1
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Kopkowski PW, Zhang Z, Saier MH. The effect of DNA-binding proteins on insertion sequence element transposition upstream of the bgl operon in Escherichia coli. Front Microbiol 2024; 15:1388522. [PMID: 38666260 PMCID: PMC11043490 DOI: 10.3389/fmicb.2024.1388522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The bglGFB operon in Escherichia coli K-12 strain BW25113, encoding the proteins necessary for the uptake and metabolism of β-glucosides, is normally not expressed. Insertion of either IS1 or IS5 upstream of the bgl promoter activates expression of the operon only when the cell is starving in the presence of a β-glucoside, drastically increasing transcription and allowing the cell to survive and grow using this carbon source. Details surrounding the exact mechanism and regulation of the IS insertional event remain unclear. In this work, the role of several DNA-binding proteins in how they affect the rate of insertion upstream of bgl are examined via mutation assays and protocols measuring transcription. Both Crp and IHF exert a positive effect on insertional Bgl+ mutations when present, active, and functional in the cell. Our results characterize IHF's effect in conjunction with other mutations, show that IHF's effect on IS insertion into bgl also affects other operons, and indicate that it may exert its effect by binding to and altering the DNA conformation of IS1 and IS5 in their native locations, rather than by directly influencing transposase gene expression. In contrast, the cAMP-CRP complex acts directly upon the bgl operon by binding upstream of the promoter, presumably altering local DNA into a conformation that enhances IS insertion.
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Affiliation(s)
| | - Zhongge Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Milton H. Saier
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
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2
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Keshavam CC, Naz S, Gupta A, Sanyal P, Kochar M, Gangwal A, Sangwan N, Kumar N, Tyagi E, Goel S, Singh NK, Sowpati DT, Khare G, Ganguli M, Raze D, Locht C, Basu-Modak S, Gupta M, Nandicoori VK, Singh Y. The heparin-binding hemagglutinin protein of Mycobacterium tuberculosis is a nucleoid-associated protein. J Biol Chem 2023; 299:105364. [PMID: 37865319 PMCID: PMC10665949 DOI: 10.1016/j.jbc.2023.105364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023] Open
Abstract
Nucleoid-associated proteins (NAPs) regulate multiple cellular processes such as gene expression, virulence, and dormancy throughout bacterial species. NAPs help in the survival and adaptation of Mycobacterium tuberculosis (Mtb) within the host. Fourteen NAPs have been identified in Escherichia coli; however, only seven NAPs are documented in Mtb. Given its complex lifestyle, it is reasonable to assume that Mtb would encode for more NAPs. Using bioinformatics tools and biochemical experiments, we have identified the heparin-binding hemagglutinin (HbhA) protein of Mtb as a novel sequence-independent DNA-binding protein which has previously been characterized as an adhesion molecule required for extrapulmonary dissemination. Deleting the carboxy-terminal domain of HbhA resulted in a complete loss of its DNA-binding activity. Atomic force microscopy showed HbhA-mediated architectural modulations in the DNA, which may play a regulatory role in transcription and genome organization. Our results showed that HbhA colocalizes with the nucleoid region of Mtb. Transcriptomics analyses of a hbhA KO strain revealed that it regulates the expression of ∼36% of total and ∼29% of essential genes. Deletion of hbhA resulted in the upregulation of ∼73% of all differentially expressed genes, belonging to multiple pathways suggesting it to be a global repressor. The results show that HbhA is a nonessential NAP regulating gene expression globally and acting as a plausible transcriptional repressor.
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Affiliation(s)
| | - Saba Naz
- Department of Zoology, University of Delhi, Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Aanchal Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Priyadarshini Sanyal
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB) Campus, Hyderabad, India
| | - Manisha Kochar
- Department of Zoology, University of Delhi, Delhi, India; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | | | - Nitika Sangwan
- Department of Zoology, University of Delhi, Delhi, India
| | - Nishant Kumar
- Department of Zoology, University of Delhi, Delhi, India
| | - Ekta Tyagi
- Department of Zoology, University of Delhi, Delhi, India
| | - Simran Goel
- Department of Zoology, University of Delhi, Delhi, India
| | | | | | - Garima Khare
- Department of Biochemistry, University of Delhi South Campus, New Delhi, India
| | - Munia Ganguli
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Dominique Raze
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Centre for Infection and Immunity of Lille, Lille, France
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Centre for Infection and Immunity of Lille, Lille, France
| | | | - Meetu Gupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
| | - Vinay Kumar Nandicoori
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB) Campus, Hyderabad, India; National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India.
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, India; Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi, India.
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3
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Rashid FZM, Crémazy FGE, Hofmann A, Forrest D, Grainger DC, Heermann DW, Dame RT. The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli. Nat Commun 2023; 14:7478. [PMID: 37978176 PMCID: PMC10656529 DOI: 10.1038/s41467-023-43322-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Nucleoid associated proteins (NAPs) maintain the architecture of bacterial chromosomes and regulate gene expression. Thus, their role as transcription factors may involve three-dimensional chromosome re-organisation. While this model is supported by in vitro studies, direct in vivo evidence is lacking. Here, we use RT-qPCR and 3C-qPCR to study the transcriptional and architectural profiles of the H-NS (histone-like nucleoid structuring protein)-regulated, osmoresponsive proVWX operon of Escherichia coli at different osmolarities and provide in vivo evidence for transcription regulation by NAP-mediated chromosome re-modelling in bacteria. By consolidating our in vivo investigations with earlier in vitro and in silico studies that provide mechanistic details of how H-NS re-models DNA in response to osmolarity, we report that activation of proVWX in response to a hyperosmotic shock involves the destabilization of H-NS-mediated bridges anchored between the proVWX downstream and upstream regulatory elements (DRE and URE), and between the DRE and ygaY that lies immediately downstream of proVWX. The re-establishment of these bridges upon adaptation to hyperosmolarity represses the operon. Our results also reveal additional structural features associated with changes in proVWX transcript levels such as the decompaction of local chromatin upstream of the operon, highlighting that further complexity underlies the regulation of this model operon. H-NS and H-NS-like proteins are wide-spread amongst bacteria, suggesting that chromosome re-modelling may be a typical feature of transcriptional control in bacteria.
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Affiliation(s)
- Fatema-Zahra M Rashid
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands
| | - Frédéric G E Crémazy
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands
- Laboratoire Infection et Inflammation, INSERM, UVSQ, Université Paris-Saclay, Versailles, 78180, France
| | - Andreas Hofmann
- Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany
| | - David Forrest
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - David C Grainger
- School of Biosciences, University of Birmingham, Edgbaston, B15 2TT, UK
| | - Dieter W Heermann
- Statistical Physics and Theoretical Biophysics, Heidelberg University, Heidelberg, D-69120, Germany
| | - Remus T Dame
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Leiden, 2333CC, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, 2333CC, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, 2333CC, The Netherlands.
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4
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Bdira FB, Erkelens AM, Qin L, Volkov AN, Lippa A, Bowring N, Boyle A, Ubbink M, Dove S, Dame R. Novel anti-repression mechanism of H-NS proteins by a phage protein. Nucleic Acids Res 2021; 49:10770-10784. [PMID: 34520554 PMCID: PMC8501957 DOI: 10.1093/nar/gkab793] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/16/2021] [Accepted: 09/01/2021] [Indexed: 12/17/2022] Open
Abstract
H-NS family proteins, bacterial xenogeneic silencers, play central roles in genome organization and in the regulation of foreign genes. It is thought that gene repression is directly dependent on the DNA binding modes of H-NS family proteins. These proteins form lateral protofilaments along DNA. Under specific environmental conditions they switch to bridging two DNA duplexes. This switching is a direct effect of environmental conditions on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of H-NS proteins. The Pseudomonas lytic phage LUZ24 encodes the protein gp4, which modulates the DNA binding and function of the H-NS family protein MvaT of Pseudomonas aeruginosa. However, the mechanism by which gp4 affects MvaT activity remains elusive. In this study, we show that gp4 specifically interferes with the formation and stability of the bridged MvaT-DNA complex. Structural investigations suggest that gp4 acts as an 'electrostatic zipper' between the oppositely charged domains of MvaT protomers, and stabilizes a structure resembling their 'half-open' conformation, resulting in relief of gene silencing and adverse effects on P. aeruginosa growth. The ability to control H-NS conformation and thereby its impact on global gene regulation and growth might open new avenues to fight Pseudomonas multidrug resistance.
