In planta vs viral expression of HCPro affects its binding of non‐plant 21‐22 nt small RNAs, but not its preference for 5´‐terminal adenines, or its effects on small RNA methylation

2021 ◽  
Author(s):  
Francisco del Toro ◽  
Hao Sun ◽  
Carmen Robinson ◽  
Álvaro Jiménez ◽  
Eva Covielles ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
In Planta ◽  
Rna Methylation ◽  
Viral Expression

scholarly journals Mechanism of Stochastic Resonance in a Quorum Sensing Network Regulated by Small RNAs

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Ya-nan Zhu ◽  
Jianwei Shen ◽  
Yong Xu
Keyword(s):  
Quorum Sensing ◽  
Stochastic Resonance ◽  
Small Rna ◽  
Small Rnas ◽  
Cell Communication ◽  
The Other ◽  
Important Process ◽  
Positive Role ◽  
Bacterial Quorum Sensing ◽  
Bacterial Quorum

Bacterial quorum sensing (QS) is an important process of cell communication and more and more attention is paid to it. Moreover, the noises are ubiquitous in nature and often play positive role. In this paper, we investigate how the noise enhances the QS though the stochastic resonance (SR) and explain the mechanism of SR in this quorum sensing network. In addition, we also discuss the interaction between the small RNA and the other genes in this network and discover the biological importance.

scholarly journals Intertissue small RNA communication mediates the acquisition and inheritance of hormesis in Caenorhabditis elegans

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Emiko Okabe ◽  
Masaharu Uno ◽  
Saya Kishimoto ◽  
Eisuke Nishida
Keyword(s):  
Caenorhabditis Elegans ◽  
Small Rna ◽  
Stress Resistance ◽  
Environmental Conditions ◽  
Production System ◽  
Small Rnas ◽  
Communication Systems ◽  
Rna Transport ◽  
Phenotypic Changes ◽  
Induced Stress

AbstractEnvironmental conditions can cause phenotypic changes, part of which can be inherited by subsequent generations via soma-to-germline communication. However, the signaling molecules or pathways that mediate intertissue communication remain unclear. Here, we show that intertissue small RNA communication systems play a key role in the acquisition and inheritance of hormesis effects – stress-induced stress resistance – in Caenorhabditis elegans. The miRNA-processing enzyme DRSH-1 is involved in both the acquisition and the inheritance of hormesis, whereas worm-specific Argonaute (WAGO) proteins, which function with endo-siRNAs, are involved only in its inheritance. Further analyses demonstrate that the miRNA production system in the neuron and the small RNA transport machinery in the intestine are both essential for its acquisition and that both the transport of small RNAs in the germline and the germline Argonaute HRDE-1 complex are required for its inheritance. Our results thus demonstrate that overlapping and distinct roles of small RNA systems in the acquisition and inheritance of hormesis effects.

scholarly journals Gain and Loss of Small RNA Classes—Characterization of Small RNAs in the Parasitic Nematode Family Strongyloididae

2017 ◽  
Vol 9 (10) ◽  
pp. 2826-2843 ◽  
Author(s):  
Anja Holz ◽  
Adrian Streit
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Parasitic Nematode ◽  
Gain And Loss

scholarly journals The Importance of the Small RNA Chaperone Hfq for Growth of Epidemic Yersinia pestis, but Not Yersinia pseudotuberculosis, with Implications for Plague Biology

2010 ◽  
Vol 192 (16) ◽  
pp. 4239-4245 ◽  
Author(s):  
Guangchun Bai ◽  
Andrey Golubov ◽  
Eric A. Smith ◽  
Kathleen A. McDonough
Keyword(s):  
Yersinia Pestis ◽  
Small Rna ◽  
Small Rnas ◽  
Yersinia Pseudotuberculosis ◽  
Etiologic Agent ◽  
Growth Restriction ◽  
Rna Chaperone ◽  
Unique Biology ◽  
Severe Growth

ABSTRACT Yersinia pestis, the etiologic agent of plague, has only recently evolved from Yersinia pseudotuberculosis. hfq deletion caused severe growth restriction at 37°C in Y. pestis but not in Y. pseudotuberculosis. Strains from all epidemic plague biovars were similarly affected, implicating Hfq, and likely small RNAs (sRNAs), in the unique biology of the plague bacillus.

scholarly journals Intergenerational metabolic priming by sperm piRNAs

2021 ◽  
Author(s):  
Adelheid Lempradl ◽  
Unn Kugelberg ◽  
Mary Iconomou ◽  
Ian Beddows ◽  
Daniel Nätt ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Target Gene ◽  
Epigenetic Inheritance ◽  
Mature Sperm ◽  
Transcriptional Reprogramming ◽  
Complementary Sequences ◽  
Specific Manner ◽  
Dietary Sugar ◽  
Pirna Pathway

