scholarly journals RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

2019 ◽  
Author(s):  
Lingting Li ◽  
Vadim Molodtsov ◽  
Wei Lin ◽  
Richard H. Ebright ◽  
Yu Zhang
Keyword(s):  
Rna Polymerase ◽  
Crystal Structures ◽  
Active Center ◽  
Protein Interactions ◽  
Transcription Initiation ◽  
Initiation Factor ◽  
Template Strand ◽  
Transcription Initiation Factor ◽  
Σ Factor ◽  
Nascent Rna

ABSTRACTAll organisms--bacteria, archaea, and eukaryotes--have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription-initiation-factor structural module pre-organizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription-initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate, and define details of, stepwise, RNA-extension-driven displacement of the “σ finger” of the bacterial transcription initiation factor σ. The structures reveal that--for both the primary σ factor and extracytoplasmic (ECF) σ factors, and for both 5’-triphosphate RNA and 5’-hydroxy RNA--the “σ finger” is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5’-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.SIGNIFICANCE STATEMENTThe “σ finger” of the bacterial initiation factor σ binds within the RNA polymerase active-center cleft and blocks the path of nascent RNA. It has been hypothesized that the σ finger must be displaced during initial transcription. By determining crystal structures defining successive steps in initial transcription, we demonstrate that the σ finger is displaced in stepwise fashion, driven by collision with the RNA 5’-end, as nascent RNA is extended from ∼5 nt to ∼10 nt during initial transcription, and we show that this is true for both the primary σ factor and alternate σ factors. Stepwise displacement of the σ finger can be conceptualized as stepwise compression of a “protein spring” that stores energy for subsequent breakage of protein-DNA and protein-protein interactions in promoter escape.

scholarly journals RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

2020 ◽  
Vol 117 (11) ◽  
pp. 5801-5809 ◽  
Author(s):  
Lingting Li ◽  
Vadim Molodtsov ◽  
Wei Lin ◽  
Richard H. Ebright ◽  
Yu Zhang
Keyword(s):  
Rna Polymerase ◽  
Crystal Structures ◽  
Active Center ◽  
Transcription Initiation ◽  
Initiation Factor ◽  
Template Strand ◽  
Bacterial Transcription ◽  
Transcription Initiation Factor ◽  
Σ Factor ◽  
Nascent Rna

All organisms—bacteria, archaea, and eukaryotes—have a transcription initiation factor that contains a structural module that binds within the RNA polymerase (RNAP) active-center cleft and interacts with template-strand single-stranded DNA (ssDNA) in the immediate vicinity of the RNAP active center. This transcription initiation-factor structural module preorganizes template-strand ssDNA to engage the RNAP active center, thereby facilitating binding of initiating nucleotides and enabling transcription initiation from initiating mononucleotides. However, this transcription initiation-factor structural module occupies the path of nascent RNA and thus presumably must be displaced before or during initial transcription. Here, we report four sets of crystal structures of bacterial initially transcribing complexes that demonstrate and define details of stepwise, RNA-extension-driven displacement of the “σ-finger” of the bacterial transcription initiation factor σ. The structures reveal that—for both the primary σ-factor and extracytoplasmic (ECF) σ-factors, and for both 5′-triphosphate RNA and 5′-hydroxy RNA—the “σ-finger” is displaced in stepwise fashion, progressively folding back upon itself, driven by collision with the RNA 5′-end, upon extension of nascent RNA from ∼5 nt to ∼10 nt.

scholarly journals Inhibition of TATA Binding Protein Dimerization by RNA Polymerase III Transcription Initiation Factor Brf1

2004 ◽  
Vol 279 (31) ◽  
pp. 32401-32406 ◽  
Author(s):  
Diane E. Alexander ◽  
David J. Kaczorowski ◽  
Amy J. Jackson-Fisher ◽  
Drew M. Lowery ◽  
Sara J. Zanton ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcription Initiation ◽  
Binding Protein ◽  
Rna Polymerase Iii ◽  
Tata Binding Protein ◽  
Initiation Factor ◽  
Protein Dimerization ◽  
Polymerase Iii ◽  
Transcription Initiation Factor

The C-terminal domain of the largest subunit of RNA polymerase II and transcription initiation

1989 ◽  
Vol 9 (12) ◽  
pp. 5750-5753
Author(s):  
M Moyle ◽  
J S Lee ◽  
W F Anderson ◽  
C J Ingles
Keyword(s):  
Monoclonal Antibodies ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Initiation Factor ◽  
Transcription Initiation Factor ◽  
Evolutionarily Conserved ◽  
Repeat Domain ◽  
Initiation Of Transcription

Monoclonal antibodies specific for the evolutionarily conserved C-terminal heptapeptide repeat domain of the largest subunit of RNA polymerase II inhibited the initiation of transcription from mammalian promoters in vitro. Since these antibodies did not inhibit elongation and randomly initiated transcription, the heptapeptide repeats may function by binding class II transcription initiation factor(s).

scholarly journals Function of the growth-regulated transcription initiation factor TIF-IA in initiation complex formation at the murine ribosomal gene promoter.

1993 ◽  
Vol 13 (11) ◽  
pp. 6723-6732 ◽  
Author(s):  
A Schnapp ◽  
G Schnapp ◽  
B Erny ◽  
I Grummt
Keyword(s):  
Cell Proliferation ◽  
Rna Polymerase ◽  
Transcription Initiation ◽  
Human Cells ◽  
Initiation Factor ◽  
Rrna Genes ◽  
Regulation Of Transcription ◽  
Initiation Complex ◽  
Transcription System ◽  
Transcription Initiation Factor

Alterations in the rate of cell proliferation are accompanied by changes in the transcription of rRNA genes. In mammals, this growth-dependent regulation of transcription of genes coding for rRNA (rDNA) is due to reduction of the amount or activity of an essential transcription factor, called TIF-IA. Extracts prepared from quiescent cells lack this factor activity and, therefore, are transcriptionally inactive. We have purified TIF-IA from exponentially growing cells and have shown that it is a polypeptide with a molecular mass of 75 kDa which exists as a monomer in solution. Using a reconstituted transcription system consisting of purified transcription factors, we demonstrate that TIF-IA is a bona fide transcription initiation factor which interacts with RNA polymerase I. Preinitiation complexes can be assembled in the absence of TIF-IA, but formation of the first phosphodiester bonds of nascent rRNA is precluded. After initiation, TIF-IA is liberated from the initiation complex and facilitates transcription from templates bearing preinitiation complexes which lack TIF-IA. Despite the pronounced species specificity of class I gene transcription, this growth-dependent factor has been identified not only in mouse but also in human cells. Murine TIF-IA complements extracts from both growth-inhibited mouse and human cells. The analogous human activity appears to be similar or identical to that of TIF-IA. Therefore, despite the fact that the RNA polymerase transcription system has evolved sufficiently rapidly that an rDNA promoter from one species will not function in another species, the basic mechanisms that adapt ribosome synthesis to cell proliferation have been conserved.

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