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Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Amanda M Erkelens
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Liang Qin
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Alexander N Volkov
- VIB-VUB Structural Biology Research Center, Pleinlaan 2, 1050 Brussels, Belgium
- Jean Jeener NMR Centre, VUB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Andrew M Lippa
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas Bowring
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Aimee L Boyle
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Simon L Dove
- Boston Children's Hospital, Division of Infectious Diseases, Harvard Medical School, Boston, MA 02115, USA
| | - Remus T Dame
- Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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5
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Son B, Patterson-West J, Arroyo-Mendoza M, Ramachandran R, Iben J, Zhu J, Rao V, Dimitriadis E, Hinton D. A phage-encoded nucleoid associated protein compacts both host and phage DNA and derepresses H-NS silencing. Nucleic Acids Res 2021; 49:9229-9245. [PMID: 34365505 PMCID: PMC8450097 DOI: 10.1093/nar/gkab678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 07/20/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleoid Associated Proteins (NAPs) organize the bacterial chromosome within the nucleoid. The interaction of the NAP H-NS with DNA also represses specific host and xenogeneic genes. Previously, we showed that the bacteriophage T4 early protein MotB binds to DNA, co-purifies with H-NS/DNA, and improves phage fitness. Here we demonstrate using atomic force microscopy that MotB compacts the DNA with multiple MotB proteins at the center of the complex. These complexes differ from those observed with H-NS and other NAPs, but resemble those formed by the NAP-like proteins CbpA/Dps and yeast condensin. Fluorescent microscopy indicates that expression of motB in vivo, at levels like that during T4 infection, yields a significantly compacted nucleoid containing MotB and H-NS. motB overexpression dysregulates hundreds of host genes; ∼70% are within the hns regulon. In infected cells overexpressing motB, 33 T4 late genes are expressed early, and the T4 early gene repEB, involved in replication initiation, is up ∼5-fold. We postulate that MotB represents a phage-encoded NAP that aids infection in a previously unrecognized way. We speculate that MotB-induced compaction may generate more room for T4 replication/assembly and/or leads to beneficial global changes in host gene expression, including derepression of much of the hns regulon.
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Affiliation(s)
- Bokyung Son
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Patterson-West
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Melissa Arroyo-Mendoza
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Revathy Ramachandran
- Laboratory of Biochemistry and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James R Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jingen Zhu
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Venigalla Rao
- Department of Biology, The Catholic University of America, Washington, DC, USA
| | - Emilios K Dimitriadis
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Deborah M Hinton
- Gene Expression and Regulation Section, Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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6
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Shen BA, Landick R. Transcription of Bacterial Chromatin. J Mol Biol 2019; 431:4040-4066. [PMID: 31153903 PMCID: PMC7248592 DOI: 10.1016/j.jmb.2019.05.041] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/22/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Abstract
Decades of research have probed the interplay between chromatin (genomic DNA associated with proteins and RNAs) and transcription by RNA polymerase (RNAP) in all domains of life. In bacteria, chromatin is compacted into a membrane-free region known as the nucleoid that changes shape and composition depending on the bacterial state. Transcription plays a key role in both shaping the nucleoid and organizing it into domains. At the same time, chromatin impacts transcription by at least five distinct mechanisms: (i) occlusion of RNAP binding; (ii) roadblocking RNAP progression; (iii) constraining DNA topology; (iv) RNA-mediated interactions; and (v) macromolecular demixing and heterogeneity, which may generate phase-separated condensates. These mechanisms are not mutually exclusive and, in combination, mediate gene regulation. Here, we review the current understanding of these mechanisms with a focus on gene silencing by H-NS, transcription coordination by HU, and potential phase separation by Dps. The myriad questions about transcription of bacterial chromatin are increasingly answerable due to methodological advances, enabling a needed paradigm shift in the field of bacterial transcription to focus on regulation of genes in their native state. We can anticipate answers that will define how bacterial chromatin helps coordinate and dynamically regulate gene expression in changing environments.
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Affiliation(s)
- Beth A Shen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, United States.
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7
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Patterson-West J, Arroyo-Mendoza M, Hsieh ML, Harrison D, Walker MM, Knipling L, Hinton DM. The Bacteriophage T4 MotB Protein, a DNA-Binding Protein, Improves Phage Fitness. Viruses 2018; 10:v10070343. [PMID: 29949907 PMCID: PMC6070864 DOI: 10.3390/v10070343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/15/2018] [Accepted: 06/25/2018] [Indexed: 01/21/2023] Open
Abstract
The lytic bacteriophage T4 employs multiple phage-encoded early proteins to takeover the Escherichia coli host. However, the functions of many of these proteins are not known. In this study, we have characterized the T4 early gene motB, located in a dispensable region of the T4 genome. We show that heterologous production of MotB is highly toxic to E. coli, resulting in cell death or growth arrest depending on the strain and that the presence of motB increases T4 burst size 2-fold. Previous work suggested that motB affects middle gene expression, but our transcriptome analyses of T4 motBam vs. T4 wt infections reveal that only a few late genes are mildly impaired at 5 min post-infection, and expression of early and middle genes is unaffected. We find that MotB is a DNA-binding protein that binds both unmodified host and T4 modified [(glucosylated, hydroxymethylated-5 cytosine, (GHme-C)] DNA with no detectable sequence specificity. Interestingly, MotB copurifies with the host histone-like proteins, H-NS and StpA, either directly or through cobinding to DNA. We show that H-NS also binds modified T4 DNA and speculate that MotB may alter how H-NS interacts with T4 DNA, host DNA, or both, thereby improving the growth of the phage.
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Affiliation(s)
- Jennifer Patterson-West
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
| | - Melissa Arroyo-Mendoza
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
| | - Meng-Lun Hsieh
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
| | - Danielle Harrison
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
| | - Morgan M Walker
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
| | - Leslie Knipling
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
| | - Deborah M Hinton
- Gene Expression and Regulation Section, Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA.
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8
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Structure and function of bacterial H-NS protein. Biochem Soc Trans 2017; 44:1561-1569. [PMID: 27913665 DOI: 10.1042/bst20160190] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/05/2016] [Accepted: 08/09/2016] [Indexed: 01/10/2023]
Abstract
The histone-like nucleoid structuring (H-NS) protein is a major component of the folded chromosome in Escherichia coli and related bacteria. Functions attributed to H-NS include management of genome evolution, DNA condensation, and transcription. The wide-ranging influence of H-NS is remarkable given the simplicity of the protein, a small peptide, possessing rudimentary determinants for self-association, hetero-oligomerisation and DNA binding. In this review, I will discuss our understanding of H-NS with a focus on these structural elements. In particular, I will consider how these interaction surfaces allow H-NS to exert its different effects.
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9
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Interaction of the histone-like nucleoid structuring protein and the general stress response regulator RpoS at Vibrio cholerae promoters that regulate motility and hemagglutinin/protease expression. J Bacteriol 2011; 194:1205-15. [PMID: 22194453 DOI: 10.1128/jb.05900-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The bacterium Vibrio cholerae colonizes the human small intestine and secretes cholera toxin (CT) to cause the rice-watery diarrhea characteristic of this illness. The ability of this pathogen to colonize the small bowel, express CT, and return to the aquatic environment is controlled by a complex network of regulatory proteins. Two global regulators that participate in this process are the histone-like nucleoid structuring protein (H-NS) and the general stress response regulator RpoS. In this study, we address the role of RpoS and H-NS in the coordinate regulation of motility and hemagglutinin (HA)/protease expression. In addition to initiating transcription of hapA encoding HA/protease, RpoS enhanced flrA and rpoN transcription to increase motility. In contrast, H-NS was found to bind to the flrA, rpoN, and hapA promoters and represses their expression. The strength of H-NS repression at the above-mentioned promoters was weaker for hapA, which exhibited the strongest RpoS dependency, suggesting that transcription initiation by RNA polymerase containing σ(S) could be more resistant to H-NS repression. Occupancy of the flrA and hapA promoters by H-NS was demonstrated by chromatin immunoprecipitation (ChIP). We show that the expression of RpoS in the stationary phase significantly diminished H-NS promoter occupancy. Furthermore, RpoS enhanced the transcription of integration host factor (IHF), which positively affected the expression of flrA and rpoN by diminishing the occupancy of H-NS at these promoters. Altogether, we propose a model for RpoS regulation of motility gene expression that involves (i) attenuation of H-NS repression by IHF and (ii) RpoS-dependent transcription initiation resistant to H-NS.
