1
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Amemiya HM, Schroeder J, Freddolino PL. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription 2021; 12:182-218. [PMID: 34499567 PMCID: PMC8632127 DOI: 10.1080/21541264.2021.1973865] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 01/21/2023] Open
Abstract
Genome architecture has proven to be critical in determining gene regulation across almost all domains of life. While many of the key components and mechanisms of eukaryotic genome organization have been described, the interplay between bacterial DNA organization and gene regulation is only now being fully appreciated. An increasing pool of evidence has demonstrated that the bacterial chromosome can reasonably be thought of as chromatin, and that bacterial chromosomes contain transcriptionally silent and transcriptionally active regions analogous to heterochromatin and euchromatin, respectively. The roles played by histones in eukaryotic systems appear to be shared across a range of nucleoid-associated proteins (NAPs) in bacteria, which function to compact, structure, and regulate large portions of bacterial chromosomes. The broad range of extant NAPs, and the extent to which they differ from species to species, has raised additional challenges in identifying and characterizing their roles in all but a handful of model bacteria. Here we review the regulatory roles played by NAPs in several well-studied bacteria and use the resulting state of knowledge to provide a working definition for NAPs, based on their function, binding pattern, and expression levels. We present a screening procedure which can be applied to any species for which transcriptomic data are available. Finally, we note that NAPs tend to play two major regulatory roles - xenogeneic silencers and developmental regulators - and that many unrecognized potential NAPs exist in each bacterial species examined.
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Affiliation(s)
- Haley M. Amemiya
- University of Michigan Medical School, Ann Arbor, MI, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter L. Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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2
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Ropers D, Métris A. Data for the qualitative modeling of the osmotic stress response to NaCl in Escherichia coli. Data Brief 2016; 9:606-612. [PMID: 27766288 PMCID: PMC5066198 DOI: 10.1016/j.dib.2016.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/09/2016] [Accepted: 09/19/2016] [Indexed: 11/30/2022] Open
Abstract
Qualitative modeling approaches allow to provide a coarse-grained description of the functioning of cellular networks when experimental data are scarce and heterogeneous. We translate the primary literature data on the response of Escherichia coli to hyperosmotic stress caused by NaCl addition into a piecewise linear (PL) model. We provide a data file of the qualitative model, which can be used for simulation of changes of protein concentrations and of DNA coiling during the physiological response of the bacterium to the stress. The qualitative model predictions are directly comparable to the available experimental data. This data is related to the research article entitled “Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens” (Metris et al., 2016) [1].
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Affiliation(s)
- Delphine Ropers
- Inria, Grenoble - Rhône-Alpes Research Center, Saint Ismier, France
| | - Aline Métris
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
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3
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Métris A, George SM, Ropers D. Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens. Int J Food Microbiol 2016; 240:63-74. [PMID: 27377009 DOI: 10.1016/j.ijfoodmicro.2016.06.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 06/09/2016] [Accepted: 06/19/2016] [Indexed: 01/08/2023]
Abstract
Addition of salt to food is one of the most ancient and most common methods of food preservation. However, little is known of how bacterial cells adapt to such conditions. We propose to use piecewise linear approximations to model the regulatory adaptation of Escherichiacoli to osmotic stress. We apply the method to eight selected genes representing the functions known to be at play during osmotic adaptation. The network is centred on the general stress response factor, sigma S, and also includes a module representing the catabolic repressor CRP-cAMP. Glutamate, potassium and supercoiling are combined to represent the intracellular regulatory signal during osmotic stress induced by salt. The output is a module where growth is represented by the concentration of stable RNAs and the transcription of the osmotic gene osmY. The time course of gene expression of transport of osmoprotectant represented by the symporter proP and of the osmY is successfully reproduced by the network. The behaviour of the rpoS mutant predicted by the model is in agreement with experimental data. We discuss the application of the model to food-borne pathogens such as Salmonella; although the genes considered have orthologs, it seems that supercoiling is not regulated in the same way. The model is limited to a few selected genes, but the regulatory interactions are numerous and span different time scales. In addition, they seem to be condition specific: the links that are important during the transition from exponential to stationary phase are not all needed during osmotic stress. This model is one of the first steps towards modelling adaptation to stress in food safety and has scope to be extended to other genes and pathways, other stresses relevant to the food industry, and food-borne pathogens. The method offers a good compromise between systems of ordinary differential equations, which would be unmanageable because of the size of the system and for which insufficient data are available, and the more abstract Boolean methods.
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Affiliation(s)
- Aline Métris
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.
| | - Susie M George
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.
| | - Delphine Ropers
- Inria Grenoble - Rhône-Alpes Research Center, Saint Ismier, France.
