Broadening the Definition of Bacterial Small RNAs: Characteristics and Mechanisms of Action

2018 ◽  
Vol 72 (1) ◽  
pp. 141-161 ◽  
Author(s):  
Marie-Claude Carrier ◽  
David Lalaouna ◽  
Eric Massé
Keyword(s):  
Small Rnas ◽  
Emerging Technologies ◽  
Mechanisms Of Action ◽  
Bacterial Cells ◽  
Clear Definition ◽  
First Report ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Definition Of

The first report of trans-acting RNA-based regulation in bacterial cells dates back to 1984. Subsequent studies in diverse bacteria unraveled shared properties of trans-acting small regulatory RNAs, forming a clear definition of these molecules. These shared characteristics have been used extensively to identify new small RNAs (sRNAs) and their interactomes. Recently however, emerging technologies able to resolve RNA-RNA interactions have identified new types of regulatory RNAs. In this review, we present a broader definition of trans-acting sRNA regulators and discuss their newly discovered intrinsic characteristics.

scholarly journals A novel computational approach for genome-wide prediction of small RNAs in bacteria

2014 ◽  
Author(s):  
Lei Li ◽  
Hoi Shan Kwan
Keyword(s):  
Small Rnas ◽  
Computational Prediction ◽  
Transcriptional Regulators ◽  
Structural Features ◽  
Extensive Study ◽  
Bacterial Physiology ◽  
Genome Wide ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Window Approach

Small regulatory RNAs (sRNAs) are the most abundant post-transcriptional regulators in bacteria. They serve ubiquitous roles that control nearly every aspects of bacterial physiology. Identification of important features from sRNAs sequences will guide the computational prediction of new sRNA sequences for a better understanding of the pervasive sRNA-mediated regulation in bacteria. In this study, we have performed systematic analyses of many sequence and structural features that are possibly related to sRNA properties and identified a subset of significant features that effectively discriminate sRNAs sequences from random sequences. we then used a neural network model that integrated these subfeatures on unlabeled testing datasets, and it had achieved a 92.2% recall and 89.8% specificity. Finally, we applied this prediction model for genome-wide identification of sRNAs-encoded genes using a sliding-window approach. We recovered multiple known sRNAs and hundreds of predicted new sRNAs. These candidate novel sRNAs deserve extensive study to better understand the sRNA-mediated regulatory network in bacteria.

scholarly journals Two GacA-Dependent Small RNAs Modulate the Quorum-Sensing Response in Pseudomonas aeruginosa

2006 ◽  
Vol 188 (16) ◽  
pp. 6026-6033 ◽  
Author(s):  
Elisabeth Kay ◽  
Bérénice Humair ◽  
Valérie Dénervaud ◽  
Kathrin Riedel ◽  
Stéphanie Spahr ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Small Rnas ◽  
Homoserine Lactone ◽  
Two Component System ◽  
Bond Forming ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Chitin Binding Protein ◽  
Biofilm Development

ABSTRACT In Pseudomonas aeruginosa, the GacS/GacA two-component system positively controls the quorum-sensing machinery and the expression of extracellular products via two small regulatory RNAs, RsmY and RsmZ. An rsmY rsmZ double mutant and a gacA mutant were similarly impaired in the synthesis of the quorum-sensing signal N-butanoyl-homoserine lactone, the disulfide bond-forming enzyme DsbA, and the exoproducts hydrogen cyanide, pyocyanin, elastase, chitinase (ChiC), and chitin-binding protein (CbpD). Both mutants showed increased swarming ability, azurin release, and early biofilm development.

scholarly journals Small Toxic Proteins and the Antisense RNAs That Repress Them

2008 ◽  
Vol 72 (4) ◽  
pp. 579-589 ◽  
Author(s):  
Elizabeth M. Fozo ◽  
Matthew R. Hemm ◽  
Gisela Storz
Keyword(s):  
Amino Acids ◽  
Small Rna ◽  
Small Rnas ◽  
Short Length ◽  
Type I ◽  
Practical Applications ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Rna Genes ◽  
Toxic Proteins

SUMMARY There has been a great expansion in the number of small regulatory RNAs identified in bacteria. Some of these small RNAs repress the synthesis of potentially toxic proteins. Generally the toxin proteins are hydrophobic and less than 60 amino acids in length, and the corresponding antitoxin small RNA genes are antisense to the toxin genes or share long stretches of complementarity with the target mRNAs. Given their short length, only a limited number of these type I toxin-antitoxin loci have been identified, but it is predicted that many remain to be found. Already their characterization has given insights into regulation by small RNAs, has suggested functions for the small toxic proteins at the cell membrane, and has led to practical applications for some of the type I toxin-antitoxin loci.

