Department of Physics, Chemistry and Biology (IFM)

Protein identification
To identify the SR proteins in Physcomitrella patens homologues of SR subfamily proteins in Arabidopsis thaliana were used as queries. The identified proteins were required to have two RNA recognition motifs (RRM) and one SR region; these three are characteristics for a protein belonging to the SR subfamily.

Phylogeny
SR subfamily proteins from Oryza sativa, Selaginella moellendorffii and Chlamydomonas reinhardtii were identified in the same approach as the P. patens proteins.
A phylogenetic analysis of these proteins was made both on protein level and RRM domain level. First a neighbor joining analysis was performed using Phylip v3 and then a maximum likelihood analysis with help of PhyML v3.0.

Expression analysis
Three weeks old P. patens were exposed for the various abiotic stresses and used for RNA extraction. The selected stress treatments were; cold, dehydration, salt stress, osmotic stress and hormone (Abscisic acid, ABA). cDNA was synthesized from the RNA and gene specific primers were used to amplify the genes using PCR.
The PCR products were visualized by gel electrophoresis and the expressions were analyzed using the program Image J 1.43u. All expression values from each replicates were normalized against the reference gene.