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10
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Bustamante VH, Villalba MI, García-Angulo VA, Vázquez A, Martínez LC, Jiménez R, Puente JL. PerC and GrlA independently regulate Ler expression in enteropathogenic Escherichia coli. Mol Microbiol 2011; 82:398-415. [DOI: 10.1111/j.1365-2958.2011.07819.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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11
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Refining the binding of the Escherichia coli flagellar master regulator, FlhD4C2, on a base-specific level. J Bacteriol 2011; 193:4057-68. [PMID: 21685294 DOI: 10.1128/jb.00442-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli flagellar master regulator, FlhD(4)C(2), binds to the promoter regions of flagellar class II genes, yet, despite extensive analysis of the FlhD(4)C(2)-regulated promoter region, a detailed consensus sequence has not emerged. We used in vitro and in vivo experimental approaches to determine the nucleotides in the class II promoter, fliAp, required for the binding and function of FlhD(4)C(2). FlhD(4)C(2) protects 48 bp (positions -76 to -29 relative to the σ(70)-dependent transcriptional start site) in the fliA promoter. We divided the 48-bp footprint region into 5 sections to determine the requirement of each DNA segment for the binding and function of FlhD(4)C(2). Results from an in vitro binding competition assay between the wild-type FlhD(4)C(2)-protected fragment and DNA fragments possessing mutations in one section of the 48-bp protected region showed that only one-third of the 48 bp protected by FlhD(4)C(2) is required for FlhD(4)C(2) binding and fliA promoter activity. This in vitro binding result was also seen in vivo with fliA promoter-lacZ fusions carrying the same mutations. Only seven bases (A(12), A(15), T(34), A(36), T(37), A(44), and T(45)) are absolutely required for the promoter activity. Moreover, A(12), A(15), T(34), T(37), and T(45) within the 7 bases are highly specific to fliA promoter activity, and those bases form an asymmetric recognition site for FlhD(4)C(2). The implications of the asymmetry of the FlhD(4)C(2) binding site and its potential impact on FlhD(4)C(2) are discussed.
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12
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Queiroz MH, Madrid C, Paytubi S, Balsalobre C, Juárez A. Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA. MICROBIOLOGY-SGM 2011; 157:2504-2514. [PMID: 21680637 DOI: 10.1099/mic.0.049197-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Coordination of the expression of Salmonella enterica invasion genes on Salmonella pathogenicity island 1 (SPI1) depends on a complex circuit involving several regulators that converge on expression of the hilA gene, which encodes a transcriptional activator (HilA) that modulates expression of the SPI1 virulence genes. Two of the global regulators that influence hilA expression are the nucleoid-associated proteins Hha and H-NS. They interact and form a complex that modulates gene expression. A chromosomal transcriptional fusion was constructed to assess the effects of these modulators on hilA transcription under several environmental conditions as well as at different stages of growth. The results obtained showed that these proteins play a role in silencing hilA expression at both low temperature and low osmolarity, irrespective of the growth phase. H-NS accounts for the main repressor activity. At high temperature and osmolarity, H-NS-mediated silencing completely ceases when cells enter the stationary phase, and hilA expression is induced. Mutants lacking IHF did not induce hilA in cells entering the stationary phase, and this lack of induction was dependent on the presence of H-NS. Band-shift assays and in vitro transcription data showed that for hilA induction under certain growth conditions, IHF is required to alleviate H-NS-mediated silencing.
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Affiliation(s)
- Mário H Queiroz
- Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Avda Diagonal, 645, 08028 Barcelona, Spain
| | - Cristina Madrid
- Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Avda Diagonal, 645, 08028 Barcelona, Spain
| | - Sònia Paytubi
- Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Avda Diagonal, 645, 08028 Barcelona, Spain
| | - Carlos Balsalobre
- Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Avda Diagonal, 645, 08028 Barcelona, Spain
| | - Antonio Juárez
- Institut de Bioenginyeria de Catalunya (IBEC), Parc Científic de Barcelona, Baldiri Reixach, 15-21, 08028 Barcelona, Spain
- Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Avda Diagonal, 645, 08028 Barcelona, Spain
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13
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Luijsterburg MS, White MF, van Driel R, Dame RT. The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 2009; 43:393-418. [PMID: 19037758 DOI: 10.1080/10409230802528488] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The genomic DNA of all organisms across the three kingdoms of life needs to be compacted and functionally organized. Key players in these processes are DNA supercoiling, macromolecular crowding and architectural proteins that shape DNA by binding to it. The architectural proteins in bacteria, archaea and eukaryotes generally do not exhibit sequence or structural conservation especially across kingdoms. Instead, we propose that they are functionally conserved. Most of these proteins can be classified according to their architectural mode of action: bending, wrapping or bridging DNA. In order for DNA transactions to occur within a compact chromatin context, genome organization cannot be static. Indeed chromosomes are subject to a whole range of remodeling mechanisms. In this review, we discuss the role of (i) DNA supercoiling, (ii) macromolecular crowding and (iii) architectural proteins in genome organization, as well as (iv) mechanisms used to remodel chromosome structure and to modulate genomic activity. We conclude that the underlying mechanisms that shape and remodel genomes are remarkably similar among bacteria, archaea and eukaryotes.
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Affiliation(s)
- Martijn S Luijsterburg
- Swammerdam Institute for Life Sciences, University of Amsterdam, Kruislaan, Amsterdam, The Netherlands
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14
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Integration host factor positively regulates virulence gene expression in Vibrio cholerae. J Bacteriol 2008; 190:4736-48. [PMID: 18456804 DOI: 10.1128/jb.00089-08] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Virulence gene expression in Vibrio cholerae is dependent upon a complex transcriptional cascade that is influenced by both specific and global regulators in response to environmental stimuli. Here, we report that the global regulator integration host factor (IHF) positively affects virulence gene expression in V. cholerae. Inactivation of ihfA and ihfB, the genes encoding the IHF subunits, decreased the expression levels of the two main virulence factors tcpA and ctx and prevented toxin-coregulated pilus and cholera toxin production. IHF was found to directly bind to and bend the tcpA promoter region at an IHF consensus site centered at position -162 by using gel mobility shift assays and DNase I footprinting experiments. Deletion or mutation of the tcpA IHF consensus site resulted in the loss of IHF binding and additionally disrupted the binding of the repressor H-NS. DNase I footprinting revealed that H-NS protection overlaps with both the IHF and the ToxT binding sites at the tcpA promoter. In addition, disruption of ihfA in an hns or toxT mutant background had no effect on tcpA expression. These results suggest that IHF may function at the tcpA promoter to alleviate H-NS repression.