Preconception parental environment can reproducibly program offspring phenotype without altering the DNA sequence, yet the mechanisms underpinning this epigenetic inheritance remains elusive. Here, we demonstrate the existence of an intact piRNA-pathway in mature Drosophila sperm and show that pathway modulation alters offspring gene transcription in a sequence-specific manner. We map a dynamic small RNA content in developing sperm and find that the mature sperm carry a highly distinct small RNA cargo. By biochemical pulldown, we identify a small RNA subset bound directly to piwi protein. And, we show that piRNA-pathway controlled sperm small RNAs are linked to target gene repression in offspring. Critically, we find that full piRNA-pathway dosage is necessary for the intergenerational metabolic and transcriptional reprogramming events triggered by high paternal dietary sugar. These data provide a direct link between regulation of endogenous mature sperm small RNAs and transcriptional programming of complementary sequences in offspring. Thus, we identify a novel mediator of paternal intergenerational epigenetic inheritance.

scholarly journals The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline

2021 ◽  
Author(s):  
Elisabeth A Marnik ◽  
Miguel Vasconcelos Almeida ◽  
P Giselle Cipriani ◽  
George Chung ◽  
Edoardo Caspani ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Small Rna ◽  
Small Rnas ◽  
Brood Size ◽  
Homologous Proteins ◽  
P Granules ◽  
Transposon Silencing ◽  
Tudor Domain ◽  
Germ Granules

LOTUS and Tudor domain containing proteins have critical roles in the germline. Proteins that contain these domains, such as Tejas/Tapas in Drosophila, help localize Vasa to the germ granules and facilitate piRNA-mediated transposon silencing. The homologous proteins in mammals, TDRD5 and TDRD7, are required during spermiogenesis. Until now, proteins containing both LOTUS and Tudor domains in Caenorhabditis elegans have remained elusive. Here we describe LOTR-1 (D1081.7), which derives its name from its LOTUS and Tudor domains. Interestingly, LOTR-1 docks next to P granules to colocalize with the broadly conserved Z-granule helicase, ZNFX-1. LOTR-1's Z-granule association requires its Tudor domain, but both LOTUS and Tudor deletions affect brood size when coupled with a knockdown of the Vasa homolog glh-1. In addition to interacting with the germ-granule components WAGO-1, PRG-1 and DEPS-1, we identified a Tudor-dependent association with ZNFX-1. Like znfx-1 mutants, lotr-1 mutants lose small RNAs from the 3' ends of WAGO and Mutator targets, reminiscent of the loss of piRNAs from the 3' ends of piRNA precursor transcripts in mouse Tdrd5 mutants. Our work suggests that LOTR-1 acts in a conserved mechanism that brings small RNA generating mechanisms towards the 3' ends of small RNA templates or precursors.

Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Yongli Qiao ◽  
Rui Xia ◽  
Jixian Zhai ◽  
Yingnan Hou ◽  
Li Feng ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Small Rna ◽  
Small Rnas ◽  
Plant Immunity ◽  
Receptor Gene ◽  
Current Status ◽  
Annual Review ◽  
Publication Date ◽  
Small Interfering Rnas ◽  
Host Pathogen

Gene silencing guided by small RNAs governs a broad range of cellular processes in eukaryotes. Small RNAs are important components of plant immunity because they contribute to pathogen-triggered transcription reprogramming and directly target pathogen RNAs. Recent research suggests that silencing of pathogen genes by plant small RNAs occurs not only during viral infection but also in nonviral pathogens through a process termed host-induced gene silencing, which involves trans-species small RNA trafficking. Similarly, small RNAs are also produced by eukaryotic pathogens and regulate virulence. This review summarizes the small RNA pathways in both plants and filamentous pathogens, including fungi and oomycetes, and discusses their role in host–pathogen interactions. We highlight secondary small interfering RNAs of plants as regulators of immune receptor gene expression and executors of host-induced gene silencing in invading pathogens. The current status and prospects of small RNAs trafficking at the host–pathogen interface are discussed. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Analysis of miRNAs in the Heads of Different Castes of the Bumblebee Bombus lantschouensis (Hymenoptera: Apidae)

Insects ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 349 ◽  
Author(s):  
Liu ◽  
Huang ◽  
Zhang ◽  
Liu ◽  
An
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Target Genes ◽  
Solexa Sequencing ◽  
Biological Functions ◽  
Putative Target ◽  
Differentially Expressed Mirnas ◽  
Rna Deep Sequencing ◽  
Small Rna Deep Sequencing ◽  
Go Terms

