Transcriptional control in the prereplicative phase of T4 development

Virology Journal

Volumn 7, Issue , 2010, Pages

  Hinton, Deborah M ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGE DNA; DNA BINDING PROTEIN; RNA; RNA POLYMERASE; MESSENGER RNA; VIRUS RNA;

BACTERIOPHAGE T4; BINDING SITE; CHLAMYDIA TRACHOMATIS; DNA BINDING; ESCHERICHIA COLI; GENE MUTATION; ISOMERIZATION; NONHUMAN; PROMOTER REGION; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; REVIEW; RNA REPLICATION; RNA SYNTHESIS; TRANSCRIPTION REGULATION; BIOSYNTHESIS; DNA REPLICATION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HOST PARASITE INTERACTION; PHYSIOLOGY; VIROLOGY; VIRUS REPLICATION;

BACTERIOPHAGE T4; DNA REPLICATION; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, VIRAL; HOST-PARASITE INTERACTIONS; PROMOTER REGIONS, GENETIC; RNA, MESSENGER; RNA, VIRAL; TRANSCRIPTION, GENETIC; VIRUS REPLICATION;

EID: 77958571327     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-7-289     Document Type: Review

References (150)

1. Regulation of middle-mode transcription. B Stitt DM Hinton, Molecular biology of bacteriophage T4 Washington, D.C.: American Society for Microbiology, Karam JD, Drake J, Kreuzer KN, Mosig G, Hall D, Eiserling F, Black L, Spicer E, Kutter E, Carlson K, Miller ES, 1994 142 160
2. Transcriptional takeover by sigma appropriation: remodelling of the sigma70 subunit of Escherichia coli RNA polymerase by the bacteriophage T4 activator MotA and co-activator AsiA. DM Hinton S Pande N Wais XB Johnson M Vuthoori A Makela I Hook-Barnard, Microbiology 2005 151 1729 1740 10.1099/mic.0.27972-0 15941982
3. Regulation of transcription of prereplicative genes. E Brody D Rabussay D Hall, Bacteriophage T4 Washington, D. C.: American Society for Microbiology, Mathews CK, Kutter EM, Mosig G, Berget PB, 1983 174 183
4. Bacteriophage T4 genome. ES Miller E Kutter G Mosig F Arisaka T Kunisawa W Ruger, Microbiol Mol Biol Rev 2003 67 86 156 10.1128/MMBR.67.1.86-156.2003 12626685
5. Transcription from early promoters. K Wilkens W Ruger, Molecular Biology of Bacteriophage T4 Washington, D. C.: American Society for Microbiology, Karam JD, Drake JW, Kreuzer KN, Mosig G, Hall DH, Eiserling FA, Black LW, Spicer EK, Kutter E, Carlson K, Miller ES, 1994 132 141
6. Transcriptional Regulation in Bacteriophage. R Weisberg DM Hinton S Adhya, Encyclopedia of Virology Oxford: Elsevier, Mahy BWJ, van Regenmortel MHV, 3 2008 174 186 174-186
7. Transcription from a bacteriophage T4 middle promoter using T4 motA protein and phage-modified RNA polymerase. DM Hinton, J Biol Chem 1991 266 18034 18044 1917941
8. Purified MotA protein binds the -30 region of a bacteriophage T4 middle-mode promoter and activates transcription in vitro. RP Schmidt KN Kreuzer, J Biol Chem 1992 267 11399 11407 1597469
9. New small polypeptides associated with DNA-dependent RNA polymerase of Escherichia coli after infection with bacteriophage T4. A Stevens, Proc Natl Acad Sci USA 1972 69 603 607 10.1073/pnas.69.3.603 4551978
10. An inhibitor of host sigma-stimulated core enzyme activity that purifies with DNA-dependent RNA polymerase of E. coli following T4 phage infection. A Stevens, Biochem Biophys Res Commun 1973 54 488 493 10.1016/0006-291X(73)91447-2 4585685
11. The asiA gene product of bacteriophage T4 is required for middle mode RNA synthesis. M Ouhammouch G Orsini EN Brody, J Bacteriol 1994 176 3956 3965 8021178
12. Bacteriophage T4 MotA and AsiA proteins suffice to direct Escherichia coli RNA polymerase to initiate transcription at T4 middle promoters. M Ouhammouch K Adelman SR Harvey G Orsini EN Brody, Proc Natl Acad Sci USA 1995 92 1451 1455 10.1073/pnas.92.5.1451 7877999
13. Bacteriophage T4 middle transcription system: T4-modified RNA polymerase; AsiA, a sigma 70 binding protein; and transcriptional activator MotA. DM Hinton R March-Amegadzie JS Gerber M Sharma, Methods Enzymol 1996 274 43 57 8902795
14. The regulation of bacterial transcription initiation. DF Browning SJ Busby, Nat Rev Microbiol 2004 2 57 65 10.1038/nrmicro787 15035009
