Clues and consequences of DNA bending in transcription.

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.

[1]  J. Dubochet,et al.  Direct visualization of supercoiled DNA molecules in solution. , 1990, The EMBO journal.

[2]  S. Kustu,et al.  The isolated catalytic domain of NIFA, a bacterial enhancer-binding protein, activates transcription in vitro: activation is inhibited by NIFL. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[3]  D. Pettijohn,et al.  RNA molecules bound to the folded bacterial genome stabilize DNA folds and segregate domains of supercoiling. , 1974, Cold Spring Harbor symposia on quantitative biology.

[4]  R. L. Baldwin,et al.  Energetics of DNA twisting. I. Relation between twist and cyclization probability. , 1983, Journal of molecular biology.

[5]  A. Schepartz Nonspecific DNA bending and the specificity of protein-DNA interactions , 1995, Science.

[6]  G. W. Hatfield,et al.  Transcriptional activation by protein-induced DNA bending: evidence for a DNA structural transmission model. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[7]  G. Rapoport,et al.  The HPr protein of the phosphotransferase system links induction and catabolite repression of the Bacillus subtilis levanase operon , 1995, Journal of bacteriology.

[8]  R. C. Johnson,et al.  DNA binding and bending are necessary but not sufficient for Fis-dependent activation of rrnB P1 , 1993, Journal of bacteriology.

[9]  J. Calvo,et al.  Sequence determinants of DNA bending in the ilvlH promoter and regulatory region of Escherichia coli. , 1994, Nucleic acids research.

[10]  Richard H. Ebright,et al.  Promoter structure, promoter recognition, and transcription activation in prokaryotes , 1994, Cell.

[11]  M. Bianchi Prokaryotic HU and eukaryotic HMG1: a kinked relationship , 1994, Molecular microbiology.

[12]  H. Buc,et al.  On the action of the cyclic AMP‐cyclic AMP receptor protein complex at the Escherichia coli lactose and galactose promoter regions. , 1984, The EMBO journal.

[13]  R Grosschedl,et al.  Assembly and function of a TCR alpha enhancer complex is dependent on LEF-1-induced DNA bending and multiple protein-protein interactions. , 1995, Genes & development.

[14]  V. de Lorenzo,et al.  The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR , 1995, Journal of bacteriology.

[15]  C. Calladine,et al.  Sequence-specific positioning of core histones on an 860 base-pair DNA. Experiment and theory. , 1987, Journal of molecular biology.

[16]  V. de Lorenzo,et al.  The amino-terminal domain of the prokaryotic enhancer-binding protein XylR is a specific intramolecular repressor. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[17]  J. Lupski,et al.  Short, interspersed repetitive DNA sequences in prokaryotic genomes , 1992, Journal of bacteriology.

[18]  S. Kustu,et al.  Expression of sigma 54 (ntrA)-dependent genes is probably united by a common mechanism. , 1989, Microbiological reviews.

[19]  A. Travers,et al.  DNA conformation and protein binding. , 1989, Annual review of biochemistry.

[20]  Dimitris Thanos,et al.  The High Mobility Group protein HMG I(Y) is required for NF-κB-dependent virus induction of the human IFN-β gene , 1992, Cell.

[21]  M. Brenowitz,et al.  DNA conformational changes associated with the cooperative binding of cI-repressor of bacteriophage lambda to OR. , 1994, Journal of molecular biology.

[22]  Phoebe A Rice,et al.  Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn , 1996, Cell.

[23]  S. Kustu,et al.  The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons , 1990, Cell.

[24]  P. Hagerman,et al.  Sequence-directed curvature of DNA. , 1986, Nature.

[25]  A. Kolb,et al.  CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli. , 1991, Journal of molecular biology.

[26]  M. Churchill,et al.  DNA chaperones: A solution to a persistence problem? , 1994, Cell.

[27]  Kano Yasunobu,et al.  Chimeric HU-IHF proteins that alter DNA-binding ability. , 1992 .

