scholarly journals A Thermus phage protein inhibits host RNA polymerase by preventing template DNA strand loading during open promoter complex formation

2017 ◽  
Vol 46 (1) ◽  
pp. 431-441 ◽  
Author(s):  
Wei-Yang Ooi ◽  
Yuko Murayama ◽  
Vladimir Mekler ◽  
Leonid Minakhin ◽  
Konstantin Severinov ◽  
...  
Keyword(s):  
Complex Formation ◽  
Rna Polymerase ◽  
Promoter Complex ◽  
Phage Protein ◽  
Dna Strand ◽  
Template Dna

β Subunit Residues 186–433 and 436–445 are Commonly Used by Eσ54 and Eσ70 RNA Polymerase for Open Promoter Complex Formation

2002 ◽  
Vol 319 (5) ◽  
pp. 1067-1083 ◽  
Author(s):  
Siva R. Wigneshweraraj ◽  
Sergei Nechaev ◽  
Konstantin Severinov ◽  
Martin Buck
Keyword(s):  
Complex Formation ◽  
Rna Polymerase ◽  
Β Subunit ◽  
Promoter Complex

scholarly journals Events during Initiation of Archaeal Transcription: Open Complex Formation and DNA-Protein Interactions

2001 ◽  
Vol 183 (10) ◽  
pp. 3025-3031 ◽  
Author(s):  
Winfried Hausner ◽  
Michael Thomm
Keyword(s):  
Complex Formation ◽  
Rna Polymerase ◽  
Protein Interactions ◽  
Dnase I ◽  
Tata Box ◽  
Noncoding Dna ◽  
Open Complex Formation ◽  
Archaeal Transcription ◽  
Tata Box Binding Protein ◽  
Dna Strand

ABSTRACT Transcription in Archaea is initiated by association of a TATA box binding protein (TBP) with a TATA box. This interaction is stabilized by the binding of the transcription factor IIB (TFIIB) orthologue TFB. We show here that the RNA polymerase of the archaeonMethanococcus, in contrast to polymerase II, does not require hydrolysis of the β-γ bond of ATP for initiation of transcription and open complex formation on linearized DNA. Permanganate probing revealed that the archaeal open complex spanned at least the DNA region from −11 to −1 at a tRNAValpromoter. The Methanococcus TBP-TFB promoter complex protected the DNA region from −40 to −14 on the noncoding DNA strand and the DNA segment from −36 to −17 on the coding DNA strand from DNase I digestion. This DNase I footprint was extended only to the downstream end by the addition of the RNA polymerase to position +17 on the noncoding strand and to position +13 on the coding DNA strand.

scholarly journals RNA polymerase III subunit architecture and implications for open promoter complex formation

2012 ◽  
Vol 109 (47) ◽  
pp. 19232-19237 ◽  
Author(s):  
C.-C. Wu ◽  
F. Herzog ◽  
S. Jennebach ◽  
Y.-C. Lin ◽  
C.-Y. Pai ◽  
...  
Keyword(s):  
Complex Formation ◽  
Rna Polymerase ◽  
Rna Polymerase Iii ◽  
Polymerase Iii ◽  
Promoter Complex

Conformational Changes of Escherichia coli σ54-RNA-Polymerase upon Closed–Promoter Complex Formation

2005 ◽  
Vol 354 (2) ◽  
pp. 201-205 ◽  
Author(s):  
Pampa Ray ◽  
Richard J. Hall ◽  
Robert D. Finn ◽  
Shaoxia Chen ◽  
Ardan Patwardhan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Complex Formation ◽  
Rna Polymerase ◽  
Conformational Changes ◽  
Promoter Complex

scholarly journals Structural basis of ribosomal RNA transcription regulation

2020 ◽  
Author(s):  
Yeonoh Shin ◽  
M. Zuhaib Qayyum ◽  
Danil Pupov ◽  
Daria Esyunina ◽  
Andrey Kulbachinskiy ◽  
...  
Keyword(s):  
Complex Formation ◽  
Ribosomal Rna ◽  
Structural Basis ◽  
Α Subunit ◽  
Rrna Transcription ◽  
Promoter Complex ◽  
Promoter Recognition ◽  
Open Complex Formation ◽  
Promoter Dna ◽  
Template Dna

Ribosomal RNA (rRNA) is the most highly expressed gene in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. To reveal the mechanism of highly regulated rRNA transcription, we determined cryo-electron microscopy structures of the Escherichia coli RNA polymerase (RNAP) σ70 holoenzyme at different steps of rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element of rRNA promoter using the dimerized α subunit carboxyl-terminal domain and scrunches the template DNA with the σfinger and β’lid to select a transcription start site favorable for rRNA expression. Promoter DNA binding to RNAP induces conformational change of the σ domain 2 that opens a gate for DNA loading and ejects σ1.1 from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding to RNAP also opens the DNA loading gate, but it is not coupled to σ1.1 ejection and impedes the open complex formation of the rRNA promoter due to its G+C rich discriminator sequence. Mutations in σ1.1 or the β’lid stabilize the RNAP and rRNA promoter complex and decrease its sensitivity to DksA/ppGpp. These results provide a molecular basis for exceptionally active rRNA transcription and for its vulnerability to DksA/ppGpp.

scholarly journals Formation of Intermediate Transcription Initiation Complexes at pfliD and pflgM by ς28 RNA Polymerase

2001 ◽  
Vol 183 (21) ◽  
pp. 6244-6252 ◽  
Author(s):  
Jennifer R. Givens ◽  
Colleen L. McGovern ◽  
Alicia J. Dombroski
Keyword(s):  
Complex Formation ◽  
Rna Polymerase ◽  
Transcription Initiation ◽  
General Phenomenon ◽  
Temperature Dependent ◽  
Binding Properties ◽  
Serovar Typhimurium ◽  
Open Complex Formation ◽  
Flagellum Biosynthesis ◽  
Dna Strand

ABSTRACT The ς subunit of prokaryotic RNA polymerase is an important factor in the control of transcription initiation. Primary ς factors are essential for growth, while alternative ς factors are activated in response to various stimuli. Expression of class 3 genes during flagellum biosynthesis in Salmonella enterica serovar Typhimurium is dependent on the alternative ς factor ς28. Previously, a novel mechanism of transcription initiation at the fliC promoter by ς28holoenzyme was proposed. Here, we have characterized the mechanism of transcription initiation by a holoenzyme carrying ς28 at the fliD and flgM promoters to determine if the mechanism of initiation observed at pfliC is a general phenomenon for all ς28-dependent promoters. Temperature-dependent footprinting demonstrated that promoter binding properties and low-temperature open complex formation are similar for pfliC, pfliD, and pflgM. However, certain aspects of DNA strand separation and complex stability are promoter dependent. Open complexes form in a concerted manner at pflgM, while a sequential pattern of open complex formation occurs at pfliD. Open and initiated complexes formed by holoenzyme carrying ς28 are generally unstable to heparin challenge, with the exception of initiated complexes at pflgM, which are stable in the presence of nucleoside triphosphates.

scholarly journals Analysis of RNA polymerase-promoter complex formation

Methods ◽  
2009 ◽  
Vol 47 (1) ◽  
pp. 13-24 ◽  
Author(s):  
Wilma Ross ◽  
Richard L. Gourse
Keyword(s):  
Complex Formation ◽  
Rna Polymerase ◽  
Promoter Complex ◽  
Rna Polymerase Promoter
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