Abstract
Telomeric repeats in fungi of the subphylum Saccharomycotina exhibit great inter- and intra-species variability in length and sequence. Such variations challenged telomeric DNA-binding proteins that co-evolved to maintain their functions at telomeres. Here, we compare the extent of co-variations in telomeric repeats, encoded in the telomerase RNAs (TERs), and the repeat-binding proteins from 13 species belonging to the Yarrowia clade. We identified putative TER loci, analyzed their sequence and secondary structure conservation, and predicted functional elements. Moreover, in vivo complementation assays with mutant TERs showed the functional importance of four novel TER substructures. The TER-derived telomeric repeat unit of all species, except for one, is 10 bp long and can be represented as 5′-TTNNNNAGGG-3′, with repeat sequence variations occuring primarily outside the vertebrate telomeric motif 5′-TTAGGG-3′. All species possess a homologue of the Yarrowia lipolytica Tay1 protein, YlTay1p. In vitro, YlTay1p displays comparable DNA-binding affinity to all repeat variants, suggesting a conserved role among these species. Taken together, these results add significant insights into the co-evolution of TERs, telomeric repeats and telomere-binding proteins in yeasts.
Highlights
Telomeres are dynamic and complex nucleoprotein structures located at the ends of linear chromosomes
In order to ensure the dynamic switching between the inaccesible and extensible states of telomeres, when the 3′ overhang can be associated with telomerase and elongated, telomeric repeats have to satisfy specific criteria: telomeric proteins need to bind them strongly enough to secure the correct assembly of shelterin, but they need to be able to transiently dissociate from telomeric DNA to allow its spatio-temporal accessibility to replication and transcription machineries[14,15,16]
Y. lipolytica may serve as a model of the ancestral tipping point, where the canonical type of telomere was converted to its divergent derivatives present in other ascomycetous yeasts. To investigate this transition in more detail, we focused on analyses of telomerase RNAs (TERs), telomeric repeats and telomere-binding proteins from 13 species belonging to the Yarrowia clade[58], i.e. twelve species of the genus Yarrowia and Candida hispaniensis, which was used as an outgroup
Summary
Telomeres are dynamic and complex nucleoprotein structures located at the ends of linear chromosomes. In order to ensure the dynamic switching between the inaccesible and extensible states of telomeres, when the 3′ overhang can be associated with telomerase and elongated, telomeric repeats have to satisfy specific criteria: telomeric proteins need to bind them strongly enough to secure the correct assembly of shelterin, but they need to be able to transiently dissociate from telomeric DNA to allow its spatio-temporal accessibility to replication and transcription machineries[14,15,16] Given their essential roles in maintaining linear chromosomes, it is not surprising that the fundamental features of telomeres are conserved. Detailed analyses of conserved domains of TERs from phylogenetically distant species, such as those of filamentous fungi[46,51], as well as the identification of novel features with potential to reveal previously unknown TER-protein interactions, are instrumental for better understanding of the evolution of yeast telomeric repeats and the entire telomere-protecting system
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