采用CodonW1.4.2软件和CUSP程序,以普通羊肚菌(Morchella conica)全基因组蛋白质编码序列(coding sequence,CDS)为对象,解析了该菌的有效密码子数(effective number of codon,ENC)、密码子3个位点的GC含量、相对同义密码子使用度(relati...采用CodonW1.4.2软件和CUSP程序,以普通羊肚菌(Morchella conica)全基因组蛋白质编码序列(coding sequence,CDS)为对象,解析了该菌的有效密码子数(effective number of codon,ENC)、密码子3个位点的GC含量、相对同义密码子使用度(relative synonymous codon usage,RSCU)和高表达优越密码子。结果表明:普通羊肚菌全基因组密码子第2位密码子的GC含量明显低于第1位和第3位,第3位密码子与第1位含量差异不大,分别为57.8%和56.8%,RSCU值大于等于1的密码子总共35个,其中以G或C结尾的25个,占71.4%,确定了25个高表达优越密码子。展开更多
The genetic code serves as one of the natural links for life＇s two conceptual frameworks--the informational and operational tracks-- bridging the nucleotide sequence of DNA and RNA to the amino acid sequence of prote...The genetic code serves as one of the natural links for life＇s two conceptual frameworks--the informational and operational tracks-- bridging the nucleotide sequence of DNA and RNA to the amino acid sequence of protein and thus its structure and function. On the informational track, DNA and its four building blocks have four basic variables： order, length, GC and purine contents; the latter two exhibit unique characteristics in prokaryotic genomes where protein-coding sequences dominate. Bridging the two tracks, tRNAs and their aminoacyl tRNA synthases that interpret each codon--nucleotide triplet, together with ribosomes, form a complex machinery that translates genetic information encoded on the messenger RNAs into proteins. On the operational track, proteins are selected in a context of cellular and organismal functions constantly. The principle of such a functional selection is to minimize the damage caused by sequence alteration in a seemingly random fashion at the nucleotide level and its function-altering consequence at the protein level; the principle also suggests that there must be complex yet sophisticated mechanisms to protect molecular interactions and cellular processes for cells and organisms from the damage in addition to both immediate or short-term eliminations and long-term selections. The two- century study of selection at species and population levels has been leading a way to understand rules of inheritance and evolution at molecular levels along the informational track, while ribogenomics, epigenomics and other operationally-defined omits （such as the metabolite-centric metabolomics） have been ushering biologists into the new millennium along the operational track.展开更多
文摘采用CodonW1.4.2软件和CUSP程序,以普通羊肚菌(Morchella conica)全基因组蛋白质编码序列(coding sequence,CDS)为对象,解析了该菌的有效密码子数(effective number of codon,ENC)、密码子3个位点的GC含量、相对同义密码子使用度(relative synonymous codon usage,RSCU)和高表达优越密码子。结果表明:普通羊肚菌全基因组密码子第2位密码子的GC含量明显低于第1位和第3位,第3位密码子与第1位含量差异不大,分别为57.8%和56.8%,RSCU值大于等于1的密码子总共35个,其中以G或C结尾的25个,占71.4%,确定了25个高表达优越密码子。
基金National Basic Research Program(973 ProgramGrant No.2011CB944100 and 2011CB944101)+3 种基金National Natural Science Foundation of China(Grant No.90919024)supported by grants from the "100-Talent Program" of Chinese Academy of Sciences(Grant No.Y1SLXb1365)National Programs for High Technology Research and Development(863 ProgramGrant No.2012AA020409)
文摘The genetic code serves as one of the natural links for life＇s two conceptual frameworks--the informational and operational tracks-- bridging the nucleotide sequence of DNA and RNA to the amino acid sequence of protein and thus its structure and function. On the informational track, DNA and its four building blocks have four basic variables： order, length, GC and purine contents; the latter two exhibit unique characteristics in prokaryotic genomes where protein-coding sequences dominate. Bridging the two tracks, tRNAs and their aminoacyl tRNA synthases that interpret each codon--nucleotide triplet, together with ribosomes, form a complex machinery that translates genetic information encoded on the messenger RNAs into proteins. On the operational track, proteins are selected in a context of cellular and organismal functions constantly. The principle of such a functional selection is to minimize the damage caused by sequence alteration in a seemingly random fashion at the nucleotide level and its function-altering consequence at the protein level; the principle also suggests that there must be complex yet sophisticated mechanisms to protect molecular interactions and cellular processes for cells and organisms from the damage in addition to both immediate or short-term eliminations and long-term selections. The two- century study of selection at species and population levels has been leading a way to understand rules of inheritance and evolution at molecular levels along the informational track, while ribogenomics, epigenomics and other operationally-defined omits （such as the metabolite-centric metabolomics） have been ushering biologists into the new millennium along the operational track.
