Prp8, the pivotal protein of the spliceosomal catalytic center, evolved from a retroelement-encoded reverse transcriptase

Abstract

Prp8 is the largest and most highly conserved protein of the spliceosome, encoded by all sequenced eukaryotic genomes but missing from prokaryotes and viruses. Despite all evidence that Prp8 is an integral part of the spliceosomal catalytic center, much remains to be learned about its molecular functions and evolutionary origin. By analyzing sequence and structure similarities between Prp8 and other protein domains, we show that its N-terminal region contains a putative bromodomain. The central conserved domain of Prp8 is related to the catalytic domain of reverse transcriptases (RTs) and is most similar to homologous enzymes encoded by prokaryotic retroelements. However, putative catalytic residues in this RT domain are only partially conserved and may not be sufficient for the nucleotidyltransferase activity. The RT domain is followed by an uncharacterized sequence region with relatives found in fungal RT-like proteins. This part of Prp8 is predicted to adopt an a-helical structure and may be functionally equivalent to diverse maturase/X domains of retroelements and to the thumb domain of retroviral RTs. Together with a previously identified C-terminal domain that has an RNaseH-like fold, our results suggest evolutionary connections between Prp8 and ancient mobile elements. Prp8 may have evolved by acquiring nucleic acid-binding domains from inactivated retroelements, and their present-day role may be in maintaining proper conformation of the bound RNA cofactors and substrates of the splicing reaction. This is only the second example-the other one being telomerase-of the RT recruitment from a genomic parasite to serve an essential cellular function.

An unanticipated early function of DEAD-box ATPase Prp28 during commitment to splicing is modulated by U5 snRNP protein Prp8

“…Suppressors of prp28-1 selected in the N-terminal quarter of Prp8. (A) Map of Prp8, showing domains identified by sequence or structural homology (Grainger and Beggs 2005;Dlakićand Mushegian 2011;Galej et al 2013). Numbers indicate amino acid residues.…”

“…We identified 15 suppressor substitutions that cluster in a proposed bromodomain (Dlakićand Mushegian 2011). To determine the precise order of spliceosome assembly defects caused by prp28-1 and to identify which defects are suppressed by the Prp8 alleles, we monitored the kinetics of cotranscriptional spliceosome assembly in vivo and post-transcriptional spliceosome assembly in vitro.…”

A Ribonucleoprotein Supercomplex Involved in trans-Splicing of Organelle Group II Introns

“…In particular, it has been hypothesized that the ancestral ribosomal group II intron fragmented into U2, U5, and U6 snRNA of the spliceosome (9). Furthermore Prp8, a nuclear key splicing factor, shows several similarities with group II intron maturases and, thus, may have evolved from an ancestral intron-encoded protein (43). It was also proposed that nuclear splicing factors and the U1 and U4 FIGURE 6.…”

Activating the branch-forming splicing pathway by reengineering the ribozyme component of a natural group II intron

“…9B), so as to shift the conformational equilibrium in favor of a structure that supports the branching process; except that unlike the destabilization that resulted from deleting the tips of domains II and VI in our constructs, the effect of the protein should be only a transient one in order for the ensuing exon ligation to proceed efficiently. What makes this model especially attractive is that Prp8, which lies at the heart of the spliceosome and shares common ancestry with group II-encoded reverse transcriptases (Dlakićand Mushegian 2011;Galej et al 2013), is also believed, based on genetic (Liu et al 2007) and biochemical (Schellenberg et al 2013) evidence, to participate in a conformational shift in between the two steps of nuclear pre-mRNA splicing.…”