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15
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Colangeli R, Helb D, Vilchèze C, Hazbón MH, Lee CG, Safi H, Sayers B, Sardone I, Jones MB, Fleischmann RD, Peterson SN, Jacobs WR, Alland D. Transcriptional regulation of multi-drug tolerance and antibiotic-induced responses by the histone-like protein Lsr2 in M. tuberculosis. PLoS Pathog 2007; 3:e87. [PMID: 17590082 PMCID: PMC1894825 DOI: 10.1371/journal.ppat.0030087] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 05/10/2007] [Indexed: 12/31/2022] Open
Abstract
Multi-drug tolerance is a key phenotypic property that complicates the sterilization of mammals infected with Mycobacterium tuberculosis. Previous studies have established that iniBAC, an operon that confers multi-drug tolerance to M. bovis BCG through an associated pump-like activity, is induced by the antibiotics isoniazid (INH) and ethambutol (EMB). An improved understanding of the functional role of antibiotic-induced genes and the regulation of drug tolerance may be gained by studying the factors that regulate antibiotic-mediated gene expression. An M. smegmatis strain containing a lacZ gene fused to the promoter of M. tuberculosis iniBAC (PiniBAC) was subjected to transposon mutagenesis. Mutants with constitutive expression and increased EMB-mediated induction of PiniBAC::lacZ mapped to the lsr2 gene (MSMEG6065), a small basic protein of unknown function that is highly conserved among mycobacteria. These mutants had a marked change in colony morphology and generated a new polar lipid. Complementation with multi-copy M. tuberculosis lsr2 (Rv3597c) returned PiniBAC expression to baseline, reversed the observed morphological and lipid changes, and repressed PiniBAC induction by EMB to below that of the control M. smegmatis strain. Microarray analysis of an lsr2 knockout confirmed upregulation of M. smegmatis iniA and demonstrated upregulation of genes involved in cell wall and metabolic functions. Fully 121 of 584 genes induced by EMB treatment in wild-type M. smegmatis were upregulated (“hyperinduced”) to even higher levels by EMB in the M. smegmatis lsr2 knockout. The most highly upregulated genes and gene clusters had adenine-thymine (AT)–rich 5-prime untranslated regions. In M. tuberculosis, overexpression of lsr2 repressed INH-mediated induction of all three iniBAC genes, as well as another annotated pump, efpA. The low molecular weight and basic properties of Lsr2 (pI 10.69) suggested that it was a histone-like protein, although it did not exhibit sequence homology with other proteins in this class. Consistent with other histone-like proteins, Lsr2 bound DNA with a preference for circular DNA, forming large oligomers, inhibited DNase I activity, and introduced a modest degree of supercoiling into relaxed plasmids. Lsr2 also inhibited in vitro transcription and topoisomerase I activity. Lsr2 represents a novel class of histone-like proteins that inhibit a wide variety of DNA-interacting enzymes. Lsr2 appears to regulate several important pathways in mycobacteria by preferentially binding to AT-rich sequences, including genes induced by antibiotics and those associated with inducible multi-drug tolerance. An improved understanding of the role of lsr2 may provide important insights into the mechanisms of action of antibiotics and the way that mycobacteria adapt to stresses such as antibiotic treatment. Understanding the cellular processes stimulated when Mycobacterium tuberculosis is treated with antibiotics may provide clues as to why months of therapy and use of several drugs simultaneously are required to prevent antibiotic resistance. Antibiotic treatment “turns on” or induces certain M. tuberculosis genes. These genes are of special interest because they appear to help M. tuberculosis survive the stress of antibiotic treatment. Our study of the regulation of antibiotic-induced genes, including iniBAC, in two mycobacterial species revealed that a small protein called Lsr2 controls iniBAC and other antibiotic-induced genes, especially ones related to the cell wall. Lsr2 binds to DNA in a relatively non-specific manner and appears to inhibit certain enzymes that must interact with DNA as part of their function. These properties differentiate Lsr2 from classical regulators of gene expression that bind to specific DNA sequences, and suggest that Lsr2 is a novel histone-like protein. These proteins regulate genes by changing the way DNA is shaped, and, indeed, we found that Lsr2 can change the shape of DNA by introducing a small number of coils into its structure. Our results suggest that Lsr2 is a major regulator of antibiotic-induced responses in mycobacteria.
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Affiliation(s)
- Roberto Colangeli
- Division of Infectious Disease and the Center for Emerging Pathogens, Department of Medicine, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, United States of America.
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16
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Dame RT. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol Microbiol 2005; 56:858-70. [PMID: 15853876 DOI: 10.1111/j.1365-2958.2005.04598.x] [Citation(s) in RCA: 274] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The bacterial chromosomal DNA is folded into a compact structure called nucleoid. The shape and size of this 'body' is determined by a number of factors. Major players are DNA supercoiling, macromolecular crowding and architectural proteins, associated with the nucleoid, which are the topic of this MicroReview. Although many of these proteins were identified more than 25 years ago, the molecular mechanisms involved in the organization and compaction of DNA have only started to become clear in recent years. Many of these new insights can be attributed to the use of recently developed biophysical techniques.
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Affiliation(s)
- Remus T Dame
- Physics of Complex Systems, Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, Amsterdam, the Netherlands.
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17
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Ilves H, Hõrak R, Teras R, Kivisaar M. IHF is the limiting host factor in transposition of Pseudomonas putida transposon Tn4652 in stationary phase. Mol Microbiol 2004; 51:1773-85. [PMID: 15009901 DOI: 10.1111/j.1365-2958.2003.03948.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transpositional activity of mobile elements is not constant. Conditional regulation of host factors involved in transposition may severely change the activity of mobile elements. We have demonstrated previously that transposition of Tn4652 in Pseudomonas putida is a stationary phase-specific event, which requires functional sigma S (Ilves et al., 2001, J Bacteriol 183: 5445-5448). We hypothesized that integration host factor (IHF), the concentration of which is increased in starving P. putida, might contribute to the transposition of Tn4652 as well. Here, we demonstrate that transposition of Tn4652 in stationary phase P. putida is essentially limited by the amount of IHF. No transposition of Tn4652 occurs in a P. putida ihfA-defective strain. Moreover, overexpression of IHF results in significant enhancement of transposition compared with the wild-type strain. This indicates that the amount of IHF is a bottleneck in Tn4652 transposition. Gel mobility shift and DNase I footprinting studies revealed that IHF is necessary for the binding of transposase to both transposon ends. In vitro, transposase can bind to inverted repeats of transposon only after the binding of IHF. The results obtained in this study indicate that, besides sigma S, IHF is another host factor that is implicated in the elevation of transposition in stationary phase.
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Affiliation(s)
- Heili Ilves
- Estonian Biocentre and Institute of Molecular and Cell Biology, Tartu University, 23 Riia Street, 51010 Tartu, Estonia
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18
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Abstract
The role of HU in Escherichia coli as both a protein involved in DNA compaction and as a protein with regulatory function seems to be firmly established. However, a critical look at the available data reveals that this is not true for each of the proposed roles of this protein. The role of HU as a regulatory or accessory protein in a number of systems has been thoroughly investigated and in many cases has been largely elucidated. However, almost 30 years after its discovery, convincing evidence for the proposed role of HU in DNA compaction is still lacking. Here we present an extensive literature survey of the available data which, in combination with novel microscopic insights, suggests that the role of HU could be the opposite as well. The protein is likely to play an architectural role, but instead of being responsible for DNA compaction it could be involved in antagonising compaction by other proteins such as H-NS.
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Affiliation(s)
- Remus Thei Dame
- Laboratory of Molecular Genetics, Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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19
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Umanski T, Rosenshine I, Friedberg D. Thermoregulated expression of virulence genes in enteropathogenic Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2002; 148:2735-2744. [PMID: 12213920 DOI: 10.1099/00221287-148-9-2735] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Enteropathogenic Escherichia coli (EPEC) causes severe diarrhoea in young children. The locus of enterocyte effacement (LEE) pathogenicity island comprises a cluster of operons encoding a type III secretion system and related proteins that are associated with EPEC virulence. The LEE1 operon encodes Ler that positively regulates the LEE2, LEE3, LEE4, LEE5 and espG transcriptional units. The LEE operons are repressed at 27 degrees C and expressed at 37 degrees C. This paper describes a regulatory cascade of the thermoregulation of LEE operons. LEE1 including ler is repressed by H-NS at 27 degrees C but not at 37 degrees C. In contrast, the expression of the LEE2, LEE3, LEE4, LEE5 and espG transcriptional units is repressed by H-NS at both 27 degrees C and 37 degrees C. Upon shifting the culture temperature from 27 degrees C to 37 degrees C, Ler is synthesized and in turn activates the expression of LEE2, LEE3, LEE4 and espG by releasing the H-NS mediated repression. In the case of LEE5, Ler acts both by alleviating the H-NS mediated repression and by an additional mechanism, as yet to be defined.
