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
|
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
I begin with the InterPro architecture. The entire polypeptide (residues 1–177) is classified as IPR016686 (Ribosome biogenesis factor, NIP7 family), establishing a dedicated role in large subunit assembly. The N-terminus carries IPR040598 (60S ribosome subunit biogenesis protein NIP7, pre-PUA domain, residues 1–83) and its eukaryote-specific refinement IPR055359 (pre-PUA domain, eukaryotes, residues 2–88). This pre-PUA segment typically forms an extended, basic, protein-interaction arm that positions the core RNA-binding module and mediates contacts with assembly factors. The C-terminal half is dominated by a PUA fold: IPR002478 (PUA domain, residues 95–171) is corroborated by IPR005155 (UPF0113, PUA domain, residues 95–172) and encompassed by PUA-related superfamily signatures IPR036974 (PUA domain superfamily, residues 94–179) and IPR015947 (PUA-like superfamily, residues 95–170). PUA domains are specialized RNA-recognition modules that bind structured RNAs and tRNA-like elements; in nucleolar biogenesis factors, this fold anchors the protein to pre-rRNA segments within pre-60S particles. The ordered layout—pre-PUA for factor docking followed by a PUA core for RNA engagement—creates a bipartite clamp that couples protein and RNA binding during 60S maturation.
This architecture causes two primary molecular activities. First, the pre-PUA and surrounding family-specific surfaces provide multivalent protein interfaces, supporting GO:0005515 protein binding. Second, the PUA fold confers high-affinity binding to structured RNA, most plausibly pre-rRNA or tRNA-like moieties present in pre-60S particles; thus RNA binding (GO:0003723) is expected. Together, these activities enable the factor to stabilize specific rRNA helices, recruit partner assembly factors, and choreograph remodeling steps on nascent 60S subunits.
From these molecular functions, the biological process follows. By binding pre-rRNA and engaging assembly proteins, the factor drives maturation of the large ribosomal subunit, a core component of ribosome biogenesis (GO:0042254) and specifically ribosomal large subunit biogenesis (GO:0042273). Ribosome production is tightly integrated with cellular stress programs. Perturbations such as UV exposure or DNA damage rapidly reprogram nucleolar activity; a nucleolar assembly factor that senses or enforces pre-rRNA checkpoints can modulate growth and ribosome output during stress. This provides a mechanistic route to participation in cellular response to DNA damage stimulus (GO:0006974) and response to UV (GO:0009411): modulation of pre-60S assembly couples ribosome biogenesis capacity to genome integrity signals, throttling output and facilitating recovery.
The cellular component is dictated by the substrate and partners. Pre-rRNA transcription and early 60S assembly occur in the nucleolus, aligning with GO:0005730 nucleolus. The absence of transmembrane features and the presence of nucleolar specialization further support a soluble nucleolar residency.
This mechanistic model predicts specific interaction partners. The pre-PUA arm can dock assembly factors such as BRX1 and WDR12 (components of the PeBoW complex), NSA2, RPF2, and RLP24, while the PUA domain anchors to pre-rRNA near sites where MRT4 (a pre-60S P-stalk placeholder) is handled during maturation. Additional contacts with an RRM domain-containing protein and coiled-coil scaffolds would stabilize transient pre-60S intermediates. In sum, the protein likely bridges pre-rRNA elements to a cohort of 60S biogenesis factors, enforcing quality control and coordinating progression through nucleolar assembly checkpoints, with stress-responsive modulation during UV or DNA-damage conditions.
## Functional Summary
A nucleolar assembly factor that promotes maturation of the large ribosomal subunit by combining an N-terminal docking module with a C-terminal RNA-recognition fold to bind pre-rRNA and recruit biogenesis factors. Through these multivalent contacts it stabilizes and remodels pre-60S particles, coordinating their progression and enforcing quality control. Its activity is expected to be tuned during UV and DNA-damage responses, coupling ribosome output to stress conditions to maintain cellular homeostasis.
## UniProt Summary
Involved in the biogenesis of the 60S ribosomal subunit.
