# Sni445 recruits box C/D snoRNPs snR4 and snR45 to guide ribosomal RNA acetylation by Kre33

**Authors:** Jutta Hafner, Ingrid Zierler, Hussein Hamze, Sébastien Favre, Matthias Thoms, Natalia Kunowska, Sarah Rimser, Benjamin Albert, Tomas Caetano, Marion Aguirrebengoa, Roland Beckmann, Ulrich Stelzl, Dieter Kressler, Anthony K Henras, Brigitte Pertschy

PMC · DOI: 10.1093/nar/gkag030 · Nucleic Acids Research · 2026-01-28

## TL;DR

The protein Sni445 helps guide specific RNA modifications in yeast ribosomes by recruiting snoRNPs and enabling acetylation of rRNA.

## Contribution

Sni445 is identified as a novel auxiliary component of snR4 and snR45 snoRNPs, essential for their stable incorporation and acetylation activity.

## Key findings

- Sni445 associates with snR4 and snR45 snoRNPs and is required for their stable incorporation into 90S pre-ribosomes.
- Sni445 interacts with Kre33 and is essential for acetylation of rRNA residues C1280 and C1773.
- Genetic interactions link Sni445 and snoRNAs to ribosomal proteins near acetylation sites.

## Abstract

Eukaryotic ribosome synthesis is a highly complex, multistep process that is best characterized in the yeast Saccharomyces cerevisiae. It is orchestrated by >200 ribosome assembly factors and 75 small nucleolar ribonucleoproteins (snoRNPs), which guide site-specific chemical modifications of precursor rRNA (pre-rRNA). While canonical box C/D snoRNPs guide 2′-O-methylation, the atypical box C/D snoRNPs snR4 and snR45 guide acetylation of 18S rRNA residues C1280 and C1773, respectively, catalyzed by the acetyltransferase Kre33. Here, we identify and characterize Ynl050c/Sni445 as a novel ribosome assembly factor and previously unrecognized auxiliary component of the snR4 and snR45 box C/D snoRNPs. Sni445 associates with snR4 and snR45 in their free form and is required for their stable incorporation into 90S pre-ribosomes. Genetic interactions link Sni445 and the snR4 and snR45 snoRNAs to ribosomal proteins Rps20 (uS10) and Rps14 (uS11), which are positioned near the respective acetylation sites in the 40S subunit. Moreover, Sni445 physically interacts with Kre33 within the 90S pre-ribosome, and its absence abolishes acetylation of C1280 and C1773. Our findings suggest that Sni445 facilitates the recruitment of snR4 and snR45 snoRNPs to 90S particles and might promote their interaction with Kre33, thereby enabling the site-specific acetylation of 18S rRNA by Kre33.

Graphical Abstract

## Linked entities

- **Genes:** YNL050C (uncharacterized protein) [NCBI Gene 855677], RPS20 (ribosomal protein S20) [NCBI Gene 6224], RPS14 (ribosomal protein S14) [NCBI Gene 6208]
- **Proteins:** NAT10 (N-acetyltransferase 10)
- **Species:** Saccharomyces cerevisiae (taxon 4932)

