51
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Xiao B, Johnson RC, Marko JF. Modulation of HU-DNA interactions by salt concentration and applied force. Nucleic Acids Res 2010; 38:6176-85. [PMID: 20497998 PMCID: PMC2952867 DOI: 10.1093/nar/gkq435] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
HU is one of the most abundant proteins in bacterial chromosomes and participates in nucleoid compaction and gene regulation. We report experiments using DNA stretching that study the dependence of DNA condensation by HU on force, salt and HU concentration. Previous experiments at sub-physiological salt levels revealed that low concentrations of HU could compact DNA, whereas larger HU concentrations formed a DNA-stiffening complex. Here we report that this bimodal binding behavior depends sensitively on salt concentration. Only the compaction mode was observed for 150 mM and higher NaCl levels, i.e. for physiological salt concentrations. Similar results were obtained for the more physiological salt K-glutamate. Real-time studies of dissociation kinetics revealed that HU unbound slowly (minutes to hours under the conditions studied) but completely for salt concentrations at or above 100 mM NaCl; the lifetime of HU complexes was observed to increase with the HU concentration at which the complexes were formed, and to decrease with salt concentration. Higher salt levels of 300 mM NaCl completely eliminated observable HU binding to DNA. Finally, we observed that the dissociation kinetics depend on force applied to the DNA: increased applied force in the sub-piconewton range accelerates dissociation, suggesting a mechanism for DNA tension to regulate chromosome structure and gene expression.
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Affiliation(s)
- Botao Xiao
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.
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52
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Karcher D, Köster D, Schadach A, Klevesath A, Bock R. The Chlamydomonas chloroplast HLP protein is required for nucleoid organization and genome maintenance. MOLECULAR PLANT 2009; 2:1223-32. [PMID: 19995727 DOI: 10.1093/mp/ssp083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The chloroplasts genome (plastome) occurs at high copy numbers per cell. Several chloroplast genome copies are densely packed into nucleoprotein particles called nucleoids. How genome packaging occurs and which proteins organize chloroplast nucleoids are largely unknown. Here, we have analyzed the Chlamydomonas reinhardtii homolog of the bacterial architectural DNA-binding protein HU, the histone-like protein HLP. We show that the Chlamydomonas HLP protein is targeted to chloroplasts and associates with nucleoids. Knockdown of HLP gene expression by RNA interference (RNAi) alters the structure of chloroplast nucleoids and appears to reduce the level of compaction of chloroplast DNA. Unexpectedly, also chloroplast genome copy numbers are significantly decreased in the RNAi strains, suggesting that, in addition to its architectural role in nucleoid formation, the HLP protein is also involved in chloroplast genome maintenance.
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Affiliation(s)
- Daniel Karcher
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476 Potsdam-Golm, Germany
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53
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Nguyen HH, de la Tour CB, Toueille M, Vannier F, Sommer S, Servant P. The essential histone-like protein HU plays a major role inDeinococcus radioduransnucleoid compaction. Mol Microbiol 2009; 73:240-52. [DOI: 10.1111/j.1365-2958.2009.06766.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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54
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Ghadam P, Shariatian N, Amoozegar MA, Rabbani A, Shahriari SH. Assaying the presence of histone-like protein HU in Halobacillus karajensis. Pak J Biol Sci 2009; 10:3380-4. [PMID: 19090154 DOI: 10.3923/pjbs.2007.3380.3384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Histone-Like Proteins (HLPs) in bacteria are small basic proteins that contribute to the control of gene expression, recombination, DNA replication and compressing the bacterial DNA in the nucleoid. Among the HLPs, HU protein as a dimer plays an important role in binding to DNA and bending it. In this study, we showed that a 9.5-10 kDa protein with the same electrophoretic mobility as HU exists in Halobacillus karajensis which is a novel gram positive moderate halophile bacterium that was recently isolated from surface saline soil of the Karaj Region, Iran. The genes encoding HU protein were also assayed during this study by Polymerase Chain Reaction.
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Affiliation(s)
- P Ghadam
- Department of Biochemistry, University of Alzahra, P.O. Box 19935-514, Tehran, Iran
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55
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Becker NA, Kahn JD, Maher LJ. Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation. Nucleic Acids Res 2008; 36:4009-21. [PMID: 18515834 PMCID: PMC2475640 DOI: 10.1093/nar/gkn353] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Revised: 05/16/2008] [Accepted: 05/16/2008] [Indexed: 01/18/2023] Open
Abstract
DNA looping is important for gene repression and activation in Escherichia coli and is necessary for some kinds of gene regulation and recombination in eukaryotes. We are interested in sequence-nonspecific architectural DNA-binding proteins that alter the apparent flexibility of DNA by producing transient bends or kinks in DNA. The bacterial heat unstable (HU) and eukaryotic high-mobility group B (HMGB) proteins fall into this category. We have exploited a sensitive genetic assay of DNA looping in living E. coli cells to explore the extent to which HMGB proteins and derivatives can complement a DNA looping defect in E. coli lacking HU protein. Here, we show that derivatives of the yeast HMGB protein Nhp6A rescue DNA looping in E. coli lacking HU, in some cases facilitating looping to a greater extent than is observed in E. coli expressing normal levels of HU protein. Nhp6A-induced changes in the DNA length-dependence of repression efficiency suggest that Nhp6A alters DNA twist in vivo. In contrast, human HMGB2-box A derivatives did not rescue looping.
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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
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56
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Mukherjee A, Sokunbi AO, Grove A. DNA protection by histone-like protein HU from the hyperthermophilic eubacterium Thermotoga maritima. Nucleic Acids Res 2008; 36:3956-68. [PMID: 18515342 PMCID: PMC2475624 DOI: 10.1093/nar/gkn348] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In mesophilic prokaryotes, the DNA-binding protein HU participates in nucleoid organization as well as in regulation of DNA-dependent processes. Little is known about nucleoid organization in thermophilic eubacteria. We show here that HU from the hyperthermophilic eubacterium Thermotoga maritima HU bends DNA and constrains negative DNA supercoils in the presence of topoisomerase I. However, while binding to a single site occludes approximately 35 bp, association of T. maritima HU with DNA of sufficient length to accommodate multiple protomers results in an apparent shorter occluded site size. Such complexes consist of ordered arrays of protomers, as revealed by the periodicity of DNase I cleavage. Association of TmHU with plasmid DNA yields a complex that is remarkably resistant to DNase I-mediated degradation. TmHU is the only member of this protein family capable of occluding a 35 bp nonspecific site in duplex DNA; we propose that this property allows TmHU to form exceedingly stable associations in which DNA flanking the kinks is sandwiched between adjacent proteins. We suggest that T. maritima HU serves an architectural function when associating with a single 35 bp site, but generates a very stable and compact aggregate at higher protein concentrations that organizes and protects the genomic DNA.
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Affiliation(s)
- Anirban Mukherjee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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57
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Benevides JM, Danahy J, Kawakami J, Thomas GJ. Mechanisms of Specific and Nonspecific Binding of Architectural Proteins in Prokaryotic Gene Regulation. Biochemistry 2008; 47:3855-62. [DOI: 10.1021/bi7009426] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- James M. Benevides
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - Jessica Danahy
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - Jessica Kawakami
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
| | - George J. Thomas
- School of Biological Sciences, University of Missouri—Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110-2499
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58
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Kamashev D, Balandina A, Mazur AK, Arimondo PB, Rouviere-Yaniv J. HU binds and folds single-stranded DNA. Nucleic Acids Res 2007; 36:1026-36. [PMID: 18096614 PMCID: PMC2241890 DOI: 10.1093/nar/gkm667] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The nucleoid-associated protein HU plays an important role in bacterial nucleoid organization and is involved in numerous processes including transposition, recombination and DNA repair. We show here that HU binds specifically DNA containing mismatched region longer than 3 bp as well as DNA bulges. HU binds single-stranded DNA (ssDNA) in a binding mode that is reminiscent but different from earlier reported specific HU interactions with double-helical DNA lesions. An HU dimer requires 24 nt of ssDNA for initial binding, and 12 nt of ssDNA for each additional dimer binding. In the presence of equimolar amounts of HU dimer and DNA, the ssDNA molecule forms an U-loop (hairpin-like) around the protein, providing contacts with both sides of the HU body. This mode differs from the binding of the single-strand-binding protein (SSB) to ssDNA: in sharp contrast to SSB, HU binds ssDNA non-cooperatively and does not destabilize double-helical DNA. Furthermore HU has a strong preference for poly(dG), while binding to poly(dA) is the weakest. HU binding to ssDNA is probably important for its capacity to cover and protect bacterial DNA both intact and carrying lesions.
