Bioinformatics Analysis Of Rice OsRacD And Its Five Putative Target Proteins

OsRacD gene is a new member of the rice Rop family which belongs to the small GTP-binding proteins,the protein coded by OsRacD gene can notably regulate the polar growth of pollen tube,thus plays a significant part in the photoperiod fertility coversion (PFC) of rice Nongken 58S. Using OsRacD as bait, the rice panicle cDNA library was screened by yeast two-hybrid system,and some cDNA sequences encoding proteins that putatively interact with OsRacD were obtained.For the sake of revealing the internal relations between OsRacD and its interactive proteins,bioinformatics methods were adopted to analyze OsRacD and its five putative interactive proteins,and these analysis can provide some references not only for the further study of pattens and characteristics of interactions between OsRacD and its interactive proteins but also for anatomising functions and regulation mechanisms of signaling pathways related to OsRacD.Genetic structure and chromosome location:OsRacD,OsRhoGDI1 and OsRhoGAP2 are in Chromosome 2,OsMY1 and OsMY2 are in Chromosome 1,while OsRhoGAP1 is in Chromosome 12.All these sequences contain multiple exons and introns. OsRacD,OsRhoGDI1 and OsRhoGAP2 are complete cDNA coding sequences,while OsMY1,OsMY2 and OsRhoGAP1 are partial cDNA who lack 5'sequence.Physical and chemical properties and protein localization:OsRacD and the other five proteins that putatively interact with OsRacD are all hydrophilic,this suggests that it is highly possible these proteins appear in cytoplasm at the same time,thus OsRacD can be close to other proteins and interact with them. Comprehensive analysis of three softwares come to the conclusion that OsRacD may interact with other proteins on the condition that they are all present in cytoplasm.Conserved domains:there is a Rho domain in OsRacD which includes G1-G5 box,switchâ…  region,switchâ…¡region,GTP/Mg2+ binding site,GAP,GEF,GDI,putative effector interaction sites;there are coiled coil regions both in OsMY1 and OsMY2;a RhoGDI conserved domain in OsRhoGDI1;a CRIB domain and a RhoGAP domain both in OsRhoGAP1 and OsRhoGAP2.OsRacD may interact with these proteins by the conserved domains above.Post-translational modification sites:there are 6 kinds of post-translational modification sites in OsRacD,among which ATP/GTP-binding site motif A (P-loop) only appears in OsRacD,the other five(N-glycosylation,protein kinase C phosphorylation,tyrosine kinase phosphorylation,casein kinase II phosphorylation and N-myristoylation sites) are found both in OsRacD and its putative interactive proteins.The common ground of post-translational modification in all these proteins above indicates that these proteins may be regulated in the same way,therefore,it is highly possible that close liaison exists between OsRacD and its putative interactive proteins when they act.However,there are 3 kinds of post-translational modification sites that don't exist in OsRacD but in other proteins:cAMP- and cGMP-dependent protein kinase phosphorylation site,amidation site and CAP-Gly domain signature.On the whole,in this study,bioinformatics methods were adopted to analyze and predict the genetic structure and chromosome location,physical and chemical properties,conserved domains,post-translational modification sites and protein localization of genes and proteins of OsRacD and its five putative interactive proteins,also,phyligenetic trees were constructed for every gene and its coding protein.All these will be helpful to intensive study on the function of the interactions between OsRacD and its putative interact proteins in the photoperiod fertility coversion (PFC) of rice Nongken 58S.