Enhanced basepair dynamics pre-disposes protein-assisted flips of key bases in DNA strand separation during transcription initiation

2018 ◽  
Vol 20 (14) ◽  
pp. 9449-9459 ◽  
Author(s):  
Neeladri Sekhar Roy ◽  
Subrata Debnath ◽  
Abhijit Chakraborty ◽  
Prasenjit Chakraborty ◽  
Indrani Bera ◽  
...  
Keyword(s):  
Transcription Initiation ◽  
Duplex Dna ◽  
Strand Separation ◽  
Dna Strand ◽  
Dependent Processes ◽  
Transcription And Replication

Localized separation of strands of duplex DNA is a necessary step in many DNA-dependent processes, including transcription and replication.

scholarly journals A DNA-binding protein from Ustilago maydis prefers duplex DNA without chain interruptions.

1983 ◽  
Vol 3 (4) ◽  
pp. 605-612 ◽  
Author(s):  
J R Rusche ◽  
W K Holloman
Keyword(s):  
Drosophila Melanogaster ◽  
Satellite Dna ◽  
Binding Assay ◽  
Ustilago Maydis ◽  
Dna Binding Protein ◽  
Double Strand Breaks ◽  
Duplex Dna ◽  
Plasmid Pbr322 ◽  
Strand Breaks ◽  
Dna Strand

Using a nitrocellulose filter binding assay, we have partially purified a protein from mitotic cells of Ustilago maydis that binds preferentially to covalently closed circular duplex DNA. DNA containing single- or double-strand breaks is bound poorly by the protein. Once formed, the DNA-protein complex is stable, resisting dissociation in high salt. However, when a DNA strand is broken, the complex appears to dissociate. The protein binds equally well to form I DNA of phi X174 or the plasmid pBR322, but has a higher affinity for a hybrid plasmid containing a cloned region of Drosophila melanogaster satellite DNA.

scholarly journals Structure of human RECQ1 helicase: identification of a putative DNA strand-separation pin

2008 ◽  
Vol 64 (a1) ◽  
pp. C306-C306
Author(s):  
A.C.W. Pike ◽  
B. Shrestha ◽  
N. Burgess-Brown ◽  
L. Muzzolini ◽  
A. Vindigni ◽  
...  
Keyword(s):  
Strand Separation ◽  
Dna Strand

Remodeling of the σ70 Subunit Non-template DNA Strand Contacts During the Final Step of Transcription Initiation

2005 ◽  
Vol 350 (5) ◽  
pp. 930-937 ◽  
Author(s):  
Konstantin Brodolin ◽  
Nikolay Zenkin ◽  
Konstantin Severinov
Keyword(s):  
Transcription Initiation ◽  
Dna Strand ◽  
Template Dna

scholarly journals RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes

2016 ◽  
Vol 113 (52) ◽  
pp. 14994-14999 ◽  
Author(s):  
Monali NandyMazumdar ◽  
Yuri Nedialkov ◽  
Dmitri Svetlov ◽  
Anastasia Sevostyanova ◽  
Georgiy A. Belogurov ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Elongation Factor ◽  
Structural Data ◽  
Duplex Dna ◽  
Structural Element ◽  
Transcript Cleavage ◽  
Σ Factor ◽  
Transcription Complexes ◽  
Dna Strand ◽  
Many Core

Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β′ clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.

scholarly journals Functional Analysis of the Genomic and Antigenomic Promoters of Human Respiratory Syncytial Virus

2000 ◽  
Vol 74 (13) ◽  
pp. 6006-6014 ◽  
Author(s):  
Rachel Fearns ◽  
Peter L. Collins ◽  
Mark E. Peeples
Keyword(s):  
Respiratory Syncytial Virus ◽  
Transcription Initiation ◽  
Rna Replication ◽  
Inhibitory Effect ◽  
Direct Transcription ◽  
Fourfold Increase ◽  
Syncytial Virus ◽  
High Degree ◽  
Pairing Potential ◽  
Transcription And Replication

ABSTRACT The promoters involved in transcription and RNA replication by respiratory syncytial virus (RSV) were examined by using a plasmid-based minireplicon system. The 3′ ends of the genome and antigenome, which, respectively, contain the 44-nucleotide (nt) leader (Le) and 155-nt trailer-complement (TrC) regions, should each contain a promoter for RNA replication. The 3′ genome end also should have the promoter for transcription. Substitution for the Le with various lengths of TrC demonstrated that the 3′-terminal 36 nt of TrC are sufficient for extensive (but not maximal) replication and that when juxtaposed with a transcription gene-start (GS) signal, this sequence was also able to direct transcription. It was also shown that the region of Le immediately preceding the GS signal of the first gene could be deleted with either no effect or with a slight decrease in transcription initiation. Thus, the TrC is competent to direct transcription even though it does not do so in nature, and the partial sequence identity it shares with the 3′ end of the genome likely represents the important elements of a conserved promoter active in both replication and transcription. Increasing the length of the introduced TrC sequence incrementally to 147 nt resulted in a fourfold increase in replication and a nearly complete inhibition of transcription. These two effects were unrelated, implying that transcription and replication are not interconvertible processes mediated by a common polymerase, but rather are independent processes. The increase in replication was specific to the TrC sequence, implying the presence of a nonessential, replication-enhancingcis-acting element. In contrast, the inhibitory effect on transcription was due solely to the altered spacing between the 3′ end of the genome and GS signal, which implies that the transcriptase recognizes the first GS signal as a promoter element. Neither the enhancement of replication nor the inhibition of transcription was due to increased base-pairing potential between the 3′ and 5′ ends. The relative strengths of the Le and TrC promoters for directing RNA synthesis were compared and found to be very similar. Thus, these findings highlighted a high degree of functional similarity between the RSV antigenomic and genomic promoters, but provided a further distinction between promoter requirements for transcription and replication.

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