Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants

Abstract

Growing interest in alternative splicing in plants and the extensive sequencing of new plant genomes necessitate more precise definition and classification of genes coding for splicing factors. SR proteins are a family of RNA binding proteins, which function as essential factors for constitutive and alternative splicing. We propose a unified nomenclature for plant SR proteins, taking into account the newly revised nomenclature of the mammalian SR proteins and a number of plant-specific properties of the plant proteins. We identify six subfamilies of SR proteins in Arabidopsis thaliana and rice (Oryza sativa), three of which are plant specific. The proposed subdivision of plant SR proteins into different subfamilies will allow grouping of paralogous proteins and simple assignment of newly discovered SR orthologs from other plant species and will promote functional comparisons in diverse plant species.

Figure 1.

Domain Architecture of the Arabidopsis and Rice SR Protein Subfamilies and the Newly Proposed Protein/Gene Symbols. The proteins of the SR subfamily (orthologs of mammalian SRSF1/SF2/ASF) possess an evolutionary conserved SWQDLKD motif in their second RRM followed by an RS domain with characteristic SR dipeptides. The RSZ subfamily (orthologs of mammalian SRSF7/9G8) consists of SR proteins with one Zn knuckle. The SC subfamily (orthologs of SRSF2/SC35) contains proteins with a single RRM followed by an RS domain. The plant-specific SCL subfamily (SC35-like) is similar to SRSF2 (RRM domain) but has an N-terminal charged extension. The proteins of the plant-specific RS2Z subfamily possess two Zn knuckles and have an additional SP-rich region following the RS domain. The plant-specific RS subfamily proteins contain two RRMs (without the SWQDLKD motif) followed by the RS domain rich in RS dipeptides. *, truncated protein; **, full-length protein. References: 1, Golovkin and Reddy (1998); 2, Golovkin and Reddy (1999); 3, Iida and Go (2006); 4, Isshiki et al. (2006); 5, Kalyna and Barta (2004); 6, Lazar et al. (1995): 7, Lopato et al. (1996); 8, Lopato et al. (1999b); 9, Lopato et al. (1999a); 10, Lopato et al. (2002); 11, Lorković and Barta (2002).