Since the genetic code is degenerate, several codons are translated to the same amino acid. Although these triplets were historically considered to be “synonymous” and therefore expected to be used at rather equal frequencies in all genomes, we now know that this is not the case. Indeed, since several coding sequences were obtained in the late ‘70s and early ‘80s in the last century, coming from either the same or different species, it was evident that (a) each genome, taken globally, displayed different codon usage patterns, which means that different genomes display a particular global codon usage table when all genes are considered together, and (b) there is a strong intragenomic diversity: in other words, within a given species the codon usage pattern can (and usually do) differ greatly among genes in the same genome. These different patterns were attributed to two main factors: first, the mutational bias characteristic of each genome, which determines that GC− poor species display a general bias towards A/T codons while the reverse is true for GC− rich species. Second, the differences in codon usage among genes from the same species are due to natural selection acting at the level of translation, in such a way that highly expressed genes tend to use codons that match with the most abundant isoacceptor tRNAs. Thus, these genes are translated at a highest rate, which in turn leads to avoid the limiting factor in translation which is the number of available ribosomes per cell. Although these explanations are still valid, new factors are almost constantly postulated to affect codon usage. In this mini review, we shall try to summarize them.

由于遗传密码是简并的，几个密码子被翻译成相同的氨基酸。尽管这些三胞胎在历史上被认为是“同义的”，因此预计在所有基因组中以相当相同的频率使用，但我们现在知道情况并非如此。事实上，由于在上个世纪 70 年代末和 80 年代初获得了来自相同或不同物种的几个编码序列，很明显（a）每个基因组，在全球范围内，显示出不同的密码子使用模式，这意味着当所有基因一起考虑时，不同的基因组显示特定的全局密码子使用表，并且 (b) 存在强大的基因组内多样性：换句话说，在给定的物种内，密码子使用模式可以（并且通常确实）有很大差异在同一基因组的基因之间。这些不同的模式归因于两个主要因素：首先，每个基因组的突变偏好特征，这决定了 GC 贫乏的物种对 A/T 密码子表现出普遍的偏见，而 GC 富集的物种则相反。其次，来自同一物种的基因之间密码子使用的差异是由于自然选择在翻译水平上起作用，因此高表达的基因倾向于使用与最丰富的同种受体 tRNA 匹配的密码子。因此，这些基因以最高的速度翻译，从而避免翻译中的限制因素，即每个细胞可用核糖体的数量。尽管这些解释仍然有效，但几乎不断假设新因素会影响密码子的使用。在这个迷你评论中，我们将尝试总结它们。