Source: http://www.asmscience.org/content/book/10.1128/9781555817640.chap8
Timestamp: 2019-04-24 05:58:52+00:00

Document:
In eukaryotes, DNA replication appears to occur in stationary factories that can be visualized as foci in the nucleus via either immunofluorescence microscopy of replication proteins or fluorescence microscopy of live cells carrying green fluorescent protein-tagged replication proteins. In bacteria, the division plane at midcell is a crucial locus where most of the events leading to cytokinesis take place. Using green fluorescent proteintagged subunits of the Pol III HE, researches have shown that the DNA polymerases assemble and replicate DNA at midcell in Bacillus subtilis. Studies on the effect of moving dif on chromosomal dimer resolution and on the tolerance of deletions and inversions in the terminus region have led to the suggestion that the chromosome is polarized, meaning that the directionality of the path taken along the chromosome away from oriC has some physical manifestation. The proteins required for restart primosome assembly—PriA, PriB, PriC, DnaT, DnaB, DnaC, and DnaG—were discovered originally because they acted to assemble a primosome on φX174 viral DNA during its conversion to the replicative form. In Escherichia coli, estimates of the probability that a replication fork formed at oriC will be arrested before completing replication of one arm of the chromosome vary from 0.15 to almost certainty.
1.. Afflerbach, H.,, O. Schroder,, and R. Wagner. 1999. Conformational changes of the upstream DNA mediated by H-NS and FIS regulate E. coli rrnB P1 promoter activity. J. Mol. Biol. 286: 339– 353.
2. Aiyar, S. E.,, S. M. McLeod,, W. Ross,, C. A. Hirvonen,, M. S. Thomas,, R. C. Johnson,, and R. L. Gourse. 2002. Architecture of Fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promoters. J. Mol. Biol. 316: 501– 516.
3. Aki, T.,, and S. Adhya. 1997. Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J. 16: 3666– 3674.
4. Ali, B. M.,, R. Amit,, I. Braslavsky,, A. B. Oppenheim,, O. Gileadi,, and J. Stavans. 2001. Compaction of single DNA molecules induced by binding of integration host factor (IHF). Proc. Natl. Acad. Sci. USA 98: 10658– 10663.
5. Allingham, J. S.,, and D. B. Haniford. 2002. Mechanisms of metal ion action in Tn 10 transposition. J. Mol. Biol. 319: 53– 65.
6. Alonso, J. C.,, F. Weise,, and F. Rojo. 1995. The Bacillus subtilis histone-like protein Hbsu is required for DNA resolution and DNA inversion mediated by the beta recombinase of plasmid pSM19035. J. Biol. Chem. 270: 2938– 2945.
7. Arfin, S. M.,, A. D. Long,, E. T. Ito,, L. Tolleri,, M. M. Riehle,, E. S. Paegle,, and G. W. Hatfield. 2000. Global gene expression profiling in Escherichia coli K12. The effects of integration host factor . J. Biol. Chem. 275: 29672– 29684.
8. Asai, T.,, D. B. Bates,, E. Boye,, and T. Kogoma. 1998. Are minichromosomes valid model systems for DNA replication control? Lessons learned from Escherichia coli. Mol. Microbiol. 29: 671– 675.
9. Atlung, T.,, and F. G. Hansen. 2002. Effect of different concentrations of H-NS protein on chromosome replication and the cell cycle in Escherichia coli. J. Bacteriol. 184: 1843– 1850.
10. Atlung, T.,, and H. Ingmer. 1997. H-NS: a modulator of environmentally regulated gene expression. Mol. Microbiol. 24: 7– 17.
11. Augustin, L. B.,, B. A. Jacobson,, and J. A. Fuchs. 1994. Escherichia coli Fis and DnaA proteins bind specifically to the nrd promoter region and affect expression of an nrd-lac fusion. J. Bacteriol. 176: 378– 387.
12. Aviv, M.,, H. Giladi,, G. Schreiber,, A. B. Oppenheim,, and G. Glaser. 1994. Expression of the genes coding for the Escherichia coli integration host factor are controlled by growth phase, RpoS, ppGpp and by autoregulation. Mol. Microbiol. 14: 1021– 1031.
13. Azaro, M. A.,, and A. Landy,. 2002. λ integrase and the λ Int family, p. 118– 148. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
14. Baker, T. A.,, and A. Kornberg. 1988. Transcriptional activation of initiation of replication from the E. coli chromosomal origin: an RNA-DNA hybrid near oriC. Cell 55: 113– 123.
15. Baker, T. A.,, and K. Mizuuchi. 1992. DNA-promoted assembly of the active tetramer of the Mu transposase. Genes Dev. 6: 2221– 2232.
16. Balandina, A.,, L. Claret,, R. Hengge-Aronis,, and J. Rouviere- Yaniv. 2001. The Escherichia coli histone-like protein HU regulates rpoS translation. Mol. Microbiol. 39: 1069– 1079.
17. Balandina, A.,, D. Kamashev,, and J. Rouviere-Yaniv. 2002. The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids. J. Biol. Chem. 277: 27622– 27628.
18. Balke, V. L.,, and J. D. Gralla. 1987. Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli. J. Bacteriol. 169: 4499– 4506.
19. Ball, C. A.,, and R. C. Johnson. 1991. Efficient excision of phage lambda from the Escherichia coli chromosome requires the Fis protein. J. Bacteriol. 173: 4027– 4031.
20. Ball, C. A.,, and R. C. Johnson. 1991. Multiple effects of Fis on integration and the control of lysogeny in phage lambda. J. Bacteriol. 173: 4032– 4038.
21. Ball, C. A.,, R. Osuna,, K. C. Ferguson,, and R. C. Johnson. 1992. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J. Bacteriol. 174: 8043– 8056.
22. Barth, M.,, C. Marschall,, A. Muffler,, D. Fischer,, and R. Hengge-Aronis. 1995. Role for the histone-like protein H-NS in growth phase-dependent and osmotic regulation of sigma S and many sigma S-dependent genes in Escherichia coli. J. Bacteriol. 177: 3455– 3464.
23. Bartlett, M. S.,, T. Gaal,, W. Ross,, and R. L. Gourse. 2000. Regulation of rRNA transcription is remarkably robust: FIS compensates for altered nucleoside triphosphate sensing by mutant RNA polymerases at Escherichia coli rrn P1 promoters. J. Bacteriol. 182: 1969– 1977.
24. Bates, D. B.,, T. Asai,, Y. Cao,, M. W. Chambers,, G. W. Cadwell,, E. Boye,, and T. Kogoma. 1995. The DnaA box R4 in the minimal oriC is dispensable for initiation of Escherichia coli chromosome replication. Nucleic Acids Res. 23: 3119– 3125.
25. Beach, M. B.,, and R. Osuna. 1998. Identification and characterization of the fis operon in enteric bacteria. J. Bacteriol. 180: 5932– 5946.
26. Bensaid, A.,, A. Almeida,, K. Drlica,, and J. Rouviere-Yaniv. 1996. Cross-talk between topoisomerase I and HU in Escherichia coli. J. Mol. Biol. 256: 292– 300.
27. Bertin, P.,, N. Benhabiles,, E. Krin,, C. Laurent-Winter,, C. Tendeng,, E. Turlin,, A. Thomas,, A. Danchin,, and R. Brasseur. 1999. The structural and functional organization of H-NS-like proteins is evolutionarily conserved in gram-negative bacteria. Mol. Microbiol. 31: 319– 329.
