101
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Kwok ACM, Zhang F, Ma Z, Chan WS, Yu VC, Tsang JSH, Wong JTY. Functional responses between PMP3 small membrane proteins and membrane potential. Environ Microbiol 2020; 22:3066-3080. [PMID: 32307863 DOI: 10.1111/1462-2920.15027] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/15/2020] [Indexed: 01/07/2023]
Abstract
The Plasma Membrane Proteolipid 3 (PMP3, UPF0057 family in Uniprot) family consists of abundant small hydrophobic polypeptides with two predicted transmembrane helices. Plant homologues were upregulated in response to drought/salt-stresses and yeast deletion mutants exhibited conditional growth defects. We report here abundant expression of Group I PMP3 homologues (PMP3(i)hs) during normal vegetative growth in both prokaryotic and eukaryotic cells, at a level comparable to housekeeping genes, implicating the regular cellular functions. Expression of eukaryotic PMP3(i)hs was dramatically upregulated in response to membrane potential (Vm) variability (Vmvar ), whereas PMP3(i)hs deletion-knockdown led to Vm changes with conditional growth defects. Bacterial PMP3(i)h yqaE deletion led to a shift of salt sensitivity; Vmvar alternations with exogenous K+ addition downregulated prokaryotic PMP3(i)hs, suggesting [K+ ]-Vmvar axis being a significant feedback element in prokaryotic ionic homeostasis. Remarkably, the eukaryotic homologues functionally suppressed the conditional growth defects in bacterial deletion mutant, demonstrating the conserved cross-kingdom membrane functions by PMP3(i)hs. These data demonstrated a direct reciprocal relationship between PMP3(i)hs expression and Vm differentials in both prokaryotic and eukaryotic cells. Cumulative with PMP3(i)hs ubiquitous abundance, their lipid-binding selectivity and membrane protein colocalization, we propose [PMP3(i)hs]-Vmvar axis as a key element in membrane homeostasis.
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Affiliation(s)
- Alvin C M Kwok
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China
| | - Fang Zhang
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China
| | - Zhiyi Ma
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China
| | - Wai Sun Chan
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China
| | - Vivian C Yu
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China
| | - Jimmy S H Tsang
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Joseph T Y Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China
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102
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Efficacy of A Poly(MeOEGMA) Brush on the Prevention of Escherichia coli Biofilm Formation and Susceptibility. Antibiotics (Basel) 2020; 9:antibiotics9050216. [PMID: 32365462 PMCID: PMC7277157 DOI: 10.3390/antibiotics9050216] [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: 04/15/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Urinary tract infections are one of the most common hospital-acquired infections, and they are often associated with biofilm formation in indwelling medical devices such as catheters and stents. This study aims to investigate the antibiofilm performance of a polymer brush—poly[oligo(ethylene glycol) methyl ether methacrylate], poly(MeOEGMA)—and evaluate its effect on the antimicrobial susceptibility of Escherichia coli biofilms formed on that surface. Biofilms were formed in a parallel plate flow chamber (PPFC) for 24 h under the hydrodynamic conditions prevailing in urinary catheters and stents and challenged with ampicillin. Results obtained with the brush were compared to those obtained with two control surfaces, polydimethylsiloxane (PDMS) and glass. The polymer brush reduced by 57% the surface area covered by E. coli after 24 h, as well as the number of total adhered cells. The antibiotic treatment potentiated cell death and removal, and the total cell number was reduced by 88%. Biofilms adapted their architecture, and cell morphology changed to a more elongated form during that period. This work suggests that the poly(MeOEGMA) brush has potential to prevent bacterial adhesion in urinary tract devices like ureteral stents and catheters, as well as in eradicating biofilms developed in these biomedical devices.
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103
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Rodríguez-Verdugo A, Lozano-Huntelman N, Cruz-Loya M, Savage V, Yeh P. Compounding Effects of Climate Warming and Antibiotic Resistance. iScience 2020; 23:101024. [PMID: 32299057 PMCID: PMC7160571 DOI: 10.1016/j.isci.2020.101024] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/11/2020] [Accepted: 03/25/2020] [Indexed: 12/18/2022] Open
Abstract
Bacteria have evolved diverse mechanisms to survive environments with antibiotics. Temperature is both a key factor that affects the survival of bacteria in the presence of antibiotics and an environmental trait that is drastically increasing due to climate change. Therefore, it is timely and important to understand links between temperature changes and selection of antibiotic resistance. This review examines these links by synthesizing results from laboratories, hospitals, and environmental studies. First, we describe the transient physiological responses to temperature that alter cellular behavior and lead to antibiotic tolerance and persistence. Second, we focus on the link between thermal stress and the evolution and maintenance of antibiotic resistance mutations. Finally, we explore how local and global changes in temperature are associated with increases in antibiotic resistance and its spread. We suggest that a multidisciplinary, multiscale approach is critical to fully understand how temperature changes are contributing to the antibiotic crisis.
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Affiliation(s)
| | - Natalie Lozano-Huntelman
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Mauricio Cruz-Loya
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Van Savage
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Pamela Yeh
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA; Santa Fe Institute, Santa Fe, NM 87501, USA.
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104
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Bittihn P, Didovyk A, Tsimring LS, Hasty J. Genetically engineered control of phenotypic structure in microbial colonies. Nat Microbiol 2020; 5:697-705. [PMID: 32284568 DOI: 10.1038/s41564-020-0686-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
Abstract
Rapid advances in cellular engineering1,2 have positioned synthetic biology to address therapeutic3,4 and industrial5 problems, but a substantial obstacle is the myriad of unanticipated cellular responses in heterogeneous real-world environments such as the gut6,7, solid tumours8,9, bioreactors10 or soil11. Complex interactions between the environment and cells often arise through non-uniform nutrient availability, which generates bidirectional coupling as cells both adjust to and modify their local environment through phenotypic differentiation12,13. Although synthetic spatial gene expression patterns14-17 have been explored under homogeneous conditions, the mutual interaction of gene circuits, growth phenotype and the environment remains a challenge. Here, we design gene circuits that sense and control phenotypic structure in microcolonies containing both growing and dormant bacteria. We implement structure modulation by coupling different downstream modules to a tunable sensor that leverages Escherichia coli's stress response and is activated on growth arrest. One is an actuator module that slows growth and thereby alters nutrient gradients. Environmental feedback in this circuit generates robust cycling between growth and dormancy in the interior of the colony, as predicted by a spatiotemporal computational model. We also use the sensor to drive an inducible gating module for selective gene expression in non-dividing cells, which allows us to radically alter population structure by eliminating the dormant phenotype with a 'stress-gated lysis circuit'. Our results establish a strategy to leverage and control microbial colony structure for synthetic biology applications in complex environments.
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Affiliation(s)
- Philip Bittihn
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA.,The San Diego Center for Systems Biology, La Jolla, CA, USA.,Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
| | - Andriy Didovyk
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA.,Vertex Pharmaceuticals, San Diego, CA, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA. .,The San Diego Center for Systems Biology, La Jolla, CA, USA.
| | - Jeff Hasty
- BioCircuits Institute, University of California, San Diego, La Jolla, CA, USA. .,The San Diego Center for Systems Biology, La Jolla, CA, USA. .,Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. .,Molecular Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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105
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Hengge R. Linking bacterial growth, survival, and multicellularity - small signaling molecules as triggers and drivers. Curr Opin Microbiol 2020; 55:57-66. [PMID: 32244175 DOI: 10.1016/j.mib.2020.02.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 02/05/2023]
Abstract
An overarching theme of cellular regulation in bacteria arises from the trade-off between growth and stress resilience. In addition, the formation of biofilms contributes to stress survival, since these dense multicellular aggregates, in which cells are embedded in an extracellular matrix of self-produced polymers, represent a self-constructed protective and homeostatic 'niche'. As shown here for the model bacterium Escherichia coli, the inverse coordination of bacterial growth with survival and the transition to multicellularity is achieved by a highly integrated regulatory network with several sigma subunits of RNA polymerase and a small number of transcriptional hubs as central players. By conveying information about the actual (micro)environments, nucleotide second messengers such as cAMP, (p)ppGpp, and in particular c-di-GMP are the key triggers and drivers that promote either growth or stress resistance and organized multicellularity in a world of limited resources.
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Affiliation(s)
- Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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106
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Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL. Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing. Front Genet 2020; 11:144. [PMID: 32211022 PMCID: PMC7066862 DOI: 10.3389/fgene.2020.00144] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/07/2020] [Indexed: 12/19/2022] Open
Abstract
Escherichia coli cells respond to a period of famine by globally reorganizing their gene expression. The changes are known as the stringent response, which is orchestrated by the alarmone ppGpp that binds directly to RNA polymerase. The resulting changes in gene expression are particularly well studied in the case of amino acid starvation. We used deep RNA sequencing in combination with spike-in cells to measure global changes in the transcriptome after valine-induced isoleucine starvation of a standard E. coli K12 strain. Owing to the whole-cell spike-in method that eliminates variations in RNA extraction efficiency between samples, we show that ribosomal RNA levels are reduced during isoleucine starvation and we quantify how the change in cellular RNA content affects estimates of gene regulation. Specifically, we show that standard data normalization relying on sample sequencing depth underestimates the number of down-regulated genes in the stringent response and overestimates the number of up-regulated genes by approximately 40%. The whole-cell spike-in method also made it possible to quantify how rapidly the pool of total messenger RNA (mRNA) decreases upon amino acid starvation. A principal component analysis showed that the first two components together described 69% of the variability of the data, underlining that large and highly coordinated regulons are at play in the stringent response. The induction of starvation by sudden addition of high valine concentrations provoked prominent regulatory responses outside of the expected ppGpp, RpoS, and Lrp regulons. This underlines the notion that with the high resolution possible in deep RNA sequencing analysis, any different starvation method (e.g., nitrogen-deprivation, removal of an amino acid from an auxotroph strain, or valine addition to E. coli K12 strains) will produce measurable variations in the stress response produced by the cells to cope with the specific treatment.
