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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
BMC Genomics. 2009; 10: 154.
Published online Apr 9, 2009. doi:  10.1186/1471-2164-10-154
PMCID: PMC2674458
Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome
Edouard I Severing,1,2 Aalt DJ van Dijk,1 Willem J Stiekema,2,3 and Roeland CHJ van Hamcorresponding author1,2
1Applied Bioinformatics, Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands
2Laboratory of Bioinformatics, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
3Centre for BioSystems Genomics, PO Box 98, 6700 AB Wageningen, The Netherlands
corresponding authorCorresponding author.
Edouard I Severing: edouard.severing/at/; Aalt DJ van Dijk: aaltjan.vandijk/at/; Willem J Stiekema: willem.stiekema/at/; Roeland CHJ van Ham: roeland.vanham/at/
Received September 8, 2008; Accepted April 9, 2009.
Alternative splicing (AS) is a widespread phenomenon in higher eukaryotes but the extent to which it leads to functional protein isoforms and to proteome expansion at large is still a matter of debate. In contrast to animal species, for which AS has been studied extensively at the protein and functional level, protein-centered studies of AS in plant species are scarce. Here we investigate the functional impact of AS in dicot and monocot plant species using a comparative approach.
Detailed comparison of AS events in alternative spliced orthologs from the dicot Arabidopsis thaliana and the monocot Oryza sativa (rice) revealed that the vast majority of AS events in both species do not result from functional conservation. Transcript isoforms that are putative targets for the nonsense-mediated decay (NMD) pathway are as likely to contain conserved AS events as isoforms that are translated into proteins. Similar results were obtained when the same comparison was performed between the two more closely related monocot species rice and Zea mays (maize).
Genome-wide computational analysis of functional protein domains encoded in alternatively and constitutively spliced genes revealed that only the RNA recognition motif (RRM) is overrepresented in alternatively spliced genes in all species analyzed. In contrast, three domain types were overrepresented in constitutively spliced genes. AS events were found to be less frequent within than outside predicted protein domains and no domain type was found to be enriched with AS introns. Analysis of AS events that result in the removal of complete protein domains revealed that only a small number of domain types is spliced-out in all species analyzed. Finally, in a substantial fraction of cases where a domain is completely removed, this domain appeared to be a unit of a tandem repeat.
The results from the ortholog comparisons suggest that the ability of a gene to produce more than one functional protein through AS does not persist during evolution. Cross-species comparison of the results of the protein-domain oriented analyses indicates little correspondence between the analyzed species. Based on the premise that functional genetic features are most likely to be conserved during evolution, we conclude that AS has only a limited role in functional expansion of the proteome in plants.
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