## InterPro Domains
- IPR016686: Ribosome biogenesis factor, NIP7 (family) [1-177]
- IPR040598: 60S ribosome subunit biogenesis protein NIP7, pre-PUA domain (domain) [1-83]
- IPR055359: 60S ribosome subunit biogenesis protein Nip7, pre-PUA domain, eukaryotes (domain) [2-88]
- IPR036974: PUA domain superfamily (homologous_superfamily) [94-179]
- IPR002478: PUA domain (domain) [95-171]
- IPR005155: UPF0113, PUA domain (domain) [95-172]
- IPR015947: PUA-like superfamily (homologous_superfamily) [95-170]
- IPR005155: UPF0113, PUA domain (domain) [96-175]
## GO Term Predictions
### Molecular Function
### Biological Process
### Cellular Component
UniProt: B0G104 | Gene: DDB_G0295477 | 179 aa, 20.7 kDa
nip7 encodes the Dictyostelium discoideum homolog of the conserved 60S ribosome subunit biogenesis protein NIP7. The protein contains two domains: an N-terminal pre-PUA domain (IPR040598, residues 1-83) and a C-terminal PUA domain (IPR002478, residues 95-171). The full-length protein is classified under IPR016686 (Ribosome biogenesis factor, NIP7 family). No direct experimental studies exist for the D. discoideum protein; all functional inferences are based on orthology to yeast and human NIP7.
The yeast NIP7 gene was first characterized by Zanchin et al. (1997). NIP7 is essential for growth, and the protein cosediments with free 60S subunits but not 80S monosomes or polysomes, confirming it is a trans-acting assembly factor rather than a ribosomal protein [PMID:9271378, "A fraction of Nip7p cosedimented through sucrose gradients with free 60S ribosomal subunits but not with 80S monosomes or polysomal ribosomes, indicating that it is not a ribosomal protein"]. Nip7p localizes primarily to the nucleolus [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"]. Depletion of Nip7p causes severe pre-rRNA processing defects: accumulation of 35S and 27S precursors, appearance of 23S aberrant precursor, decreased 20S pre-rRNA, and reduced 25S rRNA relative to 18S rRNA, resulting in a deficit of 60S subunits [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"].
Zanchin and Goldfarb (1999) identified two Nip7p-interacting proteins by yeast two-hybrid: Rrp43p (an exosome subunit) and Nop8p (a nucleolar protein also required for 60S biogenesis) [PMID:9891085, "Rrp43p and a second essential protein, Nop8p, were identified in a two-hybrid screen as Nip7p-interacting proteins"]. Physical interaction was confirmed by copurification [PMID:9891085, "Nip7p was present in IgG-Sepharose column eluates from whole-cell extracts containing either PrtA-Rrp43p or PrtA-Nop8p but not from control extract"]. The authors concluded that these proteins form a dynamic complex essential for 60S biogenesis [PMID:9891085, "Nip7p, Rrp43p, and Nop8p are subunits of a dynamic complex with essential roles in 60S subunit biogenesis"].
Coltri et al. (2007) solved the crystal structure of archaeal Nip7 (P. abyssi) and showed the PUA domain mediates RNA interaction with preference for polyuridine sequences, conserved across archaea and eukaryotes [PMID:18001138, "Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain"]. The PUA domain (named after Pseudo-Uridine synthases and Archaeosine-specific transglycosylases) is the conserved RNA-recognition module [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"].
Morello et al. (2011) showed that human NIP7 depletion affects pre-rRNA processing and causes a 40S/60S subunit imbalance [PMID:20798176, "downregulation of NIP7 affects pre-rRNA processing, causing an imbalance of the 40S/60S subunit ratio"]. Notably, in human cells NIP7 appears more involved in 40S subunit biogenesis (18S rRNA maturation) [PMID:20798176, "NIP7 is required for maturation of the 18S rRNA"], which is a functional divergence from the yeast protein's role primarily in 60S biogenesis. NIP7 localizes to the nuclear compartment and co-sediments with 40S-80S complexes [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"].
