Ectopic expression of miRNA172 in tomato (Solanum lycopersicum) reveals novel function in fruit development through regulation of an AP2 transcription factor

Abstract

Background: MicroRNAs (miRNAs) are short non-coding RNAs that can influence gene expression via diverse mechanisms. Tomato is a fruit widely consumed for its flavor, culinary attributes, and high nutritional quality. Tomato fruit are climacteric and fleshy, and their ripening is regulated by endogenous and exogenous signals operating through a coordinated genetic network. Much research has been conducted on mechanisms of tomato fruit ripening, but the roles of miRNA-regulated repression/expression of specific regulatory genes are not well documented. Results: In this study, we demonstrate that miR172 specifically targets four SlAP2 transcription factor genes in tomato. Among them, SlAP2a was repressed by the overexpression of SlmiR172, manifesting in altered flower morphology, development and accelerated ripening. miR172 over-expression lines specifically repressed SlAP2a, enhancing ethylene biosynthesis, fruit color and additional ripening characteristics. Most previously described ripening-regulatory genes, including RIN-MADS, NR, TAGL1 and LeHB-1 were not influenced by miR172 while CNR showed altered expression. Conclusions: Tomato fruit ripening is directly influenced by miR172 targeting of the APETALA2 transcription factor, SlAP2a, with minimal influence over additional known ripening-regulatory genes. miR172a-guided SlAP2a expression provides insight into another layer of genetic control of ripening and a target for modifying the quality and nutritional value of tomato and possibly other fleshy fruit crops.

MIR172d Is Required for Floral Organ Identity and Number in Tomato

“…While loss of sly-miR172d activity led to their complete transformation into sepal-like organs (slmir172c-d ), a partial loss of sly-miR172d activity caused an incomplete conversion of their identity (slmir172 CR-8-2 , slmir172 ). Previously, overexpression of sly-miR172a induced the conversion of sepals into petals in a dose-dependent manner [30]. Together, these findings suggest that sly-miR172d regulates in a quantitative manner the identity of petals and stamens.…”

“…In this study, we deciphered the functions of SlMIR172c and SlMIR172d in flower development. Still, sly-miR172 is expressed during fruit development and are predicted to guide the cleavage of SlAP2a, which is involved in fruit ripening [30,[43][44][45]. Future studies will focus on functional analysis of the remaining five tomato SlMIR172 genes, with the hope to expand the knowledge on the roles of this important miRNA family in plants.…”

“…In contrast to the comprehensive understanding of miR172 and individual MIR172 gene functions in Arabidopsis [7,17,18], only two functional studies on tomato miR172 were published to date. These describe the ectopic expression of miR172 that resulted in the development of flowers with enlarged sepals showing sepal-topetal transformation [29,30]. In the current study, we performed extensive bioinformatic analysis of public small RNA and degradome data to identify all transcriptionally active sly-miR172 coding loci in tomato and their possible target mRNAs, respectively.…”

Transcriptional regulation ofHSFA7and post-transcriptional modulation ofHSFB4aby miRNA4200 govern general and varietal thermotolerance in tomato

“…Thus, we speculate that this differential abundance of Sly-MIR4200 maintains the differential levels of HSFB4a between these cultivars in heat stress, thereby regulating the differential heat tolerance in CLN-CA4 cultivars (Supplementary figure S11). While microRNAs have been established as major regulators of transcription factors at post-transcriptional level in response to various abiotic stresses and developmental stages (Stief et al 2014; Karlova et al 2013; Chung et al 2020; Rao et al 2020), this is the first report to establish the miRNA-mediated post-transcriptional regulation of HSF by transcript cleavage. While the role of Sly-miR4200:HSFB4a is apparent in regulating thermotolerance mechanism in the tolerant and sensitive cultivars, further the expression analysis of Sly-miR4200:HSFB4a module also suggests the possible roles of this module in governing other abiotic stresses like drought and salt stress.…”

APETALA2/ethylene responsive factor in fruit ripening: Roles, interactions and expression regulation

“…In tomato, miR172 specifically targets SlAP2a . Overexpression of miR172 represses SlAP2a expression, resulting in enhanced ethylene biosynthesis and coloration ( Chung et al, 2020 ). In apple, MdAP2_1a, targeted by miR172, transactivates MdMYB10 and positively regulates anthocyanin biosynthesis.…”