28. Bertin, P.,, F. Hommais,, E. Krin,, O. Soutourina,, C. Tendeng,, S. Derzelle,, and A. Danchin. 2001. H-NS and H-NS-like proteins in Gram-negative bacteria and their multiple role in the regulation of bacterial metabolism. Biochimie 83: 235– 241.
29. Bertin, P.,, P. Lejeune,, C. Laurent-Winter,, and A. Danchin. 1990. Mutations in bglY, the structural gene for the DNA-binding protein H1, affect expression of several Escherichia coli genes. Biochimie 72: 889– 891.
30. Bertin, P.,, E. Terao,, E. H. Lee,, P. Lejeune,, C. Colson,, A. Danchin,, and E. Collatz. 1994. The H-NS protein is involved in the biogenesis of flagella in Escherichia coli. J. Bacteriol. 176: 5537– 5540.
31. Bertoni, G.,, N. Fujita,, A. Ishihama,, and V. de Lorenzo. 1998. Active recruitment of sigma54-RNA polymerase to the Pu promoter of Pseudomonas putida: role of IHF and alphaCTD. EMBO J. 17: 5120– 5128.
32. Betermier, M.,, D. J. Galas,, and M. Chandler. 1994. Interaction of Fis protein with DNA: bending and specificity of binding. Biochimie 76: 958– 967.
33. Betermier, M.,, V. Lefrere,, C. Koch,, R. Alazard,, and M. Chandler. 1989. The Escherichia coli protein, Fis: specific binding to the ends of phage Mu DNA and modulation of phage growth. Mol. Microbiol. 3: 459– 468.
34. Betermier, M.,, I. Poquet,, R. Alazard,, and M. Chandler. 1993. Involvement of Escherichia coli FIS protein in maintenance of bacteriophage Mu lysogeny by the repressor: control of early transcription and inhibition of transposition. J. Bacteriol. 175: 3798– 3811.
35. Bishop, A. C.,, J. Xu,, R. C. Johnson,, P. Schimmel,, and V. De Crecy-Lagard. 2002. Identification of the tRNA-dihydrouridine synthase family. J. Biol. Chem. 277: 25090– 25095.
36. Bliska, J. B.,, and N. R. Cozzarelli. 1987. Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. J. Mol. Biol. 194: 205– 218.
37. Bokal, A. J.,, W. Ross,, T. Gaal,, R. C. Johnson,, and R. L. Gourse. 1997. Molecular anatomy of a transcription activation patch: FIS-RNA polymerase interactions at the Escherichia coli rrnB P1 promoter. EMBO J. 16: 154– 162.
38. Bokal, A. J. T.,, W. Ross,, and R. L. Gourse. 1995. The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter. J. Mol. Biol. 245: 197– 207.
39. Bonnefoy, E.,, and J. Rouviere-Yaniv. 1991. HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments. EMBO J. 10: 687– 696.
40. Bonnefoy, E.,, and J. Rouviere-Yaniv. 1992. HU, the major histone-like protein of E. coli, modulates the binding of IHF to oriC. EMBO J. 11: 4489– 4496.
41. Bonnefoy, E.,, M. Takahashi,, and J. R. Yaniv. 1994. DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. J. Mol. Biol. 242: 116– 129.
42. Boubrik, F.,, and J. Rouviere-Yaniv. 1995. Increased sensitivity to gamma irradiation in bacteria lacking protein HU. Proc. Natl. Acad. Sci. USA 92: 3958– 3962.
43. Boye, E.,, A. Lyngstadaas,, A. Lo¨bner-Olesen,, K. Skarstad,, and S. Wold,. 1993. Regulation of DNA replication in Escherichia coli, p. 15- 26. In E. Fanning,, R. Knippers,, and E. L. Winnedler (ed.), DNA Replication and the Cell Cycle, vol. 43. Springer-Verlag KG, Berlin, Germany.
44. Bramhill, D.,, and A. Kornberg. 1988. A model for initiation at origins of DNA replication. Cell 54: 915– 918.
45.. Brandi, A.,, R. Spurio,, C. O. Gualerzi,, and C. L. Pon. 1999. Massive presence of the Escherichia coli ‘‘major cold-shock protein’’ CspA under non-stress conditions. EMBO J. 18: 1653– 1659.
46. Browning, D. F.,, C. M. Beatty,, A. J. Wolfe,, J. A. Cole,, and S. J. Busby. 2002. Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region. Mol. Microbiol. 43: 687– 701.
47. Browning, D. F.,, J. A. Cole,, and S. J. Busby. 2000. Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription initiation by a complex nucleoprotein assembly. Mol. Microbiol. 37: 1258– 1269.
49. Broyles, S. S.,, and D. E. Pettijohn. 1986. Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch. J. Mol. Biol. 187: 47– 60.
50. Bruckner, R. C.,, and M. M. Cox. 1989. The histone-like H protein of Escherichia coli is ribosomal protein S3. Nucleic Acids Res. 17: 3145– 3161.
51. Bruist, M. F.,, A. C. Glasgow,, R. C. Johnson,, and M. I. Simon. 1987. Fis binding to the recombinational enhancer of the Hin DNA inversion system. Genes Dev. 1: 762– 772.
52. Bruist, M. F.,, and M. I. Simon. 1984. Phase variation and the Hin protein: in vivo activity measurements, protein overproduction, and purification. J. Bacteriol. 159: 71– 79.
53. Busby, S.,, A. Kolb,, and H. Buc. 1979. Isolation of plasmidprotein complexes from Escherichia coli. Eur. J. Biochem. 99: 105– 111.
54. Bushman, W.,, S. Yin,, L. L. Thio,, and A. Landy. 1984. Determinants of directionality in lambda site-specific recombination. Cell 39: 699– 706.
55. Caramel, A.,, and K. Schnetz. 2000. Antagonistic control of the Escherichia coli bgl promoter by FIS and CAP in vitro. Mol. Microbiol. 36: 85– 92.
56. Caramel, A.,, and K. Schnetz. 1998. Lac and lambda repressors relieve silencing of the Escherichia coli bgl promoter. Activation by alteration of a repressing nucleoprotein complex. J. Mol. Biol. 284: 875– 883.
57. Carmona, M.,, C. Balsalobre,, F. Munoa,, M. Mourino,, Y. Jubete,, F. De la Cruz,, and A. Juarez. 1993. Escherichia coli hha mutants, DNA supercoiling and expression of the haemolysin genes from the recombinant plasmid pANN202-312. Mol. Microbiol. 9: 1011– 1018.
58. Cassler, M. R.,, J.E. Grimwade, andA.C.Leonard. 1995. Cell cycle-specific changes in nucleoprotein complexes at a chromosomal replication origin. EMBO J. 14: 5833– 5841.
59. Cassler, M. R.,, J. E. Grimwade,, K. C. McGarry,, R. T. Mott,, and A. C. Leonard. 1999. Drunken-cell footprints: nuclease treatment of ethanol-permeabilized bacteria reveals an initiation- like nucleoprotein complex in stationary phase replication origins. Nucleic Acids Res. 27: 4570– 4576.
60. Castaing, B.,, C. Zelwer,, J. Laval,, and S. Boiteux. 1995. HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps. J. Biol. Chem. 270: 10291– 10296.
61. Cayley, S.,, B. A. Lewis,, H. J. Guttman,, and M. T. Record, Jr. 1991. Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo. J. Mol. Biol. 222: 281– 300.
62. Ceschini, S.,, G. Lupidi,, M. Coletta,, C. L. Pon,, E. Fioretti,, and M. Angeletti. 2000. Multimeric self-assembly equilibria involving the histone-like protein H-NS. A thermodynamic study. J. Biol. Chem. 275: 729– 734.
