Virus versus Host Plant MicroRNAs: Who Determines the Outcome of the Interaction?

Abstract

Considering the importance of microRNAs (miRNAs) in the regulation of essential processes in plant pathogen interactions, it is not surprising that, while plant miRNA sequences counteract viral attack via antiviral RNA silencing, viruses in turn have developed antihost defense mechanisms blocking these RNA silencing pathways and establish a counter-defense. In the current study, computational and stem-loop Reverse Transcription – Polymerase Chain Reaction (RT-PCR) approaches were employed to a) predict and validate virus encoded mature miRNAs (miRs) in 39 DNA-A sequences of the bipartite genomes of African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) isolates, b) determine whether virus encoded miRs/miRs* generated from the 5′/3′ harpin arms have the capacity to bind to genomic sequences of the host plants Jatropha or cassava and c) investigate whether plant encoded miR/miR* sequences have the potential to bind to the viral genomes. Different viral pre-miRNA hairpin sequences and viral miR/miR* length variants occurring as isomiRs were predicted in both viruses. These miRNAs were located in three Open Reading Frames (ORFs) and in the Intergenic Region (IR). Moreover, various target genes for miRNAs from both viruses were predicted and annotated in the host plant genomes indicating that they are involved in biotic response, metabolic pathways and transcription factors. Plant miRs/miRs* from conserved and highly expressed families were identified, which were shown to have potential targets in the genome of both begomoviruses, representing potential plant miRNAs mediating antiviral defense. This is the first assessment of predicted viral miRs/miRs* of ACMV and EACMV-UG and host plant miRNAs, providing a reference point for miRNA identification in pathogens and their hosts. These findings will improve the understanding of host- pathogen interaction pathways and the function of viral miRNAs in Euphorbiaceous crop plants.

Geminiviruses and Plant Hosts: A Closer Examination of the Molecular Arms Race

“…Considering these facts, the genome of geminiviruses could be examined for its miRNA coding potential because geminiviruses enter the plant nucleus. Interestingly, the expression of viral derived miRNAs has been demonstrated during the infection of African cassava mosaic virus and East African cassava mosaic virus—Uganda [ 67 ]. Hence, the proof of miRNA coding potential and functional miRNAs from the genomes of a geminivirus raises questions as to who determines the outcome of the host-geminivirus interactions in the sRNA interface [ 67 ].…”

A novel miRNA analysis framework to analyze differential biological networks

“…The RNA-seq–based transcriptome scrutiny fastens the process of understanding plant systems in terms of biotic or abiotic stress, including virus infection, at the molecular level 16 . The mechanism of miRNA interaction between a virus and host plant was reported for various plant species including Jatropha 17 . The next-generation sequencing approaches substantially increase the quantity and quality of data on miRNA targets and their functional annotations.…”

“…To validate the proposed framework for various datasets, we contemplated two differential conditions of Jatropha. Various viral, fungal, and bacterial infections reduce the global average yield of J. curcas by 16% yearly 28 , the majority of which results from the occurrence of J. curcas mosaic virus, which causes leaf curling and reduction in fruit size 17 . Therefore, we considered the virus-infected (JV) tissue as one of the differential conditions.…”

Computational Identification, Characterization and Analysis of Conserved miRNAs and their Targets in Amborella Trichopoda

“…of invasive pathogens such as viroid and/or viruses that inject their genomes into the host plant [50,51]. Moreover and most likely, through evolutionary forces, genomes may have lost their corresponding target sites.Hundreds of thousands of hairpin structure in a genome exist that many of them appear to be derived from repeats, transposable elements and transposable inverted repeats as well as other evolving mechanisms that have the potential to form extremely stable miRNA like hairpin structure.…”