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Affiliation(s)
- Bertil Gummesson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shiraz Ali Shah
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Mathias Fessler
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Namiko Mitarai
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
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107
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Trösch R, Willmund F. The conserved theme of ribosome hibernation: from bacteria to chloroplasts of plants. Biol Chem 2020; 400:879-893. [PMID: 30653464 DOI: 10.1515/hsz-2018-0436] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/03/2019] [Indexed: 12/21/2022]
Abstract
Cells are highly adaptive systems that respond and adapt to changing environmental conditions such as temperature fluctuations or altered nutrient availability. Such acclimation processes involve reprogramming of the cellular gene expression profile, tuning of protein synthesis, remodeling of metabolic pathways and morphological changes of the cell shape. Nutrient starvation can lead to limited energy supply and consequently, remodeling of protein synthesis is one of the key steps of regulation since the translation of the genetic code into functional polypeptides may consume up to 40% of a cell's energy during proliferation. In eukaryotic cells, downregulation of protein synthesis during stress is mainly mediated by modification of the translation initiation factors. Prokaryotic cells suppress protein synthesis by the active formation of dimeric so-called 'hibernating' 100S ribosome complexes. Such a transition involves a number of proteins which are found in various forms in prokaryotes but also in chloroplasts of plants. Here, we review the current understanding of these hibernation factors and elaborate conserved principles which are shared between species.
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Affiliation(s)
- Raphael Trösch
- Department of Biology, Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Straße 23, D-67663 Kaiserslautern, Germany
| | - Felix Willmund
- Department of Biology, Molecular Genetics of Eukaryotes, University of Kaiserslautern, Paul-Ehrlich-Straße 23, D-67663 Kaiserslautern, Germany
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108
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Ye C, Lin H, Zhang M, Chen S, Yu X. Characterization and potential mechanisms of highly antibiotic tolerant VBNC Escherichia coli induced by low level chlorination. Sci Rep 2020; 10:1957. [PMID: 32029755 PMCID: PMC7005040 DOI: 10.1038/s41598-020-58106-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/08/2020] [Indexed: 12/29/2022] Open
Abstract
Escherichia coli is an important pathogenic indicator in drinking water. Viable but non-culturable (VBNC) E. coli induced by low level chlorination was found to have higher antibiotic tolerance. The emerging of VBNC bacteria in drinking water systems is posing challenges to the control of bio-safety. It is necessary to study the underlying mechanisms of VBNC state E. coli under actual residual chlorine condition of drinking water pipe network. In this study, we investigated the changes of morphology and gene expressions that might present such state. The results indicated that the size of VBNC E. coli was not remarkably changed or recovered culturability under favorable environmental conditions. Results from transcriptomic analysis revealed that the regulated genes related to fimbrial-like adhesin protein, putative periplasmic pilin chaperone, regulators of the transcriptional regulation, antibiotic resistance genes and stress-induced genes, rendering VBNC cells more tolerant to adverse environmental conditions. In total of 16 genes were significantly up-regulated under the VBNC state, including three genes encoding toxic protein (ygeG, ibsD, shoB), indicating that VBNC E. coil was still a threat to human. The work is of great relevance in the context of better understanding this poorly understood physiological state.
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Affiliation(s)
- Chengsong Ye
- College of the Environment&Ecology, Xiamen University, Xiamen, 361005, China
| | - Huirong Lin
- Department of Environmental Science and Engineering, College of Chemical Engineering, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Menglu Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Sheng Chen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xin Yu
- College of the Environment&Ecology, Xiamen University, Xiamen, 361005, China. .,Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China.
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109
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Kurokawa M, Ying BW. Experimental Challenges for Reduced Genomes: The Cell Model Escherichia coli. Microorganisms 2019; 8:E3. [PMID: 31861355 PMCID: PMC7022904 DOI: 10.3390/microorganisms8010003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/11/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
Genome reduction, as a top-down approach to obtain the minimal genetic information essential for a living organism, has been conducted with bacterial cells for decades. The most popular and well-studied cell models for genome reduction are Escherichia coli strains. As the previous literature intensively introduced the genetic construction and application of the genome-reduced Escherichia coli strains, the present review focuses the design principles and compares the reduced genome collections from the specific viewpoint of growth, which represents a fundamental property of living cells and is an important feature for their biotechnological application. For the extended simplification of the genomic sequences, the approach of experimental evolution and concern for medium optimization are newly proposed. The combination of the current techniques of genomic construction and the newly proposed methodologies could allow us to acquire growing Escherichia coli cells carrying the extensively reduced genome and to address the question of what the minimal genome essential for life is.
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Affiliation(s)
| | - Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 305-8572 Ibaraki, Japan;
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110
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Xu J, Cui K, Shen L, Shi J, Li L, You L, Fang C, Zhao G, Feng Y, Yang B, Zhang Y. Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor. eLife 2019; 8:50928. [PMID: 31846423 PMCID: PMC6917491 DOI: 10.7554/elife.50928] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
σS is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses including antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of σS-mediated transcription requires a σS-specific activator, Crl. In this study, we determined a 3.80 Å cryo-EM structure of an Escherichia coli transcription activation complex (E. coli Crl-TAC) comprising E. coli σS-RNA polymerase (σS-RNAP) holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with domain 2 of σS (σS2) and the RNAP core enzyme, but does not contact promoter DNA. Results from subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) indicate that Crl stabilizes key structural motifs within σS2 to promote the assembly of the σS-RNAP holoenzyme and also to facilitate formation of an RNA polymerase–promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.
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Affiliation(s)
- Juncao Xu
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kaijie Cui
- University of Chinese Academy of Sciences, Beijing, China.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Liqiang Shen
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Shi
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingting Li
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Linlin You
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chengli Fang
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China.,Department of Microbiology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, China.,State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China.,Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology,CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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111
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Sun Z, Cagliero C, Izard J, Chen Y, Zhou YN, Heinz WF, Schneider TD, Jin DJ. Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli. Nucleic Acids Res 2019; 47:3970-3985. [PMID: 30843055 DOI: 10.1093/nar/gkz159] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 11/14/2022] Open
Abstract
RNA polymerase (RNAP), the transcription machinery, shows dynamic binding across the genomic DNA under different growth conditions. The genomic features that selectively redistribute the limited RNAP molecules to dictate genome-wide transcription in response to environmental cues remain largely unknown. We chose the bacterial osmotic stress response model to determine genomic features that direct genome-wide redistribution of RNAP during the stress. Genomic mapping of RNAP and transcriptome profiles corresponding to the different temporal states after salt shock were determined. We found rapid redistribution of RNAP across the genome, primarily at σ70 promoters. Three subsets of genes exhibiting differential salt sensitivities were identified. Sequence analysis using an information-theory based σ70 model indicates that the intergenic regions of salt-responsive genes are enriched with a higher density of σ70 promoter-like sites than those of salt-sensitive genes. In addition, the density of promoter-like sites has a positive linear correlation with RNAP binding at different salt concentrations. The RNAP binding contributed by the non-initiating promoter-like sites is important for gene transcription at high salt concentration. Our study demonstrates that hyperdensity of σ70 promoter-like sites in the intergenic regions of salt-responsive genes drives the RNAP redistribution for reprograming the transcriptome to counter osmotic stress.
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Affiliation(s)
- Zhe Sun
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Cedric Cagliero
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jerome Izard
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yixiong Chen
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yan Ning Zhou
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - William F Heinz
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Thomas D Schneider
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ding Jun Jin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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112
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Physiological effects of overexpressed sigma factors on fermentative stress response of Zymomonas mobilis. Braz J Microbiol 2019; 51:65-75. [PMID: 31701383 DOI: 10.1007/s42770-019-00158-3] [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: 06/21/2019] [Accepted: 09/11/2019] [Indexed: 01/04/2023] Open
Abstract
Zymomonas mobilis is a bacterium of industrial interest due to its high ethanol productivity and high tolerance to stresses. Although the physiological parameters of fermentation are well characterized, there are few studies on the molecular mechanisms that regulate the response to fermentative stress. Z. mobilis ZM4 presents five different sigma factors identified in the genome annotation, but the absence of sigma 38 leads to the questioning of which sigma factors are responsible for its mechanism of fermentative stress response. Thus, in this study, factors sigma 32 and sigma 24, traditionally related to heat shock, were tested for their influence on the response to osmotic and ethanol stress. The overexpression of these sigma factors in Z. mobilis ZM4 strain confirmed that both are associated with heat shock response, as described in other bacteria. Moreover, sigma 32 has also a role in the adaptation to osmotic stress, increasing both growth rate and glucose influx rate. The same strain that overexpresses sigma 32 also showed a decrease in ethanol tolerance, suggesting an antagonism between these two mechanisms. It was not possible to conclude if sigma 24 really affects ethanol tolerance in Z. mobilis, but the overexpression of this sigma factor led to a decrease in ethanol productivity.
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113
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Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
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114
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Bezanson G, Mader D, Fillmore S, Bach S, Delaquis P. Reaction of Surrogate Escherichia coli Serotype O157:H7 and Non-O157 Strains to Nutrient Starvation: Variation in Phenotype and Transcription of Stress Response Genes and Behavior on Lettuce Plants in the Field. J Food Prot 2019; 82:1988-2000. [PMID: 31644333 DOI: 10.4315/0362-028x.jfp-19-072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Preharvest contamination with bacteria borne by irrigation water may result in leafy vegetables serving as vehicles for transmission of Shiga toxin-producing Escherichia coli (STEC) to humans. The influence of starvation-associated stress on the behavior of non-toxin-producing strains of E. coli serotype O157:H7 and serotypes O26, O103, O111, and O145 was examined subsequent to their introduction to the phyllosphere of field-grown romaine lettuce as inocula simulating starved (96 h in sterile deionized water) and nutrient-depleted (24 h broth culture) cells. As with E. coli O157:H7, leaf populations of the non-O157 strains declined rapidly during the first 72 h postinoculation, displaying the biphasic decay curve typical of serotype O157:H7 isolates. Preinoculation treatment appeared not to influence decay rates greatly (P > 0.5), but strain-specific differences (persistence period and attachment proficiency) indicated that serotype O103:H2 strain PARC445 was a better survivor. Also assessed was the impact of preinoculation treatment on phenotypes key to leaf colonization and survival and the expression of starvation stress-associated genes. The 96-h starvation period enhanced biofilm formation in one strain but reduced motility and autoinducer 2 formation in all five study strains relative to those characteristics in stationary-phase cells. Transcription of rpoS, dps, uspA, and gapA was reduced significantly (P < 0.05) in starvation-stressed cells relative to that for exponential- and stationary-phase cultures. Strain-specific differences were observed; serotype O103:H2 PARC445 had greater downturns than did serotype O157:H7 and other non-O157 strains. Within this particular cohort, the behavior of the representative serotype O157:H7 strain, PARC443 (ATCC 700728), was not predictive of behavior of non-O157 members of this STEC group.
