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Gene Apr 2024Argonaute (Ago) proteins act as key elements in RNA interference (RNAi) pathway, orchestrating the intricate machinery of gene regulation within eukaryotic cells. Within... (Review)
Review
Argonaute (Ago) proteins act as key elements in RNA interference (RNAi) pathway, orchestrating the intricate machinery of gene regulation within eukaryotic cells. Within the RNAi pathway, small RNA molecules, including microRNA (miRNA), small interfering RNA (siRNA), and PIWI-interacting RNA (piRNA), collaborate with Ago family member proteins such as Ago1, Ago2, and Ago3 to form the RNA-induced silencing complex (RISC). This RISC complex, in turn, either cleaves the target mRNA or inhibits the process of protein translation. The precise contributions of Ago proteins have been well-established in numerous animals and plants, although they still remain unclear in some insect species. This review aims to shed light on the specific roles played by Ago proteins within the RNAi mechanism in a destructive lepidopteran pest, the diamondback moth (Plutella xylostella). Furthermore, we explore the potential of double-stranded RNA (dsRNA)-mediated RNAi as a robust genetic tool in pest management strategies. Through an in-depth examination of Ago proteins and dsRNA-mediated RNAi, this review seeks to contribute to our understanding of innovative approaches for controlling this pest and potentially other insect species of agricultural significance.
Topics: Animals; RNA Interference; Argonaute Proteins; RNA, Small Interfering; MicroRNAs; RNA, Double-Stranded
PubMed: 38295911
DOI: 10.1016/j.gene.2024.148195 -
RNA (New York, N.Y.) Aug 2023The potential for microRNAs (miRNAs) to regulate gene expression remains incompletely understood. DROSHA initiates the biogenesis of miRNAs while variants of Argonaute...
The potential for microRNAs (miRNAs) to regulate gene expression remains incompletely understood. DROSHA initiates the biogenesis of miRNAs while variants of Argonaute (AGO) and trinucleotide repeat containing six (TNRC6) family proteins form complexes with miRNAs to facilitate RNA recognition and gene regulation. Here we investigate the fate of miRNAs in the absence of these critical RNAi protein factors. Knockout of expression reduces levels of some miRNAs annotated in miRBase but not others. The identity of miRNAs with reduced expression matches the identity of miRNAs previously identified by experimental approaches. The MirGeneDB resource offers the closest alignment with experimental results. In contrast, the loss of TNRC6 proteins had much smaller effects on miRNA levels. Knocking out AGO proteins, which directly contact the mature miRNA, decreased expression of the miRNAs most strongly associated with AGO2 as determined from enhanced crosslinking immunoprecipitation (AGO2-eCLIP). Evaluation of miRNA binding to endogenously expressed AGO proteins revealed that miRNA:AGO association was similar for AGO1, AGO2, AGO3, and AGO4. Our data emphasize the need to evaluate annotated miRNAs based on approximate cellular abundance, DROSHA-dependence, and physical association with AGO when forming hypotheses related to their function.
Topics: MicroRNAs; RNA Interference; Argonaute Proteins; Gene Expression Regulation; Trinucleotide Repeats
PubMed: 37169394
DOI: 10.1261/rna.079647.123 -
Molecular Plant Pathology Aug 2023Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many... (Review)
Review
Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.
Topics: Host-Pathogen Interactions; RNA, Small Interfering; MicroRNAs; RNA Interference; Plants
PubMed: 37026481
DOI: 10.1111/mpp.13329 -
Nature Reviews. Nephrology Oct 2023
Topics: Humans; Antihypertensive Agents; RNA Interference; Hypertension
PubMed: 37612379
DOI: 10.1038/s41581-023-00765-2 -
Microbiology Spectrum Aug 2023mosquitoes are the primary vectors for the transmission of malaria parasites, which poses a devastating burden on global public health and welfare. The recent invasion...
mosquitoes are the primary vectors for the transmission of malaria parasites, which poses a devastating burden on global public health and welfare. The recent invasion of Anopheles stephensi in Africa has made malaria eradication more challenging due to its outdoor biting behavior and widespread resistance to insecticides. To address this issue, we developed a new approach for mosquito larvae control using gut microbiota-mediated RNA interference (RNAi). We engineered a mosquito symbiotic gut bacterium, Serratia fonticola, by deleting its gene to produce double-stranded RNAs (dsRNAs) in the mosquito larval gut. We found that the engineered strains can stably colonize mosquito larval guts and produce dsRNAs ds or ds to activate RNAi and effectively suppress the expression of methoprene-tolerant gene and ecdysone receptor gene , which encode receptors for juvenile hormone and ecdysone pathways in mosquitoes, respectively. Importantly, the engineered strains markedly inhibit the development of A. stephensi larvae and leads to a high mortality, providing an effective dsRNA delivery system for silencing genes in insects and a novel RNAi-mediated pest control strategy. Collectively, our symbiont-mediated RNAi (smRNAi) approach offers an innovative and sustainable method for controlling mosquito larvae and provides a promising strategy for combating malaria. Mosquitoes are vectors for various diseases, imposing a significant threat to public health globally. The recent invasion of A. stephensi in Africa has made malaria eradication more challenging due to its outdoor biting behavior and widespread resistance to insecticides. RNA interference (RNAi) is a promising approach that uses dsRNA to silence specific genes in pests. This study presents the use of a gut symbiotic bacterium, Serratia fonticola, as an efficient delivery system of dsRNA for RNAi-mediated pest control. The knockout of , a dsRNA-specific endonuclease gene, in using CRISPR-Cas9 led to efficient dsRNA production. Engineered strains of can colonize the mosquito larval gut and effectively suppress the expression of two critical genes, and , which inhibit mosquito development and cause high mortality in mosquito larvae. This study highlights the potential of exploring the mosquito microbiota as a source of dsRNA for RNAi-based pest control.
