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Saldaña-Ahuactzi Z, Soria-Bustos J, Martínez-Santos VI, Yañez-Santos JA, Martínez-Laguna Y, Cedillo-Ramirez ML, Puente JL, Girón JA. The Fis Nucleoid Protein Negatively Regulates the Phase Variation fimS Switch of the Type 1 Pilus Operon in Enteropathogenic Escherichia coli. Front Microbiol 2022; 13:882563. [PMID: 35572706 PMCID: PMC9096935 DOI: 10.3389/fmicb.2022.882563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/23/2022] [Indexed: 01/02/2023] Open
Abstract
In Escherichia coli the expression of type 1 pili (T1P) is determined by the site-specific inversion of the fimS ON–OFF switch located immediately upstream of major fimbrial subunit gene fimA. Here we investigated the role of virulence (Ler, GrlR, and GrlA) and global regulators (H-NS, IHF, and Fis) in the regulation of the fimS switch in the human enteropathogenic E. coli (EPEC) O127:H6 strain E2348/69. This strain does not produce detectable T1P and PCR analysis of the fimS switch confirmed that it is locked in the OFF orientation. Among the regulator mutants analyzed, only the ∆fis mutant produced significantly high levels of T1P on its surface and yielded high titers of agglutination of guinea pig erythrocytes. Expression analysis of the fimA, fimB, and fimE promoters using lacZ transcriptional fusions indicated that only PfimA activity is enhanced in the absence of Fis. Collectively, these data demonstrate that Fis is a negative regulator of T1P expression in EPEC and suggest that it is required for the FimE-dependent inversion of the fimS switch from the ON-to-OFF direction. It is possible that a similar mechanism of T1P regulation exists in other intestinal and extra-intestinal pathogenic classes of E. coli.
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Affiliation(s)
- Zeus Saldaña-Ahuactzi
- Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, WA, United States
| | - Jorge Soria-Bustos
- Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Pachuca, Mexico
| | | | - Jorge A Yañez-Santos
- Facultad de Estomatología, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Ygnacio Martínez-Laguna
- Centro de Investigaciones en Ciencias Microbiológicas, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | | | - José L Puente
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Jorge A Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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2
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Ethanol as additive enhances expression of Ranibizumab in Escherichia coli: Impact on cellular physiology and transcriptome. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.11.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Tague JG, Regmi A, Gregory GJ, Boyd EF. Fis Connects Two Sensory Pathways, Quorum Sensing and Surface Sensing, to Control Motility in Vibrio parahaemolyticus. Front Microbiol 2021; 12:669447. [PMID: 34858358 PMCID: PMC8630636 DOI: 10.3389/fmicb.2021.669447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/22/2021] [Indexed: 01/13/2023] Open
Abstract
Factor for inversion stimulation (Fis) is a global regulator that is highly expressed during exponential phase growth and undetectable in stationary phase growth. Quorum sensing (QS) is a global regulatory mechanism that controls gene expression in response to changes in cell density and growth phase. In Vibrio parahaemolyticus, a marine species and a significant human pathogen, the QS regulatory sRNAs, Qrr1 to Qrr5, are expressed during exponential growth and negatively regulate the high cell density QS master regulator OpaR. OpaR is a positive regulator of capsule polysaccharide (CPS) formation, which is required for biofilm formation, and is a repressor of lateral flagella required for swarming motility. In V. parahaemolyticus, we show that Fis is a positive regulator of the qrr sRNAs expression. In an in-frame fis deletion mutant, qrr expression was repressed and opaR expression was induced. The Δfis mutant produced CPS and biofilm, but swarming motility was abolished. Also, the fis deletion mutant was more sensitive to polymyxin B. Swarming motility requires expression of both the surface sensing scrABC operon and lateral flagella laf operon. Our data showed that in the Δfis mutant both laf and scrABC genes were repressed. Fis controlled swarming motility indirectly through the QS pathway and directly through the surface sensing pathway. To determine the effects of Fis on cellular metabolism, we performed in vitro growth competition assays, and found that Δfis was outcompeted by wild type in minimal media supplemented with intestinal mucus as a sole nutrient source. The data showed that Fis positively modulated mucus components L-arabinose, D-gluconate and N-acetyl-D-glucosamine catabolism gene expression. In an in vivo colonization competition assay, Δfis was outcompeted by wild type, indicating Fis is required for fitness. Overall, these data demonstrate a global regulatory role for Fis in V. parahaemolyticus that includes QS, motility, and metabolism.
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Affiliation(s)
- Jessica G Tague
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Abish Regmi
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Gwendolyn J Gregory
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - E Fidelma Boyd
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
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4
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Mejía-Almonte C, Busby SJW, Wade JT, van Helden J, Arkin AP, Stormo GD, Eilbeck K, Palsson BO, Galagan JE, Collado-Vides J. Redefining fundamental concepts of transcription initiation in bacteria. Nat Rev Genet 2020; 21:699-714. [PMID: 32665585 PMCID: PMC7990032 DOI: 10.1038/s41576-020-0254-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.
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Affiliation(s)
- Citlalli Mejía-Almonte
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México
| | | | - Joseph T Wade
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jacques van Helden
- Aix-Marseille University, INSERM UMR S 1090, Theory and Approaches of Genome Complexity (TAGC), Marseille, France
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Gary D Stormo
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - James E Galagan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Julio Collado-Vides
- Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Morelos, Cuernavaca, México.
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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5
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Fis Contributes to Resistance of Pseudomonas aeruginosa to Ciprofloxacin by Regulating Pyocin Synthesis. J Bacteriol 2020; 202:JB.00064-20. [PMID: 32205461 DOI: 10.1128/jb.00064-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 03/16/2020] [Indexed: 12/31/2022] Open
Abstract
Factor for inversion stimulation (Fis) is a versatile DNA binding protein that plays an important role in coordinating bacterial global gene expression in response to growth phases and environmental stresses. Previously, we demonstrated that Fis regulates the type III secretion system (T3SS) in Pseudomonas aeruginosa In this study, we explored the role of Fis in the antibiotic resistance of P. aeruginosa and found that mutation of the fis gene increases the bacterial susceptibility to ciprofloxacin. We further demonstrated that genes related to pyocin biosynthesis are upregulated in the fis mutant. The pyocins are produced in response to genotoxic agents, including ciprofloxacin, and the release of pyocins results in lysis of the producer cell. Thus, pyocin biosynthesis genes sensitize P. aeruginosa to ciprofloxacin. We found that PrtN, the positive regulator of the pyocin biosynthesis genes, is upregulated in the fis mutant. Genetic experiments and electrophoretic mobility shift assays revealed that Fis directly binds to the promoter region of prtN and represses its expression. Therefore, our results revealed novel Fis-mediated regulation on pyocin production and bacterial resistance to ciprofloxacin in P. aeruginosa IMPORTANCE Pseudomonas aeruginosa is an important opportunistic pathogenic bacterium that causes various acute and chronic infections in human, especially in patients with compromised immunity, cystic fibrosis (CF), and/or severe burn wounds. About 60% of cystic fibrosis patients have a chronic respiratory infection caused by P. aeruginosa The bacterium is intrinsically highly resistant to antibiotics, which greatly increases difficulties in clinical treatment. Therefore, it is critical to understand the mechanisms and the regulatory pathways that are involved in antibiotic resistance. In this study, we elucidated a novel regulatory pathway that controls the bacterial resistance to fluoroquinolone antibiotics, which enhances our understanding of how P. aeruginosa responds to ciprofloxacin.
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Abstract
Pseudomonas putidais a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility ofP. putidamakes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes.P. putidais able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number ofP. putidastrains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the speciesP. putidaand isolation and characterization ofP. putidastrains displaying potential for biotechnological applications. This review also discusses some major findings inP. putidaresearch encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.
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Gawade P, Gunjal G, Sharma A, Ghosh P. Reconstruction of transcriptional regulatory networks of Fis and H-NS in Escherichia coli from genome-wide data analysis. Genomics 2019; 112:1264-1272. [PMID: 31356968 DOI: 10.1016/j.ygeno.2019.07.013] [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: 05/12/2019] [Revised: 07/24/2019] [Accepted: 07/25/2019] [Indexed: 11/29/2022]
Abstract
Fis (Factor for inversion stimulation) and H-NS (Histone-like nucleoid-structuring protein) are two well-known nucleoid-associated proteins (NAPs) in proteobacteria, which play crucial roles in genome organization and transcriptional regulation. We performed RNA-sequencing to identify genes regulated by these NAPs. Study reveals that Fis and H-NS affect expression of 462 and 88 genes respectively in Escherichia coli at mid-exponential growth phase. By integrating available ChIP-seq data, we identified direct and indirect regulons of Fis and H-NS proteins. Functional analysis reveals that Fis controls expression of genes involved in translation, oxidative phosphorylation, sugar metabolism and transport, amino acid metabolism, bacteriocin transport, cell division, two-component system, biofilm formation, pilus organization and lipopolysaccharide biosynthesis pathways. However, H-NS represses expression of genes in cell adhesion, recombination, biofilm formation and lipopolysaccharide biosynthesis pathways under mid-exponential growth condition. The current regulatory networks thus provide a global glimpse of coordinated regulatory roles for these two important NAPs.
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Affiliation(s)
- Priyanka Gawade
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India
| | - Gaurav Gunjal
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Anamika Sharma
- Department of Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India.
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8
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Platenkamp A, Mellies JL. Environment Controls LEE Regulation in Enteropathogenic Escherichia coli. Front Microbiol 2018; 9:1694. [PMID: 30140259 PMCID: PMC6094958 DOI: 10.3389/fmicb.2018.01694] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/09/2018] [Indexed: 12/11/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a significant cause of infant morbidity and mortality in developing regions of the world. Horizontally acquired genetic elements encode virulence structures, effectors, and regulators that promote bacterial colonization and disease. One such genetic element, the locus of enterocyte effacement (LEE), encodes the type three secretion system (T3SS) which acts as a bridge between bacterial and host cells to pass effector molecules that exert changes on the host. Due to its importance in EPEC virulence, regulation of the LEE has been of high priority and its investigation has elucidated many virulence regulators, including master regulator of the LEE Ler, H-NS, other nucleoid-associated proteins, GrlA, and PerC. Media type, environmental signals, sRNA signaling, metabolic processes, and stress responses have profound, strain-specific effects on regulators and LEE expression, and thus T3SS formation. Here we review virulence gene regulation in EPEC, which includes approaches for lessening disease by exploiting the elucidated regulatory pathways.
