| Topic | Key finding | Quantitative/statistical data | System/assay | Reference |
|---|---|---|---|---|
| Catalytic activity: primary reaction and site | **S. cerevisiae** Rtt109 is a histone acetyltransferase that uses acetyl-CoA to acetylate histone H3, with **H3K56** established as the major in vivo site; K56 acetylation is absent in **rtt109Δ** cells and Rtt109 directly acetylates H3 in vitro. | H3K56ac undetectable in **rtt109Δ**; recombinant Rtt109 shows in vitro HAT activity on H3/octamers; H3K56ac linked to ~9-fold increased GCR when RTT109 is deleted. | Yeast genetics, anti-H3K56ac immunoblot, in vitro acetylation with recombinant proteins, genome instability assays. | Driscoll et al., *Science* (Feb 2007), DOI: https://doi.org/10.1126/science.1135862 (pqac-00000002, pqac-00000006, pqac-00000013) |
| Catalytic specificity beyond K56 | Rtt109–Vps75 can also acetylate H3 tail lysines in vitro/in S phase, especially **H3K9**, with additional MS evidence for K14 and K23 acetylation; however, **H3K56** remains the canonical and dominant functional site in budding yeast. | Vps75 loss caused ~**60% reduction** in H3K9ac during S phase; H4 peptide acetylation was **28-fold slower** than H3 peptide in one study. | Mass spectrometry, peptide/substrate acetylation kinetics, S-phase histone acetylation measurements. | Berndsen et al., *Nat Struct Mol Biol* (Aug 2008), DOI: https://doi.org/10.1038/nsmb.1459 (pqac-00000000, pqac-00000007) |
| Chaperone/cofactor requirement: Asf1 and Vps75 | Rtt109 is **chaperone-dependent**: Asf1 and Vps75 each support catalysis, but in distinct ways. Asf1 is required in vivo for H3K56ac; Vps75 forms a high-affinity complex with Rtt109 and strongly stimulates catalysis. | Rtt109–Vps75: **kcat = 0.21 ± 0.04 s⁻¹**, **Km(H3) = 5.9 ± 0.8 μM**, **kcat/Km = 3.5 ± 0.9 × 10⁴ M⁻¹ s⁻¹**; Vps75 increased kcat by about **100-fold** relative to Rtt109 alone in one analysis; **Kd(Rtt109–Vps75) = 23 ± 10 nM**; **Kd(Rtt109–H3) = 17 ± 8 nM**. | Steady-state enzymology, binding assays, reconstituted HAT complexes. | Tsubota et al., *Mol Cell* (Mar 2007), DOI: https://doi.org/10.1016/j.molcel.2007.02.006; Berndsen et al., *Nat Struct Mol Biol* (Aug 2008), DOI: https://doi.org/10.1038/nsmb.1459 (pqac-00000003, pqac-00000004, pqac-00000005, pqac-00000000) |
| Chaperone specificity | Asf1 does **not** stimulate free-H3 acetylation efficiently, but promotes Rtt109 activity when **H4 is present**, consistent with Asf1 presenting **H3–H4 dimers** to Rtt109; the Rtt109–Asf1 complex is especially important for genotoxin resistance. | Rtt109–Asf1: **kcat = 0.021 ± 0.002 s⁻¹**, **Km(H3/H4) = 1.19 ± 0.34 μM**, **kcat/Km = 2.0 ± 0.5 × 10⁴ M⁻¹ s⁻¹**; Rtt109–Vps75 on H3/H4: **kcat = 0.34 ± 0.04 s⁻¹**, **Km = 0.84 ± 0.28 μM**, **kcat/Km = 4.4 ± 0.9 × 10⁵ M⁻¹ s⁻¹**. | Reconstituted HAT assays with H3/H4 dimers/tetramers and chaperones. | Tsubota et al., *Mol Cell* (Mar 2007), DOI: https://doi.org/10.1016/j.molcel.2007.02.006 (pqac-00000003, pqac-00000005) |
| Structural/evolutionary insight | Although fungal-specific in sequence, Rtt109 is structurally related to metazoan **p300/CBP**-type acetyltransferases, helping explain catalytic architecture while preserving fungal-selective biology. | Qualitative structural homology; no numeric statistic in gathered evidence. | Structural biology/review synthesis. | Bazan, *Cell Cycle* (Jun 2008), DOI: https://doi.org/10.4161/cc.7.12.6074; Tang et al., *Nat Struct Mol Biol* (2008 notice) DOI: https://doi.org/10.1038/nsmb0908-998d (contextualized in gathered set) (pqac-00000001) |
| Genome stability and DNA damage response | RTT109 promotes genome stability and resistance to replication stress/genotoxic agents; **rtt109Δ** resembles **asf1Δ** and **H3K56R** mutants, supporting a shared pathway centered on H3K56ac. | **~9-fold increase** in gross chromosomal rearrangement in **rtt109Δ**; hypersensitivity to **HU, CPT, MMS**; elevated spontaneous Rad52 foci and checkpoint activation reported. | Yeast deletion mutants, fluctuation tests, genotoxin sensitivity assays, checkpoint/Rad52 analyses. | Driscoll et al., *Science* (Feb 2007), DOI: https://doi.org/10.1126/science.1135862; Tsubota et al., *Mol Cell* (Mar 2007), DOI: https://doi.org/10.1016/j.molcel.2007.02.006 (pqac-00000001, pqac-00000002, pqac-00000013) |
| Replication-coupled nucleosome assembly | H3K56ac marks newly synthesized H3 during S phase and promotes binding of histone deposition factors **CAF-1** and **Rtt106**, linking Rtt109 directly to replication-coupled nucleosome assembly. | H3K56ac described as marking **all newly synthesized H3** in S phase; no single new percentage given in gathered evidence. | Chromatin assembly and histone chaperone pathway studies. | Duan et al., *Nat Commun* (Jan 2025; DOI minted 2024), DOI: https://doi.org/10.1038/s41467-024-55144-7; Luciano et al., *Genetics* (Feb 2015), DOI: https://doi.org/10.1534/genetics.114.173856 (pqac-00000009, pqac-00000012) |
