Defective Processing of Cytoplasmic and Chloroplast Ribosomal RNA in the Absence of Arabidopsis DXO1 [RNA-seq]

Decapping 5'-3' exoribonucleases from the DXO/Rai1 family are highly conserved among eukaryotes and exhibit diverse enzymatic activities depending on the organism. The biochemical and structural properties of the plant DXO1 differ from the yeast and animal counterparts, which is reflected in the in vivo functions of this enzyme. Here we show that Arabidopsis DXO1 contributes to the efficient processing of rRNA precursors in both nucleolar/cytosolic and chloroplast maturation pathways. However, the processing defects in DXO1-deficient plants do not depend on the catalytic activity of the enzyme but rely on its plant-specific N-terminal extension, which is responsible for the interaction with the mRNA cap methyltransferase RNMT1. Our RNA sequencing analyses show that the dxo1 mutation deregulates the expression of many ribosomal protein genes, most likely leading to inefficient or delayed pre-rRNA maturation. These phenotypes are partially suppressed by RNMT1 overexpression, suggesting that defective cap synthesis may be responsible, at least to some extent, for the observed effects. Founded by National Science Centre Grant, Poland (UMO‐2018/29/B/NZ3/01980, UMO‐2021/40/Q/NZ1/00014, UMO‐2014/13/B/NZ3/00405, MINIATURA 2017/01/X/NZ1/00332, UMO‐2021/41/B/NZ3/02605). Transcriptome profiles of Col-0 wild type, and dxo1-2, xrn3-8 and double dxo1-2 xrn3-8 mutant plants using RNA-seq (three biological replicates). Plants growth, RNA-isolation, libraries preparation and Illumina sequencing were performed in parallel for Col-0 and all mutants. However, data for different mutants were submitted as separate GEO accession along with published manuscripts describing these mutants. Data for Col-0 and xrn3-8 mutant are part of the GSE95473. Data for dxo1-2 mutant are available upon GSE99600. Here, we provide data for double dxo1-2 xrn3-8 mutant. The supplementary file contains gene counts combined for all libraries sequenced in this experiment.