyacetone kinase pathway. In addition, these results show that the alternative routes of DHA assimilation (i.e., the glycerol and fructose-6-phosphate aldolase pathways) are not fully activated under our conditions because of anaerobically mediated hierarchical control. These pathways are therefore certainly unable to sustain fluxes as high as the ones predicted in silico for optimal aerobic growth on DHA. Overexpressing some of the genes in these pathways releases these constraints and restores the predicted optimal growth on DHA. IMPORTANCE DHA is an attractive triose molecule with a wide range of applications, notably in cosmetics and the food and pharmaceutical industries. DHA is found in many species, from microorganisms to humans, and can be used by Escherichia coli as a growth substrate. However, knowledge about the mechanisms and regulation of this process is currently lacking, motivating our investigation of DHA metabolism in E. coli. We show that under aerobic conditions, E. coli growth on DHA is far from optimal and is hindered by chemical, hierarchical, and possibly allosteric constraints. We show that optimal growth on DHA can be restored by releasing the hierarchical constraint. These results improve our understanding of DHA metabolism and are likely to help unlock biotechnological applications involving DHA as an intermediate, such as the bioconversion of glycerol or C1 substrates into value-added chemicals.
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14
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Abstract
The logistics of tuberculosis therapy are difficult, requiring multiple drugs for many months. Mycobacterium tuberculosis survives in part by entering nongrowing states in which it is metabolically less active and thus less susceptible to antibiotics. Basic knowledge on how M. tuberculosis survives during these low-metabolism states is incomplete, and we hypothesize that optimized energy resource management is important. Here, we report that slowed mRNA turnover is a common feature of mycobacteria under energy stress but is not dependent on the mechanisms that have generally been postulated in the literature. Finally, we found that mRNA stability and growth status can be decoupled by a drug that causes growth arrest but increases metabolic activity, indicating that mRNA stability responds to metabolic status rather than to growth rate per se. Our findings suggest a need to reorient studies of global mRNA stabilization to identify novel mechanisms that are presumably responsible. The success of Mycobacterium tuberculosis as a human pathogen is due in part to its ability to survive stress conditions, such as hypoxia or nutrient deprivation, by entering nongrowing states. In these low-metabolism states, M. tuberculosis can tolerate antibiotics and develop genetically encoded antibiotic resistance, making its metabolic adaptation to stress crucial for survival. Numerous bacteria, including M. tuberculosis, have been shown to reduce their rates of mRNA degradation under growth limitation and stress. While the existence of this response appears to be conserved across species, the underlying bacterial mRNA stabilization mechanisms remain unknown. To better understand the biology of nongrowing mycobacteria, we sought to identify the mechanistic basis of mRNA stabilization in the nonpathogenic model Mycobacterium smegmatis. We found that mRNA half-life was responsive to energy stress, with carbon starvation and hypoxia causing global mRNA stabilization. This global stabilization was rapidly reversed when hypoxia-adapted cultures were reexposed to oxygen, even in the absence of new transcription. The stringent response and RNase levels did not explain mRNA stabilization, nor did transcript abundance. This led us to hypothesize that metabolic changes during growth cessation impact the activities of degradation proteins, increasing mRNA stability. Indeed, bedaquiline and isoniazid, two drugs with opposing effects on cellular energy status, had opposite effects on mRNA half-lives in growth-arrested cells. Taken together, our results indicate that mRNA stability in mycobacteria is not directly regulated by growth status but rather is dependent on the status of energy metabolism.
