Virus versus host plant microRNAs: who determines the outcome of the interaction?
Authors: Fatemeh Maghuly
Margit Laimer
Rose C Ramkat
Journal: PLoS ONE (2014)
Discipline: Multidisciplinary
Keywords: microRNAs; plant pathogen interactions; antiviral RNA silencing; virus encoded miRNAs; stem-loop RT-PCR
Affiliations: Plant Biotechnology Unit (PBU), Department Biotechnology, University of Natural Resources and Life Sciences, BOKU-VIBT, Vienna, Austria., Plant Biotechnology Unit (PBU), Department Biotechnology, University of Natural Resources and Life Sciences, BOKU-VIBT, Vienna, Austria; Department of Biological Sciences, Egerton University, Nakuru, Kenya.

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. 

Retracted: No

PubPeer comments:
 Could the authors clarify this image duplication in the same paper? ![file] , 
 The Western blots throughout this paper have unusual characteristics; see image below as an example, in which a splice and image editing seem apparent. In addition, these images of Figures 5A and 5B appear to be the same, but are labeled differently. *** ![file] , 
 The same gel images were used for two experimental conditions. Upper band for MCP-1 and the lower for the TNF-a. Could the authors clarify with their raw data??? ![file] ,