Alternative 3′-untranslated regions regulate high salt tolerance of Spartina alterniflora

Abstract High salt stress continues to challenge the growth and survival of many plants. Alternative polyadenylation (APA) produces mRNAs with different 3′-untranslated regions (3′ UTRs) to regulate gene expression at the post-transcriptional level. However, the roles of alternative 3′ UTRs in response to salt stress remain elusive. Here, we report the function of alternative 3′ UTRs in response to high salt stress in S. alterniflora (Spartina alterniflora), a monocotyledonous halophyte tolerant of high salt environments. We found that high salt stress induced global APA dynamics, and ∼42% of APA genes responded to salt stress. High salt stress led to 3′ UTR lengthening of 207 transcripts through increasing the usage of distal poly(A) sites. Transcripts with alternative 3′ UTRs were mainly enriched in salt stress-related ion transporters. Alternative 3′ UTRs of HIGH-AFFINITY K+ TRANSPORTER 1 (SaHKT1) increased RNA stability and protein synthesis in vivo. Regulatory AU-rich elements were identified in alternative 3′ UTRs, boosting the protein level of SaHKT1. RNAi-knock-down experiments revealed that the biogenesis of 3′ UTR lengthening in SaHKT1 was controlled by the poly(A) factor CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 30 (SaCPSF30). Over-expression of SaHKT1 with an alternative 3′ UTR in rice (Oryza sativa) protoplasts increased mRNA accumulation of salt-tolerance genes in an AU-rich element-dependent manner. These results suggest that mRNA 3′ UTR lengthening is a potential mechanism in response to high salt stress. These results also reveal complex regulatory roles of alternative 3′ UTRs coupling APA and regulatory elements at the post-transcriptional level in plants.