[28]  H. Bremer,et al.  Effects of Fis on ribosome synthesis and activity and on rRNA promoter activities in Escherichia coli. , 1996, Journal of molecular biology.

[29]  F. Rojo,et al.  Residues of the Bacillus subtilis phage phi 29 transcriptional activator required both to interact with RNA polymerase and to activate transcription. , 1993, Journal of molecular biology.

[30]  A. Segall,et al.  Architectural elements in nucleoprotein complexes: interchangeability of specific and non‐specific DNA binding proteins. , 1994, The EMBO journal.

[31]  H. Buc,et al.  Transcriptional regulation by cAMP and its receptor protein. , 1993, Annual review of biochemistry.

[32]  R. Ebright Transcription activation at Class I CAP‐dependent promoters , 1993, Molecular microbiology.

[33]  D M Crothers,et al.  Sequence elements responsible for DNA curvature. , 1994, Journal of molecular biology.

[34]  K. Timmis,et al.  An upstream XylR‐ and IHF‐induced nucleoprotein complex regulates the sigma 54‐dependent Pu promoter of TOL plasmid. , 1991, The EMBO journal.

[35]  A M Gronenborn,et al.  Intercalation, DNA Kinking, and the Control of Transcription , 1996, Science.

[36]  P. Kraulis,et al.  Structure of the HMG box motif in the B‐domain of HMG1. , 1993, The EMBO journal.

[37]  L. Kaltenbach,et al.  Leucine‐responsive regulatory protein plays dual roles as both an activator and a repressor of the Escherichia coli pap fimbrial operon , 1995, Molecular microbiology.

[38]  M. Shimizu,et al.  Characterization of the binding of HU and IHF, homologous histone-like proteins of Escherichia coli, to curved and uncurved DNA. , 1995, Biochimica et biophysica acta.

[39]  M. Suzuki,et al.  Stereochemical basis of DNA bending by transcription factors. , 1995, Nucleic acids research.

[40]  V. Corces,et al.  DNA bending is a determinant of binding specificity for a Drosophila zinc finger protein. , 1990, Genes & development.

[41]  R. Wagner,et al.  Evidence for a regulatory function of the histone‐like Escherichia coli protein H‐NS in ribosomal RNA synthesis , 1994, Molecular microbiology.

[42]  S. Kustu,et al.  Prokaryotic transcriptional enhancers and enhancer-binding proteins. , 1991, Trends in biochemical sciences.

[43]  R. C. Johnson,et al.  The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures. , 1993, Genes & development.

[44]  D. Vidal-Ingigliardi,et al.  A complex nucleoprotein structure involved in activation of transcription of two divergent Escherichia coli promoters. , 1989, Journal of molecular biology.

[45]  C. Ball,et al.  Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli , 1992, Journal of bacteriology.

[46]  C. Gutiérrez,et al.  Phage Ø29 protein p6: A viral histone-like protein , 1994 .

[47]  P. Kiley,et al.  In vitro analysis of a constitutively active mutant form of the Escherichia coli global transcription factor FNR. , 1995, Journal of molecular biology.

[48]  D. Crothers,et al.  The DNA binding domain and bending angle of E. coli CAP protein , 1986, Cell.

[49]  B. Magasanik,et al.  Positive and negative effects of DNA bending on activation of transcription from a distant site. , 1992, Journal of molecular biology.

[50]  M. Beltrame,et al.  Protein HU binds specifically to kinked DNA , 1993, Molecular microbiology.

[51]  K. Rudd,et al.  Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coli , 1993, Molecular microbiology.

[52]  Hen-Ming Wu,et al.  The locus of sequence-directed and protein-induced DNA bending , 1984, Nature.

[53]  R. Lobell,et al.  AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein. , 1991, Journal of molecular biology.

[54]  M Suzuki,et al.  An in-the-groove view of DNA structures in complexes with proteins. , 1996, Journal of molecular biology.