Morello et al. (2011) identified FTSJ3 (ortholog of yeast Spb1p) as a human NIP7-interacting protein [PMID:22195017, "FTSJ3, a putative ortholog of yeast Spb1p, as a human NIP7-interacting protein"]. Their interaction is RNA-mediated rather than direct protein-protein contact [PMID:22195017, "Incubation of the extracts with RNase abolishes the coimmunoprecipitation of NIP7 with FLAG-FTSJ3"]. Both colocalize to the nucleolus [PMID:22195017, "Both exogenous proteins colocalized to the nucleolus"].
The nip7 gene resides on chromosome 2 of D. discoideum, which was sequenced by Gloeckner et al. (2002) PMID:12097910 and subsequently the full genome was reported by Eichinger et al. (2005) PMID:15875012.
Given the high conservation of NIP7 across eukaryotes and archaea, D. discoideum nip7 is expected to function as a nucleolar assembly factor for the 60S ribosomal subunit. Its PUA domain should bind pre-rRNA (with polyuridine preference), and its pre-PUA domain should mediate protein-protein interactions with other pre-60S assembly factors. Based on the yeast ortholog, the primary role is in 27S pre-rRNA processing and 60S subunit assembly, operating within pre-60S ribosomal particles in the nucleolus. The ISS annotation (GO_REF:0000024) based on similarity to yeast Q08962 (Nip7p) is well-supported by the extensive yeast literature.
Source: nip7-deep-research-bioreason-sft.md
The BioReason functional summary states:
A nucleolar assembly factor that promotes maturation of the large ribosomal subunit by combining an N-terminal docking module with a C-terminal RNA-recognition fold to bind pre-rRNA and recruit biogenesis factors. Through these multivalent contacts it stabilizes and remodels pre-60S particles, coordinating their progression and enforcing quality control. Its activity is expected to be tuned during UV and DNA-damage responses, coupling ribosome output to stress conditions to maintain cellular homeostasis.
The first two sentences are accurate and well-supported. NIP7 is indeed a nucleolar assembly factor with a bipartite architecture: an N-terminal pre-PUA domain for protein interactions and a C-terminal PUA domain for RNA binding. Its role in 60S ribosomal subunit maturation is the core conserved function, supported by extensive experimental data from yeast showing that Nip7p depletion causes 27S pre-rRNA accumulation and 60S subunit deficit (PMID:9271378). The description of binding pre-rRNA and recruiting biogenesis factors aligns with the known interactions with Nop8p and Rrp43p (PMID:9891085).
However, the claim that NIP7 activity "is expected to be tuned during UV and DNA-damage responses, coupling ribosome output to stress conditions" is speculative and not supported by any published evidence for NIP7 specifically. The thinking trace reveals that BioReason inferred this from a generic reasoning chain: nucleolar factors can sense stress, therefore NIP7 participates in DNA damage response (GO:0006974) and UV response (GO:0009411). This is a category error -- while ribosome biogenesis is generally affected by cellular stress, there is no evidence that NIP7 specifically plays a regulatory role in stress responses. The curated annotations contain no stress-related terms, and none of the primary NIP7 literature (Zanchin et al. 1997, 1999; Coltri et al. 2007; Morello et al. 2011) mentions DNA damage or UV response functions.
The summary also omits some relevant biology. It does not mention that the PUA domain binds polyuridine RNA specifically (PMID:18001138), nor does it note the interaction with the exosome subunit Rrp43p (PMID:9891085), which connects NIP7 to the RNA degradation machinery involved in pre-rRNA quality control. It also does not mention the functional divergence between yeast NIP7 (primarily 60S) and human NIP7 (also affecting 40S/18S rRNA maturation; PMID:20798176), which would be relevant for understanding the range of NIP7 biology.
Comparison with interpro2go:
The InterPro2GO annotations (GO_REF:0000002) for this protein are:
- GO:0003723 RNA binding (from IPR002478/IPR036974, PUA domain)
- GO:0005634 nucleus (from IPR016686, NIP7 family)
- GO:0042255 ribosome assembly (from IPR016686, NIP7 family)
BioReason's functional summary covers the same core biology as interpro2go: RNA binding via the PUA domain, nuclear/nucleolar localization, and ribosome assembly. However, BioReason adds specificity beyond interpro2go by correctly identifying the large subunit (60S) as the specific target and describing the bipartite domain architecture. The interpro2go annotations are appropriately conservative (ribosome assembly rather than specifically large subunit biogenesis), while BioReason correctly narrows to 60S biogenesis.
