N ⁶-methyladenosine modifications stabilize phosphate starvation response-related mRNAs in plant adaptation to nutrient-deficient stress.

Abstract

N⁶-methyladenosine (m⁶A), an abundant internal mRNA modification, is induced by various stress conditions and post-transcriptionally regulates gene expression. However, how m⁶A modifications help plants respond to nutrient-deficiency stress remains unclear. Here, we profile high-confidence m⁶A modifications in Arabidopsis transcriptome-wide under normal and inorganic orthophosphate (Pi)-deficient conditions (-P). High-confidence m⁶A modifications are identified using synthetic modification-free RNA libraries for systematic calibration. Pi starvation induces widespread m⁶A modifications, mediated by the Pi starvation response (PSR) master regulator PHOSPHATE STARVATION RESPONSE1 (PHR1) and its family members. Many Pi starvation-induced (PSI) m⁶A modifications occur on PSR-related mRNAs, including PHR1. In addition, PHR1 proteins interact with the m⁶A writers MRNA ADENOSINE METHYLASE (MTA) and METHYLTRANSFERASE B (MTB) in nuclei under -P conditions. m⁶A modifications facilitate systemic PSR signaling, as reflected by the reduced Pi content and PSR signaling in a knockdown artificial miRNA line targeting MTA, which shows a global decrease in m⁶A. Transcriptome-wide mRNA decay analysis reveals that PSI-m⁶A increases the stability of PSR-related mRNAs, but not through alternative polyadenylation site shifts. Analysis of transgenic plants with mutations in m⁶A loci demonstrates that m⁶A stabilizes PHR1 transcripts via a positive feedback loop. Our findings indicate that PSI-m⁶A modifications facilitate PSR signaling by enhancing the stability of certain mRNAs, shedding light on the role of m⁶A modifications in nutrient stress responses in plants.