151
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Ram EVSR, Naik R, Ganguli M, Habib S. DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum. Nucleic Acids Res 2008; 36:5061-73. [PMID: 18663012 PMCID: PMC2528193 DOI: 10.1093/nar/gkn483] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Apicomplexans, including the pathogens Plasmodium and Toxoplasma, carry a nonphotosynthetic plastid of secondary endosymbiotic origin called the apicoplast. The P. falciparum apicoplast contains a 35 kb, circular DNA genome with limited coding capacity that lacks genes encoding proteins for DNA organization and replication. We report identification of a nuclear-encoded bacterial histone-like protein (PfHU) involved in DNA compaction in the apicoplast. PfHU is associated with apicoplast DNA and is expressed throughout the parasite's intra-erythocytic cycle. The protein binds DNA in a sequence nonspecific manner with a minimum binding site length of ∼27 bp and a Kd of ∼63 nM and displays a preference for supercoiled DNA. PfHU is capable of condensing Escherichia coli nucleoids in vivo indicating its role in DNA compaction. The unique 42 aa C-terminal extension of PfHU influences its DNA condensation properties. In contrast to bacterial HUs that bend DNA, PfHU promotes concatenation of linear DNA and inhibits DNA circularization. Atomic Force Microscopic study of PfHU–DNA complexes shows protein concentration-dependent DNA stiffening, intermolecular bundling and formation of DNA bridges followed by assembly of condensed DNA networks. Our results provide the first functional characterization of an apicomplexan HU protein and provide additional evidence for red algal ancestry of the apicoplast.
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Affiliation(s)
- E V S Raghu Ram
- Division of Molecular and Structural Biology, Central Drug Research Institute, Lucknow-226 001, India
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152
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Abstract
The Mre11 complex functions in double-strand break (DSB) repair, meiotic recombination, and DNA damage checkpoint pathways. Sae2 deficiency has opposing effects on the Mre11 complex. On one hand, it appears to impair Mre11 nuclease function in DNA repair and meiotic DSB processing, and on the other, Sae2 deficiency activates Mre11-complex-dependent DNA-damage-signaling via the Tel1-Mre11 complex (TM) pathway. We demonstrate that SAE2 overexpression blocks the TM pathway, suggesting that Sae2 antagonizes Mre11-complex checkpoint functions. To understand how Sae2 regulates the Mre11 complex, we screened for sae2 alleles that behaved as the null with respect to Mre11-complex checkpoint functions, but left nuclease function intact. Phenotypic characterization of these sae2 alleles suggests that Sae2 functions as a multimer and influences the substrate specificity of the Mre11 nuclease. We show that Sae2 oligomerizes independently of DNA damage and that oligomerization is required for its regulatory influence on the Mre11 nuclease and checkpoint functions.
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153
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Shiraishi K, Ogata Y, Hanada K, Kano Y, Ikeda H. Roles of the DNA binding proteins H-NS and StpA in homologous recombination and repair of bleomycin-induced damage in Escherichia coli. Genes Genet Syst 2008; 82:433-9. [PMID: 17991999 DOI: 10.1266/ggs.82.433] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The DNA binding protein H-NS promotes homologous recombination in Escherichia coli, but the role of its paralog StpA in this process remains unclear. Here we show that an hns mutant, but not an stpA mutant, are marginally defective in conjugational recombination and is sensitive to the double-strand-break-inducing agent bleomycin. Interestingly, the hns stpA double mutant is severely defective in homologous recombination and more bleomycin-sensitive than is the hns or stpA single mutant, indicating that the stpA mutation synergistically enhances the defects of homologous recombination and the increased bleomycin-sensitivity in the hns mutant. In addition, the transduction analysis in the hns stpA double mutant indicated that the stpA mutation also enhances the defect of recombination in the hns mutant. These results suggest that H-NS plays an important role in both homologous recombination and repair of bleomycin-induced damage, while StpA can substitute the H-NS function. The recombination analysis of hns single, stpA single, and hns stpA double mutants in the recBC sbcA and recBC sbcBC backgrounds suggested that the reduction of the hns single or hns stpA double mutants may not be due to the defect in a particular recombination pathway, but may be due to the defect in a common process of the pathways. The model for the functions of H-NS and StpA in homologous recombination and double-strand break repair is discussed.
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154
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Chen JM, Ren H, Shaw JE, Wang YJ, Li M, Leung AS, Tran V, Berbenetz NM, Kocíncová D, Yip CM, Reyrat JM, Liu J. Lsr2 of Mycobacterium tuberculosis is a DNA-bridging protein. Nucleic Acids Res 2008; 36:2123-35. [PMID: 18187505 PMCID: PMC2367712 DOI: 10.1093/nar/gkm1162] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Lsr2 is a small, basic protein present in Mycobacterium and related actinomycetes. Recent studies suggest that Lsr2 is a regulatory protein involved in multiple cellular processes including cell wall biosynthesis and antibiotic resistance. However, the underlying molecular mechanisms remain unknown. In this article, we performed biochemical studies of Lsr2–DNA interactions and structure–function analysis of Lsr2. Analysis by atomic force microscopy revealed that Lsr2 has the ability to bridge distant DNA segments, suggesting that Lsr2 plays a role in the overall organization and compactness of the nucleoid. Mutational analysis identified critical residues and selection of dominant negative mutants demonstrated that both DNA binding and protein oligomerization are essential for the normal functions of Lsr2 in vivo. These results provide strong evidence that Lsr2 is a DNA bridging protein, which represents the first identification of such proteins in bacteria phylogenetically distant from the Enterobacteriaceae. DNA bridging by Lsr2 also provides a mechanism of transcriptional regulation by Lsr2.
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Affiliation(s)
- Jeffrey M Chen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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155
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Hirano Y, Takahashi H, Kumeta M, Hizume K, Hirai Y, Otsuka S, Yoshimura SH, Takeyasu K. Nuclear architecture and chromatin dynamics revealed by atomic force microscopy in combination with biochemistry and cell biology. Pflugers Arch 2008; 456:139-53. [PMID: 18172599 DOI: 10.1007/s00424-007-0431-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 11/29/2007] [Accepted: 12/10/2007] [Indexed: 10/22/2022]
Abstract
The recent technical development of atomic force microscopy (AFM) has made nano-biology of the nucleus an attractive and promising field. In this paper, we will review our current understanding of nuclear architecture and dynamics from the structural point of view. Especially, special emphases will be given to: (1) How to approach the nuclear architectures by means of new techniques using AFM, (2) the importance of the physical property of DNA in the construction of the higher-order structures, (3) the significance and implication of the linker and core histones and the nuclear matrix/scaffold proteins for the chromatin dynamics, (4) the nuclear proteins that contribute to the formation of the inner nuclear architecture. Spatio-temporal analyses using AFM, in combination with biochemical and cell biological approaches, will play important roles in the nano-biology of the nucleus, as most of nuclear structures and events occur in nanometer, piconewton and millisecond order. The new applications of AFM, such as recognition imaging, fast-scanning imaging, and a variety of modified cantilevers, are expected to be powerful techniques to reveal the nanostructure of the nucleus.
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Affiliation(s)
- Yasuhiro Hirano
- Kyoto University Graduate School of Biostudies, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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156
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Mellies JL, Barron AMS, Carmona AM. Enteropathogenic and enterohemorrhagic Escherichia coli virulence gene regulation. Infect Immun 2007; 75:4199-210. [PMID: 17576759 PMCID: PMC1951183 DOI: 10.1128/iai.01927-06] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Jay L Mellies
- Biology Department, Reed College, 3203 S.E. Woodstock Boulevard, Portland, OR 97202, USA.
