Insights into the Mechanism of Pre-mRNA Splicing of Tiny Introns from the Genome of a Giant Ciliate Stentor coeruleus

Abstract

Stentor coeruleus is a ciliate known for its regenerative ability. Recent genome sequencing reveals that its spliceosomal introns are exceptionally small. We wondered whether the multimegadalton spliceosome has any unique characteristics for removal of the tiny introns. First, we analyzed intron features and identified spliceosomal RNA/protein components. We found that all snRNAs are present, whereas many proteins are conserved but slightly reduced in size. Some regulators, such as Serine/Arginine-rich proteins, are noticeably undetected. Interestingly, while most parts of spliceosomal proteins, including Prp8′s positively charged catalytic cavity, are conserved, regions of branching factors projecting to the active site are not. We conjecture that steric-clash avoidance between spliceosomal proteins and a sharply looped lariat might occur, and splicing regulation may differ from other species.

Contrasting outcomes of genome reduction in mikrocytids and microsporidians

“…The nucleomorph genome is another example of extreme genome reduction in an intracellular symbiosis and, like those of mikrocytids, its introns are not only short, but also fall into a narrow size range: 18 to 21 bp in this case. The smaller and more narrowly constrained introns of mikrocytids are matched only by the 15–16 bp introns of heterotrich ciliates [ 53 , 54 ], which, seemingly against the trend, are free-living organisms with very large cells, nuclei, and genomes.…”

“…For instance, like other non-coding sequences, introns in endosymbionts might simply gradually shrink in size due to genome erosion, where reduced DNA repair mechanisms lead to a bias for deletions over insertions. This could presumably continue until a functional threshold is hit, below which the introns might be too short to be efficiently spliced and further gradual reductions would be strongly deleterious [ 54 ]. This threshold could be slightly different in systems evolving independently, for instance because introns in organisms with lower intron densities and reduced spliceosomes also tend to evolve greater dependence on sequence conservation for spliceosomal recognition and base-pairing with the snRNAs [ 56 , 57 ]—the longer the recognition sequence, the longer the minimal intron size.…”

Decryption of the survival “black box”: gene family expansion promotes the encystment in ciliated protists

“…Pre-mRNA splicing is a crucial process in eukaryotes and is catalyzed by a spliceosome complex comprising five small nuclear ribonucleoproteins (snRNPs) and multiple non-snRNP-associated proteins [ 53 , 56 , 57 ]. Each snRNP comprises one or two snRNAs, a set of common Sm proteins, and a variable number of particle-specific proteins [ 53 , 58 ].…”

“…Each snRNP comprises one or two snRNAs, a set of common Sm proteins, and a variable number of particle-specific proteins [ 53 , 58 ]. Recently, Nuadthaisong et al (2022) identified the presence of all snRNAs and conserved protein components of the spliceosome in Stentor , suggesting that conserved pre-mRNA splicing processes and mechanisms in eukaryotes exist in Stentor [ 56 ]. Similarly, in the present study, we found the presence of all snRNAs and most protein components of the spliceosome in P. cristata and O. trifallax .…”

“…2 B) than that of other eukaryotes (median intron length: 98 bp [ Arabidopsis thaliana ] to 1,334 bp [humans]) [ 59 ]. Given that small-sized introns may cause steric clashes during pre-mRNA splicing [ 53 , 56 ], it is supposed that the splicing mechanisms in ciliates may show some divergence from those with larger introns, although the splicing mechanism should be largely conserved.…”