In silico MCMV Silencing Concludes Potential Host-Derived miRNAs in Maize.
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ABSTRACT:
SUBMITTER: Iqbal MS
PROVIDER: S-EPMC5368279 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Potato virus Y has emerged as a threatening problem in all potato growing areas around the globe. PVY reduces the yield and quality of potato cultivars. During the last 30 years, significant genetic changes in PVY strains have been observed with an increased incidence associated with crop damage. In the current study, computational approaches were applied to predict Potato derived miRNA targets in the PVY genome. The PVY genome is approximately 9 thousand nucleotides, which transcribes the following 6 genes:CI, NIa, NIb-Pro, HC-Pro, CP, and VPg. A total of 343 mature miRNAs were retrieved from the miRBase database and were examined for their target sequences in PVY genes using the minimum free energy (mfe), minimum folding energy, sequence complementarity and mRNA-miRNA hybridization approaches. The identified potato miRNAs against viral mRNA targets have antiviral activities, leading to translational inhibition by mRNA cleavage and/or mRNA blockage. We found 86 miRNAs targeting the PVY genome at 151 different sites. Moreover, only 36 miRNAs potentially targeted the PVY genome at 101 loci. The CI gene of the PVY genome was targeted by 32 miRNAs followed by the complementarity of 26, 19, 18, 16, and 13 miRNAs. Most importantly, we found 5 miRNAs (miR160a-5p, miR7997b, miR166c-3p, miR399h, and miR5303d) that could target the CI, NIa, NIb-Pro, HC-Pro, CP, and VPg genes of PVY. The predicted miRNAs can be used for the development of PVY-resistant potato crops in the future.
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Project description:Host miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses through several possible mechanisms including direct binding of viral RNA. Identification of human miRNAs involved in coronavirus-host interplay becomes important due to the ongoing COVID-19 pandemic. In this article we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. As a result, we identified six miRNAs (miR-21-3p, miR-195-5p, miR-16-5p, miR-3065-5p, miR-424-5p and miR-421) with high binding probability across all analyzed viruses. Further bioinformatic analysis of binding sites revealed high conservativity of miRNA binding regions within RNAs of human coronaviruses and their strains. In order to discover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse lungs during infection induced by SARS-CoV.
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Project description:BackgroundRecently, putative pre-miRNAs locations have been identified in the introns of plant genes, raising the question whether such genes can show a dual functionality by having both correct maturation of the host gene pre-mRNA and maturation of the miRNAs from the intron. Here, we demonstrated that such dual functionality is indeed possible, using as host gene the firefly luciferase gene with intron (ffgLUC), and different artificial intronic miRNAs (aimiRNA) placed within the intron of ffgLUC.ResultsThe miRNAs were based on the structure of the natural miR319a. Luciferase (LUC) activity in planta was used to evaluate a correct splicing of the ffgLUC mRNA. Different target sequences were inserted into the aimiRNA to monitor efficiency of silencing of different target mRNAs. After adjusting the insertion cloning strategy, the ffgLUCaimiR-319a gene showed dual functionality with correct splicing of ffgLUC and efficient silencing of TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 transcription factor genes targeted in-trans by aimiR-319a or targeting the transgene ffLUC in-cis by an aimiR-LUC. Silencing of endogenous target genes by aimiRNA or amiRNA is efficient both in transient assays and stable transformants. A behave as strong phenotype the PHYTOCHROME B (PHYB) gene was also targeted by ffgLUCaimiR-PHYB. The lack of silencing of the PHYB target was most likely due to an insensitive target site within the PHYB mRNA which can potentially form a double stranded stem structure.ConclusionThe combination of an overexpression construct with an artificial intronic microRNA allows for a simultaneous dual function in plants. The concept therefore adds new options to engineering of plant traits that require multiple gene manipulations.