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157
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Navarre WW, McClelland M, Libby SJ, Fang FC. Silencing of xenogeneic DNA by H-NS--facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev 2007; 21:1456-71. [PMID: 17575047 DOI: 10.1101/gad.1543107] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Lateral gene transfer has played a prominent role in bacterial evolution, but the mechanisms allowing bacteria to tolerate the acquisition of foreign DNA have been incompletely defined. Recent studies show that H-NS, an abundant nucleoid-associated protein in enteric bacteria and related species, can recognize and selectively silence the expression of foreign DNA with higher adenine and thymine content relative to the resident genome, a property that has made this molecule an almost universal regulator of virulence determinants in enteric bacteria. These and other recent findings challenge the ideas that curvature is the primary determinant recognized by H-NS and that activation of H-NS-silenced genes in response to environmental conditions occurs through a change in the structure of H-NS itself. Derepression of H-NS-silenced genes can occur at specific promoters by several mechanisms including competition with sequence-specific DNA-binding proteins, thereby enabling the regulated expression of foreign genes. The possibility that microorganisms maintain and exploit their characteristic genomic GC ratios for the purpose of self/non-self-discrimination is discussed.
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Affiliation(s)
- William Wiley Navarre
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, USA
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158
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Nagarajavel V, Madhusudan S, Dole S, Rahmouni AR, Schnetz K. Repression by binding of H-NS within the transcription unit. J Biol Chem 2007; 282:23622-30. [PMID: 17569663 DOI: 10.1074/jbc.m702753200] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
H-NS inhibits transcription by forming repressing nucleoprotein complexes next to promoters. We investigated repression by binding of H-NS within the transcription unit using the bgl and proU operons. Repression of both operons requires a downstream regulatory element (DRE) in addition to an upstream element (URE). In bgl, H-NS binds to a region located between 600 to 700 bp downstream of the transcription start site, whereas in proU the DRE extends up to position +270. We show that binding of H-NS to the bgl-DRE inhibits transcription initiation at a step before open complex formation, as shown before for proU. This was shown by determining the occupancy of the bgl transcription unit by RNA polymerases, expression analysis of bgl and proU reporter constructs, and chloroacetaldehyde footprinting of RNA polymerase promoter complexes. The chloroacetaldehyde footprinting also revealed that RNA polymerase is "poised" at the osmoregulated sigma70-dependent proU promoter at low osmolarity, whereas at high osmolarity poising of RNA polymerase and repression by H-NS are reduced. Furthermore, repression by H-NS via the URE and DRE is synergistic, and the efficiency of repression by H-NS via the DRE inversely correlates with the promoter activity. Repression is high for a promoter of low activity, whereas it is low for a strong promoter. Inefficient repression of strong promoters by H-NS via a DRE may account for high induction levels of proU at high osmolarity and for bgl upon disruption of the URE.
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Affiliation(s)
- V Nagarajavel
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
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159
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Becker NA, Kahn JD, Maher LJ. Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli. Nucleic Acids Res 2007; 35:3988-4000. [PMID: 17553830 PMCID: PMC1919473 DOI: 10.1093/nar/gkm419] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The intrinsic stiffness of DNA limits its ability to be bent and twisted over short lengths, but such deformations are required for gene regulation. One classic paradigm is DNA looping in the regulation of the Escherichia coli lac operon. Lac repressor protein binds simultaneously to two operator sequences flanking the lac promoter. Analysis of the length dependence of looping-dependent repression of the lac operon provides insight into DNA deformation energetics within cells. The apparent flexibility of DNA is greater in vivo than in vitro, possibly because of host proteins that bind DNA and induce sites of flexure. Here we test DNA looping in bacterial strains lacking the nucleoid proteins HU, IHF or H-NS. We confirm that deletion of HU inhibits looping and that quantitative modeling suggests residual looping in the induced operon. Deletion of IHF has little effect. Remarkably, DNA looping is strongly enhanced in the absence of H-NS, and an explanatory model is proposed. Chloroquine titration, psoralen crosslinking and supercoiling-sensitive reporter assays show that the effects of nucleoid proteins on looping are not correlated with their effects on either total or unrestrained supercoiling. These results suggest that host nucleoid proteins can directly facilitate or inhibit DNA looping in bacteria.
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Affiliation(s)
- Nicole A. Becker
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - Jason D. Kahn
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St SW, Rochester, MN 55905 and Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
- *To whom correspondence should be addressed. 507 284 9041507 284 2053
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160
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Travers A, Muskhelishvili G. A common topology for bacterial and eukaryotic transcription initiation? EMBO Rep 2007; 8:147-51. [PMID: 17268506 PMCID: PMC1796767 DOI: 10.1038/sj.embor.7400898] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 12/11/2006] [Indexed: 11/09/2022] Open
Abstract
DNA supercoiling is a major regulator of transcription in bacteria. Negative supercoiling acts both by promoting the formation of nucleoprotein structures containing wrapped DNA and by altering the twist of DNA. The latter affects the initiation of transcription by RNA polymerase as well as recombination processes. Here, we argue that although bacteria and eukaryotes differ in their mode of packaging DNA supercoils, increases in DNA twist are associated with chromatin folding and transcriptional silencing in both. Conversely, decreases in DNA twist are associated with chromatin unfolding and the acquisition of transcriptional competence. In other words, at the most fundamental level, the principles of genetic regulation are common to all organisms. The apparent differences in the details of regulation probably represent alternative methods of fine-tuning similar underlying processes.
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Affiliation(s)
- Andrew Travers
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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161
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Chan YH, Wong JTY. Concentration-dependent organization of DNA by the dinoflagellate histone-like protein HCc3. Nucleic Acids Res 2007; 35:2573-83. [PMID: 17412706 PMCID: PMC1885672 DOI: 10.1093/nar/gkm165] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The liquid crystalline chromosomes of dinoflagellates are the alternative to the nucleosome-based organization of chromosomes in the eukaryotes. These nucleosome-less chromosomes have to devise novel ways to maintain active parts of the genome. The dinoflagellate histone-like protein HCc3 has significant sequence identity with the bacterial DNA-binding protein HU. HCc3 also has a secondary structure resembling HU in silico. We have examined HCc3 in its recombinant form. Experiments on DNA-cellulose revealed its DNA-binding activity is on the C-terminal domain. The N-terminal domain is responsible for intermolecular oligomerization as demonstrated by cross-linking studies. However, HCc3 could not complement Escherichia coli HU-deficient mutants, suggesting functional differences. In ligation assays, HCc3-induced DNA concatenation but not ring closure as the DNA-bending HU does. The basic HCc3 was an efficient DNA condensing agent, but it did not behave like an ordinary polycationic compound. HCc3 also induced specific structures with DNA in a concentration-dependent manner, as demonstrated by atomic force microscopy (AFM). At moderate concentration of HCc3, DNA bridging and bundling were observed; at high concentrations, the complexes were even more condensed. These results are consistent with a biophysical role for HCc3 in maintaining extended DNA loops at the periphery of liquid crystalline chromosomes.
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Affiliation(s)
| | - Joseph T. Y. Wong
- *To whom correspondence should be addressed +86-852-2358-7343+86-852-2358-1559
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162
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Champion K, Higgins NP. Growth rate toxicity phenotypes and homeostatic supercoil control differentiate Escherichia coli from Salmonella enterica serovar Typhimurium. J Bacteriol 2007; 189:5839-49. [PMID: 17400739 PMCID: PMC1952050 DOI: 10.1128/jb.00083-07] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli and Salmonella enterica serovar Typhimurium share high degrees of DNA and amino acid identity for 65% of the homologous genes shared by the two genomes. Yet, there are different phenotypes for null mutants in several genes that contribute to DNA condensation and nucleoid formation. The mutant R436-S form of the GyrB protein has a temperature-sensitive phenotype in Salmonella, showing disruption of supercoiling near the terminus and replicon failure at 42 degrees C. But this mutation in E. coli is lethal at the permissive temperature. A unifying hypothesis for why the same mutation in highly conserved homologous genes of different species leads to different physiologies focuses on homeotic supercoil control. During rapid growth in mid-log phase, E. coli generates 15% more negative supercoils in pBR322 DNA than Salmonella. Differences in compaction and torsional strain on chromosomal DNA explain a complex set of single-gene phenotypes and provide insight into how supercoiling may modulate epigenetic effects on chromosome structure and function and on prophage behavior in vivo.
