scholarly journals Identification of a σB-Dependent Small Noncoding RNA in Listeria monocytogenes

2008 ◽  
Vol 190 (18) ◽  
pp. 6264-6270 ◽  
Author(s):  
Jesper Sejrup Nielsen ◽  
Anders Steno Olsen ◽  
Mette Bonde ◽  
Poul Valentin-Hansen ◽  
Birgitte H. Kallipolitis
Keyword(s):  
Listeria Monocytogenes ◽  
Stress Tolerance ◽  
Sigma Factor ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Alternative Sigma Factor ◽  
Dependent Manner ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas ◽  
Regulatory Circuits

ABSTRACT In Listeria monocytogenes, the alternative sigma factor σB plays important roles in stress tolerance and virulence. Here, we present the identification of SbrA, a novel small noncoding RNA that is produced in a σB-dependent manner. This finding adds the σB regulon to the growing list of stress-induced regulatory circuits that include small noncoding RNAs.

scholarly journals Of rodents and ruminants: a comparison of small noncoding RNA requirements in mouse and bovine reproduction

2021 ◽  
Vol 99 (3) ◽  
Author(s):  
Lauren G Chukrallah ◽  
Aditi Badrinath ◽  
Kelly Seltzer ◽  
Elizabeth M Snyder
Keyword(s):  
Germ Cell ◽  
Germ Cells ◽  
Noncoding Rna ◽  
Reproductive Potential ◽  
Noncoding Rnas ◽  
Model Organism ◽  
Cell Physiology ◽  
Male Germ Cells ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas

Abstract Ruminants are major producers of meat and milk, thus managing their reproductive potential is a key element in cost-effective, safe, and efficient food production. Of particular concern, defects in male germ cells and female germ cells may lead to significantly reduced live births relative to fertilization. However, the underlying molecular drivers of these defects are unclear. Small noncoding RNAs, such as piRNAs and miRNAs, are known to be important regulators of germ-cell physiology in mouse (the best-studied mammalian model organism) and emerging evidence suggests that this is also the case in a range of ruminant species, in particular bovine. Similarities exist between mouse and bovids, especially in the case of meiotic and postmeiotic male germ cells. However, fundamental differences in small RNA abundance and metabolism between these species have been observed in the female germ cell, differences that likely have profound impacts on their physiology. Further, parentally derived small noncoding RNAs are known to influence early embryos and significant species-specific differences in germ-cell born small noncoding RNAs have been observed. These findings demonstrate the mouse to be an imperfect model for understanding germ-cell small noncoding RNA biology in ruminants and highlight the need to increase research efforts in this underappreciated aspect of animal reproduction.

scholarly journals DANSR: A Tool for the Detection of Annotated and Novel Small RNAs

2022 ◽  
Vol 8 (1) ◽  
pp. 9
Author(s):  
Jin Zhang ◽  
Abdallah M. Eteleeb ◽  
Emily B. Rozycki ◽  
Matthew J. Inkman ◽  
Amy Ly ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Small Rna ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Biologically Relevant ◽  
Small Noncoding Rna ◽  
Small Noncoding Rnas ◽  
Rna Analysis ◽  
Length Range

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36–200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.

scholarly journals MicroRNA-Mediated Regulation in Biological Systems with Oscillatory Behavior

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Zhiyong Zhang ◽  
Fengdan Xu ◽  
Zengrong Liu ◽  
Ruiqi Wang ◽  
Tieqiao Wen
Keyword(s):  
Cell Cycle ◽  
Biological Systems ◽  
Noncoding Rnas ◽  
Oscillatory Behavior ◽  
Fine Tuning ◽  
Base Pairing ◽  
Periodic Behavior ◽  
Small Noncoding Rnas ◽  
Regulatory Circuits ◽  
Mrna Transcripts

As a class of small noncoding RNAs, microRNAs (miRNAs) regulate stability or translation of mRNA transcripts. Some reports bring new insights into possible roles of microRNAs in modulating cell cycle. In this paper, we focus on the mechanism and effectiveness of microRNA-mediated regulation in the cell cycle. We first describe two specific regulatory circuits that incorporate base-pairing microRNAs and show their fine-tuning roles in the modulation of periodic behavior. Furthermore, we analyze the effects ofmiR369-3on the modulation of the cell cycle, confirming thatmiR369-3plays a role in shortening the period of the cell cycle. These results are consistent with experimental observations.

scholarly journals Alternative Sigma Factor SigK Has a Role in Stress Tolerance of Group I Clostridium botulinum Strain ATCC 3502

2013 ◽  
Vol 79 (12) ◽  
pp. 3867-3869 ◽  
Author(s):  
Elias Dahlsten ◽  
David Kirk ◽  
Miia Lindström ◽  
Hannu Korkeala
Keyword(s):  
Stress Tolerance ◽  
Sigma Factor ◽  
Clostridium Botulinum ◽  
Alternative Sigma Factor ◽  
Strain Atcc ◽  
Content Type ◽  
Osmotic Stress Tolerance ◽  
Group I ◽  
Temperature Downshift

