Elongation Factor P: a Role in Posttranscriptional Control of Gene Expression

2012 ◽  
Vol 7 (10) ◽  
pp. 449-454
Author(s):  
William Wiley Navarre ◽  
Michael Ibba
Keyword(s):  
Gene Expression ◽  
Elongation Factor ◽  
Posttranscriptional Control ◽  
Control Of Gene Expression ◽  
Elongation Factor P

scholarly journals Global Analysis of Pub1p Targets Reveals a Coordinate Control of Gene Expression through Modulation of Binding and Stability

2005 ◽  
Vol 25 (13) ◽  
pp. 5499-5513 ◽  
Author(s):  
Radharani Duttagupta ◽  
Bin Tian ◽  
Carol J. Wilusz ◽  
Danny T. Khounh ◽  
Patricia Soteropoulos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Binding ◽  
Global Analysis ◽  
Affinity Purification ◽  
Mrna Turnover ◽  
Sequence Motifs ◽  
Posttranscriptional Control ◽  
Control Of Gene Expression ◽  
Transcript Stability ◽  
Distinct Sequence

ABSTRACT Regulation of mRNA turnover is an important cellular strategy for posttranscriptional control of gene expression, mediated by the interplay of cis-acting sequences and associated trans-acting factors. Pub1p, an ELAV-like yeast RNA-binding protein with homology to T-cell internal antigen 1 (TIA-1)/TIA-1-related protein (TIAR), is an important modulator of the decay of two known classes of mRNA. Our goal in this study was to determine the range of mRNAs whose stability is dependent on Pub1p, as well as to identify specific transcripts that directly bind to this protein. We have examined global mRNA turnover in isogenic PUB1 and pub1Δ strains through gene expression analysis and demonstrate that 573 genes exhibit a significant reduction in half-life in a pub1Δ strain. We also examine the binding specificity of Pub1p using affinity purification followed by microarray analysis to comprehensively distinguish between direct and indirect targets and find that Pub1p significantly binds to 368 cellular transcripts. Among the Pub1p-associated mRNAs, 53 transcripts encoding proteins involved in ribosomal biogenesis and cellular metabolism are selectively destabilized in the pub1Δ strain. In contrast, genes involved in transporter activity demonstrate association with Pub1p but display no measurable changes in transcript stability. Characterization of two candidate genes, SEC53 and RPS16B, demonstrate that both Pub1p-dependent regulation of stability and Pub1p binding require 3′ untranslated regions, which harbor distinct sequence motifs. These results suggest that Pub1p binds to discrete subsets of cellular transcripts and posttranscriptionally regulates their expression at multiple levels.

scholarly journals NusG controls transcription pausing and RNA polymerase translocation throughout theBacillus subtilisgenome

2020 ◽  
Vol 117 (35) ◽  
pp. 21628-21636 ◽  
Author(s):  
Alexander V. Yakhnin ◽  
Peter C. FitzGerald ◽  
Carl McIntosh ◽  
Helen Yakhnin ◽  
Maria Kireeva ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Polymerase ◽  
Transcription Elongation ◽  
Elongation Factor ◽  
Flavin Mononucleotide ◽  
Protein Coding ◽  
Control Of Gene Expression ◽  
Genome Wide

Transcription is punctuated by RNA polymerase (RNAP) pausing. These pauses provide time for diverse regulatory events that can modulate gene expression. Transcription elongation factors dramatically affect RNAP pausing in vitro, but the genome-wide role of such factors on pausing has not been examined. Using native elongating transcript sequencing followed by RNase digestion (RNET-seq), we analyzed RNAP pausing inBacillus subtilisgenome-wide and identified an extensive role of NusG in pausing. This universally conserved transcription elongation factor is known as Spt5 in archaeal and eukaryotic organisms.B. subtilisNusG shifts RNAP to the posttranslocation register and induces pausing at 1,600 sites containing a consensus TTNTTT motif in the nontemplate DNA strand within the paused transcription bubble. The TTNTTT motif is necessary but not sufficient for NusG-dependent pausing. Approximately one-fourth of these pause sites were localized to untranslated regions and could participate in posttranscription initiation control of gene expression as was previously shown fortlrBand thetrpEDCFBAoperon. Most of the remaining pause sites were identified in protein-coding sequences. NusG-dependent pausing was confirmed for all 10 pause sites that we tested in vitro. Putative pause hairpins were identified for 225 of the 342 strongest NusG-dependent pause sites, and some of these hairpins were shown to function in vitro. NusG-dependent pausing in theribDriboswitch provides time for cotranscriptional binding of flavin mononucleotide, which decreases the concentration required for termination upstream of theribDcoding sequence. Our phylogenetic analysis implicates NusG-dependent pausing as a widespread mechanism in bacteria.

scholarly journals Posttranscriptional Control of Gene Expression in Yeast

1998 ◽  
Vol 62 (4) ◽  
pp. 1492-1553 ◽  
Author(s):  
John E. G. McCarthy
Keyword(s):  
Gene Expression ◽  
Mrna Decay ◽  
Molecular Mechanisms ◽  
Genomic Sequence ◽  
Current Knowledge ◽  
Cellular Systems ◽  
Posttranscriptional Control ◽  
Control Of Gene Expression ◽  
Translational Initiation ◽  
Wide Range

SUMMARY Studies of the budding yeast Saccharomyces cerevisiae have greatly advanced our understanding of the posttranscriptional steps of eukaryotic gene expression. Given the wide range of experimental tools applicable to S. cerevisiae and the recent determination of its complete genomic sequence, many of the key challenges of the posttranscriptional control field can be tackled particularly effectively by using this organism. This article reviews the current knowledge of the cellular components and mechanisms related to translation and mRNA decay, with the emphasis on the molecular basis for rate control and gene regulation. Recent progress in characterizing translation factors and their protein-protein and RNA-protein interactions has been rapid. Against the background of a growing body of structural information, the review discusses the thermodynamic and kinetic principles that govern the translation process. As in prokaryotic systems, translational initiation is a key point of control. Modulation of the activities of translational initiation factors imposes global regulation in the cell, while structural features of particular 5′ untranslated regions, such as upstream open reading frames and effector binding sites, allow for gene-specific regulation. Recent data have revealed many new details of the molecular mechanisms involved while providing insight into the functional overlaps and molecular networking that are apparently a key feature of evolving cellular systems. An overall picture of the mechanisms governing mRNA decay has only very recently begun to develop. The latest work has revealed new information about the mRNA decay pathways, the components of the mRNA degradation machinery, and the way in which these might relate to the translation apparatus. Overall, major challenges still to be addressed include the task of relating principles of posttranscriptional control to cellular compartmentalization and polysome structure and the role of molecular channelling in these highly complex expression systems.

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