15. Bacterial RNA polymerases: the wholo story. KS Murakami SA Darst, Curr Opin Struct Biol 2003 13 31 39 10.1016/S0959-440X(02)00005-2 12581657
16. Views of transcription initiation. BA Young TM Gruber CA Gross, Cell 2002 109 417 420 10.1016/S0092-8674(02)00752-3 12086598
17. The sigma70 family of sigma factors. MS Paget JD Helmann, Genome Biol 2003 4 203 10.1186/gb-2003-4-1-203 12540296
18. Multiple sigma subunits and the partitioning of bacterial transcription space. TM Gruber CA Gross, Annu Rev Microbiol 2003 57 441 466 10.1146/annurev.micro.57.030502.090913 14527287
19. Regulation of bacterial RNA polymerase sigma factor activity: a structural perspective. EA Campbell LF Westblade SA Darst, Curr Opin Microbiol 2008 11 121 127 10.1016/j.mib.2008.02.016 18375176
20. Transcription Initiation by Mix and Match Elements: Flexibility for Polymerase Binding to Bacterial Promoters. IG Hook-Barnard DM Hinton, Gene Regulation and Systems Biology 2007 http://la-press.com/article.php?article-id= 481:275-293 19119427
21. RNA polymerase: a nexus of gene regulation. JD Helmann, Methods 2009 47 1 5 10.1016/j.ymeth.2008.12.001 19070783
22. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. DG Vassylyev S Sekine O Laptenko J Lee MN Vassylyeva S Borukhov S Yokoyama, Nature 2002 417 712 719 10.1038/nature752 12000971 (Pubitemid 34640620)
23. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. KS Murakami S Masuda EA Campbell O Muzzin SA Darst, Science 2002 296 1285 1290 10.1126/science.1069595 12016307 (Pubitemid 34522778)
24. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. KS Murakami S Masuda SA Darst, Science 2002 296 1280 1284 10.1126/science.1069594 12016306 (Pubitemid 34522777)
25. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. EA Campbell O Muzzin M Chlenov JL Sun CA Olson O Weinman ML Trester-Zedlitz SA Darst, Mol Cell 2002 9 527 539 10.1016/S1097-2765(02)00470-7 11931761
26. T4 AsiA blocks DNA recognition by remodeling sigma(70) region 4. LJ Lambert Y Wei V Schirf B Demeler MH Werner, Embo J 2004 23 2952 2962 10.1038/sj.emboj.7600312 15257291
27. Structure of a ternary transcription activation complex. D Jain BE Nickels L Sun A Hochschild SA Darst, Mol Cell 2004 13 45 53 10.1016/S1097- 2765(03)00483-0 14731393
28. Structural basis for transcription elongation by bacterial RNA polymerase. DG Vassylyev MN Vassylyeva A Perederina TH Tahirov I Artsimovitch, Nature 2007 448 157 162 10.1038/nature05932 17581590 (Pubitemid 47067370)
29. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. A Malhotra E Severinova SA Darst, Cell 1996 87 127 136 10.1016/S0092-8674(00)81329-X 8858155 (Pubitemid 26337397)
30. Crystal Structure of the Escherichia coli Regulator of sigma(70), Rsd, in Complex with sigma(70) Domain 4. GA Patikoglou LF Westblade EA Campbell V Lamour WJ Lane SA Darst, J Mol Biol 2007 372 649 659 10.1016/j.jmb.2007.06.081 17681541
31. KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo. S Sasse-Dwight JD Gralla, J Biol Chem 1989 264 8074 8081 2722774
32. Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subsequent conversion to RPo. WS Kontur RM Saecker CA Davis MW Capp MT Record Jr, Biochemistry 2006 45 2161 2177 10.1021/bi051835v 16475805
33. Kinetic studies and structural models of the association of E. coli sigma(70) RNA polymerase with the lambdaP(R) promoter: large scale conformational changes in forming the kinetically significant intermediates. RM Saecker OV Tsodikov KL McQuade PE Schlax Jr MW Capp MT Record Jr, J Mol Biol 2002 319 649 671 10.1016/S0022-2836(02)00293-0 12054861
34. The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription. DA Erie, Biochim Biophys Acta 2002 1577 224 239 12213654
35. The regulatory roles and mechanism of transcriptional pausing. R Landick, Biochem Soc Trans 2006 34 1062 1066 10.1042/BST0341062 17073751
36. Rho-dependent terminators and transcription termination. MS Ciampi, Microbiology 2006 152 2515 2528 10.1099/mic.0.28982-0 16946247
