Regulation of RNA editing by intracellular acidification

Malik, Turnee N; Doherty, Erin; Gaded, Vandana; Hill, Theodore M.; Beal, Peter A.; Emeson, Ronald B.

doi:10.1093/nar/gkab157

Cited by 22 publications

(15 citation statements)

References 83 publications

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“…20,23 Indeed, recently described pH effects on the deamination rates for wild-type and E488Q mutant ADAR2 support this hypothesis. 24 These observations inspired us to test orphan base analogs capable of hydrogen bonding with the wild-type E488 residue in a protonation-independent manner. By stabilizing the same contact made by the mutant enzyme, this may allow wild-type ADAR2 to elicit a similar hyperactive effect.…”

Section: ■ Resultsmentioning

confidence: 99%

“…MBP-tagged human ADAR1 p110 wild-type (hADAR1 p110 WT) was expressed as previously described. 24 Purification of hADAR1 p110 was carried out by lysing cells in buffer containing 50 mM Tris-HCl, pH 8.0, 5% glycerol, 5 mM BME, 1000 mM KCl, 50 μM ZnCl 2 , and 0.05% NP-40 using a microfluidizer. Cell lysate was clarified by centrifugation (39 000 × g for 50 min).…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position

et al. 2021

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Adenosine Deaminases Acting on RNA (ADARs) convert adenosine to inosine in double stranded RNA. Human ADARs can be directed to predetermined target sites in the transcriptome by complementary guide strands, allowing for the correction of disease-causing mutations at the RNA level. Here we use structural information available for ADAR2-RNA complexes to guide the design of nucleoside analogs for the position in the guide strand that contacts a conserved glutamic acid residue in ADARs (E488 in human ADAR2), which flips the adenosine into the ADAR active site for deamination. Mutating this residue to glutamine (E488Q) results in higher activity because of the hydrogen bond donating ability of Q488 to N3 of the orphan cytidine on the guide strand. We describe the evaluation of cytidine analogs for this position that stabilize an activated conformation of the enzyme-RNA complex and increase catalytic rate for deamination by the wild-type enzyme. A new crystal structure of ADAR2 bound to duplex RNA bearing a cytidine analog revealed a close contact between E488, stabilized by an additional hydrogen bond and altered charge distribution when compared to cytidine. In human cells and mouse primary liver fibroblasts, this single nucleotide modification increased directed editing yields when compared to an otherwise identical guide oligonucleotide. Our results show that modification of the guide RNA can mimic the effect of hyperactive mutants and advance the approach of recruiting endogenous ADARs for site-directed RNA editing.

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Section: ■ Resultsmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position

et al. 2021

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“…On the basis of increased expression of ISGs such as Ifit1 that are induced by IRF3 and IRF7, we propose that non-hematopoietic cell types as well as neutrophils initiate the IFN response in Adar1 mZα/mZα lungs. Interestingly, a recent study showed that RNA editing increases upon intracellular acidification ( Malik et al., 2021 ). Neutrophils produce different types of acids ( Ulfig and Leichert, 2021 ), which may explain the induction of type I IFN responses in these cells.…”

Section: Discussionmentioning

confidence: 99%

Adenosine-to-inosine editing of endogenous Z-form RNA by the deaminase ADAR1 prevents spontaneous MAVS-dependent type I interferon responses

et al. 2021

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“…The authors could show that intracellular acidification modulates ADAR catalytic activity directly. This is possible due to enhanced flipping out of the adenosine to be edited and additionally an increased deamination rate at a more acidic pH [ 67 ] ( Figure 2 ).…”

Section: Regulation Of Adar Activitymentioning

confidence: 99%

An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing

Vesely

Jantsch

2021

Genes

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RNA-editing by adenosine deaminases acting on RNA (ADARs) converts adenosines to inosines in structured RNAs. Inosines are read as guanosines by most cellular machineries. A to I editing has two major functions: first, marking endogenous RNAs as “self”, therefore helping the innate immune system to distinguish repeat- and endogenous retrovirus-derived RNAs from invading pathogenic RNAs; and second, recoding the information of the coding RNAs, leading to the translation of proteins that differ from their genomically encoded versions. It is obvious that these two important biological functions of ADARs will differ during development, in different tissues, upon altered physiological conditions or after exposure to pathogens. Indeed, different levels of ADAR-mediated editing have been observed in different tissues, as a response to altered physiology or upon pathogen exposure. In this review, we describe the dynamics of A to I editing and summarize the known and likely mechanisms that will lead to global but also substrate-specific regulation of A to I editing.

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Regulation of RNA editing by intracellular acidification

Cited by 22 publications

References 83 publications

Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position

Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position

Adenosine-to-inosine editing of endogenous Z-form RNA by the deaminase ADAR1 prevents spontaneous MAVS-dependent type I interferon responses

An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing

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