[55]  E. Geiduschek,et al.  Site‐specific DNA binding by the bacteriophage SP01‐encoded type II DNA‐binding protein. , 1985, The EMBO journal.

[56]  M. Suzuki,et al.  DNA conformation and its changes upon binding transcription factors. , 1996, Advances in biophysics.

[57]  A. Toussaint,et al.  Stabilization of bacteriophage Mu repressor‐operator complexes by the Escherichia coli integration host factor protein , 1992, Molecular microbiology.

[58]  S. Gottesman,et al.  An imbalance of HU synthesis induces mucoidy in Escherichia coli. , 1993, Journal of molecular biology.

[59]  C. Higgins,et al.  Histone-like protein H1 (H-NS), DNA supercoiling, and gene expression in bacteria , 1990, Cell.

[60]  D. Crothers,et al.  Detection of localized DNA flexibility , 1994, Nature.

[61]  D. Landsman,et al.  The HMG-1 box protein family: classification and functional relationships. , 1995, Nucleic acids research.

[62]  S. Maloy,et al.  Integration host factor facilitates repression of the put operon in Salmonella typhimurium. , 1992, Gene.

[63]  R. Gourse,et al.  Localization of the intrinsically bent DNA region upstream of the E.coli rrnB P1 promoter. , 1994, Nucleic acids research.

[64]  R. Simons,et al.  Chromosomal supercoiling in Escherichia coli , 1993, Molecular microbiology.

[65]  Rudolf Grosschedl,et al.  The HMG domain of lymphoid enhancer factor 1 bends DNA and facilitates assembly of functional nucleoprotein structures , 1992, Cell.

[66]  G. W. Hatfield,et al.  DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli. , 1992, Journal of molecular biology.

[67]  I. Tanaka,et al.  3-Å resolution structure of a protein with histone-like properties in prokaryotes , 1984, Nature.

[68]  D Roberts,et al.  Growth phase variation of integration host factor level in Escherichia coli , 1994, Journal of bacteriology.

[69]  J. Pérez-Martín,et al.  Correlation between DNA bending and transcriptional activation at a plasmid promoter. , 1994, Journal of molecular biology.

[70]  E. Bonnefoy,et al.  DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. , 1994, Journal of molecular biology.

[71]  P. Vignais,et al.  Cloning and sequence analyses of the genes coding for the integration host factor (IHF) and HU proteins of Pseudomonas aeruginosa. , 1995, Gene.

[72]  W. Schaffner,et al.  Transcriptional enhancers can act in trans. , 1990, Trends in genetics : TIG.

[73]  A. Ninfa,et al.  Activation of transcription initiation from the nac promoter of Klebsiella aerogenes , 1995, Journal of bacteriology.

[74]  A. Worcel,et al.  On the structure of the folded chromosome of Escherichia coli. , 1972, Journal of molecular biology.

[75]  R. D'ari,et al.  The leucine-responsive regulatory protein: more than a regulator? , 1993, Trends in biochemical sciences.

[76]  R. Gourse,et al.  Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. , 1994, Journal of molecular biology.

[77]  J. Plumbridge,et al.  Sequence of the nagBACD operon in Escherichia coli K12 and pattern of transcription within the nag regulon , 1989, Molecular microbiology.

[78]  Roberto Spurio,et al.  Expression of the gene encoding the major bacterial nucleoid protein H‐NS is subject to transcriptional auto‐repression , 1993, Molecular microbiology.

[79]  S. Long,et al.  Interactions of NodD at the nod Box: NodD binds to two distinct sites on the same face of the helix and induces a bend in the DNA. , 1993, Journal of molecular biology.

[80]  J. Pérez-Martín,et al.  The RepA repressor can act as a transcriptional activator by inducing DNA bends. , 1991, The EMBO journal.

[81]  W Hendrickson,et al.  Regulation of the Escherichia coli L-arabinose operon studied by gel electrophoresis DNA binding assay. , 1984, Journal of molecular biology.