63. Chaconas, G.,, and R. M. Harshey,. 2002. Transposition of phage Mu DNA, p. 384– 402. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C..
64. Chalmers, R.,, A. Guhathakurta,, H. Benjamin,, and N. Kleckner. 1998. IHF modulation of Tn 10 transposition: sensory transduction of supercoiling status via a proposed protein/DNA molecular spring. Cell 93: 897– 908.
65. Champagne, N.,, and J. Lapointe. 1998. Influence of FIS on the transcription from closely spaced and non-overlapping divergent promoters for an aminoacyl-tRNA synthetase gene ( gltX) and a tRNA operon ( valU) in Escherichia coli. Mol. Microbiol. 27: 1141– 1156.
66. Cheng, Q.,, N. Wesslund,, N. B. Shoemaker,, A. A. Salyers,, and J. F. Gardner. 2002. Development of an in vitro integration assay for the Bacteroides conjugative transposon CTnDOT. J. Bacteriol. 184: 4829– 4837.
67. Cheng, Y. S.,, W. Z. Yang,, R. C. Johnson,, and H. S. Yuan. 2000. Structural analysis of the transcriptional activation on Fis: crystal structures of six Fis mutants with different activation properties. J. Mol. Biol. 302: 1139– 1151.
68. Cho, E. H.,, R. I. Gumport,, and J. F. Gardner. 2002. Interactions between integrase and excisionase in the phage lambda excisive nucleoprotein complex. J. Bacteriol. 184: 5200– 5203.
69. Churchward, G., 2002. Conjugative transposons and related mobile elements, p. 177– 191. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
70. Claret, L.,, and J. Rouviere-Yaniv. 1996. Regulation of HU alpha and HU beta by CRP and FIS in Escherichia coli. J. Mol. Biol. 263: 126– 139.
71. Claret, L.,, and J. Rouviere-Yaniv. 1997. Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival. J. Mol. Biol. 273: 93– 104.
72. Condon, C.,, J. Philips,, Z. Y. Fu,, C. Squires,, and C. L. Squires. 1992. Comparison of the expression of the seven ribosomal RNA operons in Escherichia coli. EMBO J. 11: 4175– 4185.
73. Connolly, K. M.,, M. Iwahara,, and R. T. Clubb. 2002. Xis protein binding to the left arm stimulates excision of conjugative transposon Tn 916. J. Bacteriol. 184: 2088– 2099.
74. Cornelis, G. R.,, C. Sluiters,, I. Delor,, D. Geib,, K. Kaniga,, C. Lambert de Rouvroit,, M. P. Sory,, J. C. Vanooteghem,, and T. Michiels. 1991. ymoA, a Yersinia enterocolitica chromosomal gene modulating the expression of virulence functions. Mol. Microbiol. 5: 1023– 1034.
75. Corpet, F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16: 10881– 10890.
76. Craig, N. L.,, and H. A. Nash. 1984. E. coli integration host factor binds to specific sites in DNA. Cell 39: 707– 716.
77. Craigie, R.,, D. J. Arndt-Jovin,, and K. Mizuuchi. 1985. A defined system for the DNA strand-transfer reaction at the initiation of bacteriophage Mu transposition: protein and DNA substrate requirements. Proc. Natl. Acad. Sci. USA 82: 7570– 7574.
78. Crellin, P.,, and R. Chalmers. 2001. Protein-DNA contacts and conformational changes in the Tn 10 transpososome during assembly and activation for cleavage. EMBO J. 20: 3882– 3891.
79. Crisona, N. J.,, R. Kanaar,, T. N. Gonzalez,, E. L. Zechiedrich,, A. Klippel,, and N. R. Cozzarelli. 1994. Processive recombination by wild-type Gin and an enhancer-independent mutant. Insight into the mechanisms of recombination selectivity and strand exchange. J. Mol. Biol. 243: 437– 457.
80. Cukier, K. R.,, M. Jacquet,, and F. Gros. 1972. Two heat-resistant, low molecular weight proteins from Escherichia coli that stimulate DNA-directed RNA synthesis. Proc. Natl. Acad. Sci. USA 69: 3643– 3647.
81. Cunha, S.,, C. L. Woldringh,, and T. Odijk. 2001. Polymer-mediated compaction and internal dynamics of isolated Escherichia coli nucleoids. J. Struct. Biol. 136: 53– 66.
82. Cusick, M. E.,, and M. Belfort. 1998. Domain structure and RNA annealing activity of the Escherichia coli regulatory protein StpA. Mol. Microbiol. 28: 847– 857.
83. Dame, R. T.,, C. Wyman,, and N. Goosen. 2000. H-NS mediated compaction of DNA visualised by atomic force microscopy. Nucleic Acids Res. 28: 3504– 3510.
84. Dame, R. T.,, C. Wyman,, R. Wurm,, R. Wagner,, and N. Goosen. 2002. Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1. J. Biol. Chem. 277: 2146– 2150.
85. Dattananda, C. S.,, K. Rajkumari,, and J. Gowrishankar. 1991. Multiple mechanisms contribute to osmotic inducibility of proU operon expression in Escherichia coli: demonstration of two osmoresponsive promoters and of a negative regulatory element within the first structural gene. J. Bacteriol. 173: 7481– 7490.
86. Deighan, P.,, A. Free,, and C. J. Dorman. 2000. A role for the Escherichia coli H-NS-like protein StpA in OmpF porin expression through modulation of micF RNA stability. Mol. Microbiol. 38: 126– 139.
87. Delgado, J.,, S. Forst,, S. Harlocker,, and M. Inouye. 1993. Identification of a phosphorylation site and functional analysis of conserved aspartic acid residues of OmpR, a transcriptional activator for ompF and ompC in Escherichia coli. Mol. Microbiol. 10: 1037– 1047.
88. Delihas, N.,, and S. Forst. 2001. MicF: an antisense RNA gene involved in response of Escherichia coli to global stress factors. J. Mol. Biol. 313: 1– 12.
89. Dersch, P.,, S. Kneip,, and E. Bremer. 1994. The nucleoid-associated DNA-binding protein H-NS is required for the efficient adaptation of Escherichia coli K-12 to a cold environment. Mol. Gen. Genet. 245: 255– 259.
90. Dersch, P.,, K. Schmidt,, and E. Bremer. 1993. Synthesis of the Escherichia coli K-12 nucleoid-associated DNA-binding protein H-NS is subjected to growth-phase control and autoregulation. Mol. Microbiol. 8: 875– 889.
91. Dhavan, G. M.,, D. M. Crothers,, M. R. Chance,, and M. Brenowitz. 2002. Concerted binding and bending of DNA by Escherichia coli integration host factor. J. Mol. Biol. 315: 1027– 1037.
92. DiGabriele, A. D.,, M. R. Sanderson,, and T. A. Steitz. 1989. Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natl. Acad. Sci. USA 86: 1816– 1820.
93. Ditto, M. D.,, D. Roberts,, and R. A. Weisberg. 1994. Growth phase variation of integration host factor level in Escherichia coli. J. Bacteriol. 176: 3738– 3748.
94. Dixon, N. E.,, and A. Kornberg. 1984. Protein HU in the enzymatic replication of the chromosomal origin of Escherichia coli. Proc. Natl. Acad. Sci. USA 81: 424– 428.
95. Donato, G. M.,, and T. H. Kawula. 1998. Enhanced binding of altered H-NS protein to flagellar rotor protein FliG causes increased flagellar rotational speed and hypermotility in Escherichia coli. J. Biol. Chem. 273: 24030– 24036.