| Chromosome positioning/localization | Rtt109-mediated H3K56 acetylation is required for proper positioning of chromosome domains, including telomere peripheral localization, indicating a role beyond local nucleosome assembly. | Qualitative requirement; no single numeric estimate in gathered evidence. | Telomere/chromosome localization assays in yeast. | Hiraga et al., *J Cell Biol* (Nov 2008), DOI: https://doi.org/10.1083/jcb.200806065 (pqac-00000001) |
| Recent development (2024–2025): chromatin maturation | New work shows Rtt109-installed **H3K56ac** actively promotes **chromatin maturation after DNA replication** by enhancing ISWI-family remodelers and resolving disorganized nascent nucleosome arrays. | In vivo deficiency of H3K56ac caused accumulation of closely packed **di-/tetra-nucleosomes**; persistent/excess H3K56ac disrupted maturation and genome stability. | Strand-specific BrdU-IP + MNase mapping of nascent chromatin, in vitro remodeling assays with Isw1/SNF2h. | Duan et al., *Nat Commun* (Jan 2025; DOI minted 2024), DOI: https://doi.org/10.1038/s41467-024-55144-7 (pqac-00000009) |
| Recent development (2024): parental histone transfer and HR | 2024 studies use **H3K56ac as a marker of newly synthesized H3** to show that defective parental histone transfer increases free histone pools and lowers homologous recombination, connecting the Rtt109-marked new-histone pathway to epigenetic inheritance and repair outcomes. | In **dpb3Δ**, **mcm2-3A**, and double mutants, homologous recombination frequency was reported as **significantly lower**; H3K56ac is completely removed during G2 phase. | eSPAN/strand-specific chromatin analyses, HR assays, histone-mark tracking during replication. | Karri et al., *Nucleic Acids Res* (Mar 2024), DOI: https://doi.org/10.1093/nar/gkae205 (pqac-00000014) |
| Antifungal target rationale | Because Rtt109 is **fungal-specific** and central to H3K56ac-dependent genome maintenance/virulence in pathogenic fungi, it has been widely proposed as a selective antifungal target. | In *Candida albicans*, systemic candidiasis mortality cited as ~**40%** in translational discussion; Rtt109 loss causes avirulence/hypovirulence in pathogenic fungi. | Antifungal target assessment, ortholog studies, translational review/dissertation evidence. | da Rosa-Spiegler, Dissertation (Jan 2012), DOI: https://doi.org/10.13028/w35r-7869; Li et al., *Front Microbiol* (Aug 2022), DOI: https://doi.org/10.3389/fmicb.2022.980615 (pqac-00000015, pqac-00000017, pqac-00000016) |
| Chemical inhibition / screening | A selective small-molecule inhibitor **KB7** was reported for Rtt109, but later HTS experience emphasized that many apparent hits are **PAINS/thiol-reactive artifacts**, complicating inhibitor development. | **KB7 apparent Ki = 56 nM**; **IC50 ~60 nM** in dissertation summary; one screen of **300,000** compounds found one specific inhibitor, while another larger effort cited **525,000** compounds with only **2** inhibitory hits; pilot assay used **25 nM** Rtt109–Vps75, **178 μM** H3-H4 tetramers, **125 μM** compound, **7.5 μM** Ac-CoA. | High-throughput screening, ELISA-based H3K56ac readout, medicinal chemistry triage, assay-interference analysis. | da Rosa-Spiegler, Dissertation (Jan 2012), DOI: https://doi.org/10.13028/w35r-7869; Dahlin et al., *J Med Chem* (Feb 2015), DOI: https://doi.org/10.1021/jm5019093 (pqac-00000015, pqac-00000017, pqac-00000020) |
| Yeast biotechnology application | In industrially relevant **S. cerevisiae**, deleting **RTT109** improved tolerance to acetic acid stress and accelerated fermentation, showing direct engineering value even though RTT109 loss compromises DNA damage responses. | At **5.5 g/L acetic acid**, lag phase shortened by **48 h**; glucose consumption completed **36 h earlier**; ethanol production rate increased from **0.39 to 0.60 g·L⁻¹·h⁻¹**. | Stress-tolerance/fermentation assays in yeast. | Cheng et al., *FEMS Yeast Res* (Mar 2016), DOI: https://doi.org/10.1093/femsyr/fow010 (pqac-00000021) |
| Useful quantitative summary figure/table | A kinetic summary table from Berndsen et al. provides a compact quantitative comparison of Rtt109 alone versus Rtt109–Vps75 across multiple substrates and is one of the clearest single-source summaries of Rtt109 activation by Vps75. | Example values include Rtt109–Vps75 **kcat 0.21 ± 0.04 s⁻¹** for H3 vs **0.0033 ± 0.0003 s⁻¹** for Rtt109 alone. | Published kinetic table image extracted from primary paper. | Berndsen et al., *Nat Struct Mol Biol* (Aug 2008), DOI: https://doi.org/10.1038/nsmb.1459 (pqac-00000008) |


*Table: This table compiles the key mechanistic, quantitative, recent, and applied evidence for Saccharomyces cerevisiae Rtt109 (UniProt Q07794). It is useful as a compact source map linking catalytic activity, chaperone dependence, biological function, and translational relevance to specific cited studies.*