[82]  R. Grosschedl,et al.  Higher-order nucleoprotein complexes in transcription: analogies with site-specific recombination. , 1995, Current opinion in cell biology.

[83]  L. J. Maher,et al.  DNA bending by asymmetric phosphate neutralization. , 1994, Science.

[84]  E. Trifonov Curved DNA. , 1985, CRC critical reviews in biochemistry.

[85]  M. Ptashne,et al.  Transcriptional activation by recruitment , 1997, Nature.

[86]  H. Pedersen,et al.  A flexible partnership: the CytR anti‐activator and the cAMP–CRP activator protein, comrades in transcription control , 1996, Molecular microbiology.

[87]  C. Bustamante,et al.  DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity. , 1994, Science.

[88]  D M Crothers,et al.  Protein-induced bending and DNA cyclization. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[89]  E. Gilson,et al.  Palindromic units are part of a new bacterial interspersed mosaic element (BIME). , 1991, Nucleic acids research.

[90]  E. Geiduschek,et al.  DNA-bending properties of TF1. , 1991, Journal of molecular biology.

[91]  S. Kustu,et al.  Glutamate is required to maintain the steady-state potassium pool in Salmonella typhimurium. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[92]  V. Lorenzo,et al.  Regulatory noise in prokaryotic promoters: how bacteria learn to respond to novel environmental signals , 1996, Molecular microbiology.

[93]  S. Lippard,et al.  High-mobility-group 1 protein mediates DNA bending as determined by ring closures. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[94]  C. Higgins,et al.  Protein H1: a role for chromatin structure in the regulation of bacterial gene expression and virulence? , 1990, Molecular microbiology.

[95]  R. Bender The role of the NAC protein in the nitrogen regulation of Klebsiella aerogenes , 1991, Molecular microbiology.

[96]  N. Goosen,et al.  Integration host factor alleviates the H‐NS‐mediated repression of the early promoter of bacteriophage Mu , 1996, Molecular microbiology.

[97]  R. Harrington DNA curving and bending in protein–DNA recognition , 1992, Molecular microbiology.

[98]  K. Timmis,et al.  Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. , 1997, Annual review of microbiology.

[99]  M. Chandler,et al.  Escherichia coli integration host factor stabilizes bacteriophage Mu repressor interactions with operator DNA in vitro , 1992, Molecular microbiology.

[100]  Monika Tsai-Pflugfelder,et al.  A proline-rich TGF-beta-responsive transcriptional activator interacts with histone H3. , 1995, Genes & development.

[101]  A. Nakazawa,et al.  Analysis of DNA bend structure of promoter regulatory regions of xylene-metabolizing genes on the Pseudomonas TOL plasmid. , 1994, Journal of Biochemistry (Tokyo).

[102]  G. Rapoport,et al.  Two different mechanisms mediate catabolite repression of the Bacillus subtilis levanase operon , 1995, Journal of bacteriology.

[103]  T. Megraw,et al.  The mitochondrial histone HM: an evolutionary link between bacterial HU and nuclear HMG1 proteins. , 1994, Biochimie.

[104]  A. Oppenheim,et al.  Genetic and biochemical analysis of IHF/HU hybrid proteins. , 1994, Biochimie.

[105]  D. Pettijohn,et al.  Histone-like proteins and bacterial chromosome structure. , 1988, The Journal of biological chemistry.

[106]  L. Søgaard-Andersen,et al.  CRP induces the repositioning of MalT at the Escherichia coli malKp promoter primarily through DNA bending. , 1994, The EMBO journal.

[107]  K. Rudd,et al.  Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria , 1992, Journal of bacteriology.

[108]  T. Maniatis,et al.  Mechanisms of transcriptional synergism between distinct virus-inducible enhancer elements , 1993, Cell.

