Telomere DNA recognition in Saccharomycotina yeast: potential lessons for the co-evolution of ssDNA and dsDNA-binding proteins and their target sites

Olga Steinberg-Neifach,Neal F Lue

doi:10.3389/fgene.2015.00162

Olga Steinberg-Neifach, Neal F Lue

Open Access

https://doi.org/10.3389/fgene.2015.00162

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Abstract

In principle, alterations in the telomere repeat sequence would be expected to disrupt the protective nucleoprotein complexes that confer stability to chromosome ends, and hence relatively rare events in evolution. Indeed, numerous organisms in diverse phyla share a canonical 6 bp telomere repeat unit (5′-TTAGGG-3′/5′-CCCTAA-3′), suggesting common descent from an ancestor that carries this particular repeat. All the more remarkable, then, are the extraordinarily divergent telomere sequences that populate the Saccharomycotina subphylum of budding yeast. These sequences are distinguished from the canonical telomere repeat in being long, occasionally degenerate, and frequently non-G/C-rich. Despite the divergent telomere repeat sequences, studies to date indicate that the same families of single-strand and double-strand telomere binding proteins (i.e., the Cdc13 and Rap1 families) are responsible for telomere protection in Saccharomycotina yeast. The recognition mechanisms of the protein family members therefore offer an informative paradigm for understanding the co-evolution of DNA-binding proteins and the cognate target sequences. Existing data suggest three potential, inter-related solutions to the DNA recognition problem: (i) duplication of the recognition protein and functional modification; (ii) combinatorial recognition of target site; and (iii) flexibility of the recognition surfaces of the DNA-binding proteins to adopt alternative conformations. Evidence in support of these solutions and the relevance of these solutions to other DNA-protein regulatory systems are discussed.

Highlights

Linear eukaryotic chromosome termini are stabilized by telomeres, which are specialized nucleoprotein complexes that suppress the recognition of the ends as double strand breaks (DSBs; de Lange, 2009; O’Sullivan and Karlseder, 2010; Jain and Cooper, 2011)
Co-evolution of telomere DNA and proteins of tens to hundreds of nucleotides. Both the duplex region and 3′ overhang are comprised of the same short repeat unit, and both are bound by sequence-specific recognition proteins, which in turn recruit other proteins crucial for telomere protection
Because proteins recruited to the duplex telomere repeats and Gtails are both required for telomere stability, the duplex/G-tail DNA structural arrangement at chromosome ends is essential for telomere function

Summary

Introduction

The telomeres of Saccharomycotina yeast are not bound directly by TRF and POT1 family members, but rather by two other distinct protein families named Rap1 and Cdc13, suggesting that the acquisition of atypical telomere DNA sequences was accompanied by a substantial remodeling of the telomere nucleoprotein structure (Figure 1). Even though Rap1 exhibits little sequence similarity to TRF and has a distinct domain organization, it utilizes Myb-like homeodomains for telomere DNA-binding.

Results

Conclusion