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Affiliation(s)
- Amy Platenkamp
- Department of Biology, Reed College, Portland, OR, United States
| | - Jay L Mellies
- Department of Biology, Reed College, Portland, OR, United States
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9
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Ainelo H, Lahesaare A, Teppo A, Kivisaar M, Teras R. The promoter region of lapA and its transcriptional regulation by Fis in Pseudomonas putida. PLoS One 2017; 12:e0185482. [PMID: 28945818 PMCID: PMC5612765 DOI: 10.1371/journal.pone.0185482] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/13/2017] [Indexed: 12/28/2022] Open
Abstract
LapA is the biggest protein in Pseudomonas putida and a key factor for biofilm formation. Its importance and posttranslational regulation is rather thoroughly studied but less is known about the transcriptional regulation. Here we give evidence that transcription of lapA in LB-grown bacteria is initiated from six promoters, three of which display moderate RpoS-dependence. The global transcription regulator Fis binds to the lapA promoter area at six positions in vitro, and Fis activates the transcription of lapA while overexpressed in cells. Two of the six Fis binding sites, Fis-A7 and Fis-A5, are necessary for the positive effect of Fis on the transcription of lapA in vivo. Our results indicate that Fis binding to the Fis-A7 site increases the level of transcription from the most distal promoter of lapA, whereas Fis binding to the Fis-A5 site could be important for modifying the promoter area topology.
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Affiliation(s)
- Hanna Ainelo
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Andrio Lahesaare
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Annika Teppo
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maia Kivisaar
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Riho Teras
- Chair of Genetics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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10
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Casella LG, Weiss A, Pérez-Rueda E, Antonio Ibarra J, Shaw LN. Towards the complete proteinaceous regulome of Acinetobacter baumannii. Microb Genom 2017; 3:mgen000107. [PMID: 28663824 PMCID: PMC5382811 DOI: 10.1099/mgen.0.000107] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/27/2017] [Indexed: 11/18/2022] Open
Abstract
The emergence of Acinetobacter baumannii strains, with broad multidrug-resistance phenotypes and novel virulence factors unique to hypervirulent strains, presents a major threat to human health worldwide. Although a number of studies have described virulence-affecting entities for this organism, very few have identified regulatory elements controlling their expression. Previously, our group has documented the global identification and curation of regulatory RNAs in A. baumannii. As such, in the present study, we detail an extension of this work, the performance of an extensive bioinformatic analysis to identify regulatory proteins in the recently annotated genome of the highly virulent AB5075 strain. In so doing, 243 transcription factors, 14 two-component systems (TCSs), 2 orphan response regulators, 1 hybrid TCS and 5 σ factors were found. A comparison of these elements between AB5075 and other clinical isolates, as well as a laboratory strain, led to the identification of several conserved regulatory elements, whilst at the same time uncovering regulators unique to hypervirulent strains. Lastly, by comparing regulatory elements compiled in this study to genes shown to be essential for AB5075 infection, we were able to highlight elements with a specific importance for pathogenic behaviour. Collectively, our work offers a unique insight into the regulatory network of A. baumannii strains, and provides insight into the evolution of hypervirulent lineages.
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Affiliation(s)
- Leila G Casella
- 1Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL 33620-5150, USA
| | - Andy Weiss
- 1Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL 33620-5150, USA
| | - Ernesto Pérez-Rueda
- 2Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Mérida, Yucatán, Mexico.,3Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico
| | - J Antonio Ibarra
- 4Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Santo Tomás, Delegación Miguel Hidalgo, CP, 11340 Mexico, DF, Mexico
| | - Lindsey N Shaw
- 1Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 East Fowler Avenue, ISA 2015, Tampa, FL 33620-5150, USA
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11
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Brandi A, Giangrossi M, Giuliodori AM, Falconi M. An Interplay among FIS, H-NS, and Guanosine Tetraphosphate Modulates Transcription of the Escherichia coli cspA Gene under Physiological Growth Conditions. Front Mol Biosci 2016; 3:19. [PMID: 27252944 PMCID: PMC4877382 DOI: 10.3389/fmolb.2016.00019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/01/2016] [Indexed: 11/13/2022] Open
Abstract
CspA, the most characterized member of the csp gene family of Escherichia coli, is highly expressed not only in response to cold stress, but also during the early phase of growth at 37°C. Here, we investigate at molecular level the antagonistic role played by the nucleoid proteins FIS and H-NS in the regulation of cspA expression under non-stress conditions. By means of both probing experiments and immunological detection, we demonstrate in vitro the existence of binding sites for these proteins on the cspA regulatory region, in which FIS and H-NS bind simultaneously to form composite DNA-protein complexes. While the in vitro promoter activity of cspA is stimulated by FIS and repressed by H-NS, a compensatory effect is observed when both proteins are added in the transcription assay. Consistently with these findings, inactivation of fis and hns genes reversely affect the in vivo amount of cspA mRNA. In addition, by means of strains expressing a high level of the alarmone guanosine tetraphosphate ((p)ppGpp) and in vitro transcription assays, we show that the cspA promoter is sensitive to (p)ppGpp inhibition. The (p)ppGpp-mediated expression of fis and hns genes is also analyzed, thus clarifying some aspects of the regulatory loop governing cspA transcription.
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Affiliation(s)
- Anna Brandi
- Laboratory of Genetics, School of Bioscience and Veterinary Medicine, University of Camerino Camerino, Italy
| | - Mara Giangrossi
- Laboratory of Genetics, School of Bioscience and Veterinary Medicine, University of Camerino Camerino, Italy
| | - Anna M Giuliodori
- Laboratory of Genetics, School of Bioscience and Veterinary Medicine, University of Camerino Camerino, Italy
| | - Maurizio Falconi
- Laboratory of Genetics, School of Bioscience and Veterinary Medicine, University of Camerino Camerino, Italy
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12
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Horinouchi T, Suzuki S, Hirasawa T, Ono N, Yomo T, Shimizu H, Furusawa C. Phenotypic convergence in bacterial adaptive evolution to ethanol stress. BMC Evol Biol 2015; 15:180. [PMID: 26334309 PMCID: PMC4559166 DOI: 10.1186/s12862-015-0454-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 08/12/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial cells have a remarkable ability to adapt to environmental changes, a phenomenon known as adaptive evolution. During adaptive evolution, phenotype and genotype dynamically changes; however, the relationship between these changes and associated constraints is yet to be fully elucidated. RESULTS In this study, we analyzed phenotypic and genotypic changes in Escherichia coli cells during adaptive evolution to ethanol stress. Phenotypic changes were quantified by transcriptome and metabolome analyses and were similar among independently evolved ethanol tolerant populations, which indicate the existence of evolutionary constraints in the dynamics of adaptive evolution. Furthermore, the contribution of identified mutations in one of the tolerant strains was evaluated using site-directed mutagenesis. The result demonstrated that the introduction of all identified mutations cannot fully explain the observed tolerance in the tolerant strain. CONCLUSIONS The results demonstrated that the convergence of adaptive phenotypic changes and diverse genotypic changes, which suggested that the phenotype-genotype mapping is complex. The integration of transcriptome and genome data provides a quantitative understanding of evolutionary constraints.
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Affiliation(s)
- Takaaki Horinouchi
- Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Shingo Suzuki
- Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.
| | - Takashi Hirasawa
- Department of Bioengineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan. .,Graduate School of Information Science and Technology, Osaka University, 1-5 Yamada-oka, Suita, Osaka, 565-0871, Japan.
| | - Naoaki Ono
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
| | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamada-oka, Suita, Osaka, 565-0871, Japan. .,Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamada-oka, Suita, Osaka, 565-0871, Japan.
| | - Hiroshi Shimizu
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamada-oka, Suita, Osaka, 565-0871, Japan.
| | - Chikara Furusawa
- Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan. .,Graduate School of Information Science and Technology, Osaka University, 1-5 Yamada-oka, Suita, Osaka, 565-0871, Japan.
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13
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Gerganova V, Berger M, Zaldastanishvili E, Sobetzko P, Lafon C, Mourez M, Travers A, Muskhelishvili G. Chromosomal position shift of a regulatory gene alters the bacterial phenotype. Nucleic Acids Res 2015; 43:8215-26. [PMID: 26170236 PMCID: PMC4751926 DOI: 10.1093/nar/gkv709] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/30/2015] [Indexed: 12/31/2022] Open
Abstract
Recent studies strongly suggest that in bacterial cells the order of genes along the chromosomal origin-to-terminus axis is determinative for regulation of the growth phase-dependent gene expression. The prediction from this observation is that positional displacement of pleiotropic genes will affect the genetic regulation and hence, the cellular phenotype. To test this prediction we inserted the origin-proximal dusB-fis operon encoding the global regulator FIS in the vicinity of replication terminus on both arms of the Escherichia coli chromosome. We found that the lower fis gene dosage in the strains with terminus-proximal dusB-fis operons was compensated by increased fis expression such that the intracellular concentration of FIS was homeostatically adjusted. Nevertheless, despite unchanged FIS levels the positional displacement of dusB-fis impaired the competitive growth fitness of cells and altered the state of the overarching network regulating DNA topology, as well as the cellular response to environmental stress, hazardous substances and antibiotics. Our finding that the chromosomal repositioning of a regulatory gene can determine the cellular phenotype unveils an important yet unexplored facet of the genetic control mechanisms and paves the way for novel approaches to manipulate bacterial physiology.
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Affiliation(s)
- Veneta Gerganova
- Jacobs University Bremen, School of Engineering and Science, Bremen, 28758, Germany
| | - Michael Berger
- Institut für Hygiene, Universitätsklinikum Münster, Münster, 48149, Germany
| | | | - Patrick Sobetzko
- Philipps-Universität Marburg, LOEWE-Zentrum für Synthetische Mikrobiologie, Department of Chromosome Biology, Marburg, 35032, Germany
| | - Corinne Lafon
- SANOFI/ TSU Infectious Diseases, Toulouse, 31036, France
| | - Michael Mourez
- SANOFI/ TSU Infectious Diseases, Toulouse, 31036, France
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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14
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Gerganova V, Maurer S, Stoliar L, Japaridze A, Dietler G, Nasser W, Kutateladze T, Travers A, Muskhelishvili G. Upstream binding of idling RNA polymerase modulates transcription initiation from a nearby promoter. J Biol Chem 2015; 290:8095-109. [PMID: 25648898 DOI: 10.1074/jbc.m114.628131] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial gene regulatory regions often demonstrate distinctly organized arrays of RNA polymerase binding sites of ill-defined function. Previously we observed a module of closely spaced polymerase binding sites upstream of the canonical promoter of the Escherichia coli fis operon. FIS is an abundant nucleoid-associated protein involved in adjusting the chromosomal DNA topology to changing cellular physiology. Here we show that simultaneous binding of the polymerase at the canonical fis promoter and an upstream transcriptionally inactive site stabilizes a RNAP oligomeric complex in vitro. We further show that modulation of the upstream binding of RNA polymerase affects the fis promoter activity both in vivo and in vitro. The effect of the upstream RNA polymerase binding on the fis promoter activity depends on the spatial arrangement of polymerase binding sites and DNA supercoiling. Our data suggest that a specific DNA geometry of the nucleoprotein complex stabilized on concomitant binding of RNA polymerase molecules at the fis promoter and the upstream region acts as a topological device regulating the fis transcription. We propose that transcriptionally inactive RNA polymerase molecules can act as accessory factors regulating the transcription initiation from a nearby promoter.