[109]  S. Goodman,et al.  Deformation of DNA during site-specific recombination of bacteriophage lambda: replacement of IHF protein by HU protein or sequence-directed bends. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[110]  Molly B. Schmid,et al.  More than just “Histone-like” proteins , 1990, Cell.

[111]  V. de Lorenzo,et al.  Coactivation in vitro of the sigma54-dependent promoter Pu of the TOL plasmid of Pseudomonas putida by HU and the mammalian HMG-1 protein , 1997, Journal of bacteriology.

[112]  J. Calvo,et al.  Lrp, a major regulatory protein in Escherichia coli, bends DNA and can organize the assembly of a higher‐order nucleoprotein structure. , 1993, The EMBO journal.

[113]  R. Grosschedl,et al.  LEF‐1 contains an activation domain that stimulates transcription only in a specific context of factor‐binding sites. , 1993, The EMBO journal.

[114]  W. Gaastra,et al.  Regions of the CFA/I promoter involved in the activation by the transcriptional activator CfaD and repression by the histone-like protein H-NS. , 1994, Biochimie.

[115]  V. de Lorenzo,et al.  ATP binding to the sigma 54-dependent activator XylR triggers a protein multimerization cycle catalyzed by UAS DNA. , 1996, Cell.

[116]  V. de Lorenzo,et al.  Integration host factor suppresses promiscuous activation of the sigma 54-dependent promoter Pu of Pseudomonas putida. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[117]  R F Schleif,et al.  DNA looping and unlooping by AraC protein , 1990, Science.

[118]  T. Atlung,et al.  The histone-like protein H-NS acts as a transcriptional repressor for expression of the anaerobic and growth phase activator AppY of Escherichia coli , 1996, Journal of bacteriology.

[119]  H. Westerhoff,et al.  DNA supercoiling depends on the phosphorylation potential in Escherichia coli , 1996, Molecular microbiology.

[120]  M. Cayuela,et al.  High mobility group I(Y)-like DNA-binding domains on a bacterial transcription factor. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[121]  R. Kolter,et al.  A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. , 1992, Genes & development.

[122]  R. Burgess,et al.  The leucine‐responsive regulatory protein (Lrp) acts as a specific repressor for σs‐dependent transcription of the Escherichia coli aidB gene , 1996, Molecular microbiology.

[123]  R Grosschedl,et al.  HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. , 1994, Trends in genetics : TIG.

[124]  J. Kim,et al.  DNA bending by negative regulatory proteins: Gal and Lac repressors. , 1989, Genes & development.

[125]  Phillip A. Sharp,et al.  6 – Regulation of Transcription , 1991 .

[126]  Donald M. Crothers,et al.  DNA sequence determinants of CAP-induced bending and protein binding affinity , 1988, Nature.

[127]  A. Oppenheim,et al.  Enhanced activity of the bacteriophage lambda PL promoter at low temperature. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[128]  M Carmona,et al.  Activation of transcription at sigma 54-dependent promoters on linear templates requires intrinsic or induced bending of the DNA. , 1996, Journal of molecular biology.

[129]  J. Griffith,et al.  Curved helix segments can uniquely orient the topology of supertwisted DNA , 1988, Cell.

[130]  Hen-Ming Wu,et al.  DNA bending at adenine · thymine tracts , 1986, Nature.

[131]  N. Cozzarelli,et al.  Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. , 1987, Journal of molecular biology.

[132]  H. Drew,et al.  Negative supercoiling induces spontaneous unwinding of a bacterial promoter. , 1985, The EMBO journal.

[133]  M. Chandler,et al.  Mutual stabilisation of bacteriophage Mu repressor and histone-like proteins in a nucleoprotein structure. , 1995, Journal of molecular biology.

[134]  H. Nash The HU and IHF Proteins: Accessory Factors for Complex Protein-DNA Assemblies , 1996 .

