Old Circular RNAs, New Habits: Repurposing Noncoding RNAs in Parasitic Amebozoa

Eukaryotic circular RNAs (circRNAs) emerged in a common ancestor of the land-plant Arabidopsis thaliana, the fungi Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the protists Plasmodium falciparum and Dictyostelium discoideum, more than a billion years ago (Wang et al., 2014). Due to their resistance to exonucleases, these molecules are very stable, and modern-day circRNAs are capable of interacting with proteins and other RNAs (Lasda and Parker, 2014), thus regulating multiple cellular mechanisms (Qu et al., 2015) ranging from cell-cell communication (Yu and Kuo, 2019) to gene expression regulation (Garcia-Lerena et al., 2022) and, together with miRNAs and mRNAs, participating in complex regulatory networks (Cao et al., 2020). Molecular dating and species number analyses suggest that after their marine origin, some Amoebozoans colonized the land ecosystems, and others diversified with land plant radiation (FizPalacios et al., 2013; Fiz-Palacios et al., 2014). Plants and amoebozoans co-evolved and interacted within these new ecosystems generating modern-day enteric Entamoeba species such as Entamoeba histolytica, which causes dysentery in humans, and E. invadens, which invades multiple tissues of reptiles (Loftus et al., 2005; Lorenzi et al., 2010; Ehrenkaufer et al., 2013; Tanaka et al., 2019). Furthermore, the parasitic E. histolytica speciation processes culminated in a very characteristic Sulfur metabolism (Jeelani and Nozaki, 2014; Mi-Ichi and Yoshida, 2019) including sulfate activation localized in mitochondria-related organelles (mitosomes), and sulfolipid metabolism pathways. The latter is crucial for the encystation of the reptilian parasite E. invadens (Jauregui-Wade et al., 2019; Jauregui-Wade et al., 2020), which is the model of choice to study amoebic differentiation so far. Recently, 12 intronic (flicRNAs), and 748 exonic and exonic-intronic (circRNAs) circular RNAs have been identified in E. histolytica and E. invadens. In the human parasite, flicRNAs and circRNAs are differentially expressed between virulent (HM1-IMSS) and avirulent (Rahman) amoebic strains (Mendoza-Figueroa et al., 2018; López-Luis, 2022). In contrast, the reported E. invadens circRNAs correspond to 20 h encysting-induced cultures (López-Luis, 2022). As expected, in addition to strainand encystment-specific circular RNAs, numerous circRNAs derived from genes of multiple functions were reported. We reasoned that the comparison of circular RNAs indicative of species-specific Sulfur metabolism with those indicative of previously acquired differentiation mechanisms, and with those indicative of more recently acquired parasitic behavior (virulence) could suggest their episodic origin (or repurposing) and their functional relationships. Edited by: Juan David Ospina-Villa, Colombian Institute of Tropical Medicine (ICMT), Colombia