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. 2018 Jul 26;9(8):372.
doi: 10.3390/genes9080372.

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes

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Free PMC article

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes

Maria Waldl et al. Genes (Basel). .
Free PMC article

Abstract

The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here, we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina remain without annotated telomerase RNA.

Keywords: homology search; non-coding RNA; secondary structure; synteny; telomerase RNA; yeast.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure A1
Figure A1
Phylogeny of the Saccharomycetales. Bootstrap support is 100% unless otherwise indicated. The Saccharomycetacea are indicted in dark blue. A red dot at tip of the tree indicates a TER sequences listed in Table 1.
Figure 1
Figure 1
Schematic organization of telomerase RNA (TER). Contact regions for important binding sites are indicated by green circles (EST1, SM, and KU). The green ellipse denotes the contact region with the reverse transcriptase (TERT). Other major features are the template, the pseudoknot region, the template boundary element (TBE), the three-way junction (TWJ), and the Area of Required Connectivity (ARC). Adapted from [13].
Figure 2
Figure 2
Features identified in TER sequences. (KU) ku binding hairpin, (T) template region, (EST1) Est1 binding site, (TWJ) three-way junction, and (SM1) SM1 binding site. Elements not shown are either not present in the corresponding species (e.g., the TWJ in Candida glabrata) or could not be located with reasonable certainty. Species marked by * are not part of the phylogenetic tree and were placed next to their closest related neighbor based on the similarity of their TER sequences.
Figure 3
Figure 3
Alignment of the core SM-binding site motif: The common pattern of most Saccharomycetaceae (top); and species-specific variants (bottom).
Figure 4
Figure 4
Summary of the BLAST-based survey of TER genes. Blue nodes show TERs described in the literature, orange nodes represent TERs that we identified, and grey nodes are additional candidates for which we could not validate characteristic features. TERs outside the Saccharomycetaceae group are presented in light colors. The length of the edges are weighted by the inverse of the length of the BLAST hit. Note that distances in drawing between nodes not connected by an edge are not indicative of their evolutionary distance.

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