Bumblebees are important insect pollinators for many wildflowers and crops. MicroRNAs (miRNAs) are endogenous non-coding small RNAs that regulate different biological functions in insects. In this study, the miRNAs in the heads of the three castes of the bumblebee Bombus lantschouensis were identified and characterized by small RNA deep sequencing. The significant differences in the expression of miRNAs and their target genes were analyzed. The results showed that the length of the small RNA reads from males, queens, and workers was distributed between 18 and 30 nt, with a peak at 22 nt. A total of 364 known and 89 novel miRNAs were identified from the heads of the three castes. The eight miRNAs with the highest expressed levels in males, queens, and workers were identical, although the order of these miRNAs based on expression differed. The male vs. queen, male vs. worker, and worker vs. queen comparisons identified nine, fourteen, and four miRNAs with significant differences in expression, respectively. The different castes were clustered based on the differentially expressed miRNAs (DE miRNAs), and the expression levels of the DE miRNAs obtained by RT-qPCR were consistent with the read counts obtained through Solexa sequencing. The putative target genes of these DE miRNAs were enriched in 29 Gene Ontology (GO) terms, and catalytic activity was the most enriched GO term, as demonstrated by its association with 2837 target genes in the male vs. queen comparison, 3535 target genes in the male vs. worker comparison, and 2185 target genes in the worker vs. queen comparison. This study highlights the characteristics of the miRNAs in the three B. lantschouensis castes and will aid further studies on the functions of miRNAs in bumblebees.

scholarly journals Altered Fecal Small RNA Profiles in Colorectal Cancer Reflect Gut Microbiome Composition in Stool Samples

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Sonia Tarallo ◽  
Giulio Ferrero ◽  
Gaetano Gallo ◽  
Antonio Francavilla ◽  
Giuseppe Clerico ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gut Microbiota ◽  
Small Rna ◽  
Gut Microbiome ◽  
Small Rnas ◽  
Area Under The Curve ◽  
Small Rna Sequencing ◽  
Predictive Tool ◽  
Cross Sectional ◽  
Stool Samples

ABSTRACT Dysbiotic configurations of the human gut microbiota have been linked to colorectal cancer (CRC). Human small noncoding RNAs are also implicated in CRC, and recent findings suggest that their release in the gut lumen contributes to shape the gut microbiota. Bacterial small RNAs (bsRNAs) may also play a role in carcinogenesis, but their role has been less extensively explored. Here, we performed small RNA and shotgun sequencing on 80 stool specimens from patients with CRC or with adenomas and from healthy subjects collected in a cross-sectional study to evaluate their combined use as a predictive tool for disease detection. We observed considerable overlap and a correlation between metagenomic and bsRNA quantitative taxonomic profiles obtained from the two approaches. We identified a combined predictive signature composed of 32 features from human and microbial small RNAs and DNA-based microbiome able to accurately classify CRC samples separately from healthy and adenoma samples (area under the curve [AUC] = 0.87). In the present study, we report evidence that host-microbiome dysbiosis in CRC can also be observed by examination of altered small RNA stool profiles. Integrated analyses of the microbiome and small RNAs in the human stool may provide insights for designing more-accurate tools for diagnostic purposes. IMPORTANCE The characteristics of microbial small RNA transcription are largely unknown, while it is of primary importance for a better identification of molecules with functional activities in the gut niche under both healthy and disease conditions. By performing combined analyses of metagenomic and small RNA sequencing (sRNA-Seq) data, we characterized both the human and microbial small RNA contents of stool samples from healthy individuals and from patients with colorectal carcinoma or adenoma. With the integrative analyses of metagenomic and sRNA-Seq data, we identified a human and microbial small RNA signature which can be used to improve diagnosis of the disease. Our analysis of human and gut microbiome small RNA expression is relevant to generation of the first hypotheses about the potential molecular interactions occurring in the gut of CRC patients, and it can be the basis for further mechanistic studies and clinical tests.

scholarly journals Small RNA Functions as a Trafficking Effector in Plant Immunity

2019 ◽  
Vol 20 (11) ◽  
pp. 2816 ◽  
Author(s):  
Chen Zhu ◽  
Ting Liu ◽  
Ya-Nan Chang ◽  
Cheng-Guo Duan
Keyword(s):  
Small Rna ◽  
Stress Responses ◽  
Small Rnas ◽  
Plant Immunity ◽  
Arms Race ◽  
Abiotic And Biotic Stress ◽  
Plant Adaptation ◽  
Cellular Processes ◽  
Challenging Environment ◽  
Rna Export

Small RNAs represent a class of small but powerful agents that regulate development and abiotic and biotic stress responses during plant adaptation to a constantly challenging environment. Previous findings have revealed the important roles of small RNAs in diverse cellular processes. The recent discovery of bidirectional trafficking of small RNAs between different kingdoms has raised many interesting questions. The subsequent demonstration of exosome-mediated small RNA export provided a possible tool for further investigating how plants use small RNAs as a weapon during the arms race between plant hosts and pathogens. This review will focus on discussing the roles of small RNAs in plant immunity in terms of three aspects: the biogenesis of extracellular small RNAs and the transportation and trafficking small RNA-mediated gene silencing in pathogens.

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