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Affiliation(s)
- Keith Champion
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294-0024
| | - N. Patrick Higgins
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294-0024
- Corresponding author. Mailing address: KAUL-524, 720 20th Street South, Birmingham, AL 35294. Phone: (205) 934-3299. Fax: (205) 975-5955. E-mail:
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163
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Dame RT, Noom MC, Wuite GJL. Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature 2007; 444:387-90. [PMID: 17108966 DOI: 10.1038/nature05283] [Citation(s) in RCA: 290] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Accepted: 09/26/2006] [Indexed: 11/09/2022]
Abstract
Both prokaryotic and eukaryotic organisms contain DNA bridging proteins, which can have regulatory or architectural functions. The molecular and mechanical details of such proteins are hard to obtain, in particular if they involve non-specific interactions. The bacterial nucleoid consists of hundreds of DNA loops, shaped in part by non-specific DNA bridging proteins such as histone-like nucleoid structuring protein (H-NS), leucine-responsive regulatory protein (Lrp) and SMC (structural maintenance of chromosomes) proteins. We have developed an optical tweezers instrument that can independently handle two DNA molecules, which allows the systematic investigation of protein-mediated DNA-DNA interactions. Here we use this technique to investigate the abundant non-specific nucleoid-associated protein H-NS, and show that H-NS is dynamically organized between two DNA molecules in register with their helical pitch. Our optical tweezers also allow us to carry out dynamic force spectroscopy on non-specific DNA binding proteins and thereby to determine an energy landscape for the H-NS-DNA interaction. Our results explain how the bacterial nucleoid can be effectively compacted and organized, but be dynamic in nature and accessible to DNA-tracking motor enzymes. Finally, our experimental approach is widely applicable to other DNA bridging proteins, as well as to complex DNA interactions involving multiple DNA molecules.
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Affiliation(s)
- Remus T Dame
- Department of Physics and Astronomy and Laser Centre, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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164
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Abstract
Bacteria, like eukaryotic organisms, must compact the DNA molecule comprising their genome and form a functional chromosome. Yet, bacteria do it differently. A number of factors contribute to genome compaction and organization in bacteria, including entropic effects, supercoiling and DNA-protein interactions. A gamut of new experimental techniques have allowed new advances in the investigation of these factors, and spurred much interest in the dynamic response of the chromosome to environmental cues, segregation, and architecture, during both exponential and stationary phases. We review these recent developments with emphasis on the multifaceted roles that DNA-protein interactions play.
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Affiliation(s)
- Joel Stavans
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
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165
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Skoko D, Yoo D, Bai H, Schnurr B, Yan J, McLeod SM, Marko JF, Johnson RC. Mechanism of chromosome compaction and looping by the Escherichia coli nucleoid protein Fis. J Mol Biol 2006; 364:777-98. [PMID: 17045294 PMCID: PMC1988847 DOI: 10.1016/j.jmb.2006.09.043] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 09/06/2006] [Accepted: 09/15/2006] [Indexed: 11/19/2022]
Abstract
Fis, the most abundant DNA-binding protein in Escherichia coli during rapid growth, has been suspected to play an important role in defining nucleoid structure. Using bulk-phase and single-DNA molecule experiments, we analyze the structural consequences of non-specific binding by Fis to DNA. Fis binds DNA in a largely sequence-neutral fashion at nanomolar concentrations, resulting in mild compaction under applied force due to DNA bending. With increasing concentration, Fis first coats DNA to form an ordered array with one Fis dimer bound per 21 bp and then abruptly shifts to forming a higher-order Fis-DNA filament, referred to as a low-mobility complex (LMC). The LMC initially contains two Fis dimers per 21 bp of DNA, but additional Fis dimers assemble into the LMC as the concentration is increased further. These complexes, formed at or above 1 microM Fis, are able to collapse large DNA molecules via stabilization of DNA loops. The opening and closing of loops on single DNA molecules can be followed in real time as abrupt jumps in DNA extension. Formation of loop-stabilizing complexes is sensitive to high ionic strength, even under conditions where DNA bending-compaction is unaltered. Analyses of mutants indicate that Fis-mediated DNA looping does not involve tertiary or quaternary changes in the Fis dimer structure but that a number of surface-exposed residues located both within and outside the helix-turn-helix DNA-binding region are critical. These results suggest that Fis may play a role in vivo as a domain barrier element by organizing DNA loops within the E. coli chromosome.
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Affiliation(s)
- Dunja Skoko
- University of Illinois at Chicago, Department of Physics, Chicago IL 60607-7059
| | - Daniel Yoo
- David Geffen School of Medicine at UCLA, Department of Biological Chemistry, Los Angeles CA 90095-1737
| | - Hua Bai
- University of Illinois at Chicago, Department of Physics, Chicago IL 60607-7059
| | - Bernhard Schnurr
- University of Illinois at Chicago, Department of Physics, Chicago IL 60607-7059
| | - Jie Yan
- National University of Singapore, Department of Physics, Singapore 117542
| | - Sarah M. McLeod
- David Geffen School of Medicine at UCLA, Department of Biological Chemistry, Los Angeles CA 90095-1737
| | - John F. Marko
- Department of Biochemistry, Molecular Biology and Cell Biology, and Department of Physics, Northwestern University, Evanston IL 60208-3500
- *Corresponding authors: Reid C. Johnson, David Geffen School of Medicine at UCLA, Department of Biological Chemistry, Los Angeles CA 90095-1737, ph 310 825-7800, fax 310 206-5272, email , John F. Marko, Northwestern University, Department of Biochemistry, Molecular Biology and Cell Biology, Evanston IL 60208-3500 ph 847 467-1276, fax 847 467-1380, email
| | - Reid C. Johnson
- David Geffen School of Medicine at UCLA, Department of Biological Chemistry, Los Angeles CA 90095-1737
- *Corresponding authors: Reid C. Johnson, David Geffen School of Medicine at UCLA, Department of Biological Chemistry, Los Angeles CA 90095-1737, ph 310 825-7800, fax 310 206-5272, email , John F. Marko, Northwestern University, Department of Biochemistry, Molecular Biology and Cell Biology, Evanston IL 60208-3500 ph 847 467-1276, fax 847 467-1380, email
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166
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Grainger DC, Hurd D, Goldberg MD, Busby SJW. Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res 2006; 34:4642-52. [PMID: 16963779 PMCID: PMC1636352 DOI: 10.1093/nar/gkl542] [Citation(s) in RCA: 221] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Escherichia coli chromosome is condensed into an ill-defined structure known as the nucleoid. Nucleoid-associated DNA-binding proteins are involved in maintaining this structure and in mediating chromosome compaction. We have exploited chromatin immunoprecipitation and high-density microarrays to study the binding of three such proteins, FIS, H-NS and IHF, across the E.coli genome in vivo. Our results show that the distribution of these proteins is biased to intergenic parts of the genome, and that the binding profiles overlap. Hence some targets are associated with combinations of bound FIS, H-NS and IHF. In addition, many regions associated with FIS and H-NS are also associated with RNA polymerase.
