RNA–RNA interactions and pre-mRNA mislocalization as drivers of group II intron loss from nuclear genomes

Abstract

Group II introns are commonly believed to be the progenitors of spliceosomal introns, but they are notably absent from nuclear genomes. Barriers to group II intron function in nuclear genomes therefore beg examination. A previous study showed that nuclear expression of a group II intron in yeast results in nonsensemediated decay and translational repression of mRNA, and that these roadblocks to expression are group II intron-specific. To determine the molecular basis for repression of gene expression, we investigated cellular dynamics of processed group II intron RNAs, from transcription to cellular localization. Our data show pre-mRNA mislocalization to the cytoplasm, where the RNAs are targeted to foci. Furthermore, tenacious mRNA-pre-mRNA interactions, based on intron-exon binding sequences, result in reduced abundance of spliced mRNAs. Nuclear retention of pre-mRNA prevents this interaction and relieves these expression blocks. In addition to providing a mechanistic rationale for group II intronspecific repression, our data support the hypothesis that RNA silencing of the host gene contributed to expulsion of group II introns from nuclear genomes and drove the evolution of spliceosomal introns.intron-mediated nuclear gene silencing | spliceosomal intron evolution G roup II introns that reside in genomes of bacteria, archaea, and eukaryotic organelles are ribozymes that self-splice from pre-mRNA transcripts independent of protein catalysis (1-3). Group II introns are also mobile retroelements that integrate into DNAs via an RNA intermediate (2, 3). Group II intron splicing is usually facilitated in vivo by an intron-encoded protein that acts as a maturase to help form the required secondary and tertiary structures (3). The intron RNA-protein complex is also required for group II intron retromobility. Both splicing and mobility of group II introns require interactions between exon-binding sequences (EBSs) within the intron and intron-binding sequences (IBSs) in the flanking exons of RNA or DNA targets (2, 3).The chemical steps of group II intron splicing are identical to those of nuclear spliceosomal introns (4, 5). There are also similarities of RNA sequences at the splice sites and of RNA structures within the ribozyme and the spliceosome (6-9). Because of these parallels, the catalytic group II introns are believed to be the progenitors of spliceosomal introns (6, 10, 11). It is widely speculated that group II introns entered the eukaryotic lineage with the mitochondrial endosymbiosis, invaded the nucleus, and evolved from RNA catalysts into efficient spliceosomedependent introns. However, group II introns are strikingly absent from modern nuclear genomes (1), which are replete with spliceosomal introns. It is still elusive how the ancestral group II introns might have evolved into spliceosomal introns or how they were expunged from nuclear genomes.As an initial effort to answer these questions, we had probed the fate of group II introns introduced into RNA polymerase II transcripts in Saccharomyces cerevis...

Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution

“…Consistent with this hypothesis is the absence of functional group II introns from extant nuclear genes, where they appear unable to function and where silencing of gene expression and nuclear compartmentalization may have added impetus to the evolution of the spliceosome through fragmentation and reassembly (130,132,133).…”

“…The pre-mRNAs harboring the intron are not spliced in the nucleus but are spliced accurately in the cytoplasm (132), possibly reflecting higher free Mg 2+ concentrations in that compartment. Interestingly, the mRNA from which Ll.LtrB is spliced in the cytoplasm is subjected to nonsense-mediated decay, translational repression of mRNA, and targeting of the RNA to cytoplasmic foci (132,133). By contrast, a spliceosomal intron assayed in parallel evaded these surveillance mechanisms (132).…”

“…LSU/2 group IIB intron into a yeast nuclear gene results in similar silencing of spliced mRNAs (134). Tenacious intermolecular interactions between the mRNA and the pre-mRNA and/or excised intron, based on IBS-EBS base pairings, contribute to translational silencing of the spliced mRNAs (133). Whereas disruption of these pairings by mutation promoted gene expression, compensatory mutations to restore the pairings again resulted in silencing.…”

The trouble with (group II) introns

“…However, reducing gene expression levels is not always selected against; indeed, it is sometimes selected for. More importantly, group II introns in noncoding regions would not have been subject to expulsion for the reasons invoked by Qu et al (1). There are surely many more evolutionary forces at play in a story as complex as that of intron origins.…”

“…Qu et al provide new grist for the introns origin mill (1), adding one more chapter to what has become a very long narrative. Back in the day when spliceosomal introns in the protein-coding genes of eukaryotes were still very new to science (1977)(1978), some of us argued that-in an evolutionary sensethey were actually very old (2,3).…”