Phylogenetic and expression analysis of RNA-binding proteins with triple RNA recognition motifs in plants.
The superfamily of RNA binding proteins (RBPs) is vastly expanded in plants compared to other eukaryotes. A subfamily of RBPs that contain three RNA recognition motifs (RRMs) from the Arabidopsis (24), rice (19) and poplar (37) genomes was analyzed in this study. Phylogenetic analysis with full-length protein sequences of 80 RBPs identified nine clades. The largest clade, comprising 23 members, showed high homology to human RBPs involved in oxidative signaling. Digital northern analysis revealed that Arabidopsis RBPs are transcriptionally responsive to biotic, abiotic and hormonal treatments. Northern blot analysis of eight Arabidopsis RBPs belonging to the tobacco RBP45/47 family showed that these genes respond to ozone stress. AtRBP45b, which shows closest homology to the yeast oxidative stress regulatory protein, CSX1, was expressed in multiple tissues. Two novel splice variant forms of AtRBP45b were identified by 3'RACE analysis. Based on RT-PCR, splice variant AtRBP45b-SV1 was observed only in response to mechanical wounding caused by pathogen or chemical infiltrations and was not detectable in response to salt or temperature stress. Electrophoretic mobility shift assay demonstrated that recombinant full-length and splice variant forms of AtRBP45b bound synthetic RNA. Identifying in vivo RNA targets of AtRBP45b will aid in determining the precise functional role of these proteins during oxidative signaling.
Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, USA.
Lila
L
Peal
Niranjani
N
Jambunathan
Ramamurthy
R
Mahalingam
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics; D003080:Cold Temperature / Q000009:adverse effects; D018506:Gene Expression Regulation, Plant; D006358:Hot Temperature / Q000009:adverse effects; D006861:Hydrogen Peroxide / Q000009:adverse effects; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics; D018384:Oxidative Stress / Q000187:drug effects; D010126:Ozone / Q000009:adverse effects; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics*; D016012:Poisson Distribution; D032107:Populus / Q000235:genetics; D054730:Protein Interaction Domains and Motifs / Q000235:genetics*; D020033:Protein Isoforms / Q000235:genetics; D012313:RNA / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000235:genetics*; D016415:Sequence Alignment; D012965:Sodium Chloride / Q000009:adverse effects; D013312:Stress, Physiological / Q000187:drug effects; D014158:Transcription, Genetic
D029681:Arabidopsis Proteins; D010940:Plant Proteins; D020033:Protein Isoforms; C518409:RBP45b protein, Arabidopsis; D016601:RNA-Binding Proteins; D012965:Sodium Chloride; D012313:RNA; D010126:Ozone; D006861:Hydrogen Peroxide