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For: Yasuno K, Yamazaki T, Tanaka Y, Kodama TS, Matsugami A, Katahira M, Ishihama A, Kyogoku Y. Interaction of the C-terminal domain of the E. coli RNA polymerase alpha subunit with the UP element: recognizing the backbone structure in the minor groove surface. J Mol Biol 2001;306:213-25. [PMID: 11237595 DOI: 10.1006/jmbi.2000.4369] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Number Cited by Other Article(s)
1
Åberg A, Gideonsson P, Bhat A, Ghosh P, Arnqvist A. Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori. Nucleic Acids Res 2024;52:5572-5595. [PMID: 38499492 PMCID: PMC11162790 DOI: 10.1093/nar/gkae188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 03/20/2024]  Open
2
Jibiki K, Kodama TS, Yasuhara N. Importin alpha family NAAT/IBB domain: Functions of a pleiotropic long chameleon sequence. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023;134:175-209. [PMID: 36858734 DOI: 10.1016/bs.apcsb.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
3
LaFleur TL, Hossain A, Salis HM. Automated model-predictive design of synthetic promoters to control transcriptional profiles in bacteria. Nat Commun 2022;13:5159. [PMID: 36056029 PMCID: PMC9440211 DOI: 10.1038/s41467-022-32829-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/19/2022] [Indexed: 12/22/2022]  Open
4
Jibiki K, Kodama TS, Suenaga A, Kawase Y, Shibazaki N, Nomoto S, Nagasawa S, Nagashima M, Shimodan S, Kikuchi R, Okayasu M, Takashita R, Mehmood R, Saitoh N, Yoneda Y, Akagi KI, Yasuhara N. Importin α2 association with chromatin: Direct DNA binding via a novel DNA-binding domain. Genes Cells 2021;26:945-966. [PMID: 34519142 DOI: 10.1111/gtc.12896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/10/2021] [Accepted: 09/11/2021] [Indexed: 12/18/2022]
5
Camakaris H, Yang J, Fujii T, Pittard J. Activation by TyrR in Escherichia coli K-12 by Interaction between TyrR and the α-Subunit of RNA Polymerase. J Bacteriol 2021;203:e0025221. [PMID: 34309399 PMCID: PMC8425403 DOI: 10.1128/jb.00252-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022]  Open
6
Maeda M, Shimada T, Ishihama A. Strength and Regulation of Seven rRNA Promoters in Escherichia coli. PLoS One 2015;10:e0144697. [PMID: 26717514 PMCID: PMC4696680 DOI: 10.1371/journal.pone.0144697] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 11/23/2015] [Indexed: 11/18/2022]  Open
7
Positive autoregulation of mrkHI by the cyclic di-GMP-dependent MrkH protein in the biofilm regulatory circuit of Klebsiella pneumoniae. J Bacteriol 2015;197:1659-67. [PMID: 25733612 DOI: 10.1128/jb.02615-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 02/22/2015] [Indexed: 01/07/2023]  Open
8
Hashimoto M, Kodera N, Tsunaka Y, Oda M, Tanimoto M, Ando T, Morikawa K, Tate SI. Phosphorylation-coupled intramolecular dynamics of unstructured regions in chromatin remodeler FACT. Biophys J 2013;104:2222-34. [PMID: 23708362 DOI: 10.1016/j.bpj.2013.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 03/30/2013] [Accepted: 04/04/2013] [Indexed: 10/26/2022]  Open
9
Transcriptional activation of the mrkA promoter of the Klebsiella pneumoniae type 3 fimbrial operon by the c-di-GMP-dependent MrkH protein. PLoS One 2013;8:e79038. [PMID: 24244411 PMCID: PMC3828302 DOI: 10.1371/journal.pone.0079038] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 09/18/2013] [Indexed: 01/11/2023]  Open
10
Katayama S, Ishibashi K, Gotoh K, Nakamura D. Mode of binding of RNA polymerase α subunit to the phased A-tracts upstream of the phospholipase C gene promoter of Clostridium perfringens. Anaerobe 2013;23:62-9. [DOI: 10.1016/j.anaerobe.2013.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 03/31/2013] [Accepted: 06/12/2013] [Indexed: 01/17/2023]
11
