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.

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 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

Hormone-induced meiotic maturation in Xenopus oocytes occurs independently of p70s6k activation and is associated with enhanced initiation factor (eIF)-4F phosphorylation and complex formation

1995 ◽  
Vol 108 (4) ◽  
pp. 1751-1760 ◽  
Author(s):  
S.J. Morley ◽  
V.M. Pain
Keyword(s):  
Complex Formation ◽  
Mammalian Cells ◽  
De Novo ◽  
Ribosomal Subunit ◽  
Early Time ◽  
Initiation Factor ◽  
Meiotic Maturation ◽  
Initiation Factors ◽  
Ribosomal Protein S6 ◽  
Time Critical

Hormone-induced meiotic maturation of the Xenopus oocyte is regulated by complex changes in protein phosphorylation. It is accompanied by a stimulation in the rate of translation, manifest at the level of polypeptide chain initiation. At laser times in the maturation process, this reflects an increased ability for mRNA to interact with the 40 S ribosomal subunit. In mammalian cells there is growing evidence for the regulation of translation by phosphorylation of ribosomal protein S6 and of initiation factors responsible for the binding of mRNA to ribosomes. In this report, we show that although the 70 kDa form of S6 kinase is activated within 1.5 hours in response to progesterone or insulin, a time critical for protein synthesis, its activation is not required for hormone-induced stimulation of translation rates or maturation. In response to progesterone, activation of translation occurs in parallel with enhanced phosphate labelling of eIF-4 alpha and eIF-4 gamma and eIF-4F complex formation, events which are thought to facilitate the interaction of eIF-4F with the mRNA cap structure. However, with insulin, activation of translation occurs prior to detectable de novo phosphorylation of eIF-4F, although a small enhancement of turnover of phosphate on eIF-4 alpha may occur at this early time. With either hormone, enhanced phosphate labelling of eIF-4 alpha is shown to reflect activation of eIF-4 alpha kinase(s), which coincides temporally with activation of p42 MAP and p90rsk kinases. The possible role of initiation factor modification on increased translation rates during meiotic maturation is discussed.

Transcription initiation factor TBP: old friend new questions

2019 ◽  
Vol 47 (1) ◽  
pp. 411-423 ◽  
Author(s):  
Kevin Kramm ◽  
Christoph Engel ◽  
Dina Grohmann
Keyword(s):  
Transcription Initiation ◽  
Initiation Factor ◽  
Regulation Of Transcription ◽  
Eukaryotic Transcription ◽  
Initiation Factors ◽  
Transcription System ◽  
Σ Factor ◽  
Domains Of Life ◽  
Archaeal Transcription ◽  
Rnap Ii

Abstract In all domains of life, the regulation of transcription by DNA-dependent RNA polymerases (RNAPs) is achieved at the level of initiation to a large extent. Whereas bacterial promoters are recognized by a σ-factor bound to the RNAP, a complex set of transcription factors that recognize specific promoter elements is employed by archaeal and eukaryotic RNAPs. These initiation factors are of particular interest since the regulation of transcription critically relies on initiation rates and thus formation of pre-initiation complexes. The most conserved initiation factor is the TATA-binding protein (TBP), which is of crucial importance for all archaeal-eukaryotic transcription initiation complexes and the only factor required to achieve full rates of initiation in all three eukaryotic and the archaeal transcription systems. Recent structural, biochemical and genome-wide mapping data that focused on the archaeal and specialized RNAP I and III transcription system showed that the involvement and functional importance of TBP is divergent from the canonical role TBP plays in RNAP II transcription. Here, we review the role of TBP in the different transcription systems including a TBP-centric discussion of archaeal and eukaryotic initiation complexes. We furthermore highlight questions concerning the function of TBP that arise from these findings.

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.

PrimPol (Primase/Polymerase), replicating enzyme – A mini review

2020 ◽  
Vol 2 (4) ◽  
pp. 89-92
Author(s):  
Muhammad Amir ◽  
Sabeera Afzal ◽  
Alia Ishaq
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Genetic Information ◽  
Nuclear Dna ◽  
De Novo ◽  
Dna Polymerases ◽  
Test Site ◽  
Mitochondrial Dna Replication ◽  
Dna Template ◽  
Preliminary Phase

Polymerases were revealed first in 1970s. Most important to the modest perception the enzyme responsible for nuclear DNA replication that was pol , for DNA repair pol and for mitochondrial DNA replication pol  DNA construction and renovation done by DNA polymerases, so directing both the constancy and discrepancy of genetic information. Replication of genome initiate with DNA template-dependent fusion of small primers of RNA. This preliminary phase in replication of DNA demarcated as de novo primer synthesis which is catalyzed by specified polymerases known as primases. Sixteen diverse DNA-synthesizing enzymes about human perspective are devoted to replication, reparation, mutilation lenience, and inconsistency of nuclear DNA. But in dissimilarity, merely one DNA polymerase has been called in mitochondria. It has been suggest that PrimPol is extremely acting the roles by re-priming DNA replication in mitochondria to permit an effective and appropriate way replication to be accomplished. Investigations from a numeral of test site have significantly amplified our appreciative of the role, recruitment and regulation of the enzyme during DNA replication. Though, we are simply just start to increase in value the versatile roles that play PrimPol in eukaryote.

scholarly journals AAV-Mediated CRISPRi and RNAi Based Gene Silencing in Mouse Hippocampal Neurons

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 324
Author(s):  
Matthias Deutsch ◽  
Anne Günther ◽  
Rodrigo Lerchundi ◽  
Christine R. Rose ◽  
Sabine Balfanz ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Initiation ◽  
Hippocampal Neurons ◽  
De Novo ◽  
Protein Biosynthesis ◽  
Physiological Role ◽  
High Specificity ◽  
Hcn Channels ◽  
Proliferating Cells ◽  
Neuronal Tissues

Uncovering the physiological role of individual proteins that are part of the intricate process of cellular signaling is often a complex and challenging task. A straightforward strategy of studying a protein’s function is by manipulating the expression rate of its gene. In recent years, the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9-based technology was established as a powerful gene-editing tool for generating sequence specific changes in proliferating cells. However, obtaining homogeneous populations of transgenic post-mitotic neurons by CRISPR/Cas9 turned out to be challenging. These constraints can be partially overcome by CRISPR interference (CRISPRi), which mediates the inhibition of gene expression by competing with the transcription machinery for promoter binding and, thus, transcription initiation. Notably, CRISPR/Cas is only one of several described approaches for the manipulation of gene expression. Here, we targeted neurons with recombinant Adeno-associated viruses to induce either CRISPRi or RNA interference (RNAi), a well-established method for impairing de novo protein biosynthesis by using cellular regulatory mechanisms that induce the degradation of pre-existing mRNA. We specifically targeted hyperpolarization-activated and cyclic nucleotide-gated (HCN) channels, which are widely expressed in neuronal tissues and play essential physiological roles in maintaining biophysical characteristics in neurons. Both of the strategies reduced the expression levels of three HCN isoforms (HCN1, 2, and 4) with high specificity. Furthermore, detailed analysis revealed that the knock-down of just a single HCN isoform (HCN4) in hippocampal neurons did not affect basic electrical parameters of transduced neurons, whereas substantial changes emerged in HCN-current specific properties.

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