nip7 encodes the D. discoideum homolog of the conserved 60S ribosome subunit biogenesis protein NIP7. The 179-amino-acid protein contains an N-terminal pre-PUA domain for protein-protein interactions and a C-terminal PUA domain that binds pre-rRNA with polyuridine preference. Based on extensive studies of yeast and human orthologs, nip7 is predicted to function as a nucleolar trans-acting factor required for 27S pre-rRNA processing and 60S ribosomal subunit assembly. The protein associates transiently with pre-60S particles and interacts with other biogenesis factors and exosome components.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005730 nucleolus | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference (IBA) that nip7 localizes to the nucleolus is well-supported. In yeast, Nip7p-GFP localizes to the nucleolus, and in human cells NIP7 is restricted to the nuclear compartment and colocalizes with nucleolar markers. The nucleolus is the site of pre-rRNA processing and early ribosome assembly where NIP7 orthologs function. Reason: Nucleolar localization is a core conserved feature of NIP7 family proteins across eukaryotes. Supporting Evidence: file:DICDI/nip7/nip7-deep-research-bioreason-sft.md A nucleolar assembly factor that promotes maturation of the large ribosomal subunit PMID:9271378 in vivo localization of a Nip7p-green fluorescent protein fusion protein revealed that a significant amount of Nip7p is present inside the nucleus, most probably in the nucleolus PMID:22195017 Both exogenous proteins colocalized to the nucleolus |
| GO:0042273 ribosomal large subunit biogenesis | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that nip7 is involved in ribosomal large subunit biogenesis is strongly supported. Yeast Nip7p depletion causes accumulation of 27S pre-rRNA and deficit of 60S subunits. The protein cosediments with free 60S subunits, confirming direct involvement in large subunit maturation. Reason: This is the core biological process for NIP7 family proteins, extensively documented in yeast. Supporting Evidence: PMID:9271378 Delayed processing of 27S pre-rRNA appeared to be the cause of reduced synthesis of 25S rRNA relative to 18S rRNA, which may be responsible for the deficit of 60S subunits in these cells PMID:9891085 Rrp43p and a second essential protein, Nop8p, were identified in a two-hybrid screen as Nip7p-interacting proteins |
| GO:0030687 preribosome, large subunit precursor | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that nip7 is part of the preribosome, large subunit precursor is well-supported. Yeast Nip7p cosediments with free 60S subunits and interacts with other pre-60S assembly factors (Nop8p, Rrp43p). NIP7 family proteins are trans-acting factors that associate transiently with pre-60S particles during maturation. Reason: Nip7p association with pre-60S particles is demonstrated by cosedimentation and protein interaction data. Supporting Evidence: PMID:9271378 A fraction of Nip7p cosedimented through sucrose gradients with free 60S ribosomal subunits but not with 80S monosomes or polysomal ribosomes PMID:9891085 Biochemical evidence for an interaction was provided by the copurification on immunoglobulin G-Sepharose of Nip7p with protein A-tagged Rrp43p and Nop8p |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO annotation of RNA binding based on the PUA domain (IPR002478, IPR036974). The PUA domain is a well-characterized RNA-binding module. Structural and biochemical studies of archaeal and yeast Nip7 proteins confirm that the PUA domain binds RNA, with specificity for polyuridine sequences. This annotation is correct but could be more specific as rRNA binding. Reason: RNA binding via the PUA domain is experimentally verified for Nip7 orthologs. While rRNA binding (GO:0019843) would be more specific, RNA binding is not incorrect and the IEA evidence appropriately reflects the domain-level annotation. Supporting Evidence: PMID:18001138 the PUA domain mediates Nip7 interaction with RNA and reveals that the preference for interaction with polyuridine sequences is conserved in Archaea and eukaryotic Nip7 proteins |
| GO:0005634 nucleus | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO annotation of nuclear localization based on the NIP7 family signature (IPR016686). Yeast and human NIP7 proteins localize to the nucleus/nucleolus. The nucleolus annotation (GO:0005730) is more specific and also present, making this a redundant but not incorrect parent term. Reason: Correct but less specific than the nucleolus annotation. The nucleolus is within the nucleus, so this is technically true but the more informative annotation is GO:0005730 nucleolus. Supporting Evidence: PMID:9271378 in vivo localization of a Nip7p-green fluorescent protein fusion protein revealed that a significant amount of Nip7p is present inside the nucleus, most probably in the nucleolus |
