Hooper S D, Berg O G
Department of Molecular Evolution, EBC, Uppsala University, Norbyvägen 18C, SE-75236, Uppsala, Sweden.
Nucleic Acids Res. 2000 Sep 15;28(18):3517-23. doi: 10.1093/nar/28.18.3517.
The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.
密码子和核苷酸组合的使用情况在基因中各有不同，系统变异会导致使用梯度的出现。我们研究了大肠杆菌中核苷酸和核苷酸组合的此类梯度及其紧邻序列。为区分突变效应和选择效应，将基因分为具有不同密码子使用偏好的三组，并对每组中的核苷酸使用梯度进行了研究。一些可能与持续合成错误倾向相关的组合呈现出强烈的负梯度，而在密码子偏好较低的基因中这种梯度会变弱，这与对翻译效率的选择一致。最强的梯度之一是针对第三位的鸟嘌呤（G），在周围碱基的大多数情况下，其使用呈现出普遍的正梯度。