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Affiliation(s)
- Veneta Gerganova
- From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Sebastian Maurer
- From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Liubov Stoliar
- From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Aleksandre Japaridze
- the Laboratory of the Physics of Living Matter, EPFL, CH-1015 Lausanne, Switzerland
| | - Giovanni Dietler
- the Laboratory of the Physics of Living Matter, EPFL, CH-1015 Lausanne, Switzerland
| | - William Nasser
- the UMR5240 CNRS/INSA/UCB, Université de Lyon, F-69003, INSA-Lyon, Villeurbanne, F-69621, France
| | - Tamara Kutateladze
- the Ivane Beritashvili Centre of Experimental Biomedicine, Gotua str.14, Tbilisi, Georgia, and
| | - Andrew Travers
- the MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 QH, United Kingdom
| | - Georgi Muskhelishvili
- From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany,
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15
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Moor H, Teppo A, Lahesaare A, Kivisaar M, Teras R. Fis overexpression enhances Pseudomonas putida biofilm formation by regulating the ratio of LapA and LapF. MICROBIOLOGY-SGM 2014; 160:2681-2693. [PMID: 25253613 DOI: 10.1099/mic.0.082503-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bacteria form biofilm as a response to a number of environmental signals that are mediated by global transcription regulators and alarmones. Here we report the involvement of the global transcription regulator Fis in Pseudomonas putida biofilm formation through regulation of lapA and lapF genes. The major component of P. putida biofilm is proteinaceous and two large adhesive proteins, LapA and LapF, are known to play a key role in its formation. We have previously shown that Fis overexpression enhances P. putida biofilm formation. In this study, we used mini-Tn5 transposon mutagenesis to select potential Fis-regulated genes involved in biofilm formation. A total of 90 % of the studied transposon mutants carried insertions in the lap genes. Since our experiments showed that Fis-enhanced biofilm is mostly proteinaceous, the amounts of LapA and LapF from P. putida cells lysates were quantified using SDS-PAGE. Fis overexpression increases the quantity of LapA 1.6 times and decreases the amount of LapF at least 4 times compared to the wild-type cells. The increased LapA expression caused by Fis overexpression was confirmed by FACS analysis measuring the amount of LapA-GFP fusion protein. Our results suggest that the profusion of LapA in the Fis-overexpressed cells causes enhanced biofilm formation in mature stages of P. putida biofilm and LapF has a minor role in P. putida biofilm formation.
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Affiliation(s)
- Hanna Moor
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Annika Teppo
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Andrio Lahesaare
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Maia Kivisaar
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Riho Teras
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, 51010 Tartu, Estonia
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16
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Wang H, Liu B, Wang Q, Wang L. Genome-wide analysis of the salmonella Fis regulon and its regulatory mechanism on pathogenicity islands. PLoS One 2013; 8:e64688. [PMID: 23717649 PMCID: PMC3662779 DOI: 10.1371/journal.pone.0064688] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/17/2013] [Indexed: 11/19/2022] Open
Abstract
Fis, one of the most important nucleoid-associated proteins, functions as a global regulator of transcription in bacteria that has been comprehensively studied in Escherichia coli K12. Fis also influences the virulence of Salmonella enterica and pathogenic E. coli by regulating their virulence genes, however, the relevant mechanism is unclear. In this report, using combined RNA-seq and chromatin immunoprecipitation (ChIP)-seq technologies, we first identified 1646 Fis-regulated genes and 885 Fis-binding targets in the S. enterica serovar Typhimurium, and found a Fis regulon different from that in E. coli. Fis has been reported to contribute to the invasion ability of S. enterica. By using cell infection assays, we found it also enhances the intracellular replication ability of S. enterica within macrophage cell, which is of central importance for the pathogenesis of infections. Salmonella pathogenicity islands (SPI)-1 and SPI-2 are crucial for the invasion and survival of S. enterica in host cells. Using mutation and overexpression experiments, real-time PCR analysis, and electrophoretic mobility shift assays, we demonstrated that Fis regulates 63 of the 94 Salmonella pathogenicity island (SPI)-1 and SPI-2 genes, by three regulatory modes: i) binds to SPI regulators in the gene body or in upstream regions; ii) binds to SPI genes directly to mediate transcriptional activation of themselves and downstream genes; iii) binds to gene encoding OmpR which affects SPI gene expression by controlling SPI regulators SsrA and HilD. Our results provide new insights into the impact of Fis on SPI genes and the pathogenicity of S. enterica.
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Affiliation(s)
- Hui Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
| | - Bin Liu
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
| | - Quan Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
| | - Lei Wang
- TEDA School of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, P. R. China
- Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, P. R. China
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, P. R. China
- * E-mail:
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17
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Elati M, Nicolle R, Junier I, Fernández D, Fekih R, Font J, Képès F. PreCisIon: PREdiction of CIS-regulatory elements improved by gene's positION. Nucleic Acids Res 2012; 41:1406-15. [PMID: 23241390 PMCID: PMC3561985 DOI: 10.1093/nar/gks1286] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position-specific scoring matrices, which may match large numbers of sites and produce an unreliable list of target genes. To improve the prediction of binding sites, we propose to additionally use the unrelated knowledge of the genome layout. Indeed, it has been shown that co-regulated genes tend to be either neighbors or periodically spaced along the whole chromosome. This study demonstrates that respective gene positioning carries significant information. This novel type of information is combined with traditional sequence information by a machine learning algorithm called PreCisIon. To optimize this combination, PreCisIon builds a strong gene target classifier by adaptively combining weak classifiers based on either local binding sequence or global gene position. This strategy generically paves the way to the optimized incorporation of any future advances in gene target prediction based on local sequence, genome layout or on novel criteria. With the current state of the art, PreCisIon consistently improves methods based on sequence information only. This is shown by implementing a cross-validation analysis of the 20 major TFs from two phylogenetically remote model organisms. For Bacillus subtilis and Escherichia coli, respectively, PreCisIon achieves on average an area under the receiver operating characteristic curve of 70 and 60%, a sensitivity of 80 and 70% and a specificity of 60 and 56%. The newly predicted gene targets are demonstrated to be functionally consistent with previously known targets, as assessed by analysis of Gene Ontology enrichment or of the relevant literature and databases.
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Affiliation(s)
- Mohamed Elati
- Institute of Systems and Synthetic Biology, CNRS, University of Evry, Genopole, 91030 Evry, France.
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18
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Prigent-Combaret C, Zghidi-Abouzid O, Effantin G, Lejeune P, Reverchon S, Nasser W. The nucleoid-associated protein Fis directly modulates the synthesis of cellulose, an essential component of pellicle-biofilms in the phytopathogenic bacterium Dickeya dadantii. Mol Microbiol 2012; 86:172-86. [PMID: 22925161 DOI: 10.1111/j.1365-2958.2012.08182.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacteria use biofilm structures to colonize surfaces and to survive in hostile conditions, and numerous bacteria produce cellulose as a biofilm matrix polymer. Hence, expression of the bcs operon, responsible for cellulose biosynthesis, must be finely regulated in order to allow bacteria to adopt the proper surface-associated behaviours. Here we show that in the phytopathogenic bacterium, Dickeya dadantii, production of cellulose is required for pellicle-biofilm formation and resistance to chlorine treatments. Expression of the bcs operon is growth phase-regulated and is stimulated in biofilms. Furthermore, we unexpectedly found that the nucleoid-associated protein and global regulator of virulence functions, Fis, directly represses bcs operon expression by interacting with an operator that is absent from the bcs operon of animal pathogenic bacteria and the plant pathogenic bacterium Pectobacterium. Moreover, production of cellulose enhances plant surface colonization by D. dadantii. Overall, these data suggest that cellulose production and biofilm formation may be important factors for surface colonization by D. dadantii and its subsequent survival in hostile environments. This report also presents a new example of how bacteria can modulate the action of a global regulator to co-ordinate basic metabolism, virulence and modifications of lifestyle.
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19
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Batt G, Besson B, Ciron PE, de Jong H, Dumas E, Geiselmann J, Monte R, Monteiro PT, Page M, Rechenmann F, Ropers D. Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks. Methods Mol Biol 2012; 804:439-462. [PMID: 22144166 DOI: 10.1007/978-1-61779-361-5_22] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Genetic Network Analyzer (GNA) is a tool for the qualitative modeling and simulation of gene regulatory networks, based on so-called piecewise-linear differential equation models. We describe the use of this tool in the context of the modeling of bacterial regulatory networks, notably the network of global regulators controlling the adaptation of Escherichia coli to carbon starvation conditions. We show how the modeler, by means of GNA, can define a regulatory network, build a model of the network, determine the steady states of the system, perform a qualitative simulation of the network dynamics, and analyze the simulation results using model-checking tools. The example illustrates the interest of qualitative approaches for the analysis of the dynamics of bacterial regulatory networks.
