RNA helicases—central enzymes in RNA metabolism—often feature intrinsically disordered regions (IDRs) that enable phase separation and complex molecular interactions. In the bacterial pathogen Pseudomonas aeruginosa, the non-redundant RhlE1 and RhlE2 RNA helicases share a conserved REC catalytic core but differ in C-terminal IDRs. Here, we show how the IDR diversity defines RhlE RNA helicase specificity of function. Both IDRs facilitate RNA binding and phase separation, localizing proteins in cytoplasmic clusters. However, RhlE2 IDR is more efficient in enhancing REC core RNA unwinding, exhibits a greater tendency for phase separation, and interacts with the RNase E endonuclease, a crucial player in mRNA degradation. Swapping IDRs results in chimeric proteins that are biochemically active but functionally distinct as compared to their native counterparts. The RECRhlE1-IDRRhlE2 chimera improves cold growth of a rhlE1 mutant, gains interaction with RNase E and affects a subset of both RhlE1 and RhlE2 RNA targets. The RECRhlE2-IDRRhlE1 chimera instead hampers bacterial growth at low temperatures in the absence of RhlE1, with its detrimental effect linked to aberrant RNA droplets. By showing that IDRs modulate both protein core activities and subcellular localization, our study defines the impact of IDR diversity on the functional differentiation of RNA helicases.

中文翻译：

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内在无序区域调节细菌中的RhlE RNA解旋酶功能


RNA 解旋酶（RNA 代谢中的核心酶）通常具有本质无序区域 (IDR)，可实现相分离和复杂的分子相互作用。在细菌病原体铜绿假单胞菌中，非冗余的RhlE1和RhlE2 RNA解旋酶共享保守的REC催化核心，但C端IDR不同。在这里，我们展示了 IDR 多样性如何定义 RhE RNA 解旋酶功能的特异性。两种 IDR 都有利于 RNA 结合和相分离，将蛋白质定位在细胞质簇中。然而，RhlE2 IDR 在增强 REC 核心 RNA 解旋方面更有效，表现出更大的相分离趋势，并与 RNase E 核酸内切酶（mRNA 降解中的关键参与者）相互作用。交换 IDR 会产生具有生化活性的嵌合蛋白，但与其天然对应物相比，其功能不同。 RECRhlE1-IDRRhlE2 嵌合体可改善 rhlE1 突变体的冷生长，获得与 RNase E 的相互作用，并影响 RhlE1 和 RhlE2 RNA 靶标的子集。相反，在没有RhlE1的情况下，RECRhlE2-IDRRhlE1嵌合体会阻碍细菌在低温下的生长，其有害影响与异常的RNA液滴有关。通过表明 IDR 调节蛋白质核心活性和亚细胞定位，我们的研究定义了 IDR 多样性对 RNA 解旋酶功能分化的影响。