MicroRNA-mediated regulation of R-genes: Lessons from model
systems
Plants have evolved an array of resistance genetic mechanisms to cope
with pathogens and herbivores. Modern cultivars are being developed by
pyramiding multiple R-genes as well as genes involved in quantitative
mechanisms to avoid substantial economic loss to crop productivity.
However, it has been shown that constitutive expression of R-genes often
imposes high fitness costs that can have deleterious consequences to
plant growth and development. Therefore, the expression of R-genes must
be tightly regulated and activated in the right spatial and temporal
manner.
Emerging evidence suggested that the miRNAs and secondary siRNA play
important roles in the regulation of R-gene expression by silencing the
immune-response receptors in absence of pathogens. This mechanism is
important in the stabilization of the basal transcript levels in order
to limit the fitness costs of an overactive immune response (Figure 2).
Plants have evolved specific miRNAs that function in targeting the
conserved domains in R-genes. The miR472 was the first miRNA
known to be directly targeting the CC-NBS-LRRs domain-containing immune
receptor genes in Arabidopsis (Lu et al. 2006). Since its
discovery, many other miRNAs involved in R-gene regulation have been
described that optimizes the defense-fitness trade-off in plants. For
example, the sequence-specific cleavage of the TIR-NB-LRR immune
receptor of N gene transcripts that conditions resistance to tobacco
mosaic virus (TMV) were shown to be mediated by nta-miR6019 andnta-miR6020 in Solanaceae family (Li et al. 2012).
The miR482/2118 super-family targeting NB-LRR genes have also
been well characterized in tomato and its prime importance in the
regulation of immune response has been well justified (Shivaprasadet al. 2012). Recently, Osa-miR1876 has been shown to
epigenetically regulate the expression of NBS8R gene encoding a
NB-ARC domain protein that confers resistance to X. oryzae in
rice (Jiang et al. 2020).
Apart from the direct targeting of NLRs, miRNAs have also been shown to
indirectly regulate R-genes via targeting the genes that co-expressed
with R-genes (Wang & Galili 2019). The NBS-LRRs which are not primarily
recognized by miRNA triggers the production of a phased array (in a
sequential, head-to-tail manner, according to the miRNA cleavage site)
of 21-nt secondary small-interfering RNAs (phasiRNAs) to amplify the
silencing effects (Fei, Xia & Meyers 2013). These phasiRNAs are act intrans manner to silence the addition R-gene transcripts. The
fine-tuning of NBS-LRR protein expression by phasiRNA inhibits the
constitutive expressions R-genes, which is potentially detrimental for
plant growth. In the model legume Medicago truncatula, 22-nt
miRNAs including miR2275 , miR2109 , and miR2118 have
been shown to trigger the production of phasiRNA that are specifically
associated with the regulation of NBS-LRR immune receptors (Zhaiet al. 2011; Fei, Li, Teng & Meyers 2015). These miRNAs are
highly conserved in both legumes and non-legume plant species.
In rice, numerous phasiRNAs are preferentially produced and accumulated
in reproductive tissues, particularly anthers, suggesting possible roles
in reproductive development (Johnson et al. 2009; Song et
al. 2012). The rice Agronaute protein MEL1 (MEIOSIS
ARRESTED AT LEPTOTENE 1 ) plays a central role in gametogenesis.
Loss-of-function mutation in MEL1 impedes chromosome condensation
during early meiosis, causing male sterility with aberrant vacuolated
pollen mother cells. The Osa-miR2118 targets over 700
long-intergenic noncoding RNAs (lincRNAs) distributed across the rice
genome. These lincRNAs produce 21-nt phasiRNA. The Argonaute MEL1binds to phasiRNA and regulates pollen mother cell development (Komiyaet al. 2014). The Osa-miR2118 triggered the
sequence-specific cleavage of Pms1 that controls the
photoperiod-sensitive male sterile gene PSMS in rice.
Loss-of-function mutation in Pms1 affects the fertility by
accumulation of Osa-miR2118 -cleaved phasiRNA under long day
condition (Fan et al. 2016).
More recently, the Osa-miR2118 has also been shown to be involved
in 21-nt phasiRNAs, which is responsible for anther wall development in
rice (Araki et al. 2020). The miR482/2118 family was shown
to affect disease resistance in tomato through the regulation of
leucine- rich repeat proteins (Shivaprasad et al. 2012;
Canto-Pastor et al. 2019). The phasiRNA that targets the conserve
motifs of CC-NBS-LRR has been explored in diverse plant species,
including spruce, grapevine, poplar, cotton, Arabidopsis and
citrus (Källman, Chen, Gyllenstrand & Lagercrantz 2013; Boccaraet al. 2014) suggesting that highly conserved siRNAs may be
important in optimizing the expression of NBS-LRR genes, leading to
compromised plant fitness. However, the precise role of phasiRNA in
regulation of NBS-LRR immune receptors in rice is yet to be fully
understood (Fei et al. 2013).