[135]  M. Débarbouillé,et al.  The Bacillus subtilis sigL gene encodes an equivalent of sigma 54 from gram-negative bacteria. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[136]  S. Elgin,et al.  Protein/DNA architecture of the DNase I hypersensitive region of the Drosophila hsp26 promoter. , 1988, The EMBO journal.

[137]  G. Stent Molecular Genetics: An Introductory Narrative , 1971 .

[138]  V. de Lorenzo,et al.  Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. , 1994, Microbiological reviews.

[139]  D. Crothers Architectural elements in nucleoprotein complexes , 1993, Current Biology.

[140]  J. Molina-López,et al.  Geometry of the process of transcription activation at the sigma 54-dependent nifH promoter of Klebsiella pneumoniae. , 1994, The Journal of biological chemistry.

[141]  P. Valentin-Hansen,et al.  cAMP-CRP activator complex and the CytR repressor protein bind co-operatively to the cytRP promoter in Escherichia coli and CytR antagonizes the cAMP-CRP-induced DNA bend. , 1992, Journal of molecular biology.

[142]  K. Drlica,et al.  Histone-like protein HU and bacterial DNA topology: suppression of an HU deficiency by gyrase mutations. , 1996, Journal of molecular biology.

[143]  R E Harrington,et al.  The effects of sequence context on DNA curvature. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[144]  Gideon Schreiber,et al.  Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, rpoS, ppGpp and by autoregulation , 1994, Molecular microbiology.

[145]  S. Gottesman,et al.  A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[146]  C. Gutiérrez,et al.  The role of the chromatin‐associated protein Hbsu in β‐mediated DNA recombination is to facilitate the joining of distant recombination sites , 1995, Molecular microbiology.

[147]  Consejo Superior de Investigaciones The s 54 -Dependent PromoterPsof the TOL Plasmid of Pseudomonas putidaRequires HU for Transcriptional Activation In Vivo by XylR , 1995 .

[148]  R. Bender,et al.  Roles of catabolite activator protein sites centered at -81.5 and -41.5 in the activation of the Klebsiella aerogenes histidine utilization operon hutUH , 1994, Journal of bacteriology.

[149]  E. Bremer,et al.  Synthesis of the Escherichia coli K‐12 nucleoid‐associated DNA‐binding protein H‐NS is subjected to growth‐phase control and autoregulation , 1993, Molecular microbiology.

[150]  M. Brenowitz,et al.  DNA Conformational Changes Associated with the Cooperative Binding of cI-repressor of Bacteriophage λ to OR , 1994 .

[151]  J. Roth,et al.  Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium , 1996, Journal of bacteriology.

[152]  A. Travers,et al.  The Escherichia coli FIS protein is not required for the activation of tyrT transcription on entry into exponential growth. , 1993, The EMBO journal.

[153]  H. Echols,et al.  Multiple DNA-protein interactions governing high-precision DNA transactions. , 1986, Science.

[154]  S. Normark,et al.  The RpoS Sigma factor relieves H‐NS‐mediated transcriptional repression of csgA, the subunit gene of fibronectin‐binding curli in Escherichia coli , 1993, Molecular microbiology.

[155]  C. Higgins,et al.  Chromosomal domains of supercoiling in Salmonella typhimurium , 1993, Molecular microbiology.

[156]  M. Buck,et al.  Purification and in vitro activities of the native nitrogen fixation control proteins NifA and NifL , 1994, Journal of bacteriology.

[157]  M. Gilman,et al.  DNA bending and orientation-dependent function of YY1 in the c-fos promoter. , 1993, Genes & development.

[158]  G. Ames,et al.  Role of the intercistronic region in post‐transcriptional control of gene expression in the histidine transport operon of Salmonella typhimurium: involvement of REP sequences , 1988, Molecular microbiology.

[159]  P. Cary,et al.  Solution structure of a DNA-binding domain from HMG1. , 1993, Nucleic acids research.

[160]  H. Fritz,et al.  RNA polymerase and gal repressor bind simultaneously and with DNA bending to the control region of the Escherichia coli galactose operon. , 1989, The EMBO journal.

