Complex regulation of microRNAs in roots of competitively-grown isogenic Nicotiana attenuata plants with different capacities to interact with arbuscular mycorrhizal fungi

Abstract

BackgroundNicotiana attenuata is an ecological model plant whose 2.57 Gb genome has recently been sequenced and assembled and for which miRNAs and their genomic locations have been identified. To understand how this plant’s miRNAs are reconfigured during plant-arbuscular mycorrhizal fungal (AMF) interactions and whether hostplant calcium- and calmodulin dependent protein kinase (CCaMK) expression which regulates the AMF interaction also modulates miRNAs levels and regulation, we performed a large-scale miRNA analysis of this plant-AMF interaction.ResultsNext generation sequencing of miRNAs in roots of empty vector (EV) N. attenuata plants and an isogenic line silenced in CCaMK expression (irCCaMK) impaired in AMF-interactions grown under competitive conditions with and without AMF inoculum revealed a total of 149 unique miRNAs: 67 conserved and 82 novel ones. The majority of the miRNAs had a length of 21 nucleotides. MiRNA abundances were highly variable ranging from 400 to more than 25,000 reads per million. The miRNA profile of irCCaMK plants impaired in AMF colonization was distinct from fully AMF-functional EV plants grown in the same pot. Six conserved miRNAs were present in all conditions and accumulated differentially depending on treatment and genotype; five (miR6153, miR403a-3p, miR7122a, miR167-5p and miR482d, but not miR399a-3p) showed the highest accumulation in AMF inoculated EV plants compared to inoculated irCCaMK plants. Furthermore, the accumulation patterns of sequence variants of selected conserved miRNAs showed a very distinct pattern related to AMF colonization - one variant of miR473-5p specifically accumulated in AMF-inoculated plants. Also abundances of miR403a-3p, miR171a-3p and one of the sequence variants of miR172a-3p increased in AMF-inoculated EV compared to inoculated irCCaMK plants and to non-inoculated EV plants, while miR399a-3p was most strongly enriched in AMF inoculated irCCaMK plants grown in competition with EV. The analysis of putative targets of selected miRNAs revealed an involvement in P starvation (miR399), phytohormone signaling (Nat-R-PN59, miR172, miR393) and defense (e.g. miR482, miR8667, Nat-R-PN-47).ConclusionsOur study demonstrates (1) a large-scale reprograming of miRNAs induced by AMF colonization and (2) that the impaired AMF signaling due to CCaMK silencing and the resulting reduced competitive ability of irCCaMK plants play a role in modulating signal-dependent miRNA accumulation.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5338-x) contains supplementary material, which is available to authorized users.

Genomics and the future of psychopharmacology: MicroRNAs offer novel therapeutics

“…In plants, miRNAs affect root physiology and, once released in extracellular vesicles, may even affect neighboring plants and fungi. 21 The idea that interspecies effects of miRNAs take place also in animals has been put forward as a hypothesis, 22 and preliminary evidence for their cross-species communication is emerging. 23 , 24 However, our understanding on cross-species effects of miRNAs is still sketchy and requires robust confirmation.…”

microRNA390 modulates Nicotiana attenuata's tolerance response to Manduca sexta herbivory

“…After wild fires, N. attenuata germinates from long‐lived seed banks and establishes mono‐culture populations, while encountering several ecological challenges. The plant is colonized by AMF (Pandey et al, 2018 ) and is also attacked by pathogens such as Fusarium and Alternaria species (Schuck et al, 2014 ). Furthermore, N. attenuata faces an unpredictable attack by a diverse suite of herbivore species, which is thought to represent an important ecological challenge for this species; consequently, N. attenuata recruits several direct and indirect defenses (Baldwin, 2001 ; Navarro‐Quezada et al, 2020 ).…”

“…Moreover, the composition and role of the RNA‐directed RNA polymerase (RdR), DCL, and AGO components of the smRNA machinery during adaptation to these natural challenges have also been studied (Navarro‐Quezada et al, 2020 ). The composition of miRNAs in N. attenuata's genome (Xu et al, 2017 ) and its reprograming during herbivore attack, pathogen infection, and AMF colonization are also known (Pandey et al, 2018 ; Pradhan et al, 2017 , 2020 ).…”

“…miR390 has been identified in N. attenuata ; its expression is up‐regulated during simulated herbivory (Bozorov et al, 2012 ), whereas it is down‐regulated during interactions with AMF (Pandey et al, 2018 ). Yet, the biological function of this highly conserved miRNA remains poorly studied in N. attenuata and is the subject of this investigation.…”

Comparative mRNA and LncRNA Analysis of the Molecular Mechanisms Associated With Low Silk Production in Bombyx mori

“…In recent years, studies have shown that lncRNAs are involved in various biological processes, and the mechanisms of gene expression regulation mediated by lncRNAs can be roughly divided into the following three categories: (1) epigenetic modification, which involves regulation of downstream genes by histone modification (Gong and Maquat, 2011 ) and chromatin remodeling (Beniaminov et al, 2008 ; Zhao et al, 2008 ; Mercer et al, 2009 ); (2) transcriptional regulation, which involves effects on the transcription of protein-coding genes (upregulation or downregulation of the expression of the genes) via interactions with their promoters or transcription factors (Igor et al, 2007 ; Zhao et al, 2008 ; Jing et al, 2010 ); and (3) posttranscriptional regulation, which involves processing of lncRNAs into small RNAs such as siRNAs (Tiash and Chowdhury, 2018 ; Tsai et al, 2018 ) and miRNAs (Yuya et al, 2008 ; Annilo et al, 2009 ; Pandey et al, 2018 ) that function via complementary binding to coding gene transcripts. Recent research on lncRNAs has mainly concentrated on humans and mice.…”