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1
Key for protein coding sequences identification: computer analysis of codon strategy.蛋白质编码序列识别的关键：密码子策略的计算机分析
Nucleic Acids Res. 1982 Jan 11;10(1):391-402. doi: 10.1093/nar/10.1.391.
2
Codon usage in bacteria: correlation with gene expressivity.细菌中的密码子使用：与基因表达能力的相关性
Nucleic Acids Res. 1982 Nov 25;10(22):7055-74. doi: 10.1093/nar/10.22.7055.
3
Effect of structure of the initiator codon on translation in E. coli.起始密码子结构对大肠杆菌翻译的影响。
FEBS Lett. 1988 May 23;232(2):369-71. doi: 10.1016/0014-5793(88)80771-3.
4
The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences.细菌基因中碱基组成与密码子使用之间的关系及其在蛋白质编码序列简单可靠鉴定中的应用。
Gene. 1984 Oct;30(1-3):157-66. doi: 10.1016/0378-1119(84)90116-1.
5
Possible role of flanking nucleotides in recognition of the AUG initiator codon by eukaryotic ribosomes.侧翼核苷酸在真核生物核糖体识别AUG起始密码子中的可能作用。
Nucleic Acids Res. 1981 Oct 24;9(20):5233-52. doi: 10.1093/nar/9.20.5233.
6
[Characteristics of the context shift in the frequency of synonymic codons in Escherichia coli].[大肠杆菌中同义密码子频率的上下文转移特征]
Mol Biol (Mosk). 1988 May-Jun;22(3):767-79.
7
5'-Terminal nucleotide sequence of Escherichia coli lactose repressor mRNA: features of translational initiation and reinitiation sites.大肠杆菌乳糖阻遏蛋白mRNA的5′末端核苷酸序列：翻译起始和重新起始位点的特征
Proc Natl Acad Sci U S A. 1977 Oct;74(10):4163-7. doi: 10.1073/pnas.74.10.4163.
8
Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes.下游二级结构有助于真核生物核糖体识别起始密码子。
Proc Natl Acad Sci U S A. 1990 Nov;87(21):8301-5. doi: 10.1073/pnas.87.21.8301.
9
Reinitiation of translation from the triplet next to the amber termination codon in the absence of ribosome-releasing factor.在没有核糖体释放因子的情况下，从琥珀终止密码子旁边的三联体重新起始翻译。
Proc Natl Acad Sci U S A. 1981 Oct;78(10):5973-7. doi: 10.1073/pnas.78.10.5973.
10
Recognition of messenger RNA during translational initiation in Escherichia coli.大肠杆菌翻译起始过程中信使核糖核酸的识别
Biochimie. 1984 Jan;66(1):1-29. doi: 10.1016/0300-9084(84)90188-3.

引用本文的文献

1
Divergence in codon usage of Lactobacillus species.乳酸杆菌属物种密码子使用的差异。
Nucleic Acids Res. 1994 Mar 25;22(6):929-36. doi: 10.1093/nar/22.6.929.
2
Recognition of protein coding regions in DNA sequences.DNA序列中蛋白质编码区域的识别。
Nucleic Acids Res. 1982 Sep 11;10(17):5303-18. doi: 10.1093/nar/10.17.5303.
3
The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.密码子偏好性图：蛋白质编码序列的图形分析及基因表达预测
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):539-49. doi: 10.1093/nar/12.1part2.539.
4
Strong doublet preferences in nucleotide sequences and DNA geometry.核苷酸序列和DNA几何结构中强烈的双峰偏好。
J Mol Evol. 1984;20(2):111-9. doi: 10.1007/BF02257371.
5
Physical characteristics in eucaryotic promoters.真核生物启动子中的物理特征。
Nucleic Acids Res. 1983 Jul 11;11(13):4521-40. doi: 10.1093/nar/11.13.4521.
6
DNA sequences specifying the transcription of the streptococcal kanamycin resistance gene in Escherichia coli and Bacillus subtilis.指定大肠杆菌和枯草芽孢杆菌中链球菌卡那霉素抗性基因转录的DNA序列。
Mol Gen Genet. 1985;198(2):348-52. doi: 10.1007/BF00383017.
7
Analysis of the nucleotide sequence of the ereB gene encoding the erythromycin esterase type II.编码II型红霉素酯酶的ereB基因的核苷酸序列分析。
Nucleic Acids Res. 1986 Jun 25;14(12):4987-99. doi: 10.1093/nar/14.12.4987.

