Aberrant mRNA Transcripts and the Nonsense-Mediated Decay Proteins UPF2 and UPF3 Are Enriched in theArabidopsisNucleolus  

Abstract

The eukaryotic nucleolus is multifunctional and involved in the metabolism and assembly of many different RNAs and ribonucleoprotein particles as well as in cellular functions, such as cell division and transcriptional silencing in plants. We previously showed that Arabidopsis thaliana exon junction complex proteins associate with the nucleolus, suggesting a role for the nucleolus in mRNA production. Here, we report that the plant nucleolus contains mRNAs, including fully spliced, aberrantly spliced, and single exon gene transcripts. Aberrant mRNAs are much more abundant in nucleolar fractions, while fully spliced products are more abundant in nucleoplasmic fractions. The majority of the aberrant transcripts contain premature termination codons and have characteristics of nonsense-mediated decay (NMD) substrates. A direct link between NMD and the nucleolus is shown by increased levels of the same aberrant transcripts in both the nucleolus and in Up-frameshift (upf) mutants impaired in NMD. In addition, the NMD factors UPF3 and UPF2 localize to the nucleolus, suggesting that the Arabidopsis nucleolus is therefore involved in identifying aberrant mRNAs and NMD.

Cajal bodies and their role in plant stress and disease responses

“…Several lines of evidence demonstrate that in plants NMD may occur in the nucleolus whereas in animals this process is associated with cytoplasmic processing bodies. 54 Firstly, it has been shown that Arabidopsis exon junction complex proteins accumulate in the nucleolus, 55 suggesting a role for the nucleolus in mRNA production. Secondly, the plant nucleolus has been reported to contain mRNAs, including properly spliced, aberrantly spliced, and single exon gene transcripts.…”

“…54 The majority of the aberrant transcripts contain premature termination codons and exhibit characteristics of NMD substrates. 54 In addition, the NMD Up-frameshift (UPF) factors, UPF2 and UPF3 are co-localized with a nucleolar marker protein, fibrillarin, in the nucleolus, suggesting that the Arabidopsis nucleolus may be involved in recognizing aberrant mRNAs and NMD. 54 Finally, direct correlation between the accumulation of increased levels of aberrant mRNAs in the nucleolus and their turnover by NMD has been demonstrated using upf mutants, which have been shown to be impaired in NMD such that mRNAs that are normally turned over by NMD accumulate in these mutants.…”

“…Aberrant mRNAs are significantly more abundant in the nucleolus, while fully spliced products are more abundant in the nucleoplasm. 54 The majority of the aberrant transcripts contain premature termination codons and exhibit characteristics of NMD substrates. 54 In addition, the NMD Up-frameshift (UPF) factors, UPF2 and UPF3 are co-localized with a nucleolar marker protein, fibrillarin, in the nucleolus, suggesting that the Arabidopsis nucleolus may be involved in recognizing aberrant mRNAs and NMD.…”

Shedding light on the chloroplast as a remote control of nuclear gene expression

“…9 This is the only At-RS31 splice variant that is translated into the protein. 37 The other 2 transcript isoforms of At-RS31 are mRNA2, that is actively degraded by nonsense-mediated mRNA decay (NMD), 36,38 and mRNA3, that is being accumulated in the nucleus. 9,38 Alternative splicing of At-RS31 is affected in a way that mRNA3 isoform is relatively more abundant in low light intensities and in dark, likely reducing At-RS31 protein levels in these conditions.…”

“…37 The other 2 transcript isoforms of At-RS31 are mRNA2, that is actively degraded by nonsense-mediated mRNA decay (NMD), 36,38 and mRNA3, that is being accumulated in the nucleus. 9,38 Alternative splicing of At-RS31 is affected in a way that mRNA3 isoform is relatively more abundant in low light intensities and in dark, likely reducing At-RS31 protein levels in these conditions. 9 Similar alternative splicing patterns to those of dark treated seedlings are observed when DCMU (3-(3,4-dichlorophenyl)-1,1-dimethylurea) -a drug that blocks photosynthetic electron transport from Photosystem II (PSII) to plastoquinone, generating an increase in the oxidation of the PQ pool-is added under normal light conditions, indicating that a functional chloroplast with an active photosynthetic electron transport chain is needed to generate the At-RS31 alternative splicing response to light.…”