| GO:0005730 nucleolus | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular location mapping to nucleolus (IEA). This is the same term as the IBA annotation above, providing independent computational support. The nucleolus annotation is well-supported by experimental data from yeast and human orthologs. Reason: Redundant with the IBA annotation but provides independent computational evidence stream. Supporting Evidence: PMID:20798176 The NIP7 protein is restricted to the nuclear compartment and co-sediments with complexes with molecular masses in the range of 40S-80S |
| GO:0042255 ribosome assembly | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO annotation of ribosome assembly based on IPR016686 (NIP7 family). This is a parent term of the more specific ribosomal large subunit biogenesis (GO:0042273), which is already annotated. Ribosome assembly is correct but less informative. Reason: Correct parent term but less specific than GO:0042273 (ribosomal large subunit biogenesis) which is already present with IBA and ISS evidence. The InterPro2GO mapping appropriately captures the family-level biology. Supporting Evidence: PMID:9271378 Nip7-1p-depleted cells showed defective pre-rRNA processing, including accumulation of the 35S rRNA precursor, presence of a 23S aberrant precursor, decreased 20S pre-rRNA levels, and accumulation of 27S pre-rRNA |
| GO:0042273 ribosomal large subunit biogenesis | ISS GO_REF:0000024 | ACCEPT | Summary: Manual ISS annotation by dictyBase based on sequence similarity to yeast Nip7p (Q08962). This is the most informative annotation for the core biological process. The yeast ortholog has extensive experimental evidence for 60S subunit biogenesis, including 27S pre-rRNA processing defects and 60S subunit deficit upon depletion. Reason: Well-supported ISS annotation based on clear orthology to yeast NIP7, which has direct experimental evidence (IDA/IMP) for this process. Supporting Evidence: PMID:9271378 Delayed processing of 27S pre-rRNA appeared to be the cause of reduced synthesis of 25S rRNA relative to 18S rRNA, which may be responsible for the deficit of 60S subunits in these cells PMID:9891085 Rrp43p and a second essential protein, Nop8p, were identified in a two-hybrid screen as Nip7p-interacting proteins |
| GO:0019843 rRNA binding | ISS PMID:18001138 Structural insights into the interaction of the Nip7 PUA dom... | NEW | Summary: The PUA domain of Nip7 binds RNA with polyuridine preference, and this activity is conserved from archaea to eukaryotes. Given that Nip7 functions in pre-rRNA processing within pre-60S particles, the relevant RNA substrate is pre-rRNA. rRNA binding (GO:0019843) is more specific than the existing RNA binding (GO:0003723) annotation and better reflects the biological context. Reason: Structural and biochemical studies demonstrate that the PUA domain of Nip7 binds RNA, and the biological context (pre-60S particle association, 27S pre-rRNA processing) establishes pre-rRNA as the relevant substrate. This is a more specific annotation than the existing GO:0003723 RNA binding. Supporting Evidence: PMID:18001138 Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain PMID:9271378 A fraction of Nip7p cosedimented through sucrose gradients with free 60S ribosomal subunits but not with 80S monosomes or polysomal ribosomes |
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Download this section (compressed HTML)Q: Is nip7 essential for growth in D. discoideum, as it is in yeast? A knockout or knockdown experiment would clarify whether the functional requirement is conserved.
Q: Does D. discoideum nip7 function primarily in 60S subunit biogenesis (as in yeast) or does it also affect 40S biogenesis (as observed for human NIP7)?
Experiment: Generate a nip7 knockout or conditional knockdown in D. discoideum (e.g., using blasticidin cassette insertion or doxycycline-inducible RNAi). Assess growth, ribosomal subunit profiles by sucrose gradient sedimentation, and pre-rRNA processing by northern blot to determine whether 27S pre-rRNA accumulates as in yeast.
Hypothesis: nip7 is essential for growth and required for 60S ribosomal subunit biogenesis in D. discoideum.
Type: gene knockout / conditional knockdown
Experiment: Determine the subcellular localization of nip7 in D. discoideum by expressing a GFP-nip7 fusion. Verify nucleolar localization by co-staining with nucleolar markers such as fibrillarin.
Hypothesis: nip7 localizes to the nucleolus in D. discoideum.
Type: fluorescence microscopy
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