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 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.

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 Growth-Phase-Dependent Expression of the Cyclopeptide Antibiotic Microcin J25

2001 ◽  
Vol 183 (5) ◽  
pp. 1755-1764 ◽  
Author(s):  
Marı́a J. Chiuchiolo ◽  
Mónica A. Delgado ◽  
Ricardo N. Farı́as ◽  
Raúl A. Salomón
Keyword(s):  
Stationary Phase ◽  
Growth Phase ◽  
High Cell Density ◽  
Integration Host Factor ◽  
Early Stationary Phase ◽  
Stationary Phase Culture ◽  
Global Regulators ◽  
Phase Culture ◽  
Microcin J25 ◽  
Growth Induction

ABSTRACT Microcin J25 is a 2,107-Da, plasmid-encoded, cyclopeptide antibiotic produced by Escherichia coli. We have isolatedlacZ fusions to mcjA (encoding the 58-amino-acid microcin precursor) and mcjB andmcjC (which are required for microcin maturation), and the regulation of these fusions was used to identify factors that control the expression of these genes. The mcjA gene was found to be dramatically induced as cells entered the stationary phase. Expression of mcjA could be induced by resuspending uninduced exponential-phase cells in spent supernatant obtained from an early-stationary-phase culture. Induction of mcjAexpression was not dependent on high cell density, pH changes, anaerobiosis, or the buildup of some inducer. A starvation for carbon and inorganic phosphate induced mcjA expression, while under nitrogen limitation there was no induction at all. These results taken together suggest that stationary-phase induction ofmcjA is triggered by nutrient depletion. ThemcjB and mcjC genes were also regulated by the growth phase of the culture, but in contrast to mcjA, they showed substantial expression already during exponential growth. Induction of the microcin genes was demonstrated to be independent of RpoS, the cyclic AMP-Crp complex, OmpR, and H-NS. Instead, we found that the growth-phase-dependent expression of mcjA,mcjB, and mcjC may be explained by the concerted action of the positively acting transition state regulators ppGpp, Lrp, and integration host factor. Measurements of microcin J25 production by strains defective in these global regulators showed a good correlation with the reduced expression of the fusions in such mutant backgrounds.

scholarly journals The Role of Extracellular Vesicles as Shuttles of RNA and Their Clinical Significance as Biomarkers in Hepatocellular Carcinoma

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 902
Author(s):  
Eva Costanzi ◽  
Carolina Simioni ◽  
Gabriele Varano ◽  
Cinzia Brenna ◽  
Ilaria Conti ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Extracellular Vesicles ◽  
Tumor Metastasis ◽  
Biological Processes ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Non Coding Rna ◽  
Donor Cells ◽  
Relevant Role

Extracellular vesicles (EVs) have attracted interest as mediators of intercellular communication following the discovery that EVs contain RNA molecules, including non-coding RNA (ncRNA). Growing evidence for the enrichment of peculiar RNA species in specific EV subtypes has been demonstrated. ncRNAs, transferred from donor cells to recipient cells, confer to EVs the feature to regulate the expression of genes involved in differentiation, proliferation, apoptosis, and other biological processes. These multiple actions require accuracy in the isolation of RNA content from EVs and the methodologies used play a relevant role. In liver, EVs play a crucial role in regulating cell–cell communications and several pathophysiological events in the heterogeneous liver class of cells via horizontal transfer of their cargo. This review aims to discuss the rising role of EVs and their ncRNAs content in regulating specific aspects of hepatocellular carcinoma development, including tumorigenesis, angiogenesis, and tumor metastasis. We analyze the progress in EV-ncRNAs’ potential clinical applications as important diagnostic and prognostic biomarkers for liver conditions.

scholarly journals Identification of the conserved long non-coding RNAs in myogenesis

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Anupam Bhattacharya ◽  
Simang Champramary ◽  
Tanya Tripathi ◽  
Debajit Thakur ◽  
Ilya Ioshikhes ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Muscle Development ◽  
Three Dimensional ◽  
C2c12 Cells ◽  
Mouse Muscle ◽  
Rna Molecules ◽  
Expression Of Genes ◽  
Novel Approach ◽  
Non Coding Rna ◽  
Topologically Associated Domains