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Affiliation(s)
- Tatiana Umanski
- Department of Molecular Genetics and Biotechnology, The Hebrew University, Faculty of Medicine, POB 12272, Jerusalem 91120, Israel1
| | - Ilan Rosenshine
- Department of Molecular Genetics and Biotechnology, The Hebrew University, Faculty of Medicine, POB 12272, Jerusalem 91120, Israel1
| | - Devorah Friedberg
- Department of Molecular Genetics and Biotechnology, The Hebrew University, Faculty of Medicine, POB 12272, Jerusalem 91120, Israel1
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20
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Kobryn K, Watson MA, Allison RG, Chaconas G. The Mu three-site synapse: a strained assembly platform in which delivery of the L1 transposase binding site triggers catalytic commitment. Mol Cell 2002; 10:659-69. [PMID: 12408832 DOI: 10.1016/s1097-2765(02)00596-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Mu DNA transposition reaction proceeds through a three-site synaptic complex (LER), including the two Mu ends and the transpositional enhancer. We show that the LER contains highly stressed DNA regions in the enhancer and in the L1 transposase binding site. We propose that the L1 site acts as the keystone for assembly of a catalytically competent transpososome. Delivery of L1 through HU-mediated bending completes LER assembly, provides the trigger for necessary conformational transitions in transpososome formation, and allows target capture to occur. Relief of the stress at L1 and the enhancer may help drive Mu A tetramerization and engagement of the Mu ends by the transposase active site.
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Affiliation(s)
- Kerri Kobryn
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
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21
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Schröder O, Wagner R. The bacterial regulatory protein H-NS--a versatile modulator of nucleic acid structures. Biol Chem 2002; 383:945-60. [PMID: 12222684 DOI: 10.1515/bc.2002.101] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The small DNA binding protein H-NS is attracting broad interest for its profound involvement in the regulation of bacterial physiology. It is involved in the regulation of many genes in response to a changing environment and functions in the adaptation to many different kinds of stress. Many H-NS-controlled genes, including the hns gene itself, are further linked to global regulatory networks. H-NS thus plays a key role in maintaining bacterial homeostasis under conditions of a rapidly changing environment. In this review we summarize recent results from combined biochemical and biophysical efforts which have yielded new insights into the three-dimensional structure and function of H-NS. The protein consists of two distinct domains separated by an unstructured linker region, and the structural details available today have helped to understand how these domains may interact with each other or with ligand molecules. Functional studies have, in addition, revealed mechanistic clues for the various H-NS activities, like temperature- or growth phase-dependent regulation. Important elements for the specific regulatory activities of H-NS comprise different modes of DNA binding, protein oligomerization, the competition with other regulators and the fact that the topology of the target DNA is modulated during complex formation. The distinctive ability to recognize nucleic acid structures in combination with other proteins also explains H-NS-dependent post-transcriptional activities where the interaction with defined RNA structures and the interference with RNA/protein complexes during mRNA translation are crucial for regulation. Thus, protein/protein interactions, in combination with the recognition and modulation of nucleic acid structures, are key elements of the different mechanisms which make H-NS such a versatile regulator.
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Affiliation(s)
- Oliver Schröder
- Division of Biology and Center for Molecular Genetics, University of California at San Diego, La Jolla 92093-0634, USA
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22
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Dame RT, Wyman C, Wurm R, Wagner R, Goosen N. Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1. J Biol Chem 2002; 277:2146-50. [PMID: 11714691 DOI: 10.1074/jbc.c100603200] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Escherichia coli H-NS protein is a nucleoid-associated protein involved in both transcription regulation and DNA compaction. Each of these processes involves H-NS-mediated bridge formation between adjacent DNA helices. With respect to transcription regulation, preferential binding sites in the promoter regions of different genes have been reported, and generally these regions are curved. Often H-NS binding sites overlap with promoter core regions or with binding sites of other regulatory factors. Not in all cases, however, transcriptional repression is the result of preferential binding by H-NS to promoter regions leading to occlusion of the RNA polymerase. In the case of the rrnB P1, H-NS actually stimulates open complex formation by forming a ternary RNAP.H-NS.DNA complex, while simultaneously stabilizing it to such an extent that promoter clearance cannot occur. To define the mechanism by which H-NS interferes at this step in the initiation pathway, the architecture of the RNAP.H-NS.DNA complex was analyzed by scanning force microscopy (SFM). The SFM images show that the DNA flanking the RNA polymerase in open initiation complexes is bridged by H-NS. On the basis of these data, we present a model for the specific repression of transcription initiation at the rrnB P1 by H-NS.
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Affiliation(s)
- Remus Thei Dame
- Laboratory of Molecular Genetics, Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P. O. Box 9502, 2300 RA Leiden, The Netherlands
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23
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Abstract
The ability of bacterial pathogens to bind to the host mucosa is a critical step in the pathogenesis of many bacterial infections and, for Escherichia coli, a large number of different fimbrial adhesins have been implicated as virulence factors. In this chapter, our current understanding of the regulatory mechanisms that control the expression of two of the best characterized fimbrial adhesins, pyelonephritis-associated pilus (encoded by pap) and the type 1 fimbria (encoded by fim), will be described. The expression of both fimbrial adhesins is controlled by phase variation (the reversible and apparently random switching between expressing ('on') and non-expressing ('off') states), and is regulated in response to environmental conditions. The phase variation of pap (and of some other fimbriae in Escherichia coli) is determined by the formation of alternative nucleoprotein complexes that either activate (phase 'on') or suppress (phase 'off') transcription of the fimbria genes. Formation of each complex protects a single Dam methylation site (5' GATC) from modification (GATCdist in phase 'on' cells and GATCprox in phase 'off' cells). Furthermore, complex formation is inhibited by methylation of the two 5' GATC sites. Both the phase variation of pap and the transcription of the pap genes in phase 'on' cells, are regulated and expression is subject to both positive and negative feedback control. In contrast to pap, the phase variation of fim is determined by the site-specific inversion of a short element of DNA (the fim switch). In phase 'on' cells, a promoter within the invertible element directs the transcription of the fim structural genes, whereas in phase 'off' cells transcription of the fimbrial genes is silenced. Despite the very different molecular mechanisms controlling the expression of pap and fim, the two systems share many features in common and have probably evolved to fulfill the same function. In addition to details about the molecular mechanisms that control pap and fim, the possible physiological significance of the observed regulation will be discussed.
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Affiliation(s)
- I C Blomfield
- Research School of Biosciences, University of Kent at Canterbury, Canterbury, Kent, CT2 7NJ, UK.
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24
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Abstract
The Escherichia coli H-NS protein is a nucleoid-associated protein involved in transcription regulation and DNA compaction. H-NS exerts its role in DNA condensation by non-specific interactions with DNA. With respect to transcription regulation preferential binding sites in the promoter regions of different genes have been reported. In this paper we describe the analysis of H-NS-DNA complexes on a preferred H-NS binding site by atomic force microscopy. On the basis of these data we present a model for the specific recognition of DNA by H-NS as a function of DNA curvature.
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Affiliation(s)
- R T Dame
- Laboratory of Molecular Genetics, Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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25
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Dame RT, Wyman C, Goosen N. H-NS mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res 2000; 28:3504-10. [PMID: 10982869 PMCID: PMC110753 DOI: 10.1093/nar/28.18.3504] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Escherichia coli H-NS protein is a nucleoid-associated protein involved in gene regulation and DNA compaction. To get more insight into the mechanism of DNA compaction we applied atomic force microscopy (AFM) to study the structure of H-NS-DNA complexes. On circular DNA molecules two different levels of H-NS induced condensation were observed. H-NS induced lateral condensation of large regions of the plasmid. In addition, large globular structures were identified that incorporated a considerable amount of DNA. The formation of these globular structures appeared not to be dependent on any specific sequence. On the basis of the AFM images, a model for global condensation of the chromosomal DNA by H-NS is proposed.
