tRNA properties help shape codon pair preferences in open reading frames.
tRNA properties help shape codon pair preferences in open reading frames.
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DOI：
10.1093/nar/gkj488
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发表时间：
2006
影响因子：
14.9
通讯作者：
Stansfield I
中科院分区：
文献类型：
--
作者：
Buchan JR;Aucott LS;Stansfield I
翻译延伸是一个准确而快速的过程，依赖于tRNA在核糖体A-和P-位点的有效并置。在这里，我们通过检查一系列基因组开放阅读框架内密码子对选择的偏倚来寻找A和P位点tRNA相互作用的证据。三个不同的和显着的影响，揭示了一旦密码子和二肽的偏见已被扣除。首先，在大多数基因组中，密码子对偏好主要由P位点密码子的第三个核苷酸和A位点密码子的所有3个核苷酸的四核苷酸组合决定。其次，稀有密码子对通常在真核生物中使用不足，但在原核生物中过度使用。第三，分析揭示了tRNA介导的选择对单细胞真核生物、枯草芽孢杆菌和γ变形菌中密码子配对的高度显著影响。这是显而易见的，因为在这些生物体中，由相同的tRNA在A位点解码的同义密码子表现出显著相似的P位点配对偏好。因此，密码子对偏好性受到A位点tRNA的身份以及P位点密码子第三个核苷酸的影响。多变量分析确定了A位点tRNA序列内调节密码子对偏好的保守核苷酸位置。调节核糖体内tRNA几何形状的结构特征可以支配基因组密码子对模式，从而驱动增强的翻译保真度和/或速率。
Translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of tRNAs in the ribosomal A- and P-sites. Here, we sought evidence of A- and P-site tRNA interaction by examining bias in codon pair choice within open reading frames from a range of genomes. Three distinct and marked effects were revealed once codon and dipeptide biases had been subtracted. First, in the majority of genomes, codon pair preference is primarily determined by a tetranucleotide combination of the third nucleotide of the P-site codon, and all 3 nt of the A-site codon. Second, pairs of rare codons are generally under-used in eukaryotes, but over-used in prokaryotes. Third, the analysis revealed a highly significant effect of tRNA-mediated selection on codon pairing in unicellular eukaryotes, Bacillus subtilis, and the gamma proteobacteria. This was evident because in these organisms, synonymous codons decoded in the A-site by the same tRNA exhibit significantly similar P-site pairing preferences. Codon pair preference is thus influenced by the identity of A-site tRNAs, in combination with the P-site codon third nucleotide. Multivariate analysis identified conserved nucleotide positions within A-site tRNA sequences that modulate codon pair preferences. Structural features that regulate tRNA geometry within the ribosome may govern genomic codon pair patterns, driving enhanced translational fidelity and/or rate.
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DOI：
10.1073/pnas.95.23.13771
发表时间：
1998-11-10
影响因子：
11.1
作者：
Gallant, JA;Lindsley, D
通讯作者：
Lindsley, D
影响因子：
5.6
作者：
JORGENSEN, F;ADAMSKI, FM;KURLAND, CG
通讯作者：
KURLAND, CG
影响因子：
5.6
作者：
MILLER, JH;ALBERTINI, AM
通讯作者：
ALBERTINI, AM
影响因子：
1.6
作者：
McNulty, DE;Claffee, BA;Kane, JF
通讯作者：
Kane, JF
影响因子：
7.7
作者：
Dittmar, KA;Sorensen, MA;Pan, T
通讯作者：
Pan, T