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Affiliation(s)
- Grégory Batt
- INRIA Paris - Rocquencourt, Domaine de Voluceau, Le Chesnay, France
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20
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Muñiz VA, Srinivasan S, Boswell SA, Meinhold DW, Childs T, Osuna R, Colón W. The role of the local environment of engineered Tyr to Trp substitutions for probing the denaturation mechanism of FIS. Protein Sci 2011; 20:302-12. [PMID: 21280122 DOI: 10.1002/pro.561] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Factor for inversion stimulation (FIS), a 98-residue homodimeric protein, does not contain tryptophan (Trp) residues but has four tyrosine (Tyr) residues located at positions 38, 51, 69, and 95. The equilibrium denaturation of a P61A mutant of FIS appears to occur via a three-state (N(2) ⇆ I(2) ⇆ 2U) process involving a dimeric intermediate (I(2)). Although it was suggested that this intermediate had a denatured C-terminus, direct evidence was lacking. Therefore, three FIS double mutants, P61A/Y38W, P61A/Y69W, and P61A/Y95W were made, and their denaturation was monitored by circular dichroism and Trp fluorescence. Surprisingly, the P61A/Y38W mutant best monitored the N(2) ⇆ I(2) transition, even though Trp38 is buried within the dimer removed from the C-terminus. In addition, although Trp69 is located on the protein surface, the P61A/Y69W FIS mutant exhibited clearly biphasic denaturation curves. In contrast, P61A/Y95W FIS was the least effective in decoupling the two transitions, exhibiting a monophasic fluorescence transition with modest concentration-dependence. When considering the local environment of the Trp residues and the effect of each mutation on protein stability, these results not only confirm that P61A FIS denatures via a dimeric intermediate involving a disrupted C-terminus but also suggest the occurrence of conformational changes near Tyr38. Thus, the P61A mutation appears to compromise the denaturation cooperativity of FIS by failing to propagate stability to those regions involved mostly in intramolecular interactions. Furthermore, our results highlight the challenge of anticipating the optimal location to engineer a Trp residue for investigating the denaturation mechanism of even small proteins.
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Affiliation(s)
- Virginia A Muñiz
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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21
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Crozat E, Hindré T, Kühn L, Garin J, Lenski RE, Schneider D. Altered regulation of the OmpF porin by Fis in Escherichia coli during an evolution experiment and between B and K-12 strains. J Bacteriol 2011; 193:429-40. [PMID: 21097626 PMCID: PMC3019833 DOI: 10.1128/jb.01341-10] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2010] [Accepted: 11/08/2010] [Indexed: 12/19/2022] Open
Abstract
The phenotypic plasticity of global regulatory networks provides bacteria with rapid acclimation to a wide range of environmental conditions, while genetic changes in those networks provide additional flexibility as bacteria evolve across long time scales. We previously identified mutations in the global regulator-encoding gene fis that enhanced organismal fitness during a long-term evolution experiment with Escherichia coli. To gain insight into the effects of these mutations, we produced two-dimensional protein gels with strains carrying different fis alleles, including a beneficial evolved allele and one with an in-frame deletion. We found that Fis controls the expression of the major porin-encoding gene ompF in the E. coli B-derived ancestral strain used in the evolution experiment, a relationship that has not been described before. We further showed that this regulatory connection evolved over two different time scales, perhaps explaining why it was not observed before. On the longer time scale, we showed that this regulation of ompF by Fis is absent from the more widely studied K-12 strain and thus is specific to the B strain. On a shorter time scale, this regulatory linkage was lost during 20,000 generations of experimental evolution of the B strain. Finally, we mapped the Fis binding sites in the ompF regulatory region, and we present a hypothetical model of ompF expression that includes its other known regulators.
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Affiliation(s)
- Estelle Crozat
- Laboratoire Adaptation et Pathogénie des Micro-organismes, CNRS UMR 5163, Université Joseph Fourier, Grenoble 1, BP 170, F-38042 Grenoble Cedex 9, France, CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, INSERM, U880, F-38042 Grenoble Cedex 9, France, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Thomas Hindré
- Laboratoire Adaptation et Pathogénie des Micro-organismes, CNRS UMR 5163, Université Joseph Fourier, Grenoble 1, BP 170, F-38042 Grenoble Cedex 9, France, CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, INSERM, U880, F-38042 Grenoble Cedex 9, France, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Lauriane Kühn
- Laboratoire Adaptation et Pathogénie des Micro-organismes, CNRS UMR 5163, Université Joseph Fourier, Grenoble 1, BP 170, F-38042 Grenoble Cedex 9, France, CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, INSERM, U880, F-38042 Grenoble Cedex 9, France, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Jérome Garin
- Laboratoire Adaptation et Pathogénie des Micro-organismes, CNRS UMR 5163, Université Joseph Fourier, Grenoble 1, BP 170, F-38042 Grenoble Cedex 9, France, CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, INSERM, U880, F-38042 Grenoble Cedex 9, France, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Richard E. Lenski
- Laboratoire Adaptation et Pathogénie des Micro-organismes, CNRS UMR 5163, Université Joseph Fourier, Grenoble 1, BP 170, F-38042 Grenoble Cedex 9, France, CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, INSERM, U880, F-38042 Grenoble Cedex 9, France, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Dominique Schneider
- Laboratoire Adaptation et Pathogénie des Micro-organismes, CNRS UMR 5163, Université Joseph Fourier, Grenoble 1, BP 170, F-38042 Grenoble Cedex 9, France, CEA, DSV, iRTSV, Laboratoire d'Etude de la Dynamique des Protéomes, INSERM, U880, F-38042 Grenoble Cedex 9, France, Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
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22
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Role of decreased levels of Fis histone-like protein in Crohn's disease-associated adherent invasive Escherichia coli LF82 bacteria interacting with intestinal epithelial cells. J Bacteriol 2010; 192:1832-43. [PMID: 20118249 DOI: 10.1128/jb.01679-09] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The interaction of Crohn's disease (CD)-associated adherent-invasive Escherichia coli (AIEC) strain LF82 with intestinal epithelial cells depends on surface appendages, such as type 1 pili and flagella. Histone-like proteins operate as global regulators to control the expression of these virulence factors. We evaluated the role of histone-like proteins in AIEC reference strain LF82 during infection of intestinal epithelial cells, Intestine-407, and observed that the fis mRNA level was decreased. The role of Fis in AIEC LF82 was determined by studying the phenotype of an LF82 fis::Km mutant. This was the first mutant of strain LF82 that has been described thus far that is unable to express flagellin but still able to produce type 1 pili. The cyclic-di-GMP pathway linking flagella and type 1 pilus expression is not involved in Fis-mediated regulation, and we identified in the present study Fis-binding sites located upstream of the fimE gene and in the intergenic region between fimB and nanC of the fim operon encoding type 1 pili. The major consequence of decreased Fis expression in AIEC bacteria in contact with host cells is a direct downregulation of fimE expression, leading to the preferential ON phase of the fimS element. Thus, by maintaining type 1 pilus expression, AIEC bacteria, which interact with the gut mucosa, have greater ability to colonize and to induce inflammation in CD patients.
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23
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Teras R, Jakovleva J, Kivisaar M. Fis negatively affects binding of Tn4652 transposase by out-competing IHF from the left end of Tn4652. MICROBIOLOGY-SGM 2009; 155:1203-1214. [PMID: 19332822 DOI: 10.1099/mic.0.022830-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Transposition activity in bacteria is generally maintained at a low level. The activity of mobile DNA elements can be controlled by bacterially encoded global regulators. Regulation of transposition of Tn4652 in Pseudomonas putida is one such example. Activation of transposition of Tn4652 in starving bacteria requires the stationary-phase sigma factor RpoS and integration host factor (IHF). IHF plays a dual role in Tn4652 translocation by activating transcription of the transposase gene tnpA of the transposon and facilitating TnpA binding to the inverted repeats of the transposon. Our previous results have indicated that besides IHF some other P. putida-encoded global regulator(s) might bind to the ends of Tn4652 and regulate transposition activity. In this study, employing a DNase I footprint assay we have identified a binding site of P. putida Fis (factor for inversion stimulation) centred 135 bp inside the left end of Tn4652. Our results of gel mobility shift and DNase I footprint studies revealed that Fis out-competes IHF from the left end of Tn4652, thereby abolishing the binding of TnpA. Thus, the results obtained in this study indicate that the transposition of Tn4652 is regulated by the cellular amount of P. putida global regulators Fis and IHF.
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Affiliation(s)
- Riho Teras
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, 51010 Tartu, Estonia
| | - Julia Jakovleva
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, 51010 Tartu, Estonia
| | - Maia Kivisaar
- Department of Genetics, Institute of Molecular and Cell Biology, Tartu University and Estonian Biocentre, 51010 Tartu, Estonia
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24
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Galán B, Manso I, Kolb A, García JL, Prieto MA. The role of FIS protein in the physiological control of the expression of the Escherichia coli meta-hpa operon. MICROBIOLOGY-SGM 2008; 154:2151-2160. [PMID: 18599842 DOI: 10.1099/mic.0.2007/015578-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Expression from the Escherichia coli W meta-hpa operon promoter (Pg) is under a strict catabolic repression control mediated by the cAMP-catabolite repression protein (CRP) complex in a glucose-containing medium. The Pg promoter is also activated by the integration host factor (IHF) and repressed by the specific transcriptional regulator HpaR when 4-hydroxyphenylacetate (4HPA) is not present in the medium. Expression from the hpa promoter is also repressed in undefined rich medium such as LB, but the molecular basis of this mechanism is not understood. We present in vitro and in vivo studies to demonstrate the involvement of FIS protein in this catabolic repression. DNase I footprinting experiments show that FIS binds to multiple sites within the Pg promoter. FIS-site I overlaps the CRP-binding site. By using an electromobility shift assay, we demonstrated that FIS efficiently competes with CRP for binding to the Pg promoter, suggesting an antagonist/competitive mechanism. RT-PCR showed that the Pg repression effect is relieved in a FIS deleted strain. The repression role of FIS at Pg was further demonstrated by in vitro transcription assays. These results suggest that FIS contributes to silencing the Pg promoter in the exponential phase of growth in an undefined rich medium when FIS is predominantly expressed.
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Affiliation(s)
- Beatriz Galán
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Isabel Manso
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Annie Kolb
- Unité de Génétique Moléculaire-URA 2172, Institut Pasteur, Paris, France
| | - José Luis García
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - María A Prieto
- Department of Molecular Microbiology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
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25
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Shao Y, Feldman-Cohen LS, Osuna R. Functional characterization of the Escherichia coli Fis-DNA binding sequence. J Mol Biol 2007; 376:771-85. [PMID: 18178221 DOI: 10.1016/j.jmb.2007.11.101] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Revised: 11/29/2007] [Accepted: 11/30/2007] [Indexed: 12/24/2022]
Abstract
The Escherichia coli protein Fis is remarkable for its ability to interact specifically with DNA sites of highly variable sequences. The mechanism of this sequence-flexible DNA recognition is not well understood. In a previous study, we examined the contributions of Fis residues to high-affinity binding at different DNA sequences using alanine-scanning mutagenesis and identified several key residues for Fis-DNA recognition. In this work, we investigated the contributions of the 15-bp core Fis binding sequence and its flanking regions to Fis-DNA interactions. Systematic base-pair replacements made in both half sites of a palindromic Fis binding sequence were examined for their effects on the relative Fis binding affinity. Missing contact assays were also used to examine the effects of base removal within the core binding site and its flanking regions on the Fis-DNA binding affinity. The results revealed that: (1) the -7G and +3Y bases in both DNA strands (relative to the central position of the core binding site) are major determinants for high-affinity binding; (2) the C(5) methyl group of thymine, when present at the +4 position, strongly hinders Fis binding; and (3) AT-rich sequences in the central and flanking DNA regions facilitate Fis-DNA interactions by altering the DNA structure and by increasing the local DNA flexibility. We infer that the degeneracy of specific Fis binding sites results from the numerous base-pair combinations that are possible at noncritical DNA positions (from -6 to -4, from -2 to +2, and from +4 to +6), with only moderate penalties on the binding affinity, the roughly similar contributions of -3A or G and +3T or C to the binding affinity, and the minimal requirement of three of the four critical base pairs to achieve considerably high binding affinities.