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Affiliation(s)
- R T Dame
- Laboratory of Molecular Genetics, Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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26
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Rowe S, Hodson N, Griffiths G, Roberts IS. Regulation of the Escherichia coli K5 capsule gene cluster: evidence for the roles of H-NS, BipA, and integration host factor in regulation of group 2 capsule gene clusters in pathogenic E. coli. J Bacteriol 2000; 182:2741-5. [PMID: 10781541 PMCID: PMC101981 DOI: 10.1128/jb.182.10.2741-2745.2000] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/1999] [Accepted: 02/25/2000] [Indexed: 12/31/2022] Open
Abstract
The expression of Escherichia coli group 2 capsules (K antigens) is temperature dependent, with capsules only being expressed at temperatures above 20 degrees C. Thermoregulation is at the level of transcription, with no detectable transcription at 20 degrees C. Using the E. coli K5 capsule gene cluster as a model system, we have shown that the nucleoid-associated protein H-NS plays a dual role in regulating transcription of group 2 capsule gene clusters at 37 and 20 degrees C. At 37 degrees C H-NS is required for maximal transcription of group 2 capsule gene clusters, whereas at 20 degrees C H-NS functions to repress transcription. The BipA protein, previously identified as a tyrosine-phosphorylated GTPase and essential for virulence in enteropathogenic E. coli, was shown to play a similar role to H-NS in regulating transcription at 37 and 20 degrees C. The binding of integration host factor (IHF) to the region 1 promoter was necessary to potentiate transcription at 37 degrees C and IHF binding demonstrated by bandshift assays. The IHF binding site was 3' to the site of transcription initiation, suggesting that sequences in the 5' end of the first gene (kpsF) in region 1 may play a role in regulating transcription from this promoter at 37 degrees C. Two additional cis-acting sequences, conserved in both the region 1 and 3 promoters, were identified, suggesting a role for these sequences in the coordinate regulation of transcription from these promoters. These results indicate that a complex regulatory network involving a number of global regulators exists for the control of expression of group 2 capsules in E. coli.
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Affiliation(s)
- S Rowe
- School of Biological Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
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27
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Teras R, Hõrak R, Kivisaar M. Transcription from fusion promoters generated during transposition of transposon Tn4652 is positively affected by integration host factor in Pseudomonas putida. J Bacteriol 2000; 182:589-98. [PMID: 10633090 PMCID: PMC94319 DOI: 10.1128/jb.182.3.589-598.2000] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/1999] [Accepted: 10/31/1999] [Indexed: 11/20/2022] Open
Abstract
We have previously shown that both ends of the Tn3 family transposon Tn4652 contain integration host factor (IHF) binding sites and that IHF positively regulates expression of the Tn4652 transposase gene tnpA in Pseudomonas putida (R. Hõrak, and M. Kivisaar, J. Bacteriol. 180:2822-2829, 1998). Tn4652 can activate silent genes by creating fusion promoters during the transposition. The promoters are created as fusions between the -35 hexamer provided by the terminal inverted repeats of Tn4652 and the -10 hexamers in the target DNA. Two fusion promoters, PRA1 and PLA1, that contain sequences of the right and left termini of Tn4652, respectively, were chosen for the study of mechanisms of transcription activation. Gel mobility shift analysis using crude extracts from P. putida cells allowed us to detect specific binding of P. putida IHF to the ends of the transposon Tn4652. We found that the rate of transcription from the fusion promoter PRA1 is enhanced by IHF. Notably, the positive effect of IHF on transcription from the promoter PRA1 appeared only when cells of P. putida reached the stationary growth phase. We speculate that the intracellular concentration of IHF might be critical for the in vivo effect of IHF on transcription from the fusion promoters in P. putida. In the case of PLA1, the mechanism of transcription modulation by IHF is different than that observed for PRA1. Our results demonstrate that transcription of neighboring genes from outwardly directed promoters at the ends of a mobile DNA element could be influenced by the same factors that control transposition of the element.
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Affiliation(s)
- R Teras
- Department of Genetics, Institute of Molecular and Cell Biology, Estonian Biocentre and Tartu University, 51010 Tartu, Estonia
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28
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Friedberg D, Umanski T, Fang Y, Rosenshine I. Hierarchy in the expression of the locus of enterocyte effacement genes of enteropathogenic Escherichia coli. Mol Microbiol 1999; 34:941-52. [PMID: 10594820 DOI: 10.1046/j.1365-2958.1999.01655.x] [Citation(s) in RCA: 137] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Enteropathogenic Escherichia coli (EPEC) elicit changes in host cell morphology and cause actin rearrangement, a phenotype that has commonly been referred to as attaching/effacing (AE) lesions. The ability of EPEC to induce AE lesions is dependent upon a type III protein secretion/translocation system that is encoded by genes clustered in a 35.6 kb DNA segment, named the locus of enterocyte effacement (LEE). We used transcriptional fusions between the green fluorescent protein (gfp) reporter gene and LEE genes rorf2, orf3, orf5, escJ, escV and eae, together with immunoblot analysis with antibodies against Tir, intimin, EspB and EspF, to analyse the genetic regulation of the LEE. The expression of all these LEE genes was strictly dependent upon the presence of a functional integration host factor (IHF). IHF binds specifically upstream from the ler (orf1) promoter and appears to activate expression of ler, orf3, orf5 and rorf2 directly. The ler-encoded Ler protein was involved in activating the expression of escJ, escV, tir, eae, espB and espF. Expression of both IHF and Ler was needed to elicit actin rearrangement associated with AE lesions. In conclusion, IHF directly activates the expression of the ler and rorf2 transcriptional units, and Ler in turn mediates the expression of the other LEE genes.
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Affiliation(s)
- D Friedberg
- Departments of Molecular Genetics and Biotechnology, The Hebrew University, Faculty of Medicine, POB 12272, Jerusalem 91120, Israel
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29
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Marshall DG, Sheehan BJ, Dorman CJ. A role for the leucine-responsive regulatory protein and integration host factor in the regulation of the Salmonella plasmid virulence (spv ) locus in Salmonella typhimurium. Mol Microbiol 1999; 34:134-45. [PMID: 10540292 DOI: 10.1046/j.1365-2958.1999.01587.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Salmonella plasmid virulence (spv ) genes of Salmonella typhimurium are activated at the level of transcription as the bacteria enter stationary phase in vitro or in response to signals received during intracellular growth. Activation requires the LysR-like transcription factor SpvR and the alternative sigma factor RpoS. In this report, we show by biochemical and genetic analyses that two chromosomally encoded DNA-binding proteins contribute to the control of spv expression. These are the integration host factor (IHF), which binds to DNA sequences upstream of the spvR regulatory gene, and the leucine-responsive regulatory protein (Lrp), which binds to sequences upstream of the spvABCD operon. Under all conditions tested, inactivation of IHF expression reduces the level of spvR transcription by twofold. It also alters the response of the spv regulon to loss of DNA gyrase activity, consistent with a role for IHF in organizing DNA structure in the vicinity of the spvR promoter. Lrp represses spvA gene expression by up to fivefold and Lrp-mediated repression is antagonized by leucine. The Lrp binding site upstream of the spvA gene overlaps one of the binding sites for the positive regulator SpvR, suggesting a mechanism by which Lrp repression is exerted. This is a first demonstration of a role for Lrp in controlling genes that are also subject to intracellular regulation. These data show that the spv virulence genes belong simultaneously to several regulons in the cell, raising the possibility that spv expression can be fine-tuned in response to multiple environmental inputs.
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Affiliation(s)
- D G Marshall
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Ireland
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30
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Lamrani S, Ranquet C, Gama MJ, Nakai H, Shapiro JA, Toussaint A, Maenhaut-Michel G. Starvation-induced Mucts62-mediated coding sequence fusion: a role for ClpXP, Lon, RpoS and Crp. Mol Microbiol 1999; 32:327-43. [PMID: 10231489 DOI: 10.1046/j.1365-2958.1999.01352.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The formation of araB-lacZ coding sequence fusions in Escherichia coli is a particular type of chromosomal rearrangement induced by Mucts62, a thermoinducible mutant of mutator phage Mu. Fusion formation is controlled by the host physiology. It only occurs after aerobic carbon starvation and requires the phage-encoded transposase pA, suggesting that these growth conditions trigger induction of the Mucts62 prophage. Here, we show that thermal induction of the prophage accelerated araB-lacZ fusion formation, confirming that derepression is a rate-limiting step in the fusion process. Nonetheless, starvation conditions remained essential to complete fusions, suggesting additional levels of physiological regulation. Using a transcriptional fusion indicator system in which the Mu early lytic promoter is fused to the reporter E. coli lacZ gene, we confirmed that the Mucts62 prophage was derepressed in stationary phase (S derepression) at low temperature. S derepression did not apply to prophages that expressed the Mu wild-type repressor. It depended upon the host ClpXP and Lon ATP-dependent proteases and the RpoS stationary phase-specific sigma factor, but not upon Crp. None of these four functions was required for thermal induction. Crp was required for fusion formation, but only when the Mucts62 prophage encoded the transposition/replication activating protein pB. Finally, we found that thermally induced cultures did not return to the repressed state when shifted back to low temperature and, hence, remained activated for accelerated fusion formation upon starvation. The maintenance of the derepressed state required the ClpXP and Lon host proteases and the prophage Ner-regulatory protein. These observations illustrate how the cts62 mutation in Mu repressor provides the prophage with a new way to respond to growth phase-specific regulatory signals and endows the host cell with a new potential for adaptation through the controlled use of the phage transposition machinery.
