The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages.
The core and accessory Hfq interactomes across Pseudomonas aeruginosa lineages.
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DOI：
10.1038/s41467-022-28849-w
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发表时间：
2022-03-10
影响因子：
16.6
通讯作者：
Lory S
中科院分区：
文献类型：
--
作者：
Trouillon J;Han K;Attrée I;Lory S
主要rna结合蛋白Hfq可单独或与调节性小非编码rna （sRNAs）相互作用，影响细菌中mRNA的翻译和降解。然而，尽管已知存在重要的种内遗传多样性，但研究往往集中在单一参考菌株上，并假设这些发现可能适用于整个物种。在这里，我们使用RIP-seq鉴定了代表铜绿假单胞菌主要系统发育谱系的三个菌株的hfq相互作用rna。我们发现，事实上，大多数相互作用在不同菌株之间并不保守。我们确定了生长阶段特异性和菌株特异性的Hfq靶标，包括先前描述的srna。菌株特异性相互作用是由于不同的辅助基因集、RNA丰度或潜在的环境或序列依赖的调节机制。附件Hfq相互作用组包括两个菌株中编码III型分泌系统（T3SS）成分和分泌毒素的大部分mrna，以及一个菌株中的CRISPR引导rna簇。保守的Hfq靶点包括全球毒力调节因子Vfr和参与从快速到缓慢生长转变的代谢途径。此外，我们使用rGRIL-seq显示了群体感应sRNA RhlS激活Vfr翻译，从而揭示了群体感应和毒力调节之间的联系。总之，我们的工作强调了铜绿假单胞菌转录后调控网络中重要的种内多样性。Hfq蛋白通过与mRNA和小非编码rna相互作用调控细菌mRNA的翻译和稳定性。本文中，作者在代表铜绿假单胞菌主要系统发育谱系的三种菌株中鉴定了hfq相互作用的rna，突出了转录后调控网络的种内多样性。
The major RNA-binding protein Hfq interacts with mRNAs, either alone or together with regulatory small noncoding RNAs (sRNAs), affecting mRNA translation and degradation in bacteria. However, studies tend to focus on single reference strains and assume that the findings may apply to the entire species, despite the important intra-species genetic diversity known to exist. Here, we use RIP-seq to identify Hfq-interacting RNAs in three strains representing the major phylogenetic lineages of Pseudomonas aeruginosa. We find that most interactions are in fact not conserved among the different strains. We identify growth phase-specific and strain-specific Hfq targets, including previously undescribed sRNAs. Strain-specific interactions are due to different accessory gene sets, RNA abundances, or potential context- or sequence- dependent regulatory mechanisms. The accessory Hfq interactome includes most mRNAs encoding Type III Secretion System (T3SS) components and secreted toxins in two strains, as well as a cluster of CRISPR guide RNAs in one strain. Conserved Hfq targets include the global virulence regulator Vfr and metabolic pathways involved in the transition from fast to slow growth. Furthermore, we use rGRIL-seq to show that RhlS, a quorum sensing sRNA, activates Vfr translation, thus revealing a link between quorum sensing and virulence regulation. Overall, our work highlights the important intra-species diversity in post-transcriptional regulatory networks in Pseudomonas aeruginosa. Protein Hfq regulates bacterial mRNA translation and stability by interacting with mRNAs and small noncoding RNAs. Here, the authors identify Hfq-interacting RNAs in three strains representing major phylogenetic lineages of Pseudomonas aeruginosa, highlighting intra-species diversity in post-transcriptional regulatory networks.