[161]  Jay D. Gralla,et al.  DNA dynamic flexibility and protein recognition: Differential stimulation by bacterial histone-like protein HU , 1988, Cell.

[162]  V. Lorenzo,et al.  Involvement of σ54 in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter , 1996 .

[163]  F. Rojo,et al.  Bend induced by the phage phi 29 transcriptional activator in the viral late promoter is required for activation. , 1990, Journal of molecular biology.

[164]  R. C. Johnson,et al.  The Fis protein: it's not just for DNA inversion anymore , 1992, Molecular microbiology.

[165]  J. Ramos,et al.  Activation of the Pseudomonas TOL plasmid upper pathway operon. Identification of binding sites for the positive regulator XylR and for integration host factor protein. , 1991, The Journal of biological chemistry.

[166]  F. Rojo,et al.  The main early and late promoters of Bacillus subtilis phage ø29 form unstable open complexes with σA-RNA polymerase that are stabilized by DNA supercoiling , 1993 .

[167]  J. Pérez-Martín,et al.  Protein-induced bending as a transcriptional switch. , 1993, Science.

[168]  E. Yeramian,et al.  CRP fixes the rotational orientation of covalently closed DNA molecules. , 1994, The EMBO journal.

[169]  J. Wang,et al.  Action at a distance along a DNA. , 1988, Science.

[170]  R. Ebright,et al.  Transcription activation at the Escherichia coli uhpT promoter by the catabolite gene activator protein , 1995, Journal of bacteriology.

[171]  M. Débarbouillé,et al.  The transcriptional regulator LevR of Bacillus subtilis has domains homologous to both sigma 54- and phosphotransferase system-dependent regulators. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[172]  M. R. Gerrero,et al.  Site-specific HU binding in the Mu transpososome: conversion of a sequence-independent DNA-binding protein into a chemical nuclease. , 1993, Genes & development.

[173]  Paul J. Hagerman,et al.  Sequence-directed curvature of DNA , 1986, Nature.

[174]  E. Geiduschek,et al.  Specificity of the weak binding between the phage SPO1 transcription-inhibitory protein, TF1, and SPO1 DNA. , 1977, Biochemistry.

[175]  D M Crothers,et al.  Bent helical structure in kinetoplast DNA. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[176]  S. Kustu,et al.  Role of integration host factor in stimulating transcription from the sigma 54-dependent nifH promoter. , 1992, Journal of molecular biology.

[177]  D. Vidal-Ingigliardi,et al.  A new mechanism for coactivation of transcription initiation: Repositioning of an activator triggered by the binding of a second activator , 1991, Cell.

[178]  P. Hagerman,et al.  DNA ring closure mediated by protein HU. , 1989, The Journal of biological chemistry.

[179]  R. Kahmann,et al.  G inversion in bacteriophage Mu DNA is stimulated by a site within the invertase gene and a host factor , 1985, Cell.

[180]  M. Churchill,et al.  Harnessing the writhe: a role for DNA chaperones in nucleoprotein-complex formation. , 1994, Trends in biochemical sciences.

[181]  F. Rojo,et al.  A DNA curvature can substitute phage phi 29 regulatory protein p4 when acting as a transcriptional repressor. , 1991, The EMBO journal.

[182]  D. Edwards,et al.  The DNA-bending protein HMG-1 enhances progesterone receptor binding to its target DNA sequences , 1994, Molecular and cellular biology.

[183]  H. Krause,et al.  Positive and negative regulation of the Mu operator by Mu repressor and Escherichia coli integration host factor. , 1986, The Journal of biological chemistry.

[184]  H. Pedersen,et al.  Protein‐induced fit: the CRP activator protein changes sequence‐specific DNA recognition by the CytR repressor, a highly flexible LacI member , 1997, The EMBO journal.

[185]  E. Bonnefoy,et al.  HU, the major histone‐like protein of E. coli, modulates the binding of IHF to oriC. , 1992, The EMBO journal.

