title: Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing.
abstract: Alternative splicing (AS) of pre-mRNA is a fundamental molecular process that generates diversity in the transcriptome and proteome of eukaryotic organisms. SR proteins, a family of splicing regulators with one or two RNA recognition motifs (RRMs) at the N-terminus and an arg/ser-rich domain at the C-terminus, function in both constitutive and alternative splicing. We identified SR proteins in 27 eukaryotic species, which include plants, animals, fungi and "basal" eukaryotes that lie outside of these lineages. Using RNA recognition motifs (RRMs) as a phylogenetic marker, we classified 272 SR genes into robust sub-families. The SR gene family can be split into five major groupings, which can be further separated into 11 distinct sub-families. Most flowering plants have double or nearly double the number of SR genes found in vertebrates. The majority of plant SR genes are under purifying selection. Moreover, in all paralogous SR genes in Arabidopsis, rice, soybean and maize, one of the two paralogs is preferentially expressed throughout plant development. We also assessed the extent of AS in SR genes based on a splice graph approach (http://combi.cs.colostate.edu/as/gmap_SRgenes). AS of SR genes is a widespread phenomenon throughout multiple lineages, with alternative 3' or 5' splicing events being the most prominent type of event. However, plant-enriched sub-families have 57%-88% of their SR genes experiencing some type of AS compared to the 40%-54% seen in other sub-families. The SR gene family is pervasive throughout multiple eukaryotic lineages, conserved in sequence and domain organization, but differs in gene number across lineages with an abundance of SR genes in flowering plants. The higher number of alternatively spliced SR genes in plants emphasizes the importance of AS in generating splice variants in these organisms.
authors.affiliation: Department of Bioinformatics and Population Genetics, Universität zu Köln, Köln, Germany.
authors.forename: Dale N
authors.initials: DN
authors.lastname: Richardson
authors.forename: Mark F
authors.initials: MF
authors.lastname: Rogers
authors.forename: Adam
authors.initials: A
authors.lastname: Labadorf
authors.forename: Asa
authors.initials: A
authors.lastname: Ben-Hur
authors.forename: Hui
authors.initials: H
authors.lastname: Guo
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
authors.forename: Anireddy S N
authors.initials: AS
authors.lastname: Reddy
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D006801:Humans; D051379:Mice; D009687:Nuclear Proteins / Q000145:classification / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics; D016601:RNA-Binding Proteins / Q000145:classification / Q000235:genetics*; D000068103:Serine-Arginine Splicing Factors; D013025:Glycine max / Q000235:genetics; D003313:Zea mays / Q000235:genetics
chemical_list: D009687:Nuclear Proteins; D010940:Plant Proteins; D016601:RNA-Binding Proteins; D000068103:Serine-Arginine Splicing Factors