From model yeast to diverse fungal phyla
Why box C/D snoRNP and PeBoW complex?
The nucleolus is the most conspicuous nuclear domain and serves as the primary site for ribosome synthesis.
Within this hub, complex ribonucleoprotein (RNP) machineries must be precisely localized to perform specialized functions ranging from ribosomal RNA (rRNA) modification to structural maturation.
While the box C/D snoRNP core complex represents a classic system for site-specific RNA processing, the PeBoW complex provides a critical link between the assembly of ribosomal subunits and the control of cell growth and proliferation.
We selected these two systems as reference frameworks because they represent well-characterized examples of this intricate nucleolar targeting system, illustrating the utility of our database.
Biological significance
The box C/D snoRNP complex is essential for directed rRNA 2'-O-methylation, a critical step in ribosome biogenesis. This complex is composed of four highly conserved core proteins: Nop1p (fibrillarin), Snu13p, Nop56p, and Nop5p/Nop58p. Key insights from previous research highlight why these are ideal for validating out database.
In addition, the PeBoW complex (Pes1, Bop1, and WDR12) is another core complex subunits that coordinates ribosome biogenesis with the cell cycle. In yeast, its homologous core complex (Nop7p, Erb1p, and Ytm1p) is essential for the maturation of the 60S ribosomal subunit and DNA replication. The structural and functional integrity of this complex is required for proper rRNA processing and mammalian cell proliferation.
References
Lafontaine DLJ, Tollervey D. Synthesis and Assembly of the Box C+D Small Nucleolar RNPs. Mol. Cell. Biol. 2000. 20(8):2650–9.
Hölzel M, Rohrmoser M, Schlee M, Grimm T, Harasim T, Malamoussi A, Gruber-Eber A, Kremmer E, Hiddemann W, Bornkamm GW, Eick D. Mammalian WDR12 is a novel member of the Pes1–Bop1 complex and is required for ribosome biogenesis and cell proliferation. J. Cell Biol. 2005. 170(3):367–78.
FuNGI utility: From model systems to fungal proteomes
While these complexes are well-characterized in model organisms like Saccharomyces cerevisiae, FuNGI extends this knowledge across the diverse fungal phyla. By identifying how these conserved fungal orthologs are represented in our database, we can demonstrate FuNGI's possibility to capture biologically relevant proteins containing nucleolar localization signals (NoLSs).
The networks illustrate the canonical subunits of the box C/D snoRNP and PeBoW complexes. Please note that detail panels are displayed only for subunits with at least one predicted NoLS. FuNGI catalogs only proteins predicted to contain NoLSs.
Reference yeast subunits in FuNGI
Because the source organism for this tutorial is Saccharomyces cerevisiae Statistics , we first show how the reference yeast subunits are represented in FuNGI before identifying orthologs in other fungal proteomes.
| Complex | Subunit | Accession | Gene | # NoLS | # NLS | PSORT | Confidence | UniProt |
|---|---|---|---|---|---|---|---|---|
| box C/D snoRNP | NOP1 | P15646 | Kpol_1010p66 | 0 | 1 | nucl | Low (8.6) |
|
| box C/D snoRNP | NOP56 | A7TL01 | Kpol_530p27 | 1 | 1 | cyto_nucl | Medium (10.7) |
|
| box C/D snoRNP | NOP58 | A7TIF5 | NOP58 | 1 | 1 | nucl | Medium (11.2) |
|
| box C/D snoRNP | SNU13 | P39990 | Kpol_1067p31 | 0 | 0 | cyto | Low (2.3) |
|
| PeBoW | NOP7 | A7TSA8 | NOP7 | 3 | 3 | nucl | High (22) |
|
| PeBoW | ERB1 | Q04660 | ERB1 | 0 | 1 | nucl | Medium (11.4) |
|
| PeBoW | YTM1 | Q12024 | YTM1 | 0 | 1 | nucl | Medium (10.9) |
|
Interactive complex demonstration
Box C/D snoRNP subunits
NOP56
| Gene / protein | PAS_chr1-4_0403 Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes |
|---|---|
| Confidence | Medium (10.5) |
| NoLS | 1 445-496 |
| NLS | 1 452-496 |
| PSORT |
nucl: 12.000
, cyto_nucl: 13.833
, mito_nucl: 6.833
Nuclear-related sum: 32.666 |
| RBH support |
Forward: identity 78.132
, qcovs 87
Reverse: identity 78.132 , qcovs 88 |
PeBoW subunits
NOP7
| Gene / protein |
NOP7
Pescadillo homolog |
|---|---|
| Confidence | High (15.2) |
| NoLS |
2
502-534, 553-583 |
| NLS |
2
90-94, 507-575 |
| PSORT |
nucl: 16.500
, cyto_nucl: 11.166
, mito_nucl: 11.999
Nuclear-related sum: 39.665 |
| RBH support |
Forward: identity 52.649
, qcovs 99
Reverse: identity 55.762 , qcovs 88 |
| Query (Yeast Complex Subunit) | Subject (Fungal Ortholog) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Complex | Source | Subunit | UniProt | Species | FuNGI_ID | Accession | Gene Name | # NoLS | # NLS | PSORT | UniProt |
| box C/D snoRNP | S. cerevisiae | NOP56 | Q12460 | Komagataella phaffii | 0001702 | C4QYC8 | PAS_chr1-4_0403 | 1 | 1 | cyto |
|
| box C/D snoRNP | S. cerevisiae | NOP58 | Q12499 | Komagataella phaffii | 0001659 | C4R7D7 | PAS_chr4_0278 | 1 | 1 | cyto_nucl |
|
| PeBoW | S. cerevisiae | NOP7 | P53261 | Komagataella phaffii | 0001582 | C4R8Q2 | NOP7 | 2 | 2 | nucl |
|
| PeBoW | S. cerevisiae | ERB1 | Q04660 | Komagataella phaffii | 0002840 | C4QXX4 | ERB1 | 1 | 0 | nucl |
|
What this utility shows
This utility demonstrates that while prediction support may vary across conserved subunits, FuNGI effectively captures and prioritizes well-characterized proteins containing nucleolar localization signals (NoLSs).
By using established systems like the box C/D snoRNP and PeBoW complexes as reference frameworks, users can systematically explore orthologs in a target proteome and identify which candidates exhibit the strongest nucleolar localization signals.
In Magnaporthe oryzae, for instance, this approach successfully identifies NOP56 and NOP58 as high-confidence candidates. These results show FuNGI’s potentials to discover biologically relevant proteins across 769 fungal proteomes, transforming integrative predictions into functional insights.