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Since its initial characterization, Escherichia coli RNase I has been described as a single-strand specific RNA endonuclease that cleaves its substrate in a largely sequence independent manner. Here, we describe a strong calcium (Ca2+)-dependent activity of RNase I on double-stranded RNA (dsRNA), and a Ca2+-dependent novel hybridase activity, digesting the RNA strand in a DNA:RNA hybrid. Surprisingly, Ca2+ does not affect the activity of RNase I on single stranded RNA (ssRNA), suggesting a specific role for Ca2+ in the modulation of RNase I activity. Mutation of a previously overlooked Ca2+ binding site on RNase I resulted in a gain-of-function enzyme that is highly active on dsRNA and could no longer be stimulated by the metal. In summary, our data imply that native RNase I contains a bound Ca2+, allowing it to target both single- and double-stranded RNAs, thus having a broader substrate specificity than originally proposed for this traditional enzyme. In addition, the finding that the dsRNase activity, and not the ssRNase activity, is associated with the Ca2+-dependency of RNase I may be useful as a tool in applied molecular biology. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.


Sebastian Grünberg, Baptiste Coxam, Tien-Hao Chen, Nan Dai, Lana Saleh, Ivan R Corrêa, Nicole M Nichols, Erbay Yigit. E. coli RNase I exhibits a strong Ca2+-dependent inherent double-stranded RNase activity. Nucleic acids research. 2021 May 21;49(9):5265-5277

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PMID: 33885787

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