Topics: Animals; RNA Interference; Anopheles; Larva; Insecticides; Ribonuclease III; Mosquito Vectors; RNA, Double-Stranded; Malaria
PubMed: 37458601
DOI: 10.1128/spectrum.01666-23 -
Cancer Metastasis Reviews Sep 2023Cancer is a major health concern worldwide and is still in a continuous surge of seeking for effective treatments. Since the discovery of RNAi and their mechanism of... (Review)
Review
Cancer is a major health concern worldwide and is still in a continuous surge of seeking for effective treatments. Since the discovery of RNAi and their mechanism of action, it has shown promises in targeted therapy for various diseases including cancer. The ability of RNAi to selectively silence the carcinogenic gene makes them ideal as cancer therapeutics. Oral delivery is the ideal route of administration of drug administration because of its patients' compliance and convenience. However, orally administered RNAi, for instance, siRNA, must cross various extracellular and intracellular biological barriers before it reaches the site of action. It is very challenging and important to keep the siRNA stable until they reach to the targeted site. Harsh pH, thick mucus layer, and nuclease enzyme prevent siRNA to diffuse through the intestinal wall and thereby induce a therapeutic effect. After entering the cell, siRNA is subjected to lysosomal degradation. Over the years, various approaches have been taken into consideration to overcome these challenges for oral RNAi delivery. Therefore, understanding the challenges and recent development is crucial to offer a novel and advanced approach for oral RNAi delivery. Herein, we have summarized the delivery strategies for oral delivery RNAi and recent advancement towards the preclinical stages.
Topics: Humans; RNA Interference; RNA, Small Interfering; Neoplasms; Carcinogenesis; Drug Delivery Systems
PubMed: 36971908
DOI: 10.1007/s10555-023-10099-x -
ACS Synthetic Biology Oct 2023RNA-protein interactions are essential nodes of cellular regulatory circuits and play critical roles in normal physiology and disease. However, the precise roles of...
RNA-protein interactions are essential nodes of cellular regulatory circuits and play critical roles in normal physiology and disease. However, the precise roles of individual RNA-protein interactions remain elusive. Here we report a method for precise interference of endogenous RNA interacting with the RNA binding protein (RBP). TTP is an RBP that recognizes the AU-rich element (ARE) of mRNA via the binding domain TZF and represses gene expression. We engineer Cas13b, a class 2 type VI CRISPR-Cas endonuclease that exclusively targets RNA, to direct the peptide of TZF to the binding site and compete with endogenous TTP. We show that this tool specifically interferes with TTP interacting with the and 3' UTR under the guidance of the gRNA specific for the AREs. Further, precise interference with the TTP- interaction exerts a distinct effect on cell proliferation compared to transcriptome-wide interference. Thus, our work establishes a tool for deep understanding of RNA-RBP interactions.
Topics: CRISPR-Cas Systems; RNA; RNA, Messenger; RNA Interference; Peptides
PubMed: 37708031
DOI: 10.1021/acssynbio.3c00287 -
Molecular Oncology Feb 2024The F-box and WD repeat domain containing 7 (FBXW7) tumour suppressor gene encodes a substrate-recognition subunit of Skp, cullin, F-box (SCF)-containing complexes. The...
The F-box and WD repeat domain containing 7 (FBXW7) tumour suppressor gene encodes a substrate-recognition subunit of Skp, cullin, F-box (SCF)-containing complexes. The tumour-suppressive role of FBXW7 is ascribed to its ability to drive ubiquitination and degradation of oncoproteins. Despite this molecular understanding, therapeutic approaches that target defective FBXW7 have not been identified. Using genome-wide clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 screens, focussed RNA-interference screens and whole and phospho-proteome mass spectrometry profiling in multiple FBXW7 wild-type and defective isogenic cell lines, we identified a number of FBXW7 synthetic lethal targets, including proteins involved in the response to replication fork stress and proteins involved in replication origin firing, such as cell division cycle 7-related protein kinase (CDC7) and its substrate, DNA replication complex GINS protein SLD5 (GINS4). The CDC7 synthetic lethal effect was confirmed using small-molecule inhibitors. Mechanistically, FBXW7/CDC7 synthetic lethality is dependent upon the replication factor telomere-associated protein RIF1 (RIF1), with RIF1 silencing reversing the FBXW7-selective effects of CDC7 inhibition. The delineation of FBXW7 synthetic lethal effects we describe here could serve as the starting point for subsequent drug discovery and/or development in this area.