96. Donato, G. M.,, and T. H. Kawula. 1999. Phenotypic analysis of random hns mutations differentiate DNA-binding activity from properties of fimA promoter inversion modulation and bacterial motility. J. Bacteriol. 181: 941– 948.
97. Dorgai, L.,, J. Oberto,, and R. A. Weisberg. 1993. Xis and Fis proteins prevent site-specific DNA inversion in lysogens of phage HK022. J. Bacteriol. 175: 693– 700.
98. Dorman, C. J.,, N. Ni Bhriain,, and C. F. Higgins. 1990. DNA supercoiling and environmental regulation of virulence gene expression in Shigella flexneri. Nature 344: 789– 792.
99.. Dorman, C. J.,, J. C. Hinton,, and A. Free. 1999. Domain organization and oligomerization among H-NS-like nucleoid- associated proteins in bacteria. Trends Microbiol. 7: 124– 128.
100. Dri, A. M.,, J. Rouviere-Yaniv,, and P. L. Moreau. 1991. Inhibition of cell division in hupA hupB mutant bacteria lacking HU protein. J. Bacteriol. 173: 2852– 2863.
101. Drlica, K.,, and J. Rouviere-Yaniv. 1987. Histone-like proteins of bacteria. Microbiol. Rev. 51: 301– 319.
102. Eisenstein, B. I. 1981. Phase variation of type 1 fimbriae in Escherichia coli is under transcriptional control. Science 214: 337– 339.
103. Emilsson, V.,, and L. Nilsson. 1995. Factor for inversion stimulation-dependent growth rate regulation of serine and threonine tRNA species. J. Biol. Chem. 270: 16610– 16614.
104. Engelhorn, M.,, and J. Geiselmann. 1998. Maximal transcriptional activation by the IHF protein of Escherichia coli depends on optimal DNA bending by the activator. Mol. Microbiol. 30: 431– 441.
105. Esposito, D.,, A. Petrovic,, R. Harris,, S. Ono,, J. F. Eccleston,, A. Mbabaali,, I. Haq,, C. F. Higgins,, J. C. Hinton,, P. C. Driscoll,, and J. E. Ladbury. 2002. H-NS oligomerization domain structure reveals the mechanism for high order self-association of the intact protein. J. Mol. Biol. 324: 841– 850.
106. Falconi, M.,, A. Brandi,, A. La Teana,, C. O. Gualerzi,, and C. L. Pon. 1996. Antagonistic involvement of FIS and H-NS proteins in the transcriptional control of hns expression. Mol. Microbiol. 19: 965– 975.
107. Falconi, M.,, B. Colonna,, G. Prosseda,, G. Micheli,, and C. O. Gualerzi. 1998. Thermoregulation of Shigella and Escherichia coli EIEC pathogenicity. A temperature-dependent structural transition of DNA modulates accessibility of virF promoter to transcriptional repressor H-NS. EMBO J. 17: 7033– 7043.
108. Falconi, M.,, M. T. Gualtieri,, A. La Teana,, M. A. Losso,, and C. L. Pon. 1988. Proteins from the prokaryotic nucleoid: primary and quaternary structure of the 15-kD Escherichia coli DNA binding protein H-NS. Mol. Microbiol. 2: 323– 329.
109. Falconi, M.,, N. P. Higgins,, R. Spurio,, C. L. Pon,, and C. O. Gualerzi. 1993. Expression of the gene encoding the major bacterial nucleotide protein H-NS is subject to transcriptional auto-repression. Mol. Microbiol. 10: 273– 282.
110. Falconi, M.,, G. Prosseda,, M. Giangrossi,, E. Beghetto,, and B. Colonna. 2001. Involvement of FIS in the H-NS-mediated regulation of virF gene of Shigella and enteroinvasive Escherichia coli. Mol. Microbiol. 42: 439– 452.
111. Feng, J.-A.,, H. S. Yuan,, S. E. Finkel,, R. C. Johnson,, M. Kaczor-Grzeskowiak,, and R. E. Dickerson,. 1992. The interaction of Fis protein with its DNA binding sequences, p. 1– 9. In R. H. Sarma, and M. H. Sarma (ed.), Structure and Function, Proceedings of the Seventh Conversation in Biomolecular Stereodynamics, vol. 2. Adenine Press, New York, N.Y.
112. Filutowicz, M.,, W. Ross,, J. Wild,, and R. L. Gourse. 1992. Involvement of Fis protein in replication of the Escherichia coli chromosome. J. Bacteriol. 174: 398– 407.
113. Finkel, S. E.,, and R. C. Johnson. 1992. The Fis protein: it’s not just for DNA inversion anymore. Mol. Microbiol. 6: 3257– 3265.
114. Flamm, E. L.,, and R. A. Weisberg. 1985. Primary structure of the hip gene of Escherichia coli and of its product, the beta subunit of integration host factor. J. Mol. Biol. 183: 117– 128.
115. Flashner, Y.,, and J. D. Gralla. 1988. DNA dynamic flexibility and protein recognition: differential stimulation by bacterial histone-like protein HU. Cell 54: 713– 721.
116. Free, A.,, and C. J. Dorman. 1995. Coupling of Escherichia coli hns mRNA levels to DNA synthesis by autoregulation: implications for growth phase control. Mol. Microbiol. 18: 101– 113.
117. Free, A.,, and C. J. Dorman. 1997. The Escherichia coli stpA gene is transiently expressed during growth in rich medium and is induced in minimal medium and by stress conditions. J. Bacteriol. 179: 909– 918.
118. Free, A.,, M. E. Porter,, P. Deighan,, and C. J. Dorman. 2001. Requirement for the molecular adapter function of StpA at the Escherichia coli bgl promoter depends upon the level of truncated H-NS protein. Mol. Microbiol. 42: 903– 917.
119. Free, A.,, R. M. Williams,, and C. J. Dorman. 1998. The StpA protein functions as a molecular adapter to mediate repression of the bgl operon by truncated H-NS in Escherichia coli. J. Bacteriol. 180: 994– 997.
120. Frenkiel-Krispin, D.,, S. Levin-Zaidman,, E. Shimoni,, S. G. Wolf,, E. J. Wachtel,, T. Arad,, S. E. Finkel,, R. Kolter,, and A. Minsky. 2001. Regulated phase transitions of bacterial chromatin: a non-enzymatic pathway for generic DNA protection. EMBO J. 20: 1184– 1191.
121. Freundlich, M.,, N. Ramani,, E. Mathew,, A. Sirko,, and P. Tsui. 1992. The role of integration host factor in gene expression in Escherichia coli. Mol. Microbiol. 6: 2557– 2563.
122. Friedrich, K.,, C. O. Gualerzi,, M. Lammi,, M. A. Losso,, and C. L. Pon. 1988. Proteins from the prokaryotic nucleoid. Interaction of nucleic acids with the 15 kDa Escherichia coli histone-like protein H-NS. FEBS Lett. 229: 197– 202.
123. Froelich, J. M.,, T. K. Phuong,, and J. W. Zyskind. 1996. Fis binding in the dnaA operon promoter region. J. Bacteriol. 178: 6006– 6012.
124. Gaal, T.,, M. S. Bartlett,, W. Ross,, C. L. Turnbough, Jr.,, and R. L. Gourse. 1997. Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria. Science 278: 2092– 2097.
125. Gamas, P.,, M. G. Chandler,, P. Prentki,, and D. J. Galas. 1987. Escherichia coli integration host factor binds specifically to the ends of the insertion sequence IS1 and to its major insertion hot-spot in pBR322. J. Mol. Biol. 195: 261– 272.