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Affiliation(s)
- Dmitri Kamashev
- Laboratoire de Physiologie Bacterienne, CNRS UPR 9073, Laboratoire de Biochimie Théorique, CNRS UPR 9080, Paris, France
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59
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Kow YW, Imhoff B, Weiss B, Hung DCI, Hindoyan AA, Story RM, Goodman SD. Escherichia coli HU protein has a role in the repair of abasic sites in DNA. Nucleic Acids Res 2007; 35:6672-80. [PMID: 17916578 PMCID: PMC2095813 DOI: 10.1093/nar/gkm567] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HU is one of the most abundant DNA binding proteins in Escherichia coli. We find that it binds strongly to DNA containing an abasic (AP) site or tetrahydrofuran (THF) (apparent K(d) approximately 50 nM). It also possesses an AP lyase activity that cleaves at a deoxyribose but not at a THF residue. The binding and cleavage of an AP site was observed only with the HUalphabeta heterodimer. Site-specific mutations at K3 and R61 residues led to a change in substrate binding and cleavage. Both K3A(alpha)K3A(beta) and R61A(alpha)R61A(beta) mutant HU showed significant reduction in binding to DNA containing AP site; however, only R61A(alpha)R61A(beta) mutant protein exhibited significant loss in AP lyase activity. Both K3A(alpha)K3A(beta) and R61K(alpha)R61K(beta) showed slight reduction in AP lyase activities. The function of HU protein as an AP lyase was confirmed by the ability of hupA or hupB mutations to further reduce the viability of an E. coli dut(Ts) xth mutant, which generates lethal AP sites at 37 degrees C; the hupA and hupB derivatives, respectively, had a 6-fold and a 150-fold lower survival at 37 degrees C than did the parental strain. These data suggest, therefore, that HU protein plays a significant role in the repair of AP sites in E. coli.
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Affiliation(s)
- Yoke W Kow
- Department of Radiation Oncology, Emory University School of Medicine, Clifton Road NE, Atlanta, GA 30322, USA.
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60
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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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61
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Mouw KW, Rice PA. Shaping the Borrelia burgdorferi genome: crystal structure and binding properties of the DNA-bending protein Hbb. Mol Microbiol 2007; 63:1319-30. [PMID: 17244195 DOI: 10.1111/j.1365-2958.2007.05586.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The genome of the Lyme disease-causing spirochete Borrelia burgdorferi encodes only a single polypeptide from the integration host factor (IHF)/HU or 'DNABII' family of nucleoid-associated proteins - Hbb. DNABII proteins induce large bends in DNA and serve as architectural factors in a variety of prokaryotic cellular processes. We have solved the crystal structure of an Hbb-DNA complex in which the DNA is bent by over 180 degrees . We find that like IHF, Hbb relies exclusively on indirect readout to recognize its cognate site. Additional binding studies show that the sequence preferences of Hbb are related to, yet distinct from those of IHF. Defining these binding characteristics may help to uncover additional roles for Hbb in Borrelia DNA metabolism as well as further our understanding of the mechanism of indirect readout.
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Affiliation(s)
- Kent W Mouw
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
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62
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Swinger KK, Rice PA. Structure-based analysis of HU-DNA binding. J Mol Biol 2006; 365:1005-16. [PMID: 17097674 PMCID: PMC1945228 DOI: 10.1016/j.jmb.2006.10.024] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 09/25/2006] [Accepted: 10/07/2006] [Indexed: 11/29/2022]
Abstract
HU and IHF are prokaryotic proteins that induce very large bends in DNA. They are present in high concentrations in the bacterial nucleoid and aid in chromosomal compaction. They also function as regulatory cofactors in many processes, such as site-specific recombination and the initiation of replication and transcription. HU and IHF have become paradigms for understanding DNA bending and indirect readout of sequence. While IHF shows significant sequence specificity, HU binds preferentially to certain damaged or distorted DNAs. However, none of the structurally diverse HU substrates previously studied in vitro is identical with the distorted substrates in the recently published Anabaena HU(AHU)-DNA cocrystal structures. Here, we report binding affinities for AHU and the DNA in the cocrystal structures. The binding free energies for formation of these AHU-DNA complexes range from approximately 10-14.5 kcal/mol, representing K(d) values in the nanomolar to low picomolar range, and a maximum stabilization of at least approximately 6.3 kcal/mol relative to complexes with undistorted, non-specific DNA. We investigated IHF binding and found that appropriate structural distortions can greatly enhance its affinity. On the basis of the coupling of structural and relevant binding data, we estimate the amount of conformational strain in an IHF-mediated DNA kink that is relieved by a nick (at least 0.76 kcal/mol) and pinpoint the location of the strain. We show that AHU has a sequence preference for an A+T-rich region in the center of its DNA-binding site, correlating with an unusually narrow minor groove. This is similar to sequence preferences shown by the eukaryotic nucleosome.
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63
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Di Cagno R, De Angelis M, Limitone A, Fox PF, Gobbetti M. Response of Lactobacillus helveticus PR4 to heat stress during propagation in cheese whey with a gradient of decreasing temperatures. Appl Environ Microbiol 2006; 72:4503-14. [PMID: 16820437 PMCID: PMC1489348 DOI: 10.1128/aem.01829-05] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 03/16/2006] [Indexed: 11/20/2022] Open
Abstract
The heat stress response was studied in Lactobacillus helveticus PR4 during propagation in cheese whey with a gradient of naturally decreasing temperature (55 to 20 degrees C). Growth under a gradient of decreasing temperature was compared to growth at a constant temperature of 42 degrees C. Proteinase, peptidase, and acidification activities of L. helveticus PR4 were found to be higher in cells harvested when 40 degrees C was reached by a gradient of decreasing temperature than in cells grown at constant temperature of 42 degrees C. When cells grown under a temperature gradient were harvested after an initial exposure of 35 min to 55 degrees C followed by decreases in temperature to 40 (3 h), 30 (5 h 30 min), or 20 degrees C (13 h 30 min) and were then compared with cells grown for the same time at a constant temperature of 42 degrees C, a frequently transient induction of the levels of expression of 48 proteins was found by two-dimensional electrophoresis analysis. Expression of most of these proteins increased following cooling from 55 to 40 degrees C (3 h). Sixteen of these proteins were subjected to N-terminal and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses. They were identified as stress proteins (e.g., DnaK and GroEL), glycolysis-related machinery (e.g., enolase and glyceraldehyde-3-phosphate dehydrogenase), and other regulatory proteins or factors (e.g., DNA-binding protein II and ATP-dependent protease). Most of these proteins have been found to play a role in the mechanisms of heat stress adaptation in other bacteria.
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Affiliation(s)
- Raffaella Di Cagno
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Facoltà di Scienze Biotecnologiche di Bari, Via G. Amendola 165/a, 70126 Bari, Italy
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64
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López-Torrejón G, Martínez-Jiménez MI, Ayora S. Role of LrpC from Bacillus subtilis in DNA transactions during DNA repair and recombination. Nucleic Acids Res 2006; 34:120-9. [PMID: 16407330 PMCID: PMC1326243 DOI: 10.1093/nar/gkj418] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein, which binds both single-stranded (ss) and double-stranded (ds) DNA and facilitates the formation of higher order protein–DNA complexes in vitro. LrpC binds at different sites within the same DNA molecule promoting intramolecular ligation. When bound to separate molecules, it promotes intermolecular ligation, and joint molecule formation between a circular ssDNA and a homologous ssDNA-tailed linear dsDNA. LrpC binding showed a higher affinity for 4-way (Holliday) junctions in their open conformation, when compared with curved dsDNA. Consistent with these biochemical activities, an lrpC null mutant strain rendered cells sensitive to DNA damaging agents such as methyl methanesulfonate and 4-nitroquinoline-1-oxide, and showed a segregation defect. These findings collectively suggest that LrpC may be involved in DNA transactions during DNA repair and recombination.