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15
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Potts AH, Guo Y, Ahmer BMM, Romeo T. Role of CsrA in stress responses and metabolism important for Salmonella virulence revealed by integrated transcriptomics. PLoS One 2019; 14:e0211430. [PMID: 30682134 PMCID: PMC6347204 DOI: 10.1371/journal.pone.0211430] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/14/2019] [Indexed: 12/31/2022] Open
Abstract
To cause infection, Salmonella must survive and replicate in host niches that present dramatically different environmental conditions. This requires a flexible metabolism and physiology, responsive to conditions of the local milieu. The sequence specific RNA binding protein CsrA serves as a global regulator that governs gene expression required for pathogenicity, metabolism, biofilm formation, and motility in response to nutritional conditions. Its activity is determined by two noncoding small RNAs (sRNA), CsrB and CsrC, which sequester and antagonize this protein. Here, we used ribosome profiling and RNA-seq analysis to comprehensively examine the effects of CsrA on mRNA occupancy with ribosomes, a measure of translation, transcript stability, and the steady state levels of transcripts under in vitro SPI-1 inducing conditions, to simulate growth in the intestinal lumen, and under in vitro SPI-2-inducing conditions, to simulate growth in the Salmonella containing vacuole (SCV) of the macrophage. Our findings uncovered new roles for CsrA in controlling the expression of structural and regulatory genes involved in stress responses, metabolism, and virulence systems required for infection. We observed substantial variation in the CsrA regulon under the two growth conditions. In addition, CsrB/C sRNA levels were greatly reduced under the simulated intracellular conditions and were responsive to nutritional factors that distinguish the intracellular and luminal environments. Altogether, our results reveal CsrA to be a flexible regulator, which is inferred to be intimately involved in maintaining the distinct gene expression patterns associated with growth in the intestine and the macrophage.
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Affiliation(s)
- Anastasia H Potts
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States of America
| | - Yinping Guo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States of America
| | - Brian M M Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States of America
| | - Tony Romeo
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States of America
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16
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Chávez J, Vargas MH, Martínez-Zúñiga J, Falfán-Valencia R, Ambrocio-Ortiz E, Carbajal V, Sandoval-Roldán R. Allergic sensitization increases the amount of extracellular ATP hydrolyzed by guinea pig leukocytes. Purinergic Signal 2019; 15:69-76. [PMID: 30637575 DOI: 10.1007/s11302-019-09644-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 01/04/2019] [Indexed: 02/07/2023] Open
Abstract
Increased levels of ATP have been found in the bronchoalveolar lavage of patients with asthma, and subjects with this disease, but not healthy subjects, develop bronchospasm after nebulization with ATP. Because the main mechanism for controlling the noxious effects of extracellular ATP is its enzymatic hydrolysis, we hypothesized that allergic sensitization is accompanied by a decreased functioning of such hydrolysis. In the present study, peripheral blood leukocytes from sensitized and non-sensitized guinea pigs were used for determining the extracellular metabolism (as assessed by inorganic phosphate production) of ATP, ADP, AMP, or adenosine, and for detecting possible changes in the expression (qPCR and Western blot) of major ectonucleotidases (NTPDase1, NTPDase3, and NPP1) and purinoceptors (P2X1, P2X7, P2Y4, and P2Y6). Contrary to our hypothesis, we found that leukocytes from allergic animals produced higher amounts of inorganic phosphate after stimulation with ATP and ADP, as compared with leukocytes from non-sensitized animals. Although at first glance, this result suggested that sensitization caused higher efficiency of ectonucleotidases, their mRNA and protein expressions were unaffected. On the other hand, after sensitization, we found a significant increase in the protein expression of P2X7 and P2Y4, two purinoceptors known to be responsible for ATP release after activation. We concluded that allergic sensitization increased the amount of ATP hydrolyzed by ectonucleotidases, the latter probably not due to the enhanced efficiency of its enzymatic breakdown, but rather due to an increased release of endogenous ATP or other nucleotides, partly mediated by enhanced expression or P2X7 and P2Y4 receptors.