126. Giangrossi, M.,, A. M. Giuliodori,, C. O. Gualerzi,, and C. L. Pon. 2002. Selective expression of the beta-subunit of nucleoid-associated protein HU during cold shock in Escherichia coli. Mol. Microbiol. 44: 205– 216.
127. Giangrossi, M.,, C. O. Gualerzi,, and C. L. Pon. 2001. Mutagenesis of the downstream region of the Escherichia coli hns promoter. Biochimie 83: 251– 259.
128. Giladi, H.,, S. Koby,, G. Prag,, M. Engelhorn,, J. Geiselmann,, and A. B. Oppenheim. 1998. Participation of IHF and a distant UP element in the stimulation of the phage lambda PL promoter. Mol. Microbiol. 30: 443– 451.
129. Gille, H.,, J. B. Egan,, A. Roth,, and W. Messer. 1991. The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli. Nucleic Acids Res. 19: 4167– 4172.
130. Goldberg, M. D.,, M. Johnson,, J. C. Hinton,, and P. H. Williams. 2001. Role of the nucleoid-associated protein Fis in the regulation of virulence properties of enteropathogenic Escherichia coli. Mol. Microbiol. 41: 549– 559.
131. Gonzalez-Gil, G.,, P. Bringmann,, and R. Kahmann. 1996. FIS is a regulator of metabolism in Escherichia coli. Mol. Microbiol. 22: 21– 29.
132. Gonzalez-Gil, G.,, R. Kahmann,, and G. Muskhelishvili. 1998. Regulation of crp transcription by oscillation between distinct nucleoprotein complexes. EMBO J. 17: 2877– 2885.
133. Goodman, S. D.,, and O. Kay. 1999. Replacement of integration host factor protein-induced DNA bending by flexible regions of DNA. J. Biol. Chem. 274: 37004– 37011.
134. Goodman, S. D.,, and H. A. Nash. 1989. Functional replacement of a protein-induced bend in a DNA recombination site. Nature 341: 251– 254.
135. Goodrich, J. A.,, M. L. Schwartz,, and W. R. McClure. 1990. Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF). Nucleic Acids Res. 18: 4993– 5000.
136. Goransson, M.,, B. Sonden,, P. Nilsson,, B. Dagberg,, K. Forsman,, K. Emanuelsson,, and B. E. Uhlin. 1990. Transcriptional silencing and thermoregulation of gene expression in Escherichia coli. Nature 344: 682– 685.
137. Gowrishankar, J.,, and D. Manna. 1996. How is osmotic regulation of transcription of the Escherichia coli proU operon achieved? A review and a model. Genetica 97: 363– 378.
138. Granston, A. E.,, and H. A. Nash. 1993. Characterization of a set of integration host factor mutants deficient for DNA binding. J. Mol. Biol. 234: 45– 59.
139. Grant, R. A.,, D. J. Filman,, S. E. Finkel,, R. Kolter,, and J. M. Hogle. 1998. The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nat. Struct. Biol. 5: 294– 303.
140. Green, J.,, M. F. Anjum,, and J. R. Guest. 1996. The ndh-binding protein (Nbp) regulates the ndh gene of Escherichia coli in response to growth phase and is identical to Fis. Mol. Microbiol. 20: 1043– 1055.
141. Griffo, G.,, A. B. Oppenheim,, and M. E. Gottesman. 1989. Repression of the lambda Pcin promoter by integrative host factor. J. Mol. Biol. 209: 55– 64.
142. Grimwade, J. E.,, V. T. Ryan,, and A. C. Leonard. 2000. IHF redistributes bound initiator protein, DnaA, on supercoiled oriC of Escherichia coli. Mol. Microbiol. 35: 835– 844.
143. Haffter, P.,, and T. A. Bickle. 1988. Enhancer-independent mutants of the Cin recombinase have a relaxed topological specificity. EMBO J. 7: 3991– 3996.
144. Hales, L. M.,, R. I. Gumport,, and J. F. Gardner. 1994. Determining the DNA sequence elements required for binding integration host factor to two different target sites. J. Bacteriol. 176: 2999– 3006.
145. Hales, L. M.,, R. I. Gumport,, and J. F. Gardner. 1996. Examining the contribution of a dAþdT element to the conformation of Escherichia coli integration host factor- DNA complexes. Nucleic Acids Res. 24: 1780– 1786.
146. Haykinson, M. J.,, L. M. Johnson,, J. Soong,, and R. C. Johnson. 1996. The Hin dimer interface is critical for Fis-mediated activation of the catalytic steps of sitespecific DNA inversion. Curr. Biol. 6: 163– 177.
147. Haykinson, M. J.,, and R. C. Johnson. 1993. DNA looping and the helical repeat in vitro and in vivo: effect of HU protein and enhancer location on Hin invertasome assembly. EMBO J. 12: 2503– 2512.
148. Heichman, K. A.,, and R. C. Johnson. 1990. The Hin invertasome: protein-mediated joining of distant recombination sites at the enhancer. Science 249: 511– 517.
149. Heichman, K. A.,, I. P. Moskowitz,, and R. C. Johnson. 1991. Configuration of DNA strands and mechanism of strand exchange in the Hin invertasome as revealed by analysis of recombinant knots. Genes Dev. 5: 1622– 1634.
150. Hengen, P. N.,, S. L. Bartram,, L. E. Stewart,, and T. D. Schneider. 1997. Information analysis of Fis binding sites. Nucleic Acids Res. 25: 4994– 5002.
151. Hengge-Aronis, R. 1999. Interplay of global regulators and cell physiology in the general stress response of Escherichia coli. Curr. Opin. Microbiol. 2: 148– 152.
152. Hengge-Aronis, R. 2002. Signal transduction and regulatory mechanisms involved in control of the sigma S (RpoS) subunit of RNA polymerase. Microbiol. Mol. Biol. Rev. 66: 373– 395.
153. Hiasa, H.,, and K. J. Marians. 1994. Fis cannot support oriC DNA replication in vitro. J. Biol. Chem. 269: 24999– 25003.
154. Hiestand-Nauer, R.,, and S. Iida. 1983. Sequence of the sitespecific recombinase gene cin and of its substrates serving in the inversion of the C segment of bacteriophage P1. EMBO J. 2: 1733– 1740.
155. Higgins, C. F.,, C. J. Dorman,, D. A. Stirling,, L. Waddell,, I. R. Booth,, G. May,, and E. Bremer. 1988. A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli. Cell 52: 569– 584.
156. Higgins, C. F.,, J. C. Hinton,, C. S. Hulton,, T. Owen- Hughes,, G. D. Pavitt,, and A. Seirafi. 1990. Protein H1: a role for chromatin structure in the regulation of bacterial gene expression and virulence? Mol. Microbiol. 4: 2007- 2012.
157. Higgins, N. P.,, X. Yang,, Q. Fu,, and J. R. Roth. 1996. Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium. J. Bacteriol. 178: 2825– 2835.
158. Hillyard, D. R.,, M. Edlund,, K. T. Hughes,, M. Marsh,, and N. P. Higgins. 1990. Subunit-specific phenotypes of Salmonella typhimurium HU mutants. J. Bacteriol. 172: 5402– 5407.
159. Hinton, J. C.,, D. S. Santos,, A. Seirafi,, C. S. Hulton,, G. D. Pavitt,, and C. F. Higgins. 1992. Expression and mutational analysis of the nucleoid-associated protein H-NS of Salmonella typhimurium. Mol. Microbiol. 6: 2327– 2337.
160. Hiraga, S.,, H. Niki,, T. Ogura,, C. Ichinose,, H. Mori,, B. Ezaki,, and A. Jaffe. 1989. Chromosome partitioning in Escherichia coli: novel mutants producing anucleate cells. J. Bacteriol. 171: 1496– 1505.