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Affiliation(s)
- Gema López-Torrejón
- Department of Microbial Biotechnology, Centro Nacional Biotecnología, CSICDarwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - María I. Martínez-Jiménez
- Department of Microbial Biotechnology, Centro Nacional Biotecnología, CSICDarwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional Biotecnología, CSICDarwin 3, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- Department of Molecular Biology, Universidad Autónoma de MadridDarwin 2, Cantoblanco, 28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91585 4528; Fax: +34 91585 4506,
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65
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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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66
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Preobrajenskaya OV, Starodubova ES, Karpov VL, Rouviere-Yaniv J. Comparison of the Local Concentration of the HU Protein for Particular Regions of Genomic DNA in Escherichia coli Cells in Vivo. Mol Biol 2005. [DOI: 10.1007/s11008-005-0074-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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67
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Kepple KV, Boldt JL, Segall AM. Holliday junction-binding peptides inhibit distinct junction-processing enzymes. Proc Natl Acad Sci U S A 2005; 102:6867-72. [PMID: 15867153 PMCID: PMC1100769 DOI: 10.1073/pnas.0409496102] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Holliday junctions (HJ) are the central intermediates in both homologous recombination and site-specific recombination performed by tyrosine recombinases such as the bacteriophage lambda Integrase (Int) protein. Previously, our lab identified peptide inhibitors of Int-mediated recombination that prevent the resolution of HJ intermediates. We now show that two of these inhibitors bind HJ DNA in the square-planar conformation even in the absence of Int protein. The peptides prevent unwinding of branched DNA substrates by the RecG helicase of Escherichia coli and interfere with the resolution of HJ substrates by the RuvABC complex. Our results suggest that these peptides target all proteins that process HJ in the square-planar conformation. These inhibitors should be extremely useful for dissecting homologous recombination and recombination-dependent repair in vitro and in vivo.
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Affiliation(s)
- Kevin V Kepple
- Center for Microbial Sciences and Department of Biology, San Diego State University, San Diego, CA 92182-4614, USA
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68
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Westfall LW, Luna AM, Francisco MS, Diggle SP, Worrall KE, Williams P, Cámara M, Hamood AN. The Pseudomonas aeruginosa global regulator MvaT specifically binds to the ptxS upstream region and enhances ptxS expression. Microbiology (Reading) 2004; 150:3797-3806. [PMID: 15528665 DOI: 10.1099/mic.0.27270-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Exotoxin A production inPseudomonas aeruginosais regulated positively or negatively by several genes. Two such regulatory genes,ptxRandptxS, which are divergently transcribed from each other, have been described previously. While computer analysis suggested that theptxR-ptxSintergenic region contains potential binding sites for several regulatory proteins, the mechanism that regulates the expression of eitherptxRorptxSinP. aeruginosais not known. The presence of aP. aeruginosaprotein complex that specifically binds to a segment within this region was determined. In this study the binding region was localized to a 150 bp fragment of the intergenic region and the proteins that constitute the binding complex were characterized asP. aeruginosaHU and MvaT. Recombinant MvaT was purified as a fusion protein (MAL-MvaT) and shown to specifically bind to theptxR-ptxSintergenic region. A PAO1 isogenic mutant defective inmvaT, PAOΔmvaT, was constructed and characterized. The lysate of PAOΔmvaTfailed to bind to the 150 bp probe. The effect ofmvaTonptxSandptxRexpression was examined using real-time PCR experiments. The expression ofptxSwas lower in PAOΔmvaTthan in PAO1, but no difference was detected inptxRexpression. These results suggest that MvaT positively regulatesptxSexpression by binding specifically to theptxSupstream region.
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Affiliation(s)
- Landon W Westfall
- Department of Microbiology and Immunology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - A Marie Luna
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
- Department of Microbiology and Immunology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Stephen P Diggle
- Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kathryn E Worrall
- Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Paul Williams
- Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Miguel Cámara
- Institute of Infection, Immunity and Inflammation, Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Abdul N Hamood
- Department of Microbiology and Immunology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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69
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Abstract
The energetic cost of bending short segments of DNA is very high. This bending is critical for the packaging of DNA and is exploited to regulate many cellular processes. In prokaryotes, IHF and HU are key architectural proteins present at high concentrations. New protein-DNA co-crystal structures, and the adaptation of advanced biophysical and biochemical techniques have led to an improved understanding of how these proteins interact with DNA. These techniques include time-resolved synchrotron X-ray footprinting, differential scanning calorimetry, isothermal titration calorimetry and single-molecule experiments.
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Affiliation(s)
- Kerren K Swinger
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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70
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Ghosh S, Grove A. Histone-like Protein HU from Deinococcus radiodurans Binds Preferentially to Four-way DNA Junctions. J Mol Biol 2004; 337:561-71. [PMID: 15019777 DOI: 10.1016/j.jmb.2004.02.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Revised: 01/23/2004] [Accepted: 02/05/2004] [Indexed: 01/31/2023]
Abstract
The histone-like protein HU from Escherichia coli is involved in DNA compaction and in processes such as DNA repair and recombination. Its participation in these events is reflected in its ability to bend DNA and in its preferred binding to DNA junctions and DNA with single-strand breaks. Deinococcus radiodurans is unique in its ability to reconstitute its genome from double strand breaks incurred after exposure to ionizing radiation. Using electrophoretic mobility shift assays (EMSA), we show that D.radiodurans HU (DrHU) binds preferentially only to DNA junctions, with half-maximal saturation of 18 nM. In distinct contrast to E.coli HU, DrHU does not exhibit a marked preference for DNA with nicks or gaps compared to perfect duplex DNA, nor is it able to mediate circularization of linear duplex DNA. These unexpected properties identify DrHU as the first member of the HU protein family not to serve an architectural role and point to its potential participation in DNA recombination events. Our data also point to a mechanism whereby differential target site selection by HU proteins is achieved and suggest that the substrate specificity of HU proteins should be expected to vary as a consequence of their individual capacity for inducing the required DNA bend.
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Affiliation(s)
- Sharmistha Ghosh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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71
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De Angelis M, Di Cagno R, Huet C, Crecchio C, Fox PF, Gobbetti M. Heat shock response in Lactobacillus plantarum. Appl Environ Microbiol 2004; 70:1336-46. [PMID: 15006751 PMCID: PMC368309 DOI: 10.1128/aem.70.3.1336-1346.2004] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2003] [Accepted: 12/05/2003] [Indexed: 11/20/2022] Open
Abstract
Heat stress resistance and response were studied in strains of Lactobacillus plantarum. Stationary-phase cells of L. plantarum DPC2739 had decimal reduction times (D values) (D value was the time that it took to reduce the number of cells by 1 log cycle) in sterile milk of 32.9, 14.7, and 7.14 s at 60, 72, and 75 degrees C, respectively. When mid-exponential-phase cells were used, the D values decreased. The temperature increases which caused a 10-fold reduction in the D value ranged from 9 to 20 degrees C, depending on the strain. Part of the cell population treated at 72 degrees C for 90 s recovered viability during incubation at 7 degrees C in sterile milk for 20 days. When mid-exponential- or stationary-phase cells of L. plantarum DPC2739 were adapted to 42 degrees C for 1 h, the heat resistance at 72 degrees C for 90 s increased ca. 3 and 2 log cycles, respectively. Heat-adapted cells also showed increased growth at pH 5 and in the presence of 6% NaCl. Two-dimensional gel electrophoresis of proteins expressed by control and heat-adapted cells revealed changes in the levels of expression of 31 and 18 proteins in mid-exponential- and stationary-phase cells, respectively. Twelve proteins were commonly induced. Nine proteins induced in the heat-adapted mid-exponential- and/or stationary-phase cells of L. plantarum DPC2739 were subjected to N-terminal sequencing. These proteins were identified as DnaK, GroEL, trigger factor, ribosomal proteins L1, L11, L31, and S6, DNA-binding protein II HlbA, and CspC. All of these proteins have been found to play a role in the mechanisms of stress adaptation in other bacteria. Antibodies against GroES detected a protein which was induced moderately, while antibodies against DnaJ and GrpE reacted with proteins whose level of expression did not vary after heat adaptation. This study showed that the heat resistance of L. plantarum is a complex process involving proteins with various roles in cell physiology, including chaperone activity, ribosome stability, stringent response mediation, temperature sensing, and control of ribosomal function. The physiological mechanisms of response to pasteurization in L. plantarum are fundamental for survival in cheese during manufacture.
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Affiliation(s)
- Maria De Angelis
- Institute of Sciences of Food Production, CNR, 70125 Bari, Italy
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72
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Abstract
Proteins of the Sac10b family, which is highly conserved among hyperthermophilic archaea, have been regarded as DNA-binding proteins. Based on their in vitro DNA-binding properties, these proteins are thought to be involved in chromosomal organization or DNA repair/recombination. We show that Ssh10b, a member of the Sac10b family from Sulfolobus shibatae, bound with similar affinities to double-stranded DNA, single-stranded DNA and RNA in vitro. However, the protein was exclusively bound to RNA in S. shibatae cells, as revealed by in vivo UV cross-linking and co-immunoprecipitation. Ribosomal RNAs were among the RNA species co-immunoprecipitated with Ssh10b. Consistent with this observation, Ssh10b was co-purified with ribosomes under low salt conditions. Furthermore, we demonstrate by UV-cross-linking hybridization that, when the cells were irradiated with UV, Ssh10b became cross-linked to 16S, 23S rRNAs and mRNAs. Our data indicate that RNA is the physiological binding target of the Sac10b family.