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Affiliation(s)
- Jaime Chávez
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, 14080, Mexico City, Mexico.
| | - Mario H Vargas
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, 14080, Mexico City, Mexico
| | - Jesús Martínez-Zúñiga
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, 14080, Mexico City, Mexico
| | - Ramcés Falfán-Valencia
- Laboratorio HLA, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, 14080, Mexico City, Mexico
| | - Enrique Ambrocio-Ortiz
- Laboratorio HLA, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, 14080, Mexico City, Mexico
| | - Verónica Carbajal
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, 14080, Mexico City, Mexico
| | - Rosa Sandoval-Roldán
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Calzada de Tlalpan 4502, 14080, Mexico City, Mexico
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17
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Emerson DF, Woolston BM, Liu N, Donnelly M, Currie DH, Stephanopoulos G. Enhancing hydrogen-dependent growth of and carbon dioxide fixation by Clostridium ljungdahlii through nitrate supplementation. Biotechnol Bioeng 2018; 116:294-306. [PMID: 30267586 DOI: 10.1002/bit.26847] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 09/23/2018] [Accepted: 09/28/2018] [Indexed: 12/15/2022]
Abstract
Synthesis gas (syngas) fermentation via the Wood-Ljungdahl pathway is receiving growing attention as a possible platform for the fixation of CO 2 and renewable production of fuels and chemicals. However, the pathway operates near the thermodynamic limit of life, resulting in minimal adenosine triphosphate (ATP) production and long doubling times. This calls into question the feasibility of producing high-energy compounds at industrially relevant levels. In this study, we investigated the possibility of co-utilizing nitrate as an inexpensive additional electron acceptor to enhance ATP production during H 2 -dependent growth of Clostridium ljungdahlii, Moorella thermoacetica, and Acetobacterium woodii. In contrast to other acetogens tested, growth rate and final biomass titer were improved for C. ljungdahlii growing on a mixture of H 2 and CO 2 when supplemented with nitrate. Transcriptomic analysis, 13 CO 2 labeling, and an electron balance were used to understand how electron flux was partitioned between CO 2 and nitrate. We further show that, with nitrate supplementation, the ATP/adenosine diphosphate (ADP) ratio and acetyl-CoA pools were increased by fivefold and threefold, respectively, suggesting that this strategy could be useful for the production of ATP-intensive heterologous products from acetyl-CoA. Finally, we propose a pathway for enhanced ATP production from nitrate and use this as a basis to calculate theoretical yields for a variety of products. This study demonstrates a viable strategy for the decoupling of ATP production from carbon dioxide fixation, which will serve to significantly improve the CO 2 fixation rate and the production metrics of other chemicals from CO 2 and H 2 in this host.
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Affiliation(s)
- David F Emerson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Benjamin M Woolston
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Mackenzie Donnelly
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Devin H Currie
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
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18
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Dressaire C, Pobre V, Laguerre S, Girbal L, Arraiano CM, Cocaign-Bousquet M. PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli. BMC Genomics 2018; 19:848. [PMID: 30486791 PMCID: PMC6264599 DOI: 10.1186/s12864-018-5259-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 11/16/2018] [Indexed: 12/02/2022] Open
Abstract
Background Exoribonucleases are crucial for RNA degradation in Escherichia coli but the roles of RNase R and PNPase and their potential overlap in stationary phase are not well characterized. Here, we used a genome-wide approach to determine how RNase R and PNPase affect the mRNA half-lives in the stationary phase. The genome-wide mRNA half-lives were determined by a dynamic analysis of transcriptomes after transcription arrest. We have combined the analysis of mRNA half-lives with the steady-state concentrations (transcriptome) to provide an integrated overview of the in vivo activity of these exoribonucleases at the genome-scale. Results The values of mRNA half-lives demonstrated that the mRNAs are very stable in the stationary phase and that the deletion of RNase R or PNPase caused only a limited mRNA stabilization. Intriguingly the absence of