Nigam Akanksha, Oron-Gottesman Adi, Engelberg-Kulka Hanna
Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University, Hadassah Medical School, Jerusalem91120, Israel.
Curr Genomics. 2020 May;21(4):311-318. doi: 10.2174/1389202921999200606215305.
Escherichia coli (E. coli) mazEF, a stress-induced toxin-antitoxin (TA) system, has been studied extensively. The MazF toxin is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a Stress-induced Translation Machinery (STM), composed of MazF processed mRNAs and selective ribosomes that specifically translate the processed mRNAs.
Based on the data from the EcoCyc website of the National Center for Biotechnology Information (NCBI), the sequence of all E. coli MG1655 genes were scanned for ACA sites upstream from the initiation codons. Among these sequences, the fuzznuc program of the "European Molecular Biology Open Software Suite" (EMBOSS) was used to find the "ACA" pattern. The distribution of the ACA threonine codon, both in-frame and out-of-frame, was determined by using the HTML Script Program (Supplementary Material).
Here it is reported that for most of the E. coli proteins mediated by stress-induced MazF, the ACA threonine codon in their mRNAs is not in-frame but rather out-of-frame; in these same RNAs, the three synonymous threonine codons, ACG, ACU, and ACC, are in-frame. In contrast, for proteins translated by the canonical translation system, in the majority of mRNAs, the ACA codon is located in-frame.
The described bias in the genetic code is a characteristic of E. coli genes specifying for stress-induced MazF-mediated proteins.
大肠杆菌（E. coli）mazEF是一种应激诱导的毒素-抗毒素（TA）系统，已得到广泛研究。MazF毒素是一种内切核糖核酸酶，可在ACA位点切割RNA。因此，在应激状态下，诱导产生的MazF会生成一种应激诱导翻译机制（STM），该机制由MazF加工后的mRNA和特异性翻译这些加工后mRNA的选择性核糖体组成。
基于美国国立生物技术信息中心（NCBI）的EcoCyc网站的数据，扫描了大肠杆菌MG1655所有基因的序列，以查找起始密码子上游的ACA位点。在这些序列中，使用了“欧洲分子生物学开放软件套件”（EMBOSS）的fuzznuc程序来查找“ACA”模式。通过使用HTML脚本程序（补充材料）确定了框内和框外ACA苏氨酸密码子的分布。
据报道，对于大多数由应激诱导的MazF介导的大肠杆菌蛋白质，其mRNA中的ACA苏氨酸密码子不在框内，而是框外；在这些相同的RNA中，三个同义苏氨酸密码子ACG、ACU和ACC在框内。相比之下，对于由经典翻译系统翻译的蛋白质，在大多数mRNA中，ACA密码子位于框内。
所描述的遗传密码偏差是大肠杆菌中指定应激诱导的MazF介导蛋白质的基因的一个特征。