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Affiliation(s)
- David C. Grainger
- To whom correspondence should be addressed. Tel: +44 121 414 5435; Fax: +44 121 414 5925;
| | - Douglas Hurd
- Oxford Gene Technology, Begbroke Science ParkSandy Lane, Yarnton, Oxford OX5 1PF, UK
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167
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Limanskaya LA, Limanskii AP. Compaction of single supercoiled DNA molecules adsorbed onto amino mica. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2006. [DOI: 10.1134/s1068162006050074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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168
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Erol I, Jeong KC, Baumler DJ, Vykhodets B, Ho Choi S, Kaspar CW. H-NS controls metabolism and stress tolerance in Escherichia coli O157:H7 that influence mouse passage. BMC Microbiol 2006; 6:72. [PMID: 16911800 PMCID: PMC1560139 DOI: 10.1186/1471-2180-6-72] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 08/15/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND H-NS is a DNA-binding protein with central roles in gene regulation and nucleoid structuring in Escherichia coli. There are over 60 genes that are influenced by H-NS many of which are involved in metabolism. To determine the significance of H-NS-regulated genes in metabolism and stress tolerance, an hns mutant of E. coli O157:H7 was generated (hns::nptI, FRIK47001P) and its growth, metabolism, and gastrointestinal passage compared to the parent strain (43895) and strain FRIK47001P harboring pSC0061 which contains a functional hns and 90-bp upstream of the open-reading frame. RESULTS The hns mutant grew slower and was non-motile in comparison to the parent strain. Carbon and nitrogen metabolism was significantly altered in the hns mutant, which was incapable of utilizing 42 carbon, and 19 nitrogen sources that the parent strain metabolized. Among the non-metabolized substrates were several amino acids, organic acids, and key metabolic intermediates (i.e., pyruvate) that limit carbon acquisition and energy generation. Growth studies determined that the parent strain grew in LB containing 14 to 15% bile or bile salts, while the hns mutant grew in 6.5 and 9% of these compounds, respectively. Conversely, log-phase cells of the hns mutant were significantly (p < 0.05) more acid tolerant than the parent strain and hns mutant complemented with pSC0061. In mouse passage studies, the parent strain was recovered at a higher frequency (p < 0.01) than the hns mutant regardless of whether log- or stationary-phase phase cells were orally administered. CONCLUSION These results demonstrate that H-NS is a powerful regulator of carbon and nitrogen metabolism as well as tolerance to bile salts. It is likely that the metabolic impairments and/or the reduced bile tolerance of the E. coli O157:H7 hns mutant decreased its ability to survive passage through mice. Collectively, these results expand the influence of H-NS on carbon and nitrogen metabolism and highlight its role in the ability of O157:H7 strains to respond to changing nutrients and conditions encountered in the environment and its hosts.
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Affiliation(s)
- Irfan Erol
- Department of Food Hygiene and Technology, University of Ankara, Ankara, Turkey
| | - Kwang-Cheol Jeong
- Department of Food Microbiology and Toxicology, University of Wisconsin, Madison, Wisconsin 53706-1187, USA
| | - David J Baumler
- Cellular and Molecular Biology, University of Wisconsin, Madison, Wisconsin 53706-1187, USA
| | - Boris Vykhodets
- Department of Food Microbiology and Toxicology, University of Wisconsin, Madison, Wisconsin 53706-1187, USA
| | - Sang Ho Choi
- Department of Food Science and Technology, Seoul National University, Seoul 151-742, South Korea
| | - Charles W Kaspar
- Department of Food Microbiology and Toxicology, University of Wisconsin, Madison, Wisconsin 53706-1187, USA
- Cellular and Molecular Biology, University of Wisconsin, Madison, Wisconsin 53706-1187, USA
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169
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Cozzarelli NR, Cost GJ, Nöllmann M, Viard T, Stray JE. Giant proteins that move DNA: bullies of the genomic playground. Nat Rev Mol Cell Biol 2006; 7:580-8. [PMID: 16936698 DOI: 10.1038/nrm1982] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As genetic material DNA is wonderful, but as a macromolecule it is unruly, voluminous and fragile. Without the action of DNA replicases, topoisomerases, helicases, translocases and recombinases, the genome would collapse into a topologically entangled random coil that would be useless to the cell. We discuss the organization, movement and energetics of these proteins that are crucial to the preservation of a molecule that has such beautiful biological but challenging physical properties.
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Affiliation(s)
- Nicholas R Cozzarelli
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720-3204, USA
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170
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Wang Q, Mordukhova EA, Edwards AL, Rybenkov VV. Chromosome condensation in the absence of the non-SMC subunits of MukBEF. J Bacteriol 2006; 188:4431-41. [PMID: 16740950 PMCID: PMC1482961 DOI: 10.1128/jb.00313-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
MukBEF is a bacterial SMC (structural maintenance of chromosome) complex required for chromosome partitioning in Escherichia coli. We report that overproduction of MukBEF results in marked chromosome condensation. This condensation is rapid and precedes the effects of overproduction on macromolecular synthesis. Condensed nucleoids are often mispositioned; however, cell viability is only mildly affected. The overproduction of MukB leads to a similar chromosome condensation, even in the absence of MukE and MukF. Thus, the non-SMC subunits of MukBEF play only an auxiliary role in chromosome condensation. MukBEF, however, was often a better condensin than MukB. Furthermore, the chromosome condensation by MukB did not rescue the temperature sensitivity of MukEF-deficient cells, nor did it suppress the high frequency of anucleate cell formation. We infer that the role of MukBEF in stabilizing chromatin architecture is more versatile than its role in controlling chromosome size. We further propose that MukBEF could be directly involved in chromosome segregation.
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Affiliation(s)
- Qinhong Wang
- University of Oklahoma, Department of Chemistry and Biochemistry, 620 Parrington Oval, Norman, OK 73019, USA
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171
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Zimmerman SB. Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase. J Struct Biol 2005; 153:160-75. [PMID: 16384714 DOI: 10.1016/j.jsb.2005.10.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 09/23/2005] [Accepted: 10/18/2005] [Indexed: 12/29/2022]
Abstract
The genomic DNA of Escherichia coli occurs in compact bodies known as nucleoids. Organization and structure of nucleoids are poorly understood. Compact, characteristically shaped, nucleoids isolated by the polylysine-spermidine procedure were visualized by DNA fluorescence microscopy. Treatment with urea or trypsin converted compact nucleoids to partially expanded forms. The transition in urea solutions was accompanied by release of most DNA-associated proteins; the transition point between compact and partially expanded forms was not changed by the loss of the proteins nor was it changed in nucleoids isolated from cells after exposure to chloramphenicol or from cells in which Dps, Fis, or H-NS and StpA had been deleted. Partially expanded forms became dispersed upon RNase exposure, indicating a role of RNA in maintaining the partial expansion. Partially expanded forms that had been stripped of most DNA-associated proteins were recompacted by polyethylene glycol 8,000, a macromolecular crowding agent, in a cooperative transition. DNA-associated proteins are suggested to have relatively little effect on the phase-like behavior of the cellular nucleoid. Changes in the urea transition indicate that a previously described procedure for compaction of polylysine-spermidine nucleoids may have an artifactual basis, and raise questions about reports of repetitive local structures involving the DNA of lysed cells.
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Affiliation(s)
- Steven B Zimmerman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0560, USA
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172
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Hardy CD, Cozzarelli NR. A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure. Mol Microbiol 2005; 57:1636-52. [PMID: 16135230 DOI: 10.1111/j.1365-2958.2005.04799.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chromosomes are divided into topologically independent regions, called domains, by the action of uncharacterized barriers. With the goal of identifying domain barrier components, we designed a genetic selection for mutants with reduced negative supercoiling of the Escherichia coli chromosome. We employed a strain that contained two chromosomally located reporter genes under the control of a supercoiling-sensitive promoter and used transposon mutagenesis to generate a wide range of mutants. We subjected the selected mutants to a series of secondary screens and identified five proteins as modulators of chromosomal supercoiling in vivo. Three of these proteins: H-NS, Fis and DksA, have clear ties to chromosome biology. The other two proteins, phosphoglucomutase (Pgm) and transketolase (TktA), are enzymes involved in carbohydrate metabolism and have not previously been shown to affect DNA. Deletion of any of the identified genes specifically affected chromosome topology, without affecting plasmid supercoiling. We suggest that at least H-NS, Fis and perhaps TktA assist directly in the supercoiling of domains by forming topological barriers on the E. coli chromosome.
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Affiliation(s)
- Christine D Hardy
- Department of Molecular and Cell Biology, 16 Barker Hall, University of California, Berkeley, CA 94720-3204, USA
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173
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Abstract
During a normal cell cycle, chromosomes are exposed to many biochemical reactions that require specific types of DNA movement. Separation forces move replicated chromosomes into separate sister cell compartments during cell division, and the contemporaneous acts of DNA replication, RNA transcription and cotranscriptional translation of membrane proteins cause specific regions of DNA to twist, writhe and expand or contract. Recent experiments indicate that a dynamic and stochastic mechanism creates supercoil DNA domains soon after DNA replication. Domain structure is subsequently reorganized by RNA transcription. Examples of transcription-dependent chromosome remodelling are also emerging from eukaryotic cell systems.