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Affiliation(s)
- Rong Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
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73
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Ramstein J, Hervouet N, Coste F, Zelwer C, Oberto J, Castaing B. Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure. J Mol Biol 2003; 331:101-21. [PMID: 12875839 DOI: 10.1016/s0022-2836(03)00725-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Escherichia coli histone-like HU protein pool is composed of three dimeric forms: two homodimers, EcHUalpha(2) and EcHUbeta(2), and a heterodimer, EcHUalphabeta. The relative abundance of these dimeric forms varies during cell growth and in response to environmental changes, suggesting that each dimer plays different physiological roles. Here, differential scanning calorimetry and circular dichroism (CD) were used to study the thermal stability of the three E.coli HU dimers and show that each of them has its own thermodynamic signature. Unlike the other HU proteins studied so far, which melt through a single step (N(2)<-->2D), this present thermodynamic study shows that the three E.coli dimers melt according to a two-step mechanism (N(2)<-->I(2)<-->2D). The native dimer, N(2), melts partially into a dimeric intermediate, I(2), which in turn yields the unfolded monomers, D. In addition, the crystal structure of the EcHUalpha(2) dimer has been solved. Comparative thermodynamic and structural analysis between EcHUalpha(2) and the HU homodimer from Bacillus stearothermophilus suggests that the E.coli dimer is constituted by two subdomains of different energetic properties. The CD study indicates that the intermediate, I(2), corresponds to an HU dimer having partly lost its alpha-helices. The partially unfolded dimer I(2) is unable to complex with high-affinity, single-stranded break-containing DNA. These structural, thermodynamic and functional results suggest that the N(2)<-->I(2) equilibrium plays a central role in the physiology of E.coli HU. The I(2) molecular species seems to be the EcHUbeta(2) preferential conformation, possibly related to its role in the E.coli cold-shock adaptation. Besides, I(2) might be required in E.coli for the HU chain exchange, which allows the heterodimer formation from homodimers.
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Affiliation(s)
- Jean Ramstein
- Centre de Biophysique Moléculaire, CNRS, affiliated to the University of Orléans, rue Charles Sadron, 45071 Orléans cedex 02, France
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74
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Abstract
HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence-specific (IHF) or non-specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation, transcription regulation and site-specific recombination, and is associated with bacterial nucleoids. Cocrystal structures of Anabaena HU bound to DNA (1P71, 1P78, 1P51) reveal that while underlying proline intercalation and asymmetric charge neutralization mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles ( approximately 105-140 degrees ). The two bend angles within a single HU complex are not coplanar, and the resulting dihedral angle is consistent with negative supercoiling. Comparison of HU-DNA and IHF-DNA structures suggests that sharper bending is correlated with longer DNA binding sites and smaller dihedral angles. An HU-induced bend may be better modeled as a hinge, not a rigid bend. The ability to induce or stabilize varying bend angles is consistent with HU's role as an architectural cofactor in many different systems that may require differing geometries.
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Affiliation(s)
- Kerren K Swinger
- Department of Biochemistry and Molecular Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA
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75
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Li G, Tolstonog GV, Sabasch M, Traub P. Type III intermediate filament proteins interact with four-way junction DNA and facilitate its cleavage by the junction-resolving enzyme T7 endonuclease I. DNA Cell Biol 2003; 22:261-91. [PMID: 12823903 DOI: 10.1089/104454903321908656] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The isolation from proliferating mouse and human embryo fibroblasts of SDS-stable crosslinkage products of vimentin with DNA fragments containing inverted repeats capable of cruciform formation under superhelical stress and the competitive effect of a synthetic Holliday junction on the binding of cytoplasmic intermediate filament (cIF) proteins to supercoiled DNA prompted a detailed investigation of the proteins' capacity to associate with four-way junction DNA and to influence its processing by junction-resolving endonucleases. Electrophoretic mobility shift analysis of reaction products obtained from vimentin and Holliday junctions under varying ionic conditions revealed efficient complex formation of the filament protein not only with the unstacked, square-planar configuration of the junctions but also with their coaxially stacked X-conformation. Glial fibrillary acidic protein (GFAP) was less efficient and desmin virtually inactive in complex formation. Electron microscopy showed binding of vimentin tetramers or octamers almost exclusively to the branchpoint of the Holliday junctions under physiological ionic conditions. Even at several hundredfold molar excess, sequence-related single- and double-stranded DNAs were unable to chase Holliday junctions from their complexes with vimentin. Vimentin also stimulated bacteriophage T7 endonuclease I in introducing single-strand cuts diametrically across the branchpoint and thus in the resolution of the Holliday junctions. This effect is very likely due to vimentin-induced structural distortion of the branchpoint, as suggested by the results of hydroxyl radical footprinting of Holliday junctions in the absence and the presence of vimentin. Moreover, vimentin, and to a lesser extent GFAP and desmin, interacted with the cruciform structures of inverted repeats inserted into a supercoiled vector plasmid, thereby changing their configuration via branch migration and sensibilizing them to processing by T7 endonuclease I. This refers to both plasmid relaxation caused by unilateral scission and, particularly, linearization via bilateral scission at primary and cIF protein-induced secondary cruciform branchpoints that were identified by T7 endonuclease I footprinting. cIF proteins share these activities with a variety of other architectural proteins interacting with and structurally modulating four-way DNA junctions. In view of the known and hypothetical functions of four-way DNA junctions and associated protein factors in DNA metabolism, cIF proteins as complementary nuclear matrix proteins may play important roles in such nuclear matrix-associated processes as DNA replication, recombination, repair, and transcription, with special emphasis on both the preservation and evolution of the genome.
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Affiliation(s)
- Guohong Li
- Max-Planck-Institut für Zellbiologie, Rosenhof, 68526 Ladenburg, Germany
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76
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Abstract
A synthetic cruciform DNA (X-DNA) was used for screening cellular extracts of Saccharomyces cerevisiae for X-DNA-binding activity. Three X-DNA-binding proteins with apparent molecular mass of 28kDa, 26kDa and 24kDa, estimated by SDS-PAGE, were partially purified. They were identified as N-terminal fragments originating from the same putative protein, encoded by the open reading frame YHR146W, which we named CRP1 (cruciform DNA-recognising protein 1). Expression of CRP1 in Escherichia coli showed that Crp1p is subject to efficient proteolysis at one specific site. Cleavage leads to an N-terminal subpeptide of approximately 160 amino acid residues that is capable of binding specifically X-DNA with an estimated dissociation constant (K(d)) of 800nM, and a C-terminal subpeptide of approximately 305 residues without intrinsic X-DNA-binding activity. The N-terminal subpeptide is of a size similarly to that of the fragments identified in yeast, suggesting that the same cleavage process occurs in the yeast and the E.coli background. This makes the action of a site-specific protease unlikely and favours the possibility of an autoproteolytic activity of Crp1p. The DNA-binding domain of Crp1p was mapped to positions 120-141. This domain can act autonomously as an X-DNA-binding peptide and provides a new, lysine-rich DNA-binding domain different from those of known cruciform DNA-binding proteins (CBPs). As reported earlier for several other CBPs, Crp1p exerts an enhancing effect on the cleavage of X-DNA by endonuclease VII from bacteriophage T4.
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Affiliation(s)
- Ulrich Rass
- Institut für Genetik der Universität zu Köln, Zülpicher Strasse 47, Köln, Germany.
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77
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Balandina A, Kamashev D, Rouviere-Yaniv J. The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids. J Biol Chem 2002; 277:27622-8. [PMID: 12006568 DOI: 10.1074/jbc.m201978200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
HU, a major component of the bacterial nucleoid, shares properties with histones, high mobility group proteins (HMGs), and other eukaryotic proteins. HU, which participates in many major pathways of the bacterial cell, binds without sequence specificity to duplex DNA but recognizes with high affinity DNA repair intermediates. Here we demonstrate that HU binds to double-stranded DNA, double-stranded RNA, and linear DNA-RNA duplexes with a similar low affinity. In contrast to this nonspecific binding to total cellular RNA and to supercoiled DNA, HU specifically recognizes defined structures common to both DNA and RNA. In particular HU binds specifically to nicked or gapped DNA-RNA hybrids and to composite RNA molecules such as DsrA, a small non-coding RNA. HU, which modulates DNA architecture, may play additional key functions in the bacterial machinery via its RNA binding capacity. The simple, straightforward structure of its binding domain with two highly flexible beta-ribbon arms and an alpha-helical platform is an alternative model for the elaborate binding domains of the eukaryotic proteins that display dual DNA- and RNA-specific binding capacities.
