In bacteria, σ²⁸ is the flagella‐specific sigma factor that targets RNA polymerase (RNAP ) to control the expression of flagella‐related genes involving bacterial motility and chemotaxis. However, the structural mechanism of σ²⁸‐dependent promoter recognition remains uncharacterized. Here, we report cryo‐EM structures of E. coli σ²⁸‐dependent transcribing complexes on a complete flagella‐specific promoter. These structures reveal how σ²⁸‐RNAP recognizes promoter DNA through strong interactions with the −10 element, but weak contacts with the −35 element, to initiate transcription. In addition, we observed a distinct architecture in which the β′ zinc‐binding domain (ZBD ) of RNAP stretches out from its canonical position to interact with the upstream non‐template strand. Further in vitro and in vivo assays demonstrate that this interaction has the overall effect of facilitating closed‐to‐open isomerization of the RNAP –promoter complex by compensating for the weak interaction between σ4 and −35 element. This suggests that ZBD relocation may be a general mechanism employed by σ⁷⁰ family factors to enhance transcription from promoters with weak σ4/−35 element interactions.

中文翻译：

---

细菌σ28介导的转录的结构基础揭示了RNA聚合酶锌结合域的作用。

在细菌中，σ ²⁸是鞭毛特异性σ因子即目标RNA聚合酶（RNAP）来控制的，涉及细菌运动性和趋化性鞭毛相关基因的表达。然而，σ的结构机构²⁸依赖性启动子识别仍然未表征。在这里，我们报告的冷冻电镜结构大肠杆菌σ ^28种上完成特定的鞭毛启动子依赖性转录复合物。这些结构揭示如何σ ²⁸‐RNAP通过与−10元素的强相互作用而与−35元素的弱接触来识别启动子DNA，从而启动转录。此外，我们观察到了一种独特的结构，其中RNAP的β'锌结合结构域（ZBD）从其规范位置伸出，与上游非模板链相互作用。进一步的体外和体内试验表明，这种相互作用具有总体作用，可通过补偿σ4和-35元素之间的弱相互作用来促进RNA聚合酶-启动子复合物的封闭-开放异构化。这表明，ZBD重定位可以是由σ采用一般的机构^70个家庭因素，以增强从与弱σ4/ -35元件相互作用的启动子转录。