Proteomic Analysis of Zebrafish Protein Recoding via mRNA Editing by ADAR Enzymes

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Shamsudin S. Nasaev^1,2, Anna S. Kopeykina³, Ksenia G. Kuznetsova⁴, Lev I. Levitsky⁵, and Sergei A. Moshkovskii^1,3,a*

¹Federal Research and Clinical Center of Physical-Chemical Medicine, 119435 Moscow, Russia

²Institute of Biomedical Chemistry, 119121 Moscow, Russia

³Pirogov Russian National Research Medical University, 117997 Moscow, Russia

⁴University of Bergen, NO-5020, Bergen, Norway

⁵Talrose Institute for Energy Problems of Chemical Physics, Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia

^* To whom correspondence should be addressed.

Received September 20, 2022; Revised October 8, 2022; Accepted October 8, 2022

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RNA editing by adenosine deaminases of the ADAR family can lead to protein recoding, since inosine formed from adenosine in mRNA is complementary to cytosine; the resulting codon editing might introduce amino acid substitutions into translated proteins. Proteome recoding can have functional consequences which have been described in many animals including humans. Using protein recoding database derived from publicly available transcriptome data, we identified for the first time the recoding sites in the zebrafish shotgun proteomes. Out of more than a hundred predicted recoding events, ten substitutions were found in six used datasets. Seven of them were in the AMPA glutamate receptor subunits, whose recoding has been well described, and are conserved among vertebrates. Three sites were specific for zebrafish proteins and were found in the transmembrane receptors astrotactin 1 and neuregulin 3b (proteins involved in the neuronal adhesion and signaling) and in the rims2b gene product (presynaptic membrane protein participating in the neurotransmitter release), respectively. Further studies are needed to elucidate the role of recoding of the said three proteins in the zebrafish.

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KEY WORDS: proteogenomics, shotgun proteomics, zebrafish, ADAR, RNA-dependent adenosine deaminase, RNA editing

DOI: 10.1134/S0006297922110098

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