Where BioReason diverges negatively from interpro2go is the fabricated stress-response claims. InterPro2GO makes no such claims because the domain signatures do not predict stress responsiveness. BioReason appears to have over-interpreted the nucleolar localization to generate these additional biological process predictions, which is a hallmark reasoning error where plausible-sounding inferences are made without supporting evidence.
In summary, BioReason recapitulates the core interpro2go biology with improved specificity (60S rather than generic ribosome assembly), adds reasonable structural interpretation of the domain architecture, but then extends into unsupported stress-response territory.
The thinking trace demonstrates reasonable domain-level interpretation. The analysis of the pre-PUA and PUA domain architecture is sound: identifying the pre-PUA as a "protein-interaction arm" and the PUA as an "RNA-recognition module" that together create "a bipartite clamp that couples protein and RNA binding during 60S maturation." This is consistent with the structural data (PMID:18001138).
The trace goes off track when it predicts "participation in cellular response to DNA damage stimulus (GO:0006974) and response to UV (GO:0009411)" through a chain of reasoning that nucleolar factors "can modulate growth and ribosome output during stress." This is generic nucleolar biology reasoning applied without specific evidence for NIP7. The trace also predicts specific interaction partners (BRX1, WDR12/PeBoW complex, NSA2, RPF2, RLP24, MRT4) that are not documented for NIP7 -- these are known pre-60S factors but their specific interaction with NIP7 is speculative.
The protein binding prediction (GO:0005515) in the trace is also noted. Per curation guidelines, protein binding is uninformative and should be avoided in favor of more specific molecular function terms.
id: B0G104
gene_symbol: nip7
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:44689
label: Dictyostelium discoideum
description: 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.
references:
- id: PMID:9271378
title: Saccharomyces cerevisiae Nip7p is required for efficient 60S ribosome
subunit biogenesis
findings:
- statement: NIP7 is essential for growth and required for 60S ribosomal
subunit biogenesis in yeast.
supporting_text: 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
- statement: Nip7p cosediments with free 60S subunits and localizes to the
nucleolus.
supporting_text: A fraction of Nip7p cosedimented through sucrose gradients
with free 60S ribosomal subunits but not with 80S monosomes or polysomal
ribosomes, indicating that it is not a ribosomal protein
- statement: Nip7p is a nucleolar protein.
supporting_text: 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
- id: PMID:9891085
title: Nip7p interacts with Nop8p, an essential nucleolar protein required for
60S ribosome biogenesis, and the exosome subunit Rrp43p
findings:
- statement: Nip7p interacts with nucleolar protein Nop8p and exosome subunit
Rrp43p.
supporting_text: Rrp43p and a second essential protein, Nop8p, were
identified in a two-hybrid screen as Nip7p-interacting proteins
- statement: The three proteins form a dynamic complex in 60S biogenesis.
supporting_text: Biochemical evidence for an interaction was provided by the
copurification on immunoglobulin G-Sepharose of Nip7p with protein
A-tagged Rrp43p and Nop8p
- id: PMID:18001138
title: Structural insights into the interaction of the Nip7 PUA domain with
polyuridine RNA
findings:
- statement: The PUA domain mediates Nip7 interaction with RNA, with conserved
polyuridine preference.
supporting_text: Both proteins can bind specifically to polyuridine, and RNA
interaction requires specific residues of the PUA domain
- statement: Polyuridine binding is conserved from archaea to eukaryotes.
supporting_text: 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
- id: PMID:20798176
title: The NIP7 protein is required for accurate pre-rRNA processing in human
cells
findings:
- statement: Human NIP7 is required for pre-rRNA processing and ribosome
subunit biogenesis.
supporting_text: downregulation of NIP7 affects pre-rRNA processing, causing
an imbalance of the 40S/60S subunit ratio
- statement: NIP7 localizes to the nuclear compartment and associates with
pre-ribosomal particles.