161. Hirvonen, C. A.,, W. Ross,, C. E. Wozniak,, E. Marasco,, J. R. Anthony,, S. E. Aiyar,, V. H. Newburn,, and R. L. Gourse. 2001. Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli. J. Bacteriol. 183: 6305– 6314.
163. Hodges-Garcia, Y.,, P. J. Hagerman,, and D. E. Pettijohn. 1989. DNA ring closure mediated by protein HU. J. Biol. Chem. 264: 14621– 14623.
164. Holmes, V. F.,, and N. R. Cozzarelli. 2000. Closing the ring: links between SMC proteins and chromosome partitioning, condensation, and supercoiling. Proc. Natl. Acad. Sci. USA 97: 1322– 1234.
165. Hommais, F.,, E. Krin,, C. Laurent-Winter,, O. Soutourina,, A. Malpertuy,, J. P. Le Caer,, A. Danchin,, and P. Bertin. 2001. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol. Microbiol. 40: 20– 36.
166. Hoover, T. R.,, E. Santero,, S. Porter,, and S. Kustu. 1990. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell 63: 11– 22.
167. Hsieh, L. S.,, J. Rouviere-Yaniv,, and K. Drlica. 1991. Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock. J. Bacteriol. 173: 3914– 3917.
168. Hu, K. H.,, E. Liu,, K. Dean,, M. Gingras,, W. DeGraff,, and N. J. Trun. 1996. Overproduction of three genes leads to camphor resistance and chromosome condensation in Escherichia coli. Genetics 143: 1521– 1532.
169. Huisman, O.,, P. R. Errada,, L. Signon,, and N. Kleckner. 1989. Mutational analysis of IS10’s outside end. EMBO J. 8: 2101– 2109.
170. Huisman, O.,, M. Faelen,, D. Girard,, A. Jaffe,, A. Toussaint,, and J. Rouviere-Yaniv. 1989. Multiple defects in Escherichia coli mutants lacking HU protein. J. Bacteriol. 171: 3704– 3712.
171. Hulton, C. S.,, A. Seirafi,, J. C. Hinton,, J. M. Sidebotham,, L. Waddell,, G. D. Pavitt,, T. Owen-Hughes,, A. Spassky,, H. Buc,, and C. F. Higgins. 1990. Histone-like protein H1 (H-NS), DNA supercoiling, and gene expression in bacteria. Cell 63: 631– 642.
172. Hwang, D. S.,, and A. Kornberg. 1992. Opening of the replication origin of Escherichia coli by DnaA protein with protein HU or IHF. J. Biol. Chem. 267: 23083– 23086.
173. Igo, M. M.,, A. J. Ninfa,, and T. J. Silhavy. 1989. A bacterial environmental sensor that functions as a protein kinase and stimulates transcriptional activation. Genes Dev. 3: 598– 605.
174. Ishihama, A. 1999. Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival. Genes Cells 4: 135– 143.
175. Jacobson, B. A.,, and J. A. Fuchs. 1998. Multiple cis-acting sites positively regulate Escherichia coli nrd expression. Mol. Microbiol. 28: 1315– 1322.
176. Jaffe, A.,, D. Vinella,, and R. D’Ari. 1997. The Escherichia coli histone-like protein HU affects DNA initiation, chromosome partitioning via MukB, and cell division via Min- CDE. J. Bacteriol. 179: 3494– 3499.
177. Jaquet, M.,, K. R. Cukier,, J. Pla,, and F. Gros. 1971. A thermostable protein factor acting on in vitro DNA transcription. Biochem. Biophys. Res. Commun. 45: 1597– 1607.
178. Jeon, Y. H.,, T. Negishi,, M. Shirakawa,, T. Yamazaki,, N. Fujita,, A. Ishihama,, and Y. Kyogoku. 1995. Solution structure of the activator contact domain of the RNA polymerase alpha subunit. Science 270: 1495– 1497.
179. Johansson, J.,, B. Dagberg,, E. Richet,, and B. E. Uhlin. 1998 . H-NS and StpA proteins stimulate expression of the maltose regulon in Escherichia coli. J. Bacteriol. 180: 6117– 6125.
180. Johansson, J.,, S. Eriksson,, B. Sonden,, S. N. Wai,, and B. E. Uhlin. 2001. Heteromeric interactions among nucleoid- associated bacterial proteins: localization of StpA-stabilizing regions in H-NS of Escherichia coli. J. Bacteriol. 183: 2343– 2347.
181. Johansson, J.,, and B. E. Uhlin. 1999. Differential proteasemediated turnover of H-NS and StpA revealed by a mutation altering protein stability and stationary-phase survival of Escherichia coli. Proc.Natl. Acad. Sci.USA 96: 10776– 10781.
182. Johnson, R. C., 2002. Bacterial site-specific DNA inversion systems, p. 230– 271. In N. L. Craig,, R. Craigie,, M. Gellert,, and A. M. Lambowitz (ed.), Mobile DNA II. ASM Press, Washington, D.C.
183. Johnson, R. C.,, C. A. Ball,, D. Pfeffer,, and M. I. Simon. 1988. Isolation of the gene encoding the Hin recombinational enhancer binding protein. Proc. Natl. Acad. Sci. USA 85: 3484– 3488.
184. Johnson, R. C.,, M. F. Bruist,, and M. I. Simon. 1986. Host protein requirements for in vitro site-specific DNA inversion. Cell 46: 531– 539.
185. Johnson, R. C.,, A. C. Glasgow,, and M. I. Simon. 1987. Spatial relationship of the Fis binding sites for Hin recombinational enhancer activity. Nature 329: 462– 465.
186. Johnson, R. C.,, and M. I. Simon. 1985. Hin-mediated sitespecific recombination requires two 26 bp recombination sites and a 60 bp recombinational enhancer. Cell 41: 781– 791.
187. Jordi, B. J.,, A. E. Fielder,, C. M. Burns,, J. C. Hinton,, N. Dover,, D. W. Ussery,, and C. F. Higgins. 1997. DNA binding is not sufficient for H-NS-mediated repression of proU expression. J. Biol. Chem. 272: 12083– 12090.
188. Jordi, B. J.,, and C. F. Higgins. 2000. The downstream regulatory element of the proU operon of Salmonella typhimurium inhibits open complex formation by RNA polymerase at a distance. J. Biol. Chem. 275: 12123– 12128.
189. Kahmann, R.,, F. Rudt,, C. Koch,, and G. Mertens. 1985. G inversion in bacteriophageMu DNA is stimulated by a site within the invertase gene and a host factor. Cell 41: 771– 780.
190. Kahmann, R.,, F. Rudt,, and G. Mertens. 1984. Substrate and enzyme requirements for in vitro site-specific recombination in bacteriophage mu. Cold Spring Harbor Symp. Quant. Biol. 49: 285– 294.
191. Kaidow, A.,, M. Wachi,, J. Nakamura,, J. Magae,, and K. Nagai. 1995. Anucleate cell production by Escherichia coli delta hns mutant lacking a histone-like protein, H-NS. J. Bacteriol. 177: 3589– 3592.
192. Kamashev, D.,, and J. Rouviere-Yaniv. 2000. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J. 19: 6527– 6535.
193. Kanaar, R.,, A. Klippel,, E. Shekhtman,, J. M. Dungan,, R. Kahmann,, and N. R. Cozzarelli. 1990. Processive recombination by the phage Mu Gin system: implications for the mechanisms of DNA strand exchange, DNA site alignment, and enhancer action. Cell 62: 353– 366.