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4
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Engineering Synthetic Multistress Tolerance in Escherichia coli by Using a Deinococcal Response Regulator, DR1558. Appl Environ Microbiol 2015; 82:1154-1166. [PMID: 26655758 DOI: 10.1128/aem.03371-15] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/20/2015] [Indexed: 12/15/2022] Open
Abstract
Cellular robustness is an important trait for industrial microbes, because the microbial strains are exposed to a multitude of different stresses during industrial processes, such as fermentation. Thus, engineering robustness in an organism in order to push the strains toward maximizing yield has become a significant topic of research. We introduced the deinococcal response regulator DR1558 into Escherichia coli (strain Ec-1558), thereby conferring tolerance to hydrogen peroxide (H2O2). The reactive oxygen species (ROS) level in strain Ec-1558 was reduced due to the increased KatE catalase activity. Among four regulators of the oxidative-stress response, OxyR, RpoS, SoxS, and Fur, we found that the expression of rpoS increased in Ec-1558, and we confirmed this increase by Western blot analysis. Electrophoretic mobility shift assays showed that DR1558 bound to the rpoS promoter. Because the alternative sigma factor RpoS regulates various stress resistance-related genes, we performed stress survival analysis using an rpoS mutant strain. Ec-1558 was able to tolerate a low pH, a high temperature, and high NaCl concentrations in addition to H2O2, and the multistress tolerance phenotype disappeared in the absence of rpoS. Microarray analysis clearly showed that a variety of stress-responsive genes that are directly or indirectly controlled by RpoS were upregulated in strain Ec-1558. These findings, taken together, indicate that the multistress tolerance conferred by DR1558 is likely routed through RpoS. In the present study, we propose a novel strategy of employing an exogenous response regulator from polyextremophiles for strain improvement.
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5
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Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomic identification of a novel salt tolerance gene from the human gut microbiome which encodes a membrane protein with homology to a brp/blh-family β-carotene 15,15'-monooxygenase. PLoS One 2014; 9:e103318. [PMID: 25058308 PMCID: PMC4110020 DOI: 10.1371/journal.pone.0103318] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/29/2014] [Indexed: 12/30/2022] Open
Abstract
The human gut microbiome consists of at least 3 million non-redundant genes, 150 times that of the core human genome. Herein, we report the identification and characterisation of a novel stress tolerance gene from the human gut metagenome. The locus, assigned brpA, encodes a membrane protein with homology to a brp/blh-family β-carotene monooxygenase. Cloning and heterologous expression of brpA in Escherichia coli confers a significant salt tolerance phenotype. Furthermore, when cultured in the presence of exogenous β-carotene, cell pellets adopt a red/orange pigmentation indicating the incorporation of carotenoids in the cell membrane.
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Affiliation(s)
- Eamonn P. Culligan
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Roy D. Sleator
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
- * E-mail: (CH); (RDS); (JRM)
| | - Julian R. Marchesi
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- Department of Hepatology and Gastroenterology, Imperial College London, London, United Kingdom
- * E-mail: (CH); (RDS); (JRM)
| | - Colin Hill
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- * E-mail: (CH); (RDS); (JRM)
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6
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Culligan EP, Marchesi JR, Hill C, Sleator RD. Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome. Front Microbiol 2014; 5:189. [PMID: 24808895 PMCID: PMC4010731 DOI: 10.3389/fmicb.2014.00189] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 04/07/2014] [Indexed: 12/13/2022] Open
Abstract
In the current study, a number of salt-tolerant clones previously isolated from a human gut metagenomic library were screened using Phenotype MicroArray (PM) technology to assess their functional capacity. PM's can be used to study gene function, pathogenicity, metabolic capacity and identify drug targets using a series of specialized microtitre plate assays, where each well of the microtitre plate contains a different set of conditions and tests a different phenotype. Cellular respiration is monitored colorimetrically by the reduction of a tetrazolium dye. One clone, SMG 9, was found to be positive for utilization/transport of L-carnitine (a well-characterized osmoprotectant) in the presence of 6% w/v sodium chloride (NaCl). Subsequent experiments revealed a significant growth advantage in minimal media containing NaCl and L-carnitine. Fosmid sequencing revealed putative candidate genes responsible for the phenotype. Subsequent cloning of two genes did not replicate the L-carnitine-associated phenotype, although one of the genes, a σ54-dependent transcriptional regulator, did confer salt tolerance to Escherichia coli when expressed in isolation. The original clone, SMG 9, was subsequently found to have lost the original observed phenotype upon further investigation. Nevertheless, this study demonstrates the usefulness of a phenomic approach to assign a functional role to metagenome-derived clones.