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Affiliation(s)
- Anna Balandina
- Laboratoire de Physiologie Bactérienne, CNRS UPR 9073, Institut de Biologie Physico-Chimique, 13 Rue Pierre et Marie CURIE, 75005 Paris, France
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78
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Giangrossi M, Giuliodori AM, Gualerzi CO, Pon CL. Selective expression of the beta-subunit of nucleoid-associated protein HU during cold shock in Escherichia coli. Mol Microbiol 2002; 44:205-16. [PMID: 11967080 DOI: 10.1046/j.1365-2958.2002.02868.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Expression of Escherichia coli hupA and hupB, the structural genes encoding the most abundant nucleoid-associated proteins HUalpha and HUbeta has been studied during cold shock. This article demonstrates that: (i) transcriptional expression of hupA is blocked following a sudden temperature downshift (from 37 degrees C to 10 degrees C), whereas transcription of hupB from the P2 and P3 promoters is maintained at a constitutive level and is activated de novo from the P4 promoter; (ii) all three hupB mRNAs (transcribed from the three natural promoters P2, P3 and P4) become much more stable than the single hupA transcript; and (iii) the hupB transcripts, unlike that of hupA, are efficiently translated in vivo during cold acclimation and can be actively translated in vitro at low temperature. Taken together, the results indicate that during cold shock the expression of the HUbeta subunit is preferentially stimulated and that of HUalpha repressed, suggesting that an altered HUalpha to HUbeta expression ratio resulting in an increase of HUalpha/HUbeta heterodimers and/or (HUbeta)2 homodimers may play an important role during cold adaptation.
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Affiliation(s)
- Mara Giangrossi
- Laboratory of Genetics, Department of Biology MCA, University of Camerino, Camerino (MC), Italy
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79
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Grove A, Lim L. High-affinity DNA binding of HU protein from the hyperthermophile Thermotoga maritima. J Mol Biol 2001; 311:491-502. [PMID: 11493003 DOI: 10.1006/jmbi.2001.4763] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Prokaryotic genomes are compacted by association with small basic proteins, generating what has been termed bacterial chromatin. The ubiquitous DNA-binding protein HU serves this function. DNA-binding properties of HU from the hyperthermophilic eubacterium Thermotoga maritima are shown here to differ significantly from those characteristic of previously described HU homologs. Electrophoretic mobility shift analyses show that T. maritima HU (TmHU) binds double-stranded DNA with high affinity (K(d)=5.6(+/-0.7) nM for 37 bp DNA). Equivalent affinity is observed between 4 degrees C and 45 degrees C. TmHU has higher affinity for DNA containing a set of 4 nt loops separated by 9 bp (K(d)=1.4(+/-0.3) nM), consistent with its introduction of two DNA kinks. Using DNA probes of varying length, the optimal binding site for TmHU is estimated at 37 bp, in sharp contrast to the 9-10 bp binding site reported for other HU homologs. Alignment of >60 HU sequences demonstrates significant sequence conservation: A DNA-intercalating proline residue is almost universally conserved, and it is preceded by arginine and asparagine in most sequences, generating a highly conserved RNP motif; V substitutes for R only in HU from Thermotoga, Thermus and Deinococcus. A fivefold increase in DNA-binding affinity is observed for TmHU in which V is replaced with R (TmHU-V61R; K(d)=1.1(+/-0.2) nM), but a change in the trajectory of DNA flanking the sites of DNA intercalation is inferred from analysis of TmHU-V61R binding to DNA modified with 4 nt loops or with substitutions of 5-hydroxymethyluracil for thymine. Survival in extreme environments places unique demands on protection of genomic DNA from thermal destabilization and on access of DNA to the cellular machinery, demands that may be fulfilled by the specific DNA-binding properties of HU and by the fine structure of the bacterial chromatin.
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Affiliation(s)
- A Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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80
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Balandina A, Claret L, Hengge-Aronis R, Rouviere-Yaniv J. The Escherichia coli histone-like protein HU regulates rpoS translation. Mol Microbiol 2001; 39:1069-79. [PMID: 11251825 DOI: 10.1046/j.1365-2958.2001.02305.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Escherichia coli HU protein is a major component of the bacterial nucleoid. HU stabilizes higher order nucleoprotein complexes and belongs to a family of DNA architectural proteins. Here, we report that HU is required for efficient expression of the sigma S subunit of RNA polymerase. This rpoS-encoded alternative sigmaS factor induces a number of genes implicated in cell survival in stationary phase and in multiple stress resistance. By analysis of rpoS-lacZ fusions and by pulse-chase experiments, we show that the efficiency of rpoS translation is reduced in cells lacking HU, whereas neither rpoS transcription nor protein stability is affected by HU. Gel mobility shift assays show that HU is able to bind specifically an RNA fragment containing the translational initiation region of rpoS mRNA 1000-fold more strongly than double-stranded DNA. Together with the in vivo data, this finding strongly suggests that, by binding to rpoS mRNA, HU directly stimulates rpoS translation. We demonstrate here that HU, an abundant DNA-binding, histone-like protein, is able specifically to recognize an RNA molecule and therefore play a role in post-transcriptional regulation.
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Affiliation(s)
- A Balandina
- Laboratoire de Physiologie Bactérienne, CNRS, UPR 9073, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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81
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Kamashev D, Rouviere-Yaniv J. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J 2000; 19:6527-35. [PMID: 11101525 PMCID: PMC305869 DOI: 10.1093/emboj/19.23.6527] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The heterodimeric HU protein associated with the Escherichia coli nucleoid shares some properties with histones and HMG proteins. HU binds DNA junctions and DNA containing a nick much more avidly than double-stranded (ds-) DNA. Cells lacking HU are extremely sensitive to gamma irradiation and we wondered how HU could play a role in maintaining the integrity of the bacterial chromosome. We show that HU binds with high affinity to DNA repair and recombination intermediates, including DNA invasions, DNA overhangs and DNA forks. The DNA structural motif that HU specifically recognizes in all these structures consists of a ds-DNA module joined to a second module containing either ds- or single-stranded (ss-) DNA. The two modules rotate freely relative to one another. Binding specificity results from the simultaneous interaction of HU with these two modules: HU arms bind the ds-DNA module whereas the HU body contacts the 'variable' module containing either ds- or ss-DNA. Both structural motifs are recognized by HU at least 1000-fold more avidly than duplex DNA.
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Affiliation(s)
- D Kamashev
- Laboratoire de Physiologie Bactérienne, CNRS, UPR 9073, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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82
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Lilley DM, Wilson TJ. Fluorescence resonance energy transfer as a structural tool for nucleic acids. Curr Opin Chem Biol 2000; 4:507-17. [PMID: 11006537 DOI: 10.1016/s1367-5931(00)00124-1] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence resonance energy transfer is a spectroscopic method that provides distance information on macromolecules in solution in the range 20-80 A. It is particularly suited to the analysis of the global structure of nucleic acids because the long-range distance information provides constraints when modelling these important structures. The application of fluorescence resonance energy transfer to nucleic acid structure has seen a resurgence of interest in the past decade, which continues to increase. An especially exciting development is the recent extension to single-molecule studies.
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Affiliation(s)
- D M Lilley
- CRC Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 4HN, UK.
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83
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Azam TA, Hiraga S, Ishihama A. Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid. Genes Cells 2000; 5:613-26. [PMID: 10947847 DOI: 10.1046/j.1365-2443.2000.00350.x] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND The genome DNA of Escherichia coli is folded into the nucleosome-like structure, often called a nucleoid, by the binding of several DNA-binding proteins. We previously determined the specificity and affinity of DNA-binding for 12 species of the E. coli DNA-binding protein, and their intracellular concentrations at various growth phases. The intracellular localization of these proteins in E. coli could be predicted from these data, but no attempt has been made thus far to directly observe the intracellular distribution of the DNA-binding proteins. RESULTS The intracellular localization in Escherichia coli of 10 species of the nucleoid-associated protein, three components of the transcripton apparatus, and three components of the translation machinery was investigated by indirect immuno-fluorescence microscopy. The DNA-binding proteins could be classified into two groups. The group-I proteins, including the major nucleoid-structural proteins, H-NS, HU, IHF, StpA and Dps, are distributed uniformly within the entire nucleoid. In contrast, the group-II proteins, which are presumed to possess regulatory activities of DNA functions accumulate at specific loci within the nucleoid, forming 2 (SeqA), 3-4 (CbpA and CbpB) and 6-10 (Fis and IciA) immuno-stained dots. Each immuno-stained dot may represent either the association of a hundred to one thousand molecules of each DNA-binding protein at a specific locus of the genome DNA or the assembly of protein-associated DNA segments from different domains of the folded genome. Both the RNA polymerase core enzyme and the sigma70 subunit are mainly associated with the nucleoid, but the anti-sigma70 factor (Rsd) appears to be accumulated at the boundary between the nucleoid and the cytosol in the stationary-phase cells. Here we show that the majority of Hfq is present in cytoplasm together with ribosomal proteins L7/L12 and RMF. CONCLUSION The DNA-binding proteins of E. coli could be classified into two groups. One group proteins was distributed uniformly within the nucleoid, but the other group of proteins showed an irregular distribution, forming immuno-stained spots or clumps.