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Affiliation(s)
- Greg Bezanson
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, 32 Main Street, Kentville, Nova Scotia, Canada B4N 1J
| | - David Mader
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, 32 Main Street, Kentville, Nova Scotia, Canada B4N 1J
| | - Sherry Fillmore
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, 32 Main Street, Kentville, Nova Scotia, Canada B4N 1J
| | - Susan Bach
- Agriculture and Agri-Food Canada, Brandon Research and Development Centre, 2701 Grand Valley Road, Brandon, Manitoba, Canada R7A 5Y3
| | - Pascal Delaquis
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, 4200 Highway 97, Summerland, British Columbia, Canada V0H 1Z0
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Huang J, Chen Y, Chen J, Liu C, Zhang T, Luo S, Huang M, Min X. Exploration of the effects of a degS mutant on the growth of Vibrio cholerae and the global regulatory function of degS by RNA sequencing. PeerJ 2019; 7:e7959. [PMID: 31660280 PMCID: PMC6815195 DOI: 10.7717/peerj.7959] [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: 06/20/2019] [Accepted: 09/29/2019] [Indexed: 01/25/2023] Open
Abstract
Background DegS is a periplasmic serine protease that is considered to be the initiator of the σE stress response pathway, and this protein plays an important role in the regulation of the stress response in E. coli. However, knowledge of the biological function and global regulatory network of DegS in Vibrio cholerae remains limited. In this study, we aimed to characterize the molecular functions and further investigate the regulatory network of degS in V. cholerae. Methods A deletion mutant of degS was constructed in the V. cholerae HN375 strain. Bacterial colony morphology was observed by a plate-based growth experiment, and bacterial growth ability was observed by a growth curve experiment. High-throughput RNA sequencing (RNA-Seq) technology was used to analyze the differential transcriptomic profiles between the wild-type and degS mutant strains. Gene ontology (GO), pathway analysis and Gene-Act-network analysis were performed to explore the main functions of the differentially expressed genes. Quantitative real-time PCR (qRT-PCR) was performed to validate the reliability and accuracy of the RNA-Seq analysis. The complementation experiments were used to test the roles of degS and ropS in the small colony degS mutant phenotype. Results When degS was deleted, the degS mutant exhibited smaller colonies on various media and slower growth than the wild-type strain. A total of 423 differentially expressed genes were identified, including 187 genes that were upregulated in the degS mutant compared to the wild-type strain and 236 genes that were relatively downregulated. GO categories and pathway analysis showed that many differentially expressed genes were associated with various cellular metabolic pathways and the cell cycle. Furthermore, Gene-Act network analysis showed that many differentially expressed genes were involved in cellular metabolic pathways and bacterial chemotaxis. The cAMP-CRP-RpoS signaling pathway and the LuxPQ signal transduction system were also affected by the degS mutant. The expression patterns of nine randomly selected differentially expressed genes were consistent between the qRT-PCR and RNA-seq results. The complementation experiments showed that the small colony degS mutant phenotype could be partially restored by complementation with the pBAD24-degS or pBAD24-rpoS plasmid. Discussion These results suggest that the degS gene is important for normal growth of V. cholerae. Some of the differentially expressed genes were involved in various cellular metabolic processes and the cell cycle, which may be associated with bacterial growth. Several new degS-related regulatory networks were identified. In addition, our results suggested that the cAMP-CRP-RpoS signaling pathway may be involved in the small colony degS mutant phenotype. Overall, we believe that these transcriptomic data will serve as useful genetic resources for research on the functions of degS in V. cholerae.
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Affiliation(s)
- Jian Huang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yuxi Chen
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jie Chen
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Changjin Liu
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Tao Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Shilu Luo
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Meirong Huang
- Department of Blood Transfusion, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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Hu X, Li X, Yang L, Zhu Y, Shi Y, Li Y, Wang H, Gong Q. Conformation and mechanical property of rpoS mRNA inhibitory stem studied by optical tweezers and X-ray scattering. PLoS One 2019; 14:e0222938. [PMID: 31557220 PMCID: PMC6762075 DOI: 10.1371/journal.pone.0222938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/10/2019] [Indexed: 02/02/2023] Open
Abstract
3' downstream inhibitory stem plays a crucial role in locking rpoS mRNA 5' untranslated region in a self-inhibitory state. Here, we used optical tweezers to study the unfolding/refolding of rpoS inhibitory stem in the absence and presence of Mg2+. We found adding Mg2+ decreased the free energy of the RNA junction without re-arranging its secondary structure, through confirming that this RNA formed a canonical RNA three-way junction. We suspected increased free energy might change the relative orientation of different stems of rpoS and confirmed this by small angle X-ray scattering. Such changed conformation may improve Hfq-bridged annealing between sRNA and rpoS RNA inhibitory stem. We established a convenient route to analyze the changes of RNA conformation and folding dynamics by combining optical tweezers with X-ray scattering methods. This route can be easily applied in the studies of other RNA structure and ligand-RNA.
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Affiliation(s)
- Xinyao Hu
- Department of Optics and Optical Engineering, University of Science and Technology of China and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, P. R. China
| | - Xuanling Li
- Department of Optics and Optical Engineering, University of Science and Technology of China and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, P. R. China
| | - Lingna Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Yilin Zhu
- Department of Optics and Optical Engineering, University of Science and Technology of China and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, P. R. China
| | - Yunyu Shi
- Department of Optics and Optical Engineering, University of Science and Technology of China and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, P. R. China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
| | - Yinmei Li
- Department of Optics and Optical Engineering, University of Science and Technology of China and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, P. R. China
| | - Haowei Wang
- Department of Optics and Optical Engineering, University of Science and Technology of China and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, P. R. China
| | - Qingguo Gong
- Department of Optics and Optical Engineering, University of Science and Technology of China and Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, Anhui, P. R. China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P. R. China
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Hackley RK, Schmid AK. Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response. J Mol Biol 2019; 431:4147-4166. [PMID: 31437442 PMCID: PMC7419163 DOI: 10.1016/j.jmb.2019.07.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023]
Abstract
The environmental stress response (ESR), a global transcriptional program originally identified in yeast, is characterized by a rapid and transient transcriptional response composed of large, oppositely regulated gene clusters. Genes induced during the ESR encode core components of stress tolerance, macromolecular repair, and maintenance of homeostasis. In this review, we investigate the possibility for conservation of the ESR across the eukaryotic and archaeal domains of life. We first re-analyze existing transcriptomics data sets to illustrate that a similar transcriptional response is identifiable in Halobacterium salinarum, an archaeal model organism. To substantiate the archaeal ESR, we calculated gene-by-gene correlations, gene function enrichment, and comparison of temporal dynamics. We note reported examples of variation in the ESR across fungi, then synthesize high-level trends present in expression data of other archaeal species. In particular, we emphasize the need for additional high-throughput time series expression data to further characterize stress-responsive transcriptional programs in the Archaea. Together, this review explores an open question regarding features of global transcriptional stress response programs shared across domains of life.
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Affiliation(s)
- Rylee K Hackley
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Amy K Schmid
- Department of Biology, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomics and Computational Biology, Duke University, Durham, NC 27708, USA.
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Shi H, Zhang R, Lan L, Chen Z, Kan J. Zinc mediates resuscitation of lactic acid-injured Escherichia coli by relieving oxidative stress. J Appl Microbiol 2019; 127:1741-1750. [PMID: 31487417 DOI: 10.1111/jam.14433] [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: 06/12/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 01/10/2023]
Abstract
AIMS Lactic acid is a natural antimicrobial in food industry, and also exists in fermented food. It was reported that sublethally injured Escherichia coli could survive in acidic conditions. When conditions become advantageous, injured E. coli can restore physiological function, which is a potential threat in food industry. Recovery is a necessary step for discriminating injured bacteria, but the resuscitation mechanism of injured bacteria is still unknown. METHODS AND RESULTS In our study, sublethal lactic acid treatment (pH 4·2, 60 min) posed oxidative stress on E. coli by decrease of superoxide dismutase (SOD) activity and overproduction of reactive oxygen species (ROS). Zinc with low concentration (1·0 mmol l-1 ) significantly increased the recovery ratio of injured E.coli induced by lactic acid. The recovery ratios of injured cell in minimal A medium (minA) with 1·0 mmol l-1 zinc reached to that with 3·0 mmol l-1 catalase (CAT). Conversely, the addition of zinc chelator N, N, N', N'-tetrakis (2-pyridylmethyl) decreased the recovery ratio. Zinc accelerated resuscitation of injured E. coli by improving SOD activity, and decreasing ROS production. Deletion of sodC encoding Cu/ZnSOD, katE/katG encoding CAT or regulating gene rpoS significantly decreased the recovery ratio. Among all of the mutants in this study, ΔrpoS and ΔsodC showed the lowest recovery ratio, which means they played significant roles in the process of resuscitation. CONCLUSION We provided direct evidence that zinc mediated resuscitation of lactic acid-injured E. coli by relieving oxidative stress. Zinc can be used as a low-cost and effective agent to improve recovery ratio and detection efficiency of injured bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY Antibacterial agents are a challenge for bacteria, but bacteria can survive as a sublethally injured state under stresses. Using injured E. coli induced by lactic acid as a model organism, we validated the significant role of zinc on resuscitation of injured cells.
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Affiliation(s)
- H Shi
- College of Food Science, Southwest University, Chongqing, China
| | - R Zhang
- College of Food Science, Southwest University, Chongqing, China
| | - L Lan
- College of Food Science, Southwest University, Chongqing, China
| | - Z Chen
- College of Food Science, Southwest University, Chongqing, China
| | - J Kan
- College of Food Science, Southwest University, Chongqing, China
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119
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King T, Vockler CJ, Allnutt TR, Fegan N. Transcriptomic response of Escherichia coli O157 isolates on meat: Comparison between a typical Australian isolate from cattle and a pathogenic clinical isolate. Food Microbiol 2019; 82:378-387. [DOI: 10.1016/j.fm.2019.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 02/25/2019] [Accepted: 03/07/2019] [Indexed: 02/02/2023]
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120
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Caimano MJ, Groshong AM, Belperron A, Mao J, Hawley KL, Luthra A, Graham DE, Earnhart CG, Marconi RT, Bockenstedt LK, Blevins JS, Radolf JD. The RpoS Gatekeeper in Borrelia burgdorferi: An Invariant Regulatory Scheme That Promotes Spirochete Persistence in Reservoir Hosts and Niche Diversity. Front Microbiol 2019; 10:1923. [PMID: 31507550 PMCID: PMC6719511 DOI: 10.3389/fmicb.2019.01923] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/05/2019] [Indexed: 11/28/2022] Open
Abstract
Maintenance of Borrelia burgdorferi within its enzootic cycle requires a complex regulatory pathway involving the alternative σ factors RpoN and RpoS and two ancillary trans-acting factors, BosR and Rrp2. Activation of this pathway occurs within ticks during the nymphal blood meal when RpoS, the effector σ factor, transcribes genes required for tick transmission and mammalian infection. RpoS also exerts a 'gatekeeper' function by repressing σ70-dependent tick phase genes (e.g., ospA, lp6.6). Herein, we undertook a broad examination of RpoS functionality throughout the enzootic cycle, beginning with modeling to confirm that this alternative σ factor is a 'genuine' RpoS homolog. Using a novel dual color reporter system, we established at the single spirochete level that ospA is expressed in nymphal midguts throughout transmission and is not downregulated until spirochetes have been transmitted to a naïve host. Although it is well established that rpoS/RpoS is expressed throughout infection, its requirement for persistent infection has not been demonstrated. Plasmid retention studies using a trans-complemented ΔrpoS mutant demonstrated that (i) RpoS is required for maximal fitness throughout the mammalian phase and (ii) RpoS represses tick phase genes until spirochetes are acquired by a naïve vector. By transposon mutant screening, we established that bba34/oppA5, the only OppA oligopeptide-binding protein controlled by RpoS, is a bona fide persistence gene. Lastly, comparison of the strain 297 and B31 RpoS DMC regulons identified two cohorts of RpoS-regulated genes. The first consists of highly conserved syntenic genes that are similarly regulated by RpoS in both strains and likely required for maintenance of B. burgdorferi sensu stricto strains in the wild. The second includes RpoS-regulated plasmid-encoded variable surface lipoproteins ospC, dbpA and members of the ospE/ospF/elp, mlp, revA, and Pfam54 paralogous gene families, all of which have evolved via inter- and intra-strain recombination. Thus, while the RpoN/RpoS pathway regulates a 'core' group of orthologous genes, diversity within RpoS regulons of different strains could be an important determinant of reservoir host range as well as spirochete virulence.
