We cloned and analyzed the two genes of the 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase(HDR) gene family from Huperzia serrate.The two transcripts coding HDR,named Hs HDR1 and Hs HDR2,were discovered in t...We cloned and analyzed the two genes of the 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase(HDR) gene family from Huperzia serrate.The two transcripts coding HDR,named Hs HDR1 and Hs HDR2,were discovered in the transcriptome dataset of H.serrate and were cloned by reverse transcription-polymerase chain reaction(RT-PCR).The physicochemical properties,protein domains,protein secondary structure,and 3D structure of the putative Hs HDR1 and Hs HDR2 proteins were analyzed.The full-length c DNA of the Hs HDR1 gene contained 1431 bp encoding a putative protein with 476 amino acids,whereas the Hs HDR2 gene contained 1428 bp encoding a putative protein of 475 amino acids.These two proteins contained the conserved domain of 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase(PF02401),but without the transmembrane region and signal peptide.The most abundant expression of Hs HDR1 and Hs HDR2 was detected in H.serrate roots,followed by the stems and leaves.Our results provide a foundation for exploring the function of Hs HDR1 and Hs HDR2 in terpenoid and sterol biosynthesis in Huperziaceae plants.展开更多
In this study,we identified the most deleterious nsSNP in RB1 gene through structural and functional properties of its protein (pRB) and investigated its binding affinity with E2F-2.Out of 956 SNPs,we investigated 12 ...In this study,we identified the most deleterious nsSNP in RB1 gene through structural and functional properties of its protein (pRB) and investigated its binding affinity with E2F-2.Out of 956 SNPs,we investigated 12 nsSNPs in coding region in which three of them (SNPids rs3092895,rs3092903 and rs3092905) are commonly found to be damaged by I-Mutant 2.0,SIFT and PolyPhen programs.With this effort,we modeled the mutant pRB proteins based on these deleterious nsSNPs.From a comparison of total energy,stabilizing residues and RMSD of these three mutant proteins with native pRB protein,we identified that the major mutation is from Glutamic acid to Glycine at the residue position of 746 of pRB.Further,we compared the binding efficiency of both native and mutant pRB (E746G) with E2F-2.We found that mutant pRB has less binding affinity with E2F-2 as compared to native type.This is due to sixteen hydrogen bonding and two salt bridges that exist between native type and E2F-2,whereas mutant type makes only thirteen hydrogen bonds and one salt bridge with E2F-2.Based on our investigation,we propose that the SNP with an id rs3092905 could be the most deleterious nsSNP in RB1 gene causing retinoblastoma.展开更多
基金supported by the National Nature Science Foundation of China(No.30900113)the Program for Innovative Research Team in the Institute of Medicinal Plant Development(No.IT1304)
文摘We cloned and analyzed the two genes of the 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase(HDR) gene family from Huperzia serrate.The two transcripts coding HDR,named Hs HDR1 and Hs HDR2,were discovered in the transcriptome dataset of H.serrate and were cloned by reverse transcription-polymerase chain reaction(RT-PCR).The physicochemical properties,protein domains,protein secondary structure,and 3D structure of the putative Hs HDR1 and Hs HDR2 proteins were analyzed.The full-length c DNA of the Hs HDR1 gene contained 1431 bp encoding a putative protein with 476 amino acids,whereas the Hs HDR2 gene contained 1428 bp encoding a putative protein of 475 amino acids.These two proteins contained the conserved domain of 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase(PF02401),but without the transmembrane region and signal peptide.The most abundant expression of Hs HDR1 and Hs HDR2 was detected in H.serrate roots,followed by the stems and leaves.Our results provide a foundation for exploring the function of Hs HDR1 and Hs HDR2 in terpenoid and sterol biosynthesis in Huperziaceae plants.
文摘In this study,we identified the most deleterious nsSNP in RB1 gene through structural and functional properties of its protein (pRB) and investigated its binding affinity with E2F-2.Out of 956 SNPs,we investigated 12 nsSNPs in coding region in which three of them (SNPids rs3092895,rs3092903 and rs3092905) are commonly found to be damaged by I-Mutant 2.0,SIFT and PolyPhen programs.With this effort,we modeled the mutant pRB proteins based on these deleterious nsSNPs.From a comparison of total energy,stabilizing residues and RMSD of these three mutant proteins with native pRB protein,we identified that the major mutation is from Glutamic acid to Glycine at the residue position of 746 of pRB.Further,we compared the binding efficiency of both native and mutant pRB (E746G) with E2F-2.We found that mutant pRB has less binding affinity with E2F-2 as compared to native type.This is due to sixteen hydrogen bonding and two salt bridges that exist between native type and E2F-2,whereas mutant type makes only thirteen hydrogen bonds and one salt bridge with E2F-2.Based on our investigation,we propose that the SNP with an id rs3092905 could be the most deleterious nsSNP in RB1 gene causing retinoblastoma.