scholarly journals Compensatory sequence variation between trans-species small RNAs and their target sites

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Nathan R Johnson ◽  
Claude W dePamphilis ◽  
Michael J Axtell
Keyword(s):  
Small Rnas ◽  
Synonymous Site ◽  
Protein Coding ◽  
Coding Regions ◽  
Target Sites ◽  
Site Variation ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Multiple Species ◽  
Multiple Variants

Trans-species small regulatory RNAs (sRNAs) are delivered to host plants from diverse pathogens and parasites and can target host mRNAs. How trans-species sRNAs can be effective on diverse hosts has been unclear. Multiple species of the parasitic plant Cuscuta produce trans-species sRNAs that collectively target many host mRNAs. Confirmed target sites are nearly always in highly conserved, protein-coding regions of host mRNAs. Cuscuta trans-species sRNAs can be grouped into superfamilies that have variation in a three-nucleotide period. These variants compensate for synonymous-site variation in host mRNAs. By targeting host mRNAs at highly conserved protein-coding sites, and simultaneously expressing multiple variants to cover synonymous-site variation, Cuscuta trans-species sRNAs may be able to successfully target multiple homologous mRNAs from diverse hosts.

scholarly journals RNA-dependent RNA polymerases in the black-legged tick produce Argonaute-dependent small RNAs and regulate genes

2021 ◽  
Author(s):  
Canran Feng ◽  
Kyosuke Torimaru ◽  
Mandy Yu Theng Lim ◽  
Li-Ling Chak ◽  
Kosuke Tsuji ◽  
...  
Keyword(s):  
Small Rnas ◽  
Rna Polymerase Iii ◽  
Feedback Regulation ◽  
Rna Polymerases ◽  
Effector Proteins ◽  
Protein Coding ◽  
C Elegans ◽  
Animal Pathogens ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

Small regulatory RNAs (sRNAs) are involved in anti-viral defense and gene regulation. Although RNA-dependent RNA Polymerases (RdRPs) are known to produce sRNA in nematodes, plants and fungi, whether they play roles in sRNA biogenesis in other animals remains controversial. In this study, we study sRNAs in the ISE6 cell line, which is derived from the black-legged tick, an important vector of human and animal pathogens. We identify abundant classes of ~22nt sRNAs that require specific combinations of RdRPs and sRNA effector proteins (Argonautes or AGOs). RdRP-dependent sRNAs are mainly derived from sense and antisense strands of RNA polymerase III-transcribed genes and repetitive elements. Unlike C. elegans sRNA pathways, 5′-tri-phosphorylated sRNAs are not detected, suggesting that the tick pathways are distinct from the pathways known in worms. Knockdown of one of the RdRPs unexpectedly results in downregulation of a subset of viral transcripts, in contrast to their upregulation by AGO knockdown. Furthermore, we show that knockdown of AGO/RdRP causes misregulation of protein-coding genes including RNAi-related genes, suggesting feedback regulation. Luciferase assays demonstrate that one of the RdRP-regulated genes, the MEK1 ortholog IscDsor1 is regulated through its 3′UTR, where a putative sRNA target site resides. These results provide evidence that arachnid RdRPs are important sRNA biogenesis factors, and the discovery of novel pathways underscores the importance of characterizing sRNA biogenesis in various organisms to understand virus-vector interactions and to exploit RNAi for pest control.

scholarly journals Sensitive whole mount in situ localization of small RNAs in plants

2016 ◽  
Author(s):  
Mouli Ghosh Dastidar ◽  
Magdalena Mosiolek ◽  
Michael D Nodine ◽  
Alexis Maizel
Keyword(s):  
Small Rnas ◽  
Direct Detection ◽  
Expression Patterns ◽  
Systematic Investigation ◽  
Indirect Detection ◽  
Whole Mount ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
In Situ Detection

Small regulatory RNAs are pivotal regulators of gene expression and play important roles in many plant processes. Although our knowledge of their biogenesis and mode of action has significantly progressed, we comparatively still know little about their biological functions. In particular, knowledge about their spatiotemporal patterns of expression rely on either indirect detection by use of reporter constructs or labor-intensive direct detection by in situ hybridization on sectioned material. None of the current approaches allows for a systematic investigation of small RNAs expression patterns.Here, we present a method for the sensitive in situ detection of micro- and siRNAs in intact plant tissues that utilizes both double-labelled probes and a specific cross linker. We determined the expression patterns of several small RNAs in plant roots and embryos.