37. Derailing the locomotive: transcription termination. DS Gilmour R Fan, J Biol Chem 2008 283 661 664 10.1074/jbc.R700032200 17998201
38. Control of transcription termination. S Adhya M Gottesman, Annu Rev Biochem 1978 47 967 996 10.1146/annurev.bi.47.070178.004535 354508
39. Characterization of bacteriophage T4 early promoters in vivo with a new promoter probe vector. K Wilkens W Ruger, Plasmid 1996 35 108 120 10.1006/plas.1996.0013 8700964
40. Overexpression, purification, and characterization of the ADP-ribosyltransferase (gpAlt) of bacteriophage T4: ADP-ribosylation of E. coli RNA polymerase modulates T4 "early" transcription. T Koch A Raudonikiene K Wilkens W Ruger, Gene Expr 1995 4 253 264 7787417
41. Bacteriophage T4 mutants deficient in alteration and modification of the Escherichia coli RNA polymerase. HR Horvitz, J Mol Biol 1974 90 739 750 10.1016/0022-2836(74)90537-3 4615179
42. Control by bacteriophage T4 of two sequential phosphorylations of the alpha subunit of Escherichia coli RNA polymerase. HR Horvitz, J Mol Biol 1974 90 727 738 10.1016/0022-2836(74)90536-1 4615178
43. The mono-ADP-ribosyltransferases Alt and ModB of bacteriophage T4: target proteins identified. R Depping C Lohaus HE Meyer W Ruger, Biochem Biophys Res Commun 2005 335 1217 1223 10.1016/j.bbrc.2005.08.023 16112649
44. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. W Ross KK Gosink J Salomon K Igarashi C Zou A Ishihama K Severinov RL Gourse, Science 1993 262 1407 1413 10.1126/science. 8248780 8248780
45. DNA-binding determinants of the alpha subunit of RNA polymerase: novel DNA-binding domain architecture. T Gaal W Ross EE Blatter H Tang X Jia VV Krishnan N Assa-Munt RH Ebright RL Gourse, Genes Dev 1996 10 16 26 10.1101/gad.10.1.16 8557191
46. Transcription factor recognition surface on the RNA polymerase alpha subunit is involved in contact with the DNA enhancer element. K Murakami N Fujita A Ishihama, EMBO J 1996 15 4358 4367 8861963
47. Mapping the cAMP receptor protein contact site on the alpha subunit of Escherichia coli RNA polymerase. C Zou N Fujita K Igarashi A Ishihama, Mol Microbiol 1992 6 2599 2605 10.1111/j.1365-2958.1992.tb01437.x 1333035
48. ModA and ModB, two ADP-ribosyltransferases encoded by bacteriophage T4: catalytic properties and mutation analysis. B Tiemann R Depping E Gineikiene L Kaliniene R Nivinskas W Ruger, J Bacteriol 2004 186 7262 7272 10.1128/JB.186.21.7262-7272.2004 15489438
49. ADP-ribosylation and early transcription regulation by bacteriophage T4. K Wilkens B Tiemann F Bazan W Ruger, Adv Exp Med Biol 1997 419 71 82 9193638
50. T4 early promoter strength probed in vivo with unribosylated and ADP-ribosylated Escherichia coli RNA polymerase: a mutation analysis. N Sommer V Salniene E Gineikiene R Nivinskas W Ruger, Microbiology 2000 146 2643 2653 11021939
51. Bacteriophage T4 Alc protein: a transcription termination factor sensing local modification of DNA. M Kashlev E Nudler A Goldfarb T White E Kutter, Cell 1993 75 147 154 8402894
52. A non-essential domain of Escherichia coli RNA polymerase required for the action of the termination factor Alc. K Severinov M Kashlev E Severinova I Bass K McWilliams E Kutter V Nikiforov L Snyder A Goldfarb, J Biol Chem 1994 269 14254 14259 8188709
53. Overexpression, purification, and partial characterization of ADP-ribosyltransferases modA and modB of bacteriophage T4. B Tiemann R Depping W Ruger, Gene Expr 1999 8 187 196 10634320
54. The bacteriophage T4 anti-sigma factor AsiA is not necessary for the inhibition of early promoters in vivo. C Pene M Uzan, Mol Microbiol 2000 35 1180 1191 10.1046/j.1365-2958.2000.01787.x 10712698
55. Dual role of the sequence-specific bacteriophage T4 endoribonuclease RegB. mRNA inactivation and mRNA destabilization. B Sanson M Uzan, J Mol Biol 1993 233 429 446 10.1006/jmbi.1993.1522 8411154
56. Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis. N Hirano H Ohshima H Takahashi, Nucleic Acids Res 2006 34 4743 4751 10.1093/nar/gkl553 16971463