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Affiliation(s)
- Eamonn P Culligan
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork Cork, Ireland ; School of Microbiology, University College Cork Cork, Ireland
| | - Julian R Marchesi
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork Cork, Ireland ; Cardiff School of Biosciences, Cardiff University Cardiff, UK ; Department of Surgery and Cancer, Centre for Digestive and Gut Health, Imperial College London London, UK
| | - Colin Hill
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork Cork, Ireland ; School of Microbiology, University College Cork Cork, Ireland
| | - Roy D Sleator
- Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork Cork, Ireland ; Department of Biological Sciences, Cork Institute of Technology Cork, Ireland
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7
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Sheidy DT, Zielke RA. Analysis and expansion of the role of the Escherichia coli protein ProQ. PLoS One 2013; 8:e79656. [PMID: 24205389 PMCID: PMC3808355 DOI: 10.1371/journal.pone.0079656] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022] Open
Abstract
The decrease in proline transport by the proline porter ProP in a ΔproQ strain has been well documented; however, the reason for this phenotype remains undefined. Previous studies have speculated that ProQ facilitates translation of proP mRNA. Here, we demonstrate that ProQ is enriched in the polysome fractions of sucrose gradient separations of E. coli lysates and the 30S fractions of lysates separated under conditions causing ribosomal subunit dissociation. Thus, ProQ is a bona fide ribosome associated protein. Analysis of proQ constructs lacking predicted structural domains implicates the N-terminal domain in ribosome association. Association with the ribosome appears to be mediated by an interaction with the mRNA being translated, as limited treatment of lysates with Micrococcal Nuclease maintains ribosome integrity but disrupts ProQ localization with polysomes. ProQ also fails to robustly bind to mRNA-free 70S ribosomes in vitro. Interestingly, deletion of proP does not disrupt the localization of ProQ with translating ribosomes, and deletion of proP in combination with the proU operon has no effect on ProQ localization. We also demonstrate that ProQ is necessary for robust biofilm formation, and this phenotype is independent of ProP. Binding studies were carried out using tryptophan fluorescence and in vitro transcribed proP mRNAs. proP is transcribed from two differentially regulated promoters, and ProQ interacts with proP mRNA transcribed from both promoters, as well as a control mRNA with similar affinities. In total, these data suggest that ProQ is positioned to function as a novel translational regulator, and its cellular role extends beyond its effects on proline uptake by ProP.
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Affiliation(s)
- Daniel T. Sheidy
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
| | - Ryszard A. Zielke
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon, United States of America
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8
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Crozat E, Winkworth C, Gaffe J, Hallin PF, Riley MA, Lenski RE, Schneider D. Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli. Mol Biol Evol 2010; 27:2113-28. [DOI: 10.1093/molbev/msq099] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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9
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Tan HJ, Liu SH, Oliver JD, Wong HC. Role of RpoS in the susceptibility of low salinity-adapted Vibrio vulnificus to environmental stresses. Int J Food Microbiol 2009; 137:137-42. [PMID: 20051307 DOI: 10.1016/j.ijfoodmicro.2009.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 11/02/2009] [Accepted: 12/03/2009] [Indexed: 11/19/2022]
Abstract
Vibrio vulnificus is an opportunistic pathogen commonly found in oyster and marine environments, which frequently encounters low salinity stress in its natural and food processing environment. In this study, the responses of a V. vulnificus wild-type strain C78140o and its rpoS isogenic mutant AH1 to sublethal low salinity were examined to investigate the role of rpoS in this response. Both strains, adapted in low salinity (0.4% NaCl), were protected against the lethal low salinity (0.1% NaCl), but were not protected against heat (45 degrees C) or acid stress (pH 3.5), and were sensitized against 5% bile. Protection of the adapted cells against the lethal low salinity was not inhibited by the addition of chloramphenicol. Hemolysis was detected only in the adapted C78140o cells and its spent medium, and was inhibited by chloramphenicol. Transcription of the mechanosensitive channels (VVl_1542 and VVl_2579) and an aquaporin gene (VVl_2010) was markedly increased in the wild-type cells adapted in low salinity medium, while transcription of these genes was slightly enhanced or inhibited in AH1 cells. Results of this study support the active role of rpoS in the low salinity adaptation of V. vulnificus by regulating the expression of virulence and low salinity-associated factors, although rpoS is not related to the immediate protection of the adapted cells against lethal low salinity.
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Affiliation(s)
- Hao-Jen Tan
- Department of Microbiology, Soochow University, Taipei 111, Taiwan, ROC
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10
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Calderón MI, Vargas C, Rojo F, Iglesias-Guerra F, Csonka LN, Ventosa A, Nieto JJ. Complex regulation of the synthesis of the compatible solute ectoine in the halophilic bacterium Chromohalobacter salexigens DSM 3043T. MICROBIOLOGY-SGM 2005; 150:3051-3063. [PMID: 15347763 DOI: 10.1099/mic.0.27122-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The synthesis of the compatible solute ectoine, mediated by the ectABC gene products, is the main mechanism used by the halophilic bacterium Chromohalobacter salexigens to cope with osmotic stress. Evidence was found that this process is regulated at the transcriptional level. S1 protection analyses performed with RNA extracted from cells grown in minimal medium at low (0.75 M NaCl) or high (2.5 M NaCl) osmolarity suggested the existence of four promoters upstream of ectA. Two of these (PectA1 and PectA2) might be recognized by the main vegetative sigma factor sigma(70), and one (PectA3) might be dependent on the general stress sigma factor sigma(S). The S1 protection assays suggest that PectA1 and PectA3 may be osmoregulated promoters. In addition, an internal promoter showing sequences homologous to promoters dependent on the heat-shock sigma factor sigma(32) was found upstream of ectB. Transcription from PectA in C. salexigens followed a pattern typical of sigma(S)-dependent promoters, and was reduced by 50 % in an E. coli rpoS background. These data strongly suggest the involvement of the general stress sigma factor sigma(S) in ectABC transcription in C. salexigens. Expression of PectA-lacZ and PectB-lacZ trancriptional fusions was very high at low salinity, suggesting that ectABC may be a partially constitutive system. Both transcriptional fusions were induced during continuous growth at high temperature and their expression was reduced in cells grown in the presence of osmoprotectants (ectoine or glycine betaine) or the DNA gyrase inhibitor nalidixic acid. Moreover, PectA-lacZ expression was negatively modulated in cells grown with an excess of iron (FeCl(3)). Measurement of ectoine levels in the presence of glycine betaine at different NaCl concentrations suggests that an additional post-transcriptional control may occur as well.
