scholarly journals Anti-pausing activity of region 4 of the RNA polymerase σ subunit and its regulation by σ-remodeling factors

2020 ◽  
Author(s):  
Konstantin Brodolin ◽  
Zakia Morichaud
Keyword(s):  
Transcription Factors ◽  
Transcription Initiation ◽  
Rna Synthesis ◽  
De Novo ◽  
Initiation Factor ◽  
Exit Channel ◽  
Β Subunit ◽  
High Propensity ◽  
Rna:Dna Hybrids ◽  
Basal Transcription Factors

ABSTRACTThe basal transcription factors of cellular RNA polymerases (RNAPs) stimulate the initial RNA synthesis via poorly understood mechanisms. Here, we explored the mechanism employed by the bacterial factor σ in promoter-independent initial transcription. We found that the RNAP holoenzyme lacking the promoter-binding domain σ4 is ineffective in de novo transcription initiation and displays high propensity to pausing upon extension of RNAs 3 to 7 nucleotides in length. The σ4 domain stabilizes short RNA:DNA hybrids and suppresses pausing by stimulating RNAP active-center translocation. The anti-pausing activity of σ4 is modulated by its interaction with the β subunit flap domain and by the σ remodeling factors AsiA and RbpA. Our results suggest that the presence of σ4 within the RNA exit channel compensates for the intrinsic instability of short RNA:DNA hybrids by increasing RNAP processivity, thus favoring productive transcription initiation. This “RNAP boosting” activity of the initiation factor is shaped by the the thermodynamics of RNA:DNA interactions and thus, should be relevant for any factor-dependent RNAP.

scholarly journals Region 4 of the RNA polymerase σ subunit counteracts pausing during initial transcription

2020 ◽  
pp. jbc.RA120.016299
Author(s):  
Konstantin Brodolin ◽  
Zakia Morichaud
Keyword(s):  
Genetic Information ◽  
Transcription Initiation ◽  
Rna Synthesis ◽  
De Novo ◽  
Initiation Factor ◽  
Exit Channel ◽  
Β Subunit ◽  
Initiation Factors ◽  
High Propensity ◽  
Rna:Dna Hybrids

All cellular genetic information is transcribed into RNA by multisubunit RNA polymerases (RNAPs). The basal transcription initiation factors of cellular RNAPs stimulate the initial RNA synthesis via poorly understood mechanisms. Here, we explored the mechanism employed by the bacterial factor σ in promoter-independent initial transcription. We found that the RNAP holoenzyme lacking the promoter-binding domain σ4 is ineffective in de novo transcription initiation and displays high propensity to pausing upon extension of RNAs 3 to 7 nucleotides in length. The nucleotide at the RNA 3' end determines the pause lifetime. The σ4 domain stabilizes short RNA:DNA hybrids and suppresses pausing by stimulating RNAP active-center translocation. The anti-pausing activity of σ4 is modulated by its interaction with the β subunit flap domain and by the σ remodeling factors AsiA and RbpA. Our results suggest that the presence of σ4 within the RNA exit channel compensates for the intrinsic instability of short RNA:DNA hybrids by increasing RNAP processivity, thus favoring productive transcription initiation. This “RNAP boosting” activity of the initiation factor is shaped by the thermodynamics of RNA:DNA interactions and thus, should be relevant for any factor-dependent RNAP.

The Long Road to Understanding RNAPII Transcription Initiation and Related Syndromes

2021 ◽  
Vol 90 (1) ◽  
pp. 193-219
Author(s):  
Emmanuel Compe ◽  
Jean-Marc Egly
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase Ii ◽  
Chromatin Remodeling ◽  
Transcription Initiation ◽  
Rna Synthesis ◽  
Regulatory Elements ◽  
Initiation Mechanism ◽  
Protein Coding ◽  
Core Promoters ◽  
General Transcription Factors

In eukaryotes, transcription of protein-coding genes requires the assembly at core promoters of a large preinitiation machinery containing RNA polymerase II (RNAPII) and general transcription factors (GTFs). Transcription is potentiated by regulatory elements called enhancers, which are recognized by specific DNA-binding transcription factors that recruit cofactors and convey, following chromatin remodeling, the activating cues to the preinitiation complex. This review summarizes nearly five decades of work on transcription initiation by describing the sequential recruitment of diverse molecular players including the GTFs, the Mediator complex, and DNA repair factors that support RNAPII to enable RNA synthesis. The elucidation of the transcription initiation mechanism has greatly benefited from the study of altered transcription components associated with human diseases that could be considered transcription syndromes.

scholarly journals Structural Insights into Transcription Initiation from De Novo RNA Synthesis to Transitioning into Elongation

iScience ◽  
2020 ◽  
Vol 23 (9) ◽  
pp. 101445
Author(s):  
Yuhong Zuo ◽  
Swastik De ◽  
Yingang Feng ◽  
Thomas A. Steitz
Keyword(s):  
Transcription Initiation ◽  
Rna Synthesis ◽  
De Novo ◽  
Structural Insights

scholarly journals Direct Modulation of RNA Polymerase Core Functions by Basal Transcription Factors

