RNase III nucleases from diverse kingdoms serve as antiviral effectors

Aguado, Lauren C.; Schmid, Sonja; May, Jared; Sabin, Leah R.; Panis, Maryline; Blanco-Melo, Daniel; Shim, Jaehee; Sachs, David; Cherry, Sara; Simon, Anne; Levraud, Jean‐Pierre; tenOever, Benjamin R.

doi:10.1038/nature22990

Cited by 55 publications

(57 citation statements)

References 39 publications

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“…To test this hypothesis, we cloned the 3′UTR of the BHRF1 protein, which encompasses these two pri-miRNAs, either from WT EBV or from the Δ123 EBV mutant in which the pri-miR-BHRF1-2 and 1-3 stem-loops have been mutationally inactivated, 3′ to the FLuc indicator gene. These two constructs, and a control “empty” FLuc vector lacking any inserted EBV sequences, were then transfected into wildtype 293T cells, as well as into a previously described 293T derivative in which both Drosha and Dicer expression had been blocked by gene editing, called RNaseIII−/− cells (Aguado et al, 2017). FLuc expression was then determined relative to a co-transfected NanoLuc control vector.…”

Section: Resultsmentioning

confidence: 99%

“…293T cells were grown in Dulbecco’s modified Eagle medium (DMEM) supplemented with 5% FBS, 50 μg/ml gentamicin, and 1x Antibiotic-Antimycotic. NoDice/ΔPKR cells (Kennedy et al, 2015) and RNaseIII−/− 293T cells (Aguado et al, 2017) were grown in DMEM supplemented with 10% FBS, 50 μg/ml gentamicin, and 1x Antibiotic-Antimycotic.. All cells were grown at 37°C with 5% CO 2 .…”

Section: Methodsmentioning

confidence: 99%

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The Epstein-Barr virus miR-BHRF1 microRNAs regulate viral gene expression in cis

et al. 2017

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The Epstein-Barr virus (EBV) miR-BHRF1 microRNA (miRNA) cluster has been shown to facilitate B-cell transformation and promote the rapid growth of the resultant lymphoblastoid cell lines (LCLs). However, we find that expression of physiological levels of the miR-BHRF1 miRNAs in LCLs transformed with a miR-BHRF1 null mutant (Δ123) fails to increase their growth rate. We demonstrate that the pri-miR-BHRF1-2 and 1-3 stem-loops are present in the 3′UTR of transcripts encoding EBNA-LP and that excision of pre-miR-BHRF1-2 and 1-3 by Drosha destabilizes these mRNAs and reduces expression of the encoded protein. Therefore, mutational inactivation of pri-miR-BHRF1-2 and 1-3 in the Δ123 mutant upregulates the expression of not only EBNA-LP but also EBNA-LP-regulated mRNAs and proteins, including LMP1. We hypothesize that this overexpression causes the reduced transformation capacity of the Δ123 EBV mutant. Thus, in addition to regulating cellular mRNAs in trans, miR-BHRF1-2 and 1-3 also regulate EBNA-LP mRNA expression in cis.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The Epstein-Barr virus miR-BHRF1 microRNAs regulate viral gene expression in cis

et al. 2017

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“…We have experimentally analyzed two well‐known biochemical factors, RNase P and RNase III . Their basic domains are present in all three domains of life (although functional RNase III is limited to a subset of archaeal species), so that it is assumed that they were likely operating in the last universal common ancestor (LUCA) of past and current biodiversity . All our reaction assays were performed in vitro using purified factors.…”