[186]  P. Valentin-Hansen,et al.  The cyclic AMP (cAMP)-cAMP receptor protein complex functions both as an activator and as a corepressor at the tsx-p2 promoter of Escherichia coli K-12 , 1991, Journal of bacteriology.

[187]  J T Finch,et al.  Role of base‐backbone and base‐base interactions in alternating DNA conformations , 1996, FEBS letters.

[188]  D M Crothers,et al.  Intrinsically bent DNA. , 1990, The Journal of biological chemistry.

[189]  B. Magasanik,et al.  Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[190]  D. K. Hawley,et al.  DNA bending is an important component of site-specific recognition by the TATA binding protein. , 1995, Journal of molecular biology.

[191]  V. de Lorenzo,et al.  Modulation of gene expression through chromosomal positioning in Escherichia coli. , 1997, Microbiology.

[192]  A. Wolffe,et al.  A nucleosome‐dependent static loop potentiates estrogen‐regulated transcription from the Xenopus vitellogenin B1 promoter in vitro. , 1993, The EMBO journal.

[193]  P. Kraulis,et al.  Structure of the HMG box motif in the B‐domain of HMG1. , 1993, EMBO Journal.

[194]  W. Szybalski,et al.  Repression of transcription from the b2-att region of coliphage lambda by integration host factor. , 1989, Virology.

[195]  S. Elgin,et al.  The formation and function of DNase I hypersensitive sites in the process of gene activation. , 1988, The Journal of biological chemistry.

[196]  Steven D. Goodman,et al.  Functional replacement of a protein-induced bend in a DNA recombination site , 1989, Nature.

[197]  R E Harrington,et al.  Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[198]  G. Węgrzyn,et al.  An Additional Role of Transcriptional Activation of ori-λ in the Regulation of λ-Plasmid Replication in Escherichia coli , 1994 .

[199]  Nora Goosen,et al.  The regulation of transcription initiation by integration host factor , 1995, Molecular microbiology.

[200]  R. Lurz,et al.  Induced bending of plasmid pLS1 DNA by the plasmid-encoded protein RepA. , 1989, The Journal of biological chemistry.

[201]  L. Shapiro,et al.  Integration host factor is required for the activation of developmentally regulated genes in Caulobacter. , 1990, Genes & development.

[202]  P. Sharp,et al.  Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor , 1995, Nature.

[203]  K. Drlica,et al.  Histonelike proteins of bacteria. , 1987, Microbiological reviews.

[204]  F. Rojo,et al.  The Bacillussubtilis Histone-like Protein Hbsu Is Required for DNA Resolution and DNA Inversion Mediated by the Recombinase of Plasmid pSM19035 (*) , 1995, The Journal of Biological Chemistry.

[205]  M. Yaniv,et al.  E. coli DNA binding protein HU forms nucleosome-like structure with circular double-stranded DNA , 1979, Cell.

[206]  M. Salas,et al.  Transcription activation at a distance by phage ø29 protein p4 , 1991 .

[207]  H R Drew,et al.  Structural junctions in DNA: the influence of flanking sequence on nuclease digestion specificities. , 1985, Nucleic acids research.

[208]  V. de Lorenzo,et al.  Co-regulation by bent DNA. Functional substitutions of the integration host factor site at sigma 54-dependent promoter Pu of the upper-TOL operon by intrinsically curved sequences. , 1994, The Journal of biological chemistry.

[209]  D. Friedman,et al.  Integration host factor: A protein for all reasons , 1988, Cell.

[210]  G. del Solar,et al.  Plasmid pLS1-encoded RepA protein regulates transcription from repAB promoter by binding to a DNA sequence containing a 13-base pair symmetric element. , 1990, The Journal of biological chemistry.

[211]  A. Oppenheim,et al.  Enhanced activity of the bacteriophage λ PL promoter at low temperature , 1995 .