PNPase provoked also the destabilization of many mRNAs. These changes in mRNA half-lives in the PNPase deletion strain were associated with a massive reorganization of mRNA levels and also variation in several ncRNA concentrations. Finally, the in vivo activity of the degradation machinery was found frequently saturated by mRNAs in the PNPase mutant unlike in the RNase R mutant, suggesting that the degradation activity is limited by the deletion of PNPase but not by the deletion of RNase R. Conclusions This work had identified PNPase as a central player associated with mRNA degradation in stationary phase. Electronic supplementary material The online version of this article (10.1186/s12864-018-5259-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clémentine Dressaire
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | - Laurence Girbal
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - Cecilia Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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Laguerre S, González I, Nouaille S, Moisan A, Villa-Vialaneix N, Gaspin C, Bouvier M, Carpousis AJ, Cocaign-Bousquet M, Girbal L. Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay. Methods Enzymol 2018; 612:47-66. [PMID: 30502954 DOI: 10.1016/bs.mie.2018.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, we compared different computational methods used for genome-wide determination of mRNA half-lives in Escherichia coli with a special focus on the impact on considering a delay before the onset of mRNA decay after transcription arrest. A wide variety of datasets were analyzed coming from different technical methods for mRNA quantification (microarrays, RNA-seq, and RT-qPCR) and different bacterial growth conditions. The exponential decay of mRNA levels was fitted using both linear and exponential models and with or without a delay. We showed that for all the models, independently of mRNA quantification methods and growth conditions, ignoring the delay resulted in only a modest overestimation of the half-life. For approximately 80% of the mRNAs, differences in mRNA half-life values were less than 34s. The correlation between half-lives estimated with and without a delay was extremely high. However, the slope of the linear regression between the half-lives with and without a delay tended to decrease with the delay. For the few mRNAs for which taking into account the delay influenced the estimated half-life, the impact was dependent on the model and the growth condition. The smallest impact was obtained for the linear model.
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Affiliation(s)
| | | | | | - Annick Moisan
- MIAT, Université de Toulouse, INRA, Castanet-Tolosan, France
| | | | | | - Marie Bouvier
- LMGM, CBI, Université de Toulouse, CNRS, Toulouse, France
| | | | | | - Laurence Girbal
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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20
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Arraes MLBDM, Holanda MVD, Lima LNGC, Sabadia JAB, Duarte CR, Almeida RLF, Kendall C, Kerr LRS, Frota CC. Natural environmental water sources in endemic regions of northeastern Brazil are potential reservoirs of viable Mycobacterium leprae. Mem Inst Oswaldo Cruz 2017; 112:805-811. [PMID: 29211240 PMCID: PMC5719548 DOI: 10.1590/0074-02760170117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/30/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The detection of live Mycobacterium leprae in soil and animals other than humans suggests that the environment plays a role in the transmission of leprosy. OBJECTIVE The objective of this study was to investigate the presence of viable M. leprae in natural water sources used by the local population in five municipalities in the state of Ceará, northeastern Brazil. METHODS Samples were collected from 30 different sources. Viable bacilli were identified by reverse transcriptase polymerase chain reaction (PCR) of the M. leprae gyrA gene and sequencing of the PCR products. Physicochemical properties of each water source were also assessed. FINDINGS M. leprae gyrA mRNA was found in 23 (76.7%) of the water sources. No association was found between depth of the water and sample positivity, nor was there any association between the type of water used by the population and sample positivity. An association between viable M. leprae and temperature and pH was found. Georeferencing showed a relation between the residences of leprosy cases and water source containing the bacterium. MAIN CONCLUSIONS The finding of viable M. leprae in natural water sources associated with human contact suggests that the environment plays an important role in maintaining endemic leprosy in the study region.
