Posttranscriptional regulation of cellulose synthase genes by small RNAs derived from cellulose synthase antisense transcripts

ABSTRACT Small RNAs (sRNAs) have been discovered in every bacterium examined and have been shown to play important roles in the regulation of a diverse range of behaviors, from metabolism to infection. However, despite a wide range of available techniques for discovering and validating sRNA regulatory interactions, only a minority of these molecules have been well characterized. In part, this is due to the nature of posttranscriptional regulation: the activity of an sRNA depends on the state of the transcriptome as a whole, so characterization is best carried out under the conditions in which it is naturally active. In this issue of mSystems, Arrieta-Ortiz and colleagues (M. L. Arrieta-Ortiz, C. Hafemeister, B. Shuster, N. S. Baliga, et al., mSystems 5:e00057-20, 2020, https://doi.org/10.1128/mSystems.00057-20) present a network inference approach based on estimating sRNA activity across transcriptomic compendia. This shows promise not only for identifying new sRNA regulatory interactions but also for pinpointing the conditions in which these interactions occur, providing a new avenue toward functional characterization of sRNAs.

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σ28-dependent small RNAs regulate timing of flagella biosynthesis

10.1101/2021.08.05.455139 ◽

2021 ◽

Author(s):

Sahar Melamed ◽

Aixia Zhang ◽

Michal Jarnik ◽

Joshua Mills ◽

Hongen Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Transcriptional Regulation ◽

Cell Motility ◽

Sigma Factor ◽

Small Rnas ◽

Posttranscriptional Regulation ◽

Bacterial Motility ◽

Coding Sequences ◽

Protein Levels ◽

Opposing Effects

Flagella are important for bacterial motility as well as for pathogenesis. Synthesis of these structures is energy intensive and, while extensive transcriptional regulation has been described, little is known about the posttranscriptional regulation. Small RNAs (sRNAs) are widespread posttranscriptional regulators, most base pairing with mRNAs to affect their stability and/or translation. Here we describe four UTR-derived sRNAs (UhpU, MotR, FliX and FlgO) whose expression is controlled by the flagella sigma factor σ28 (fliA) in Escherichia coli. Interestingly, MotR and FliX have opposing effects on flagellin protein levels, flagella number and cell motility, with MotR accelerating flagella synthesis and FliX decelerating flagella synthesis. Unlike most sRNAs, MotR and FliX base pair within the coding sequences of target mRNAs. They also uniquely act on ribosomal protein mRNAs thus coordinating flagella synthesis with ribosome production. The study shows how sRNA-mediated regulation can overlay a complex network enabling nuanced control of flagella synthesis.

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Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-09-15-0212-fi ◽

2016 ◽

Vol 29 (3) ◽

pp. 165-169 ◽

Cited By ~ 47

Author(s):

Qili Fei ◽

Yu Zhang ◽

Rui Xia ◽

Blake C. Meyers

Keyword(s):

Small Rnas ◽

Posttranscriptional Regulation ◽

Defense Responses ◽

Ongoing Work ◽

Target Disease ◽

The Rich ◽

Regulatory Effects ◽

Functional Relevance ◽

Cis And Trans ◽

In Cis

Plant small RNAs play important roles in transcriptional and posttranscriptional regulation, with ongoing work demonstrating their functions in diverse pathways. Their roles in defense responses are a topic of active investigation, particularly the rich set of micro (mi)RNAs that target disease resistance genes such as nucleotide binding/leucine-rich repeat (NB-LRR) genes. The miRNA–NB-LRR interactions result in the production of phased, secondary small interfering (phasi)RNAs, and phasiRNAs function in both cis and trans to propagate negative regulatory effects across additional members of the target gene family. Yet, while phasiRNAs have the capacity to trigger targeted decay of specific targets, both in cis and trans, their functional relevance in NB-LRR regulation remains largely a matter of speculation.