Schweimer K, Prasch S, Sujatha PS, Bubunenko M, Gottesman ME, Rösch P. NusA interaction with the α subunit of E. coli RNA polymerase is via the UP element site and releases autoinhibition. Structure 2011;19:945-54. [PMID: 21742261 PMCID: PMC3134791 DOI: 10.1016/j.str.2011.03.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 02/28/2011] [Accepted: 03/05/2011] [Indexed: 10/18/2022]
12
The unique structure of A-tracts and intrinsic DNA bending. Q Rev Biophys 2009;42:41-81. [DOI: 10.1017/s0033583509004752] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
13
The UP element is necessary but not sufficient for growth rate-dependent control of the Escherichia coli guaB promoter. J Bacteriol 2008;190:2450-7. [PMID: 18203835 DOI: 10.1128/jb.01732-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
14
Olivares-Zavaleta N, Jáuregui R, Merino E. Genome analysis of Escherichia coli promoter sequences evidences that DNA static curvature plays a more important role in gene transcription than has previously been anticipated. Genomics 2006;87:329-37. [PMID: 16413165 DOI: 10.1016/j.ygeno.2005.11.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Revised: 10/24/2005] [Accepted: 11/30/2005] [Indexed: 12/30/2022]
15
Husnain SI, Meng W, Busby SJW, Thomas MS. Escherichia coli can tolerate insertions of up to 16 amino acids in the RNA polymerase alpha subunit inter-domain linker. ACTA ACUST UNITED AC 2005;1678:47-56. [PMID: 15093137 DOI: 10.1016/j.bbaexp.2004.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2003] [Revised: 01/28/2004] [Accepted: 01/30/2004] [Indexed: 11/17/2022]
16
Sclavi B, Zaychikov E, Rogozina A, Walther F, Buckle M, Heumann H. Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter. Proc Natl Acad Sci U S A 2005;102:4706-11. [PMID: 15738402 PMCID: PMC555702 DOI: 10.1073/pnas.0408218102] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Indexed: 11/18/2022]  Open
17
Dangi B, Gronenborn AM, Rosner JL, Martin RG. Versatility of the carboxy-terminal domain of the alpha subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA. Mol Microbiol 2004;54:45-59. [PMID: 15458404 DOI: 10.1111/j.1365-2958.2004.04250.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
18
Meijer WJJ, Salas M. Relevance of UP elements for three strong Bacillus subtilis phage phi29 promoters. Nucleic Acids Res 2004;32:1166-76. [PMID: 14973248 PMCID: PMC373416 DOI: 10.1093/nar/gkh290] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
19
Kaji M, Matsushita O, Tamai E, Miyata S, Taniguchi Y, Shimamoto S, Katayama S, Morita S, Okabe A. A novel type of DNA curvature present in a Clostridium perfringens ferredoxin gene: characterization and role in gene expression. MICROBIOLOGY-SGM 2004;149:3083-3091. [PMID: 14600220 DOI: 10.1099/mic.0.26503-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
20
Lee DJ, Busby SJW, Lloyd GS. Exploitation of a Chemical Nuclease to Investigate the Location and Orientation of the Escherichia coli RNA Polymerase α Subunit C-terminal Domains at Simple Promoters That Are Activated by Cyclic AMP Receptor Protein. J Biol Chem 2003;278:52944-52. [PMID: 14530288 DOI: 10.1074/jbc.m308300200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
21
Macchi R, Montesissa L, Murakami K, Ishihama A, De Lorenzo V, Bertoni G. Recruitment of sigma54-RNA polymerase to the Pu promoter of Pseudomonas putida through integration host factor-mediated positioning switch of alpha subunit carboxyl-terminal domain on an UP-like element. J Biol Chem 2003;278:27695-702. [PMID: 12754257 DOI: 10.1074/jbc.m303031200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
22
Ross W, Schneider DA, Paul BJ, Mertens A, Gourse RL. An intersubunit contact stimulating transcription initiation by E coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4. Genes Dev 2003;17:1293-307. [PMID: 12756230 PMCID: PMC196054 DOI: 10.1101/gad.1079403] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
