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 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 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 Small RNAs Worm Up Transgenerational Epigenetics Research

DNA ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 37-48
Author(s):  
Alla Grishok
Keyword(s):  
Small Rnas ◽  
Epigenetic Inheritance ◽  
Control Mechanisms ◽  
C Elegans ◽  
Sensory Experiences ◽  
New Findings ◽  
Regulatory Rnas ◽  
Living Organisms ◽  
Flow Of Information ◽  
Self Replication

DNA is central to the propagation and evolution of most living organisms due to the essential process of its self-replication. Yet it also encodes factors that permit epigenetic (not included in DNA sequence) flow of information from parents to their offspring and beyond. The known mechanisms of epigenetic inheritance include chemical modifications of DNA and chromatin, as well as regulatory RNAs. All these factors can modulate gene expression programs in the ensuing generations. The nematode Caenorhabditis elegans is recognized as a pioneer organism in transgenerational epigenetic inheritance research. Recent advances in C. elegans epigenetics include the discoveries of control mechanisms that limit the duration of RNA-based epigenetic inheritance, periodic DNA motifs that counteract epigenetic silencing establishment, new mechanistic insights into epigenetic inheritance carried by sperm, and the tantalizing examples of inheritance of sensory experiences. This review aims to highlight new findings in epigenetics research in C. elegans with the main focus on transgenerational epigenetic phenomena dependent on small RNAs.

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 Co-surveillance of ribosomal RNA by the exosome complex and nucleolar RNAi in C. elegans

2020 ◽  
Author(s):  
Shimiao Liao ◽  
Xiangyang Chen ◽  
Ting Xu ◽  
Qile Jin ◽  
Zongxiu Xu ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Degradation ◽  
Rna Polymerase I ◽  
C Elegans ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Rna Exosome ◽  
Polymerase I ◽  
Nuclear Rnai ◽  
Novel Model

AbstractEukaryotic cells express a wide variety of endogenous small regulatory RNAs that function in the nucleus. We previously found that erroneous rRNAs induce the generation of antisense ribosomal siRNAs (risiRNAs) which silence the expression of rRNAs via the nuclear RNAi defective (Nrde) pathway. To further understand the biological roles and mechanisms of this class of small regulatory RNAs, we conducted forward genetic screening to identify factors involved in risiRNA generation in Caenorhabditis elegans. We found that risiRNAs accumulated in the RNA exosome mutants. risiRNAs directed a NRDE-dependent silencing of pre-rRNAs in the nucleolus. In the presence of risiRNA, NRDE-2 accumulated in the nucleolus and colocalized with RNA polymerase I. risiRNA inhibited the transcription elongation of RNA polymerase I by decreasing RNAP I occupancy downstream of the site of RNAi. Meanwhile, exosome mislocalized from the nucleolus to nucleoplasm in suppressor of siRNA (susi) mutants, in which erroneous rRNAs accumulated. These results establish a novel model of rRNA surveillance by combining ribonuclease-mediated RNA degradation with small RNA-directed nucleolar RNAi system.

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 Analysis of the Caenorhabditis elegans rpc-1 gene

2005 ◽  
Author(s):  
◽  
Qun Zheng
Keyword(s):  
Gene Expression ◽  
Promoter Activity ◽  
Rna Polymerase Iii ◽  
Transgenic Animals ◽  
Rna Polymerases ◽  
Pol Ii ◽  
C Elegans ◽  
Pol I ◽  
Genes Encoding ◽  
Pol Iii

In eukaryotes, two large subunits form the core catalytic structure of RNA polymerase III (Pol III), which is conserved in other RNA polymerases, Pol I and Pol II. It has been found that Pol III activity is tightly associated to cell growth. TFIII B has been shown to be one of main mediators in this process. No regulation of the Pol III largest subunit gene has been found. In C. elegans, the rpc-1 gene encodes the largest subunit of Pol III. Here, I identified two critical structural components of RPC-1, Gly644 and Gly1055, whose mutations result in larval lethal arrestment. These two amino acid residues are universally conserved in RNA polymerases, indicating their overall involvement in gene transcription mechanism. Also, I found that maternally inherited, not embryonically expressed, rpc-1 gene products survive early development. Starvation was found to suppress rpc-1 gene expression and re-feeding treatment enhances rpc-1 gene expression rapidly. No similar regulation was detected in genes encoding largest subunits of Pol I and Pol II. This is the first time that rpc-1 gene regulation has been reported. Insulin signaling may not be involved in this regulation. Also, I found that rpc-1 promoter is not ubiquitously active in C. elegans. Using the rpc-1p::gfp transgene, the rpc-1 promoter activity is only detected in a subset of neurons in the head and the tail and the intestine. While starvation silences the rpc-1 promoter activity in most tissues and cells, ASK neurons still show GFP staining in the rpc-1p::gfp transgenic animals, indicating that rpc-1 transcription in ASK neurons is continuously active under starvation conditions. Further studies suggest that TGF-[beta] signaling is involved in mediating the rpc-1 promoter activity in ASK neurons.

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.

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.

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