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

N(6)-methyladenosine (m(6)A), an abundant internal mRNA modification, is induced by various stress conditions and post-transcriptionally regulates gene expression. However, how m(6)A modifications help plants respond to nutrient-deficiency stress remains unclear. Here, we profile high-confidence m(6)A modifications in Arabidopsis transcriptome-wide under normal and inorganic orthophosphate (Pi)-deficient conditions (-P). High-confidence m(6)A modifications are identified using synthetic modification-free RNA libraries for systematic calibration. Pi starvation induces widespread m(6)A modifications, mediated by the Pi starvation response (PSR) master regulator PHOSPHATE STARVATION RESPONSE1 (PHR1) and its family members. Many Pi starvation-induced (PSI) m(6)A modifications occur on PSR-related mRNAs, including PHR1. In addition, PHR1 proteins interact with the m(6)A writers MRNA ADENOSINE METHYLASE (MTA) and METHYLTRANSFERASE B (MTB) in nuclei under -P conditions. m(6)A 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 m(6)A. Transcriptome-wide mRNA decay analysis reveals that PSI-m(6)A increases the stability of PSR-related mRNAs, but not through alternative polyadenylation site shifts. Analysis of transgenic plants with mutations in m(6)A loci demonstrates that m(6)A stabilizes PHR1 transcripts via a positive feedback loop. Our findings indicate that PSI-m(6)A modifications facilitate PSR signaling by enhancing the stability of certain mRNAs, shedding light on the role of m(6)A modifications in nutrient stress responses in plants.