Arabidopsis DXO1 possesses deNADding and exonuclease activities and its mutation affects defense‐related and photosynthetic gene expression

Abstract

RNA capping and decapping tightly coordinate with transcription, translation, and RNA decay to regulate gene expression. Proteins in the DXO/Rai1 family have been implicated in mRNA decapping and decay, and mammalian DXO was recently found to also function as a decapping enzyme for NAD+‐capped RNAs (NAD‐RNA). The Arabidopsis genome contains a single gene encoding a DXO/Rai1 protein, AtDXO1. Here we show that AtDXO1 possesses both NAD‐RNA decapping activity and 5ʹ‐3ʹ exonuclease activity but does not hydrolyze the m7G cap. The atdxo1 mutation increased the stability of NAD‐RNAs and led to pleiotropic phenotypes, including severe growth retardation, pale color, and multiple developmental defects. Transcriptome profiling analysis showed that the atdxo1 mutation resulted in upregulation of defense‐related genes but downregulation of photosynthesis‐related genes. The autoimmunity phenotype of the mutant could be suppressed by either eds1 or npr1 mutation. However, the various phenotypes associated with the atdxo1 mutant could be complemented by an enzymatically inactive AtDXO1. The atdxo1 mutation apparently enhances post‐transcriptional gene silencing by elevating levels of siRNAs. Our study indicates that AtDXO1 regulates gene expression in various biological and physiological processes through its pleiotropic molecular functions in mediating RNA processing and decay.

TheArabidopsismediator complex subunit 8 regulates oxidative stress responses

“…The dxo1 mutation results in up-regulation of defense-related genes. Interestingly, the dxo1-dependent autoimmunity phenotype is also suppressed by the manipulation of SA signaling through npr1 or eds1 mutation (Pan et al, 2020). The interaction of MED8 and the Mediator complex with the CCR4-NOT complex as well as its interactor PUMILIO HOMOLOG2 (Arae et al, 2019) now also links MED8 to miRNA biogenesis.…”

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD + -capped transcripts

“…SPAAC-NAD-seq will aid future studies on NAD-RNA metabolism and molecular functions. The RNA NAD + cap can be removed by at least two classes of decapping enzymes, Nudix family proteins present in both prokaryotes and eukaryotes (8,(33)(34)(35) and DXO proteins found only in eukaryotes (9,33,36,37). NAD-RNAs transfected into human cells and Arabidopsis protoplasts undergo DXO-dependent degradation (9,37).…”

“…The RNA NAD + cap can be removed by at least two classes of decapping enzymes, Nudix family proteins present in both prokaryotes and eukaryotes (8,(33)(34)(35) and DXO proteins found only in eukaryotes (9,33,36,37). NAD-RNAs transfected into human cells and Arabidopsis protoplasts undergo DXO-dependent degradation (9,37). In an Arabidopsis dxo mutant, NAD + -capped transcripts are channeled to RNA silencing for degradation (32,36).…”

NAD+capping of RNA in Archaea and Mycobacteria

“…NAD + cap removing enzymes have been identified in bacteria, mammals, yeast and plants (4, 7, 13, 47, 71–73). They are often represented by members of the Nudix family (3, 14, 74).…”