A comparative study of variation in codon 33 of the rpoS gene in Escherichia coli K12 stocks:: implications for the synthesis of σs
A comparative study of variation in codon 33 of the rpoS gene in Escherichia coli K12 stocks:: implications for the synthesis of σs
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DOI：
10.1007/s00438-003-0944-x
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发表时间：
2004-01-01
影响因子：
3.1
通讯作者：
Sarkar, M
中科院分区：
文献类型：
--
作者：
Subbarayan, PR;Sarkar, M
大肠杆菌rpoS基因编码稳定期基因表达所需的RNA聚合酶sigma因子（sigma S或sigma（S））。在首次发表的E. coliK-12密码子33以CAG给出。然而，随后的几项独立研究发现琥珀密码子TAG位于该位置（rpoSAm）。除了这个琥珀密码子，在rpoS的这个位置还发现了其他密码子，如达特。比较基因组分析现在使我们提出TAG作为E. coli K-12中表达。研究了菌株W3110的五种不同的原种，它们表达的sigma（S）蛋白水平不同。我们对这些rpoS基因进行了测序，发现五个股票中有四个在核苷酸位置97处为T，五个股票中有三个在位置99处为G。W3110的亲本菌株W1485和W3110的衍生物W3350也是rpoSAm突变体。预期此类rpoSAm突变体不显示RpoS活性。因此，无抑制子的rpoSAm突变体保留部分或中间σ（S）活性是令人困惑的。我们提出，一个功能性的，N-末端截短的，sigma（S）（Delta 1 - 53 sigma（S））可以从位于琥珀密码子33下游的二级翻译起始区（STIR）翻译。最近有报道称，缺少前53个氨基酸的RpoS片段（Delta 1 - 53 sigma（S））在体内合成时是有功能的。综上所述，我们的结果支持了大肠杆菌rpoS基因的原始密码子33的假设。coli K-12菌株的琥珀密码子为TAG。
The Escherichia coli rpoS gene encodes an RNA polymerase sigma factor (sigma S or sigma(S)) required for the expression of stationary-phase genes. In the first published rpoS sequence from E. coli K-12 codon 33 is given as CAG. However, several subsequent independent studies found the amber codon TAG at this position ( rpoSAm). Besides this amber codon, other codons such as TAT have also been found at this location in rpoS. Comparative genome analysis now leads us to propose TAG as the parental codon 33 in rpoS in E. coli K-12. Five different stocks of the strain W3110, which differ in the levels of sigma(S) protein they express, were investigated. We sequenced the rpoS gene from these, and found a T at nucleotide position 97 in four out of the five stocks and a G at position 99 in three out of the five. W1485, a parental strain of W3110, and W3350, a derivative of W3110, are also rpoSAm mutants. Such rpoSAm mutants would be expected to show no RpoS activity. The retention of partial or intermediate sigma(S) activity by suppressor-free rpoSAm mutants is therefore puzzling. We propose that a functional, N-terminally truncated, sigma(S) (Delta1-53sigma(S)) can be translated from a Secondary Translation Initiation Region (STIR) located downstream of the amber codon 33. It has recently been reported that a fragment of RpoS (Delta1-53sigma(S)) that lacks the first 53 amino acids is functional when synthesized in vivo. Taken together, our results support the hypothesis that the original codon 33 of the rpoS gene in E. coli K-12 strains is the amber codon TAG.