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Affiliation(s)
- Yongping Shao
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
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26
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Bradley MD, Beach MB, de Koning APJ, Pratt TS, Osuna R. Effects of Fis on Escherichia coli gene expression during different growth stages. MICROBIOLOGY-SGM 2007; 153:2922-2940. [PMID: 17768236 DOI: 10.1099/mic.0.2007/008565-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fis is a nucleoid-associated protein in Escherichia coli that is abundant during early exponential growth in rich medium but is in short supply during stationary phase. Its role as a transcriptional regulator has been demonstrated for an increasing number of genes. In order to gain insight into the global effects of Fis on E. coli gene expression during different stages of growth in rich medium, DNA microarray analyses were conducted in fis and wild-type strains during early, mid-, late-exponential and stationary growth phases. The results uncovered 231 significantly regulated genes that were distributed over 15 functional categories. Regulatory effects were observed at all growth stages examined. Coordinate upregulation was observed for a number of genes involved in translation, flagellar biosynthesis and motility, nutrient transport, carbon compound metabolism, and energy metabolism at different growth stages. Coordinate down-regulation was also observed for genes involved in stress response, amino acid and nucleotide biosynthesis, energy and intermediary metabolism, and nutrient transport. As cells transitioned from the early to the late-exponential growth phase, different functional categories of genes were regulated, and a gradual shift occurred towards mostly down-regulation. The results demonstrate that the growth phase-dependent Fis expression triggers coordinate regulation of 15 categories of functionally related genes during specific stages of growth of an E. coli culture.
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Affiliation(s)
- Meranda D Bradley
- Department of Biological Science, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Michael B Beach
- Department of Biology, Chemistry, and Physics, Southern Polytechnic State University, 1100 South Marietta Parkway, Marietta, GA 30060-2896, USA
| | - A P Jason de Koning
- Department of Biological Science, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Timothy S Pratt
- New York University - School of Medicine, Department of Environmental Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - Robert Osuna
- Department of Biological Science, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
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27
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Lautier T, Nasser W. The DNA nucleoid-associated protein Fis co-ordinates the expression of the main virulence genes in the phytopathogenic bacterium Erwinia chrysanthemi. Mol Microbiol 2007; 66:1474-90. [PMID: 18028311 DOI: 10.1111/j.1365-2958.2007.06012.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Erwinia chrysanthemi strain 3937 is a necrotrophic bacterial plant pathogen. Pectinolytic enzymes and, in particular, pectate lyases (Pels) play a key role in soft rot symptoms but the efficient colonization of plants by E. chrysanthemi requires additional factors. These factors include the harpin HrpN, the cellulase Cel5, proteases (Prts), flagellar proteins and the Sap system, involved in the detoxification of plant antimicrobial peptides. HrpN and flagellum are mostly involved in the early steps of infection whereas the degradative enzymes (Pels, Cel5, Prts) are mainly required in the advanced stages. Production of these virulence factors is tightly regulated by environmental conditions. This report shows that the nucleoid-associated protein Fis plays a pivotal role in the expression of the main virulence genes. Its production is regulated in a growth phase-dependent manner and is under negative autoregulation. An E. chrysanthemi fis mutant displays a reduced motility and expression of hrpN, prtC and the sap operon. In contrast, the expression of the cel5 gene is increased in this mutant. Furthermore, the induction of the Pel activity is delayed and increased during the stationary growth phase in the fis mutant. Most of these controls occur through a direct effect because purified Fis binds to the promoter regions of fis, hrpN, sapA, cel5 and fliC. Moreover, potassium permanganate footprinting and in vitro transcription assays have revealed that Fis prevents transcription initiation at the fis promoter and also transcript elongation from the cel5 promoter. Finally, the fis mutant has a decreased virulence. These results suggest a co-ordinated regulation by Fis of virulence factors involved in certain key steps of infection, early (asymptomatic) and advanced (symptomatic) phases.
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Affiliation(s)
- Thomas Lautier
- Université de Lyon, F-69003, France; Université Lyon 1, F-69622, France; INSA-Lyon, Villeurbanne, F-69621, France; CNRS, UMR 5240, Unité Microbiologie Adaptation et Pathogénie, F-69622, France
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28
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Lei GS, Chen CJ, Yuan HS, Wang SH, Hu ST. Inhibition of IS 2transposition by factor for inversion stimulation. FEMS Microbiol Lett 2007; 275:98-105. [PMID: 17666068 DOI: 10.1111/j.1574-6968.2007.00864.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The effect of factor for inversion stimulation (Fis) protein on IS2 transposition was investigated. A full-length IS2 was found to transpose at a frequency 64 times lower in a normal Escherichia coli than in a fis- mutant. To investigate whether Fis affects IS2 transposition by DNA binding, gel retardation and DNase I footprinting experiments were performed. Analysis of Fis binding to the left terminus of IS2 revealed that Fis binds to nucleotide number 44-60 located between the -35 and -10 regions of the major IS2 promoter. To further determine whether Fis binding affects IS2 transcription, the major IS2 promoter was fused to a luciferase gene and assayed for its transcription efficiency in the presence or absence of Fis. The results showed that Fis reduced transcription from the major IS2 promoter by approximately sixfold. Analysis of Fis binding to the right terminal repeat of IS2 revealed that Fis binds to the inner end of the repeat, which is the same region as the place where the IS2 transposase binds. These results suggest that Fis inhibits IS2 transposition by blocking the binding sites of IS2 transposase and by repressing the transcription of IS2 genes.
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Affiliation(s)
- Guang-Sheng Lei
- Graduate Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan, Republic of China
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29
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Abstract
We previously reported that the P1 promoter of topA encoding topoisomerase I of Escherichia coli is activated in response to oxidative stress, in a Fis-dependent manner. Here we show that Fis regulation of topA varies with the intracellular concentrations of Fis. Thus, when Fis levels are low, hydrogen peroxide treatment results in topA activation, whereas at high Fis levels hydrogen peroxide treatment renders topA P1 inactive. In vivo DMS footprinting indicates that only at low Fis levels, when exposed to the stress, the region of the topA promoter changes and P1 becomes active. Potassium permanganate experiments indicate that low levels of Fis activate P1 transcription by facilitating the formation of open complexes, while high levels of this protein shut off the promoter. DNase I footprinting show that Fis binds the promoter region of topA at eight sites with different affinities. One low affinity site overlaps the -10, -35 hexamers of RNA polymerase. We propose that in response to oxidative stress, when present at low levels, Fis binds the promoter region of topA at its high affinity sites, thereby facilitating the recruitment of RNA polymerase to P1, while at high levels, Fis occupies the low affinity sites as well, and thus prevents the binding of RNA polymerase. Our results indicate that the oxidative stress response varies in response to changes in growth phase and nutritional environment.
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Affiliation(s)
- Dalit Weinstein-Fischer
- Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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30
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Deutscher J, Francke C, Postma PW. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2007; 70:939-1031. [PMID: 17158705 PMCID: PMC1698508 DOI: 10.1128/mmbr.00024-06] [Citation(s) in RCA: 989] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
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Affiliation(s)
- Josef Deutscher
- Microbiologie et Génétique Moléculaire, INRA-CNRS-INA PG UMR 2585, Thiverval-Grignon, France.
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31
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Typas A, Stella S, Johnson RC, Hengge R. The ?35 sequence location and the Fis?sigma factor interface determine ?Sselectivity of the proP (P2) promoter in Escherichia coli. Mol Microbiol 2007; 63:780-96. [PMID: 17302803 DOI: 10.1111/j.1365-2958.2006.05560.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The P2 promoter of proP, encoding a transporter for proline and glycine betaine in Escherichia coli, is a unique paradigm, where master regulators of different growth stages, Fis and sigma(S) (RpoS), collaborate to achieve promoter activation. It is also the only case described where Fis functions as class II transcriptional activator (centred at -41). Here we show that the degenerate -35 sequence, and the location of the Fis binding site, which forces a suboptimal 16 bp spacing between the -35 and -10 elements, allow only sigma(S) but not sigma(70) to function at proP (P2). Moreover, the interface between Fis and sigma(S) seems better suited to sigma(S), due to a single residue difference between sigma(S) and sigma(70). Nevertheless, Fis can activate RNA polymerase containing sigma(70) at a proP (P2) promoter variant, in which a typical sigma(70)-35 recognition sequence has been introduced at a 17 bp distance from the -10 hexamer. In summary, we elucidate the rules that govern sigma factor selectivity in the presence of a class II activator, provide new insight into transcriptional activation by Fis from this position, and clarify, why the proP (P2) promoter is precisely activated during a short time window of the growth cycle, when Fis and sigma(S) are both present.
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Affiliation(s)
- Athanasios Typas
- Institut für Biologie, Mikrobiologie, Freie Universität Berlin, Königin-Luise-Str. 12-16, 14195 Berlin, Germany
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32
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Mallik P, Paul BJ, Rutherford ST, Gourse RL, Osuna R. DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J Bacteriol 2006; 188:5775-82. [PMID: 16885445 PMCID: PMC1540068 DOI: 10.1128/jb.00276-06] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
DksA is a critical transcription factor in Escherichia coli that binds to RNA polymerase and potentiates control of rRNA promoters and certain amino acid promoters. Given the kinetic similarities between rRNA promoters and the fis promoter (Pfis), we investigated the possibility that DksA might also control transcription from Pfis. We show that the absence of dksA extends transcription from Pfis well into the late logarithmic and stationary growth phases, demonstrating the importance of DksA for growth phase-dependent regulation of fis. We also show that transcription from Pfis increases with steady-state growth rate and that dksA is absolutely required for this regulation. In addition, both DksA and ppGpp are required for inhibition of Pfis promoter activity following amino acid starvation, and these factors act directly and synergistically to negatively control Pfis transcription in vitro. DksA decreases the half-life of the intrinsically short-lived fis promoter-RNA polymerase complex and increases its sensitivity to the concentration of CTP, the predominant initiating nucleotide triphosphate for this promoter. This work extends our understanding of the multiple factors controlling fis expression and demonstrates the generality of the DksA requirement for regulation of kinetically similar promoters.
