Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme.
Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme.
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DOI：
10.1093/molbev/mss273
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发表时间：
2013-03
影响因子：
10.7
通讯作者：
Marx CJ
中科院分区：
文献类型：
--
作者：
Agashe D;Martinez-Gomez NC;Drummond DA;Marx CJ
蛋白质编码基因中密码子使用的偏差是普遍存在的，氨基酸主要由可能密码子的特定子集编码。在单个基因中，密码子偏倚在进化上保守的残基上更强，有利于被丰富的 tRNA 识别的密码子。尽管这一观察表明翻译速度和/或准确性的总体选择模式，但其他工作表明转录物结构或结合基序驱动密码子的使用。然而，我们对密码子偏倚进化的理解受到关于改变功能基因密码子的适应性影响的有限实验数据的限制。为了弥补这一差距，我们在扭扭甲基杆菌中生成了关键酶编码基因的同义变体。我们发现突变型基因表达、酶产量、酶活性和适应度均显着低于野生型。令人惊讶的是，仅使用稀有密码子编码的基因使适合度降低了 40%，而完全由频繁密码子编码的等位基因使适合度降低了 90% 以上。增加基因表达可以不同程度地恢复突变体的适应性，这表明同义突变体的适应性劣势是由于缺乏有益的蛋白质而不是蛋白质生产的成本造成的。蛋白质产量与抗Shine-Dalgarno序列具有高亲和力的基序频率呈负相关，表明核糖体暂停是低突变体适应性的主要原因。总之，我们的数据支持这样的观点：虽然一组特定的密码子在整个基因组中平均受到青睐，但在单个基因选择中，可以根据密码子的局部情况支持或反对密码子。
Biased codon usage in protein-coding genes is pervasive, whereby amino acids are largely encoded by a specific subset of possible codons. Within individual genes, codon bias is stronger at evolutionarily conserved residues, favoring codons recognized by abundant tRNAs. Although this observation suggests an overall pattern of selection for translation speed and/or accuracy, other work indicates that transcript structure or binding motifs drive codon usage. However, our understanding of codon bias evolution is constrained by limited experimental data on the fitness effects of altering codons in functional genes. To bridge this gap, we generated synonymous variants of a key enzyme-coding gene in Methylobacterium extorquens. We found that mutant gene expression, enzyme production, enzyme activity, and fitness were all significantly lower than wild-type. Surprisingly, encoding the gene using only rare codons decreased fitness by 40%, whereas an allele coded entirely by frequent codons decreased fitness by more than 90%. Increasing gene expression restored mutant fitness to varying degrees, demonstrating that the fitness disadvantage of synonymous mutants arose from a lack of beneficial protein rather than costs of protein production. Protein production was negatively correlated with the frequency of motifs with high affinity for the anti-Shine-Dalgarno sequence, suggesting ribosome pausing as the dominant cause of low mutant fitness. Together, our data support the idea that, although a particular set of codons are favored on average across a genome, in an individual gene selection can either act for or against codons depending on their local context.
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影响因子：
56.9
作者：
Lind, Peter A.;Berg, Otto G.;Andersson, Dan I.
通讯作者：
Andersson, Dan I.
DOI：
10.1016/s0006-291x(02)00226-7
发表时间：
2002-04-26
影响因子：
3.1
作者：
Cortazzo, P;Cerve単ansky, C;Deana, A
通讯作者：
Deana, A
影响因子：
3.2
作者：
Marx, CJ;Chistoserdova, L;Lidstrom, ME
通讯作者：
Lidstrom, ME
DOI：
10.1038/nrg2899
发表时间：
2011-01
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
5.6
作者：
CURRAN, JF;YARUS, M
通讯作者：
YARUS, M