Enhanced Loss of Retinoic Acid Network Genes in Xenopus laevis Achieves a Tighter Signal Regulation

Abstract

Retinoic acid (RA) is a major regulatory signal during embryogenesis produced from vitamin A (retinol) by an extensive, autoregulating metabolic and signaling network to prevent fluctuations that result in developmental malformations. Xenopus laevis is an allotetraploid hybrid frog species whose genome includes L (long) and S (short) chromosomes from the originating species. Evolutionarily, the X. laevis subgenomes have been losing either L or S homoeologs in about 43% of genes to generate singletons. In the RA network, out of the 47 genes, about 47% have lost one of the homoeologs, like the genome average. Interestingly, RA metabolism genes from storage (retinyl esters) to retinaldehyde production exhibit enhanced gene loss with 75% singletons out of 28 genes. The effect of this gene loss on RA signaling autoregulation was studied. Employing transient RA manipulations, homoeolog gene pairs were identified in which one homoeolog exhibits enhanced responses or looser regulation than the other, while in other pairs both homoeologs exhibit similar RA responses. CRISPR/Cas9 targeting of individual homoeologs to reduce their activity supports the hypothesis where the RA metabolic network gene loss results in tighter network regulation and more efficient RA robustness responses to overcome complex regulation conditions.

Retinoic Acid and Retinoid X Receptors

“…Using a differential transcriptomic screening approach based on pharmacological treatments with synthetic RAR paralog-specific agonists, they identify RARα as the dominant RAR to control positional identity in the regenerating limb and define a list of candidates acting downstream of RARα during this process. RAR-dependent signaling is also at the center of the study by Abbou and colleagues [ 20 ]. The focus of this study, however, is on the evolutionary conservation of the RA metabolic and gene regulatory networks in the African clawed frog Xenopus laevis .…”