RNA-binding proteins (RBPs) play important roles in bacterial gene expression and physiology but their true number and functional scope remain little understood even in model microbes. To advance global RBP discovery in bacteria, we here establish glycerol gradient sedimentation with RNase treatment and mass spectrometry (GradR). Applied to Salmonella enterica, GradR confirms many known RBPs such as CsrA, Hfq and ProQ by their RNase-sensitive sedimentation profiles, and discovers the FopA protein as a new member of the emerging family of FinO/ProQ-like RBPs. FopA, encoded on resistance plasmid pCol1B9, primarily targets a small RNA associated with plasmid replication. The target suite of FopA dramatically differs from the related global RBP ProQ, revealing context-dependent selective RNA recognition by FinO-domain RBPs. Numerous other unexpected RNase-induced changes in gradient profiles suggest that cellular RNA helps to organize macromolecular complexes in bacteria. By enabling poly(A)-independent generic RBP discovery, GradR provides an important element in the quest to build a comprehensive catalogue of microbial RBPs.

中文翻译：

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通过 RNase 敏感梯度图谱全球发现细菌 RNA 结合蛋白报告了一种新的 FinO 结构域蛋白

RNA 结合蛋白 (RBP) 在细菌基因表达和生理学中发挥重要作用，但即使在模型微生物中，它们的真实数量和功能范围仍然知之甚少。为了推进细菌中的全球 RBP 发现，我们在这里建立了带有 RNase 处理和质谱 (GradR) 的甘油梯度沉降。GradR 应用于肠道沙门氏菌，通过其 RNase 敏感的沉降曲线证实了许多已知的 RBP，例如 CsrA、Hfq 和 ProQ，并发现 FopA 蛋白是新兴的 FinO/ProQ 样 RBP 家族的新成员。FopA 由抗性质粒 pCol1B9 编码，主要靶向与质粒复制相关的小 RNA。FopA 的目标套件与相关的全局 RBP ProQ 显着不同，揭示了 FinO 域 RBP 对上下文依赖的选择性 RNA 识别。许多其他意外的 RNase 诱导的梯度变化表明细胞 RNA 有助于组织细菌中的大分子复合物。通过启用与 poly(A) 无关的通用 RBP 发现，GradR 为构建微生物 RBP 的综合目录提供了重要元素。