57. Bacteriophage T4 endonuclease II: concerted single-strand nicks yield double-strand cleavage. K Carlson P Lagerback AC Nystrom, Mol Microbiol 2004 52 1403 1411 10.1111/j.1365-2958.2004.04062.x 15165242
58. Characterization of an inhibitor causing potassium chloride sensitivity of an RNA polymerase from T4 phage-infected Escherichia coli. A Stevens JC Rhoton, Biochemistry 1975 14 5074 5079 10.1021/bi00694a007 1103966
59. The asiA gene of bacteriophage T4 codes for the anti-sigma 70 protein. G Orsini M Ouhammouch JP Le Caer EN Brody, J Bacteriol 1993 175 85 93 8416914
60. The interaction between the AsiA protein of bacteriophage T4 and the sigma70 subunit of Escherichia coli RNA polymerase. K Adelman G Orsini A Kolb L Graziani EN Brody, J Biol Chem 1997 272 27435 27443 10.1074/jbc.272.43.27435 9341196
61. Domain organization of the Escherichia coli RNA polymerase sigma 70 subunit. E Severinova K Severinov D Fenyo M Marr EN Brody JW Roberts BT Chait SA Darst, J Mol Biol 1996 263 637 647 10.1006/jmbi.1996.0604 8947564 (Pubitemid 26395056)
62. The bacteriophage T4 AsiA protein: a molecular switch for sigma 70-dependent promoters. F Colland G Orsini EN Brody H Buc A Kolb, Mol Microbiol 1998 27 819 829 10.1046/j.1365-2958.1998.00729.x 9515707
63. Expressed protein ligation, a novel method for studying protein-protein interactions in transcription. K Severinov TW Muir, J Biol Chem 1998 273 16205 16209 10.1074/jbc.273.26.16205 9632677
64. Study of the interaction between bacteriophage T4 asiA and Escherichia coli sigma(70), using the yeast two-hybrid system: neutralization of asiA toxicity to E. coli cells by coexpression of a truncated sigma(70) fragment. UK Sharma S Ravishankar RK Shandil PV Praveen TS Balganesh, J Bacteriol 1999 181 5855 5859 10482532
65. Conserved regions 4.1 and 4.2 of sigma(70) constitute the recognition sites for the anti-sigma factor AsiA, and AsiA is a dimer free in solution. JL Urbauer K Adelman RJ Urbauer MF Simeonov JM Gilmore M Zolkiewski EN Brody, J Biol Chem 2001 276 41128 41132 10.1074/jbc.M106400200 11518715
66. Interaction of bacteriophage T4 AsiA protein with Escherichia coli sigma70 and its variant. S Pahari D Chatterji, FEBS Lett 1997 411 60 62 10.1016/S0014-5793(97)00668-6 9247142
67. Characterization of the interactions between the bacteriophage T4 AsiA protein and RNA polymerase. MF Simeonov RJ Bieber Urbauer JM Gilmore K Adelman EN Brody A Niedziela-Majka L Minakhin T Heyduk JL Urbauer, Biochemistry 2003 42 7717 7726 10.1021/bi0340797 12820881
68. Both regions 4.1 and 4.2 of E. coli sigma(70) are together required for binding to bacteriophage T4 AsiA in vivo. UK Sharma D Chatterji, Gene 2006 376 133 143 10.1016/j.gene.2006.02.017 16545925
69. Interaction of T4 AsiA with its target sites in the RNA polymerase sigma70 subunit leads to distinct and opposite effects on transcription. L Minakhin A Niedziela-Majka K Kuznedelov K Adelman JL Urbauer T Heyduk K Severinov, J Mol Biol 2003 326 679 690 10.1016/S0022-2836(02)01442-0 12581632
70. Bacterial two-hybrid analysis of interactions between region 4 of the sigma(70) subunit of RNA polymerase and the transcriptional regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa. SL Dove A Hochschild, J Bacteriol 2001 183 6413 6421 10.1128/JB.183.21.6413-6421.2001 11591686
71. Solution structure and stability of the anti-sigma factor AsiA: implications for novel functions. JL Urbauer MF Simeonov RJ Urbauer K Adelman JM Gilmore EN Brody, Proc Natl Acad Sci USA 2002 99 1831 1835 10.1073/pnas. 032464699 11830637
72. Analysis of regions within the bacteriophage T4 AsiA protein involved in its binding to the sigma70 subunit of E. coli RNA polymerase and its role as a transcriptional inhibitor and co-activator. D Pal M Vuthoori S Pande D Wheeler DM Hinton, J Mol Biol 2003 325 827 841 10.1016/S0022-2836(02)01307-4 12527294
73. Flipping a genetic switch by subunit exchange. LJ Lambert V Schirf B Demeler M Cadene MH Werner, Embo J 2001 20 7149 7159 10.1093/emboj/20.24.7149 11742991