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Affiliation(s)
| | | | - N. Patrick Higgins
- *For correspondence. E-mail; Tel. (+1) 205 934 3299; Fax (+1) 205 975 5955
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174
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Keatch SA, Leonard PG, Ladbury JE, Dryden DTF. StpA protein from Escherichia coli condenses supercoiled DNA in preference to linear DNA and protects it from digestion by DNase I and EcoKI. Nucleic Acids Res 2005; 33:6540-6. [PMID: 16299353 PMCID: PMC1289078 DOI: 10.1093/nar/gki951] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The nucleoid-associated protein, StpA, of Escherichia coli binds non-specifically to double-stranded DNA (dsDNA) and apparently forms bridges between adjacent segments of the DNA. Such a coating of protein on the DNA would be expected to hinder the action of nucleases. We demonstrate that StpA binding hinders dsDNA cleavage by both the non-specific endonuclease, DNase I, and by the site-specific type I restriction endonuclease, EcoKI. It requires approximately one StpA molecule per 250–300 bp of supercoiled DNA and approximately one StpA molecule per 60–100 bp on linear DNA for strong inhibition of the nucleases. These results support the role of StpA as a nucleoid-structuring protein which binds DNA segments together. The inhibition of EcoKI, which cleaves DNA at a site remote from its initial target sequence after extensive DNA translocation driven by ATP hydrolysis, suggests that these enzymes would be unable to function on chromosomal DNA even during times of DNA damage when potentially lethal, unmodified target sites occur on the chromosome. This supports a role for nucleoid-associated proteins in restriction alleviation during times of cell stress.
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Affiliation(s)
| | - P. G. Leonard
- Department of Biochemistry and Molecular Biology, University College LondonGower Street, London WC1E 6BT, UK
| | - J. E. Ladbury
- Department of Biochemistry and Molecular Biology, University College LondonGower Street, London WC1E 6BT, UK
| | - D. T. F. Dryden
- To whom correspondence should be addressed. Tel: +44 131 650 4735; Fax: +44 131 650 6453;
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175
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Ono S, Goldberg M, Olsson T, Esposito D, Hinton J, Ladbury J. H-NS is a part of a thermally controlled mechanism for bacterial gene regulation. Biochem J 2005; 391:203-13. [PMID: 15966862 PMCID: PMC1276917 DOI: 10.1042/bj20050453] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 06/20/2005] [Accepted: 06/21/2005] [Indexed: 01/03/2023]
Abstract
Temperature is a primary environmental stress to which micro-organisms must be able to adapt and respond rapidly. Whereas some bacteria are restricted to specific niches and have limited abilities to survive changes in their environment, others, such as members of the Enterobacteriaceae, can withstand wide fluctuations in temperature. In addition to regulating cellular physiology, pathogenic bacteria use temperature as a cue for activating virulence gene expression. This work confirms that the nucleoid-associated protein H-NS (histone-like nucleoid structuring protein) is an essential component in thermoregulation of Salmonella. On increasing the temperature from 25 to 37 degrees C, more than 200 genes from Salmonella enterica serovar Typhimurium showed H-NS-dependent up-regulation. The thermal activation of gene expression is extremely rapid and change in temperature affects the DNA-binding properties of H-NS. The reduction in gene repression brought about by the increase in temperature is concomitant with a conformational change in the protein, resulting in the decrease in size of high-order oligomers and the appearance of increasing concentrations of discrete dimers of H-NS. The present study addresses one of the key complex mechanisms by which H-NS regulates gene expression.
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Affiliation(s)
- Shusuke Ono
- *Department of Biochemistry and Molecular Biology, and Institute of Structural Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - Martin D. Goldberg
- †Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, U.K
| | - Tjelvar Olsson
- *Department of Biochemistry and Molecular Biology, and Institute of Structural Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - Diego Esposito
- *Department of Biochemistry and Molecular Biology, and Institute of Structural Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - Jay C. D. Hinton
- †Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, U.K
| | - John E. Ladbury
- *Department of Biochemistry and Molecular Biology, and Institute of Structural Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
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176
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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: 239] [Impact Index Per Article: 12.6] [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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177
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Zhang W, Carneiro MJVM, Turner IJ, Allen S, Roberts CJ, Soultanas P. The Bacillus subtilis DnaD and DnaB proteins exhibit different DNA remodelling activities. J Mol Biol 2005; 351:66-75. [PMID: 16002087 PMCID: PMC3034352 DOI: 10.1016/j.jmb.2005.05.065] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2005] [Revised: 05/23/2005] [Accepted: 05/24/2005] [Indexed: 11/21/2022]
Abstract
Primosomal protein cascades load the replicative helicase onto DNA. In Bacillus subtilis a putative primosomal cascade involving the DnaD-DnaB-DnaI proteins has been suggested to participate in both the DnaA and PriA-dependent loading of the replicative helicase DnaC onto the DNA. Recently we discovered that DnaD has a global remodelling DNA activity suggesting a more widespread role in bacterial nucleoid architecture. Here, we show that DnaB forms a "square-like" tetramer with a hole in the centre and suggest a model for its interaction with DNA. It has a global DNA remodelling activity that is different from that of DnaD. Whereas DnaD opens up supercoiled DNA, DnaB acts as a lateral compaction protein. The two competing activities can act together on a supercoiled plasmid forming two topologically distinct poles; one compacted with DnaB and the other open with DnaD. We propose that the primary roles of DnaB and DnaD are in bacterial nucleoid architecture control and modulation, and their effects on the initiation of DNA replication are a secondary role resulting from architectural perturbations of chromosomal DNA.
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Affiliation(s)
- Wenke Zhang
- Centre for Biomolecular Sciences, School of Chemistry University of Nottingham University Park, Nottingham NG7, 2RD, UK
| | - Maria J. V. M. Carneiro
- Centre for Biomolecular Sciences, School of Chemistry University of Nottingham University Park, Nottingham NG7, 2RD, UK
| | - Ian J. Turner
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, University Park Nottingham NG7 2RD, UK
| | - Stephanie Allen
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, University Park Nottingham NG7 2RD, UK
| | - Clive J. Roberts
- Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, University Park Nottingham NG7 2RD, UK
| | - Panos Soultanas
- Centre for Biomolecular Sciences, School of Chemistry University of Nottingham University Park, Nottingham NG7, 2RD, UK
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178
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Stella S, Spurio R, Falconi M, Pon CL, Gualerzi CO. Nature and mechanism of the in vivo oligomerization of nucleoid protein H-NS. EMBO J 2005; 24:2896-905. [PMID: 16052211 PMCID: PMC1187939 DOI: 10.1038/sj.emboj.7600754] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2004] [Accepted: 06/29/2005] [Indexed: 11/08/2022] Open
Abstract
Two types of two-hybrid systems demonstrate that the transcriptional repressor, nucleoid-associated protein H-NS (histone-like, nucleoid structuring protein) forms dimers and tetramers in vivo, the latter being the active form of the protein. The H-NS 'protein oligomerization' domain (N-domain) is unable to oligomerize in the absence of the intradomain linker while the 'DNA-binding' C-domain clearly displays a protein-protein interaction capacity, which contributes to H-NS tetramerization and which is lost following Pro115 mutation. Linker deletion or substitution with KorB linker abolishes H-NS oligomerization. A model describing H-NS dimerization and tetramerization based on all available data and suggesting the existence in the tetramer of a bundle of four alpha-helices, each contributed by an H-NS monomer, is presented.