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Affiliation(s)
- S Lamrani
- Laboratoire de Génétique des Procaryotes, Département de Biologie Moléculaire, Université Libre de Bruxelles, 67 rue des Chevaux, B1640 Rhode St Genèse, Belgium
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31
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Caramel A, Schnetz K. Lac and lambda repressors relieve silencing of the Escherichia coli bgl promoter. Activation by alteration of a repressing nucleoprotein complex. J Mol Biol 1998; 284:875-83. [PMID: 9837711 DOI: 10.1006/jmbi.1998.2191] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Escherichia coli bgl promoter is kept in a repressed state by silencer sequences which flank the promoter and by the histone-like protein H-NS. Silencing of the bgl promoter is likely due to the formation of a repressing nucleoprotein complex of which H-NS is an essential component. Here, we show that silencing is abolished by the binding of Lac or lambda repressors to their respective operators that were inserted within the bgl upstream silencer. Efficient activation of bgl operon transcription by Lac and lambda repressors was independent of the position and phasing of the operators with respect to the promoter. Activation by Lac and lambda repressors as shown here is unprecedented. We conclude that the activation of bgl transcription by both repressors is achieved by a novel mechanism, that is by alteration of the repressing nucleoprotein complex rather than by protein-protein interactions with RNA polymerase and the catabolite activator protein, CAP.
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Affiliation(s)
- A Caramel
- Institut für Genetik, Universität zu Köln, Köln, Weyertal 121, D-50931, Germany
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32
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Gowrishankar J, Pittard AJ. Superimposition of tyrR protein-mediated regulation on osmoresponsive transcription of Escherichia coli proU in vivo. J Bacteriol 1998; 180:6743-8. [PMID: 9852023 PMCID: PMC107782 DOI: 10.1128/jb.180.24.6743-6748.1998] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Osmotic regulation of proU expression in the enterobacteria is achieved, at least in part, by a repression mechanism involving the histone-like nucleoid protein H-NS. By the creation of binding sites for the TyrR regulator protein in the vicinity of the sigma70-controlled promoter of proU in Escherichia coli, we were able to demonstrate a superposed TyrR-mediated activation by L-phenylalanine (Phe), as well as repression by L-tyrosine, of proU expression in vivo. Based on the facts that pronounced activation in the presence of Phe was observed even at a low osmolarity and that the affinity of binding of TyrR to its cognate sites on DNA is not affected by Phe, we argue that H-NS-mediated repression of proU at a low osmolarity may not involve a classical silencing mechanism. Our data also suggest the involvement of recruited RNA polymerase in the mechanism of antirepression in E. coli.
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Affiliation(s)
- J Gowrishankar
- Centre for Cellular & Molecular Biology, Hyderabad 500007, India.
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33
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Giladi H, Koby S, Prag G, Engelhorn M, Geiselmann J, Oppenheim AB. Participation of IHF and a distant UP element in the stimulation of the phage lambda PL promoter. Mol Microbiol 1998; 30:443-51. [PMID: 9791187 DOI: 10.1046/j.1365-2958.1998.01079.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have previously identified a UP element in the phage lambda PL promoter, centred at position -90 from the transcription start site. Integration host factor (IHF), a heterodimeric DNA-binding and -bending protein, binds upstream of the lambda PL promoter in a region overlapping the UP element. Stimulation of transcription by IHF requires an intact alphaCTD and affects the initial binding of RNA polymerase to the promoter. We propose a model for the stimulation of PL by IHF in which IHF bends the DNA to bring the distal UP sequence in closer proximity to the promoter core sequences to allow the docking of the alphaCTD of RNA polymerase. Furthermore, IHF may also participate in protein-protein interactions with the alphaCTD. In support of this model, we found that alanine substitutions in alphaCTD at positions 265, 268, 270 and 275 reduced PL promoter activity. Mutations in the IHF DNA binding site, as well as IHF mutant proteins exhibiting a decreased ability to bend the DNA, were both defective in stimulating the PL promoter. In addition, some of the mutated IHF residues are clustered at a protein surface that interacts with the UP DNA sequence. These residues may also participate in protein-protein interactions with the alphaCTD.
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Affiliation(s)
- H Giladi
- Department of Molecular Genetics, The Hebrew University - Hadassah Medical School, PO Box 12272, Jerusalem, 91120, Israel
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34
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Bertoni G, Fujita N, Ishihama A, de Lorenzo V. Active recruitment of sigma54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and alphaCTD. EMBO J 1998; 17:5120-8. [PMID: 9724648 PMCID: PMC1170840 DOI: 10.1093/emboj/17.17.5120] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The sequence elements determining the binding of the sigma54-containing RNA polymerase (sigma54-RNAP) to the Pu promoter of Pseudomonas putida have been examined. Contrary to previous results in related systems, we show that the integration host factor (IHF) binding stimulates the recruitment of the enzyme to the -12/-24 sequence motifs. Such a recruitment, which is fully independent of the activator of the system, XylR, requires the interaction of the C-terminal domain of the alpha subunit of RNAP with specific DNA sequences upstream of the IHF site which are reminiscent of the UP elements in sigma70 promoters. Our data show that this interaction is mainly brought about by the distinct geometry of the promoter region caused by IHF binding and the ensuing DNA bending. These results support the view that binding of sigma54-RNAP to a promoter is a step that can be subjected to regulation by factors (e.g. IHF) other than the sole intrinsic affinity of sigma54-RNAP for the -12/-24 site.
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Affiliation(s)
- G Bertoni
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología CSIC, Campus de Cantoblanco, 28049 Madrid, Spain
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35
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Kakikawa M, Watanabe N, Funawatashi T, Oki M, Yasukawa H, Taketo A, Kodaira KI. Promoter/repressor system of Lactobacillus plantarum phage og1e: characterization of the promoters pR49-pR-pL and overproduction of the cro-like protein cng in Escherichia coli. Gene 1998; 215:371-9. [PMID: 9714836 DOI: 10.1016/s0378-1119(98)00289-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The Lactobacillus plantarum phage og1e (42<HSP SP = "0. 25">259<HSP SP = "0.25">bp) has two repressor-like genes cng and cpg oriented oppositely, accompanied by three potential promoters pR, pL and pR49, and seven operator-like sequences (GATAC-boxes) (Kodaira et al., 1997). In this study, the og1e putative promoters were introduced into the Escherichia coli promoter-detecting plasmid pKK232-8. In E. coli CK111, pR (pKPR1), pL (pKPL1) and pR49 (pKPR49) exhibited distinct CAT activities. When pKPR1 or pKPL1 was coexistent with a compatible plasmid pACYC184 carrying pR-cng (pA4PRCN1), the CAT activity was decreased significantly. On the other hand, cng directed a protein (Cng) of 10.1 kDa in E. coli under the control of T7 promoter. Gel mobility-shift assays demonstrated that Cng binds specifically to a DNA region containing the GATAC-boxes. In addition, primer extension analyses demonstrated that the two sequences pR and pL act as a promoter in L. plantarum as well as in E. coli. These results suggested that the potential promoters pR and pL probably function for the lytic and lysogenic pathways, respectively, and Cng may act as a repressor presumably through the GATAC-boxes as operators.
