Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals

Abstract

The GW182 proteins are a key component of the miRNA-dependent post-transcriptional silencing pathway in animals. They function as scaffold proteins to mediate the interaction of Argonaute (AGO)-containing complexes with cytoplasmic poly(A)-binding proteins (PABP) and PAN2-PAN3 and CCR4-NOT deadenylases. The AGO-GW182 complexes mediate silencing of the target mRNA through induction of translational repression and/or mRNA degradation. Although the GW182 proteins are a subject of extensive experimental research in the recent years, very little is known about their origin and evolution. Here, based on complex functional annotation and phylogenetic analyses, we reveal 448 members of the GW182 protein family from the earliest animals to humans. Our results indicate that a single-copy GW182/TNRC6C progenitor gene arose with the emergence of multicellularity and it multiplied in the last common ancestor of vertebrates in 2 rounds of whole genome duplication (WGD) resulting in 3 genes. Before the divergence of vertebrates, both the AGO- and CCR4-NOT-binding regions of GW182s showed significant acceleration in the accumulation of amino acid changes, suggesting functional adaptation toward higher specificity to the molecules of the silencing complex. We conclude that the silencing ability of the GW182 proteins improves with higher position in the taxonomic classification and increasing complexity of the organism. The first reconstruction of the molecular journey of GW182 proteins from the ancestral metazoan protein to the current mammalian configuration provides new insight into development of the miRNA-dependent post-transcriptional silencing pathway in animals.

Comprehensive Evolutionary Analysis of the Major RNA-Induced Silencing Complex Members

“…In this study, the full-length sequences of GW182 and its orthologues were used for a reliable phylogenetic reconstruction, which was consistent with previous results (Supplementary Fig. S7 ) 17 . The results indicate that mammalian TNRC6C is the founding member of the chordate gene family representing and diverging from the orthologue of nonchordate GW182 genes.…”

“…Previously, few phylogenetic analyses of RISC members have been performed. Several conclusions are summarized as follows: (I) vertebrates lack siRNA-class AGO proteins and vertebrate AGOs display low rates of molecular evolution 15 ; (II) Dicers might have duplicated and diversified independently and have evolved for various functions in invertebrates 16 ; (III) Loquacious identified in insects may be ancestral to both TRBP and PACT; and (IV) significant acceleration in the accumulation of amino acid changes of GW182-binding regions indicates its early origin and adaptive evolution 17 . However, a systematic, integrative evolutionary analysis is still lacking.…”

Poly(A)-binding proteins are required for microRNA-mediated silencing and to promote target deadenylation inC. elegans

“…C. elegans GW182 orthologs AIN-1 and AIN-2 lack PAM2 or PG-L motifs. In fact, AIN-1 and AIN-2 primary sequences diverge so much from GW182 that several authors still question whether they are homologs at all ( 43 , 44 ). Yet, our results presented here (see Figure 2 ) and early studies on AIN-1 and AIN-2 clearly establish their importance in miRNA-mediated silencing ( 14 , 18 ).…”

The Role of Dynamic miRISC During Neuronal Development

“…GW182, a critical component of this pathway, is a large Glycine Tryptophan (GW) repeats containing protein. The structure and function of different domains of GW182 have been critically reviewed (Ding and Han, 2007;Baillat and Shiekhattar, 2009;Chekulaeva et al, 2009;Eulalio et al, 2009;Bazzini et al, 2012;Zielezinski and Karlowski, 2015;Niaz and Hussain, 2018). GW182 binds to AGO2 through its N-terminal domain following which it interacts with Polyadenylate Binding Protein (PABP) on the 3 ′ end of mRNA.…”