Evolution and Functional Trajectory of Sir1 in Gene Silencing

Abstract

We used the budding yeasts Saccharomyces cerevisiae and Torulaspora delbrueckii to examine the evolution of Sir-based silencing, focusing on Sir1, silencers, the molecular topography of silenced chromatin, and the roles of SIR and RNA interference (RNAi) genes in T. delbrueckii. Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) analysis of Sir proteins in T. delbrueckii revealed a different topography of chromatin at the HML and HMR loci than was observed in S. cerevisiae. S. cerevisiae Sir1, enriched at the silencers of HML␣ and HMRa, was absent from telomeres and did not repress subtelomeric genes. In contrast to S. cerevisiae SIR1's partially dispensable role in silencing, the T. delbrueckii SIR1 paralog KOS3 was essential for silencing. KOS3 was also found at telomeres with T. delbrueckii Sir2 (Td-Sir2) and Td-Sir4 and repressed subtelomeric genes. Silencer mapping in T. delbrueckii revealed single silencers at HML and HMR, bound by Td-Kos3, Td-Sir2, and Td-Sir4. The KOS3 gene mapped near HMR, and its expression was regulated by Sir-based silencing, providing feedback regulation of a silencing protein by silencing. In contrast to the prominent role of Sir proteins in silencing, T. delbrueckii RNAi genes AGO1 and DCR1 did not function in heterochromatin formation. These results highlighted the shifting role of silencing genes and the diverse chromatin architectures underlying heterochromatin.

Evolution of DNA replication origin specification and gene silencing mechanisms

“…Budding yeasts that lack sequence-specific origins, such as the pathogenic yeast Candida albicans and the industrial yeast Yarrowia lipolytica that can metabolize unusual hydrocarbons, have lost, or are in the process of losing RNAi 29,30 . Some retain a non-canonical Dicer (Dcr*) that has an RNase III domain and has been shown in C. albicans to exhibit RNAi to silence transposable elements and sub-telomeric repeated sequences 29 .…”

“…The whole genome duplication (WGD) event is indicated in the tree. Table inspired by previous studies on gene silencing 30 . Positive symbol indicates the exist of genes, negative symbol indicates the absent of genes, asterisk symbol indicates exist of noncanonical dicer.…”

Evolution of DNA Replication Origin Specification and Gene Silencing Mechanisms

“…Budding yeasts that lack sequence-specific origins, such as the pathogenic yeast Candida albicans and the industrial yeast Yarrowia lipolytica that can metabolize unusual hydrocarbons, have lost, or are in the process of losing RNAi 28,29 . Some retain a non-canonical Dicer (Dcr*) that has an RNase III domain and has been shown in C. albicans to exhibit RNAi to silence transposable elements and sub-telomeric repeated sequences 28 .…”

“…The budding yeasts that have acquired sequence specific origins and ORC-Sir4-mediated gene silencing system are likely to have lost RNAi completely, albeit some retained the non-canonical Dicer (Dcr*). One budding yeast, T. delbrueckii, has ORC-Sir4 silencing and has retained Dcr* and Ago, but the latter are not involved in transcriptional gene silencing 29 . As species lost RNAi with a concomitant reduction in repeated sequences in the genome, including centromere associated repeated sequences, we suggest that in the Saccharomyces-related, ORC-Sir4 containing budding yeast that ORC evolved to bind DNA in a sequence specific manner, providing a mechanism to locate origins of DNA replication in intergenic regions 6 .…”

“…The "AG" dinucleotide at position 29-30 in the motif logo is not utilized in mutants that change Y486 to alanine or glutamine. Table inspired by previous studies on gene silencing 29 . "+" indicates the exist of genes, "-" indicates the absent of genes, "*" indicates exist of noncanonical dicer.…”