MicroRNA840 (MIR840) accelerates leaf senescence by targeting the overlapping 3′UTRs of PPR and WHIRLY3 in Arabidopsis thaliana

• Published in: The Plant journal : for cell and molecular biology 2022-01, Vol.109 (1), p.126-143
• Main Authors: Ren, Yujun, Li, Mengsi, Wang, Wanzhen, Lan, Wei, Schenke, Dirk, Cai, Daguang, Miao, Ying
• Format: Article
• Language: English
• Subjects: 3' Untranslated regions; Arabidopsis; Cellular stress response; Cleavage; Environmental stress; Gene expression; Genes; genetics; microRNA; miRNA; Phenotypes; post‐transcriptional control; Proteins; Reduction; Senescence; Transcription
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/tpj.15559

SUMMARY MicroRNAs negatively regulate gene expression by promoting target mRNA cleavage and/or impairing its translation, thereby playing a crucial role in plant development and environmental stress responses. In Arabidopsis, the MIR840 gene is located within the overlapping 3′UTR of the PPR and WHIRLY3 (WHY3) genes, both being predicted targets of miR840* and miR840, the short maturation products of MIR840. Gain‐ and loss‐of‐function of MIR840 in Arabidopsis resulted in opposite senescence phenotypes. The highest expression levels of the MIR840 precursor transcript pre‐miR840 were observed at senescence initiation, and pre‐miR840 expression is significantly correlated with a reduction in PPR, but not WHY3, transcript levels. Although a reduction of transcript level of PPR, but not WHY3 transcript levels were not significantly affected by MIR840 overexpression, its protein levels were strongly reduced. Mutating the cleavage sites or replacing the target sequences abolishes the miR840*/miR840‐mediated degradation of PPR transcripts and accumulation of WHY3 protein. In support for this, concurrent knockdown of both PPR and WHY3 in wild‐type plants resulted in a senescence phenotype resembling that of the MIR840‐overexpressing plant. This indicates that both PRR and WHY3 are targets in the MIR840‐mediated senescence pathway. Moreover, single knockout mutants of PPR and WHY3 show a convergent upregulated subset of senescence‐associated genes, which are also found among those induced by MIR840 overexpression. Our data provide evidence for a regulatory role of MIR840 in plant senescence. Significance Statement MIR840 is highly expressed at the onset of plant senescence. Both PPR and WHIRLY3 transcripts are specifically targeted within their 3′UTR region by mature miR840* or miR840 in vivo. miR840* represses PPR transcript levels by promoting cleavage, while miR840 inhibits WHIRLY3 protein expression at the translational level. MIR840 accelerates plant senescence via post‐transcriptional gene silencing of PPR and WHIRLY3, which are novel negative joint regulators of plant senescence. A working model showing how MIR840 accelerates plant senescence in Arabidopsis.Increased expression of MIR840 may be activated by developmental or environmental signals. Processing of pre‐miR840 (generating mature miR840) involves many factors; this process is controlled by DCL1, DCL4, and to a lesser extent DCL2, but not DCL3. Accumulated miR840 or its star strand miR840* is targete