Rapid gene evolution in an ancient post-transcriptional and translational regulatory system compensates for meiotic X chromosomal inactivation

Abstract

It is conventionally assumed that conserved pathways evolve slowly with little participation of gene evolution. Nevertheless, it has been recently observed that young genes can take over fundamental functions in essential biological processes, for example, development and reproduction. It is unclear how newly duplicated genes are integrated into ancestral networks and reshape the conserved pathways of important functions. Here, we investigated origination and function of two autosomal genes that evolved recently in Drosophila: Poseidon and Zeus, which were created by RNA-based duplications from the X-linked CAF40, a subunit of the conserved CCR4-NOT deadenylase complex involved in post-transcriptional and translational regulation. Knockdown and knockout assays show that the two genes quickly evolved critically important functions in viability and male fertility. Moreover, our transcriptome analysis demonstrates that the three genes have a broad and distinct effect in the expression of hundreds of genes, with almost half of the differentially expressed genes being perturbed exclusively by one paralog, but not the others. Co-immunoprecipitation and tethering assays show that the CAF40 paralog Poseidon maintains the ability to interact with the CCR4-NOT deadenylase complex and might act in post-transcriptional mRNA regulation. The rapid gene evolution in the ancient post-transcriptional and translational regulatory system may be driven by evolution of sex chromosomes to compensate for the meiotic X chromosomal inactivation (MXCI) in Drosophila.

Rapid Cis–Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4–NOT Component in Drosophila

“…The CAZAM frequency of both Dmel_Zeus ChIP-Seq genes and Dsim_Zeus ChIP-Seq genes shows a drastic fluctuation ( Figure 5 D). Taken together, we speculate that Zeus exhibits a rapid, dynamic and species-differential coevolution with specific motif for its neofunctionalization, as is consistent with what we recently observed [ 13 ].…”

“…To test this, we generated Zeus loss-of-function lines by using CRISPR-Cas9 (see Methods section and Figure 5 A). We found that the KO lines had significantly reduced (22%) viability ( p < 0.05, t-test) [ 13 ], suggesting an important functional role of Zeus. We further conducted RNA-Seq on adult male whole testes, in which Zeus is normally expressed, from control injection and Zeus knockout (KO) lines in biological triplicate.…”

“…However, several studies suggest that Caf40 in Drosophila may also act indirectly with nucleic acids as a member of the larger CCR4–NOT complex, which has roles in mRNA processing and degradation [ 66 , 67 , 68 , 69 , 70 ]. Dramatically, a recent study conducting a co-immunoprecipitation in Dm S2 cells by expressing a GFP-tagged version of three paralogs ( Caf40 and its two retroduplicates, Zeus and Poseidon ) assayed their interaction with HA-tagged NOT1, which is the central scaffold subunit of the CCR4–NOT complex [ 13 ]. Their result suggested that Poseidon conserved Caf40’s ability to interact with the CCR4–NOT complex, while Zeus almost lost its CCR4–NOT recruitment ability [ 13 ].…”

“…Dramatically, a recent study conducting a co-immunoprecipitation in Dm S2 cells by expressing a GFP-tagged version of three paralogs ( Caf40 and its two retroduplicates, Zeus and Poseidon ) assayed their interaction with HA-tagged NOT1, which is the central scaffold subunit of the CCR4–NOT complex [ 13 ]. Their result suggested that Poseidon conserved Caf40’s ability to interact with the CCR4–NOT complex, while Zeus almost lost its CCR4–NOT recruitment ability [ 13 ]. Moreover, mRNA-tethering assay also displayed similar pattern: Poseidon has conserved the same repressive effect on targeted mRNAs observed for CAF40, while Zeus exhibits a significantly weaker repressive ability [ 13 ].…”

“…Retrogene movement within and between chromosomes plays a remarkable role in contributing to genetic novelty [ 10 , 11 , 12 ]. Case studies suggest that those retrogenes rapidly evolved essential developmental function [ 5 , 13 ]. The autosome gene Zeus ( CG9573 , also known as Rcd-1r , required for cell differentiation 1 related) is a testis-specific young gene that arose via a “out of X” retroposition event approximately 5 million years ago in the lineage, leading to Drosophila melanogaster and its closest relatives.…”