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Affiliation(s)
- Melissa J. Caimano
- Department of Medicine, UConn Health, Farmington, CT, United States,Department of Pediatrics, UConn Health, Farmington, CT, United States,Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States,*Correspondence: Melissa J. Caimano,
| | | | - Alexia Belperron
- Department of Internal Medicine, Section of Rheumatology, Allergy and Immunology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Jialing Mao
- Department of Internal Medicine, Section of Rheumatology, Allergy and Immunology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Kelly L. Hawley
- Department of Pediatrics, UConn Health, Farmington, CT, United States,Division of Infectious Diseases and Immunology, Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Amit Luthra
- Department of Medicine, UConn Health, Farmington, CT, United States
| | - Danielle E. Graham
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher G. Earnhart
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA, United States
| | - Richard T. Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA, United States
| | - Linda K. Bockenstedt
- Department of Internal Medicine, Section of Rheumatology, Allergy and Immunology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Jon S. Blevins
- Department of Microbiology and Immunology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Justin D. Radolf
- Department of Medicine, UConn Health, Farmington, CT, United States,Department of Pediatrics, UConn Health, Farmington, CT, United States,Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States,Department of Genetics and Genome Science, UConn Health, Farmington, CT, United States,Department of Immunology, UConn Health, Farmington, CT, United States
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121
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Chiok KLR, Shah DH. Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis. Poult Sci 2019; 98:2948-2963. [PMID: 30953073 DOI: 10.3382/ps/pez119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/27/2019] [Indexed: 01/02/2023] Open
Abstract
Chickens are the reservoir host of Salmonella Enteritidis. Salmonella Enteritidis colonizes the gastro-intestinal tract of chickens and replicates within macrophages without causing clinically discernable illness. Persistence of S. Enteritidis in the hostile environments of intestinal tract and macrophages allows it to disseminate extra-intestinally to liver, spleen, and reproductive tract. Extra-intestinal dissemination into reproductive tract leads to contamination of internal contents of eggs, which is a major risk factor for human infection. Understanding the genes that contribute to S. Enteritidis persistence in the chicken host is central to elucidate the genetic basis of the unique pathobiology of this public health pathogen. The aim of this study was to identify a succinct set of genes associated with infection-relevant in vitro environments to provide a rational foundation for subsequent biologically-relevant research. We used in silico prediction of gene expression and RNA-seq technology to identify a core set of 73 S. Enteritidis genes that are consistently highly expressed in multiple S. Enteritidis strains cultured at avian physiologic temperature under conditions that represent intestinal and intracellular environments. These common highly expressed (CHX) genes encode proteins involved in bacterial metabolism, protein synthesis, cell-envelope biogenesis, stress response, and a few proteins with uncharacterized functions. Further studies are needed to dissect the contribution of these CHX genes to the pathobiology of S. Enteritidis in the avian host. Several of the CHX genes could serve as promising targets for studies towards the development of immunoprophylactic and novel therapeutic strategies to prevent colonization of chickens and their environment with S. Enteritidis.
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Affiliation(s)
- Kim Lam R Chiok
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040
| | - Devendra H Shah
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA 99164-7040
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122
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Gaballa A, Guariglia-Oropeza V, Dürr F, Butcher BG, Chen AY, Chandrangsu P, Helmann JD. Modulation of extracytoplasmic function (ECF) sigma factor promoter selectivity by spacer region sequence. Nucleic Acids Res 2019; 46:134-145. [PMID: 29069433 PMCID: PMC5758882 DOI: 10.1093/nar/gkx953] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 10/05/2017] [Indexed: 11/27/2022] Open
Abstract
The ability of bacteria to adapt to stress depends on the conditional expression of specific sets of genes. Bacillus subtilis encodes seven extracytoplasmic function (ECF) sigma (σ) factors that regulate functions important for survival under conditions eliciting cell envelope stress. Of these, four have been studied in detail: σM, σW, σX and σV. These four σ factors recognize overlapping sets of promoters, although the sequences that determine this overlapping recognition are incompletely understood. A major role in promoter selectivity has been ascribed to the core −10 and −35 promoter elements. Here, we demonstrate that a homopolymeric T-tract motif, proximal to the −35 element, functions in combination with the core promoter sequences to determine selectivity for ECF sigma factors. This motif is most critical for promoter activation by σV, and contributes variably to activation by σM, σX and σW. We propose that this motif, which is a feature of the deduced promoter consensus for a subset of ECF σ factors from many species, imparts intrinsic DNA curvature to influence promoter activity. The differential effect of this region among ECF σ factors thereby provides a mechanism to modulate the nature and extent of regulon overlap.
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Affiliation(s)
- Ahmed Gaballa
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | | | - Franziska Dürr
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Bronwyn G Butcher
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Albert Y Chen
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - Pete Chandrangsu
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
| | - John D Helmann
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
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Gottschlich L, Geiser P, Bortfeld-Miller M, Field CM, Vorholt JA. Complex general stress response regulation in Sphingomonas melonis Fr1 revealed by transcriptional analyses. Sci Rep 2019; 9:9404. [PMID: 31253827 PMCID: PMC6599016 DOI: 10.1038/s41598-019-45788-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/12/2019] [Indexed: 01/31/2023] Open
Abstract
The general stress response (GSR) represents an important trait to survive in the environment by leading to multiple stress resistance. In alphaproteobacteria, the GSR is under the transcriptional control of the alternative sigma factor EcfG. Here we performed transcriptome analyses to investigate the genes controlled by EcfG of Sphingomonas melonis Fr1 and the plasticity of this regulation under stress conditions. We found that EcfG regulates genes for proteins that are typically associated with stress responses. Moreover, EcfG controls regulatory proteins, which likely fine-tune the GSR. Among these, we identified a novel negative GSR feedback regulator, termed NepR2, on the basis of gene reporter assays, phenotypic analyses, and biochemical assays. Transcriptional profiling of signaling components upstream of EcfG under complex stress conditions showed an overall congruence with EcfG-regulated genes. Interestingly however, we found that the GSR is transcriptionally linked to the regulation of motility and biofilm formation via the single domain response regulator SdrG and GSR-activating histidine kinases. Altogether, our findings indicate that the GSR in S. melonis Fr1 underlies a complex regulation to optimize resource allocation and resilience in stressful and changing environments.
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Affiliation(s)
- Lisa Gottschlich
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Petra Geiser
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Miriam Bortfeld-Miller
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Christopher M Field
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093, Zurich, Switzerland.
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Gottesman S. Trouble is coming: Signaling pathways that regulate general stress responses in bacteria. J Biol Chem 2019; 294:11685-11700. [PMID: 31197038 DOI: 10.1074/jbc.rev119.005593] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria can rapidly and reversibly respond to changing environments via complex transcriptional and post-transcriptional regulatory mechanisms. Many of these adaptations are specific, with the regulatory output tailored to the inducing signal (for instance, repairing damage to cell components or improving acquisition and use of growth-limiting nutrients). However, the general stress response, activated in bacterial cells entering stationary phase or subjected to nutrient depletion or cellular damage, is unique in that its common, broad output is induced in response to many different signals. In many different bacteria, the key regulator for the general stress response is a specialized sigma factor, the promoter specificity subunit of RNA polymerase. The availability or activity of the sigma factor is regulated by complex regulatory circuits, the majority of which are post-transcriptional. In Escherichia coli, multiple small regulatory RNAs, each made in response to a different signal, positively regulate translation of the general stress response sigma factor RpoS. Stability of RpoS is regulated by multiple anti-adaptor proteins that are also synthesized in response to different signals. In this review, the modes of signaling to and levels of regulation of the E. coli general stress response are discussed. They are also used as a basis for comparison with the general stress response in other bacteria with the aim of extracting key principles that are common among different species and highlighting important unanswered questions.
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Affiliation(s)
- Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
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125
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Herr CQ, Macomber L, Kalliri E, Hausinger RP. Glutarate L-2-hydroxylase (CsiD/GlaH) is an archetype Fe(II)/2-oxoglutarate-dependent dioxygenase. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 117:63-90. [PMID: 31564307 DOI: 10.1016/bs.apcsb.2019.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The Escherichia coli gene initially named ygaT is located adjacent to lhgO, encoding L-2-hydroxyglutarate oxidase/dehydrogenase, and the gabDTP gene cluster, utilized for γ-aminobutyric acid (GABA) metabolism. Because this gene is transcribed specifically during periods of carbon starvation, it was renamed csiD for carbon starvation induced. The CsiD protein was structurally characterized and shown to possess a double-stranded ß-helix fold, characteristic of a large family of non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases. Consistent with a role in producing the substrate for LhgO, CsiD was shown to be a glutarate L-2-hydroxylase. We review the kinetic and structural properties of glutarate L-2-hydroxylase from E. coli and other species, and we propose a catalytic mechanism for this archetype 2OG-dependent hydroxylase. Glutarate can be derived from l-lysine within the cell, with the gabDT genes exhibiting expanded reactivities beyond those known for GABA metabolism. The complete CsiD-containing pathway provides a means for the cell to obtain energy from the metabolism of l-lysine during periods of carbon starvation. To reflect the role of this protein in the cell, a renaming of csiD to glaH has been proposed.