Topics: Humans; F-Box-WD Repeat-Containing Protein 7; Cell Line, Tumor; Cell Cycle Proteins; Ubiquitination; RNA Interference; Protein Domains; Ubiquitin-Protein Ligases; Neoplasms; Protein Serine-Threonine Kinases; Chromosomal Proteins, Non-Histone
PubMed: 37866880
DOI: 10.1002/1878-0261.13537 -
Journal of Virology Feb 2024During the life cycle of mosquito-borne flaviviruses, substantial subgenomic flaviviral RNA (sfRNA) is produced incomplete degradation of viral genomic RNA by host...
During the life cycle of mosquito-borne flaviviruses, substantial subgenomic flaviviral RNA (sfRNA) is produced incomplete degradation of viral genomic RNA by host XRN1. Zika virus (ZIKV) sfRNA has been detected in mosquito and mammalian somatic cells. Human neural progenitor cells (hNPCs) in the developing brain are the major target cells of ZIKV, and antiviral RNA interference (RNAi) plays a critical role in hNPCs. However, whether ZIKV sfRNA was produced in ZIKV-infected hNPCs as well as its function remains not known. In this study, we demonstrate that abundant sfRNA was produced in ZIKV-infected hNPCs. RNA pulldown and mass spectrum assays showed ZIKV sfRNA interacted with host proteins RHA and PACT, both of which are RNA-induced silencing complex (RISC) components. Functionally, ZIKV sfRNA can antagonize RNAi by outcompeting small interfering RNAs (siRNAs) in binding to RHA and PACT. Furthermore, the 3' stem loop (3'SL) of sfRNA was responsible for RISC components binding and RNAi inhibition, and 3'SL can enhance the replication of a viral suppressor of RNAi (VSR)-deficient virus in a RHA- and PACT-dependent manner. More importantly, the ability of binding to RISC components is conversed among multiple flaviviral 3'SLs. Together, our results identified flavivirus 3'SL as a potent VSR in RNA format, highlighting the complexity in virus-host interaction during flavivirus infection.IMPORTANCEZika virus (ZIKV) infection mainly targets human neural progenitor cells (hNPCs) and induces cell death and dysregulated cell-cycle progression, leading to microcephaly and other central nervous system abnormalities. RNA interference (RNAi) plays critical roles during ZIKV infections in hNPCs, and ZIKV has evolved to encode specific viral proteins to antagonize RNAi. Herein, we first show that abundant sfRNA was produced in ZIKV-infected hNPCs in a similar pattern to that in other cells. Importantly, ZIKV sfRNA acts as a potent viral suppressor of RNAi (VSR) by competing with siRNAs for binding RISC components, RHA and PACT. The 3'SL of sfRNA is responsible for binding RISC components, which is a conserved feature among mosquito-borne flaviviruses. As most known VSRs are viral proteins, our findings highlight the importance of viral non-coding RNAs during the antagonism of host RNAi-based antiviral innate immunity.
Topics: Animals; Humans; Mammals; RNA Interference; RNA, Small Interfering; RNA, Viral; RNA-Induced Silencing Complex; Subgenomic RNA; Viral Proteins; Virus Replication; Zika Virus; Zika Virus Infection
PubMed: 38289102
DOI: 10.1128/jvi.01954-23 -
Plant, Cell & Environment Sep 2023RNA interference (RNAi) technology is a promising and effective approach for pest insect management. Owing to its sequence-guided working mechanism, RNAi has a high... (Review)
Review
RNA interference (RNAi) technology is a promising and effective approach for pest insect management. Owing to its sequence-guided working mechanism, RNAi has a high degree of species-selectivity, thus minimizing potential adverse effects on nontarget organisms. Recently, engineering plastid (chloroplast) genome, rather than the nuclear genome, to produce double-stranded RNAs has emerged as a powerful way to protect plants from multiple arthropod pests. Here, we review the recent progresses in the plastid-mediated RNAi (PM-RNAi) approach for pest control and the factors influencing its efficacy, and propose the strategies for further efficiency improvement. We also discuss the current challenges and the biosafety-related issues of PM-RNAi technology that need to be addressed for commercial production.
Topics: Animals; RNA Interference; Pest Control; Insecta; Plastids; RNA, Double-Stranded
PubMed: 37332196
DOI: 10.1111/pce.14652