The SR protein family

Abstract

The processing of pre-mRNAs is a fundamental step required for the expression of most metazoan genes. Members of the family of serine/arginine (SR)-rich proteins are critical components of the machineries carrying out these essential processing events, highlighting their importance in maintaining efficient gene expression. SR proteins are characterized by their ability to interact simultaneously with RNA and other protein components via an RNA recognition motif (RRM) and through a domain rich in arginine and serine residues, the RS domain. Their functional roles in gene expression are surprisingly diverse, ranging from their classical involvement in constitutive and alternative pre-mRNA splicing to various post-splicing activities, including mRNA nuclear export, nonsense-mediated decay, and mRNA translation. These activities point up the importance of SR proteins during the regulation of mRNA metabolism.

Figure 1

The human SR protein family. The structural organization of the nine human SR proteins is shown. RRM, RNA recognition motif; RRMH, RRM homology; RS, arginine/serine-rich domain; Zn, Zinc knuckle.

Figure 2

Evolutionary relationship between members of the SR family. The phylogeny was inferred using the neighbor-joining method. ClustalW was used to align sequences and perform phylogenetic analysis. Trees were drawn by CTree. The horizontal lines in each panel indicate the similarity between SR proteins. (a) Phylogenetic tree based on the alignment of the human (Hs) SR protein family. The numbers above each bar indicate the degree of similarity. (b) Phylogenetic tree based on the alignment of Homo sapiens (Hs), Drosophila melanogaster (Dm), Caenorhabditis elegans (Ce), Arabidopsis thaliana (At), and Schizosaccharomyces pombe (Sp) SR protein sequences. Green and blue lines indicate different clusters. Cluster set selection is based on minimizing the subtype diversity ratio, a measure that groups related subclasses.

Figure 3

Solution structure of an SR protein RRM from human SRp20 (blue) in complex with the RNA sequence 5'-CAUC-3' (red). All four nucleotides present are contacted by the RRM, but only the 5' cytosine is recognized specifically. The structure was generated using the Visual Molecular Dynamics program [78] from coordinates deposited in the Brookhaven National Laboratory Protein Data Bank [30].

Figure 4

Localization of SR proteins within the nucleus. Left panel: HeLa cells transfected with GFP-SRp20. The GFP fluorescence is visualized directly. Middle panel: cells are also stained with anti-SC35 hybridoma supernatant to highlight clusters of SR proteins in the nucleus (red), which are referred to as nuclear speckles. Speckles are believed to be storage compartments for SR proteins and other splicing factors. Right panel: merge of GFP-SRp20 and SC35 images. The bar in each panel indicates the scale. Images courtesy of Lin Li and Rozanne Sandri-Goldin.

Figure 5

Splicing functions of SR proteins. (a) SR proteins (green) bound to an exonic splicing enhancer (ESE) may function in constitutive splicing by interacting with the splicing factors U2AF bound at the upstream 3' splice site and U1 snRNP bound to the downstream 5' splice site. Py represents the polypyrimidine tract, the binding site for U2AF. (b) Exon-independent functions of SR proteins. SR proteins may have two exon-independent functions. SR proteins facilitate splice-site pairing by simultaneously interacting with U1 snRNP and U2AF across the intron. SR proteins also assist in recruiting the U4/U6U5 tri-snRNP. (c) Splicing repression is mediated when SR proteins associate with intronic sequences close to the splice sites. Recruitment of spliceosomal components is inhibited through steric hindrance or nonproductive spliceosomal assembly. Adapted with permission from [79].

Figure 6

SR protein functions other than splicing. (a) mRNA export. SR proteins associate site-specifically with intronless mRNAs, such as histone H2A mRNA [63], to promote their export (left-hand side). The export machinery is as yet unknown. For intron-containing pre-mRNAs (right-hand side), SR protein association with the spliced mRNA has also been suggested to mediate nuclear export through interactions with the RNA export factor ALY/REF and Tip-containing protein (TAP). (b) Translation initiation. Interactions between mRNA-bound SF2/ASF and the protein kinase mTOR trigger phosphorylation of 4E-BP (eIF4E-binding protein). In its phosphorylated form 4E-BP dissociates from the translation initiation factor eIF4E, thereby releasing eIF4E and activating initiation of cap-dependent translation (green arrow) [71].