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Affiliation(s)
- M Isabel Calderón
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Carmen Vargas
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Fernando Iglesias-Guerra
- Department of Organic Chemistry and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Laszlo N Csonka
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-1392, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
| | - Joaquín J Nieto
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
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11
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Checroun C, Gutierrez C. Ïs-Dependent regulation of yehZYXW, which encodes a putative osmoprotectant ABC transporter of Escherichia coli. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09650.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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12
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Eguchi Y, Okada T, Minagawa S, Oshima T, Mori H, Yamamoto K, Ishihama A, Utsumi R. Signal transduction cascade between EvgA/EvgS and PhoP/PhoQ two-component systems of Escherichia coli. J Bacteriol 2004; 186:3006-14. [PMID: 15126461 PMCID: PMC400602 DOI: 10.1128/jb.186.10.3006-3014.2004] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional analysis of a constitutively active mutant of the EvgA/EvgS two-component system of Escherichia coli resulted in enhanced expression of 13 PhoP/PhoQ-regulated genes, crcA, hemL, mgtA, ompT, phoP, phoQ, proP, rstA, rstB, slyB, ybjG, yrbL, and mgrB. This regulatory network between the two systems also occurred as a result of overproduction of the EvgA regulator; however, enhanced transcription of the phoPQ genes did not further activate expression of the PhoP/PhoQ-regulated genes. These results demonstrated signal transduction from the EvgA/EvgS system to the PhoP/PhoQ system in E. coli and also identified the genes that required the two systems for enhanced expression. This is one example of the intricate signal transduction networks that are posited to exist in E. coli.
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Affiliation(s)
- Yoko Eguchi
- Department of Bioscience and Biotechnology, Graduate School of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan
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13
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Lee SJ, Gralla JD. Osmo-regulation of bacterial transcription via poised RNA polymerase. Mol Cell 2004; 14:153-62. [PMID: 15099515 DOI: 10.1016/s1097-2765(04)00202-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Revised: 02/27/2004] [Accepted: 03/08/2004] [Indexed: 11/30/2022]
Abstract
Adaptation to high-salt environments is critical for the survival of a wide range of cells, especially for pathogenic bacteria that colonize the animal gut and urinary tract. The adaptation strategy involves production of the salt potassium glutamate, which induces a specific gene expression program that produces electro-neutral osmolytes while inhibiting general sigma(70) transcription. These data show that in Escherichia coli potassium glutamate stimulates transcription by disengaging inhibitory polymerase interactions at a sigma(38) promoter. These occur in an upstream region that is marked by an osmotic shock promoter DNA consensus sequence. The disruption activates a poised RNA polymerase to transcribe. This transcription program leads to the production of osmolytes that are shown to have only minor effects on transcription and therefore help to restore normal cell function. An osmotic shock gene expression cycle is discussed.
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Affiliation(s)
- Shun Jin Lee
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, P.O. Box 951569, Los Angeles, CA 90095, USA
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14
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Romeo Y, Obis D, Bouvier J, Guillot A, Fourçans A, Bouvier I, Gutierrez C, Mistou MY. Osmoregulation in Lactococcus lactis: BusR, a transcriptional repressor of the glycine betaine uptake system BusA. Mol Microbiol 2003; 47:1135-47. [PMID: 12581365 DOI: 10.1046/j.1365-2958.2003.03362.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The busA (opuA) locus of Lactococcus lactis encodes a glycine betaine uptake system. Transcription of busA is osmotically inducible and its induction after an osmotic stress is reduced in the presence of glycine betaine. Using a genetic screen in CLG802, an Escherichia coli strain carrying a lacZ transcriptional fusion expressed under the control of the busA promoter, we isolated a genomic fragment from the L. lactis subsp. cremoris strain MG1363, which represses transcription from busAp. The cloned locus responsible for this repression was identified as a gene present upstream from the busA operon, encoding a putative DNA binding protein. This gene was named busR. Electrophoretic mobility shift and footprinting experiments showed that BusR is able to bind a site that overlaps the busA promoter. Overexpression of busR in L. lactis reduced expression of busA. Its disruption led to increased and essentially constitutive transcription of busA at low osmolarity. Therefore, BusR is a major actor of the osmotic regulation of busA in L. lactis.