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Affiliation(s)
- Prabhat Mallik
- Department of Biological Sciences, University at Albany, 1400 Washington Avenue, Albany, NY 12222, USA
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33
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Yuste L, Hervás AB, Canosa I, Tobes R, Jiménez JI, Nogales J, Pérez-Pérez MM, Santero E, Díaz E, Ramos JL, de Lorenzo V, Rojo F. Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Environ Microbiol 2006; 8:165-77. [PMID: 16343331 DOI: 10.1111/j.1462-2920.2005.00890.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial transcriptional networks are built on a hierarchy of regulators, on top of which lie the components of the RNA polymerase (in particular the sigma factors) and the global control elements, which play a pivotal role. We have designed a genome-wide oligonucleotide-based DNA microarray for Pseudomonas putida KT2440. In combination with real-time reverse transcription polymerase chain reaction (RT-PCR), we have used it to analyse the expression pattern of the genes encoding the RNA polymerase subunits (the core enzyme and the 24 sigma factors), and various proteins involved in global regulation (Crc, Lrp, Fur, Anr, Fis, CsrA, IHF, HupA, HupB, HupN, BipA and several MvaT-like proteins), during the shift from exponential growth in rich medium into starvation and stress brought about by the entry into stationary phase. Expression of the genes encoding the RNA polymerase core and the vegetative sigma factor decreased in stationary phase, while that of sigma(S) increased. Data obtained for sigma(N), sigma(H), FliA and for the 19 extracytoplasmic function (ECF)-like sigma factors suggested that their mRNA levels change little upon entry into stationary phase. Expression of Crc, BipA, Fis, HupB, HupN and the MvaT-like protein PP3693 decreased in stationary phase, while that of HupA and the MvaT-like protein PP3765 increased significantly. Expression of IHF was indicative of post-transcriptional control. These results provide the first global study of the expression of the transcriptional machinery through the exponential stationary-phase shift in P. putida.
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Affiliation(s)
- Luis Yuste
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 - Madrid, Spain
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34
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Pelosi L, Kühn L, Guetta D, Garin J, Geiselmann J, Lenski RE, Schneider D. Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli. Genetics 2006; 173:1851-69. [PMID: 16702438 PMCID: PMC1569701 DOI: 10.1534/genetics.105.049619] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2005] [Accepted: 05/11/2006] [Indexed: 02/06/2023] Open
Abstract
Twelve populations of Escherichia coli evolved in and adapted to a glucose-limited environment from a common ancestor. We used two-dimensional protein electrophoresis to compare two evolved clones, isolated from independently derived populations after 20,000 generations. Exceptional parallelism was detected. We compared the observed changes in protein expression profiles with previously characterized global transcription profiles of the same clones; this is the first time such a comparison has been made in an evolutionary context where these changes are often quite subtle. The two methodologies exhibited some remarkable similarities that highlighted two different levels of parallel regulatory changes that were beneficial during the evolution experiment. First, at the higher level, both methods revealed extensive parallel changes in the same global regulatory network, reflecting the involvement of beneficial mutations in genes that control the ppGpp regulon. Second, both methods detected expression changes of identical gene sets that reflected parallel changes at a lower level of gene regulation. The protein profiles led to the discovery of beneficial mutations affecting the malT gene, with strong genetic parallelism across independently evolved populations. Functional and evolutionary analyses of these mutations revealed parallel phenotypic decreases in the maltose regulon expression and a high level of polymorphism at this locus in the evolved populations.
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Affiliation(s)
- Ludovic Pelosi
- Laboratoire Adaptation et Pathogénie des Microorganismes, Université Joseph Fourier, Grenoble, France
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35
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Blot N, Mavathur R, Geertz M, Travers A, Muskhelishvili G. Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome. EMBO Rep 2006; 7:710-5. [PMID: 16799466 PMCID: PMC1500834 DOI: 10.1038/sj.embor.7400729] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Revised: 04/10/2006] [Accepted: 05/09/2006] [Indexed: 11/09/2022] Open
Abstract
Regulation of cellular growth implies spatiotemporally coordinated programmes of gene transcription. A central question, therefore, is how global transcription is coordinated in the genome. The growth of the unicellular organism Escherichia coli is associated with changes in both the global superhelicity modulated by cellular topoisomerase activity and the relative proportions of the abundant DNA-architectural chromatin proteins. Using a DNA-microarray-based approach that combines mutations in the genes of two important chromatin proteins with induced changes of DNA superhelicity, we demonstrate that genomic transcription is tightly associated with the spatial distribution of supercoiling sensitivity, which in turn depends on chromatin proteins. We further demonstrate that essential metabolic pathways involved in the maintenance of growth respond distinctly to changes of superhelicity. We infer that a homeostatic mechanism organizing the supercoiling sensitivity is coordinating the growth-phase-dependent transcription of the genome.
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Affiliation(s)
- Nicolas Blot
- International University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ramesh Mavathur
- International University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Marcel Geertz
- International University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | - Georgi Muskhelishvili
- International University Bremen, Campus Ring 1, 28759 Bremen, Germany
- Tel: +49 421 200 3143; Fax: +49 421 200 3249; E-mail:
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36
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Ropers D, de Jong H, Page M, Schneider D, Geiselmann J. Qualitative simulation of the carbon starvation response in Escherichia coli. Biosystems 2006; 84:124-52. [PMID: 16325332 DOI: 10.1016/j.biosystems.2005.10.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Revised: 09/28/2005] [Accepted: 10/04/2005] [Indexed: 10/25/2022]
Abstract
In case of nutritional stress, like carbon starvation, Escherichia coli cells abandon their exponential-growth state to enter a more resistant, non-growth state called stationary phase. This growth-phase transition is controlled by a genetic regulatory network integrating various environmental signals. Although E. coli is a paradigm of the bacterial world, it is little understood how its response to carbon starvation conditions emerges from the interactions between the different components of the regulatory network. Using a qualitative method that is able to overcome the current lack of quantitative data on kinetic parameters and molecular concentrations, we model the carbon starvation response network and simulate the response of E. coli cells to carbon deprivation. This allows us to identify essential features of the transition between exponential and stationary phase and to make new predictions on the qualitative system behavior following a carbon upshift.
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Affiliation(s)
- Delphine Ropers
- Institut National de Recherche en Informatique et en Automatique (INRIA), Unité de recherche Rhône-Alpes, 655 Avenue de l 'Europe, Montbonnot, 38334 Saint Ismier Cedex, France.
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37
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Feldman-Cohen LS, Shao Y, Meinhold D, Miller C, Colón W, Osuna R. Common and variable contributions of Fis residues to high-affinity binding at different DNA sequences. J Bacteriol 2006; 188:2081-95. [PMID: 16513738 PMCID: PMC1428148 DOI: 10.1128/jb.188.6.2081-2095.2006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fis is a nucleoid-associated protein that interacts with poorly related DNA sequences with a high degree of specificity. A difference of more than 3 orders of magnitude in apparent Kd values was observed between specific (Kd, approximately 1 to 4 nM) and nonspecific (Kd, approximately 4 microM) DNA binding. To examine the contributions of Fis residues to the high-affinity binding at different DNA sequences, 13 alanine substitutions were generated in or near the Fis helix-turn-helix DNA binding motif, and the resulting proteins were purified. In vitro binding assays at three different Fis sites (fis P II, hin distal, and lambda attR) revealed that R85, T87, R89, K90, and K91 played major roles in high-affinity DNA binding and that R85, T87, and K90 were consistently vital for binding to all three sites. Other residues made variable contributions to binding, depending on the binding site. N84 was required only for binding to the lambda attR Fis site, and the role of R89 was dramatically altered by the lambda attR DNA flanking sequence. The effects of Fis mutations on fis P II or hin distal site binding in vitro generally correlated with their abilities to mediate fis P repression or DNA inversion in vivo, demonstrating that the in vitro DNA-binding effects are relevant in vivo. The results suggest that while Fis is able to recognize a minimal common set of DNA sequence determinants at different binding sites, it is also equipped with a number of residues that contribute to the binding strength, some of which play variable roles.
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Affiliation(s)
- Leah S Feldman-Cohen
- Department of Chemistry, College of Staten Island and Macromolecular Assemblies Institute of the City, University of New York, Staten Island 10314, USA
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38
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Walker KA, Mallik P, Pratt TS, Osuna R. The Escherichia coli Fis promoter is regulated by changes in the levels of its transcription initiation nucleotide CTP. J Biol Chem 2004; 279:50818-28. [PMID: 15385561 DOI: 10.1074/jbc.m406285200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Expression of the Escherichia coli nucleoid-associated protein Fis (factor for inversion stimulation) is controlled at the transcriptional level in accordance with the nutritional availability. It is highly expressed during early logarithmic growth phase in cells growing in rich medium but poorly expressed in late logarithmic and stationary phase. However, fis mRNA expression is prolonged at high levels throughout the logarithmic and early stationary phase when the preferred transcription initiation site (+1C) is replaced with A or G, indicating that initiation with CTP is a required component of the regulation pattern. We show that RNA polymerase-fis promoter complexes are short lived and that transcription is stimulated over 20-fold from linear or supercoiled DNA if CTP is present during formation of initiation complexes, which serves to stabilize these complexes. Use of fis promoter fusions to lacZ indicated that fis promoter transcription is sensitive to the intracellular pool of the predominant initiating NTP. Growth conditions resulting in increases in CTP pools also result in corresponding increases in fis mRNA levels. Measurements of NTP pools performed throughout the growth of the bacterial culture in rich medium revealed a dramatic increase in all four NTP levels during the transition from stationary to logarithmic growth phase, followed by reproducible oscillations in their levels during logarithmic growth, which later decrease during the transition from logarithmic to stationary phase. In particular, CTP pools fluctuate in a manner consistent with a role in regulating fis expression. These observations support a model whereby fis expression is subject to regulation by the availability of its initiating NTP.