ABSTRACTThe role of the alternative sigma factor SigK in cold and osmotic stress tolerance ofClostridium botulinumATCC 3502 was demonstrated by induction ofsigKafter temperature downshift and exposure to hyperosmotic conditions and by impaired growth of thesigKmutants under the respective conditions.

scholarly journals Sigma B Contributes to PrfA-Mediated Virulence in Listeria monocytogenes

2002 ◽  
Vol 70 (7) ◽  
pp. 3948-3952 ◽  
Author(s):  
Celine A. Nadon ◽  
Barbara M. Bowen ◽  
Martin Wiedmann ◽  
Kathryn J. Boor
Keyword(s):  
Listeria Monocytogenes ◽  
Sigma Factor ◽  
Deletion Mutation ◽  
Alternative Sigma Factor ◽  
Regulatory Factor ◽  
Virulence Phenotype ◽  
Sigma B

ABSTRACT Transcription of the Listeria monocytogenes positive regulatory factor A protein (PrfA) is initiated from either of two promoters immediately upstream of prfA (prfAp 1 and prfAp 2) or from the upstream plcA promoter. We demonstrate that prfAp 2 is a functional σB-dependent promoter and that a sigB deletion mutation affects the virulence phenotype of L. monocytogenes. Thus, the alternative sigma factor σB contributes to virulence in L. monocytogenes.

scholarly journals Identification and Gene Disruption of Small Noncoding RNAs in Streptomyces griseus

2009 ◽  
Vol 191 (15) ◽  
pp. 4896-4904 ◽  
Author(s):  
Takeaki Tezuka ◽  
Hirofumi Hara ◽  
Yasuo Ohnishi ◽  
Sueharu Horinouchi
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Noncoding Rnas ◽  
Streptomyces Griseus ◽  
Streptomyces Avermitilis ◽  
Dependent Manner ◽  
Wild Type ◽  
Srna Candidate ◽  
Small Noncoding Rnas ◽  
Nuclease Mapping

ABSTRACT Small noncoding RNAs (sRNAs) have been shown to control diverse cellular processes in prokaryotes. To identify and characterize novel bacterial sRNAs, a gram-positive, soil-inhabiting, filamentous bacterium, Streptomyces griseus, was examined, on the assumption that Streptomyces should express sRNAs as important regulators of morphological and physiological differentiation. By bioinformatics investigation, 54 sRNA candidates, which were encoded on intergenic regions of the S. griseus chromosome and were highly conserved in those of both Streptomyces coelicolor A3(2) and Streptomyces avermitilis, were selected. Of these 54 sRNA candidates, 17 transcripts were detected by Northern blot analysis of the total RNAs isolated from cells grown on solid medium. Then, the direction of transcription of each sRNA candidate gene was determined by S1 nuclease mapping, followed by exclusion of four sRNA candidates that were considered riboswitches of their downstream open reading frames (ORFs). Finally, a further sRNA candidate was excluded because it was cotranscribed with the upstream ORF determined by reverse transcription-PCR. Thus, 12 sRNAs ranging in size from 40 to 300 nucleotides were identified in S. griseus. Seven of them were apparently transcribed in a growth phase-dependent manner. Furthermore, of the 12 sRNAs, the expression profiles of 7 were significantly influenced by a mutation of adpA, which encodes the central transcriptional regulator of the A-factor regulatory cascade involved in both morphological differentiation and secondary metabolism in S. griseus. However, disruption of all 12 sRNA genes showed no detectable phenotypic changes; all the disruptants grew and formed aerial mycelium and spores with the same time course as the wild-type strain on various media and produced streptomycin similarly to the wild-type strain.

scholarly journals Home Alone: Elimination of All but One Alternative Sigma Factor in Listeria monocytogenes Allows Prediction of New Roles for σB

2017 ◽  
Vol 8 ◽  
Author(s):  
Yichang Liu ◽  
Renato H. Orsi ◽  
Kathryn J. Boor ◽  
Martin Wiedmann ◽  
Veronica Guariglia-Oropeza
Keyword(s):  
Listeria Monocytogenes ◽  
Sigma Factor ◽  
Alternative Sigma Factor

scholarly journals Listeria monocytogenes σHContributes to Expression of Competence Genes and Intracellular Growth

2016 ◽  
Vol 198 (8) ◽  
pp. 1207-1217 ◽  
Author(s):  
Veronica Medrano Romero ◽  
Kazuya Morikawa
Keyword(s):  
Transcription Factor ◽  
Listeria Monocytogenes ◽  
Sigma Factor ◽  
Physiological Role ◽  
Population Level ◽  
Alternative Sigma Factor ◽  
Intracellular Growth ◽  
Content Type ◽  
Gram Positive Bacteria ◽  
Regulation Scheme