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Affiliation(s)
- T A Azam
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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84
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Pedersen AG, Jensen LJ, Brunak S, Staerfeldt HH, Ussery DW. A DNA structural atlas for Escherichia coli. J Mol Biol 2000; 299:907-30. [PMID: 10843847 DOI: 10.1006/jmbi.2000.3787] [Citation(s) in RCA: 178] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have performed a computational analysis of DNA structural features in 18 fully sequenced prokaryotic genomes using models for DNA curvature, DNA flexibility, and DNA stability. The structural values that are computed for the Escherichia coli chromosome are significantly different from (and generally more extreme than) that expected from the nucleotide composition. To aid this analysis, we have constructed tools that plot structural measures for all positions in a long DNA sequence (e.g. an entire chromosome) in the form of color-coded wheels (http://www.cbs.dtu. dk/services/GenomeAtlas/). We find that these "structural atlases" are useful for the discovery of interesting features that may then be investigated in more depth using statistical methods. From investigation of the E. coli structural atlas, we discovered a genome-wide trend, where an extended region encompassing the terminus displays a high of level curvature, a low level of flexibility, and a low degree of helix stability. The same situation is found in the distantly related Gram-positive bacterium Bacillus subtilis, suggesting that the phenomenon is biologically relevant. Based on a search for long DNA segments where all the independent structural measures agree, we have found a set of 20 regions with identical and very extreme structural properties. Due to their strong inherent curvature, we suggest that these may function as topological domain boundaries by efficiently organizing plectonemically supercoiled DNA. Interestingly, we find that in practically all the investigated eubacterial and archaeal genomes, there is a trend for promoter DNA being more curved, less flexible, and less stable than DNA in coding regions and in intergenic DNA without promoters. This trend is present regardless of the absolute levels of the structural parameters, and we suggest that this may be related to the requirement for helix unwinding during initiation of transcription, or perhaps to the previously observed location of promoters at the apex of plectonemically supercoiled DNA. We have also analyzed the structural similarities between groups of genes by clustering all RNA and protein-encoding genes in E. coli, based on the average structural parameters. We find that most ribosomal genes (protein-encoding as well as rRNA genes) cluster together, and we suggest that DNA structure may play a role in the transcription of these highly expressed genes.
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MESH Headings
- Bacterial Proteins/genetics
- Base Pairing/genetics
- Color
- Computational Biology
- Computer Simulation
- Crystallography, X-Ray
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Superhelical/chemistry
- DNA, Superhelical/genetics
- Deoxyribonuclease I/metabolism
- Escherichia coli/genetics
- Genes, Bacterial/genetics
- Genome, Bacterial
- Models, Molecular
- Nucleic Acid Conformation
- Nucleosomes/chemistry
- Nucleosomes/genetics
- Pattern Recognition, Automated
- Phylogeny
- Pliability
- Promoter Regions, Genetic/genetics
- RNA, Bacterial/genetics
- Software
- Statistics as Topic
- Thermodynamics
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Affiliation(s)
- A G Pedersen
- Center for Biological Sequence Analysis, Department of Biotechnology, The Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark
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85
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Azam TA, Ishihama A. Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J Biol Chem 1999; 274:33105-13. [PMID: 10551881 DOI: 10.1074/jbc.274.46.33105] [Citation(s) in RCA: 347] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The genome of Escherichia coli is composed of a single molecule of circular DNA with the length of about 47,000 kilobase pairs, which is associated with about 10 major DNA-binding proteins, altogether forming the nucleoid. We expressed and purified 12 species of the DNA-binding protein, i.e. CbpA (curved DNA-binding protein A), CbpB or Rob (curved DNA-binding protein B or right arm of the replication origin binding protein), DnaA (DNA-binding protein A), Dps (DNA-binding protein from starved cells), Fis (factor for inversion stimulation), Hfq (host factor for phage Q(beta)), H-NS (histone-like nucleoid structuring protein), HU (heat-unstable nucleoid protein), IciA (inhibitor of chromosome initiation A), IHF (integration host factor), Lrp (leucine-responsive regulatory protein), and StpA (suppressor of td(-) phenotype A). The sequence specificity of DNA binding was determined for all the purified nucleoid proteins using gel-mobility shift assays. Five proteins (CbpB, DnaA, Fis, IHF, and Lrp) were found to bind to specific DNA sequences, while the remaining seven proteins (CbpA, Dps, Hfq, H-NS, HU, IciA, and StpA) showed apparently sequence-nonspecific DNA binding activities. Four proteins, CbpA, Hfq, H-NS, and IciA, showed the binding preference for the curved DNA. From the apparent dissociation constant (K(d)) determined using the sequence-specific or nonspecific DNA probes, the order of DNA binding affinity were determined to be: HU > IHF > Lrp > CbpB(Rob) > Fis > H-NS > StpA > CbpA > IciA > Hfq/Dps, ranging from 25 nM (HU binding to the non-curved DNA) to 250 nM (Hfq binding to the non-curved DNA), under the assay conditions employed.
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Affiliation(s)
- T A Azam
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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86
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Dixon-Fyle SM, Caro L. Characterization in vitro and in vivo of a new HU family protein from Streptococcus thermophilus ST11. Plasmid 1999; 42:159-73. [PMID: 10545259 DOI: 10.1006/plas.1999.1423] [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: 11/22/2022]
Abstract
Streptococcus thermophilus is a thermophilic gram-positive bacterium belonging to the lactic acid group. We report the isolation and characterization of a new 9.6-kDa DNA-binding protein, HSth, belonging to the HU family of nucleoid-associated proteins. The hsth gene was isolated in a 2.5-kb genomic region, upstream of a gene with strong homology to Lactococcus lactis pyrD. It is transcribed from a single E. coli sigma(70)-like promoter. Based on its high level of sequence similarity to B. subtilis and E. coli HU, HSth appears to be an HU homologue. The HSth protein shows biochemical and functional properties typical of HU proteins from gram-positive bacteria, being heat-stable, acid-soluble, and homodimeric. When expressed in HU-deficient E. coli cells, HSth supported the growth of bacteriophage Mu as efficiently as E. coli HU homo- and heterodimeric proteins. It did not, however, display any IHF-specific functions. Finally, we show that HSth binds to linear DNA with no apparent specificity, forming protein-DNA complexes similar but not identical to those observed with E. coli HU proteins.
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Affiliation(s)
- S M Dixon-Fyle
- Department of Molecular Biology, University of Geneva, Geneva 4, 1211, Switzerland.
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87
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Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 1999; 181:6361-70. [PMID: 10515926 PMCID: PMC103771 DOI: 10.1128/jb.181.20.6361-6370.1999] [Citation(s) in RCA: 674] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome DNA of Escherichia coli is associated with about 10 DNA-binding structural proteins, altogether forming the nucleoid. The nucleoid proteins play some functional roles, besides their structural roles, in the global regulation of such essential DNA functions as replication, recombination, and transcription. Using a quantitative Western blot method, we have performed for the first time a systematic determination of the intracellular concentrations of 12 species of the nucleoid protein in E. coli W3110, including CbpA (curved DNA-binding protein A), CbpB (curved DNA-binding protein B, also known as Rob [right origin binding protein]), DnaA (DNA-binding protein A), Dps (DNA-binding protein from starved cells), Fis (factor for inversion stimulation), Hfq (host factor for phage Q(beta)), H-NS (histone-like nucleoid structuring protein), HU (heat-unstable nucleoid protein), IciA (inhibitor of chromosome initiation A), IHF (integration host factor), Lrp (leucine-responsive regulatory protein), and StpA (suppressor of td mutant phenotype A). Intracellular protein levels reach a maximum at the growing phase for nine proteins, CbpB (Rob), DnaA, Fis, Hfq, H-NS, HU, IciA, Lrp, and StpA, which may play regulatory roles in DNA replication and/or transcription of the growth-related genes. In descending order, the level of accumulation, calculated in monomers, in growing E. coli cells is Fis, Hfq, HU, StpA, H-NS, IHF*, CbpB (Rob), Dps*, Lrp, DnaA, IciA, and CbpA* (stars represent the stationary-phase proteins). The order of abundance, in descending order, in the early stationary phase is Dps*, IHF*, HU, Hfq, H-NS, StpA, CbpB (Rob), DnaA, Lrp, IciA, CbpA, and Fis, while that in the late stationary phase is Dps*, IHF*, Hfq, HU, CbpA*, StpA, H-NS, CbpB (Rob), DnaA, Lrp, IciA, and Fis. Thus, the major protein components of the nucleoid change from Fis and HU in the growing phase to Dps in the stationary phase. The curved DNA-binding protein, CbpA, appears only in the late stationary phase. These changes in the composition of nucleoid-associated proteins in the stationary phase are accompanied by compaction of the genome DNA and silencing of the genome functions.