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Affiliation(s)
- Caitlyn Q Herr
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Lee Macomber
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Efthalia Kalliri
- Department of Chemistry, Michigan State University, East Lansing, MI, United States
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
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127
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Santos-Zavaleta A, Pérez-Rueda E, Sánchez-Pérez M, Velázquez-Ramírez DA, Collado-Vides J. Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes. BMC Genomics 2019; 20:299. [PMID: 30991941 PMCID: PMC6469107 DOI: 10.1186/s12864-019-5619-z] [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: 02/14/2019] [Accepted: 03/18/2019] [Indexed: 02/08/2023] Open
Abstract
Background Crl, identified for curli production, is a small transcription factor that stimulates the association of the σS factor (RpoS) with the RNA polymerase core through direct and specific interactions, increasing the transcription rate of genes during the transition from exponential to stationary phase at low temperatures, using indole as an effector molecule. The lack of a comprehensive collection of information on the Crl regulon makes it difficult to identify a dominant function of Crl and to generate any hypotheses concerning its taxonomical distribution in archaeal and bacterial organisms. Results In this work, based on a systematic literature review, we identified the first comprehensive dataset of 86 genes under the control of Crl in the bacterium Escherichia coli K-12; those genes correspond to 40% of the σS regulon in this bacterium. Based on an analysis of orthologs in 18 archaeal and 69 bacterial taxonomical divisions and using E. coli K-12 as a framework, we suggest three main events that resulted in this regulon’s actual form: (i) in a first step, rpoS, a gene widely distributed in bacteria and archaea cellular domains, was recruited to regulate genes involved in ancient metabolic processes, such as those associated with glycolysis and the tricarboxylic acid cycle; (ii) in a second step, the regulon recruited those genes involved in metabolic processes, which are mainly taxonomically constrained to Proteobacteria, with some secondary losses, such as those genes involved in responses to stress or starvation and cell adhesion, among others; and (iii) in a posterior step, Crl might have been recruited in Enterobacteriaceae; because its taxonomical pattern constrained to this bacterial order, however further analysis are necessary. Conclusions Therefore, we suggest that the regulon Crl is highly flexible for phenotypic adaptation, probably as consequence of the diverse growth environments associated with all organisms in which members of this regulatory network are present. Electronic supplementary material The online version of this article (10.1186/s12864-019-5619-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A Santos-Zavaleta
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico.
| | - E Pérez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Sede Mérida, Universidad Nacional Autónoma de México, Unidad Académica de Ciencias y Tecnología, 97302, Mérida, Yucatán, Mexico. .,Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.
| | - M Sánchez-Pérez
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - D A Velázquez-Ramírez
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - J Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
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128
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Dorich V, Brugger C, Tripathi A, Hoskins JR, Tong S, Suhanovsky MM, Sastry A, Wickner S, Gottesman S, Deaconescu AM. Structural basis for inhibition of a response regulator of σ S stability by a ClpXP antiadaptor. Genes Dev 2019; 33:718-732. [PMID: 30975721 PMCID: PMC6546054 DOI: 10.1101/gad.320168.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 03/19/2019] [Indexed: 11/25/2022]
Abstract
Dorich et al. present the first crystal structure of RssB bound to an antiadaptor, the DNA damage-inducible IraD. The structural data, together with mechanistic studies, suggest that RssB plasticity is critical for regulation of σS degradation. The stationary phase promoter specificity subunit σS (RpoS) is delivered to the ClpXP machinery for degradation dependent on the adaptor RssB. This adaptor-specific degradation of σS provides a major point for regulation and transcriptional reprogramming during the general stress response. RssB is an atypical response regulator and the only known ClpXP adaptor that is inhibited by multiple but dissimilar antiadaptors (IraD, IraP, and IraM). These are induced by distinct stress signals and bind to RssB in poorly understood manners to achieve stress-specific inhibition of σS turnover. Here we present the first crystal structure of RssB bound to an antiadaptor, the DNA damage-inducible IraD. The structure reveals that RssB adopts a compact closed architecture with extensive interactions between its N-terminal and C-terminal domains. The structural data, together with mechanistic studies, suggest that RssB plasticity, conferred by an interdomain glutamate-rich flexible linker, is critical for regulation of σS degradation. Structural modulation of interdomain linkers may thus constitute a general strategy for tuning response regulators.
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Affiliation(s)
- Victoria Dorich
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
| | - Christiane Brugger
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
| | - Arti Tripathi
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Joel R Hoskins
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Song Tong
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Margaret M Suhanovsky
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
| | - Amita Sastry
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
| | - Sue Wickner
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Susan Gottesman
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Alexandra M Deaconescu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA
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Coxiella burnetii RpoS Regulates Genes Involved in Morphological Differentiation and Intracellular Growth. J Bacteriol 2019; 201:JB.00009-19. [PMID: 30745369 DOI: 10.1128/jb.00009-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/30/2019] [Indexed: 12/19/2022] Open
Abstract
Coxiella burnetii, the etiological agent of Q fever, undergoes a unique biphasic developmental cycle where bacteria transition from a replicating (exponential-phase) large cell variant (LCV) form to a nonreplicating (stationary-phase) small cell variant (SCV) form. The alternative sigma factor RpoS is an essential regulator of stress responses and stationary-phase physiology in several bacterial species, including Legionella pneumophila, which has a developmental cycle superficially similar to that of C. burnetii Here, we used a C. burnetii ΔrpoS mutant to define the role of RpoS in intracellular growth and SCV development. Growth yields following infection of Vero epithelial cells or THP-1 macrophage-like cells with the rpoS mutant in the SCV form, but not the LCV form, were significantly lower than that of wild-type bacteria. RNA sequencing and whole-cell mass spectrometry of the C. burnetii ΔrpoS mutant revealed that a substantial portion of the C. burnetii genome is regulated by RpoS during SCV development. Regulated genes include those involved in stress responses, arginine transport, peptidoglycan remodeling, and synthesis of the SCV-specific protein ScvA. Genes comprising the dot/icm locus, responsible for production of the Dot/Icm type 4B secretion system, were also dysregulated in the rpoS mutant. These data were corroborated with independent assays demonstrating that the C. burnetii ΔrpoS strain has increased sensitivity to hydrogen peroxide and carbenicillin and a thinner cell wall/outer membrane complex. Collectively, these results demonstrate that RpoS is an important regulator of genes involved in C. burnetii SCV development and intracellular growth.IMPORTANCE The Q fever bacterium Coxiella burnetii has spore-like environmental stability, a characteristic that contributes to its designation as a potential bioweapon. Stability is likely conferred by a highly resistant, small cell variant (SCV) stationary-phase form that arises during a biphasic developmental cycle. Here, we define the role of the alternative sigma factor RpoS in regulating genes associated with SCV development. Genes involved in stress responses, amino acid transport, cell wall remodeling, and type 4B effector secretion were dysregulated in the rpoS mutant. Cellular impairments included defects in intracellular growth, cell wall structure, and resistance to oxidants. These results support RpoS as a central regulator of the Coxiella developmental cycle and identify developmentally regulated genes involved in morphological differentiation.
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130
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A sigma factor RpoD negatively regulates temperature-dependent metalloprotease expression in a pathogenic Vibrio splendidus. Microb Pathog 2019; 128:311-316. [DOI: 10.1016/j.micpath.2019.01.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/18/2018] [Accepted: 01/16/2019] [Indexed: 11/24/2022]
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131
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Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile. Antimicrob Agents Chemother 2019; 63:AAC.01363-18. [PMID: 30455241 DOI: 10.1128/aac.01363-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/04/2018] [Indexed: 01/08/2023] Open
Abstract
Clostridium difficile is a potentially lethal gut pathogen that causes nosocomial and community-acquired infections. Limited treatment options and reports of reduced susceptibility to current treatment emphasize the necessity for novel antimicrobials. The DNA polymerase of Gram-positive organisms is an attractive target for the development of antimicrobials. ACX-362E [N 2-(3,4-dichlorobenzyl)-7-(2-[1-morpholinyl]ethyl)guanine; MorE-DCBG] is a DNA polymerase inhibitor in preclinical development as a novel therapeutic against C. difficile infection. This synthetic purine shows preferential activity against C. difficile PolC over those of other organisms in vitro and is effective in an animal model of C. difficile infection. In this study, we have determined its efficacy against a large collection of clinical isolates. At concentrations below the MIC, the presumed slowing (or stalling) of replication forks due to ACX-362E leads to a growth defect. We have determined the transcriptional response of C. difficile to replication inhibition and observed an overrepresentation of upregulated genes near the origin of replication in the presence of PolC inhibitors, but not when cells were subjected to subinhibitory concentrations of other antibiotics. This phenomenon can be explained by a gene dosage shift, as we observed a concomitant increase in the ratio between origin-proximal and terminus-proximal gene copy number upon exposure to PolC inhibitors. Moreover, we show that certain genes differentially regulated under PolC inhibition are controlled by the origin-proximal general stress response regulator sigma factor B. Together, these data suggest that genome location both directly and indirectly determines the transcriptional response to replication inhibition in C. difficile.
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132
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Abstract
The ability of bacteria to thrive in diverse habitats and to adapt to ever-changing environmental conditions relies on the rapid and stringent modulation of gene expression. It has become evident in the past decade that small regulatory RNAs (sRNAs) are central components of networks controlling the bacterial responses to stress. Functioning at the posttranscriptional level, sRNAs base-pair with cognate mRNAs to alter translation, stability, or both to either repress or activate the targeted transcripts; the RNA chaperone Hfq participates in stabilizing sRNAs and in promoting pairing between target and sRNA. In particular, sRNAs act at the heart of crucial stress responses, including those dedicated to overcoming membrane damage and oxidative stress, discussed here. The bacterial cell envelope is the outermost protective barrier against the environment and thus is constantly monitored and remodeled. Here, we review the integration of sRNAs into the complex networks of several major envelope stress responses of Gram-negative bacteria, including the RpoE (σE), Cpx, and Rcs regulons. Oxidative stress, caused by bacterial respiratory activity or induced by toxic molecules, can lead to significant damage of cellular components. In Escherichia coli and related bacteria, sRNAs also contribute significantly to the function of the RpoS (σS)-dependent general stress response as well as the specific OxyR- and SoxR/S-mediated responses to oxidative damage. Their activities in gene regulation and crosstalk to other stress-induced regulons are highlighted.