23
Schneider DA, Ross W, Gourse RL. Control of rRNA expression in Escherichia coli. Curr Opin Microbiol 2003;6:151-6. [PMID: 12732305 DOI: 10.1016/s1369-5274(03)00038-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
24
McAlister V, Zou C, Winslow RH, Christie GE. Purification and in vitro characterization of the Serratia marcescens NucC protein, a zinc-binding transcription factor homologous to P2 Ogr. J Bacteriol 2003;185:1808-16. [PMID: 12618444 PMCID: PMC150115 DOI: 10.1128/jb.185.6.1808-1816.2003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2002] [Accepted: 12/16/2002] [Indexed: 11/20/2022]  Open
25
Boucher PE, Maris AE, Yang MS, Stibitz S. The response regulator BvgA and RNA polymerase alpha subunit C-terminal domain bind simultaneously to different faces of the same segment of promoter DNA. Mol Cell 2003;11:163-73. [PMID: 12535530 DOI: 10.1016/s1097-2765(03)00007-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
26
Lloyd GS, Niu W, Tebbutt J, Ebright RH, Busby SJW. Requirement for two copies of RNA polymerase alpha subunit C-terminal domain for synergistic transcription activation at complex bacterial promoters. Genes Dev 2002;16:2557-65. [PMID: 12368266 PMCID: PMC187446 DOI: 10.1101/gad.237502] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
27
Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH. Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science 2002;297:1562-6. [PMID: 12202833 DOI: 10.1126/science.1076376] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
28
Finney AH, Blick RJ, Murakami K, Ishihama A, Stevens AM. Role of the C-terminal domain of the alpha subunit of RNA polymerase in LuxR-dependent transcriptional activation of the lux operon during quorum sensing. J Bacteriol 2002;184:4520-8. [PMID: 12142422 PMCID: PMC135237 DOI: 10.1128/jb.184.16.4520-4528.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
29
Savery NJ, Lloyd GS, Busby SJW, Thomas MS, Ebright RH, Gourse RL. Determinants of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit important for transcription at class I cyclic AMP receptor protein-dependent promoters. J Bacteriol 2002;184:2273-80. [PMID: 11914359 PMCID: PMC134954 DOI: 10.1128/jb.184.8.2273-2280.2002] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
30
Aiyar SE, McLeod SM, Ross W, Hirvonen CA, Thomas MS, Johnson RC, Gourse RL. Architecture of Fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promoters. J Mol Biol 2002;316:501-16. [PMID: 11866514 DOI: 10.1006/jmbi.2001.5390] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
31
Ozoline ON, Fujita N, Ishihama A. Mode of DNA-protein interaction between the C-terminal domain of Escherichia coli RNA polymerase alpha subunit and T7D promoter UP element. Nucleic Acids Res 2001;29:4909-19. [PMID: 11812819 PMCID: PMC97620 DOI: 10.1093/nar/29.24.4909] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
32
Katayama S, Matsushita O, Tamai E, Miyata S, Okabe A. Phased A-tracts bind to the alpha subunit of RNA polymerase with increased affinity at low temperature. FEBS Lett 2001;509:235-8. [PMID: 11741595 DOI: 10.1016/s0014-5793(01)03148-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
33
Meng W, Belyaeva T, Savery NJ, Busby SJ, Ross WE, Gaal T, Gourse RL, Thomas MS. UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker. Nucleic Acids Res 2001;29:4166-78. [PMID: 11600705 PMCID: PMC60210 DOI: 10.1093/nar/29.20.4166] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
34
Yamamoto K, Yata K, Fujita N, Ishihama A. Novel mode of transcription regulation by SdiA, an Escherichia coli homologue of the quorum-sensing regulator. Mol Microbiol 2001;41:1187-98. [PMID: 11555297 DOI: 10.1046/j.1365-2958.2001.02585.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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