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Affiliation(s)
- Yves Romeo
- Laboratoire de Microbiologie et Génétique Moléculaire, UMR 5100 CNRS-Université Toulouse III 118, route de Narbonne 31062 Toulouse Cedex, France
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15
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Lacour S, Kolb A, Boris Zehnder AJ, Landini P. Mechanism of specific recognition of the aidB promoter by sigma(S)-RNA polymerase. Biochem Biophys Res Commun 2002; 292:922-30. [PMID: 11944903 DOI: 10.1006/bbrc.2002.6744] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Transcription of the Escherichia coli aidB gene is controlled by an Esigma(S)-dependent promoter (PaidB) and is poorly transcribed by the Esigma(70) form of RNA polymerase in the absence of additional factors. In this report, we investigate the interaction between PaidB and either the Esigma(70) or the Esigma(S) forms of RNA polymerase in vitro. We show that although Esigma(70) can bind the aidB promoter, its interaction with the promoter results in the formation of an open complex inefficient in transcription initiation and sensitive to heparin challenge. Deletion of the C residue at position -13 of PaidB (Delta-13C) slightly impaired transcription initiation by Esigma(S), consistent with the role of -13C as a specific feature of Esigma(S)-dependent promoters. However, Esigma(S) could still bind and initiate transcription from the Delta-13C mutant aidB promoter more efficiently than Esigma(70), suggesting that sequence elements other than the -13C play an important role in specific promoter recognition by Esigma(S).
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Affiliation(s)
- Stephan Lacour
- Swiss Federal Institute of Environmental Technology (EAWAG), Uberlandstrasse 133, CH-8600 Dübendorf, Switzerland
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16
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McLeod SM, Aiyar SE, Gourse RL, Johnson RC. The C-terminal domains of the RNA polymerase alpha subunits: contact site with Fis and localization during co-activation with CRP at the Escherichia coli proP P2 promoter. J Mol Biol 2002; 316:517-29. [PMID: 11866515 DOI: 10.1006/jmbi.2001.5391] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fis is a versatile transactivator that functions at many different promoters. Fis activates transcription at the RpoS-dependent proP P2 promoter when bound to a site that overlaps the minus sign35 hexamer by a mechanism that requires the C-terminal domain of the alpha subunit of RNA polymerase (alphaCTD). The region on Fis responsible for activating transcription through the alphaCTD has been localized to a short beta-turn near the DNA-binding determinant on one subunit of the Fis homodimer. We report here that Fis-dependent activation of proP P2 transcription requires two discrete regions on the alphaCTD. One region, consisting of residues 264-265 and 296-297, mediates DNA binding. A second patch, comprising amino acid residues 271-273, forms a ridge on the surface of the alphaCTD that we propose interacts with Fis. The accompanying paper shows that these same regions on alphaCTD are utilized for transcriptional activation at the rrnB and rrnE P1 promoters by Fis bound to a site upstream of the core promoter (centered at minus sign71/minus sign72). In addition to stimulation of proP P2 transcription by Fis, CRP co-activates this promoter when bound to a remote site upstream from the promoter (centered at -121.5). RNA polymerase preparations lacking one alphaCTD of the alpha dimer were employed to demonstrate that the beta'-associated alpha(II)CTD was utilized preferentially by Fis at proP P2 in the presence and absence of CRP. These experiments define the overall architecture of the proP P2 initiation complex where Fis and CRP each function through a different alphaCTD.
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Affiliation(s)
- Sarah M McLeod
- Department of Biological Chemistry, UCLA School of Medicine, Los Angeles, CA 90095-1737, USA
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17
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Lee SJ, Gralla JD. Sigma38 (rpoS) RNA polymerase promoter engagement via -10 region nucleotides. J Biol Chem 2001; 276:30064-71. [PMID: 11375988 DOI: 10.1074/jbc.m102886200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Band shift assays using DNA probes that mimic closed and open complexes were used to explore the determinants of promoter recognition by sigma38 (rpoS) RNA polymerase. Duplex recognition was found to be much weaker than that observed in sigma70 promoter usage. However, binding to fork junction probes, which attempt to mimic melted DNA, was very strong. This binding occurs via the non-template strand with the identity of the two conserved junction nucleotides (-12T and -11A) being of paramount importance. A modified promoter consensus sequence identified these two nucleotides as among only four (underlined) that are highly conserved, and all four were in the -10 region (CTAcacT from -13 to -7). The remaining two nucleotides were shown to have different roles, -13C in preventing recognition by the heterologous sigma70 polymerase and -7T in directing enzyme isomerization. These -10 region nucleotides appear to have their primary function prior to full melting because probes that had a melted start site were relatively insensitive to substitution at these positions. These results suggest the sigma38 mechanism differs from the sigma70 mechanism, and this difference likely contributes to selective use of sigma38 under conditions that exist during stationery phase.