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133
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Bischof LF, Haurat MF, Hoffmann L, Albersmeier A, Wolf J, Neu A, Pham TK, Albaum SP, Jakobi T, Schouten S, Neumann-Schaal M, Wright PC, Kalinowski J, Siebers B, Albers SV. Early Response of Sulfolobus acidocaldarius to Nutrient Limitation. Front Microbiol 2019; 9:3201. [PMID: 30687244 PMCID: PMC6335949 DOI: 10.3389/fmicb.2018.03201] [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: 10/08/2018] [Accepted: 12/10/2018] [Indexed: 01/13/2023] Open
Abstract
In natural environments microorganisms encounter extreme changes in temperature, pH, osmolarities and nutrient availability. The stress response of many bacterial species has been described in detail, however, knowledge in Archaea is limited. Here, we describe the cellular response triggered by nutrient limitation in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius. We measured changes in gene transcription and protein abundance upon nutrient depletion up to 4 h after initiation of nutrient depletion. Transcript levels of 1118 of 2223 protein coding genes and abundance of approximately 500 proteins with functions in almost all cellular processes were affected by nutrient depletion. Our study reveals a significant rerouting of the metabolism with respect to degradation of internal as well as extracellular-bound organic carbon and degradation of proteins. Moreover, changes in membrane lipid composition were observed in order to access alternative sources of energy and to maintain pH homeostasis. At transcript level, the cellular response to nutrient depletion in S. acidocaldarius seems to be controlled by the general transcription factors TFB2 and TFEβ. In addition, ribosome biogenesis is reduced, while an increased protein degradation is accompanied with a loss of protein quality control. This study provides first insights into the early cellular response of Sulfolobus to organic carbon and organic nitrogen depletion.
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Affiliation(s)
- Lisa F Bischof
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - M Florencia Haurat
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Lena Hoffmann
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jacqueline Wolf
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Astrid Neu
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Trong Khoa Pham
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Stefan P Albaum
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Jakobi
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Stefan Schouten
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute of Sea Research, Den Burg, Netherlands.,Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Meina Neumann-Schaal
- Department of Bioinformatics and Biochemistry, Braunschweig University of Technology, Braunschweig, Germany
| | - Phillip C Wright
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany
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134
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Matanza XM, Osorio CR. Transcriptome changes in response to temperature in the fish pathogen Photobacterium damselae subsp. damselae: Clues to understand the emergence of disease outbreaks at increased seawater temperatures. PLoS One 2018; 13:e0210118. [PMID: 30596794 PMCID: PMC6312309 DOI: 10.1371/journal.pone.0210118] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/17/2018] [Indexed: 01/22/2023] Open
Abstract
The marine bacterium Photobacterium damselae subsp. damselae (Pdd) is a generalist and facultative pathogen that causes disease in a wide range of marine animals including fish species of importance in aquaculture. Disease outbreaks in fish farms have been correlated with an increased water temperature during summer months. In this study, we have used RNA sequencing to analyze the transcriptome of Pdd RM-71 cultured at two different temperatures, which simulated temperature conditions experienced during free swimming lifestyle at mid latitudes in winter months (15°C) and during outbreaks in aquaculture in warm summer months (25°C). The enhanced bacterial growth of Pdd observed at 25°C in comparison to 15°C suggests that an elevated seawater temperature contributes to the build-up of a sufficient bacterial population to cause disease. In comparison to growth at 15°C, growth at 25°C resulted in the upregulation of genes involved in DNA synthesis, nutrient uptake, chemotaxis, flagellar motility, secretion systems and antimicrobial resistance. Plasmid-encoded virulence factors, which include a putative adhesin/invasin OmpU, a transferrin receptor and a serum resistance protein, were also upregulated. Transcription factor RpoS, genes involved in cold shock response, modulation of cell envelope and amino acid metabolism, as well as genes of yet unknown function were downregulated at 25°C. Notably, the gene encoding damselysin cytotoxin (Dly) was among the most highly transcribed genes at the two assayed temperatures, at levels comparable to the most highly expressed housekeeping genes. This study contributes to our understanding of the regulatory networks and biology of a generalist marine bacterial pathogen, and provides evidence that temperature regulates multiple physiological and virulence-related functions in Pdd.
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Affiliation(s)
- Xosé M. Matanza
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Carlos R. Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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135
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The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase. Sci Rep 2018; 8:17875. [PMID: 30552341 PMCID: PMC6294744 DOI: 10.1038/s41598-018-35756-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/08/2018] [Indexed: 12/02/2022] Open
Abstract
Only a few overlapping gene pairs are known in the best-analyzed bacterial model organism Escherichia coli. Automatic annotation programs usually annotate only one out of six reading frames at a locus, allowing only small overlaps between protein-coding sequences. However, both RNAseq and RIBOseq show signals corresponding to non-trivially overlapping reading frames in antisense to annotated genes, which may constitute protein-coding genes. The transcription and translation of the novel 264 nt gene asa, which overlaps in antisense to a putative TEGT (Testis-Enhanced Gene Transfer) transporter gene is detected in pathogenic E. coli, but not in two apathogenic E. coli strains. The gene in E. coli O157:H7 (EHEC) was further analyzed. An overexpression phenotype was identified in two stress conditions, i.e. excess in salt or arginine. For this, EHEC overexpressing asa was grown competitively against EHEC with a translationally arrested asa mutant gene. RT-qPCR revealed conditional expression dependent on growth phase, sodium chloride, and arginine. Two potential promoters were computationally identified and experimentally verified by reporter gene expression and determination of the transcription start site. The protein Asa was verified by Western blot. Close homologues of asa have not been found in protein databases, but bioinformatic analyses showed that it may be membrane associated, having a largely disordered structure.
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136
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New insights into the adaptive transcriptional response to nitrogen starvation in Escherichia coli. Biochem Soc Trans 2018; 46:1721-1728. [PMID: 30514772 PMCID: PMC6299236 DOI: 10.1042/bst20180502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/14/2018] [Accepted: 10/17/2018] [Indexed: 12/11/2022]
Abstract
Bacterial adaptive responses to biotic and abiotic stresses often involve large-scale reprogramming of the transcriptome. Since nitrogen is an essential component of the bacterial cell, the transcriptional basis of the adaptive response to nitrogen starvation has been well studied. The adaptive response to N starvation in Escherichia coli is primarily a 'scavenging response', which results in the transcription of genes required for the transport and catabolism of nitrogenous compounds. However, recent genome-scale studies have begun to uncover and expand some of the intricate regulatory complexities that underpin the adaptive transcriptional response to nitrogen starvation in E. coli The purpose of this review is to highlight some of these new developments.
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137
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Jousset AB, Rosinski-Chupin I, Takissian J, Glaser P, Bonnin RA, Naas T. Transcriptional Landscape of a bla KPC-2 Plasmid and Response to Imipenem Exposure in Escherichia coli TOP10. Front Microbiol 2018; 9:2929. [PMID: 30559731 PMCID: PMC6286996 DOI: 10.3389/fmicb.2018.02929] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/14/2018] [Indexed: 12/15/2022] Open
Abstract
The diffusion of KPC-2 carbapenemase is closely related to the spread of Klebsiella pneumoniae of the clonal-group 258 and linked to IncFIIK plasmids. Little is known about the biology of multi-drug resistant plasmids and the reasons of their successful dissemination. Using E. coli TOP10 strain harboring a multi-replicon IncFIIK-IncFIB blaKPC−2-gene carrying plasmid pBIC1a from K. pneumoniae ST-258 clinical isolate BIC-1, we aimed to identify basal gene expression and the effects of imipenem exposure using whole transcriptome approach by RNA sequencing (RNA-Seq). Independently of the antibiotic pressure, most of the plasmid-backbone genes were expressed at low levels. The most expressed pBIC1a genes were involved in antibiotic resistance (blaKPC−2, blaTEM and aph(3′)-I), in plasmid replication and conjugation, or associated to mobile elements. After antibiotic exposure, 34% of E. coli (pBIC1a) genome was differentially expressed. Induction of oxidative stress response was evidenced, with numerous upregulated genes of the SoxRS/OxyR oxydative stress regulons, the Fur regulon (for iron uptake machinery), and IscR regulon (for iron sulfur cluster synthesis). Nine genes carried by pBIC1a were up-regulated, including the murein DD-endopeptidase mepM and the copper resistance operon. Despite the presence of a carbapenemase, we observed a major impact on E. coli (pBIC1a) whole transcriptome after imipenem exposure, but no effect on the level of transcription of antimicrobial resistance genes. We describe adaptive responses of E. coli to imipenem-induced stress, and identified plasmid-encoded genes that could be involved in resistance to stressful environments.
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Affiliation(s)
- Agnès B Jousset
- Department of Bacteriology-Parasitology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Faculty of Medicine, Paris-Sud University, Le Kremlin-Bicêtre, France.,Joint Research Unit Evolution and Ecology of Resistance to Antibiotics, Institut Pasteur-APHP-University Paris Sud, Paris, France
| | - Isabelle Rosinski-Chupin
- Joint Research Unit Evolution and Ecology of Resistance to Antibiotics, Institut Pasteur-APHP-University Paris Sud, Paris, France.,CNRS, UMRS 3525, Paris, France
| | - Julie Takissian
- EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Faculty of Medicine, Paris-Sud University, Le Kremlin-Bicêtre, France.,Joint Research Unit Evolution and Ecology of Resistance to Antibiotics, Institut Pasteur-APHP-University Paris Sud, Paris, France
| | - Philippe Glaser
- Joint Research Unit Evolution and Ecology of Resistance to Antibiotics, Institut Pasteur-APHP-University Paris Sud, Paris, France.,CNRS, UMRS 3525, Paris, France
| | - Rémy A Bonnin
- Associated French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Faculty of Medicine, Paris-Sud University, Le Kremlin-Bicêtre, France.,Joint Research Unit Evolution and Ecology of Resistance to Antibiotics, Institut Pasteur-APHP-University Paris Sud, Paris, France
| | - Thierry Naas
- Department of Bacteriology-Parasitology-Hygiene, Bicêtre Hospital, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France.,Associated French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France.,EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases", Faculty of Medicine, Paris-Sud University, Le Kremlin-Bicêtre, France.,Joint Research Unit Evolution and Ecology of Resistance to Antibiotics, Institut Pasteur-APHP-University Paris Sud, Paris, France
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138
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Moser F, Espah Borujeni A, Ghodasara AN, Cameron E, Park Y, Voigt CA. Dynamic control of endogenous metabolism with combinatorial logic circuits. Mol Syst Biol 2018; 14:e8605. [PMID: 30482789 PMCID: PMC6263354 DOI: 10.15252/msb.20188605] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 11/09/2022] Open
Abstract
Controlling gene expression during a bioprocess enables real-time metabolic control, coordinated cellular responses, and staging order-of-operations. Achieving this with small molecule inducers is impractical at scale and dynamic circuits are difficult to design. Here, we show that the same set of sensors can be integrated by different combinatorial logic circuits to vary when genes are turned on and off during growth. Three Escherichia coli sensors that respond to the consumption of feedstock (glucose), dissolved oxygen, and by-product accumulation (acetate) are constructed and optimized. By integrating these sensors, logic circuits implement temporal control over an 18-h period. The circuit outputs are used to regulate endogenous enzymes at the transcriptional and post-translational level using CRISPRi and targeted proteolysis, respectively. As a demonstration, two circuits are designed to control acetate production by matching their dynamics to when endogenous genes are expressed (pta or poxB) and respond by turning off the corresponding gene. This work demonstrates how simple circuits can be implemented to enable customizable dynamic gene regulation.