2005 ◽  
Vol 25 (18) ◽  
pp. 8344-8355 ◽  
Author(s):  
Finn Werner ◽  
Robert O. J. Weinzierl
Keyword(s):  
Transcription Factors ◽  
Transcription Initiation ◽  
Catalytic Properties ◽  
Active Role ◽  
Nucleic Acid Binding ◽  
Independent Function ◽  
Binding Properties ◽  
Basal Transcription ◽  
Additional Function ◽  
Basal Transcription Factors

ABSTRACT Archaeal RNA polymerases (RNAPs) are recruited to promoters through the joint action of three basal transcription factors: TATA-binding protein, TFB (archaeal homolog of TFIIB), and TFE (archaeal homolog of TFIIE). Our results demonstrate several new insights into the mechanisms of TFB and TFE during the transcription cycle. (i) The N-terminal Zn ribbon of TFB displays a surprising degree of redundancy for the recruitment of RNAP during transcription initiation in the archaeal system. (ii) The B-finger domain of TFB participates in transcription initiation events by stimulating abortive and productive transcription in a recruitment-independent function. TFB thus combines physical recruitment of the RNAP with an active role in influencing the catalytic properties of RNAP during transcription initiation. (iii) TFB mutations are complemented by TFE, thereby demonstrating that both factors act synergistically during transcription initiation. (iv) An additional function of TFE is to dynamically alter the nucleic acid-binding properties of RNAP by stabilizing the initiation complex and destabilizing elongation complexes.

scholarly journals Archaeal TFEα/β is a hybrid of TFIIE and the RNA polymerase III subcomplex hRPC62/39

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Fabian Blombach ◽  
Enrico Salvadori ◽  
Thomas Fouqueau ◽  
Jun Yan ◽  
Julia Reimann ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Rna Polymerase ◽  
Transcription Initiation ◽  
Rna Polymerase Iii ◽  
Promoter Sequence ◽  
Dna Melting ◽  
Β Subunit ◽  
Primary Sequence ◽  
Eukaryotic Transcription ◽  
Basal Transcription Factors

Transcription initiation of archaeal RNA polymerase (RNAP) and eukaryotic RNAPII is assisted by conserved basal transcription factors. The eukaryotic transcription factor TFIIE consists of α and β subunits. Here we have identified and characterised the function of the TFIIEβ homologue in archaea that on the primary sequence level is related to the RNAPIII subunit hRPC39. Both archaeal TFEβ and hRPC39 harbour a cubane 4Fe-4S cluster, which is crucial for heterodimerization of TFEα/β and its engagement with the RNAP clamp. TFEα/β stabilises the preinitiation complex, enhances DNA melting, and stimulates abortive and productive transcription. These activities are strictly dependent on the β subunit and the promoter sequence. Our results suggest that archaeal TFEα/β is likely to represent the evolutionary ancestor of TFIIE-like factors in extant eukaryotes.

EARLY STEPS IN THE FORMATION OF A TRANSLATION INITIATION COMPLEX ON NEWLY TRANSCRIBED MESSENGER RNA

1973 ◽  
Vol 74 (Suppl) ◽  
pp. S33-S53 ◽  
Author(s):  
Michel Crépin ◽  
Jean-Claude Lelong ◽  
François Gros
Keyword(s):  
Translation Initiation ◽  
Transcription Initiation ◽  
Messenger Rna ◽  
Rna Synthesis ◽  
Initiation Factor ◽  
Initiation Complex ◽  
Initiator Trna ◽  
Transcription System ◽  
Run Off

ABSTRACT The aim of this study is to investigate how formation of a translation initiation complex affects the rate of transcription from a phage DNA template (λ plac or Ø 80 dlac DNA). Addition of "native" 30S ribosomes to a Ø 80 dlac in vitro transcription system (including limiting amounts of purified E. coli RNA polymerase and the requisite substrates) markedly enhances the rate of RNA synthesis. Factor free, 1 M NH4Cl washed 30S or 70S ribosomes show a weak albeit detectable activity, "run off 70S" or washed 50S being inefficient. Single addition of purified initiation factor IF3 greatly magnifies (about 2–3 fold) the stimulation obtained with washed 30S subunits, the effect being catalytic with respect to IF3; IF2 addition causes a weaker and stoichiometrical effect. Maximum stimulation (up to 6 fold) is achieved by the combined addition of washed ribosomes (30S or 70S), IF1, IF2, IF3 plus the highly purified fMet-tRNAfMet species. Under such conditions, very efficient initiator tRNA binding to nascent RNA does occur. Initiation factors show no activity in the absence of ribosomes. Kasugamycin greatly reduces the stimulation of RNA synthesis in the presence of the various translation elements. This system provides a new and very sensitive means to study the various factor dependent ribosome-messenger interactions even in the absence of initiator tRNA, thereby enabling one to analyze early translation initiation steps. Both the frequency of transcription initiation and the rate of RNA chain propagation appear to be enhanced when RNA synthesis and initiation of protein synthesis are coupled.

Sign in / Sign up

Export Citation Format

Share Document