194. Kanaar, R.,, P. van de Putte,, and N. R. Cozzarelli. 1988. Gin-mediated DNA inversion: product structure and the mechanism of strand exchange. Proc. Natl. Acad. Sci. USA 85: 752– 756.
195. Kanaar, R.,, P. van de Putte,, and N. R. Cozzarelli. 1989. Gin-mediated recombination of catenated and knotted DNA substrates: implications for the mechanism of interaction between cis-acting sites. Cell 58: 147– 159.
196. Kano, Y.,, and F. Imamoto. 1990. Requirement of integration host factor (IHF) for growth of Escherichia coli deficient in HU protein. Gene 89: 133– 137.
198. Kano, Y.,, K. Osato,, M. Wada,, and F. Imamoto. 1987. Cloning and sequencing of the HU-2 gene of Escherichia coli. Mol. Gen. Genet. 209: 408– 410.
199. Kano, Y.,, M. Wada,, T. Nagase,, and F. Imamoto. 1986. Genetic characterization of the gene hupB encoding the HU-1 protein of Escherichia coli. Gene 45: 37– 44.
200. Kano, Y.,, K. Yasuzawa,, H. Tanaka,, and F. Imamoto. 1993. Propagation of phage Mu in IHF-deficient Escherichia coli in the absence of the H-NS histone-like protein. Gene 126: 93– 97.
201. Kano, Y.,, S. Yoshino,, M. Wada,, K. Yokoyama,, M. Nobuhara,, and F. Imamoto. 1985. Molecular cloning and nucleotide sequence of the HU-1 gene of Escherichia coli. Mol. Gen. Genet. 201: 360– 362.
202. Kar, S.,, and S. Adhya. 2001. Recruitment of HU by piggyback: a special role of GalR in repressosome assembly. Genes Dev. 15: 2273– 2281.
203. Katayama, T.,, M. Takata,, and K. Sekimizu. 1996. The nucleoid protein H-NS facilitates chromosome DNA replication in Escherichia coli dnaA mutants. J. Bacteriol. 178: 5790– 5792.
204. Kavenoff, R.,, and B. C. Bowen. 1976. Electron microscopy of membrane-free folded chromosomes from Escherichia coli. Chromosoma 59: 89– 101.
205. Kawula, T. H.,, and P. E. Orndorff. 1991. Rapid sitespecific DNA inversion in Escherichia coli mutants lacking the histonelike protein H-NS. J. Bacteriol. 173: 4116– 4123.
206. Kellenberger, E., 1990. Intracellular organization of the bacterial genome, p. 173– 186. In K. Drlica, and M. Riley (ed.), The Bacterial Chromosome. American Society for Microbiology, Washington, D.C.
207. Kikuchi, A.,, E. Flamm,, and R. A. Weisberg. 1985. An Escherichia coli mutant unable to support site-specific recombination of bacteriophage lambda. J. Mol. Biol. 183: 129– 140.
208. Kikuchi, Y.,, and H. A. Nash. 1978. The bacteriophage lambda int gene product. A filter assay for genetic recombination, purification of Int, and specific binding to DNA. J. Biol. Chem. 253: 7149– 7157.
209. Kim, S.,, and A. Landy. 1992. Lambda Int protein bridges between higher order complexes at two distant chromosomal loci attL and attR. Science 256: 198– 203.
211. Kim, S.,, L. Moitoso de Vargas,, S. E. Nunes-Duby,, and A. Landy. 1990. Mapping of a higher order protein-DNA complex: two kinds of long-range interactions in lambda attL. Cell 63: 773– 781.
212. Klippel, A.,, K. Cloppenborg,, and R. Kahmann. 1988. Isolation and characterization of unusual Gin mutants. EMBO J. 7: 3983– 3989.
213. Klippel, A.,, R. Kanaar,, R. Kahmann,, and N. R. Cozzarelli. 1993. Analysis of strand exchange and DNA binding of enhancer-independent Gin recombinase mutants. EMBO J. 12: 1047– 1057.
214. Klose, K. E.,, A. K. North,, K. M. Stedman,, and S. Kustu. 1994. The major dimerization determinants of the nitrogen regulatory protein NTRC from enteric bacteria lie in its carboxy-terminal domain. J. Mol. Biol. 241: 233– 245.
215. Ko, M.,, and C. Park. 2000. Two novel flagellar components and H-NS are involved in the motor function of Escherichia coli. J. Mol. Biol. 303: 371– 382.
216. Kobryn, K.,, B. D. Lavoie,, and G. Chaconas. 1999. Supercoiling- dependent site-specific binding of HU to naked Mu DNA. J. Mol. Biol. 289: 777– 784.
217. Koch, C.,, and R. Kahmann. 1986. Purification and properties of the Escherichia coli host factor required for inversion of the G segment in bacteriophage Mu. J. Biol. Chem. 261: 15673– 15678.
218. Koch, C.,, G. Mertens,, F. Rudt,, R. Kahmann,, R. Kanaar,, R. H. Plasterk,, P. van de Putte,, R. Sandulache,, and D. Kamp,. 1987. The invertible G segment, p. 75– 91. In N. Symonds,, A. Toussaint,, P. van de Putte,, and M. M. Howe (ed.), Phage Mu. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
219. Koch, C.,, O. Ninnemann,, H. Fuss,, and R. Kahmann. 1991. The N-terminal part of the E. coli DNA binding protein FIS is essential for stimulating site-specific DNA inversion but is not required for specific DNA binding. Nucleic Acids Res. 19: 5915– 5922.
220. Koch, C.,, J. Vandekerckhove,, and R. Kahmann. 1988. Escherichia coli host factor for site-specific DNA inversion: cloning and characterization of the fis gene. Proc. Natl. Acad. Sci. USA 85: 4237– 4241.
221. Kohno, K.,, M. Wada,, Y. Kano,, and F. Imamoto. 1990. Promoters and autogenous control of the Escherichia coli hupA and hupB genes. J. Mol. Biol. 213: 27– 36.
222. Kolesnikow, T.,, I. Schroder,, and R. P. Gunsalus. 1992. Regulation of narK gene expression in Escherichia coli in response to anaerobiosis, nitrate, iron, and molybdenum. J. Bacteriol. 174: 7104– 7111.
223. Kornberg, T.,, A. Lockwood,, and A. Worcel. 1974. Replication of the Escherichia coli chromosome with a soluble enzyme system. Proc. Natl. Acad. Sci. USA 71: 3189– 3193.
224. Kostrewa, D.,, J. Granzin,, C. Koch,, H. W. Choe,, S. Raghunathan,, W. Wolf,, J. Labahn,, R. Kahmann,, and W. Saenger. 1991. Three-dimensional structure of the E. coli DNA-binding protein FIS. Nature 349: 178– 180.
225. Kostrewa, D.,, J. Granzin,, D. Stock,, H. W. Choe,, J. Labahn,, and W. Saenger. 1992. Crystal structure of the factor for inversion stimulation FIS at 2.0 Å resolution. J. Mol. Biol. 226: 209– 226.
226. Krause, H. M.,, and N. P. Higgins. 1986. Positive and negative regulation of the Mu operator by Mu repressor and Escherichia coli integration host factor. J. Biol. Chem. 261: 3744– 3752.
227. Kur, J.,, N. Hasan,, and W. Szybalski. 1989. Physical and biological consequences of interactions between integration host factor (IHF) and coliphage lambda late p'R promoter and its mutants. Gene 81: 1– 15.