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Project description:Maize chlorotic mottle virus (MCMV) has been occurring frequently worldwide and causes severe yield losses in maize (Zea mays). To better investigate the destructive effects of MCMV infection on maize plants, isobaric tagging for relative and absolute quantitation (iTRAQ)-based comparative proteomic analysis was performed on MCMV infected maize cv. B73. A total of 972 differentially abundant proteins (DAPs), including 661 proteins with increased abundance and 311 proteins with reduced abundance, were identified in response to MCMV infection. Functional annotations of DAPs and measurement of photosynthetic activity revealed that photosynthesis was decreased, while the abundance of ribosomal proteins, proteins related to stress responses, oxidation-reduction and redox homeostasis was altered significantly during MCMV infection. Two DAPs, disulfide isomerases like protein ZmPDIL-1 and peroxiredoxin family protein ZmPrx5, were further analyzed for their roles during MCMV infection through cucumber mosaic virus-based virus-induced gene silencing (CMV-VIGS). The accumulation of MCMV was suppressed in ZmPDIL-1-silenced or ZmPrx5-silenced B73 maize, suggesting ZmPDIL-1 and ZmPrx5 might enhance host susceptibility to MCMV infection.
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Project description:Maize lethal necrosis is attributed to the accumulation of maize chlorotic mottle virus (MCMV), an invasive virus transmitted by insect vectors. The western flower thrips (WFT) can shift host to maize, thus promoting the spread of MCMV. However, our understanding of the characteristics and interactions involved in the transmission of MCMV is still limited. This study finds that non-viruliferous WFTs showed a 57.56% higher preference for MCMV-infected maize plants compared to healthy maize plants, while viruliferous WFTs showed a 53.70% higher preference for healthy maize plants compared to MCMV-infected maize plants. We also show for the first time that both adults and larvae of WFT could successfully acquire MCMV after 1 min of acquisition access period (AAP), and after 48 h of AAP, WFT could transmit MCMV in an inoculation access period of 1 h without a latent period. Both adults and larvae of WFT can transmit MCMV for up to 2 days. Furthermore, the decreasing number of viruliferous WFTs and transmission rates as time progressed, together with the transcriptomic evidence, collectively suggest that WFTs transmit MCMV in a semi-persistent method, a mode of transmission requiring minutes to several hours for acquisition access and having a retention time of several hours to a few days. Additionally, β-myrcene can attract WFTs significantly and is detected in Nicotiana benthamiana plants transiently expressing MCMV CP (coat protein), which is consistent with results in MCMV-infected maize plants through the metabolomic profiling and the preference analyses of WFT. Therefore, this study demonstrates the indirect interaction between MCMV and WFT by inducing maize to synthesize β-myrcene to attract insect vectors. The exploration of specific interactions between MCMV and WFT could help to expand the mechanism studies of virus-vector-host plant interaction and put forward a new insight for the combined control of MCMV and WFT through the manipulation of plant volatiles and key insect genes.
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Project description:In late December 2019, several cases of pneumonia of unknown etiology (COVID-19) were reported in Wuhan, Hubei province, China. Based on clinical findings, blood tests and chest radiographs, this disease was diagnosed as a virus-associated pneumonia. Sequence analysis revealed a novel coronavirus, called SARS-CoV-2 (formerly called 2019-nCoV), as the causative agent of pneumonia of unknown etiology. So far, the SARS-CoV-2 infection continues to spread, and this virus poses a serious public health threat. In this study, it was aimed to reveal potential miRNA targets for the regulation of SARS-CoV-2 host cell receptor ACE2. For the identification of potential miRNA targets for the ACE2 gene, TarBase v.8 (DIANA Tools), TargetScan, miRTarBase and miRDB miRNA-target prediction algorithms were used. FANTOM5 CAGE was used for the cellular ontology analysis. Expression levels of these miRNAs were determined using OncomiR Pan-Cancer miRNome Atlas. The results suggest that members of miR-200 family of miRNAs, especially miR-200c-3p, are strong candidate targets for the regulation of ACE2 in respiratory system cells. Consequently, the present study for the first time emphasizes potential use of miRNA-based therapeutics in the battle against SARS-CoV-2 infection and its deadly disease, COVID-19.
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