Dramatically reduced spliceosome, intronome, and splicing efficiency in Cyanidiococcus yangmingshanensis and Cyanidium caldarium

Abstract

Eukaryotic pre-mRNA splicing is catalyzed by the spliceosome, whose ribonucleoprotein composition and the number of intron substrates it acts upon vary widely across eukaryotic lineages. The red alga Cyanidioschyzon merolae possesses a reduced spliceosome lacking the U1 snRNP, and an unusually small intron repertoire. We asked whether these traits are unique to C. merolae or shared across the related Cyanidiales and Cyanidioschyzonales lineages, as well as how they relate to splicing efficiency under light conditions relevant to photosynthetic growth. Genomic and transcriptomic analysis of C. merolae, Cyanidiococcus yangmingshanensis, and Cyanidium caldarium reveal that all three species harbour a reduced, but broadly conserved, set of splicing proteins. Strikingly, covariance model searches failed to detect U1 snRNA in either C. yangmingshanensis or C. caldarium, establishing U1 loss as a shared feature of all three lineages. We identified only 39 introns in C. merolae, 40 in C. yangmingshanensis, and 54 in C. caldarium. Splicing efficiencies were 42-50%, substantially lower than most organisms in which splicing has been measured, but low splicing is compensated by 2-4x higher expression of intron-containing genes than intron-lacking genes. Notably, light can enhance splicing efficiency in C. merolae and C. yangmingshanensis by up to 100%. Furthermore, the splice site and branch site consensus sequences are highly conserved and similar to those found in hemiascomycetous yeasts such as Saccharomyces cerevisiae. 85% of introns contain an in-frame stop codon with a strong bias towards the 5' end of the intron. These results indicate that dramatic streamlining of the spliceosome and intronome, together with inefficient splicing, predated the divergence of these lineages [~]320 million years ago, and is therefore a defining molecular trait of these extremophilic red algae.