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Affiliation(s)
- S J Lee
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095-1569, USA
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18
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Marianovsky I, Aizenman E, Engelberg-Kulka H, Glaser G. The regulation of the Escherichia coli mazEF promoter involves an unusual alternating palindrome. J Biol Chem 2001; 276:5975-84. [PMID: 11071896 DOI: 10.1074/jbc.m008832200] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Escherichia coli mazEF system is a chromosomal "addiction module" that, under starvation conditions in which guanosine-3',5'-bispyrophosphate (ppGpp) is produced, is responsible for programmed cell death. This module specifies for the toxic stable protein MazF and the labile antitoxic protein MazE. Upstream from the mazEF module are two promoters, P(2) and P(3) that are strongly negatively autoregulated by MazE and MazF. We show that the expression of this module is positively regulated by the factor for inversion stimulation. What seems to be responsible for the negative autoregulation of mazEF is an unusual DNA structure, which we have called an "alternating palindrome." The middle part, "a," of this structure may complement either the downstream fragment, "b," or the upstream fragment, "c". When the MazE.MazF complex binds either of these arms of the alternating palindrome, strong negative autoregulation results. We suggest that the combined presence of the two promoters, the alternating palindrome structure and the factor for inversion stimulation-binding site, all permit the expression of the mazEF module to be sensitively regulated under various growth conditions.
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Affiliation(s)
- I Marianovsky
- Department of Cellular Biochemistry, Hebrew University-Hadassah Medical School, Ein Kerem, Jerusalem, 91120 Israel
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19
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Cheng YS, Yang WZ, Johnson RC, Yuan HS. Structural analysis of the transcriptional activation region on Fis: crystal structures of six Fis mutants with different activation properties. J Mol Biol 2000; 302:1139-51. [PMID: 11183780 DOI: 10.1006/jmbi.2000.4123] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Fis protein regulates gene expression in Escherichia coli by activating or repressing transcription of a variety of genes. Fis can activate transcription when bound to DNA upstream of the RNA-polymerase-binding site, such as in the rrnB P1 promoter, or when bound to a site overlapping the -35 RNA polymerase binding site, such as in the proP P2 promoter. It has been suggested that transcriptional activation in both promoters results from interactions between specific amino acids within a turn connecting the B and C helices (the BC turn) in Fis and the C-terminal domain of the alpha-subunit of RNA polymerase (alphaCTD of RNAP). Here, crystal structures of six Fis BC turn mutants with different transcriptional activation properties, Q68A, R71Y, R71L, G72A, G72D and Q74A, were determined at 1.9 to 2.8 A resolution. Two of these mutants, R71Y and R71L, crystallized in unit cells which are different from that of wild-type Fis, and the structure of R71L offers the most complete Fis model to date in that the extended structure of the N-terminal region is revealed. The BC turn in all of these mutant structures remains in a nearly identical gamma gamma beta-turn conformation as present in wild-type Fis. Analyses of the molecular surfaces of the transactivation region of the mutants suggest that several residues in or near the BC turn, including Gln68, Arg71, Gly72 and Gln74, form a ridge that could contact the alphaCTD of RNAP on one side. The structures and biochemical properties of the mutants suggest that Arg71 is the most critical residue for contacting RNAP within this ridge and that the glycine at position 72 helps to stabilize the structure.
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Affiliation(s)
- Y S Cheng
- Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan, Republic of China
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20
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Culham DE, Tripet B, Racher KI, Voegele RT, Hodges RS, Wood JM. The role of the carboxyl terminal alpha-helical coiled-coil domain in osmosensing by transporter ProP of Escherichia coli. J Mol Recognit 2000; 13:309-22. [PMID: 10992293 DOI: 10.1002/1099-1352(200009/10)13:5<309::aid-jmr505>3.0.co;2-r] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Concentrative uptake of osmoprotectants via transporter ProP contributes to the rehydration of Escherichia coli cells that encounter high osmolality media. A member of the major facilitator superfamily, ProP is activated by osmotic upshifts in whole bacteria, in cytoplasmic membrane vesicles and in proteoliposomes prepared with the purified protein. Soluble protein ProQ is also required for full osmotic activation of ProP in vivo. ProP is differentiated from structural and functional homologues by its osmotic activation and its C-terminal extension, which is predicted to form an alpha-helical coiled-coil. A synthetic polypeptide corresponding to the C-terminus of ProP (ProP-p) formed a dimeric alpha-helical coiled-coil. A derivative of transporter ProP lacking 26 C-terminal amino acids was expressed but inactive. A derivative harbouring amino acid changes K460I, Y467I and H495I (each at the core, coiled-coil 'a' position) required a larger osmotic upshift for activation than did the wild type transporter. The same changes extended, stabilized and altered the oligomeric state of the coiled-coil formed by ProP-p. Amino acid change R488I (also at the 'a' position) further increased the magnitude of the osmotic upshift required to activate ProP, reduced the activity attained and rendered ProP activation transient. Unexpectedly, replacement R488I destabilized the coiled-coil formed by ProP-p. The activity and osmotic activation of ProP were even more strongly attenuated by helix-destabilizing change I474P. These data demonstrate that the carboxyl terminal domain of ProP can form a homodimeric alpha-helical coiled-coil with unusual properties. They implicate the C-terminal domain in the osmotic activation of ProP.