74. Determinants of Affinity and Activity of the Anti-Sigma Factor AsiA. JM Gilmore RJ Bieber Urbauer L Minakhin V Akoyev M Zolkiewski K Severinov JL Urbauer, Biochemistry 2010 20545305
75. Mutational analysis of bacteriophage T4 AsiA: involvement of N- and C-terminal regions in binding to sigma(70) of Escherichia coli in vivo. UK Sharma PV Praveen TS Balganesh, Gene 2002 295 125 134 10.1016/S0378-1119(02) 00831-4 12242019
76. A salt-promoted inhibitor of RNA polymerase isolated from T4 phage-infected E. coli. A Stevens, RNA Polymerase Cold Spring Harbor, N. Y.: Cold Spring Harbor Laboratory, Losick R, Chamberlin M, 1976 617 627
77. Mutational Analysis of sigma(70) Region 4 Needed for Appropriation by the Bacteriophage T4 Transcription Factors AsiA and MotA. K Baxter J Lee L Minakhin K Severinov DM Hinton, J Mol Biol 2006 363 931 944 10.1016/j.jmb.2006.08.074 16996538
78. Mapping the molecular interface between the sigma(70) subunit of E. coli RNA polymerase and T4 AsiA. L Minakhin JA Camarero M Holford C Parker TW Muir K Severinov, J Mol Biol 2001 306 631 642 10.1006/jmbi.2001.4445 11243776
79. A regulator that inhibits transcription by targeting an intersubunit interaction of the RNA polymerase holoenzyme. BD Gregory BE Nickels SJ Garrity E Severinova L Minakhin RJ Urbauer JL Urbauer T Heyduk K Severinov A Hochschild, Proc Natl Acad Sci USA 2004 101 4554 4559 10.1073/pnas.0400923101 15070756
80. Inhibition of Escherichia coli RNA polymerase by bacteriophage T4 AsiA. E Severinova K Severinov SA Darst, J Mol Biol 1998 279 9 18 10.1006/jmbi.1998. 1742 9636696
81. Replacement of potassium chloride by potassium glutamate dramatically enhances protein-DNA interactions in vitro. S Leirmo C Harrison DS Cayley RR Burgess MT Record Jr, Biochemistry 1987 26 2095 2101 10.1021/bi00382a006 2887198
82. Enhancement of transcription termination factor rho activity with potassium glutamate. LL Zou JP Richardson, J Biol Chem 1991 266 10201 10209 1709928
83. The Escherichia coli RNA polymerase.anti-sigma 70 AsiA complex utilizes alpha-carboxyl-terminal domain upstream promoter contacts to transcribe from a -10/-35 promoter. G Orsini A Kolb H Buc, J Biol Chem 2001 276 19812 19819 10.1074/jbc.M010105200 11278617
84. Phage T4 early promoters are resistant to inhibition by the anti-sigma factor AsiA. G Orsini S Igonet C Pene B Sclavi M Buckle M Uzan A Kolb, Mol Microbiol 2004 52 1013 1028 10.1111/j.1365-2958.2004.04038.x 15130121
85. Sigma competition: the contest between bacteriophage T4 middle and late transcription. S Kolesky M Ouhammouch EN Brody EP Geiduschek, J Mol Biol 1999 291 267 281 10.1006/jmbi.1999.2953 10438620
86. Mutant of bacteriophage T4D affecting expression of many early genes. T Mattson J Richardson D Goodin, Nature 1974 250 48 50 10.1038/250048a0 4601455
87. Isolation and characterization of conditional lethal mutations in the mot gene of bacteriophage T4. T Mattson G Van Houwe RH Epstein, J Mol Biol 1978 126 551 570 10.1016/0022-2836(78)90058-X 745239
88. Nucleotide sequence and control of transcription of the bacteriophage T4 motA regulatory gene. M Uzan E Brody R Favre, Mol Microbiol 1990 4 1487 1496 10.1111/j.1365-2958.1990.tb02059.x 2287273
89. Characterization of pre-transcription complexes made at a bacteriophage T4 middle promoter: involvement of the T4 MotA activator and the T4 AsiA protein, a sigma 70 binding protein, in the formation of the open complex. DM Hinton R March-Amegadzie JS Gerber M Sharma, J Mol Biol 1996 256 235 248 10.1006/jmbi.1996.0082 8594193
90. The bacteriophage T4 middle promoter PuvsX: analysis of regions important for binding of the T4 transcriptional activator MotA and for activation of transcription. R March-Amegadzie DM Hinton, Mol Microbiol 1995 15 649 660 10.1111/j.1365-2958.1995.tb02374.x 7783637
91. Middle promoters constitute the most abundant and diverse class of promoters in bacteriophage T4. G Stoskiene L Truncaite A Zajanckauskaite R Nivinskas, Mol Microbiol 2007 64 421 434 10.1111/j.1365-2958.2007.05659.x 17371501
