Distinct non‐coding RNAs confer root‐dependent sense transgene‐induced post‐transcriptional gene silencing and nitrogen‐dependent post‐transcriptional regulation to AtAMT1;1 transcripts in Arabidopsis roots. (28th January 2020)

• Record Type: Journal Article
• Authors: Zhang, Yongjian; Wu, Xiangyu; Yuan, Lixing
• Is Part Of: Plant journal. Volume 102:Number 4(2020)
• Page Start: 823
• Page End: 837
• Publication Date: 2020-01-28
• Subjects: post‐transcriptional gene silencing -- post‐transcriptional regulation -- ammonium transporter -- mRNA turnover -- ncRNA; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.14667
• Languages: English
• ISSNs: 0960-7412

Abstract

SUMMARY: High‐affinity ammonium uptake in roots mediate by AMT1‐type ammonium transporters, which are tightly controlled at multiple regulatory levels for adapting various nitrogen availability. For Arabidopsis AtAMT1;1 gene, in addition to the transcriptional and post‐translational controls, an organ‐dependent and N‐dependent post‐transcriptional regulation was suggested as an additional regulatory step for fine tuning ammonium uptake, but the underlying mechanisms remain to be elucidated. Here, we showed that degradation of AtAMT1;1 transcript in roots of Pro35s:AtAMT1;1‐ transformed atamt1;1‐1 Arabidopsis plants resulted from RDR6‐dependent sense transgene‐induced post‐transcriptional gene silencing (S‐PTGS). The siRNAs for S‐PTGS may derive from the aberrant RNA, of which the production was co‐determined by sequence feature and excessive expression of AtAMT1;1 . Switching to the expression of AtAMT1;1 driven by ProAtUBQ10 or of AtAMT1;1 mutated at two siRNA‐targeted hotspots reduced AtAMT1;1 ‐specific siRNAs and overcame S‐PTGS in roots. In roots of these lines, however, the steady‐state transcript levels of AtAMT1;1 still significantly decreased under conditions of N‐sufficiency compared with N‐deficiency, confirming a N‐dependent post‐transcriptional regulatory manner. A crucial role of the 207‐bp 3′‐end sequence of AtAMT1;1 was further demonstrated by N‐dependent accumulation of chimeric‐ AtAMT1;1 transcript in T‐DNA insertion lines and of GFP ‐tagged chimeric‐ AtAMT1;1 transcript in transgenic lines. A novel non‐coding RNA (ncRNA), which was highly abundant in N‐sufficient roots, may target the above‐identified 3′‐end region for the degrading AtAMT1;1 transcript. This degradation could be prevented by a mutation on the AtAMT1;1 transcript at a potential cleavage site ( + 1458). These results suggested two distinct mechanisms of regulating AtAMT1;1 mRNA turnover by ncRNA for strictly control of ammonium uptake in roots. Significance Statement: Post‐transcriptional regulation of ammonium transporter AtAMT1;1 is a critical step for controlling ammonium uptake in Arabidopsis roots, but the underlying mechanism remains unclear. Here, we show that two distinct types of non‐coding RNAs in roots, the RDR6‐dependent transgene‐induced siRNAs and nitrogen‐induced ncRNA, were involved in the degradation of AtAMT1;1 transcripts by targeting the 3′‐end region, preventing from the over‐accumulation of AtAMT1;1 transcripts.