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Affiliation(s)
- Felix Moser
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amin Espah Borujeni
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amar N Ghodasara
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ewen Cameron
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yongjin Park
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, USA
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139
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Switzer A, Evangelopoulos D, Figueira R, de Carvalho LPS, Brown DR, Wigneshweraraj S. A novel regulatory factor affecting the transcription of methionine biosynthesis genes in Escherichia coli experiencing sustained nitrogen starvation. Microbiology (Reading) 2018; 164:1457-1470. [DOI: 10.1099/mic.0.000683] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Amy Switzer
- 1MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Dimitrios Evangelopoulos
- 2Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Rita Figueira
- 1MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Luiz Pedro S. de Carvalho
- 2Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Daniel R. Brown
- 1MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
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140
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Ji F, Shen Y, Tang L, Cai Z. Determination of intracellular metabolites concentrations in Escherichia coli under nutrition stress using liquid chromatography-tandem mass spectrometry. Talanta 2018; 189:1-7. [DOI: 10.1016/j.talanta.2018.06.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/07/2018] [Accepted: 06/13/2018] [Indexed: 11/26/2022]
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141
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Aguilar C, Martínez-Batallar G, Flores N, Moreno-Avitia F, Encarnación S, Escalante A, Bolívar F. Analysis of differentially upregulated proteins in ptsHIcrr - and rppH - mutants in Escherichia coli during an adaptive laboratory evolution experiment. Appl Microbiol Biotechnol 2018; 102:10193-10208. [PMID: 30284012 DOI: 10.1007/s00253-018-9397-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 11/25/2022]
Abstract
The previous deletion of the cytoplasmic components of the phosphotransferase system (PTS) in Escherichia coli JM101 resulted in the PTS- derivative strain PB11 with severely impaired growth capability in glucose as the sole carbon source. Previous adaptive laboratory evolution (ALE) experiment led to select a fast-growing strain named PB12 from PB11. Comparative genome analysis of PB12 showed a chromosomal deletion, which result in the loss of several genes including rppH which codes for the RNA pyrophosphohydrolase RppH, involved in the preparation of hundreds of mRNAs for further degradation by RNase E. Previous inactivation of rppH in PB11 (PB11rppH-) improved significantly its growing capabilities and increased several mRNAs respect its parental strain PB11. These previous results led to propose to the PB11rppH- mutant as an intermediate between PB11 and PB12 strains merged during the early ALE experiment. In this contribution, we report the metabolic response to the PTS- and rppH- mutations in the deep of a proteomic approach to understanding the relevance of rppH- phenotype during an ALE experiment. Differentially upregulated proteins between the wild-type JM101/PB11, PB11/PB11rppH-, and PB11/PB12 comparisons led to identifying 45 proteins between strain comparisons. Downregulated or upregulated proteins in PB11rppH- were found expressed at an intermediate level with respect to PB11 and PB12. Many of these proteins were found involved in non-previously metabolic traits reported in the study of the PTS- strains, including glucose, amino acids, ribose transport; amino acid biosynthesis; NAD biosynthesis/salvage pathway, biosynthesis of Ac-CoA precursors; detoxification and degradation pathways; stress response; protein synthesis; and possible mutator activities between comparisons. No changes were found in the expression of galactose permease GalP, previously proposed as the primary glucose transporter in the absence of PTS selected by the PTS- derivatives during the ALE experiment. This result suggests that the evolving PTS- population selected other transporters such as LamB, MglB, and ManX instead of GalP for glucose uptake during the early ALE experiment. Analysis of the biological relevance of the metabolic traits developed by the studied strains provided valuable information to understand the relevance of the rppH- mutation in the PTS- background during an ALE experiment as a strategy for the selection of valuable phenotypes for metabolic engineering purposes.
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Affiliation(s)
- César Aguilar
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Gabriel Martínez-Batallar
- Programa de Genómica Funcional de Procariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico
| | - Fabián Moreno-Avitia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico
| | - Sergio Encarnación
- Programa de Genómica Funcional de Procariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico.
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico.,Member of El Colegio Nacional, Ciudad de México, México
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142
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Liu H, Yan H, Xiao Y, Nie H, Huang Q, Chen W. The exopolysaccharide gene cluster pea is transcriptionally controlled by RpoS and repressed by AmrZ in Pseudomonas putida KT2440. Microbiol Res 2018; 218:1-11. [PMID: 30454651 DOI: 10.1016/j.micres.2018.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/29/2018] [Accepted: 09/05/2018] [Indexed: 10/28/2022]
Abstract
In Pseudomonas putida KT2440, the exopolysaccharide Pea is associated with biofilm stability and pellicle formation; however, little is known about its regulatory pathway. In this study, we identified that the gene cluster pea was transcribed from 25 bp upstream of the operon and the stationary phase alternative sigma factor RpoS regulated the transcription of pea. When RpoS was absent, another sigma factor, likely the housekeeping sigma factor RpoD, could also mediate pea transcription but at a low level. The function of Pea polysaccharide was further confirmed to be necessary for full production of biofilm, formation of pellicle and c-di-GMP-dependent wrinkly colony morphology. Additionally, evidences were provided to demonstrate that the transcriptional regulator AmrZ was a negative regulator for pea expression. DNase I footprinting studies verified that AmrZ bound directly to the site overlapping the pea promoter, which might interfere with the binding of RNA polymerase to the promoter and resulted in inhibition of transcription initiation.
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Affiliation(s)
- Huizhong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Huaduo Yan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Yujie Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Hailing Nie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Qiaoyun Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
| | - Wenli Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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143
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Smith A, Kaczmar A, Bamford RA, Smith C, Frustaci S, Kovacs-Simon A, O'Neill P, Moore K, Paszkiewicz K, Titball RW, Pagliara S. The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli. Front Microbiol 2018; 9:1739. [PMID: 30158905 PMCID: PMC6104134 DOI: 10.3389/fmicb.2018.01739] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/11/2018] [Indexed: 11/13/2022] Open
Abstract
Microorganisms shape the composition of the medium they are growing in, which in turn has profound consequences on the reprogramming of the population gene-expression profile. In this paper, we investigate the progressive changes in pH and sugar availability in the medium of a growing Escherichia coli (E. coli) culture. We show how these changes have an effect on both the cellular heterogeneity within the microbial community and the gene-expression profile of the microbial population. We measure the changes in gene-expression as E. coli moves from lag, to exponential, and finally into stationary phase. We found that pathways linked to the changes in the medium composition such as ribosomal, tricarboxylic acid cycle (TCA), transport, and metabolism pathways are strongly regulated during the different growth phases. In order to quantify the corresponding temporal changes in the population heterogeneity, we measure the fraction of E. coli persisters surviving different antibiotic treatments during the various phases of growth. We show that the composition of the medium in which β-lactams or quinolones, but not aminoglycosides, are dissolved strongly affects the measured phenotypic heterogeneity within the culture. Our findings contribute to a better understanding on how the composition of the culture medium influences both the reprogramming in the population gene-expression and the emergence of phenotypic variants.
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Affiliation(s)
- Ashley Smith
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | - Agnieszka Kaczmar
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rosemary A Bamford
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Simona Frustaci
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - Paul O'Neill
- Biosciences, University of Exeter, Exeter, United Kingdom
| | - Karen Moore
- Biosciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,Biosciences, University of Exeter, Exeter, United Kingdom
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144
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Amar A, Pezzoni M, Pizarro RA, Costa CS. New envelope stress factors involved in σ E activation and conditional lethality of rpoE mutations in Salmonella enterica. MICROBIOLOGY-SGM 2018; 164:1293-1307. [PMID: 30084765 DOI: 10.1099/mic.0.000701] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Salmonella enterica serovar Typhimurium (S. typhimurium) can cause food- and water-borne illness with diverse clinical manifestations. One key factor for S. typhimurium pathogenesis is the alternative sigma factor σE, which is encoded by the rpoE gene and controls the transcription of genes required for outer-membrane integrity in response to alterations in the bacterial envelope. The canonical pathway for σE activation involves proteolysis of the antisigma factor RseA, which is triggered by unfolded outer-membrane porins (OMPs) and lipopolysaccharides (LPS) that have accumulated in the periplasm. This study reports new stress factors that are able to activate σE expression. We demonstrate that UVA radiation induces σE activity in a pathway that is dependent on the stringent response regulator ppGpp. Survival assays revealed that rpoE has a role in the defence against lethal UVA doses that is mediated by functions that are dependent on and independent of the alternative sigma factor RpoS. We also report that the envelope stress generated by phage infection requires a functional rpoE gene for optimal bacterial tolerance and that it is able to induce σE activity in an RseA-dependent fashion. σE activity is also induced by hypo-osmotic shock in the absence of osmoregulated periplasmic glucans (OPGs). It is known that the rpoE gene is not essential in S. typhimurium. However, we report here two cases of the conditional lethality of rpoE mutations in this micro-organism. We demonstrate that rpoE mutations are not tolerated in the absence of OPGs (at low to moderate osmolarity) or LPS O-antigen. The latter case resembles that of the prototypic Escherichia coli strain K12, which neither synthesizes a complete LPS nor tolerates null rpoE mutations.