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The Pseudomonas aeruginosa Two-Component Regulator AlgR Directly Activates rsmA Expression in a Phosphorylation-Independent Manner

Journal of Bacteriology ◽

10.1128/jb.00048-17 ◽

2017 ◽

Vol 199 (18) ◽

Cited By ~ 11

Author(s):

Sean D. Stacey ◽

Danielle A. Williams ◽

Christopher L. Pritchett

Keyword(s):

Pseudomonas Aeruginosa ◽

Small Rnas ◽

Posttranscriptional Regulation ◽

Regulatory System ◽

Chronic Infections ◽

Independent Manner ◽

Content Type ◽

Alginate Production ◽

Two Component ◽

Mechanisms Of Persistence

ABSTRACTPseudomonas aeruginosais an important pathogen of the immunocompromised, causing both acute and chronic infections. In cystic fibrosis (CF) patients,P. aeruginosacauses chronic disease. The impressive sensory network ofP. aeruginosaallows the bacterium to sense and respond to a variety of stimuli found in diverse environments. Transcriptional regulators, including alternative sigma factors and response regulators, integrate signals changing gene expression, allowingP. aeruginosato cause infection. The two-component transcriptional regulator AlgR is important inP. aeruginosapathogenesis in both acute and chronic infections. In chronic infections, AlgR and the alternative sigma factor AlgU activate the genes responsible for alginate production. Previous work demonstrated that AlgU controlsrsmAexpression. RsmA is a posttranscriptional regulator that is antagonized by two small RNAs, RsmY and RsmZ. In this work, we demonstrate that AlgR directly activatesrsmAexpression from the same promoter as AlgU. In addition, phosphorylation was not necessary for AlgR activation ofrsmAusingalgRandalgZmutant strains. AlgU and AlgR appear to affect the antagonizing small RNAsrsmYandrsmZindirectly. RsmA was active in amucA22mutant strain using leader fusions of two RsmA targets,tssA1andhcnA. AlgU and AlgR were necessary for posttranscriptional regulation oftssA1andhcnA. Altogether, our work demonstrates that the alginate regulators AlgU and AlgR are important in the control of the RsmA posttranscriptional regulatory system. These findings suggest that RsmA plays an unknown role in mucoid strains due to AlgU and AlgR activities.IMPORTANCEP. aeruginosainfections are difficult to treat and frequently cause significant mortality in CF patients. Understanding the mechanisms of persistence is important. Our work has demonstrated that the alginate regulatory system also significantly impacts the posttranscriptional regulator system RsmA/Y/Z. We demonstrate that AlgR directly activatesrsmAexpression, and this impacts the RsmA regulon. This leads to the possibility that the RsmA/Y/Z system plays a role in helpingP. aeruginosapersist during chronic infection. In addition, this furthers our understanding of the reach of the alginate regulators AlgU and AlgR.

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Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans

Science ◽

10.1126/science.1132839 ◽

2006 ◽

Vol 315 (5809) ◽

pp. 241-244 ◽

Cited By ~ 375

Author(s):

Julia Pak ◽

Andrew Fire

Keyword(s):

Rna Interference ◽

Small Rnas ◽

De Novo ◽

Messenger Rnas ◽

Cellular Regulation ◽

Rdrp Activity ◽

Antisense Transcripts ◽

Double Stranded Rna ◽

C Elegans ◽

Secondary Sirnas

RNA interference (RNAi) is a phylogenetically widespread gene-silencing process triggered by double-stranded RNA. In plants and Caenorhabditis elegans, two distinct populations of small RNAs have been proposed to participate in RNAi: “Primary siRNAs” (derived from DICER nuclease-mediated cleavage of the original trigger) and “secondary siRNAs” [additional small RNAs whose synthesis requires an RNA-directed RNA polymerase (RdRP)]. Analyzing small RNAs associated with ongoing RNAi in C. elegans, we found that secondary siRNAs constitute the vast majority. The bulk of secondary siRNAs exhibited structure and sequence indicative of a biosynthetic mode whereby each molecule derives from an independent de novo initiation by RdRP. Analysis of endogenous small RNAs indicated that a fraction derive from a biosynthetic mechanism that is similar to that of secondary siRNAs formed during RNAi, suggesting that small antisense transcripts derived from cellular messenger RNAs by RdRP activity may have key roles in cellular regulation.

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Identification of BvgA-Dependent and BvgA-Independent Small RNAs (sRNAs) in Bordetella pertussis Using the Prokaryotic sRNA Prediction Toolkit ANNOgesic

Microbiology Spectrum ◽

10.1128/spectrum.00044-21 ◽

2021 ◽

Author(s):

Kyung Moon ◽

Minji Sim ◽

Chin-Hsien Tai ◽

Kyungyoon Yoo ◽

Charlotte Merzbacher ◽

...