228. Lambert de Rouvroit, C.,, C. Sluiters,, and G. R. Cornelis. 1992. Role of the transcriptional activator, VirF, and temperature in the expression of the pYV plasmid genes of Yersinia enterocolitica. Mol. Microbiol. 6: 395– 409.
229. Landis, L.,, J. Xu,, and R. C. Johnson. 1999. The cAMP receptor protein CRP can function as an osmoregulator of transcription in Escherichia coli. Genes Dev. 13: 3081– 3091.
230. Landy, A. 1989. Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu. Rev. Biochem. 58: 913– 949.
231. Lange, R.,, and R. Hengge-Aronis. 1994. The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability. Genes Dev. 8: 1600– 1612.
232. La Teana, A.,, A. Brandi,, M. Falconi,, R. Spurio,, C. L. Pon,, and C. O. Gualerzi. 1991. Identification of a cold shock transcriptional enhancer of the Escherichia coli gene encoding nucleoid protein H-NS. Proc. Natl. Acad. Sci. USA 88: 10907– 10911.
233. Laurent-Winter, C.,, P. Lejeune,, and A. Danchin. 1995. The Escherichia coli DNA-binding protein H-NS is one of the first proteins to be synthesized after a nutritional upshift. Res. Microbiol. 146: 5– 16.
234. Lavoie, B. D.,, and G. Chaconas. 1990. Immunoelectron microscopic analysis of the A, B, and HU protein content of bacteriophage Mu transpososomes. J. Biol. Chem. 265: 1623– 1627.
235. Lavoie, B. D.,, and G. Chaconas. 1993. Site-specific HU binding in the Mu transpososome: conversion of a sequence-independent DNA-binding protein into a chemical nuclease. Genes Dev. 7: 2510– 2519.
236. Lavoie, B. D.,, G. S. Shaw,, A. Millner,, and G. Chaconas. 1996. Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate. Cell 85: 761– 771.
237. Lazarus, L. R.,, and A. A. Travers. 1993. The Escherichia coli FIS protein is not required for the activation of tyrT transcription on entry into exponential growth. EMBO J. 12: 2483– 2494.
238. Lease, R. A.,, and M. Belfort. 2000. Riboregulation by DsrA RNA: trans-actions for global economy. Mol. Microbiol. 38: 667– 672.
239. Lease, R. A.,, M. E. Cusick,, and M. Belfort. 1998. Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc. Natl. Acad. Sci. USA 95: 12456– 12461.
240. Lee, E. C.,, L. M. Hales,, R. I. Gumport,, and J. F. Gardner. 1992. The isolation and characterization of mutants of the integration host factor (IHF) of Escherichia coli with altered, expanded DNA-binding specificities. EMBO J. 11: 305– 313.
242. Leng, F.,, and R. McMacken. 2002. Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins. Proc. Natl. Acad. Sci. USA 99: 9139– 9144.
243. Lewis, D. E.,, and S. Adhya. 2002. In vitro repression of the gal promoters by GalR and HU depends on the proper helical phasing of the two operators. J. Biol. Chem. 277: 2498– 2504.
244. Lewis, D. E.,, M. Geanacopoulos,, and S. Adhya. 1999. Role of HU and DNA supercoiling in transcription repression: specialized nucleoprotein repression complex at gal promoters in Escherichia coli. Mol. Microbiol. 31: 451– 461.
245. Li, S.,, and R. Waters. 1998. Escherichia coli strains lacking protein HU are UV sensitive due to a role for HU in homologous recombination. J. Bacteriol. 180: 3750– 3756.
246. Liu, Q.,, and C. C. Richardson. 1993. Gene 5.5 protein of bacteriophage T7 inhibits the nucleoid protein H-NS of Escherichia coli. Proc. Natl. Acad. Sci. USA 90: 1761– 1765.
247. Lorenz, M.,, A. Hillisch,, S. D. Goodman,, and S. Diekmann. 1999. Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer. Nucleic Acids Res. 27: 4619– 4625.
248. Lu, M.,, J. L. Campbell,, E. Boye,, and N. Kleckner. 1994. SeqA: a negative modulator of replication initiation in E. coli. Cell 77: 413– 426.
249. Lucht, J. M.,, P. Dersch,, B. Kempf,, and E. Bremer. 1994. Interactions of the nucleoid-associated DNA-binding protein H-NS with the regulatory region of the osmotically controlled proU operon of Escherichia coli. J. Biol. Chem. 269: 6578– 6578.
250. MacWilliams, M. P.,, R. I. Gumport,, and J. F. Gardner. 1996. Genetic analysis of the bacteriophage lambda attL nucleoprotein complex. Genetics 143: 1069– 1079.
251. Malik, M.,, A. Bensaid,, J. Rouviere-Yaniv,, and K. Drlica. 1996. Histone-like protein HU and bacterial DNA topology: suppression of an HU deficiency by gyrase mutations. J. Mol. Biol. 256: 66– 76.
252. Margulies, C.,, and J. M. Kaguni. 1998. The FIS protein fails to block the binding of DnaA protein to oriC, the Escherichia coli chromosomal origin. Nucleic Acids Res. 26: 5170– 5175.
253. Marykwas, D. L.,, S. A. Schmidt,, and H. C. Berg. 1996. Interacting components of the flagellar motor of Escherichia coli revealed by the two-hybrid system in yeast. J. Mol. Biol. 256: 564– 576.
254. Mattison, K.,, R. Oropeza,, N. Byers,, and L. J. Kenney. 2002. A phosphorylation site mutant of OmpR reveals different binding conformations at ompF and ompC. J. Mol. Biol. 315: 497– 511.
255. McLeod, S. M. 2001. Architecture of the Fis and CRP Coactivated proP P2 Transcription Initiation Complex. Ph.D. thesis. University of California, Los Angeles.
256. McLeod, S. M.,, S. E. Aiyar,, R. L. Gourse,, and R. C. Johnson. 2002. The C-terminal domains of the RNA polymerase alpha subunits: contact site with Fis and localization during co-activation with CRP at the Escherichia coli proP P2 promoter. J. Mol. Biol. 316: 517– 529.
257. McLeod, S. M.,, and R. C. Johnson. 2001. Control of transcription by nucleoid proteins. Curr. Opin. Microbiol. 4: 152– 159.
258. McLeod, S. M.,, J. Xu,, S. E. Cramton,, T. Gaal,, R. L. Gourse,, and R. C. Johnson. 1999. Localization of amino acids required for Fis to function as a class II transcriptional activator at the RpoS-dependent proP P2 promoter. J. Mol. Biol. 294: 333– 346.
259. McLeod, S. M.,, J. Xu,, and R. C. Johnson. 2000. Coactivation of the RpoS-dependent proP P2 promoter by Fis and cyclic AMP receptor protein. J. Bacteriol. 182: 4180– 4187.
260. Mechulam, Y.,, S. Blanquet,, and G. Fayat. 1987. Dual level control of the Escherichia coli pheST-himA operon expression. tRNA(Phe)-dependent attenuation and transcriptional operator-repressor control by himA and the SOS network. J. Mol. Biol. 197: 453– 470.
261. Megraw, T. L.,, and C. B. Chae. 1993. Functional complementarity between the HMG1-like yeast mitochondrial histone HM and the bacterial histone-like protein HU. J. Biol. Chem. 268: 12758– 12763.
262. Membrillo-Hernandez, J.,, O. Kwon,, P. De Wulf,, S. E. Finkel,, and E. C. Lin. 1999. Regulation of adhE (encoding ethanol oxidoreductase) by the Fis protein in Escherichia coli. J. Bacteriol. 181: 7390– 7393.

References: V. 
 V. 
 V. 
 V. 
 V. 
 V. 
 V.