Structural and Virus Regulatory Insights Into Avian N6-Methyladenosine (m6A) Machinery

Abstract

The addition of a methyl group to the N6 position of adenosine (m6A) is the most common posttranscriptional RNA modification, and it regulates most steps of RNA metabolism including splicing, stability, translation, nuclear-export, and RNA structures. Besides cellular RNA, m6A modifications have also been detected on viral RNA. A range of recent studies have demonstrated the crucial roles of m6A in the virushost interactions; however, m6A cellular machineries are only characterized in limited mammalian species. Herein, we aim to present comprehensive evolutionary insights into major m6A writers, erasers, and readers and draw a comparative structural analysis between avian and mammalian m6A-associated machineries. The comparative collinearity on the chromosomal scale revealed that the majority of m6A-related genes were found less syntenic even among avian species. Genetic analysis of avian m6A erasers revealed a distinct phylogenetic clustering compared to mammalian orthologs and shared a weak percent (55%) identity with mammalian species with low identity percentage (55%). The overall comparative three-dimensional (3D) structure analyses among different mammalian species were maintained through synonymous structural mutations. Unlike erasers, the putative 3D structures in the active sites as for the aromatic cage in YTH-domain of YTHDC1 and two pivotal loops in MTD-domains in METTL3 exhibited structural alterations in chicken. In conjunction with in silico investigations, influenza viruses significantly downregulated gene the transcription of m6A writers and erasers, whereas m6A readers were moderately regulated in chicken fibroblasts. In light of these findings, future detailed biochemical and crystallographic studies are warranted to define the roles of m6A machinery in regulating both viral and cellular RNA metabolism in avian species.

Evolutionary conservation of the DRACH signatures of potential N6-methyladenosine (m6A) sites among influenza A viruses

“…The epigenetic m 6 A mark is the most abundant internal chemical modification installed onto both cellular and viral mRNA that dictate various cell behaviours and the fate of the virus-host interaction 2 , 39 . The significance of m 6 A has been highlighted by the fact that this modification is evolutionarily conserved among vertebrates 31 , besides, a high degree of conservation in the majority of m6A machinery has recently been confirmed among vertebrates 9 . Furthermore, the overall inhibition of m 6 A has various detrimental effects on animals' life 13 .…”

“…The addition of the m 6 A marks on both cellular and viral RNA is governed by a complex group of nuclear methyltransferases (writers); these marks can be removed by another group of demethylases (erasers). Ultimately, a third group able to bind and generate a recognizable effect on the methylated transcripts (readers), all groups are collectively known as m 6 A machinery 9 , 25 – 27 . Installation of m 6 A is predominantly restricted to consensus sequence motif, the putative m 6 A sites significantly reported to be enriched in some 5′-DRA*CH-3′ sequences (where A* denotes the methylatable adenosine, D denotes A, G or U, R denotes A and G, and H denotes A, C or U) 24 , 28 , 29 .…”

Structural Insights Into m6A-Erasers: A Step Toward Understanding Molecule Specificity and Potential Antiviral Targeting

“…A higher degree of conservation to the residues surrounding the methylated base in both H. sapiens and avian species was noticed, indicating a highly conserved catalytic mechanism even in various organisms exhibiting evolutionary changes. Moreover, we have found that the pincer-like structure in avian species suggests a higher binding affinity with more stabilizing property compared with H. sapiens (Bayoumi et al, 2020 ).…”

“…Our group has performed a recent comprehensive analysis of the m 6 A demethylases among various orders of animals, especially the avian species (Bayoumi et al, 2020 ). The study revealed multiple evolutionary changes when compared with Homo sapiens .…”

“…We have revealed that m 6 A-erasers shared the lowest identity percent among the m 6 A-related machinery. However, the overall demethylases' structures were maintained through synonymous structural mutations (Bayoumi et al, 2020 ). The entire human AlkB-homolog-5 (hALKBH5) protein comprises a polypeptide chain of 394 amino acids (Zheng et al, 2013 ; Huang and Yin, 2018 ).…”