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MESH Headings
- Base Sequence
- Blotting, Northern
- Chromatography, Thin Layer
- Cytidine/chemistry
- Cytidine Triphosphate/chemistry
- DNA Primers/chemistry
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- DNA-Directed RNA Polymerases/chemistry
- DNA-Directed RNA Polymerases/metabolism
- Dose-Response Relationship, Drug
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Factor For Inversion Stimulation Protein/genetics
- Gene Expression Regulation, Enzymologic
- Kinetics
- Lac Operon
- Models, Biological
- Models, Genetic
- Molecular Sequence Data
- Oscillometry
- Plasmids/metabolism
- Promoter Regions, Genetic
- RNA, Messenger/metabolism
- Salts/pharmacology
- Time Factors
- Transcription, Genetic
- beta-Galactosidase/metabolism
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Affiliation(s)
- Kimberly A Walker
- Department of Biological Sciences, University at Albany, Albany, New York 12222, USA
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39
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Owens RM, Pritchard G, Skipp P, Hodey M, Connell SR, Nierhaus KH, O'Connor CD. A dedicated translation factor controls the synthesis of the global regulator Fis. EMBO J 2004; 23:3375-85. [PMID: 15297874 PMCID: PMC514516 DOI: 10.1038/sj.emboj.7600343] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Accepted: 07/05/2004] [Indexed: 11/09/2022] Open
Abstract
BipA is a highly conserved protein with global regulatory properties in Escherichia coli. We show here that it functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of elongation factor G and has a GTPase activity that is sensitive to high GDP:GTP ratios and stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion. We propose a model in which BipA destabilizes unusually strong interactions between the 5' untranslated region of fis mRNA and the ribosome. Since BipA spans phylogenetic domains, transcript-selective translational control for the 'fast-track' expression of specific mRNAs may have wider significance.
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Affiliation(s)
- Róisín M Owens
- School of Biological Sciences, University of Southampton, Southampton, UK
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | - Gareth Pritchard
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Paul Skipp
- School of Biological Sciences, University of Southampton, Southampton, UK
- Centre for Proteomic Research, University of Southampton, Southampton, UK
| | - Michelle Hodey
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Sean R Connell
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | | | - C David O'Connor
- School of Biological Sciences, University of Southampton, Southampton, UK
- Centre for Proteomic Research, University of Southampton, Southampton, UK
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40
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Kelly A, Goldberg MD, Carroll RK, Danino V, Hinton JCD, Dorman CJ. A global role for Fis in the transcriptional control of metabolism and type III secretion in Salmonella enterica serovar Typhimurium. Microbiology (Reading) 2004; 150:2037-2053. [PMID: 15256548 DOI: 10.1099/mic.0.27209-0] [Citation(s) in RCA: 165] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fis is a key DNA-binding protein involved in nucleoid organization and modulation of many DNA transactions, including transcription in enteric bacteria. The regulon of genes whose expression is influenced by Fis inSalmonella entericaserovar Typhimurium (S. typhimurium) has been defined by DNA microarray analysis. These data suggest that Fis plays a central role in coordinating the expression of both metabolic and type III secretion factors. The genes that were most strongly up-regulated by Fis were those involved in virulence and located in the pathogenicity islands SPI-1, SPI-2, SPI-3 and SPI-5. Similarly, motility and flagellar genes required Fis for full expression. This was shown to be a direct effect as purified Fis protein bound to the promoter regions of representative flagella and SPI-2 genes. Genes contributing to aspects of metabolism known to assist the bacterium during survival in the mammalian gut were also Fis-regulated, usually negatively. This category included components of metabolic pathways for propanediol utilization, biotin synthesis, vitamin B12transport, fatty acids and acetate metabolism, as well as genes for the glyoxylate bypass of the tricarboxylic acid cycle. Genes found to be positively regulated by Fis included those for ethanolamine utilization. The data reported reveal the central role played by Fis in coordinating the expression of both housekeeping and virulence factors required byS. typhimuriumduring life in the gut lumen or during systemic infection of host cells.
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Affiliation(s)
- Arlene Kelly
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Martin D Goldberg
- Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Ronan K Carroll
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Vittoria Danino
- Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Jay C D Hinton
- Molecular Microbiology Group, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, UK
| | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Ireland
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41
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Mallik P, Pratt TS, Beach MB, Bradley MD, Undamatla J, Osuna R. Growth phase-dependent regulation and stringent control of fis are conserved processes in enteric bacteria and involve a single promoter (fis P) in Escherichia coli. J Bacteriol 2004; 186:122-35. [PMID: 14679232 PMCID: PMC303451 DOI: 10.1128/jb.186.1.122-135.2004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The intracellular concentration of the Escherichia coli factor for inversion stimulation (Fis), a global regulator of transcription and a facilitator of certain site-specific DNA recombination events, varies substantially in response to changes in the nutritional environment and growth phase. Under conditions of nutritional upshift, fis is transiently expressed at very high levels, whereas under induced starvation conditions, fis is repressed by stringent control. We show that both of these regulatory processes operate on the chromosomal fis genes of the enterobacteria Klebsiella pneumoniae, Serratia marcescens, Erwinia carotovora, and Proteus vulgaris, strongly suggesting that the physiological role of Fis is closely tied to its transcriptional regulation in response to the nutritional environment. These transcriptional regulatory processes were previously shown to involve a single promoter (fis P) preceding the fis operon in E. coli. Recent work challenged this notion by presenting evidence from primer extension assays which appeared to indicate that there are multiple promoters upstream of fis P that contribute significantly to the expression and regulation of fis in E. coli. Thus, a rigorous analysis of the fis promoter region was conducted to assess the contribution of such additional promoters. However, our data from primer extension analysis, S1 nuclease mapping, beta-galactosidase assays, and in vitro transcription analysis all indicate that fis P is the sole E. coli fis promoter in vivo and in vitro. We further show how certain conditions used in the primer extension reactions can generate artifacts resulting from secondary annealing events that are the likely source of incorrect assignment of additional fis promoters.
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Affiliation(s)
- Prabhat Mallik
- Department of Biological Sciences, University at Albany, SUNY, Albany, New York 12222, USA
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42
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Zhang K, Showalter M, Revollo J, Hsu FF, Turk J, Beverley SM. Sphingolipids are essential for differentiation but not growth in Leishmania. EMBO J 2004; 22:6016-26. [PMID: 14609948 PMCID: PMC275442 DOI: 10.1093/emboj/cdg584] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sphingolipids (SLs) play critical roles in eukaryotic cells in the formation of lipid rafts, membrane trafficking, and signal transduction. Here we created a SL null mutant in the protozoan parasite Leishmania major through targeted deletion of the key de novo biosynthetic enzyme serine palmitoyltransferase subunit 2 (SPT2). Although SLs are typically essential, spt2- Leishmania were viable, yet were completely deficient in de novo sphingolipid synthesis, and lacked inositol phosphorylceramides and other SLs. Remarkably, spt2- parasites maintained 'lipid rafts' as defined by Triton X-100 detergent resistant membrane formation. Upon entry to stationary phase spt2- failed to differentiate to infective metacyclic parasites and died instead. Death occurred not by apoptosis or changes in metacyclic gene expression, but from catastrophic problems leading to accumulation of small vesicles characteristic of the multivesicular body/multivesicular tubule network. Stage specificity may reflect changes in membrane structure as well as elevated demands in vesicular trafficking required for parasite remodeling during differentiation. We suggest that SL-deficient Leishmania provide a useful biological setting for tests of essential SL enzymes in other organisms where SL perturbation is lethal.
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Affiliation(s)
- Kai Zhang
- Department of Molecular Microbiology, Box 8230, Washington University School of Medicine, 660 S. Euclid Ave, St Louis, MO 63110, USA
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43
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Auner H, Buckle M, Deufel A, Kutateladze T, Lazarus L, Mavathur R, Muskhelishvili G, Pemberton I, Schneider R, Travers A. Mechanism of transcriptional activation by FIS: role of core promoter structure and DNA topology. J Mol Biol 2003; 331:331-44. [PMID: 12888342 DOI: 10.1016/s0022-2836(03)00727-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Escherichia coli DNA architectural protein FIS activates transcription from stable RNA promoters on entry into exponential growth and also reduces the level of negative supercoiling. Here we show that such a reduction decreases the activity of the tyrT promoter but that activation by FIS rescues tyrT transcription at non-optimal superhelical densities. Additionally we show that three different "up" mutations in the tyrT core promoter either abolish or reduce the dependence of tyrT transcription on both high negative superhelicity and FIS in vivo and infer that the specific sequence organisation of the core promoter couples the control of transcription initiation by negative superhelicity and FIS. In vitro all the mutations potentiate FIS-independent untwisting of the -10 region while at the wild-type promoter FIS facilitates this step. We propose that this untwisting is a crucial limiting step in the initiation of tyrT RNA synthesis. The tyrT core promoter structure is thus optimised to combine high transcriptional activity with acute sensitivity to at least three major independent regulatory inputs: negative superhelicity, FIS and ppGpp.
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Affiliation(s)
- Helge Auner
- Institut für Genetik und Mikrobiologie, LMU, München, Maria-Ward-Str 1a, 80638, München, Germany
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44
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Shin D, Cho N, Heu S, Ryu S. Selective regulation of ptsG expression by Fis. Formation of either activating or repressing nucleoprotein complex in response to glucose. J Biol Chem 2003; 278:14776-81. [PMID: 12588863 DOI: 10.1074/jbc.m213248200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription of ptsG encoding glucose-specific permease, enzyme IICB(Glc), in Escherichia coli is initiated from two promoters, P1 and P2. ptsG transcription is repressed by Mlc, a glucose-inducible regulator of carbohydrate metabolism. The regulation of ptsG P1 transcription is also under positive control by cyclic AMP receptor protein and cyclic AMP complex (CRP.cAMP) as observed in other Mlc regulon. We report here that Fis, one of the nucleoid-associated proteins, plays a key role in glucose induction of Mlc regulon. ptsG transcription was induced when wild-type cells were grown in the presence of glucose. However, in a fis mutant, the basal level of ptsG transcription was higher but decreased when cells were grown in the presence of glucose, which implies the possibility of regulatory interactions among Fis, Mlc, and CRP.cAMP. Footprinting experiments with various probes and transcription assays revealed that Fis assists both Mlc repression and CRP.cAMP activation of ptsG P1 through the formation of Fis.CRP.Mlc or Fis.CRP nucleoprotein complexes at ptsG P1 promoter depending on the availability of glucose in the growth medium. ptsG P2 transcription was inhibited by Fis and Mlc. Tighter Mlc repression and enhanced CRP.cAMP activation of ptsG P1 by Fis enable cells to regulate Mlc regulon efficiently by selectively controlling the concentration of enzyme IICB(Glc) that modulates Mlc activity.
