Cloning and bioinformatics analysis of tillering-related gene NpD53 from Narenga porphyrocoma(Hance) Bor

Objective This research was aimed to clone tillering-related gene NpD53 from Narenga porphyrocoma(Hance) Bor,and analyze the sequence characteristics of NpD53 and provide theoretical basis for the study on molecular mechanism of wild sugarcane tillering.MethodTotal RNA was isolated from the leaves ofN.porphyrocoma and the cDNA was obtained by reverse transcription.NpD53 was amplified by RACE (rapid amplification of cDNA end) and its nucleotide sequence and amino acid sequence of encoding protein were analyzed by bioinformatics methods.ResultThe cloned Gene NpD53 (GeneBank accession No.MF593461) contained midregion sequence of 760 bp,5'terminal sequence of 1497 bp,3'terminal sequence of 1233 bp.Combining the three parts,its cDNA sequence full-length was 2597 bp.It contained an open reading frame(ORF) of 2037 bp,encoded 678 amino acids with molecular mass of 75.02 KD,pI of 6.59,and average hydrophilicity of-0.506,which meant it was a hydrophilic protein.The protein was situated in cell nucleus (94.1% confidence).The encoding protein (NpD53) of NpD53 had two super family core sequences,namely P-loop_NT-Pase and ClpB_D2-small,with four non-specific sites,and shared the same ClpB_D2-small conserved domain with D53 protein of other species.Its secondary structure had only four coil types,among which random coils were in the majority,accounting for 42.77%,followed by alpha helix,accounting for 35.55%,while extended strand and beta turn accounted for 15.34% and 6.34% respectively.According to the homology comparison and phylogenetic tree analysis for amino acid sequences of NpD53 protein,N.porphyrocoma had a close phylogenetic relationship with gramineous plants(Sorghum bicolor andAegilops tauschii),and had a distant phylogenetic relationship with Phoenix dactylifera,Elaeis guineensis and Musa acuminate.Conclusion The encoding protein of tillering-related gene NpD53 from N.porphyrocoma shares the same conserved domain with D53 protein of other species,and has two non-specific sites of class-Ⅰ Clp ATPase.It is predicted that NpD53 may be a molecular chaperone,and is related to heat resistance ofN.porphyrocoma.