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Affiliation(s)
- M Kakikawa
- Molecular Biology Group, Faculty of Engineering, Toyama University, 3190, Gofuku, Toyama 930, Japan
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36
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Hõrak R, Kivisaar M. Expression of the transposase gene tnpA of Tn4652 is positively affected by integration host factor. J Bacteriol 1998; 180:2822-9. [PMID: 9603867 PMCID: PMC107244 DOI: 10.1128/jb.180.11.2822-2829.1998] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/1997] [Accepted: 03/29/1998] [Indexed: 02/07/2023] Open
Abstract
Tn4652 is a derivative of the toluene degradation transposon Tn4651 that belongs to the Tn3 family of transposons (M. Tsuda and T. Iino, Mol. Gen. Genet. 210:270-276, 1987). We have sequenced the transposase gene tnpA of transposon Tn4652 and mapped its promoter to the right end of the element. The deduced amino acid sequence of tnpA revealed 96.2% identity with the putative transposase of Tn5041. Homology with other Tn3 family transposases was only moderate (about 20 to 24% identity), suggesting that Tn4652 and Tn5041 are distantly related members of the Tn3 family. Functional analysis of the tnpA promoter revealed that it is active in Pseudomonas putida but silent in Escherichia coli, indicating that some P. putida-specific factor is required for the transcription from this promoter. Additionally, tnpA promoter activity was shown to be modulated by integration host factor (IHF). The presence of an IHF-binding site upstream of the tnpA promoter enhanced the promoter activity. The positive role of IHF was also confirmed by the finding that the enhancing effect of IHF was not detected in the P. putida ihfA-deficient strain A8759. Moreover, the Tn4652 terminal sequences had a negative effect on transcription from the tnpA promoter in the ihfA-defective strain. This finding suggests that IHF not only enhances transcription from the tnpA promoter but also alleviates the negative effect of terminal sequences of Tn4652 on the promoter activity. Also, an in vitro binding assay demonstrated that both ends of Tn4652 bind IHF from a cell lysate of E. coli.
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Affiliation(s)
- R Hõrak
- Estonian Biocentre and Institute of Molecular and Cell Biology, Tartu University, EE2400 Tartu, Estonia.
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37
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Howe MM. Bacteriophage Mu. Mol Microbiol 1998. [DOI: 10.1007/978-3-642-72071-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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38
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Porter ME, Dorman CJ. Positive regulation of Shigella flexneri virulence genes by integration host factor. J Bacteriol 1997; 179:6537-50. [PMID: 9352898 PMCID: PMC179577 DOI: 10.1128/jb.179.21.6537-6550.1997] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In Shigella flexneri, expression of the plasmid-encoded virulence genes is regulated via a complex cascade involving DNA topology, specific transactivators, and the nucleoid-associated protein H-NS, which represses transcription under inappropriate environmental conditions. We have investigated the involvement of a second nucleoid-associated protein, integration host factor (IHF), in virulence gene expression. We found that transcription of the invasion-specific genes is repressed in a strain harboring an ihfA mutation, particularly on entry into the stationary phase. Expression of the virB gene, whose product is required for the activation of these structural genes, is also enhanced by IHF in the stationary phase. In contrast, the virF gene, which encodes an activator of virB, is stimulated by IHF in both the logarithmic and early stationary phases of growth, as is another virF-regulated gene, icsA. We have identified regions of the virF, virB, and icsA promoters which form IHF-dependent protein-DNA complexes in vitro and have located sequences within these regions with similarity to the consensus IHF binding site. Moreover, results from experiments in which the virF or virB gene was expressed constitutively confirm that IHF has a direct input at the level of both virF and virB transcription. Finally, we provide evidence that at the latter promoter, the primary role of IHF may be to overcome repression by the H-NS protein. To our knowledge, this is the first report of a role for IHF in controlling gene expression in S. flexneri.
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Affiliation(s)
- M E Porter
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Republic of Ireland
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39
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Abstract
This review attempts to substantiate the notion that nonlinear DNA structures allow prokaryotic cells to evolve complex signal integration devices that, to some extent, parallel the transduction cascades employed by higher organisms to control cell growth and differentiation. Regulatory cascades allow the possibility of inserting additional checks, either positive or negative, in every step of the process. In this context, the major consequence of DNA bending in transcription is that promoter geometry becomes a key regulatory element. By using DNA bending, bacteria afford multiple metabolic control levels simply through alteration of promoter architecture, so that positive signals favor an optimal constellation of protein-protein and protein-DNA contacts required for activation. Additional effects of regulated DNA bending in prokaryotic promoters include the amplification and translation of small physiological signals into major transcriptional responses and the control of promoter specificity for cognate regulators.
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Affiliation(s)
- J Pérez-Martín
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus de Cantoblanco, Madrid, Spain
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40
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van Ulsen P, Hillebrand M, Zulianello L, van de Putte P, Goosen N. The integration host factor-DNA complex upstream of the early promoter of bacteriophage Mu is functionally symmetric. J Bacteriol 1997; 179:3073-5. [PMID: 9139933 PMCID: PMC179079 DOI: 10.1128/jb.179.9.3073-3075.1997] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Inversion of the ihf site in the promoter region of the early promoter of bacteriophage Mu did not influence the integration host factor (IHF)-mediated functions. IHF bound to this inverted site could counteract H-NS-mediated repression, directly activate transcription, and support lytic growth of bacteriophage Mu. This implies that the IHF heterodimer and its asymmetrical binding site form a functionally symmetrical complex.
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Affiliation(s)
- P van Ulsen
- Laboratory of Molecular Genetics, Leiden University, The Netherlands
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41
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van Ulsen P, Hillebrand M, Kainz M, Collard R, Zulianello L, van de Putte P, Gourse RL, Goosen N. Function of the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase in basal expression and integration host factor-mediated activation of the early promoter of bacteriophage Mu. J Bacteriol 1997; 179:530-7. [PMID: 8990307 PMCID: PMC178725 DOI: 10.1128/jb.179.2.530-537.1997] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Integration host factor (IHF) can activate transcription from the early promoter (Pe) of bacteriophage Mu both directly and indirectly. Indirect activation occurs through alleviation of H-NS-mediated repression of the Pe promoter (P. Van Ulsen, M. Hillebrand, L. Zulianello, P. Van de Putte, and N. Goosen, Mol. Microbiol. 21:567-578, 1996). The direct activation involves the C-terminal domain of the alpha subunit (alphaCTD) of RNA polymerase. We investigated which residues in the alphaCTD are important for IHF-mediated activation of the Pe promoter. Initial in vivo screening, using a set of substitution mutants derived from an alanine scan (T. Gaal, W. Ross, E. E. Blatter, T. Tang, X. Jia, V. V. Krishnan, N. Assa-Munt, R. Ebright, and R. L. Gourse, Genes Dev. 10:16-26, 1996; H. Tang, K. Severinov, A. Goldfarb, D. Fenyo, B. Chait, and R. H. Ebright, Genes Dev. 8:3058-3067, 1994), indicated that the residues, which are required for transcription activation by the UP element of the rrnB P1 promoter (T. Gaal, W. Ross, E. E. Blatter, T. Tang, X. Jia, V. V. Krishnan, N. Assa-Munt, R. Ebright, and R. L. Gourse, Genes Dev. 10:16-26, 1996), are also important for Pe expression in the presence of IHF. Two of the RNA polymerase mutants, alphaR265A and alphaG296A, that affected Pe expression most in vivo were subsequently tested in in vitro transcription experiments. Mutant RNA polymerase with alphaR265A showed no IHF-mediated activation and a severely reduced basal level of transcription from the Pe promoter. Mutant RNA polymerase with alphaG296A resulted in a slightly reduced transcription from the Pe promoter in the absence of IHF but could still be activated by IHF. These results indicate that interaction of the alphaCTD with DNA is involved not only in the IHF-mediated activation of Pe transcription but also in maintaining the basal level of transcription from this promoter. Mutational analysis of the upstream region of the Pe promoter identified a sequence, positioned from -39 to -51 with respect to the transcription start site, that is important for basal Pe expression, presumably through binding of the alphaCTD. The role of the alphaCTD in IHF-mediated stimulation of transcription from the Pe promoter is discussed.
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Affiliation(s)
- P van Ulsen
- Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, The Netherlands
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