SWAP pre-mRNA splicing regulators are a novel, ancient protein family sharing a highly conserved sequence motif with the prp21 family of constitutive splicing proteins

Abstract

Regulators responsible for the pervasive, nonsex-specific alternative pre-mRNA splicing characteristic of metazoans are almost entirely unknown or uncertain. We describe here a novel family of splicing regulators present throughout metazoans. Specifically, we analyze two nematode (Caenorhabditis elegans) genes. One, CeSWAP, is a cognate of the suppressor-of-white-apricot (DmSWAP) splicing regulator from the arthropod Drosophila. Our results define the ancient, conserved SWAP protein family whose members share a colinearly arrayed series of novel sequence motifs. Further, we describe evidence that the CeSWAP protein autoregulates its levels by feedback control of splicing of its own pre-mRNA analogously to the DmSWAP protein and as expected of a splicing regulator. The second nematode gene, Ceprp21, encodes an abundant nuclear cognate of the constitutive yeast splicing protein, prp21, on the basis of several lines of evidence. Our analysis defines prp21 as a second novel, ancient protein family. One of the motifs conserved in prp21 proteins--designated surp--is shared with SWAP proteins. Several lines of evidence indicate that both new families of surp-containing proteins act at the same (or very similar) step in early prespliceosome assembly. We discuss implications of our results for regulated metazoan pre-mRNA splicing.

The Evolutionarily Conserved TOUGH Protein Is Required for Proper Development ofArabidopsis thaliana

“…TGH is an evolutionarily conserved regulator with a G-patch and a SWAP domain, and both domains are exclusively found in RNA binding and processing proteins (Figure 1) (Denhez and Lafyatis, 1994;Spikes et al, 1994;Aravind and Koonin, 1999). TGH colocalizes with the SR protein SRp34 to subnuclear particles and the enrichment of Ser and Arg residues in the KRDES domain of TGH is reminiscent of the Arg-and Ser-rich RS domains found in SR proteins (Figures 1 and 2).…”

“…In addition to the highly conserved and specific TGH domain, the TGH orthologs contain two recognizable conserved protein domains, a G-patch and a Suppressor-of-white-apricot (SWAP) domain ( Figures 1A, 1C, and 1D) (Denhez and Lafyatis, 1994;Spikes et al, 1994;Aravind and Koonin, 1999). The G-patch is defined by a series of conserved Gly residues, and G-patches are exclusively found in proteins with a predicted or known role in RNA binding or RNA processing (Aravind and Koonin, 1999) ( Figure 1C).…”

“…The G-patch is defined by a series of conserved Gly residues, and G-patches are exclusively found in proteins with a predicted or known role in RNA binding or RNA processing (Aravind and Koonin, 1999) ( Figure 1C). The SWAP domain is a conserved domain with a presumed function in RNA binding that was first identified in the splicing regulator SWAP from Drosophila melanogaster (Denhez and Lafyatis, 1994;Spikes et al, 1994) (Figure 1D). The G-patch and the SWAP domains have unknown biochemical properties or functions.…”

The Small Ubiquitin-Like Modifier (SUMO) and SUMO-Conjugating System ofChlamydomonas reinhardtii

“…These fusion proteins, thus, can bind to ubiquitin-binding domains (UBDs) and carry along their fusion partner to perform a particular function. Two examples of proteins with ubiquitin sequences at their C termini, both involved in pre-mRNA splicing, are SF3a120 (Kramer et al 1995) and CePRP21 (Spikes et al 1994). Whether the three CrSUMO-like proteins perform functions analogous to ubiquitin-containing fusion proteins remains to be determined.…”

“…CrSUMO148 represents a unique SUMO-like protein with tandem repeats of Cterminal domains each with a potential GG maturation cleavage site. CrSUMO-like89A, CrSUMO-like89B, and CrSUMO-like90 appear to encode proteins that may be fusions of SUMO sequences with the C termini of different proteins and, thus, represent a newly discovered class of SUMO-containing molecules that are akin to previously identified proteins containing ubiquitinassociated (UBA) domains (Spikes et al 1994;Kerscher et al 2006). Heat and osmotic pressure stress conditions increase the appearance of proteins recognized by CrSUMO96 antibodies, indicating that SUMOylation may be an important modification system for responses to stress conditions and in the regulation of gene expression in C. reinhardtii.…”