本文引用的文献

1
The ribosome binding sites recognized by E. coli ribosomes have regions with signal character in both the leader and protein coding segments.大肠杆菌核糖体识别的核糖体结合位点在前导序列和蛋白质编码序列中都有具有信号特征的区域。
Nucleic Acids Res. 1980 Sep 11;8(17):3895-907. doi: 10.1093/nar/8.17.3895.
2
The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites.大肠杆菌16S核糖体RNA的3'末端序列：与无义三联体及核糖体结合位点的互补性
Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342-6. doi: 10.1073/pnas.71.4.1342.
3
Sequence and symmetry in ribosome binding sites of bacteriophage f1 RNA.噬菌体f1 RNA核糖体结合位点的序列与对称性
J Mol Biol. 1974 Dec 5;90(2):191-124. doi: 10.1016/0022-2836(74)90368-4.
4
Nucleotide sequence of bacteriophage fd DNA.噬菌体fd DNA的核苷酸序列。
Nucleic Acids Res. 1978 Dec;5(12):4495-503. doi: 10.1093/nar/5.12.4495.
5
The nucleotide sequence of bacteriophage phiX174.噬菌体φX174的核苷酸序列。
J Mol Biol. 1978 Oct 25;125(2):225-46. doi: 10.1016/0022-2836(78)90346-7.
6
Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs.RNA分子中配对方案的预测——环的贡献以及摆动和非摆动配对的能量
Biochimie. 1979;61(10):1133-50. doi: 10.1016/s0300-9084(80)80227-6.
7
Correlation of local stability of DNA during melting with environmental conditions.DNA解链过程中局部稳定性与环境条件的相关性。
Nature. 1979 Aug 9;280(5722):515-7. doi: 10.1038/280515a0.

蛋白质编码序列识别的关键：密码子策略的计算机分析

Key for protein coding sequences identification: computer analysis of codon strategy.

作者信息

Rodier F, Gabarro-Arpa J, Ehrlich R, Reiss C

出版信息

Nucleic Acids Res. 1982 Jan 11;10(1):391-402. doi: 10.1093/nar/10.1.391.

DOI:10.1093/nar/10.1.391
PMID:7038623
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC326141/
Abstract

The signal qualifying an AUG or GUG as an initiator in mRNAs processed by E. coli ribosomes is not found to be a systematic, literal homology sequence. In contrast, stability analysis reveals that initiators always occur within nucleic acid domains of low stability, for which a high A/U content is observed. Since no aminoacid selection pressure can be detected at N-termini of the proteins, the A/U enrichment results from a biased usage of the code degeneracy. A computer analysis is presented which allows easy detection of the codon strategy. N-terminal codons carry rather systematically A or U in third position, which suggests a mechanism for translation initiation and helps to detect protein coding sequences in sequenced DNA.

摘要

在由大肠杆菌核糖体加工的mRNA中，将AUG或GUG鉴定为起始密码子的信号并非系统的、字面上的同源序列。相反，稳定性分析表明，起始密码子总是出现在低稳定性的核酸结构域内，在这些结构域中观察到较高的A/U含量。由于在蛋白质的N端检测不到氨基酸选择压力，A/U富集是由于密码子简并性的偏向使用所致。本文提出了一种计算机分析方法，可轻松检测密码子策略。N端密码子在第三位相当系统地携带A或U，这提示了一种翻译起始机制，并有助于在测序DNA中检测蛋白质编码序列。