Keyword(s):

Gene Expression ◽

Small Rnas ◽

Posttranscriptional Regulation ◽

Transcriptome Sequencing ◽

Regulation Of Gene Expression ◽

Bacterial Virulence ◽

Human Pathogen ◽

Rna Seq ◽

Content Type ◽

Search Program

Noncoding small RNAs (sRNAs) are crucial for posttranscriptional regulation of gene expression in all organisms and are known to be involved in the regulation of bacterial virulence. We have investigated the presence of sRNAs in the obligate human pathogen B. pertussis , using transcriptome sequencing (RNA-seq) and the recently developed prokaryotic sRNA search program ANNOgesic.

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Endoribonuclease YbeY Is Essential for RNA Processing and Virulence in Pseudomonas aeruginosa

mBio ◽

10.1128/mbio.00659-20 ◽

2020 ◽

Vol 11 (3) ◽

Author(s):

Yushan Xia ◽

Yuding Weng ◽

Congjuan Xu ◽

Dan Wang ◽

Xiaolei Pan ◽

...

Keyword(s):

Oxidative Stress ◽

Pseudomonas Aeruginosa ◽

Stress Response ◽

Small Rnas ◽

Posttranscriptional Regulation ◽

Oxidative Stress Response ◽

Bacterial Virulence ◽

Rrna Processing ◽

Content Type ◽

Stress Response Genes

ABSTRACT Posttranscriptional regulation plays an essential role in the quick adaptation of pathogenic bacteria to host environments, and RNases play key roles in this process by modifying small RNAs and mRNAs. We find that the Pseudomonas aeruginosa endonuclease YbeY is required for rRNA processing and the bacterial virulence in a murine acute pneumonia model. Transcriptomic analyses reveal that knocking out the ybeY gene results in downregulation of oxidative stress response genes, including the catalase genes katA and katB. Consistently, the ybeY mutant is more susceptible to H2O2 and neutrophil-mediated killing. Overexpression of katA restores the bacterial tolerance to H2O2 and neutrophil killing as well as virulence. We further find that the downregulation of the oxidative stress response genes is due to defective expression of the stationary-phase sigma factor RpoS. We demonstrate an autoregulatory mechanism of RpoS and find that ybeY mutation increases the level of a small RNA, ReaL, which directly represses the translation of rpoS through the 5′ UTR of its mRNA and subsequently reduces the expression of the oxidative stress response genes. In vitro assays demonstrate direct degradation of ReaL by YbeY. Deletion of reaL or overexpression of rpoS in the ybeY mutant restores the bacterial tolerance to oxidative stress and the virulence. We also demonstrate that YbeZ binds to YbeY and is involved in the 16S rRNA processing and regulation of reaL and rpoS as well as the bacterial virulence. Overall, our results reveal pleiotropic roles of YbeY and the YbeY-mediated regulation of rpoS through ReaL. IMPORTANCE The increasing bacterial antibiotic resistance imposes a severe threat to human health. For the development of effective treatment and prevention strategies, it is critical to understand the mechanisms employed by bacteria to grow in the human body. Posttranscriptional regulation plays an important role in bacterial adaptation to environmental changes. RNases and small RNAs are key players in this regulation. In this study, we demonstrate critical roles of the RNase YbeY in the virulence of the pathogenic bacterium Pseudomonas aeruginosa. We further identify the small RNA ReaL as the direct target of YbeY and elucidate the YbeY-regulated pathway on the expression of bacterial virulence factors. Our results shed light on the complex regulatory network of P. aeruginosa and indicate that inference with the YbeY-mediated regulatory pathway might be a valid strategy for the development of a novel treatment strategy.

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Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis

BMC Molecular Biology ◽

10.1186/1471-2199-9-6 ◽

2008 ◽

Vol 9 (1) ◽

Cited By ~ 82

Author(s):

Hailing Jin ◽

Vladimir Vacic ◽

Thomas Girke ◽

Stefano Lonardi ◽

Jian-Kang Zhu

Keyword(s):

Small Rnas ◽

Antisense Transcripts ◽

Natural Antisense Transcripts

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