噬菌体通过与RNA和DNA结合的螺旋–转角–螺旋（HTH）蛋白抵抗CRISPR，这一成果由新西兰奥塔戈大学Peter C. Fineran团队经过不懈努力而取得。相关论文于2024年7月10日发表在《自然》杂志上。

研究人员发现调节因子抗CRISPR相关（Aca）2蛋白的HTH结构域，除了通过结合DNA调控Acr的转录合成外，还通过结合保守的RNA环和阻断核糖体的进入来抑制mRNA的翻译。约40 kDa的Aca2-RNA复合物冷冻电镜结构展示了，多功能 HTH 结构域如何从DNA结合位点特异性地识别RNA。

这些组合调控模式在Aca2家族中非常普遍，有助于在噬菌体DNA快速复制的情况下抑制CRISPR-Cas，而不会出现有毒的acr过表达。鉴于含HTH结构域蛋白的普遍性，预计会有更多的含HTH结构域的蛋白通过DNA和RNA的双重结合实现调控。

研究人员表示，在所有生物体中，基因表达的调控都必须根据细胞的需要进行调整，这通常与含有螺旋-转角-螺旋结构域蛋白有关。例如，在细菌和噬菌体的竞争中，噬菌体抵抗CRISPR (acr)的基因在感染后迅速表达，从而逃避CRISPR-Cas的防御；转录随后被含有HTH结构域的抗CRISPR相关蛋白抑制，这可能是为了降低蛋白过表达所带来危害。然而，目前尚不清楚单个HTH调节因子如何调整抗CRISPR的产生，以应对噬菌体基因组拷贝数增加和acr mRNA的积累。

附：英文原文

Title: Phage anti-CRISPR control by an RNA- and DNA-binding helix–turn–helix protein

Author: Birkholz, Nils, Kamata, Kotaro, Feussner, Maximilian, Wilkinson, Max E., Cuba Samaniego, Christian, Migur, Angela, Kimanius, Dari, Ceelen, Marijn, Went, Sam C., Usher, Ben, Blower, Tim R., Brown, Chris M., Beisel, Chase L., Weinberg, Zasha, Fagerlund, Robert D., Jackson, Simon A., Fineran, Peter C.

Issue&Volume: 2024-07-10

Abstract: In all organisms, regulation of gene expression must be adjusted to meet cellular requirements and frequently involves helix–turn–helix (HTH) domain proteins1. For instance, in the arms race between bacteria and bacteriophages, rapid expression of phage anti-CRISPR (acr) genes upon infection enables evasion from CRISPR–Cas defence; transcription is then repressed by an HTH-domain-containing anti-CRISPR-associated (Aca) protein, probably to reduce fitness costs from excessive expression2,3,4,5. However, how a single HTH regulator adjusts anti-CRISPR production to cope with increasing phage genome copies and accumulating acr mRNA is unknown. Here we show that the HTH domain of the regulator Aca2, in addition to repressing Acr synthesis transcriptionally through DNA binding, inhibits translation of mRNAs by binding conserved RNA stem-loops and blocking ribosome access. The cryo-electron microscopy structure of the approximately 40kDa Aca2–RNA complex demonstrates how the versatile HTH domain specifically discriminates RNA from DNA binding sites. These combined regulatory modes are widespread in the Aca2 family and facilitate CRISPR–Cas inhibition in the face of rapid phage DNA replication without toxic acr overexpression. Given the ubiquity of HTH-domain-containing proteins, it is anticipated that many more of them elicit regulatory control by dual DNA and RNA binding.

DOI: 10.1038/s41586-024-07644-1

Source: https://www.nature.com/articles/s41586-024-07644-1