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Affiliation(s)
- Stefano Stella
- Department of Biology MCA, Laboratory of Genetics, University of Camerino, Camerino (MC), Italy
| | - Roberto Spurio
- Department of Biology MCA, Laboratory of Genetics, University of Camerino, Camerino (MC), Italy
| | - Maurizio Falconi
- Department of Biology MCA, Laboratory of Genetics, University of Camerino, Camerino (MC), Italy
| | - Cynthia L Pon
- Department of Biology MCA, Laboratory of Genetics, University of Camerino, Camerino (MC), Italy
| | - Claudio O Gualerzi
- Department of Biology MCA, Laboratory of Genetics, University of Camerino, Camerino (MC), Italy
- Department of Biology MCA, Laboratory of Genetics, University of Camerino, 62032 Camerino (MC), Italy. Tel.: +39 0737 403240; Fax: +39 0737 636216; E-mail:
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179
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Marek J, Demjénová E, Tomori Z, Janácek J, Zolotová I, Valle F, Favre M, Dietler G. Interactive measurement and characterization of DNA molecules by analysis of AFM images. Cytometry A 2005; 63:87-93. [PMID: 15648079 DOI: 10.1002/cyto.a.20105] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND In the past few years, computer-based analysis of atomic-force microscopic images has acquired increasing importance for studying biomolecules such as DNA. On the one hand, fully automated methods do not allow analysis of complex shapes; on the other hand, manual methods are usually time consuming and inaccurate. The semiautomated approach presented in this report overcomes the drawbacks of both methods. METHODS Two kinds of images were analyzed: computer-generated filaments that modeled circular DNA molecules on a surface and real atomic-force microscopic images of DNA molecules adsorbed on an appropriate substrate surface. RESULTS The algorithm was tested on a group of 140 simulated and 189 real plasmids with a nominal length of 913 nm. The accuracy of the length measurement was statistically evaluated on the ensemble of molecules, with particular attention to the influence of the noise. Mean contour lengths of 912 +/- 5 nm and 910 +/- 47 nm were found for simulated and real plasmids, respectively. The measured end-to-end distance of lambda-DNA molecules as a function of their contour length is reported, from which it is possible to estimate the stiffness of the DNA molecules adsorbed onto a surface; the value obtained for the DNA persistence length (42 +/- 5 nm) is consistent with values measured by other imaging techniques. CONCLUSIONS An interactive algorithm for DNA molecule measurements based on the detection of the filament ridge line in a digitized image is presented. The simulation of artificial filaments combined with the experimental data demonstrates that the proposed method can be a valuable tool for the DNA contour length evaluation, especially in the case of complex shapes where the use of automatic methods is not possible.
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Affiliation(s)
- J Marek
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 043 53 Kosice, Slovak Republic.
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180
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Thanbichler M, Viollier PH, Shapiro L. The structure and function of the bacterial chromosome. Curr Opin Genet Dev 2005; 15:153-62. [PMID: 15797198 DOI: 10.1016/j.gde.2005.01.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Advances in microscopic and cell biological techniques have considerably improved our understanding of bacterial chromosome organization and dynamics. The nucleoid was formerly perceived to be an amorphous entity divided into ill-defined domains of supercoiling that are randomly deposited in the cell. Recent work, however, has demonstrated a remarkable degree of spatial organization. A highly ordered chromosome structure, established while DNA replication and partitioning are in progress, is maintained and propagated during growth. Duplication of the chromosome and partitioning of the newly generated daughter strands are interwoven processes driven by the dynamic interplay between the synthesis, segregation and condensation of DNA. These events are intimately coupled with the bacterial cell cycle and exhibit a previously unanticipated complexity reminiscent of eukaryotic systems.
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Affiliation(s)
- Martin Thanbichler
- Department of Developmental Biology, Stanford University School of Medicine, Beckman Center B300, 279 Campus Drive, Stanford, CA 94305-5329, USA
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181
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Giangrossi M, Zattoni S, Tramonti A, De Biase D, Falconi M. Antagonistic role of H-NS and GadX in the regulation of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli. J Biol Chem 2005; 280:21498-505. [PMID: 15795232 DOI: 10.1074/jbc.m413255200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
One of the most efficient systems of acid resistance in Escherichia coli, the gad system, is based on the coordinated action of two isoforms of glutamate decarboxylase (GadA and GadB) and of a specific glutamate/gamma-aminobutyrate antiporter (GadC). The gadA/BC genes, activated in response to acid stress and in stationary phase cells, are subjected to complex circuits of regulation involving sigma70, sigmaS, cAMP receptor protein, H-NS, EvgAS, TorRS, GadE, GadX, GadW, and YdeO. Herein, we provide evidence that the nucleoid-associated protein H-NS directly functions as repressor of gadA, one of the structural genes, and gadX, a regulatory gene encoding one of the primary activators of the gad system. Band shift and DNase I footprints reveal that H-NS indeed binds to specific sites in the promoter regions of gadA and gadX and represses the transcription of these genes both in an in vitro system and in vivo. Moreover, we show that a maltose-binding protein MalE-GadX fusion is able to stimulate the promoter activity of gadA/BC, thus indicating that GadX is by itself able to up-regulate the gad genes and that a functional competition between H-NS and GadX takes place at the gadA promoter. Altogether, our results indicate that H-NS directly inhibits gadA and gadX transcription and, by controlling the intracellular level of the activator GadX, indirectly affects the expression of the whole gad system.
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Affiliation(s)
- Mara Giangrossi
- Laboratorio di Genetica, Dipartimento di Biologia MCA, Università di Camerino, 62032 Camerino (MC), Italy
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182
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Dame RT, Luijsterburg MS, Krin E, Bertin PN, Wagner R, Wuite GJL. DNA bridging: a property shared among H-NS-like proteins. J Bacteriol 2005; 187:1845-8. [PMID: 15716456 PMCID: PMC1064010 DOI: 10.1128/jb.187.5.1845-1848.2005] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleoid-associated protein H-NS is thought to play an essential role in the organization of bacterial chromatin in Escherichia coli. Homologues, often with very low sequence identity, are found in most gram-negative bacteria. Microscopic analysis reveals that, despite limited sequence identity, their structural organization results in similar DNA binding properties.
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Affiliation(s)
- Remus T Dame
- Physics of Complex Systems, Department of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, NL-1081 HV Amsterdam, The Netherlands.
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183
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Amit R, Oppenheim AB, Stavans J. Single molecule elasticity measurements: a biophysical approach to bacterial nucleoid organization. Biophys J 2005; 87:1392-3. [PMID: 15298941 PMCID: PMC1304477 DOI: 10.1529/biophysj.104.039503] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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184
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Vijayakumar SRV, Kirchhof MG, Patten CL, Schellhorn HE. RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis. J Bacteriol 2005; 186:8499-507. [PMID: 15576800 PMCID: PMC532425 DOI: 10.1128/jb.186.24.8499-8507.2004] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RpoS is a conserved alternative sigma factor that regulates the expression of many stress response genes in Escherichia coli. The RpoS regulon is large but has not yet been completely characterized. In this study, we report the identification of over 100 RpoS-dependent fusions in a genetic screen based on the differential expression of an operon-lacZ fusion bank in rpoS mutant and wild-type backgrounds. Forty-eight independent gene fusions were identified, including several in well-characterized RpoS-regulated genes, such as osmY, katE, and otsA. Many of the other fusions mapped to genes of unknown function or to genes that were not previously known to be under RpoS control. Based on the homology to other known bacterial genes, some of the RpoS-regulated genes of unknown functions are likely important in nutrient scavenging.
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185
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Song Y, Li Z, Liu Z, Wei G, Wang L, Sun L. Immobilization of DNA on 11-mercaptoundecanoic acid-modified gold (111) surface for atomic force microscopy imaging. Microsc Res Tech 2005; 68:59-64. [PMID: 16228986 DOI: 10.1002/jemt.20235] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Immobilized DNA on preformed 11-mercaptoundecanoic acids (MUDA) self-assembled monolayers (SAMs) on a gold (111) surface was bound by a divalent cation bridges was imaged by atomic force microscopy (AFM). The DNA immobilization was attributed to the formation of ionic bridges between the carboxylate groups of MUDA and the phosphate groups of DNA. AFM images revealed that DNA molecules could be immobilized strongly enough to permit stable and reproducible imaging. The effect of different bridge cations, such as Mg(2+), Zn(2+) and Cu(2+), and the pH of DNA assembled solution on immobilization and conformation of DNA was studied. Plasmid DNA pBR 322/Pst I molecules were straightened by using a molecular combing technique on the MUDA surface.
