Dek42 encodes an RNA‐binding protein that affects alternative pre‐mRNA splicing and maize kernel development

Abstract

RNA‐binding proteins (RBPs) play an important role in post‐transcriptional gene regulation. However, the functions of RBPs in plants remain poorly understood. Maize kernel mutant dek42 has small defective kernels and lethal seedlings. Dek42 was cloned by Mutator tag isolation and further confirmed by an independent mutant allele and clustered regularly interspaced short palindromic repeats (CRISPR)‐CRISPR‐associated protein 9 materials. Dek42 encodes an RRM_RBM48 type RNA‐binding protein that localizes to the nucleus. Dek42 is constitutively expressed in various maize tissues. The dek42 mutation caused a significant reduction in the accumulation of DEK42 protein in mutant kernels. RNA‐seq analysis showed that the dek42 mutation significantly disturbed the expression of thousands of genes during maize kernel development. Sequence analysis also showed that the dek42 mutation significantly changed alternative splicing in expressed genes, which were especially enriched for the U12‐type intron‐retained type. Yeast two‐hybrid screening identified SF3a1 as a DEK42‐interacting protein. DEK42 also interacts with the spliceosome component U1‐70K. These results suggested that DEK42 participates in the regulation of pre‐messenger RNA splicing through its interaction with other spliceosome components. This study showed the function of a newly identified RBP and provided insights into alternative splicing regulation during maize kernel development.

DEK43 is a P‐type pentatricopeptide repeat (PPR) protein responsible for the Cis‐splicing of nad4 in maize mitochondria

“…RNA binding proteins (RBPs) function in post‐transcriptional gene regulation and are involved in seed development. For example, Dek42 encodes an RBP that affects alternative pre‐mRNA splicing and regulates maize kernel development (Zuo et al 2019). PPR proteins, which represent a type of RBP, are also essential for seed development (Sosso et al 2012; Xiu et al 2016; Li et al 2019).…”

The ALBA RNA-binding proteins function redundantly to promote growth and flowering in Arabidopsis

“…For example, the indirect phenotypic affects were reported for the maize RBP Dek42 that regulates pre-mRNA splicing. The dek42 mutant predominantly affects starch metabolic processes, but perturbation of this process resulted in seedling lethality (Zuo et al, 2019). The dek42 mutant caused differential expression to approximately 6% of the transcriptome (Zuo et al, 2019).…”

“…The dek42 mutant predominantly affects starch metabolic processes, but perturbation of this process resulted in seedling lethality (Zuo et al, 2019). The dek42 mutant caused differential expression to approximately 6% of the transcriptome (Zuo et al, 2019). Similarly, other examples of mutations of RBPs resulted in global changes to the transcriptome.…”

Maize biology: From functional genomics to breeding application

“…Two kernel mutant genes were identified and verified (Song et al ; Zuo et al ). OS1 ( opaque endosperm and small germ 1 ), encoding a putative RWP‐RK transcription factor, expresses highly in the nutrient‐allocation cell types of maize endosperm (Song et al ).…”

“…A similar finding was also recently reported for the same gene (Mimura et al ). Dek42 is a new gene, encoding an RRM_RBM48 type RNA binding protein, and mainly functions in intron‐alternative splicing particularly for the U12‐type introns (Zuo et al ). The study provides evidence that DEK42 regulates alternative intron splicing via interacting with the spliceosome components SF3a1 and U1–70K.…”