Predicting the impact of alternative splicing on plant MADS domain protein function

• Published in: PloS one 2012-01, Vol.7 (1), p.e30524-e30524
• Main Authors: Severing, Edouard I, van Dijk, Aalt D J, Morabito, Giuseppa, Busscher-Lange, Jacqueline, Immink, Richard G H, van Ham, Roeland C H J
• Format: Article
• Language: English
• Subjects: Alternative Splicing; Analysis; Annotations; Arabidopsis; Arabidopsis - genetics; Arabidopsis - metabolism; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Arabidopsis thaliana; Bioinformatics; Biology; box genes; Complex formation; Complexity; Computational Biology; Deoxyribonucleic acid; DNA; Evolution; Evolution, Molecular; evolutionary analysis; exon duplication; flowering time; Gene expression; Gene families; Gene regulation; Genes; Genomes; Genomics; Identification; Impact prediction; Isoforms; Laboratories; MADS domain protein; MADS Domain Proteins - genetics; MADS Domain Proteins - metabolism; messenger-rna; Nucleotide sequence; organ identity; Oryza sativa; Phylogenetics; Physics; Plants (botany); Protein interaction; Protein Isoforms - genetics; Protein Isoforms - metabolism; Protein-protein interactions; Proteins; Reproducibility of Results; sequence; Studies; Transcription factors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0030524

Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of AS on the functional diversity of proteins is difficult to assess using genome-wide approaches. The availability of detailed sequence annotations for specific genes and gene families allows for a more detailed assessment of the potential effect of AS on their function. One example is the plant MADS-domain transcription factor family, members of which interact to form protein complexes that function in transcription regulation. Here, we perform an in silico analysis of the potential impact of AS on the protein-protein interaction capabilities of MIKC-type MADS-domain proteins. We first confirmed the expression of transcript isoforms resulting from predicted AS events. Expressed transcript isoforms were considered functional if they were likely to be translated and if their corresponding AS events either had an effect on predicted dimerisation motifs or occurred in regions known to be involved in multimeric complex formation, or otherwise, if their effect was conserved in different species. Nine out of twelve MIKC MADS-box genes predicted to produce multiple protein isoforms harbored putative functional AS events according to those criteria. AS events with conserved effects were only found at the borders of or within the K-box domain. We illustrate how AS can contribute to the evolution of interaction networks through an example of selective inclusion of a recently evolved interaction motif in the MADS AFFECTING FLOWERING1-3 (MAF1-3) subclade. Furthermore, we demonstrate the potential effect of an AS event in SHORT VEGETATIVE PHASE (SVP), resulting in the deletion of a short sequence stretch including a predicted interaction motif, by overexpression of the fully spliced and the alternatively spliced SVP transcripts. For most of the AS events we were able to formulate hypotheses about the potential impact on the interaction capabilities of the encoded MIKC proteins.