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Affiliation(s)
- T Ali Azam
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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88
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Elías-Arnanz M, Salas M. Functional interactions between a phage histone-like protein and a transcriptional factor in regulation of phi29 early-late transcriptional switch. Genes Dev 1999; 13:2502-13. [PMID: 10521395 PMCID: PMC317075 DOI: 10.1101/gad.13.19.2502] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/1999] [Accepted: 08/06/1999] [Indexed: 11/24/2022]
Abstract
Protein p6 is a nonspecific DNA-binding protein occurring in high abundance in phage phi29-infected cells. Here, we demonstrate a novel role for this versatile histone-like protein: its involvement in regulating the viral switch between early and late transcription. p6 performs this role by exhibiting a reciprocal functional interaction with the regulatory protein p4, also phage encoded, which is required for repression of the early A2b and A2c promoters and activation of the late A3 promoter. On the one hand, p6 promotes p4-mediated repression of the A2b promoter and activation of the A3 promoter by enhancing binding of p4 to its recognition site at PA3; on the other, p4 promotes p6-mediated repression of the A2c promoter by favoring the formation of a stable p6-nucleoprotein complex that interferes with RNA polymerase binding to PA2c. We propose that the observed interplay between proteins p6 and p4 is based on their DNA architectural properties.
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Affiliation(s)
- M Elías-Arnanz
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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89
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Esser D, Rudolph R, Jaenicke R, Böhm G. The HU protein from Thermotoga maritima: recombinant expression, purification and physicochemical characterization of an extremely hyperthermophilic DNA-binding protein. J Mol Biol 1999; 291:1135-46. [PMID: 10518949 DOI: 10.1006/jmbi.1999.3022] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The histone-like protein TmHU from the hyperthermophilic eubacterium Thermotoga maritima was cloned, expressed to high levels in Escherichia coli, and purified to homogeneity by heat precipitation and cation exchange chromatography. CD spectroscopical studies with secondary structure analysis as well as comparative modeling demonstrate that the dimeric TmHU has a tertiary structure similar to other homologous HU proteins. The Tm of the protein was determined to be 96 degrees C, and thermal unfolding is nearly completely reversible. Surface plasmon resonance measurements for TmHU show that the protein binds to DNA in a highly cooperative manner, with a KD of 73 nM and a Hill coefficient of 7.6 for a 56 bp DNA fragment. It is demonstrated that TmHU is capable to increase the melting point of a synthetic, double-stranded DNA (poly[d(A-T)]) by 47 degrees C, thus suggesting that DNA stabilization may be a major function of this protein in hyperthermophiles. The significant in vitro protection of double-helical DNA may be useful for biotechnological applications.
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Affiliation(s)
- D Esser
- Institut für Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Saale, Germany.
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90
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Kobryn K, Lavoie BD, Chaconas G. Supercoiling-dependent site-specific binding of HU to naked Mu DNA. J Mol Biol 1999; 289:777-84. [PMID: 10369760 DOI: 10.1006/jmbi.1999.2805] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using HU chemical nucleases to probe HU-DNA interactions, we report here for the first time site-specific binding of HU to naked DNA. An unique feature of this interaction is the absolute requirement for negative DNA supercoiling for detectable levels of site-specific DNA binding. The HU binding site is the Mu spacer between the L1 and L2 transposase binding sites. Our results suggest recognition of an altered DNA structure which is induced by DNA supercoiling. We propose that recruitment of HU to this naked DNA site induces the DNA bending required for productive synapsis and transpososome assembly. Implications of HU as a supercoiling sensor with a potential in vivo regulatory role are discussed. Finally, using HU nucleases we have also shown that non-specific DNA binding by HU is stimulated by increasing levels of supercoiling.
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Affiliation(s)
- K Kobryn
- Department of Biochemistry, University of Western Ontario, London, Ontario, N6A 5C1, Canada
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91
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Pinson V, Takahashi M, Rouviere-Yaniv J. Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA. J Mol Biol 1999; 287:485-97. [PMID: 10092454 DOI: 10.1006/jmbi.1999.2631] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have shown recently that the relative abundance of the three dimeric forms (alpha2, alphabeta and beta2) of the HU protein from Escherichia coli varies during growth and in response to environmental changes. Using gel retardation assays we have compared the DNA binding properties of the three dimers with different DNA substrates. The determination of their DNA binding parameters shows that the relative affinities of HUalphabeta and HUalpha2 are comparable. Both recognize, with a high degree of affinity under stringent conditions, cruciform structures or DNA molecules with a nick or a gap, whereas they bind to linear DNA only at low salt. DNA containing a gap of two nucleotides is in fact the substrate recognized with the highest degree of affinity by these two forms under all conditions. Conversely, HUbeta2 binds very poorly to duplex DNA and shows a much lower affinity for nicked or gapped DNAs. However, HUbeta2 binds to cruciform DNA structures almost as well as HUalphabeta and HUalpha2. This almost exclusive binding of HUbeta2 to a unique substrate is surprising in regards of the quasi identity, in the three forms, of the flexible arms considered as the DNA-binding domains of the three forms of HU. Cruciform DNA may stabilize HUbeta2 structure which could be structurally defective.
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Affiliation(s)
- V Pinson
- Laboratoire de Physiologie Bactérienne, CNRS, UPR 9073, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris, 75005, France
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92
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Tominaga T, Nakagawa A, Tanaka I, Kawamura S, Kimura M. High-resolution crystals of the HU mutant K38N from Bacillus stearothermophilus. J Struct Biol 1999; 125:86-9. [PMID: 10196119 DOI: 10.1006/jsbi.1998.4076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The DNA-binding protein HU is ubiquitous in the prokaryotic cell. It is a major protein component of isolated nucleoids and is believed to control the tertiary structure of prokaryotic DNA. The Bacillus stearothermophilus HU (BstHU) mutants obtained by mutagenesis have been investigated. Crystallization experiments of BstHU-K38N (Lys38 is substituted with Asn) resulted in two forms of crystals suitable for high-resolution x-ray analysis. The first form belongs to the monoclinic space group C2 with unit-cell dimensions of a = 90.1 A, b = 43.5 A, c = 63.7 A, and beta = 135.1 degrees, and it diffracts x rays to 1.5-A resolution. The second form belongs to the tetragonal space group I41 with a = b = 62.6 A and c = 43.3 A, and it diffracts up to 1.8-A resolution.
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Affiliation(s)
- T Tominaga
- Graduate School of Science, Hokkaido University, Sapporo, 060-0810, Japan
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93
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Dorman CJ, Hinton JC, Free A. Domain organization and oligomerization among H-NS-like nucleoid-associated proteins in bacteria. Trends Microbiol 1999; 7:124-8. [PMID: 10203842 DOI: 10.1016/s0966-842x(99)01455-9] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The bacterial nucleoid-associated proteins H-NS and StpA can form homomeric or heteromeric complexes, a parallel with protein HU. Thus, functional modulation of H-NS and StpA by one another and by other proteins with appropriate interaction domains is possible. This has implications for bacterial pathogenesis and adaptation to environmental stress.
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Affiliation(s)
- C J Dorman
- Dept of Microbiology, Moyne Institute of Preventive Medicine, University of Dublin, Trinity College, Ireland.