92. The MotA transcriptional activator of bacteriophage T4 binds to its specific DNA site as a monomer. MP Cicero KA Alexander KN Kreuzer, Biochemistry 1998 37 4977 4984 10.1021/bi972337s 9538016
93. The MotA transcription factor from bacteriophage T4 contains a novel DNA-binding domain: the 'double wing' motif. N Li EA Sickmier R Zhang A Joachimiak SW White, Mol Microbiol 2002 43 1079 1088 10.1046/j.1365-2958.2002. 02809.x 11918797
94. Solution structure of the transcriptional activation domain of the bacteriophage T4 protein, MotA. N Li W Zhang SW White RW Kriwacki, Biochemistry 2001 40 4293 4302 10.1021/bi0028284 11284685
95. The MotA protein from bacteriophage T4 contains two domains. Preliminary structural analysis by X-ray diffraction and nuclear magnetic resonance. MS Finnin DW Hoffman KN Kreuzer SJ Porter RP Schmidt SW White, J Mol Biol 1993 232 301 304 10.1006/jmbi.1993.1384 8331666
96. An N-terminal mutation in the bacteriophage T4 motA gene yields a protein that binds DNA but is defective for activation of transcription. JS Gerber DM Hinton, J Bacteriol 1996 178 6133 6139 8892810
97. The bacteriophage T4 transcription activator MotA interacts with the far-C-terminal region of the sigma70 subunit of Escherichia coli RNA polymerase. S Pande A Makela SL Dove BE Nickels A Hochschild DM Hinton, J Bacteriol 2002 184 3957 3964 10.1128/JB.184.14.3957-3964.2002 12081968
98. The activation domain of the MotA transcription factor from bacteriophage T4. MS Finnin MP Cicero C Davies SJ Porter SW White KN Kreuzer, Embo J 1997 16 1992 2003 10.1093/emboj/16.8.1992 9155025
99. Transcriptional activation of bacteriophage T4 middle promoters by the motA protein. N Guild M Gayle R Sweeney T Hollingsworth T Modeer L Gold, J Mol Biol 1988 199 241 258 10.1016/0022-2836(88)90311-7 3280803
100. The bacteriophage T4 transcriptional activator MotA accepts various base-pair changes within its binding sequence. P Marshall M Sharma DM Hinton, J Mol Biol 1999 285 931 944 10.1006/jmbi.1998.2373 9918715
101. Twelve new MotA-dependent middle promoters of bacteriophage T4: consensus sequence revised. L Truncaite L Piesiniene G Kolesinskiene A Zajanckauskaite A Driukas V Klausa R Nivinskas, J Mol Biol 2003 327 335 346 10.1016/S0022-2836(03) 00125-6 12628241
102. Identification of two middle promoters upstream DNA ligase gene 30 of bacteriophage T4. L Truncaite A Zajanckauskaite R Nivinskas, J Mol Biol 2002 317 179 190 10.1006/jmbi.2002.5407 11902835
103. Binding of the bacteriophage T4 transcriptional activator, MotA, to T4 middle promoter DNA: evidence for both major and minor groove contacts. M Sharma P Marshall DM Hinton, J Mol Biol 1999 290 905 915 10.1006/jmbi.1999.2928 10438591
104. A basic/hydrophobic cleft of the T4 activator MotA interacts with the C-terminus of E. coli sigma70 to activate middle gene transcription. RP Bonocora G Caignan C Woodrell MH Werner DM Hinton, Mol Microbiol 2008 69 331 343 10.1111/j.1365-2958.2008.06276.x 18485078
105. Amino acid substitutions in the -35 recognition motif of sigma 70 that result in defects in phage lambda repressor-stimulated transcription. N Kuldell A Hochschild, J Bacteriol 1994 176 2991 2998 8188599
106. Target of the transcriptional activation function of phage lambda cI protein. M Li H Moyle MM Susskind, Science 1994 263 75 77 10.1126/science. 8272867 8272867
107. Protein-protein and protein-DNA interactions of sigma70 region 4 involved in transcription activation by lambda cI. BE Nickels SL Dove KS Murakami SA Darst A Hochschild, J Mol Biol 2002 324 17 34 10.1016/S0022-2836(02)01043-4 12421556
108. Interactions between activating region 3 of the Escherichia coli cyclic AMP receptor protein and region 4 of the RNA polymerase sigma(70) subunit: application of suppression genetics. VA Rhodius SJ Busby, J Mol Biol 2000 299 311 324 10.1006/jmbi.2000.3737 10860740
109. Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase sigma70 subunit. MA Lonetto V Rhodius K Lamberg P Kiley S Busby C Gross, J Mol Biol 1998 284 1353 1365 10.1006/jmbi.1998.2268 9878355
