Regulatory sRNAs in photosynthetic cyanobacteria have been reported, but the lack of plausible RNA chaperones involved in this regulation appears enigmatic. Here, we analyzed the full ensemble of cellular RNAs and proteins using gradient profiling by sequencing (Grad-seq) in Synechocystis 6803. Complexes with overlapping subunits such as the CpcG1-type versus the CpcL-type phycobilisomes or the PsaK1 versus PsaK2 photosystem I pre(complexes) could be distinguished supporting a high quality of the approach. Clustering of the in-gradient distribution profiles followed by several additional criteria yielded a short list of potential RNA chaperones that include a YlxR homolog and a cyanobacterial homolog of the KhpA/B complex. The data suggest previously undetected complexes between accessory proteins and CRISPR-Cas systems, such as a Csx1-Csm6 ribonucleolytic defense complex. Moreover, the exclusive association of either RpoZ or 6S RNA with the core RNA polymerase complex and the existence of a reservoir of inactive sigma-antisigma complexes is suggested. The Synechocystis Grad-seq resource is available online at https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/ providing a comprehensive resource for the functional assignment of RNA-protein complexes and multisubunit protein complexes in a photosynthetic organism.

中文翻译：

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内膜系统中富含光合作用的蓝细菌的梯度测序分析（Grad-seq）

已经报道了光合作用蓝细菌中的调节性sRNA，但是缺乏参与该调节的合理的RNA分子伴侣似乎是莫名其妙的。在这里，我们使用Synechocystis 6803中的测序（Grad-seq）方法通过梯度分析（Grad-seq）分析了细胞RNA和蛋白质的完整集合。具有重叠亚基的复合物，例如CpcG1型与CpcL型藻胆体或PsaK1与PsaK2光系统I pre （复杂）可以区分，以支持该方法的高质量。渐进分布分布图的聚类以及随后的几个其他标准产生了潜在的RNA伴侣的简短列表，其中包括KhpA / B复合体的YlxR同源物和蓝细菌同源物。数据表明先前未发现附件蛋白和CRISPR-Cas系统之间的复合物，如Csx1-Csm6核糖核酸防御复合物。此外，建议RpoZ或6S RNA与核心RNA聚合酶复合物的排他性关联，以及存在无活性sigma-antisigma复合物的储库。可通过https://sunshine.biologie.uni-freiburg.de/GradSeqExplorer/在线获取Synechocystis Grad-seq资源，它为光合生物中RNA蛋白质复合物和多亚基蛋白质复合物的功能分配提供了全面的资源。