ABSTRACTThe alternative sigma factor σHhas two functions in Gram-positive bacteria: it regulates sporulation and the development of genetic competence.Listeria monocytogenesis a nonsporulating species in which competence has not yet been detected. Nevertheless, the main competence regulators and a series of orthologous genes that form the competence machinery are present in its genome; some of the competence genes play a role in optimal phagosomal escape. In this study, strains overexpressing σHand strains with a σHdeletion were used to elucidate the contribution of σHto the expression of the competence machinery genes inL. monocytogenes. Gene expression analysis showed that σHis, indeed, involved incomGandcomEregulation. Unexpectedly, we observed a unique regulation scheme in which σHand the transcription factor ComK were involved. Population-level analysis showed that even with the overexpression of both factors, only a fraction of the cells expressed the competence machinery genes. Although we could not detect competence, σHwas crucial for phagosomal escape, which implies that this alternative sigma factor has specifically evolved to regulate theL. monocytogenesintracellular life cycle.IMPORTANCEListeria monocytogenescan be an intracellular pathogen capable of causing serious infections in humans and animal species. Recently, the competence machinery genes were described as being necessary for optimal phagosomal escape, in which the transcription factor ComK plays an important role. On the other hand, our previous phylogenetic analysis suggested that the alternative sigma factor σHmight play a role in the regulation of competence genes. The present study shows that some of the competence genes belong to the σHregulon and, importantly, that σHis essential for intracellular growth, implying a unique physiological role of σHamongFirmicutes.

scholarly journals piRNAs Coordinate poly(UG) Tailing to Prevent Aberrant and Permanent Gene Silencing

2021 ◽  
Author(s):  
Aditi Shukla ◽  
Roberto Perales ◽  
Scott Kennedy
Keyword(s):  
Gene Silencing ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
Epigenetic Inheritance ◽  
The Self ◽  
Specific Class ◽  
Transgenerational Epigenetic Inheritance ◽  
Small Noncoding Rna ◽  
C Elegans ◽  
Inheritance System

AbstractNoncoding RNAs have emerged as mediators of transgenerational epigenetic inheritance (TEI) in a number of organisms. A robust example of RNA-directed TEI is the inheritance of gene silencing states following RNA interference (RNAi) in the metazoan C. elegans. During RNAi inheritance, gene silencing is transmitted by a self-perpetuating cascade of siRNA-directed poly(UG) tailing of mRNA fragments (pUGylation), followed by siRNA synthesis from poly(UG)-tailed mRNA templates (termed pUG RNA/siRNA cycling). Despite the self-perpetuating nature of pUG RNA/siRNA cycling, RNAi inheritance is finite, suggesting that systems likely exist to prevent permanent RNAi-triggered gene silencing. Here we show that, in the absence of Piwi-interacting RNAs (piRNAs), an animal-specific class of small noncoding RNA, RNAi-based gene silencing can become essentially permanent, lasting at near 100% penetrance for more than five years and hundreds of generations. This permanent gene silencing is mediated by perpetual activation of the pUG RNA/siRNA TEI pathway. Further, we find that piRNAs coordinate endogenous RNAi pathways to prevent germline-expressed genes, which are not normally subjected to TEI, from entering a state of permanent and irreversible epigenetic silencing also mediated by perpetual activation of pUG RNA/siRNA cycling. Together, our results show that one function of C. elegans piRNAs is to insulate germline-expressed genes from aberrant and runaway inactivation by the pUG RNA/siRNA epigenetic inheritance system.

Long and small noncoding RNAs during oocyte-to-embryo transition in mammals

2017 ◽  
Vol 45 (5) ◽  
pp. 1117-1124 ◽  
Author(s):  
Petr Svoboda
Keyword(s):  
Noncoding Rna ◽  
Transcriptional Control ◽  
Noncoding Rnas ◽  
Rna Degradation ◽  
Early Embryo ◽  
Protein Coding ◽  
Small Noncoding Rnas ◽  
Major Genome ◽  
Silencing Pathways ◽  
And Function

Oocyte-to-embryo transition is a process during which an oocyte ovulates, is fertilized, and becomes a developing embryo. It involves the first major genome reprogramming event in life of an organism where gene expression, which gave rise to a differentiated oocyte, is remodeled in order to establish totipotency in blastomeres of an early embryo. This remodeling involves replacement of maternal RNAs with zygotic RNAs through maternal RNA degradation and zygotic genome activation. This review is focused on expression and function of long noncoding RNAs (lncRNAs) and small RNAs during oocyte-to-embryo transition in mammals. LncRNAs are an assorted rapidly evolving collection of RNAs, which have no apparent protein-coding capacity. Their biogenesis is similar to mRNAs including transcriptional control and post-transcriptional processing. Diverse molecular and biological roles were assigned to lncRNAs although most of them probably did not acquire a detectable biological role. Since some lncRNAs serve as precursors for small noncoding regulatory RNAs in RNA silencing pathways, both types of noncoding RNA are reviewed together.

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