scholarly journals Bacterial chaperone protein Hfq facilitates the annealing of sponge RNAs to small regulatory RNAs

2021 ◽  
Author(s):  
Ewelina M. Małecka ◽  
Daria Sobańska ◽  
Mikołaj Olejniczak
Keyword(s):  
Environmental Conditions ◽  
Small Rnas ◽  
Base Pairing ◽  
Biochemical Methods ◽  
Target Mrnas ◽  
Chaperone Protein ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Posttranscriptional Level

ABSTRACTBacterial small RNAs (sRNAs) in association with the chaperone protein Hfq regulate the expression of many target mRNAs. Since sRNAs’ action is crucial to engender a response to changing environmental conditions, their activity needs to be regulated. One such mechanism occurs at posttranscriptional level and involves sponge RNAs (or anti-sRNAs) which sequester sRNAs affecting their regulatory output. Both types of RNAs were identified on Hfq, but it is not known how Hfq interacts with RNA sponges and stimulates their base-pairing with sRNAs. Here, we used biochemical methods to demonstrate that anti-sRNAs resemble sRNAs by their structure and their modes of Hfq binding. Hfq facilitates sponge RNA annealing to sRNA, and each surface of the protein plays a particular role in the process. Moreover, we found that the efficiency of sponge RNA interactions with sRNAs can be improved, therefore, we propose that natural RNA sponges might not sequester sRNAs optimally.

scholarly journals Bacterial nucleoid protein Dps binds structured RNA molecules

2016 ◽  
Vol 11 (2) ◽  
pp. 311-322
Author(s):  
А.А. Быков ◽  
A.A. Bykov
Keyword(s):  
Bacterial Genome ◽  
Bacterial Cells ◽  
Dna Structures ◽  
Rna Molecules ◽  
Controlled Processing ◽  
Short Rnas ◽  
Phosphate Backbone ◽  
Bacterial Nucleoid ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas

Architectural protein Dps of the bacterial nucleoid employs side groups of lysines at its N-terminal modules for interacting with the sugar-phosphate backbone of the DNA. Electrostatic nature of interaction assumes the potential ability of Dps to bind with any nucleotide sequence including RNA. The available data also indicate that Dps exhibits enhanced affinity to branched DNA structures. In RNA molecules such structures are formed more frequently than in DNA. Hence, the aim of this investigation was studying the ability of purified Dps immobilized on acrylate spheres to bind with short RNAs isolated from bacterial cells. It appeared that transport and small regulatory RNAs forming stable secondary structures are preferential targets for such interaction. Among RNAs identified in complexes with Dps 8 transcripts corresponded to intergenic spaces, which might indicate the presence of novel genes. Moreover, products 9-13 nucleotides long belonging to small untranslated RNAs SdsR and RyeA and transcribed from both strands of the same locus were registered. Since the number of longer transcripts from this region was at least five-fold lower, it can be presumed that two counter-synthesized products form a partly complementary duplex subjected to controlled processing. The selectivity of Dps to these molecules, as well as to other structured RNAs, indicates a possibility of its involvement not only in bacterial genome condensation, but also in maintaining the functional state of the transcriptome.

scholarly journals Pathogenetic Role and Clinical Implications of Regulatory RNAs in Biliary Tract Cancer

Cancers ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 12
Author(s):  
Nduka Ofoeyeno ◽  
Emmanuel Ekpenyong ◽  
Chiara Braconi
Keyword(s):  
Biliary Tract ◽  
Biliary Tract Cancer ◽  
Transcriptional Repression ◽  
Small Rnas ◽  
Mechanisms Of Action ◽  
Clinical Implications ◽  
Tract Cancer ◽  
Non Coding Rna ◽  
Regulatory Rnas

Biliary tract cancer (BTC) is characterised by poor prognosis and low overall survival in patients. This is generally due to minimal understanding of its pathogenesis, late diagnosis and limited therapeutics in preventing or treating BTC patients. Non-coding RNA (ncRNA) are small RNAs (mRNA) that are not translated to proteins. ncRNAs were considered to be of no importance in the genome, but recent studies have shown they play essential roles in biology and oncology such as transcriptional repression and degradation, thus regulating mRNA transcriptomes. This has led to investigations into the role of ncRNAs in the pathogenesis of BTC, and their clinical implications. In this review, the mechanisms of action of ncRNA are discussed and the role of microRNAs in BTC is summarised. The scope of this review will be limited to miRNA as they have been shown to play the most significant roles in BTC progression. There is huge potential in miRNA-based biomarkers and therapeutics in BTC, but more studies, research and technological advancements are required before it can be translated into clinical practice for patients.

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