Discovery, annotation and expression analysis of arginine/serine (SR) proteins in maize and sorghum using the Plant Genome Database PlantGDB
Discovery, annotation and expression analysis of arginine/serine (SR) proteins in maize and sorghum using the Plant Genome Database PlantGDB (Computational and Large-Scale Biology)
Klusman, Katarina1; Patrick, Tara1; Rauch, Hypaitia1; Lal, Shailesh1
1 Oakland University; Department of Biological Sciences; Rochester, MI, 48309-4401
The arginine/serine (SR)-rich family of conserved proteins across plant species plays an important role in plant growth and development and in response to environmental stress. We have searched and discovered candidate SR genes in different plant species available at the Plant Genome Database PlantGDB. These were manually annotated and the gene structures were determined by splice alignment of the available ESTs with the cognate gene using the computer software GeneSeqer. Expression validation of maize and sorghum SR genes by RT-PCR analysis using SR gene specific primers revealed tissue specificity in mRNA extracted from etiolated roots and shoots. Intriguingly, ~35 percent of the cloned RT-PCR products of these SR genes were not represented in the available EST collection. The majority of these new transcripts represent alternatively spliced isoforms generated by differential selection of splice sites during pre-mRNA processing. Several of these transcripts utilized non-canonical splice sites. Our data indicates that alternative splicing profile of SR genes display evolutionary conservation between maize and sorghum. These findings suggest an important biological relevance of this process in gene expression.
Funding acknowledgement: National Science Foundation (NSF)