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Affiliation(s)
- Yonghai Song
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences
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186
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Thanbichler M, Wang SC, Shapiro L. The bacterial nucleoid: A highly organized and dynamic structure. J Cell Biochem 2005; 96:506-21. [PMID: 15988757 DOI: 10.1002/jcb.20519] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent advances in bacterial cell biology have revealed unanticipated structural and functional complexity, reminiscent of eukaryotic cells. Particular progress has been made in understanding the structure, replication, and segregation of the bacterial chromosome. It emerged that multiple mechanisms cooperate to establish a dynamic assembly of supercoiled domains, which are stacked in consecutive order to adopt a defined higher-level organization. The position of genetic loci on the chromosome is thereby linearly correlated with their position in the cell. SMC complexes and histone-like proteins continuously remodel the nucleoid to reconcile chromatin compaction with DNA replication and gene regulation. Moreover, active transport processes ensure the efficient segregation of sister chromosomes and the faithful restoration of nucleoid organization while DNA replication and condensation are in progress.
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Affiliation(s)
- Martin Thanbichler
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305-5329, USA
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187
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Klungsøyr HK, Skarstad K. Positive supercoiling is generated in the presence of Escherichia coli SeqA protein. Mol Microbiol 2004; 54:123-31. [PMID: 15458410 DOI: 10.1111/j.1365-2958.2004.04239.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In Escherichia coli, the SeqA protein is known as a negative regulator of chromosome replication. This protein is also suggested to have a role in chromosome organization. SeqA preferentially binds to hemi-methylated DNA and is by immunofluorescence microscopy seen as foci situated at the replication factories. Loss of SeqA leads to increased negative supercoiling of the DNA. We show that purified SeqA protein bound to fully methylated, covalently closed or nicked circular DNA generates positive supercoils in vitro in the presence of topoisomerase I or ligase respectively. This means that binding of SeqA changes either the twist or the writhe of the DNA. The ability to affect the topology of DNA suggests that SeqA may take part in the organization of the chromosome in vivo. The topology change performed by SeqA occurred also on unmethylated plasmids. It is, however, reasonable to suppose that in vivo the major part of such activity is performed on hemi-methylated DNA at the replication factories and presumably forms the basis for the characteristic SeqA foci observed by fluorescence microscopy.
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188
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Will WR, Lu J, Frost LS. The role of H-NS in silencing F transfer gene expression during entry into stationary phase. Mol Microbiol 2004; 54:769-82. [PMID: 15491366 DOI: 10.1111/j.1365-2958.2004.04303.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conjugative ability of the F plasmid of Escherichia coli is highly growth phase dependent, with plasmid transfer efficiency dropping rapidly as donor cells progress through the growth cycle towards stationary phase. Transfer is dependent on the expression of the plasmid transfer (tra) genes, which are controlled by three plasmid-encoded regulatory proteins: TraJ, TraY and TraM. Here, we show that the nucleoid-associated host protein, H-NS, acts to repress the expression of traM and traJ as cells enter stationary phase, thereby decreasing mating ability to barely detectable levels. Sequence analysis identified regions of predicted intrinsic curvature, to which H-NS preferentially binds, at the promoters of both traM and traJ. H-NS binding at these regions was then confirmed by electrophoretic mobility shift and DNase I protection footprinting assays. Immunoblot assays displayed a significant increase in TraJ and TraM levels in an hns mutant strain. These findings were further supported by Northern and primer extension analyses which showed that whereas both genes were only expressed in early exponential phase in wild-type cells, hns mutant cells exhibited drastic derepression throughout the growth cycle. Transcriptional fusion studies of the individual promoters demonstrated that H-NS-mediated repression was observed when the promoters of both traM and traJ were present in cis to each other. This suggests that H-NS may bind to an extended region of the F plasmid, acting as a regional silencer of promoters for traJ and traM.
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Affiliation(s)
- William R Will
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G2E9, Canada
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189
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Dame RT, Wuite GJL. On the role of H-NS in the organization of bacterial chromatin: from bulk to single molecules and back. Biophys J 2004; 85:4146-8. [PMID: 14645101 PMCID: PMC1303713 DOI: 10.1016/s0006-3495(03)74826-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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190
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Dole S, Nagarajavel V, Schnetz K. The histone-like nucleoid structuring protein H-NS represses the Escherichia coli bgl operon downstream of the promoter. Mol Microbiol 2004; 52:589-600. [PMID: 15066043 DOI: 10.1111/j.1365-2958.2004.04001.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Specificity of repression by the histone-like nucleoid structuring protein and pleiotropic regulator, H-NS, is exceptionally high in case of the Escherichia coli bgl (beta-glucoside) operon. Here we present evidence that H-NS represses the operon at two levels. The binding of H-NS to an upstream silencer results in an approximately threefold repression of the catabolite gene regulator protein (CRP) dependent bgl promoter. In addition, H-NS binds to a silencer region located approximately 600-700 base pairs downstream of the promoter, within the coding region of first gene, bglG, resulting in a approximately sevenfold further decrease of expression. Repression by H-NS at the downstream silencer requires termination factor Rho and is reduced by translation of the bglG mRNA, but is independent of the promoter. This suggests that H-NS induces polarity of transcription by acting as a roadblock to the elongating RNA polymerase. The control of the bgl operon by H-NS at two levels results in a highly specific repression.
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Affiliation(s)
- Sudhanshu Dole
- Institute for Genetics, University Cologne,Weyertal 121, 50931 Cologne, Germany
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191
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Rimsky S. Structure of the histone-like protein H-NS and its role in regulation and genome superstructure. Curr Opin Microbiol 2004; 7:109-14. [PMID: 15063845 DOI: 10.1016/j.mib.2004.02.001] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
H-NS belongs to the group of histone-like proteins in Gram-negative bacteria and is also a pleiotropic regulator of genes implicated in many responses to environmental changes. It plays a dual role in structuring DNA and in regulating transcription. Recent advances have been made in elucidating the structure and oligomerisation properties of this protein, thus aiding in the understanding of the molecular relationship between its two major functions.
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Affiliation(s)
- Sylvie Rimsky
- Enzymologie et Cinétique Structurale, LBPA, UMR 8113, Ecole Normale Supérieure de Cachan/CNRS/ Université Paris XI, 61 Avenue du Président Wilsons, 94235 Cachan cedex, France.
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192
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Affiliation(s)
- Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College, University of Dublin, Dublin 2, Ireland.
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193
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Prosseda G, Falconi M, Giangrossi M, Gualerzi CO, Micheli G, Colonna B. The virF promoter in Shigella: more than just a curved DNA stretch. Mol Microbiol 2004; 51:523-37. [PMID: 14756791 DOI: 10.1046/j.1365-2958.2003.03848.x] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the human enteropathogen Shigella transcription of virF, the primary regulator of the invasion functions, is strictly temperature-dependent and is antagonistically mediated by H-NS and FIS, which bind to specific sites on the virF promoter. Here we report on the relevance of DNA geometry to the thermoregulation of virF and demonstrate that the virF promoter hosts a major DNA bend halfway between two H-NS sites. The bent region has been mutagenized in vitro to mimic temperature-induced changes of DNA curvature. Functional analysis of curvature mutants and of promoter constructs in which the two H-NS sites are phased-out by a half-helix turn reveals that modifying the spatial relationships between these sites severely affects the interaction of H-NS with the virF promoter, as well as its in vivo and in vitro temperature-dependent activity. The role of promoter curvature as thermosensor is also compatible with the present observation that, with increasing temperature, the virF bending centre moves downstream at a rate having its maximum around the transition temperature, abruptly unmasking a binding site for the transcriptional activator FIS.
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Affiliation(s)
- Gianni Prosseda
- Dip. Biologia Cellulare e dello Sviluppo, University La Sapienza, 00185 Roma, Italy
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194
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van Noort J, Verbrugge S, Goosen N, Dekker C, Dame RT. Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc Natl Acad Sci U S A 2004; 101:6969-74. [PMID: 15118104 PMCID: PMC406450 DOI: 10.1073/pnas.0308230101] [Citation(s) in RCA: 228] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nucleoid-associated protein HU is one of the most abundant proteins in Escherichia coli and has been suggested to play an important role in bacterial nucleoid organization and regulation. Although the regulatory aspects of HU have been firmly established, much less is understood about the role of HU in shaping the bacterial nucleoid. In both functions (local) modulation of DNA architecture seems an essential feature, but information on the mechanical properties of this type of sequence-independent nucleoprotein complex is scarce. In this study we used magnetic tweezers and atomic force microscopy to quantify HU-induced DNA bending and condensation. Both techniques revealed that HU can have two opposing mechanical effects depending on the protein concentration. At concentrations <100 nM, individual HU dimers induce very flexible bends in DNA that are responsible for DNA compaction up to 50%. At higher HU concentrations, a rigid nucleoprotein filament is formed in which HU appears to arrange helically around the DNA without inducing significant condensation.
