scholarly journals 6S RNA Regulation of Transcription

2009 ◽  
Vol 23 (S1) ◽  
Author(s):  
Karen M Wassarman ◽  
Andrew D Klocko ◽  
Amy Cavanagh
Keyword(s):  
Regulation Of Transcription ◽  
Rna Regulation ◽  
6S Rna

scholarly journals 6S RNA regulation of relA alters ppGpp levels in early stationary phase

Microbiology ◽  
2010 ◽  
Vol 156 (12) ◽  
pp. 3791-3800 ◽  
Author(s):  
Amy T. Cavanagh ◽  
Pete Chandrangsu ◽  
Karen M. Wassarman
Keyword(s):  
Amino Acid ◽  
Stationary Phase ◽  
Regulation Of Transcription ◽  
Early Stationary Phase ◽  
Rna Regulation ◽  
Global Regulators ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
6S Rna ◽  
Altered Regulation

6S RNA is a small, non-coding RNA that interacts directly with σ 70-RNA polymerase and regulates transcription at many σ 70-dependent promoters. Here, we demonstrate that 6S RNA regulates transcription of relA, which encodes a ppGpp synthase. The 6S RNA-dependent regulation of relA expression results in increased ppGpp levels during early stationary phase in cells lacking 6S RNA. These changes in ppGpp levels, although modest, are sufficient to result in altered regulation of transcription from σ 70-dependent promoters sensitive to ppGpp, including those promoting expression of genes involved in amino acid biosynthesis and rRNA. These data place 6S RNA as another player in maintaining appropriate gene expression as cells transition into stationary phase. Independent of this ppGpp-mediated 6S RNA-dependent regulation, we also demonstrate that in later stationary phase, 6S RNA continues to downregulate transcription in general, and specifically at a subset of the amino acid promoters, but through a mechanism that is independent of ppGpp and which we hypothesize is through direct regulation. In addition, 6S RNA-dependent regulation of σ S activity is not mediated through observed changes in ppGpp levels. We suggest a role for 6S RNA in modulating transcription of several global regulators directly, including relA, to downregulate expression of key pathways in response to changing environmental conditions.

scholarly journals 6S RNA Regulation of pspF Transcription Leads to Altered Cell Survival at High pH

2006 ◽  
Vol 188 (11) ◽  
pp. 3936-3943 ◽  
Author(s):  
Amy E. Trotochaud ◽  
Karen M. Wassarman
Keyword(s):  
Direct Interaction ◽  
Independent Manner ◽  
Rna Regulation ◽  
Altered Expression ◽  
High Ph ◽  
6S Rna ◽  
Altered Cell ◽  
Similar Growth ◽  
Better Than

ABSTRACT 6S RNA is a highly abundant small RNA that regulates transcription through direct interaction with RNA polymerase. Here we show that 6S RNA directly inhibits transcription of pspF, which subsequently leads to inhibition of pspABCDE and pspG expression. Cells without 6S RNA are able to survive at elevated pH better than wild-type cells due to loss of 6S RNA-regulation of pspF. This 6S RNA-dependent phenotype is eliminated in pspF-null cells, indicating that 6S RNA effects are conferred through PspF. Similar growth phenotypes are seen when PspF levels are increased in a 6S RNA-independent manner, signifying that changes to pspF expression are sufficient. Changes in survival at elevated pH most likely result from altered expression of pspABCDE and/or pspG, both of which require PspF for transcription and are indirectly regulated by 6S RNA. 6S RNA provides another layer of regulation in response to high pH during stationary phase. We propose that the normal role of 6S RNA at elevated pH is to limit the extent of the psp response under conditions of nutrient deprivation, perhaps facilitating appropriate allocation of diminishing resources.

scholarly journals Regulation of transcription from two ssrS promoters in 6S RNA biogenesis

2013 ◽  
Vol 36 (3) ◽  
pp. 227-234 ◽  
Author(s):  
Ji Young Lee ◽  
Hongmarn Park ◽  
Geunu Bak ◽  
Kwang-sun Kim ◽  
Younghoon Lee
Keyword(s):  
Regulation Of Transcription ◽  
6S Rna ◽  
Rna Biogenesis

scholarly journals 6S RNA Function Enhances Long-Term Cell Survival

2004 ◽  
Vol 186 (15) ◽  
pp. 4978-4985 ◽  
Author(s):  
Amy E. Trotochaud ◽  
Karen M. Wassarman
Keyword(s):  
Stationary Phase ◽  
Molecular Mechanisms ◽  
Physiological Role ◽  
Rna Regulation ◽  
Competitive Fitness ◽  
Growth Defects ◽  
6S Rna ◽  
Rna Inhibition

