An Arabidopsispre-RNA processing8a (prp8a)missense allele restores splicing of a subset of mis-spliced mRNAs

Abstract

Eukaryotic precursor mRNAs often harbor noncoding introns that must be removed prior to translation. Accurate splicing of precursor messenger RNA depends on placement and assembly of small nuclear ribonucleoprotein (snRNP) sub-complexes of the spliceosome. Yeast (Saccharomyces cerevisiae) studies established a role in splice-site selection for PRE-RNA PROCESSING8 (PRP8), a conserved spliceosome scaffolding protein of the U5 snRNP. However, analogous splice-site selection studies in multicellular eukaryotes are lacking. Such studies are crucial for a comprehensive understanding of alternative splicing, which is extensive in plants and animals but limited in yeast. In this work, we describe an Arabidopsis (Arabidopsis thaliana) prp8a mutant that modulates splice-site selection. We isolated prp8a-14 from a screen for suppressors of pex14-6, which carries a splice-site mutation in the PEROXIN14 (PEX14) peroxisome biogenesis gene. To elucidate Arabidopsis PRP8A function in spliceosome fidelity, we combined prp8a-14 with various pex14 splice-site mutations and monitored the double mutants for physiological and molecular consequences of dysfunctional and functional peroxisomes that correspond to impaired and recovered splicing, respectively. prp8a-14 restored splicing and PEX14 function to alleles with mutations in the exonic guanine of the 5′-splice site but did not restore splicing or function to alleles with mutations in the intronic guanine of 5′- or 3′-splice sites. We used RNA-seq to reveal the systemic impact of prp8a-14 and found hundreds of differentially spliced transcripts and thousands of transcripts with significantly altered levels. Among differentially spliced transcripts, prp8a-14 significantly altered 5′- and 3′-splice-site utilization to favor sites resulting in shorter introns. This study provides a genetic platform for probing splicing in plants and hints at a role for plant PRP8 in splice-site selection.

CXIP4 depletion causes early lethality and pre-mRNA missplicing in Arabidopsis

“…We also found that most of the detected differential AS events do not deregulate the expression of the affected genes, as is the case with the prp8a-14 mutant of the PRP8 gene (Llinas et al, 2022). It is possible that the missplicing events that we found in cxip4-2 plants cause a reduction of functional mRNAs and alter the relative concentrations of the resulting protein isoforms, which may have diverse functional consequences.…”

Genome-Wide Association Study and Prediction of Tassel Weight of Tropical Maize Germplasm in Multi-Parent Population

“…In double mutants of PRP8A and PRP8B, ovules fail to attract pollen tubes, and pollen tubes lose the ability to perceive signals released by the ovules [49]. Additionally, other studies have identified PRP8A as a target gene for alternative splicing [50]. Notably, the PRP8A-14 variant significantly altered the selection of 5 ′ -and 3 ′ -splice sites, displaying a preference for shorter introns.…”