Genome-Wide microRNA Profiling Using Oligonucleotide Microarray Reveals Regulatory Networks of microRNAs in Nicotiana benthamiana During Beet Necrotic Yellow Vein Virus Infection

Abstract

Beet necrotic yellow vein virus (BNYVV) infections induce stunting and leaf curling, as well as root and floral developmental defects and leaf senescence in Nicotiana benthamiana. A microarray analysis with probes capable of detecting 1596 candidate microRNAs (miRNAs) was conducted to investigate differentially expressed miRNAs and their targets upon BNYVV infection of N. benthamiana plants. Eight species-specific miRNAs of N. benthamiana were identified. Comprehensive characterization of the N. benthamiana microRNA profile in response to the BNYVV infection revealed that 129 miRNAs were altered, including four species-specific miRNAs. The targets of the differentially expressed miRNAs were predicted accordingly. The expressions of miR164, 160, and 393 were up-regulated by BNYVV infection, and those of their target genes, NAC21/22, ARF17/18, and TIR, were down-regulated. GRF1, which is a target of miR396, was also down-regulated. Further genetic analysis of GRF1, by Tobacco rattle virus-induced gene silencing, assay confirmed the involvement of GRF1 in the symptom development during BNYVV infection. BNYVV infection also induced the up-regulation of miR168 and miR398. The miR398 was predicted to target umecyanin, and silencing of umecyanin could enhance plant resistance against viruses, suggesting the activation of primary defense response to BNYVV infection in N. benthamiana. These results provide a global profile of miRNA changes induced by BNYVV infection and enhance our understanding of the mechanisms underlying BNYVV pathogenesis.

Whole-Transcriptome RNA Sequencing Reveals the Global Molecular Responses and CeRNA Regulatory Network of mRNAs, lncRNAs, miRNAs and circRNAs in Response to Salt Stress in Sugar Beet (Beta vulgaris)

“…We confirmed cleavage of these two genes by mtr-miR164d by degradation sequencing. This down-regulation may activate multiple downstream genes, which is in agreement with a Nicotiana benthamiana study infected by beet necrotic yellow vein virus [ 61 ]. PC-5P-3682_979 regulates the expression of tocopherol cyclase in leaves, where it may perform a different function.…”

Turnip mosaic virus in oilseed rape activates networks of sRNA-mediated interactions between viral and host genomes

“…Certain virus-and viroid-derived siRNAs interact with host-mRNA targets to direct sequencespecific regulation [19][20][21][22][23][24] , whereas virus-induced changes in miRNA expression reflect changes in the expression of their mRNA targets (e.g., see refs. [25][26][27] ). Also, secondary siRNAs with potential to guide silencing events are produced from multiple endogenous mRNA transcripts in response to viral infections 28 .…”

“…However, whereas the cross-talk interaction between plants, viruses and RNA silencing has been primarily studied in systemically infected plants (e.g., see refs. [24][25][26][27][29][30][31][32][33][34][35][36][37][38][39] ), very little is known about the regulatory layers that operate between the virus and host cells at the infection front.…”

Manipulation of auxin signalling by plant viruses

“…These questions require further investigation. However, additional alternatives deserve consideration as small RNA sequencing and subsequent validation of the data revealed an up-regulation of miR396 (in both species in question), resulting in down-regulation of the TIR1 auxin receptor transcript, the cleavage target of miR396 (Fan et al, 2015;Liu et al, 2020). The repression of the auxin response by reducing the expression of the auxin receptor may indicate a host-specific effect of BNYVV on the auxin signalling pathway in hosts other than sugar beet.…”