ABSTRACT 6S RNA was identified in Escherichia coli >30 years ago, but the physiological role of this RNA has remained elusive. Here, we demonstrate that 6S RNA-deficient cells are at a disadvantage for survival in stationary phase, a time when 6S RNA regulates transcription. Growth defects were most apparent as a decrease in the competitive fitness of cells lacking 6S RNA. To decipher the molecular mechanisms underlying the growth defects, we have expanded studies of 6S RNA effects on transcription. 6S RNA inhibition of σ70-dependent transcription was not ubiquitous, in spite of the fact that the vast majority of σ70-RNA polymerase is bound by 6S RNA during stationary phase. The σ70-dependent promoters inhibited by 6S RNA contain an extended −10 promoter element, suggesting that this feature may define a class of 6S RNA-regulated genes. We also discovered a secondary effect of 6S RNA in the activation of σS-dependent transcription at several promoters. We conclude that 6S RNA regulation of both σ70 and σS activities contributes to increased cell persistence during nutrient deprivation.

A highly conserved 6S RNA structure is required for regulation of transcription

2005 ◽  
Vol 12 (4) ◽  
pp. 313-319 ◽  
Author(s):  
Amy E Trotochaud ◽  
Karen M Wassarman
Keyword(s):  
Rna Structure ◽  
Regulation Of Transcription ◽  
6S Rna

High resolution mapping of nucleic acid containing complexes in vitro and in situ

1996 ◽  
Vol 54 ◽  
pp. 48-49
Author(s):  
D. P. Bazett-Jones ◽  
M. J. Hendzel
Keyword(s):  
Nucleic Acid ◽  
High Resolution ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Heavy Atom ◽  
Regulation Of Transcription ◽  
High Exposure ◽  
Resolution Mapping ◽  
Tata Sequence

Structural analysis of combinations of nucleosomes and transcription factors on promoter and enhancer elements is necessary in order to understand the molecular mechanisms responsible for the regulation of transcription initiation. Such complexes are often not amenable to study by high resolution crystallographic techniques. We have been applying electron spectroscopic imaging (ESI) to specific problems in molecular biology related to transcription regulation. There are several advantages that this technique offers in studies of nucleoprotein complexes. First, an intermediate level of spatial resolution can be achieved because heavy atom contrast agents are not necessary. Second, mass and stoichiometric relationships of protein and nucleic acid can be estimated by phosphorus detection, an element in much higher proportions in nucleic acid than protein. Third, wrapping or bending of the DNA by the protein constituents can be observed by phosphorus mapping of the complexes. Even when ESI is used with high exposure of electrons to the specimen, important macromolecular information may be provided. For example, an image of the TATA binding protein (TBP) bound to DNA is shown in the Figure (top panel). It can be seen that the protein distorts the DNA away from itself and much of its mass sits off the DNA helix axis. Moreover, phosphorus and mass estimates demonstrate whether one or two TBP molecules interact with this particular promoter TATA sequence.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

Protein expression changes in cells inoculated with Equine Influenza Virus: antibody microarray analysis

2013 ◽  
Vol 16 (4) ◽  
pp. 663-669
Author(s):  
W. Rozek ◽  
M. Kwasnik ◽  
J.F. Zmudzinski
Keyword(s):  
Influenza Virus ◽  
Protein Quality ◽  
Biological Properties ◽  
Regulation Of Transcription ◽  
Equine Influenza Virus ◽  
Virus Antibody ◽  
Antibody Microarray ◽  
Equine Influenza ◽  
Microarray Technique ◽  
In Cells

AbstractChanges in the level of cellular proteins in cells inoculated with equine influenza virus H7N7 and H3N8 were studied with microarray technique. H3N8 induced pro-apoptotic proteins while H7N7 induced both pro- as well as anti-apoptotic factors. The higher level of some cytoskeleton components and proteins involved in the protein quality control was recorded. Relatively high number of proteins involved in the regulation of transcription was down-regulated. The pattern of changes observed for H7N7 and H3N8 may reflect differences in the biological properties of both serotypes.

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