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Affiliation(s)
- Agustina Amar
- Dpto. de Radiobiología, Comisión Nacional de Energía Atómica, General San Martín, Argentina
| | - Magdalena Pezzoni
- Dpto. de Radiobiología, Comisión Nacional de Energía Atómica, General San Martín, Argentina
| | - Ramón A Pizarro
- Dpto. de Radiobiología, Comisión Nacional de Energía Atómica, General San Martín, Argentina
| | - Cristina S Costa
- Dpto. de Radiobiología, Comisión Nacional de Energía Atómica, General San Martín, Argentina
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145
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Mateus A, Bobonis J, Kurzawa N, Stein F, Helm D, Hevler J, Typas A, Savitski MM. Thermal proteome profiling in bacteria: probing protein state in vivo. Mol Syst Biol 2018; 14:e8242. [PMID: 29980614 PMCID: PMC6056769 DOI: 10.15252/msb.20188242] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Increasing antibiotic resistance urges for new technologies for studying microbes and antimicrobial mechanism of action. We adapted thermal proteome profiling (TPP) to probe the thermostability of Escherichia coli proteins in vivoE. coli had a more thermostable proteome than human cells, with protein thermostability depending on subcellular location-forming a high-to-low gradient from the cell surface to the cytoplasm. While subunits of protein complexes residing in one compartment melted similarly, protein complexes spanning compartments often had their subunits melting in a location-wise manner. Monitoring the E. coli meltome and proteome at different growth phases captured changes in metabolism. Cells lacking TolC, a component of multiple efflux pumps, exhibited major physiological changes, including differential thermostability and levels of its interaction partners, signaling cascades, and periplasmic quality control. Finally, we combined in vitro and in vivo TPP to identify targets of known antimicrobial drugs and to map their downstream effects. In conclusion, we demonstrate that TPP can be used in bacteria to probe protein complex architecture, metabolic pathways, and intracellular drug target engagement.
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Affiliation(s)
- André Mateus
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jacob Bobonis
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Nils Kurzawa
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Johannes Hevler
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Mikhail M Savitski
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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146
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Run S, Tian P. Improved Tolerance of Escherichia coli to Propionic Acid by Overexpression of Sigma Factor RpoS. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818030122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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147
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Regulation of Global Transcription in Escherichia coli by Rsd and 6S RNA. G3-GENES GENOMES GENETICS 2018; 8:2079-2089. [PMID: 29686109 PMCID: PMC5982834 DOI: 10.1534/g3.118.200265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In Escherichia coli, the sigma factor σ70 directs RNA polymerase to transcribe growth-related genes, while σ38 directs transcription of stress response genes during stationary phase. Two molecules hypothesized to regulate RNA polymerase are the protein Rsd, which binds to σ70, and the non-coding 6S RNA which binds to the RNA polymerase-σ70 holoenzyme. Despite multiple studies, the functions of Rsd and 6S RNA remain controversial. Here we use RNA-Seq in five phases of growth to elucidate their function on a genome-wide scale. We show that Rsd and 6S RNA facilitate σ38 activity throughout bacterial growth, while 6S RNA also regulates widely different genes depending upon growth phase. We discover novel interactions between 6S RNA and Rsd and show widespread expression changes in a strain lacking both regulators. Finally, we present a mathematical model of transcription which highlights the crosstalk between Rsd and 6S RNA as a crucial factor in controlling sigma factor competition and global gene expression.
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148
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Shaw JA, Henard CA, Liu L, Dieckman LM, Vázquez-Torres A, Bourret TJ. Salmonella enterica serovar Typhimurium has three transketolase enzymes contributing to the pentose phosphate pathway. J Biol Chem 2018; 293:11271-11282. [PMID: 29848552 DOI: 10.1074/jbc.ra118.003661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/23/2018] [Indexed: 11/06/2022] Open
Abstract
The genus Salmonella is responsible for many illnesses in humans and other vertebrate animals. We report here that Salmonella enterica serovar Typhimurium harbors three transketolases that support the non-oxidative branch of the pentose phosphate pathway. BLAST analysis identified two genes, STM14_2885 and STM14_2886, that together encode a putative transketolase (TktC) with 46-47% similarity to the known TktA and TktB isoforms. Assessing the mRNA and protein expression for each of the three transketolases, we determined that all are expressed in WT cells and regulated to varying extents by the alternative sigma factor RpoS. Enzyme assays with lysates from WT and transketolase-knockout strains established that TktA is responsible for >88% of the transketolase activity in WT cells. We purified recombinant forms of each isoenzyme to assess the kinetics for canonical transketolase reactions. TktA and TktB had comparable values for Vmax (539-1362 μm NADH consumed/s), Km (80-739 μm), and catalytic efficiency (1.02 × 108-1.06 × 109 m-1/s) for each substrate tested. The recombinant form of TktC had lower Km values (23-120 μm), whereas the Vmax (7.8-16 μm NADH consumed/s) and catalytic efficiency (5.58 × 106 to 6.07 × 108 m-1/s) were 10-100-fold lower. Using a murine model of Salmonella infection, we showed that a strain lacking all three transketolases is avirulent in C57BL/6 mice. These data provide evidence that S Typhimurium possesses three transketolases that contribute to pathogenesis.
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Affiliation(s)
- Jeff A Shaw
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Calvin A Henard
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011
| | - Lin Liu
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011
| | - Lynne M Dieckman
- Department of Chemistry, Creighton University, Omaha, Nebraska 68178
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011; Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado 80220
| | - Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178.
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149
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Guebel DV, Torres NV. Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response of Escherichia coli: Assessment by an Optimized Factorial Microarray Analysis. Front Microbiol 2018; 9:941. [PMID: 29875739 PMCID: PMC5974110 DOI: 10.3389/fmicb.2018.00941] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Background: While in eukaryotes acetylation/deacetylation regulation exerts multiple pleiotropic effects, in Escherichia coli it seems to be more limited and less known. Hence, we aimed to progress in the characterization of this regulation by dealing with three convergent aspects: the effector enzymes involved, the master regulator CRP, and the dependence on glucose availability. Methods: The transcriptional response of E. coli BW25113 was analyzed across 14 relevant scenarios. These conditions arise when the wild type and four isogenic mutants (defective in deacetylase CobB, defective in N(ε)-lysine acetyl transferase PatZ, Q- and R-type mutants of protein CRP) are studied under three levels of glucose availability (glucose-limited chemostat and glucose-excess or glucose-exhausted in batch culture). The Q-type emulates a permanent stage of CRPacetylated, whereas the R-type emulates a permanent stage of CRPdeacetylated. The data were analyzed by an optimized factorial microarray method (Q-GDEMAR). Results: (a) By analyzing one mutant against the other, we were able to unravel the true genes that participate in the interaction between ΔcobB/ΔpatZ mutations and glucose availability; (b) Increasing stages of glucose limitation appear to be associated with the up-regulation of specific sets of target genes rather than with the loss of genes present when glucose is in excess; (c) Both CRPdeacetylated and CRPacetylated produce extensive changes in specific subsets of genes, but their number and identity depend on the glucose availability; (d) In other sub-sets of genes, the transcriptional effect of CRP seems to be independent of its acetylation or deacetylation; (e) Some specific ontology functions can be associated with each of the different sets of genes detected herein. Conclusions: CRP cannot be thought of only as an effector of catabolite repression, because it acts along all the glucose conditions tested (excess, limited, and exhausted), exerting both positive and negative effects through different sets of genes. Acetylation of CRP does not seem to be a binary form of regulation, as there is not a univocal relationship between its activation/inhibitory effect and its acetylation/deacetylation stage. All the combinatorial possibilities are observed. During the exponential growth phase, CRP also exerts a very significant transcriptional effect, mainly on flagellar assembly and chemotaxis (FDR = 7.2 × 10−44).
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Affiliation(s)
| | - Néstor V Torres
- Systems Biology and Mathematical Modelling Group, Department of Biochemistry, Microbiology, Cellular Biology and Genetics, Institute of Biomedical Technologies, Center for Biomedical Research of the Canary Islands, University of La Laguna, San Cristóbal de La Laguna, Spain
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150
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Wytock TP, Fiebig A, Willett JW, Herrou J, Fergin A, Motter AE, Crosson S. Experimental evolution of diverse Escherichia coli metabolic mutants identifies genetic loci for convergent adaptation of growth rate. PLoS Genet 2018; 14:e1007284. [PMID: 29584733 PMCID: PMC5892946 DOI: 10.1371/journal.pgen.1007284] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 04/10/2018] [Accepted: 03/02/2018] [Indexed: 01/08/2023] Open
Abstract
Cell growth is determined by substrate availability and the cell’s metabolic capacity to assimilate substrates into building blocks. Metabolic genes that determine growth rate may interact synergistically or antagonistically, and can accelerate or slow growth, depending on genetic background and environmental conditions. We evolved a diverse set of Escherichia coli single-gene deletion mutants with a spectrum of growth rates and identified mutations that generally increase growth rate. Despite the metabolic differences between parent strains, mutations that enhanced growth largely mapped to core transcription machinery, including the β and β’ subunits of RNA polymerase (RNAP) and the transcription elongation factor, NusA. The structural segments of RNAP that determine enhanced growth have been previously implicated in antibiotic resistance and in the control of transcription elongation and pausing. We further developed a computational framework to characterize how the transcriptional changes that occur upon acquisition of these mutations affect growth rate across strains. Our experimental and computational results provide evidence for cases in which RNAP mutations shift the competitive balance between active transcription and gene silencing. This study demonstrates that mutations in specific regions of RNAP are a convergent adaptive solution that can enhance the growth rate of cells from distinct metabolic states. The loss of a metabolic function caused by gene deletion can be compensated, in certain cases, by the concurrent mutation of a second gene. Whether such gene pairs share a local chemical or regulatory relationship or interact via a non-local mechanism has implications for the co-evolution of genetic changes, development of alternatives to gene therapy, and the design of combination antimicrobial therapies that select against resistance. Yet, we lack a comprehensive knowledge of adaptive responses to metabolic mutations, and our understanding of the mechanisms underlying genetic rescue remains limited. We present results of a laboratory evolution approach that has the potential to address both challenges, showing that mutations in specific regions of RNA polymerase enhance growth rates of distinct mutant strains of Escherichia coli with a spectrum of growth defects. Several of these adaptive mutations are deleterious when engineered directly into the original wild-type strain under alternative cultivation conditions, and thus have epistatic rescue properties when paired with the corresponding primary metabolic gene deletions. Our combination of adaptive evolution, directed genetic engineering, and mathematical analysis of transcription and growth rate distinguishes between rescue interactions that are specific or non-specific to a particular deletion. Our study further supports a model for RNA polymerase as a locus of convergent adaptive evolution from different sub-optimal metabolic starting points.
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Affiliation(s)
- Thomas P. Wytock
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
| | - Aretha Fiebig
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Jonathan W. Willett
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Julien Herrou
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Aleksandra Fergin
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Adilson E. Motter
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois, United States of America
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, Illinois, United States of America
- * E-mail: (AEM); (SC)
| | - Sean Crosson
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (AEM); (SC)
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