Evolutionary driving forces of <scp>A‐to‐I</scp> editing in metazoans

Duan, Yuange; Tang, Xiaolu; Lü, Jian

doi:10.1002/wrna.1666

Cited by 25 publications

(29 citation statements)

References 128 publications

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“…The proteoforms arising from RNA editing were deduced from RNA sequences soon after discovery of this modification type (Sommer et al 1991). ADAR2 is an isoform encoded by a distinct gene in mammals, which is prone to editing exonic RNA sequences, thereby recoding proteins (Duan, Tang, and Lu 2022). Despite thousands of potential recoded sites being deduced from RNA sequencing, a few of them are characterized functionally.…”

Section: Introductionmentioning

confidence: 99%

Massive proteogenomic reanalysis of publicly available proteomic datasets of human tissues in search for protein recoding via adenosine-to-inosine RNA editing

Levitsky

Ivanov

Goncharov³

et al. 2022

Preprint

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The proteogenomic search pipeline developed in this work has been applied for re-analysis of 40 publicly available shotgun proteomic datasets from various human tissues comprising more than 8,000 individual LC-MS/MS runs, of which 5442 .raw data files were processed in total. The scope of this re-analysis was focused on searching for ADAR-mediated RNA editing events, their clustering across samples of different origin, and classification. In total, 33 recoded protein sites were identified in 21 datasets. Of those, 18 sites were detected in at least two datasets representing the core human protein editome. In agreement with prior art works, neural and cancer tissues were found being enriched with recoded proteins. Quantitative analysis indicated that recoding of specific sites did not directly depend on the levels of ADAR enzymes or targeted proteins themselves, rather it was provided by differential and yet undescribed regulation of interaction of enzymes with mRNA. Nine recoding sites conservative between human and rodents were validated by targeted proteomics using stable isotope standards in murine brain cortex and cerebellum, and an additional one was validated in human cerebrospinal fluid. In addition to previous data of the same type from cancer proteomes, we provide a comprehensive catalog of recoding events caused by ADAR RNA editing in the human proteome.

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Section: Introductionmentioning

confidence: 99%

Massive proteogenomic reanalysis of publicly available proteomic datasets of human tissues in search for protein recoding via adenosine-to-inosine RNA editing

Levitsky

Ivanov

Goncharov³

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…A-to-I RNA editing events have been reported in tRNA from several domains. All deaminases have evolved from the bacterial ancestor enzyme TadA, and it is considered that ADAT1 contains the evolutionary clade of ADARs, while ADAT2 and ADAT3 belong to the evolutionary clade of the activation-induced deaminase (AID) or apolipoprotein B mRNA editing enzyme catalytic peptide-like (APOBEC) ( Gerber and Keller, 1999 ; Jin et al, 2009 ; Iyer et al, 2011 ; Torres et al, 2014 ; Duan et al, 2022 ). In eukaryotes, the A-to-I RNA editing events are mediated by the ADAT1 homologous dimer at position 37 (A 37 ) in the anticodon loop of tRNA Ala ( Grosjean et al, 1996 ; Gerber et al, 1998 ; Maas et al, 1999 ; Jühling et al, 2009 ).…”

Section: Introductionmentioning

confidence: 99%

The occurrence, characteristics, and adaptation of A-to-I RNA editing in bacteria: A review

et al. 2023

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A-to-I RNA editing is a very important post-transcriptional modification or co-transcriptional modification that creates isoforms and increases the diversity of proteins. In this process, adenosine (A) in RNA molecules is hydrolyzed and deaminated into inosine (I). It is well known that ADAR (adenosine deaminase acting on RNA)-dependent A-to-I mRNA editing is widespread in animals. Next, the discovery of A-to-I mRNA editing was mediated by TadA (tRNA-specific adenosine deaminase) in Escherichia coli which is ADAR-independent event. Previously, the editing event S128P on the flagellar structural protein FliC enhanced the bacterial tolerance to oxidative stress in Xoc. In addition, the editing events T408A on the enterobactin iron receptor protein XfeA act as switches by controlling the uptake of Fe3+ in response to the concentration of iron in the environment. Even though bacteria have fewer editing events, the great majority of those that are currently preserved have adaptive benefits. Interestingly, it was found that a TadA-independent A-to-I RNA editing event T408A occurred on xfeA, indicating that there may be other new enzymes that perform a function like TadA. Here, we review recent advances in the characteristics, functions, and adaptations of editing in bacteria.

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“…26 ADAR2 is an isoform encoded by a distinct gene in mammals, which is known to edit exonic RNA sequences, thereby recoding proteins. 27 Despite thousands of potential recoded sites being deduced from RNA sequencing, only few of them are characterized functionally. For instance, a gene knockout of ADAR2 which causes early death by excitotoxicity in mice can be reversed by the genomic knockin of a single Arg-607 residue into the GRIA2 glutamate receptor subunit instead of glycine, thereby mimicking Gln-to-Arg substitution via RNA editing.…”

Section: ■ Introductionmentioning

confidence: 99%

Massive Proteogenomic Reanalysis of Publicly Available Proteomic Datasets of Human Tissues in Search for Protein Recoding via Adenosine-to-Inosine RNA Editing

et al. 2023

View full text Add to dashboard Cite

The proteogenomic search pipeline developed in this work has been applied for reanalysis of 40 publicly available shotgun proteomic datasets from various human tissues comprising more than 8000 individual LC–MS/MS runs, of which 5442 .raw data files were processed in total. This reanalysis was focused on searching for ADAR-mediated RNA editing events, their clustering across samples of different origins, and classification. In total, 33 recoded protein sites were identified in 21 datasets. Of those, 18 sites were detected in at least two datasets, representing the core human protein editome. In agreement with prior artworks, neural and cancer tissues were found to be enriched with recoded proteins. Quantitative analysis indicated that recoding the rate of specific sites did not directly depend on the levels of ADAR enzymes or targeted proteins themselves, rather it was governed by differential and yet undescribed regulation of interaction of enzymes with mRNA. Nine recoding sites conservative between humans and rodents were validated by targeted proteomics using stable isotope standards in the murine brain cortex and cerebellum, and an additional one was validated in human cerebrospinal fluid. In addition to previous data of the same type from cancer proteomes, we provide a comprehensive catalog of recoding events caused by ADAR RNA editing in the human proteome.

show abstract

Evolutionary driving forces of A‐to‐I editing in metazoans

Cited by 25 publications

References 128 publications

Massive proteogenomic reanalysis of publicly available proteomic datasets of human tissues in search for protein recoding via adenosine-to-inosine RNA editing

Massive proteogenomic reanalysis of publicly available proteomic datasets of human tissues in search for protein recoding via adenosine-to-inosine RNA editing

The occurrence, characteristics, and adaptation of A-to-I RNA editing in bacteria: A review

Massive Proteogenomic Reanalysis of Publicly Available Proteomic Datasets of Human Tissues in Search for Protein Recoding via Adenosine-to-Inosine RNA Editing

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