Abstract Background Our understanding of genome regulation is ever-evolving with the continuous discovery of new modes of gene regulation, and transcriptomic studies of mammalian genomes have revealed the presence of a considerable population of non-coding RNA molecules among the transcripts expressed. One such non-coding RNA molecule is long non-coding RNA (lncRNA). However, the function of lncRNAs in gene regulation is not well understood; moreover, finding conserved lncRNA across species is a challenging task. Therefore, we propose a novel approach to identify conserved lncRNAs and functionally annotate these molecules. Results In this study, we exploited existing myogenic transcriptome data and identified conserved lncRNAs in mice and humans. We identified the lncRNAs expressing differentially between the early and later stages of muscle development. Differential expression of these lncRNAs was confirmed experimentally in cultured mouse muscle C2C12 cells. We utilized the three-dimensional architecture of the genome and identified topologically associated domains for these lncRNAs. Additionally, we correlated the expression of genes in domains for functional annotation of these trans-lncRNAs in myogenesis. Using this approach, we identified conserved lncRNAs in myogenesis and functionally annotated them. Conclusions With this novel approach, we identified the conserved lncRNAs in myogenesis in humans and mice and functionally annotated them. The method identified a large number of lncRNAs are involved in myogenesis. Further studies are required to investigate the reason for the conservation of the lncRNAs in human and mouse while their sequences are dissimilar. Our approach can be used to identify novel lncRNAs conserved in different species and functionally annotated them.

Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA

Microbiology ◽  
2011 ◽  
Vol 157 (9) ◽  
pp. 2504-2514 ◽  
Author(s):  
Mário H. Queiroz ◽  
Cristina Madrid ◽  
Sònia Paytubi ◽  
Carlos Balsalobre ◽  
Antonio Juárez
Keyword(s):  
Stationary Phase ◽  
Salmonella Enterica ◽  
Growth Conditions ◽  
Integration Host Factor ◽  
Band Shift ◽  
Global Regulators ◽  
Serovar Typhimurium ◽  
Associated Proteins ◽  
Transcription Data

Coordination of the expression of Salmonella enterica invasion genes on Salmonella pathogenicity island 1 (SPI1) depends on a complex circuit involving several regulators that converge on expression of the hilA gene, which encodes a transcriptional activator (HilA) that modulates expression of the SPI1 virulence genes. Two of the global regulators that influence hilA expression are the nucleoid-associated proteins Hha and H-NS. They interact and form a complex that modulates gene expression. A chromosomal transcriptional fusion was constructed to assess the effects of these modulators on hilA transcription under several environmental conditions as well as at different stages of growth. The results obtained showed that these proteins play a role in silencing hilA expression at both low temperature and low osmolarity, irrespective of the growth phase. H-NS accounts for the main repressor activity. At high temperature and osmolarity, H-NS-mediated silencing completely ceases when cells enter the stationary phase, and hilA expression is induced. Mutants lacking IHF did not induce hilA in cells entering the stationary phase, and this lack of induction was dependent on the presence of H-NS. Band-shift assays and in vitro transcription data showed that for hilA induction under certain growth conditions, IHF is required to alleviate H-NS-mediated silencing.

scholarly journals Short communication: Colostrum versus formula: Effects on mRNA expression of genes related to branched-chain amino acid metabolism in neonatal dairy calves

2020 ◽  
Vol 103 (10) ◽  
pp. 9656-9666 ◽  
Author(s):  
Morteza H. Ghaffari ◽  
Hassan Sadri ◽  
Harald M. Hammon ◽  
Julia Steinhoff-Wagner ◽  
Nico Henschel ◽  
...  
Keyword(s):  
Amino Acid ◽  
Mrna Expression ◽  
Amino Acid Metabolism ◽  
Short Communication ◽  
Acid Metabolism ◽  
Dairy Calves ◽  
Branched Chain Amino Acid ◽  
Expression Of Genes ◽  
Branched Chain

scholarly journals Spread and survival of promiscuous IncP-1 plasmids.

2003 ◽  
Vol 50 (2) ◽  
pp. 425-453 ◽  
Author(s):  
Małgorzata Adamczyk ◽  
Grazyna Jagura-Burdzy
Keyword(s):  
Unique Feature ◽  
Central Control ◽  
Conjugative Transfer ◽  
Incompatibility Group ◽  
Global Regulators ◽  
Current State ◽  
Expression Of Genes ◽  
Low Copy Number ◽  
Coordinated Expression ◽  
Stable Maintenance

Plasmids classified to the IncP-1 incompatibility group belong to the most stably maintained mobile elements among low copy number plasmids known to date. The remarkable persistence is achieved by various tightly controlled stability mechanisms like active partitioning, efficient conjugative transfer system, killing of plasmid-free segregants and multimer resolution. The unique feature of IncP-1 plasmids is the central control operon coding for global regulators which control the expression of genes involved in vegetative replication, stable maintenance and conjugative transfer. The multivalent regulatory network provides means for coordinated expression of all plasmid functions. The current state of knowledge about two fully sequenced plasmids RK2 and R751, representatives of the IncP-1alpha and IncP-1beta subgroups, is presented.

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