110. The Escherichia coli Ada protein can interact with two distinct determinants in the sigma70 subunit of RNA polymerase according to promoter architecture: identification of the target of Ada activation at the alkA promoter. P Landini SJ Busby, J Bacteriol 1999 181 1524 1529 10049384
111. Genetic evidence that transcription activation by RhaS involves specific amino acid contacts with sigma 70. PM Bhende SM Egan, J Bacteriol 2000 182 4959 4969 10.1128/JB.182.17.4959-4969.2000 10940041
112. Amino acid contacts between sigma 70 domain 4 and the transcription activators RhaS and RhaR. JR Wickstrum SM Egan, J Bacteriol 2004 186 6277 6285 10.1128/JB.186.18.6277-6285.2004 15342598
113. The secret to 6S: regulating RNA polymerase by ribo-sequestration. KB Decker DM Hinton, Mol Microbiol 2009 73 137 140 10.1111/j.1365-2958.2009.06759.x 19538446
114. Host - virus interactions in the control of T4 prereplicative transcription. II. Interaction between tabC (rho) mutants and T4 mot mutants. JF Pulitzer A Coppo M Caruso, J Mol Biol 1979 135 979 997 10.1016/0022-2836(79) 90523-0 395323
115. Substitutions in bacteriophage T4 AsiA and Escherichia coli sigma(70) that suppress T4 motA activation mutations. MP Cicero MM Sharp CA Gross KN Kreuzer, J Bacteriol 2001 183 2289 2297 10.1128/JB.183.7.2289-2297.2001 11244069
116. The bacteriophage T4 AsiA protein contacts the beta-flap domain of RNA polymerase. AH Yuan BE Nickels A Hochschild, Proc Natl Acad Sci USA 2009 106 6597 6602 10.1073/pnas.0812832106 19366670
117. Direct activator/co-activator interaction is essential for bacteriophage T4 middle gene expression. AH Yuan A Hochschild, Mol Microbiol 2009 74 1018 1030 10.1111/j.1365-2958.2009.06916.x 19843221
118. Direct activator/co-activator interaction is essential for bacteriophage T4 middle gene expression. AH Yuan A Hochschild, Mol Microbiol 2009 19843221
119. A family of anti-sigma70 proteins in T4-type phages and bacteria that are similar to AsiA, a Transcription inhibitor and co-activator of bacteriophage T4. M Pineda BD Gregory B Szczypinski KR Baxter A Hochschild ES Miller DM Hinton, J Mol Biol 2004 344 1183 1197 10.1016/j.jmb.2004.10.003 15561138
120. A mutation within the subunit of Escherichia coli RNA polymerase impairs transcription from bacteriophage T4 middle promoters. TD James M Cashel DM Hinton, J Bacteriol 2010 20729353
121. Stimulation of bacteriophage T4 middle transcription by the T4 proteins MotA and AsiA occurs at two distinct steps in the transcription cycle. K Adelman EN Brody M Buckle, Proc Natl Acad Sci USA 1998 95 15247 15252 10.1073/pnas.95.26.15247 9860954
122. Efficient inhibition of Escherichia coli RNA polymerase by the bacteriophage T4 AsiA protein requires that AsiA binds first to free sigma70. DM Hinton S Vuthoori, J Mol Biol 2000 304 731 739 11188759
123. Association of RNA polymerase with transcribed regions in Escherichia coli. JT Wade K Struhl, Proc Natl Acad Sci USA 2004 101 17777 17782 10.1073/pnas.0404305101 15596728
124. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. ES Miller JF Heidelberg JA Eisen WC Nelson AS Durkin A Ciecko TV Feldblyum O White IT Paulsen WC Nierman,, et al. J Bacteriol 2003 185 5220 5233 10.1128/JB.185.17.5220-5233.2003 12923095
125. A regulator from Chlamydia trachomatis modulates the activity of RNA polymerase through direct interaction with the beta subunit and the primary sigma subunit. X Rao P Deighan Z Hua X Hu J Wang M Luo Y Liang G Zhong A Hochschild L Shen, Genes Dev 2009 23 1818 1829 10.1101/gad.1784009 19651989
126. Deletion analysis of bacteriophage T4 tertiary origins. A promoter sequence is required for a rifampicin-resistant replication origin. AE Menkens KN Kreuzer, J Biol Chem 1988 263 11358 11365 3403531
127. Role of MotA transcription factor in bacteriophage T4 DNA replication. KH Benson KN Kreuzer, J Mol Biol 1992 228 88 100 10.1016/0022-2836(92)90493-4 1447797
128. Microarray analysis of gene expression during bacteriophage T4 infection. K Luke A Radek X Liu J Campbell M Uzan R Haselkorn Y Kogan, Virology 2002 299 182 191 10.1006/viro.2002.1409 12202221