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Affiliation(s)
| | - Maísa Viana de Holanda
- Universidade Federal do Ceará, Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Fortaleza, CE, Brasil
| | | | | | | | | | - Carl Kendall
- Tulane University, School of Public Health and Tropical Medicine, Department of Global Community Health and Behavioral Sciences, New Orleans, LA, USA
| | - Ligia Regina Sansigolo Kerr
- Universidade Federal do Ceará, Faculdade de Medicina, Departamento de Saúde Comunitária, Fortaleza, CE, Brasil
| | - Cristiane Cunha Frota
- Universidade Federal do Ceará, Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Fortaleza, CE, Brasil
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21
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Peterson JR, Thor S, Kohler L, Kohler PR, Metcalf WW, Luthey-Schulten Z. Genome-wide gene expression and RNA half-life measurements allow predictions of regulation and metabolic behavior in Methanosarcina acetivorans. BMC Genomics 2016; 17:924. [PMID: 27852217 PMCID: PMC5112694 DOI: 10.1186/s12864-016-3219-8] [Citation(s) in RCA: 16] [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: 07/15/2016] [Accepted: 10/26/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND While a few studies on the variations in mRNA expression and half-lives measured under different growth conditions have been used to predict patterns of regulation in bacterial organisms, the extent to which this information can also play a role in defining metabolic phenotypes has yet to be examined systematically. Here we present the first comprehensive study for a model methanogen. RESULTS We use expression and half-life data for the methanogen Methanosarcina acetivorans growing on fast- and slow-growth substrates to examine the regulation of its genes. Unlike Escherichia coli where only small shifts in half-lives were observed, we found that most mRNA have significantly longer half-lives for slow growth on acetate compared to fast growth on methanol or trimethylamine. Interestingly, half-life shifts are not uniform across functional classes of enzymes, suggesting the existence of a selective stabilization mechanism for mRNAs. Using the transcriptomics data we determined whether transcription or degradation rate controls the change in transcript abundance. Degradation was found to control abundance for about half of the metabolic genes underscoring its role in regulating metabolism. Genes involved in half of the metabolic reactions were found to be differentially expressed among the substrates suggesting the existence of drastically different metabolic phenotypes that extend beyond just the methanogenesis pathways. By integrating expression data with an updated metabolic model of the organism (iST807) significant differences in pathway flux and production of metabolites were predicted for the three growth substrates. CONCLUSIONS This study provides the first global picture of differential expression and half-lives for a class II methanogen, as well as provides the first evidence in a single organism that drastic genome-wide shifts in RNA half-lives can be modulated by growth substrate. We determined which genes in each metabolic pathway control the flux and classified them as regulated by transcription (e.g. transcription factor) or degradation (e.g. post-transcriptional modification). We found that more than half of genes in metabolism were controlled by degradation. Our results suggest that M. acetivorans employs extensive post-transcriptional regulation to optimize key metabolic steps, and more generally that degradation could play a much greater role in optimizing an organism's metabolism than previously thought.
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Affiliation(s)
- Joseph R. Peterson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Ave, Urbana, 60801 IL USA
| | - ShengShee Thor
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 60801 IL USA
| | - Lars Kohler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Ave, Urbana, 60801 IL USA
| | - Petra R.A. Kohler
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S Goodwin AveIL, Urbana, 60801 USA
| | - William W. Metcalf
- Department of Microbiology, University of Illinois at Urbana-Champaign, 601 S Goodwin AveIL, Urbana, 60801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory DrIL, Urbana, 60801 USA
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Ave, Urbana, 60801 IL USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 1110 W Green St, Urbana, 60801 IL USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory DrIL, Urbana, 60801 USA
- Beckman Institute, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, Urbana, 60801 IL USA
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22
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Esquerré T, Bouvier M, Turlan C, Carpousis AJ, Girbal L, Cocaign-Bousquet M. The Csr system regulates genome-wide mRNA stability and transcription and thus gene expression in Escherichia coli. Sci Rep 2016; 6:25057. [PMID: 27112822 PMCID: PMC4844966 DOI: 10.1038/srep25057] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/08/2016] [Indexed: 11/08/2022] Open
Abstract
Bacterial adaptation requires large-scale regulation of gene expression. We have performed a genome-wide analysis of the Csr system, which regulates many important cellular functions. The Csr system is involved in post-transcriptional regulation, but a role in transcriptional regulation has also been suggested. Two proteins, an RNA-binding protein CsrA and an atypical signaling protein CsrD, participate in the Csr system. Genome-wide transcript stabilities and levels were compared in wildtype E. coli (MG1655) and isogenic mutant strains deficient in CsrA or CsrD activity demonstrating for the first time that CsrA and CsrD are global negative and positive regulators of transcription, respectively. The role of CsrA in transcription regulation may be indirect due to the 4.6-fold increase in csrD mRNA concentration in the CsrA deficient strain. Transcriptional action of CsrA and CsrD on a few genes was validated by transcriptional fusions. In addition to an effect on transcription, CsrA stabilizes thousands of mRNAs. This is the first demonstration that CsrA is a global positive regulator of mRNA stability. For one hundred genes, we predict that direct control of mRNA stability by CsrA might contribute to metabolic adaptation by regulating expression of genes involved in carbon metabolism and transport independently of transcriptional regulation.