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Affiliation(s)
- Dongwoo Shin
- Department of Food Science and Technology, School of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National University, Suwon 441-744, Korea
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45
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Hobart SA, Ilin S, Moriarty DF, Osuna R, Colón W. Equilibrium denaturation studies of the Escherichia coli factor for inversion stimulation: implications for in vivo function. Protein Sci 2002; 11:1671-80. [PMID: 12070319 PMCID: PMC2373661 DOI: 10.1110/ps.5050102] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2001] [Revised: 04/04/2002] [Accepted: 04/10/2002] [Indexed: 10/14/2022]
Abstract
The Factor for Inversion Stimulation (FIS) is a dimeric DNA binding protein found in enteric bacteria that is involved in various cellular processes, including stimulation of certain specialized DNA recombination events and transcription regulation of a large number of genes. The intracellular FIS concentration, when cells are grown in rich media, varies dramatically during the early logarithmic growth phase. Its broad range of concentrations could potentially affect the nature of its quaternary structure, which in turn, could affect its ability to function in vivo. Thus, we examined the stability of FIS homodimers under a wide range of concentrations relevant to in vivo expression levels. Its urea-induced equilibrium denaturation was monitored by far- and near-UV circular dichroism (CD), tyrosine fluorescence, and tyrosine fluorescence anisotropy. The denaturation transitions obtained were concentration-dependent and showed similar midpoints (C(m)) and m values, suggesting a two-state denaturation process involving the native dimer and unfolded monomers (N(2) <--> 2U). The DeltaG(H(2)O) for the unfolding of FIS determined from global and individual curve fitting was 14.2 kcal/mole. At concentrations <9 microM, the FIS dimer began to dissociate, as noted by the change in CD signal and size-exclusion high-pressure liquid chromatography retention times and peak width. The estimated dimer dissociation constant based on the CD and size-exclusion chromatography data is in the micromolar range, resulting in a DeltaG(H(2)O) of at least 5 kcal/mole less than that calculated from the urea denaturation data. This discrepancy suggests a deviation from a two-state denaturation model, perhaps due to a marginally stable monomeric intermediate. These observations have implications for the stability and function of FIS in vivo.
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Affiliation(s)
- Sarah A Hobart
- Rensselaer Polytechnic Institute, Department of Chemistry, 110 8th Street, Troy, NY 12180, USA
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46
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Nasser W, Rochman M, Muskhelishvili G. Transcriptional regulation of fis operon involves a module of multiple coupled promoters. EMBO J 2002; 21:715-24. [PMID: 11847119 PMCID: PMC125868 DOI: 10.1093/emboj/21.4.715] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The transcription of the Escherichia coli fis gene is strongly activated during the outgrowth of cells from stationary phase. The high activity of the promoter of the fis operon requires the transcription factor IHF. Previously, we identified a divergent promoter, div, located upstream of the fis promoter. In this study we demonstrate that at least two additional promoters, designated fis P2 and fis P3, are located in the control region of the fis operon. The fis P2 and div promoters overlap completely, whereas fis P3 and div P are arranged as face-to-face divergent promoters. We show that the div and the tandem fis promoters counterbalance each other, such that their activity is kept on a lower than potentially attainable level. Furthermore, we demonstrate an unusual activation mechanism by IHF, involving a coordinated shift in the balance of promoter activities. We infer that these coupled promoters represent a regulatory module and propose a novel "dynamic balance" mechanism involved in the transcriptional control of the fis operon.
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Affiliation(s)
- William Nasser
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
Present address: UMG, UMR-CNRS5122, INSA bât Louis Pasteur, 11 Av. Jean Cappelle, F-69621 Villeurbanne Cedex, France Present address: Department of Cellular Biochemistry, The Hebrew University-Hadassah Medical School, Jerusalem 90101, Israel Corresponding author e-mail:
| | - Mark Rochman
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
Present address: UMG, UMR-CNRS5122, INSA bât Louis Pasteur, 11 Av. Jean Cappelle, F-69621 Villeurbanne Cedex, France Present address: Department of Cellular Biochemistry, The Hebrew University-Hadassah Medical School, Jerusalem 90101, Israel Corresponding author e-mail:
| | - Georgi Muskhelishvili
- Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany
Present address: UMG, UMR-CNRS5122, INSA bât Louis Pasteur, 11 Av. Jean Cappelle, F-69621 Villeurbanne Cedex, France Present address: Department of Cellular Biochemistry, The Hebrew University-Hadassah Medical School, Jerusalem 90101, Israel Corresponding author e-mail:
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47
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Falconi M, Prosseda G, Giangrossi M, Beghetto E, Colonna B. Involvement of FIS in the H-NS-mediated regulation of virF gene of Shigella and enteroinvasive Escherichia coli. Mol Microbiol 2001; 42:439-52. [PMID: 11703666 DOI: 10.1046/j.1365-2958.2001.02646.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The mechanism of pathogenicity in Shigella and enteroinvasive Escherichia coli (EIEC) requires the co-ordinated expression of several genes located on both the virulence plasmid and the chromosome. We found that cells lacking a functional FIS protein (factor for inversion stimulation) are partially impaired in expressing the virulence genes and that full expression is totally restored when Shigella wild-type fis gene is offered in trans. We also identified virF, among the virulence genes, as a target of FIS-mediated activation and showed that FIS binds to four specific sites in the promoter region of virF. Previous studies have demonstrated that the expression of VirF, the first positive activator of a multistep regulatory cascade, is subject to temperature-dependent regulation by H-NS, one of the main nucleoid-associated proteins. We now demonstrate that two of the four FIS sites overlap one of the two H-NS sites responsible for thermoregulation (H-NS site I). FIS was found to exercise a direct positive transcriptional control at permissive temperature (37 degrees C), when H-NS fails to repress virF, as well as an indirect effect by partially counteracting H-NS inhibition at the transition temperature (32 degrees C). Our data indicate that FIS may be relevant for the rapid increase in virF expression after penetration of bacteria into the host.
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Affiliation(s)
- M Falconi
- Laboratorio di Genetica, Dipartimento di Biologia MCA, Università di Camerino, 62032 Camerino (MC), Italy
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48
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Goldberg MD, Johnson M, Hinton JC, Williams PH. Role of the nucleoid-associated protein Fis in the regulation of virulence properties of enteropathogenic Escherichia coli. Mol Microbiol 2001; 41:549-59. [PMID: 11532124 DOI: 10.1046/j.1365-2958.2001.02526.x] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Virulence gene expression in enteropathogenic Escherichia coli (EPEC) is governed by a combination of environmental factors and virulence regulators. These factors control the expression of the bundle-forming pili (BFP), intimin, the type III secretion apparatus and the secreted proteins EspA, EspB, EspD and Tir. Expression of the bfp genes occurs for a short period in early exponential phase during growth in tissue culture medium. The nucleoid-associated regulator protein, Fis, is also expressed transiently during this period. To determine whether Fis was responsible for the growth phase-dependent expression of bfp, fis was deleted from the EPEC strain E2348/69S. Paradoxically, the Delta fis mutant retained the ability to colonize HEp-2 cells in a characteristic localized adherence pattern, and Fis was found negatively to regulate the expression of BFP. However, the Delta fis mutant failed to induce the accretion of filamentous actin, which is associated with attaching and effacing lesions. Using a combination of Western blotting and a novel multiplex primer extension assay (MPEA), we showed that, although the expression of intimin and Tir was not affected, transcription of the LEE4 operon encoding espADB and the virulence activator, Ler, were found to be Fis dependent.
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MESH Headings
- Adhesins, Bacterial/genetics
- Adhesins, Bacterial/metabolism
- Blotting, Western
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Escherichia coli/metabolism
- Escherichia coli/pathogenicity
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Factor For Inversion Stimulation Protein
- Fimbriae, Bacterial/genetics
- Fimbriae, Bacterial/metabolism
- Fluorescent Antibody Technique, Indirect
- Gene Expression Regulation, Bacterial
- Humans
- Integration Host Factors
- Mutation/genetics
- Operon/genetics
- Phenotype
- RNA, Bacterial/analysis
- RNA, Bacterial/genetics
- Tumor Cells, Cultured
- Virulence
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Affiliation(s)
- M D Goldberg
- Department of Microbiology and Immunology, School of Medicine, Maurice Shock Building, PO Box 138, University Road, Leicester LE1 9HN, UK.
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49
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Nasser W, Schneider R, Travers A, Muskhelishvili G. CRP modulates fis transcription by alternate formation of activating and repressing nucleoprotein complexes. J Biol Chem 2001; 276:17878-86. [PMID: 11279109 DOI: 10.1074/jbc.m100632200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The DNA architectural proteins FIS and CRP are global regulators of transcription in Escherichia coli involved in the adjustment of cellular metabolism to varying growth conditions. We have previously demonstrated that FIS modulates the expression of the crp gene by functioning as its transcriptional repressor. Here we show that in turn, CRP is required to maintain the growth phase pattern of fis expression. We demonstrate the existence of a divergent promoter in the fis regulatory region, which reduces transcription of the fis promoter. In the absence of FIS, CRP activates fis transcription, thereby displacing the polymerase from the divergent promoter, whereas together FIS and CRP synergistically repress fis gene expression. These results provide evidence for a direct cross-talk between global regulators of cellular transcription during the growth phase. This cross-talk is manifested in alternate formation of functional nucleoprotein complexes exerting either activating or repressing effects on transcription.
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Affiliation(s)
- W Nasser
- Institut für Genetik und Mikrobiologie, Ludwig-Maximilians-Univesitaet, Maria-Ward-Strasse 1a, 80638 München, Germany
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50
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Prüss BM, Liu X, Hendrickson W, Matsumura P. FlhD/FlhC-regulated promoters analyzed by gene array and lacZ gene fusions. FEMS Microbiol Lett 2001; 197:91-7. [PMID: 11287152 DOI: 10.1111/j.1574-6968.2001.tb10588.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The Escherichia coli transcriptional regulatory complex FlhD/FlhC, initially identified as a flagella-specific activator, is a global regulator involved in many cellular processes. Using gene arrays, lacZ gene fusions and enzyme assays, eight new targets of FlhD/FlhC were recognized. These are the transporter for galactose (MglBAC), the rod-shape determination proteins (MreBCD), malate dehydrogenase, and several enzymes involved in anaerobic respiration (glycerol 3-phosphate dehydrogenase, GlpABC; periplasmic nitrate reductase, NapFAGHBC; nitrite reductase, NrfABCDEFG; dimethyl sulfoxide reductase, DmsABC; and the modulator for hydrogenases, HydNHypF).
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Affiliation(s)
- B M Prüss
- Department of Microbiology and Immunology (M/C 790), College of Medicine, University of Illinois at Chicago, E-603 Medical Sciences Building, 835 S. Wolcott, Chicago, IL 60612-7344, USA.
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