129. Transcription and messenger RNA processing upstream of bacteriophage T4 gene 32. AJ Carpousis EA Mudd HM Krisch, Mol Gen Genet 1989 219 39 48 10.1007/BF00261155 2615764
130. Sequence and characterization of the bacteriophage T4 comC alpha gene product, a possible transcription antitermination factor. B Sanson M Uzan, J Bacteriol 1992 174 6539 6547 1400206
131. Characterisation of the bacteriophage T4 comC alpha 55.6 and comCJ mutants. A possible role in an antitermination process. M Chiurazzi JF Pulitzer, FEMS Microbiol Lett 1998 166 187 195 9770273
132. Revisited gene regulation in bacteriophage lambda. IB Dodd KE Shearwin JB Egan, Curr Opin Genet Dev 2005 15 145 152 10.1016/j.gde.2005.02.001 15797197
133. In vitro characterization of transcription termination factor Rho from Escherichia coli rho(nusD) mutants. RS Washburn BL Stitt, J Mol Biol 1996 260 332 346 10.1006/jmbi.1996.0404 8757797
134. Effects on mRNA degradation by Escherichia coli transcription termination factor Rho and pBR322 copy number control protein Rop. S Sozhamannan BL Stitt, J Mol Biol 1997 268 689 703 10.1006/jmbi.1997.1004 9175854
135. RNA-binding proteins and post-transcriptional gene regulation. T Glisovic JL Bachorik J Yong G Dreyfuss, FEBS Lett 2008 582 1977 1986 10.1016/j.febslet.2008.03.004 18342629
136. Transcription termination factor Pcf11 limits the processivity of Pol II on an HIV provirus to repress gene expression. Z Zhang A Klatt AJ Henderson DS Gilmour, Genes Dev 2007 21 1609 1614 10.1101/gad.1542707 17606639
137. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. RH Ebright, J Mol Biol 2000 304 687 698 10.1006/jmbi.2000.4309 11124018
138. Structural evolution of multisubunit RNA polymerases. F Werner, Trends Microbiol 2008 16 247 250 10.1016/j.tim.2008.03.008 18468900
139. Requirement of tissue-selective TBP-associated factor TAFII105 in ovarian development. RN Freiman SR Albright S Zheng WC Sha RE Hammer R Tjian, Science 2001 293 2084 2087 10.1126/science.1061935 11557891
140. Transcription of histone gene cluster by differential core-promoter factors. Y Isogai S Keles M Prestel A Hochheimer R Tjian, Genes Dev 2007 21 2936 2949 10.1101/gad.1608807 17978101
141. The rIIA gene of bacteriophage T4. II. Regulation of its messenger RNA synthesis. P Daegelen E Brody, Genetics 1990 125 249 260 2379818
142. The rIIA gene of bacteriophage T4. I. Its DNA sequence and discovery of a new open reading frame between genes 60 and rIIA. P Daegelen E Brody, Genetics 1990 125 237 248 2379817
143. Transcriptional mapping of a DNA replication gene cluster in bacteriophage T4. Sites for initiation, termination, and mRNA processing. T Hsu JD Karam, J Biol Chem 1990 265 5303 5316 2180963
144. Regulation of two nested proteins from gene 49 (recombination endonuclease VII) and of a lambda RexA-like protein of bacteriophage T4. KA Barth D Powell M Trupin G Mosig, Genetics 1988 120 329 343 2974005
145. Sequence and transcripts of the bacteriophage T4 DNA repair gene uvsY. ME Gruidl G Mosig, Genetics 1986 114 1061 1079 3026891
146. A new early gene in front of the middle gene 31 of bacteriophage T4: cloning and expression. RG Nivinskas AA Raudonikene N Guild, Mol Biol (Mosk) 1989 23 739 749 2671675
147. Genes within genes: independent expression of phage T4 intron open reading frames and the genes in which they reside. JM Gott A Zeeh D
148. Bacteriophage T4 nrdA and nrdB genes, encoding ribonucleotide reductase, are expressed both separately and coordinately: characterization of the nrdB promoter. MJ Tseng P He JM Hilfinger GR Greenberg, J Bacteriol 1990 172 6323 6332 2228963
149. Sense and antisense transcription of bacteriophage T4 gene 32. Processing and stability of the mRNAs. D Belin EA Mudd P Prentki Y Yi-Yi HM Krisch, J Mol Biol 1987 194 231 243 10.1016/0022-2836(87)90371-8 3612804
150. Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. ST Estrem W Ross T Gaal ZW Chen W Niu RH Ebright RL Gourse, Genes Dev 1999 13 2134 2147 10.1101/gad.13.16.2134 10465790