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Affiliation(s)
- Thomas Esquerré
- Université de Toulouse, INSA, UPS, INP, LISBP, 135, avenue de Rangueil, 31077 Toulouse, France
- INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France
- CNRS, UMR5504, 31400 Toulouse, France
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France
| | - Catherine Turlan
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France
| | - Agamemnon J. Carpousis
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre National de la Recherche Scientifique et Université Paul Sabatier, 118 Route de Narbonne, 31062, Toulouse, France
| | - Laurence Girbal
- Université de Toulouse, INSA, UPS, INP, LISBP, 135, avenue de Rangueil, 31077 Toulouse, France
- INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France
- CNRS, UMR5504, 31400 Toulouse, France
| | - Muriel Cocaign-Bousquet
- Université de Toulouse, INSA, UPS, INP, LISBP, 135, avenue de Rangueil, 31077 Toulouse, France
- INRA, UMR792 Ingénierie des systèmes biologiques et des procédés, 31400 Toulouse, France
- CNRS, UMR5504, 31400 Toulouse, France
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Córdoba-Rodríguez G, Vargas MH, Ruiz V, Carbajal V, Campos-Bedolla P, Mercadillo-Herrera P, Arreola-Ramírez JL, Segura-Medina P. Allergic sensitization modifies the pulmonary expression of 5-hydroxytryptamine receptors in guinea pigs. Respir Physiol Neurobiol 2015; 223:9-15. [PMID: 26657047 DOI: 10.1016/j.resp.2015.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 10/22/2022]
Abstract
There is mounting evidence that 5-hydroxytryptamine (5-HT) plays a role in asthma. However, scarce information exists about the pulmonary expression of 5-HT receptors and its modification after allergic sensitization. In the present work, we explored the expression of 5-HT1A, 5-HT2A, 5-HT3, 5-HT4, 5-ht5a, 5-HT6, and 5-HT7 receptors in lungs from control and sensitized guinea pigs through qPCR and Western blot. In control animals, mRNA from all receptors was detectable in lung homogenates, especially from 5-HT2A and 5-HT4 receptors. Sensitized animals had decreased mRNA expression of 5-HT2A and 5-HT4 receptors and increased that of 5-HT7 receptor. In contrast, they had increased protein expression of 5-HT2A receptor in bronchial epithelium and of 5-HT4 receptor in lung parenchyma. The degree of airway response to the allergic challenge was inversely correlated with mRNA expression of the 5-HT1A receptor. In summary, our results showed that major 5-HT receptor subtypes are constitutively expressed in the guinea pig lung, and that allergic sensitization modifies the expression of 5-HT2A, 5-HT4, and 5-HT7 receptors.
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Affiliation(s)
- Guadalupe Córdoba-Rodríguez
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias, México DF, Mexico
| | - Mario H Vargas
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias, México DF, Mexico
| | - Víctor Ruiz
- Laboratorio de Biología Molecular, Departamento de Investigación en Fibrosis Pulmonar, Instituto Nacional de Enfermedades Respiratorias, México DF, Mexico
| | - Verónica Carbajal
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias, México DF, Mexico
| | - Patricia Campos-Bedolla
- Unidad de Investigación Médica en Enfermedades Neurológicas, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México DF, Mexico
| | | | - José Luis Arreola-Ramírez
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias, México DF, Mexico
| | - Patricia Segura-Medina
- Departamento de Investigación en Hiperreactividad Bronquial, Instituto Nacional de Enfermedades Respiratorias, México DF, Mexico.
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