Dual activities of a silencing information regulator complex in yeast transcriptional regulation and DNA-damage response

Abstract

The Saccharomyces cerevisiae silencing information regulator (SIR) complex contains up to four proteins, namely Sir1, Sir2, Sir3, and Sir4. While Sir2 encodes a NAD-dependent histone deacetylase, other SIR proteins mainly function as structural and scaffold components through physical interaction with various proteins. The SIR complex displays different conformation and composition, including Sir2 homotrimer, Sir1-4 heterotetramer, Sir2-4 heterotrimer, and their derivatives, which recycle and relocate to different chromosomal regions. Major activities of the SIR complex are transcriptional silencing through chromosomal remodeling and modulation of DNA double-strand-break repair pathways. These activities allow the SIR complex to be involved in mating-type maintenance and switching, telomere and subtelomere gene silencing, promotion of nonhomologous end joining, and inhibition of homologous recombination, as well as control of cell aging. This review explores the potential link between epigenetic regulation and DNA damage response conferred by the SIR complex under various conditions aiming at understanding its roles in balancing cell survival and genomic stability in response to internal and environmental stresses. As core activities of the SIR complex are highly conserved in eukaryotes from yeast to humans, knowledge obtained in the yeast may apply to mammalian Sirtuin homologs and related diseases.

Keywords: DNA‐damage response; SIR complex; chromatin remodeling; transcriptional silencing; yeast.

Figure 1

Domain structure of Sir proteins and their associated proteins. (A) The Sir2 structure with mapped Sir4 binding domain (Sir4^BD, aa99–237) and a Sirtuin‐type deacetylase domain (aa237–562). (B) The Sir3 structure with a bromo‐adjacent homology (BAH) domain (aa1–214), a Rap1 binding domain (aa456–483), an ATPase‐like (AAAL)/nucleosome interacting domain (aa532–834), a winged‐helix (wH) domain (aa840–978) for Sir3 homodimerization, a Sae2 binding domain (aa531–723), and Sir4 interacting region (aa456–834). (C) The Sir4 structure. Its N‐terminal region (aa1–270) contains DNA‐binding, Sir1, and Yku80 interacting activities. A Sir2‐binding domain (Sir2^BD) is mapped to aa787–893. It also contains a partitioning and anchoring domain (PAD) (aa960–1262) and a C‐terminal coiled‐coil (CC) domain (aa1262–1346) for Sir4 homodimerization. This C‐terminal CC domain is also required for physical interaction with Sir3 and Yku70. In addition, a noncanonical BRCA1 C‐terminal helix (H‐BRCT) functional unit is mapped to aa961–1085, which is also required for the Esc1 interaction. Rap1 interacting regions are mapped to two regions at aa1–270 and aa787–1262, and the C‐terminal aa787–1346 region is required for binding DNA and nucleosome, as well as Yku80. BRCA1, breast cancer susceptibility gene 1.

Figure 2

Chromosomal structures for a rDNA array and two mating‐type loci. (A) Chromosome XII contains approximately 150 copies of the rDNA repeats with one 9.1‐kb rDNA repeat consisting of 35S and 5S RNA coding genes, an autonomous replication sequence (ARS), and two nontranscribed spacer (NTS) regions 1 and 2. The mapped Sir2 interacting region is shown. (B) Each yeast HMR a and HMLα mating‐type locus contains two coding sequences, silencer regions E and I, two autonomically replicating consensus sites (ACSs), and Rap1 and Abf1 binding sites.

Figure 3

Diagram illustrating signaling events fostering the switch between Sir2 homotrimer formation and Sir2–Sir3–Sir4 heterotrimer formation between nucleolus and telomeres. Initially, Sir2 can dimerize with Sir4 and be further recruited to complex with Sir3. Upon trimeric complex formation, Rap1 signaling causes complex re‐localization to acetylated lysine residues on telomeric ends upon Rap1 interacting with Sir3. Alternately, Sir2 may dissociate from Sir4 and favor homotrimerization at nuclear‐acetylated lysine residues upon signaling from Net1. Upon homotrimerization or complex formation with Sir3 and Sir4, Sir2 deacetylates bound lysine and spreads along chromatin for transcriptional repression.

Figure 4

Dual activities of the silencing information regulator (SIR) complex and the resultant functions. (1) The SIR complex is recruited to mating‐type loci at consensus sequences within silencers, where Sir2 deacetylates bound lysine residues and the complex spreads along the chromatin at those loci to repress transcription, allowing expression of the opposite mating type at the MAT locus. (2) Sir2–Sir4 are recruited to acetylated histone tails to deacetylate H4K16 and repress transcription. (3) Sir2 binds to Sir2 responsive regions at rDNA arrays at telomeric or non‐telomeric ends, preventing the formation of extra‐ribosomal circles (ERCs) and chromosomal degradation. (4) Recruitment of Sir3 by Rap1 to double‐strand break (DSB) regions and subsequent complex formation with Sir2 and Sir4. Complex formation leads to the reorganization of chromatin and the telomere position effect, promoting DSB resection and repair. (5) The recruitment of Sir3 to DSB ends upon signaling from Mec1 and/or Rad9 and the competitive inhibition of Sae2, blocking homologous recombination (HR) at free DSB ends. (6) Initial Sir4 binding to Yku70/80 around free DSB ends before recruitment of Sir2 and Sir3 for the SIR complex formation, which is followed by Yku70/80‐mediated nonhomologous end joining (NHEJ) at the damaged region.