A plant 5S ribosomal RNA mimic regulates alternative splicing of transcription factor IIIA pre-mRNAs

Abstract

Transcription factor IIIA (TFIIIA) is required for eukaryotic synthesis of 5S ribosomal RNA by RNA polymerase III. Here we report the discovery of a structured RNA element with striking resemblance to 5S rRNA that is conserved within TFIIIA precursor mRNAs (pre-mRNAs) from diverse plant lineages. TFIIIA protein expression is controlled by alternative splicing of the exon containing the plant 5S rRNA mimic (P5SM). P5SM triggers exon skipping upon binding of ribosomal protein L5, a natural partner of 5S rRNA, which demonstrates the functional adaptation of its structural mimicry. Since the exon-skipped splice product encodes full-length TFIIIA protein, these results reveal a ribosomal protein-mRNA interaction that is involved in 5S rRNA synthesis and has implications for cross-coordination of ribosomal components. This study also provides insight into the origin and function of a newfound class of structured RNA that regulates alternative splicing.

Polypyrimidine Tract Binding Protein Homologs from Arabidopsis Are Key Regulators of Alternative Splicing with Implications in Fundamental Developmental Processes

“…Furthermore, while downregulation of PTB1/2 had similar quantitative effects for most events, more variation was observed for the OE lines, suggesting that PTB-dependent cassette exons respond differently to varying levels of PTB proteins in vivo. To exclude a general perturbation of AS upon PTB misexpression, splice form patterns for the previously characterized cassette exon event within At1g72050 (Hammond et al, 2009) were determined ( Figure 3B). …”

A conserved alternative splicing event in plants reveals an ancient exonization of 5S rRNA that regulates TFIIIA

“…Elegant biochemical analysis by Hammond et al 20 demonstrated that ribosomal protein L5 directly binds the conserved helix III-like structure of the 5S rRNA like element associated with the alternative exon, which parallels a known binding interaction between L5 and 5S rRNA. 22 Hammond et al further determined that the binding of L5 to the 5srRNA like element is responsible for structure elements including Helix III and loop D that are required for ribosomal protein L5 binding, and helix IV and loop E that can interact with TFIIIA protein 19,22 ( Fig.…”

“…Multiple sequence analysis identifies highly conserved sequence blocks between all 5S-like alternative exons and 5S rRNA sequences, suggesting that the 5S rRNAlike element may adopt a similar secondary structure to that of 5S rRNA. 19,20 Computational 19,20 and experimental 20 evidence suggests that the 5S rRNA-like element associated with the alternative exon adopts many 5S rRNA secondary and experimentally isolated sequences identified 52 TFIIIA orthologues from a diverse group of land plants that include many flowering plants, the bryophyte moss (Physcomitrella patens), and an early vascular plant (Selaginella moellendorffii) that last shared a common ancestor with angiosperms over 400 Mya. No evidence for the alternative exon was found in the green alga Chlamydomonas or other non plant genomes.…”

“…Conversely, the binding of L5 to AtTFIIIA pre-mRNA influences the splicing machinery to favor production of the ES isoform. This regulatory logic coordinates the levels of 5S rRNA with L5 ribosomal protein and makes sense in light of the observation that 5S rRNA must be bound with L5 prior to its incorporation into the ribosome 22 Hammond et al 20 suggest that L5 binding may displace an exonic splice factor from the pre-mRNA, thus effecting the splicing decision. However, it may be the secondary structure of the 5S rRNAlike element that actually influences the splicing decision.…”

“…9 However, it is not clear to what extent PTC containing isoforms are indeed coupled to NMD as a mode of post-transcriptional gene regulation versus simply being the by-products of noisy splicing. Recent studies suggest that a large fraction of AS events are a result of noise in the splicing machinery and lead to unstable protein products if translated 11,12 rather than being Because genes whose protein expression levels are truly modulated by regulated unproductive splicing coupled to a highly conserved sequence element associated with an alternatively spliced cassette exon in the gene encoding the TFIIIA transcription factor in rice (Oryza sativa) and Arabidopsis thaliana 19,20 that diverged 140-150 Mya. 21 Hammond et al 20 searched for structured cis-regulatory RNA elements based on nucleotide and secondary structure conservation between noncoding regions in rice and Arabidopsis orthologous genes.…”