Section: A Methods For Mrna Archaeologymentioning

confidence: 99%

The archaeology of coding RNA

Ariza-Mateos

Briones

Perales

et al. 2019

Annals of the New York Academy of Sciences

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Different theories concerning the origin of RNA (and, in particular, mRNA) point to the concatenation and expansion of proto‐tRNA−like structures. Different biochemical and biophysical tools have been used to search for ancient‐like RNA elements with a specific structure in genomic viral RNAs, including that of the hepatitis C virus, as well as in cellular mRNA populations, in particular those of human hepatocytes. We define this method as “archaeological,” and it has been designed to discover evolutionary patterns through a nonphylogenetic and nonrepresentational strategy. tRNA‐like elements were found in structurally or functionally relevant positions both in viral RNA and in one of the liver mRNAs examined, the antagonist interferon‐alpha subtype 5 (IFNA5) mRNA. Additionally, tRNA‐like elements are highly represented within the hepatic mRNA population, which suggests that they could have participated in the formation of coding RNAs in the distant past. Expanding on this finding, we have observed a recurring dsRNA‐like motif next to the tRNA‐like elements in both viral RNAs and IFNA5 mRNA. This suggested that the concatenation of these RNA motifs was an activity present in the RNA pools that might have been relevant in the RNA world. The extensive alteration of sequences that likely triggered the transition from the predecessors of coding RNAs to the first fully functional mRNAs (which was not the case in the stepwise construction of noncoding rRNAs) hinders the phylogeny‐based identification of RNA elements (both sequences and structures) that might have been active before the advent of protein synthesis. Therefore, our RNA archaeological method is presented as a way to better understand the structural/functional versatility of a variety of RNA elements, which might represent “the losers” in the process of RNA evolution as they had to adapt to the selective pressures favoring the coding capacity of the progressively longer mRNAs.

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“…Since DDX17 also interacts with enzymes in the canonical mRNA degradation machinery, it was proposed that Rm62/DDX17 may function as an RNA sensor of RVFV infection to facilitate (RNAi-independent) degradation [112]. Finally, an ancient antiviral role was demonstrated for Drosha, the RNase III component of the microprocessor complex that processes primary miRNA transcripts in the nucleus [120]. However, Drosha is proposed to act as an antiviral factor through direct recognition/processing of RNA stem loops, conform to its ancestral function, independently of the antiviral RNAi machinery (Dcr-2, Ago-2) or its role in primary miRNA processing, that both later evolved.…”

Section: No Identification Of Rnai Machinery Componentsmentioning

confidence: 99%

“…Furthermore, it was regularly observed that host factors in Drosophila cells were conserved in mammalian (human) cells [112][113][114][117][118][119][120]. The results of the screens with respect to the (validated) identification of both new resistance mechanisms (VRFs, "antiviral genes") as well as (often virus-specific) cellular processes that are limiting to viral infection (VSFs, "proviral genes") are summarized in Table 1.…”

Section: Identification Of Host Factors That Restrict Viral Infectionmentioning

confidence: 99%

Defense Mechanisms against Viral Infection in <em>Drosophila</em>: RNAi versus Non-RNAi

Swevers¹,

Liu²,

Smagghe³

2018

Preprint

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RNAi is considered a major antiviral defense mechanism in insects but its relative importance compared to other antiviral pathways has not been evaluated comprehensively. Here, it is attempted to give an overview of the antiviral defense mechanisms in Drosophila that involve both RNAi and non-RNAi to acquire a sense of their relative importance. While RNAi is considered important in most viral infections, many other pathways can exist that confer antiviral resistance. It is noted that very few direct recognition mechanisms of virus infections have been identified in Drosophila and that the activation of immune pathways may be accomplished indirectly through cell damage incurred by viral replication. In several cases, protection against viral infection can be obtained in RNAi mutants by non-RNAi mechanisms, confirming the variability of the RNAi defense mechanism according to the type of infection and the physiological status of the host. This analysis invites to investigate more systematically the relative contribution of RNAi in the antiviral response and more specifically to ask whether RNAi efficiency is affected when other defense mechanisms predominate. While Drosophila can function as a useful model, this issue may be more critical for economically important insects that are either controlled (agricultural pests and vectors of diseases) or protected from parasite infection (beneficial insects as bees) by RNAi products.

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RNase III nucleases from diverse kingdoms serve as antiviral effectors

Cited by 55 publications

References 39 publications

The Epstein-Barr virus miR-BHRF1 microRNAs regulate viral gene expression in cis

The Epstein-Barr virus miR-BHRF1 microRNAs regulate viral gene expression in cis

The archaeology of coding RNA

Defense Mechanisms against Viral Infection in <em>Drosophila</em>: RNAi versus Non-RNAi

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