Universität zu Köln

Richardson, Dale N., Rogers, Mark F., Labadorf, Adam ORCID: 0000-0002-0753-8992, Ben-Hur, Asa ORCID: 0000-0001-8269-6942, Guo, Hui ORCID: 0000-0001-7830-8564, Paterson, Andrew H. and Reddy, Anireddy S. N. (2011). Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing. PLoS One, 6 (9). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1932-6203

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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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Richardson, Dale N. UNSPECIFIED UNSPECIFIED UNSPECIFIED Rogers, Mark F. UNSPECIFIED UNSPECIFIED UNSPECIFIED Labadorf, Adam UNSPECIFIED orcid.org/0000-0002-0753-8992 UNSPECIFIED Ben-Hur, Asa UNSPECIFIED orcid.org/0000-0001-8269-6942 UNSPECIFIED Guo, Hui UNSPECIFIED orcid.org/0000-0001-7830-8564 UNSPECIFIED Paterson, Andrew H. UNSPECIFIED UNSPECIFIED UNSPECIFIED Reddy, Anireddy S. N. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-489052
DOI:	10.1371/journal.pone.0024542
Journal or Publication Title:	PLoS One
Volume:	6
Number:	9
Date:	2011
Publisher:	PUBLIC LIBRARY SCIENCE
Place of Publication:	SAN FRANCISCO
ISSN:	1932-6203
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language PRE-MESSENGER-RNA; SR PROTEINS; GENOME SEQUENCE; CONSERVED FAMILY; GENE-EXPRESSION; RS DOMAIN; EVOLUTION; DATABASE; BINDING; TRANSCRIPTOME Multiple languages Multidisciplinary Sciences Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/48905