Divergence in codon usage of Lactobacillus species.
Divergence in codon usage of Lactobacillus species.
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DOI：
10.1093/nar/22.6.929
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发表时间：
1994-03
影响因子：
14.9
通讯作者：
P. Pouwels;J. Leunissen
中科院分区：
文献类型：
--
作者：
P. Pouwels;J. Leunissen
我们已经分析了70个测序基因的密码子使用模式，从不同的乳酸杆菌物种。乳酸杆菌中的密码子使用是高度偏倚的。种间和种内的异质性的密码子使用偏好进行了观察。L. acidophilus与L. helveticus，但与L. bulgaricus、保加利亚湖L.干酪湖（L. casei）pentosus和L.植物后三种生物的密码子使用没有显著差异，但与L.保加利亚人。种间密码子使用的差异至少可以部分地由突变漂移的差异来解释。L. bulgaricus表现为GC漂移，而所有其他物种都表现为AT漂移。L.嗜酸乳杆菌和L.与所有其他物种相比，瑞士亚种很少在家族盒（一组同义）密码子中使用NNG。这个结果可以通过假设L.嗜酸乳杆菌和L. helveticus，而不是其他物种检查，使用一个单一的tRNA物种的家族盒密码子的翻译。基因表达水平的差异与密码子使用偏性呈正相关。高表达基因显示高度偏好的密码子使用，而弱表达基因显示少得多的偏好密码子使用。乳酸杆菌基因5 '端的密码子使用模式与整个基因的密码子使用模式没有显著差异。密码子2-6的GC含量与基因的其余部分相比显著降低。降低GC含量的翻译效率的控制可能产生的影响进行了讨论。
We have analyzed codon usage patterns of 70 sequenced genes from different Lactobacillus species. Codon usage in lactobacilli is highly biased. Both inter-species and intra-species heterogeneity of codon usage bias was observed. Codon usage in L. acidophilus is similar to that in L. helveticus, but dissimilar to that in L. bulgaricus, L. casei, L. pentosus and L. plantarum. Codon usage in the latter three organisms is not significantly different, but is different from that in L. bulgaricus. Inter-species differences in codon usage can, at least in part, be explained by differences in mutational drift. L. bulgaricus shows GC drift, whereas all other species show AT drift. L. acidophilus and L. helveticus rarely use NNG in family-box (a set of synonymous) codons, in contrast to all other species. This result may be explained by assuming that L. acidophilus and L. helveticus, but not other species examined, use a single tRNA species for translation of family-box codons. Differences in expression level of genes are positively correlated with codon usage bias. Highly expressed genes show highly biased codon usage, whereas weakly expressed genes show much less biased codon usage. Codon usage patterns at the 5'-end of Lactobacillus genes is not significantly different from that of entire genes. The GC content of codons 2-6 is significantly reduced compared with that of the remainder of the gene. The possible implications of a reduced GC content for the control of translation efficiency are discussed.