Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different specie...Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.展开更多
为探究甜龙竹叶绿体基因组密码子的偏好性及影响因素,以甜龙竹叶绿体基因组50个蛋白编码序列为研究对象,利用Codon W 1.4.2、CUSP、Excel等软件分析密码子第1、第2和第3位碱基的GC含量(GC1、GC2、GC3)、有效密码子数(effective number o...为探究甜龙竹叶绿体基因组密码子的偏好性及影响因素,以甜龙竹叶绿体基因组50个蛋白编码序列为研究对象,利用Codon W 1.4.2、CUSP、Excel等软件分析密码子第1、第2和第3位碱基的GC含量(GC1、GC2、GC3)、有效密码子数(effective number of codons,ENC)、密码子适应系数(codon adaptation index,CAI)、密码子偏性指数(codon bias index,CBI)、最优密码子使用频率(frequency of optimal codons,Fop)及相对同义密码子使用度(relative synonymous codon usage,RSCU)。结果显示,GC含量呈现出GC1(47.70%)>GC2(39.39%)>GC3(30.99%)的趋势;平均GC含量为39.36%,表明甜龙竹叶绿体基因组中GC含量分布不均匀。密码子偏好以A/U结尾,且第3位碱基(GC3)比第1和第2位碱基更偏好使用A/U。ENC、CAI、CBI、Fop的均值分别为50.41、0.17、-0.09和0.36,表明甜龙竹叶绿体基因密码子使用偏好性较弱。中性绘图、ENC-plot和PR2-plot绘图分析结果表明,甜龙竹叶绿体基因组密码子使用偏好性主要受自然选择影响;确定了GCU、UGU、GGU等11个最优密码子。以上结果为甜龙竹的基因组学研究提供了参考依据,并为相关领域的后续研究奠定了基础。展开更多
Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational proper...Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.展开更多
基金This work was supported by the National Major Basic Research and Development Program(No.TG1999016004)Jiangsu Provincial Natural Science Foundation(No.BK2003213).
文摘Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence （CDS） of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. ＆ Gray., is used to analyze the relative frequency of synonymous codon （RFSC）. High-frequency codons are selected by high-frequency （HF） codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.
文摘为探究甜龙竹叶绿体基因组密码子的偏好性及影响因素,以甜龙竹叶绿体基因组50个蛋白编码序列为研究对象,利用Codon W 1.4.2、CUSP、Excel等软件分析密码子第1、第2和第3位碱基的GC含量(GC1、GC2、GC3)、有效密码子数(effective number of codons,ENC)、密码子适应系数(codon adaptation index,CAI)、密码子偏性指数(codon bias index,CBI)、最优密码子使用频率(frequency of optimal codons,Fop)及相对同义密码子使用度(relative synonymous codon usage,RSCU)。结果显示,GC含量呈现出GC1(47.70%)>GC2(39.39%)>GC3(30.99%)的趋势;平均GC含量为39.36%,表明甜龙竹叶绿体基因组中GC含量分布不均匀。密码子偏好以A/U结尾,且第3位碱基(GC3)比第1和第2位碱基更偏好使用A/U。ENC、CAI、CBI、Fop的均值分别为50.41、0.17、-0.09和0.36,表明甜龙竹叶绿体基因密码子使用偏好性较弱。中性绘图、ENC-plot和PR2-plot绘图分析结果表明,甜龙竹叶绿体基因组密码子使用偏好性主要受自然选择影响;确定了GCU、UGU、GGU等11个最优密码子。以上结果为甜龙竹的基因组学研究提供了参考依据,并为相关领域的后续研究奠定了基础。
文摘Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.