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Affiliation(s)
- D E Culham
- Department of Microbiology and Guelph-Waterloo Centre for Graduate Work in Chemistry, University of Guelph, Guelph, Ontario, Canada
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21
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McLeod SM, Xu J, Johnson RC. Coactivation of the RpoS-dependent proP P2 promoter by fis and cyclic AMP receptor protein. J Bacteriol 2000; 182:4180-7. [PMID: 10894725 PMCID: PMC101903 DOI: 10.1128/jb.182.15.4180-4187.2000] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli proP P2 promoter, which directs the expression of an integral membrane transporter of proline, glycine betaine, and other osmoprotecting compounds, is induced upon entry into stationary phase to protect cells from osmotic shock. Transcription from the P2 promoter is completely dependent on RpoS (sigma(38)) and Fis. Fis activates transcription by binding to a site centered at -41, which overlaps the promoter, where it makes a specific contact with the C-terminal domain of the alpha subunit of RNA polymerase (alpha-CTD). We show here that Fis and cyclic AMP (cAMP) receptor protein (CRP)-cAMP collaborate to activate transcription synergistically in vitro. Coactivation both in vivo and in vitro is dependent on CRP binding to a site centered at -121.5, but CRP without Fis provides little activation. The contribution by CRP requires the correct helical phasing of the CRP site and a functional activation region 1 on CRP. We provide evidence that coactivation is achieved by Fis and CRP independently contacting each of the two alpha-CTDs. Efficient transcription in vitro requires that both activators must be preincubated with the DNA prior to addition of RNA polymerase.
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Affiliation(s)
- S M McLeod
- Department of Biological Chemistry, UCLA School of Medicine, Los Angeles, California 90095-1737, USA
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22
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Landis L, Xu J, Johnson RC. The cAMP receptor protein CRP can function as an osmoregulator of transcription in Escherichia coli. Genes Dev 1999; 13:3081-91. [PMID: 10601034 PMCID: PMC317180 DOI: 10.1101/gad.13.23.3081] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transcription of the P1 promoter of the Escherichia coli proP gene, which encodes a transporter of osmoprotectants, is strongly induced by a shift to hyperosmotic media. Unlike most other osmotically regulated promoters, the induction occurs for a brief period of time, corresponding to the replacement of intracellular K(+) glutamate with osmoprotecting compounds. This burst of proP transcription is correlated with the osmolarity-dependent binding of the cAMP receptor protein CRP to a site within the proP P1 promoter. We show that CRP-cAMP functions as an osmotically sensitive repressor of proP P1 transcription in vitro. Binding of CRP to the proP promoter in vivo is transiently destabilized after a hyperosmotic shift with kinetics that correspond to the derepression of transcription, whereas Fis and Lac repressor binding is not osmotically sensitive. Similar osmotic regulation of proP P1 transcription by the CRP* mutant implies that binding of cAMP is not responsible for the unusual osmotic sensitivity of CRP activity. Osmotic regulation of CRP activity is not limited to proP. Activation of the lac promoter by CRP is also transiently inhibited after an osmotic upshift, as is the binding of CRP to the galdelta4P1 promoter. These findings suggest that CRP functions in certain contexts to regulate gene expression in response to osmotic changes, in addition to its role in catabolite control.
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Affiliation(s)
- L Landis
- Department of Biological Chemistry, School of Medicine, University of California, Los Angeles, Los Angeles, California 90095-1737, USA
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23
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McLeod SM, Xu J, Cramton SE, Gaal T, Gourse RL, Johnson RC. Localization of amino acids required for Fis to function as a class II transcriptional activator at the RpoS-dependent proP P2 promoter. J Mol Biol 1999; 294:333-46. [PMID: 10610762 DOI: 10.1006/jmbi.1999.3262] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
ProP is an integral membrane transporter of proline, glycine betaine, and several other osmoprotecting compounds. Fis plus RpoS collaborate to promote a burst of proP transcription in late exponential growth phase. This brief period of ProP synthesis enables stationary phase cells to cope with a potential hyperosmotic shock. Fis activates the RpoS (sigma(38))-dependent proP P2 promoter by binding to a site within the promoter region centered at -41 and thus functions as a class II activator. We show here that activation by Fis at this promoter is completely dependent upon the alpha-CTD of RNA polymerase and that the activation domain on Fis is localized to a four amino acid ridge on the surface of Fis adjacent to the helix-turn-helix DNA binding domain in only one subunit of the homodimer. Fis mutants containing amino acid substitutions within this region are defective in cooperative binding interactions with the sigma(38)-form of RNA polymerase. Some of these substitutions also alter interactions with DNA sequences flanking the core binding site, but we show that changes in Fis-mediated curvature do not affect promoter activity. We conclude that the same amino acids are used by Fis to activate transcription from a class I (-71, rrnB P1) and class II (-41, proP P2) location, but this region is distinct from that required to regulate the Hin site-specific DNA inversion reaction.