## Full-text entities

- **Genes:** ADE2 (phosphoribosylaminoimidazole carboxylase ADE2) [NCBI Gene 854295], NOP10 (snoRNP complex protein NOP10) [NCBI Gene 856471], SNU13 (RNA binding protein SNU13) [NCBI Gene 856687], SNR10 (ncRNA) [NCBI Gene 9164894], KRI1 (Kri1p) [NCBI Gene 855408], HIS3 (imidazoleglycerol-phosphate dehydratase HIS3) [NCBI Gene 854377] {aka HIS10, HIS8}, MAK21 (RNA-binding ribosome biosynthesis protein MAK21) [NCBI Gene 851632] {aka NOC1}, YNL050C (uncharacterized protein) [NCBI Gene 855677], CUP1-1 (metallothionein CUP1-1) [NCBI Gene 856450] {aka CUP1}, UTP22 (rRNA-processing protein UTP22) [NCBI Gene 852982], URB1 (Urb1p) [NCBI Gene 853855] {aka NPA1}, SSF1 (rRNA-binding ribosome biosynthesis protein) [NCBI Gene 856463], DHR2 (RNA helicase) [NCBI Gene 853784], NHP2 (snoRNA-binding protein NHP2) [NCBI Gene 851319], PWP2 (snoRNA-binding rRNA-processing protein PWP2) [NCBI Gene 850422] {aka UTP1, YCR055C, YCR058C}, RRP9 (ribosomal RNA-processing protein RRP9) [NCBI Gene 856255], SNR45 (ncRNA) [NCBI Gene 9164982], KRR1 (ribosome biosynthesis protein KRR1) [NCBI Gene 850298], NOP56 (snoRNP complex protein NOP56) [NCBI Gene 850894] {aka SIK1}, FKBP1AP4 (FKBP prolyl isomerase 1A pseudogene 4) [NCBI Gene 2285] {aka FKBP12, FKBP1P4}, SNR35 (ncRNA) [NCBI Gene 9164977], RPS31 (ubiquitin-40S ribosomal protein eS31 RPS31 fusion protein) [NCBI Gene 850864] {aka RPS37, UBI3}, NOP1 (rRNA methyltransferase NOP1) [NCBI Gene 851548] {aka LOT3}, RPS20 (40S ribosomal protein uS10 RPS20) [NCBI Gene 856371] {aka URP2}, PAF1 (Paf1p) [NCBI Gene 852582], UTP10 (snoRNA-binding rRNA-processing protein UTP10) [NCBI Gene 853335], SNR190 (ncRNA) [NCBI Gene 9164910], RPS12 (40S ribosomal protein eS12 RPS12) [NCBI Gene 854551], NSA1 (ribosome biosynthesis protein NSA1) [NCBI Gene 852767], ERB1 (ribosome biogenesis protein ERB1) [NCBI Gene 855068], SNR4 (ncRNA) [NCBI Gene 9164882], TAN1 (putative tRNA acetyltransferase) [NCBI Gene 852619], ENP1 (snoRNA-binding rRNA-processing protein ENP1) [NCBI Gene 852549] {aka MEG1}, RPS22A (40S ribosomal protein uS8 RPS22A) [NCBI Gene 853249] {aka RPS24}, NOP58 (NOP58 ribonucleoprotein) [NCBI Gene 51602] {aka HSPC120, NOP5, NOP5/NOP58}, NSA2 (rRNA-processing protein NSA2) [NCBI Gene 856863], KRE33 (ribosome biosynthesis protein KRE33) [NCBI Gene 855591] {aka RRA1}, UTP5 (Utp5p) [NCBI Gene 852007], UTP23 (rRNA-binding ribosome biosynthesis protein UTP23) [NCBI Gene 854165], RPS14A (40S ribosomal protein uS11 RPS14A) [NCBI Gene 850397] {aka CRY1, RPL59}, CTR9 (Ctr9p) [NCBI Gene 854020] {aka CDP1}, RTF1 (RNA polymerase-associated protein) [NCBI Gene 852607] {aka CSL3}, SNR77 (ncRNA) [NCBI Gene 9164954], GAR1 (H/ACA snoRNP pseudouridylase subunit GAR1) [NCBI Gene 856489], RRP17 (rRNA-processing protein RRP17) [NCBI Gene 852021], NOP12 (rRNA-processing protein NOP12) [NCBI Gene 854116], TRP1 (phosphoribosylanthranilate isomerase TRP1) [NCBI Gene 851570], CMD1 (calmodulin) [NCBI Gene 852406], LOC1 (Loc1p) [NCBI Gene 850551], RNH203 (Rnh203p) [NCBI Gene 850847], RRP5 (Rrp5p) [NCBI Gene 855269], CBF5 (pseudouridine synthase CBF5) [NCBI Gene 850872], NOP58 (RNA-processing protein NOP58) [NCBI Gene 854487] {aka NOP5}, RNH202 (Rnh202p) [NCBI Gene 851873], LEO1 (Paf1-complex subunit LEO1) [NCBI Gene 854290], LEU2 (3-isopropylmalate dehydrogenase) [NCBI Gene 850342], RPS13 (40S ribosomal protein uS15 RPS13) [NCBI Gene 851636] {aka RPS13B, RPS13C}, RRP12 (mRNA-binding protein RRP12) [NCBI Gene 856095], RPS14B (40S ribosomal protein uS11 RPS14B) [NCBI Gene 853248] {aka CRY2}, RIO1 (protein kinase RIO1) [NCBI Gene 854286] {aka RRP10}
- **Chemicals:** cycloheximide (MESH:D003513), NaCl (MESH:D012965), histidine (MESH:D006639), KCl (MESH:D011189), H2O (MESH:D014867), Bis-Tris (MESH:C026272), 32P (MESH:C000615311), adenine (MESH:D000225), 90S (MESH:C015262), DTT (MESH:D004229), polyacrylamide (MESH:C016679), DMS (MESH:C007482), phenol (MESH:D019800), oligonucleotides (MESH:D009841), ethidium bromide (MESH:D004996), agar (MESH:D000362), Coomassie blue (MESH:C048139), EGTA (MESH:D004533), copper (MESH:D003300), Urea (MESH:D014508), glycerol (MESH:D005990), nylon (MESH:D009757), CaCl2 (MESH:D002122), EDTA (MESH:D004492), ethanol (MESH:D000431), chloroform (MESH:D002725), NP-40 (MESH:C010615), FOA (MESH:C001242), 3-(N-morpholino)-propanesulfonic acid (MESH:C008550), sodium acetate (MESH:D019346), Hygromycin (MESH:C026273), His6 (MESH:C471213), Peptides (MESH:D010455), acetonitrile (MESH:C032159), MgCl2 (MESH:D015636), isoamyl alcohol (MESH:C029683), Coomassie (-), Sepharose (MESH:D012685), 35S (MESH:C000615320), rapamycin (MESH:D020123), HCl (MESH:D006851), Leu (MESH:D007930), formic acid (MESH:C030544), Trp (MESH:D014364), sodium borohydride (MESH:C025364), SDS (MESH:D012967), N (MESH:D009584), formaldehyde (MESH:D005557)
- **Species:** Homo sapiens (human, species) [taxon 9606], Saccharomyces cerevisiae (baker's yeast, species) [taxon 4932], Tobacco etch virus (no rank) [taxon 12227], Mus musculus (house mouse, species) [taxon 10090]
- **Mutations:** C for 3-6, R136, R637A, K69, R132A, R68E, K69E, R132, R136A, 637 (R > A)
- **Cell lines:** YDK11 — Capra hircus (Goat), Spontaneously immortalized cell line (CVCL_6F17), tor1-1 — Mus musculus (Mouse), Hybridoma (CVCL_C3BY), PJ69 — Homo sapiens (Human), Ovarian adenocarcinoma, Cancer cell line (CVCL_A8KJ)

## Full text

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## Figures

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## References

51 references — full list in the complete paper: https://tomesphere.com/paper/PMC12848939/full.md

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Source: https://tomesphere.com/paper/PMC12848939