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Affiliation(s)
- John van Noort
- Molecular Biophysics, Kavli Institute of Nanoscience, Delft University of Technology, NL-2628 CJ, Delft, The Netherlands.
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195
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Trun N, Johnston D. Folding chromosomes in bacteria: examining the role of Csp proteins and other small nucleic acid-binding proteins. Curr Top Dev Biol 2004; 55:173-201. [PMID: 12959196 DOI: 10.1016/s0070-2153(03)01004-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Nancy Trun
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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196
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Beloin C, Deighan P, Doyle M, Dorman CJ. Shigella flexneri 2a strain 2457T expresses three members of the H-NS-like protein family: characterization of the Sfh protein. Mol Genet Genomics 2003; 270:66-77. [PMID: 12898223 DOI: 10.1007/s00438-003-0897-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2003] [Accepted: 07/02/2003] [Indexed: 11/28/2022]
Abstract
Shigella flexneri 2a is known to express the H-NS nucleoid-structuring protein and the paralogous protein StpA. Using bioinformatic analysis we have now discovered a third member of the H-NS protein family, Sfh (Shigella flexneri H-NS-like protein), in strain 2457T. This protein is encoded by the sfh gene, which is located on a high-molecular-mass plasmid that is closely related to the self-transmissible plasmid R27. When expressed in Escherichia coli, the Sfh protein can complement an hns null mutation, restoring wild-type Bgl, porin protein, and mucoidy phenotypes, and wild-type expression of the fliC and proU genes. While a knockout mutation in the sfh gene alone had no effect on the expression of virulence genes in S. flexneri, an additive effect on virulence gene derepression was seen when the sfh lesion was combined with a mutation in hns. Over-expression of the sfh gene repressed expression of the VirB virulence regulatory protein and transcription of a VirB-dependent structural gene promoter. The purified Sfh protein bound specifically to DNA sequences containing the promoters of the virF and virB virulence regulatory genes. These findings show that Sfh has the ability to influence genetic events beyond the genetic element that encodes it, including the expression of the S. flexneri virulence genes. They raise the possibility of a triangular relationship among three closely related proteins with broad consequences for genetic events in the bacterium that harbours them.
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Affiliation(s)
- C Beloin
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Dublin 2, Ireland
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197
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Leliveld SR, Dame RT, Mommaas MA, Koerten HK, Wyman C, Danen-van Oorschot AAAM, Rohn JL, Noteborn MHM, Abrahams JP. Apoptin protein multimers form distinct higher-order nucleoprotein complexes with DNA. Nucleic Acids Res 2003; 31:4805-13. [PMID: 12907722 PMCID: PMC169900 DOI: 10.1093/nar/gkg661] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The chicken anaemia virus-derived protein apoptin is a tumour-specific cell-killing agent. It is biologically active as a highly stable, multimeric complex, consisting of 30-40 monomers. In tumour cells, but negligibly in normal cells, apoptin is imported into the nucleus prior to the induction of apoptosis. Immunoelectron microscopic data we report here indicate that apoptin predominantly co-localises with heterochromatin and nucleoli within tumour cells. Apoptin's preference for these DNA-dense nuclear bodies may be explained by our finding that apoptin cooperatively forms distinct superstructures with DNA in vitro. These superstructures do not grow beyond a diameter of approximately 200 nm, containing up to 20 multimeric apoptin complexes and approximately 3 kb of DNA. Furthermore, we show a single apoptin multimer to have eight independent, non-specific DNA-binding sites which preferentially bind strand ends, but which can also collaborate to bind longer stretches of DNA. Apoptin's high affinity for naked, undecorated double- and single-stranded DNA and for DNA fibre ends suggests that it may also capture such DNA in superstructures in vivo. Since these forms of DNA are predominantly found in transcriptionally active, replicating and damaged DNA, apoptin could be triggering apoptosis by interfering with DNA transcription and synthesis.
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198
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Stuger R, Woldringh CL, van der Weijden CC, Vischer NOE, Bakker BM, van Spanning RJM, Snoep JL, Westerhoff HV. DNA supercoiling by gyrase is linked to nucleoid compaction. Mol Biol Rep 2003; 29:79-82. [PMID: 12241080 DOI: 10.1023/a:1020318705894] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The genes of E. coli are located on a circular chromosome of 4.6 million basepairs. This 1.6 mm long molecule is compressed into a nucleoid to fit inside the 1-2 microm cell in a functional format. To examine the role of DNA supercoiling as nucleoid compaction force we modulated the activity of DNA gyrase by electronic, genetic, and chemical means. A model based on physical properties of DNA and other cell components predicts that relaxation of supercoiling expands the nucleoid. Nucleoid size did not increase after reduction of DNA gyrase activity by genetic or chemical means, but nucleoids did expand upon chemical inhibition of gyrase in chloramphenicol-treated cells, indicating that supercoiling may help to compress the genome.
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Affiliation(s)
- Rogier Stuger
- Molecular Cell Physiology, Free University, Amsterdam, The Netherlands
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199
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Amit R, Oppenheim AB, Stavans J. Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor. Biophys J 2003; 84:2467-73. [PMID: 12668454 PMCID: PMC1302812 DOI: 10.1016/s0006-3495(03)75051-6] [Citation(s) in RCA: 152] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Histonelike nucleoid structuring protein (H-NS) is an abundant prokaryotic protein participating in nucleoid structure, gene regulation, and silencing. It plays a key role in cell response to changes in temperature and osmolarity. Force-extension measurements of single, twist-relaxed lambda-DNA-H-NS complexes show that these adopt more extended configurations compared to the naked DNA substrates. Crosslinking indicates that H-NS can decorate DNA molecules at one H-NS dimer per 15-20 bp. These results suggest that H-NS polymerizes along DNA, forming a complex of higher bending rigidity. These effects are not observed above 32 degrees C or at high osmolarity, supporting the hypothesis that a direct H-NS-DNA interaction plays a key role in gene silencing. Thus, we propose that H-NS plays a unique structural role, different from that of HU and IHF, and functions as one of the environmental sensors of the cell.
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Affiliation(s)
- Roee Amit
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel
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200
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Beloin C, Dorman CJ. An extended role for the nucleoid structuring protein H-NS in the virulence gene regulatory cascade of Shigella flexneri. Mol Microbiol 2003; 47:825-38. [PMID: 12535079 DOI: 10.1046/j.1365-2958.2003.03347.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The H-NS nucleoid structuring protein has been shown previously to play a negative role in controlling virulence gene expression in Shigella flexneri by repressing transcription of the virF and virB regulatory genes and the VirF-dependent icsA structural gene under non-permissive growth conditions. Here, we show that H-NS also acts at the promoters of the VirB-dependent structural genes in the regulatory cascade. H-NS protein binds to the promoter regions in vivo and in vitro. The promoters were shown physically and by in silico analysis to contain regions of DNA curvature, a feature of H-NS binding sites. H-NS binding sites were determined by DNase I footprinting at the icsB and the virA promoters. The locations of these sites were consistent with a role for H-NS as a transcription repressor. The VirB-dependent structural gene promoters were found to respond directly to the H-NS repressor, revealing a level of control that is additional to that exerted by the H-NS-dependent virB activator gene. Moreover, the promoters were sensitive to the level of VirB protein in the cell, requiring a threshold level of VirB to be reached before becoming active. A model is discussed in which the levels of expression of the structural genes reflect the outcome of competition between the countervailing regulatory activities of the H-NS and VirB proteins.
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Affiliation(s)
- Christophe Beloin
- Department of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Dublin2, Ireland
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