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Affiliation(s)
- S M McLeod
- Department of Biological Chemistry, UCLA School of Medicine, Los Angeles, CA 90095-1737, USA
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24
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Hengge-Aronis R. Interplay of global regulators and cell physiology in the general stress response of Escherichia coli. Curr Opin Microbiol 1999; 2:148-52. [PMID: 10322169 DOI: 10.1016/s1369-5274(99)80026-5] [Citation(s) in RCA: 182] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Under various stress conditions, two sigma subunits of RNA polymerase, sigmaS and sigma70, coexist in Escherichia coli cells. In contrast to sigma70, sigmaS is subject to intricate regulation and coordinates an emergency reaction to stress as well as long term stress adaptation. In vivo, the two sigma factors clearly control different genes. Yet, they are structurally and functionally very similar and basically recognize the same promoter sequences. Recent data suggest that sigma factor specificity at stress-activated promoters is affected by the interplay of the two RNA polymeraseholoenzymes with additional regulatory factors, such as H-NS, Lrp, CRP, IHF or Fis, that differentially affect transcription initiation by sigmaS or sigma70 in a promoter-specific manner.
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Affiliation(s)
- R Hengge-Aronis
- Institute of Plant Physiology and Microbiology, Department of Biology, Free University of Berlin, Königin-Luise-Str 12-16a, 14195, Berlin, Germany.
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25
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Kunte HJ, Crane RA, Culham DE, Richmond D, Wood JM. Protein ProQ influences osmotic activation of compatible solute transporter ProP in Escherichia coli K-12. J Bacteriol 1999; 181:1537-43. [PMID: 10049386 PMCID: PMC93544 DOI: 10.1128/jb.181.5.1537-1543.1999] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/1998] [Accepted: 12/09/1998] [Indexed: 11/20/2022] Open
Abstract
ProP is an osmoregulatory compatible solute transporter in Escherichia coli K-12. Mutation proQ220::Tn5 decreased the rate constant for and the extent of ProP activation by an osmotic upshift but did not alter proP transcription or the ProP protein level. Allele proQ220::Tn5 was isolated, and the proQ sequence was determined. Locus proQ is upstream from prc (tsp) at 41.2 centisomes on the genetic map. The proQ220::Tn5 and prc phenotypes were different, however. Gene proQ is predicted to encode a 232-amino-acid, basic, hydrophilic protein (molecular mass, 25,876 Da; calculated isoelectric point, 9.66; 32% D, E, R, or K; 54.5% polar amino acids). The insertion of PCR-amplified proQ into vector pBAD24 produced a plasmid containing the wild-type proQ open reading frame, the expression of which yielded a soluble protein with an apparent molecular mass of 30 kDa. Antibodies raised against the overexpressed ProQ protein detected cross-reactive material in proQ+ bacteria but not in proQ220::Tn5 bacteria. ProQ may be a structural element that influences the osmotic activation of ProP at a posttranslational level.
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Affiliation(s)
- H J Kunte
- Department of Microbiology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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26
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Abstract
Our research has focused on bacterial gene products that protect cells from damage by near-ultraviolet radiation (near-UV) including gene products involved in the subsequent recovery process. Protective gene products include such anti-oxidants as catalases, superoxide dismutases and glutathione reductase. Near-UV damage recovery products include exonuclease III and DNA-glycosylases. Perhaps more critical than the products of structural genes are certain regulatory gene products that are triggered upon excess near-UV oxidation and lead to synthesis of entire batteries of anti-oxidant enzymes, DNA repair enzymes, and DNA-integrity proteins. Our recent experiments have focused on RpoS and its interaction with OxyR, two proteins that regulate the synthesis of molecules that protect cells from near-UV and other oxidative stresses.
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Affiliation(s)
- A Eisenstark
- Cancer Research Center, Columbia, MO 65201, USA.
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27
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Cases I, de Lorenzo V. Expression systems and physiological control of promoter activity in bacteria. Curr Opin Microbiol 1998; 1:303-10. [PMID: 10066491 DOI: 10.1016/s1369-5274(98)80034-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Promoter activity in vivo is not just dependent on the performance of the regulator/promoter pair which may predominantly control transcription initiation in response to a given signal, it also relies on overimposed mechanisms that connect the activity of individual promoters to the metabolic and energetic status of the bacterial cells. Such mechanisms - which frequently become limiting for biotechnological applications involving regulated promoters - include classic (i.e. cAMP/CRP-mediated) or alternative catabolite control checks, recruitment of protein intermediates of the phosphotransferase sugar transport system, coregulation through protein-induced DNA bending and the interplay of sigma factors during various growth stages.
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Affiliation(s)
- I Cases
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones, Cientificas Campus de Cantoblanco, 28049 Madrid, Spain
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