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94
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Timsit Y, Duplantier B, Jannink G, Sikorav JL. Symmetry and chirality in topoisomerase II-DNA crossover recognition. J Mol Biol 1998; 284:1289-99. [PMID: 9878350 DOI: 10.1006/jmbi.1998.2281] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Several experimental data support the notion that the recognition of DNA crossovers play an important role in the multiple functions of topoisomerase II. Here, a theoretical analysis of the possible modes of assembly of yeast topoisomerase II with right and left-handed tight DNA crossovers is performed, using the crystal coordinates of the docking partners. The DNA crossovers are assumed to be clamped into the central hole of the enzyme. Taking into account the rules for building symmetric ternary complexes and the structural constraints imposed by DNA-DNA and protein-DNA interactions, this analysis shows that two geometric solutions could exist, depending on the chirality of the DNA crossovers. In the first one, the two DNA segments are symmetrically recognized by the enzyme while each single double helix binds asymmetrically the protein dimer. In the second one, each double helix is symmetrically recognized by the protein around its dyad axis, while the two DNA segments have their own binding modes. The finding of potential DNA-binding domains which could interact with the crossovers provides structural supports for each model. The structural similarity of a loop containing a cluster of conserved basic residues pointing into the central hole of topoisomerase II and the second DNA-binding site of histone H5 which binds DNA crossover is of particular interest. Each solution, which is consistent with different sets of experimental data found in the literature, could either correspond to different functions of the enzyme or different steps of the reaction. This work provides structural insights for better understanding the role of chirality and symmetry in topoisomerase II-DNA crossover recognition, suggests testable experiments to further elucidate the structure of ternary complexes, and raises new questions about the relationships between the mechanism of strand-passage and strand-exchange catalyzed by the enzyme.
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Affiliation(s)
- Y Timsit
- Institut de Biologie Physico-Chimique, CNRS, Paris, France.
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95
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Bouet JY, Krisch HM, Louarn JM. Ndd, the bacteriophage T4 protein that disrupts the Escherichia coli nucleoid, has a DNA binding activity. J Bacteriol 1998; 180:5227-30. [PMID: 9748458 PMCID: PMC107561 DOI: 10.1128/jb.180.19.5227-5230.1998] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Early in a bacteriophage T4 infection, the phage ndd gene causes the rapid destruction of the structure of the Escherichia coli nucleoid. Even at very low levels, the Ndd protein is extremely toxic to cells. In uninfected E. coli, overexpression of the cloned ndd gene induces disruption of the nucleoid that is indistinguishable from that observed after T4 infection. A preliminary characterization of this protein indicates that it has a double-stranded DNA binding activity with a preference for bacterial DNA rather than phage T4 DNA. The targets of Ndd action may be the chromosomal sequences that determine the structure of the nucleoid.
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Affiliation(s)
- J Y Bouet
- Laboratoire de Microbiologie et de Génétique Moléculaire du CNRS, Toulouse, France
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96
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Fenley MO, Manning GS, Marky NL, Olson WK. Excess counterion binding and ionic stability of kinked and branched DNA. Biophys Chem 1998; 74:135-52. [PMID: 9760723 DOI: 10.1016/s0301-4622(98)00171-9] [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: 02/09/2023]
Abstract
We compute the excess number of counterions associated with kinked and branched DNA, and the ionic stabilities of these structures as a function of chain length and both sodium and magnesium salt concentration, using numerical counterion condensation theory. The DNA structures are modeled as two or more finite lines of phosphate charges radiating from the kink or junction center. The number of excess counterions around the (40-90 degrees) kinked duplex is very small (at most four). The geometries of large three- and four-way DNA junctions (with > 50 base pairs per arm) in solutions containing low to moderate NaCl concentrations, by contrast, accumulate a substantial number of excess sodium ions (> 20) but no more than 15 magnesium counterions. The excess number of counterions surrounding the kinked linear chain and the branched DNA structures either remains invariant or increases with chain length, tending to reach a plateau value. Open configurations, such as the planar Y-shaped three-way junction (with three 120 degrees inter-arm angles) and the 90 degrees cross-shaped four-way junction, are ionically more stable than compact geometries, such as pyramidal three-way junctions and X-shaped four-way junctions, over the entire range of salt concentration considered (10(-5)-10(-1) M NaCl or MgCl2). The ionic stabilities of the compact forms increase with increasing salt concentration and become comparable to those of the extended geometries at high salt (especially when magnesium is the supporting salt).
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Affiliation(s)
- M O Fenley
- Department of Chemistry, Rutgers, State University of New Jersey, Wright-Rieman Laboratories, Piscataway 08854-8087, USA
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97
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Liu ST, Chang WZ, Cao HM, Hu HL, Chen ZH, Ni FD, Lu HF, Hong GF. A HU-like protein binds to specific sites within nod promoters of Rhizobium leguminosarum. J Biol Chem 1998; 273:20568-74. [PMID: 9685414 DOI: 10.1074/jbc.273.32.20568] [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: 11/06/2022] Open
Abstract
Nodulation genes (nod) of rhizobia are essential for establishment of its symbiosis with specific legume hosts and are usually located on the Sym(biosis) megaplasmid. In this work we identified a new Sym plasmid independent protein in Rhizobium leguminosarum, Px, by its ability to bind to nod promoters and induce DNA bending. Depending upon its concentrations relative to DNA templates, Px could either stimulate or inhibit in vitro transcription of the major regulatory nodulation gene nodD. This may result from its property to bind to specific sites within nod promoters at lower concentration or in the presence of competitor calf thymus DNA but nonspecifically associate with DNA at higher levels or in the absence of competitors. Its binding sites within nodD and nodF promoters were determined by DNase I footprinting but showed no sequence consensus. N-terminal sequencing and Western blot revealed that Px belongs to the HU class of prokaryotic histone-like proteins. Its binding feature and functioning mechanism were discussed in the light of this discovery.
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Affiliation(s)
- S T Liu
- Shanghai Institute of Biochemistry, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
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98
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Whitby MC, Lloyd RG. Targeting Holliday junctions by the RecG branch migration protein of Escherichia coli. J Biol Chem 1998; 273:19729-39. [PMID: 9677403 DOI: 10.1074/jbc.273.31.19729] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The RecG protein of Escherichia coli is a junction-specific DNA helicase that drives branch migration of Holliday intermediates in genetic recombination and DNA repair. The reaction was investigated using synthetic X-junctions. RecG dissociates X-junctions to flayed duplex products, although DNA unwinding of the heterologous arms is limited to </=30 base pairs. Junction unwinding requires Mg2+ and the hydrolysis of ATP. X-junction DNA stimulates the ATPase activity of RecG. ATPase activity is also stimulated by linear duplex DNA, although to a lesser extent than by X-DNA, but not by linear single-stranded DNA. In situ 1,10-phenanthroline-copper footprinting shows that RecG binds to the strand cross-over point at the center of the X-junction. Substrate recognition by RecG was investigated using DNAs that represented the various component parts of an X-junction. The minimal DNA structure that RecG forms a stable complex with is a flayed duplex, suggesting that this is the critical feature for junction recognition by RecG. Junction binding and unwinding also depend critically on the concentration of free Mg2+, excess free cation dramatically inhibiting both processes. These inhibitory effects are not mediated specifically by Mg2+; e.g. both Ca2+ and hexamminecobalt(III) chloride also inhibit X-junction binding and unwinding by RecG. The relative abilities of these cations to inhibit RecG-junction binding is correlated with their respective abilities to stack X-junction DNA. From this we conclude that RecG is unable to bind or binds very poorly to fully stacked X-junctions.
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Affiliation(s)
- M C Whitby
- Microbiology Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.
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99
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Canosa I, Lurz R, Rojo F, Alonso JC. beta Recombinase catalyzes inversion and resolution between two inversely oriented six sites on a supercoiled DNA substrate and only inversion on relaxed or linear substrates. J Biol Chem 1998; 273:13886-91. [PMID: 9593735 DOI: 10.1074/jbc.273.22.13886] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The beta recombinase, in the presence of a chromatin-associated protein such as Hbsu, catalyzes DNA resolution or DNA inversion on supercoiled substrates containing two directly or inversely oriented six sites. Hbsu stabilizes the formation of the recombination complex (Alonso, J. C., Weise, F., and Rojo, F. (1995) J. Biol. Chem. 270, 2938-2945). In this study we show that resolution by beta recombinase strictly requires supercoiled DNA, but inversion does not. On a substrate with two inversely oriented six sites, beta recombinase catalyzed both resolution and inversion if the DNA was supercoiled but only inversion if the substrate was relaxed or linear. Hbsu was critical for the formation of synaptic complexes; its concentration relative to that of the supercoiled DNA substrate determined whether resolution or inversion products were preferentially formed. The results suggest that the beta recombinase forms unproductive short-lived synaptic complexes between two juxtaposed inversely oriented six sites; the presence of 3 to 13 Hbsu dimers per supercoiled DNA molecule would stabilize a synaptic complex with a relative geometry of the six sites allowing beta recombinase preferentially to achieve resolution. Supercoiling probably helps to overcome an energetic barrier, since resolution does not occur in relaxed DNA. The presence of >30 Hbsu dimers per DNA molecule probably favors the formation of a recombination complex with a different geometry since the reaction is directed preferentially toward DNA inversion.
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Affiliation(s)
- I Canosa
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, C.S.I.C., Campus de la Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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100
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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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