supporting_text: The NIP7 protein is restricted to the nuclear compartment
and co-sediments with complexes with molecular masses in the range of
40S-80S
- id: PMID:22195017
title: The human nucleolar protein FTSJ3 associates with NIP7 and functions in
pre-rRNA processing
findings:
- statement: NIP7 and FTSJ3 interact and colocalize in the nucleolus.
supporting_text: Both exogenous proteins colocalized to the nucleolus
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with
GO terms
findings: []
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data to
orthologs by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular
Location vocabulary mapping, accompanied by conservative changes to GO terms
applied by UniProt
findings: []
- id: PMID:12097910
title: Sequence and analysis of chromosome 2 of Dictyostelium discoideum
findings:
- statement: Genomic sequence of D. discoideum chromosome 2 where nip7
resides.
supporting_text: the chromosome codes for 2,799 predicted protein coding
genes and 73 transfer RNA genes
- id: PMID:15875012
title: The genome of the social amoeba Dictyostelium discoideum
findings:
- statement: Complete genome of D. discoideum encoding approximately 12,500
predicted proteins.
supporting_text: chromosomes of this organism encode approximately 12,500
predicted proteins
- id: file:DICDI/nip7/nip7-deep-research-bioreason-sft.md
title: BioReason-Pro SFT prediction for nip7 (D. discoideum)
findings:
- statement: BioReason SFT trace identifies nip7 as a nucleolar assembly
factor for 60S ribosomal subunit maturation with bipartite pre-PUA and PUA
domain architecture.
existing_annotations:
- term:
id: GO:0005730
label: nucleolus
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
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.
action: ACCEPT
reason: Nucleolar localization is a core conserved feature of NIP7 family
proteins across eukaryotes.
supported_by:
- reference_id: file:DICDI/nip7/nip7-deep-research-bioreason-sft.md
supporting_text: A nucleolar assembly factor that promotes maturation of
the large ribosomal subunit
- reference_id: PMID:9271378
supporting_text: 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
- reference_id: PMID:22195017
supporting_text: Both exogenous proteins colocalized to the nucleolus
- term:
id: GO:0042273
label: ribosomal large subunit biogenesis
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
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.
action: ACCEPT
reason: This is the core biological process for NIP7 family proteins,
extensively documented in yeast.
supported_by:
- reference_id: PMID:9271378
supporting_text: 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
- reference_id: PMID:9891085
supporting_text: Rrp43p and a second essential protein, Nop8p, were
identified in a two-hybrid screen as Nip7p-interacting proteins
- term:
id: GO:0030687
label: preribosome, large subunit precursor
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
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.
action: ACCEPT
reason: Nip7p association with pre-60S particles is demonstrated by
cosedimentation and protein interaction data.
supported_by:
- reference_id: PMID:9271378
supporting_text: A fraction of Nip7p cosedimented through sucrose
gradients with free 60S ribosomal subunits but not with 80S monosomes or
polysomal ribosomes
- reference_id: PMID:9891085
supporting_text: Biochemical evidence for an interaction was provided by
the copurification on immunoglobulin G-Sepharose of Nip7p with protein
A-tagged Rrp43p and Nop8p
- term:
id: GO:0003723
label: RNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: ACCEPT
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.
supported_by:
- reference_id: PMID:18001138
supporting_text: 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
- term:
id: GO:0005634
label: nucleus
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: KEEP_AS_NON_CORE
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.
supported_by:
- reference_id: PMID:9271378
supporting_text: 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
- term:
id: GO:0005730
label: nucleolus
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
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.
action: ACCEPT
reason: Redundant with the IBA annotation but provides independent
computational evidence stream.
supported_by:
- reference_id: PMID:20798176
supporting_text: The NIP7 protein is restricted to the nuclear compartment
and co-sediments with complexes with molecular masses in the range of
40S-80S
- term:
id: GO:0042255
label: ribosome assembly
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: KEEP_AS_NON_CORE
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.
supported_by:
- reference_id: PMID:9271378
supporting_text: 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
- term:
id: GO:0042273
label: ribosomal large subunit biogenesis
evidence_type: ISS
original_reference_id: GO_REF:0000024
review:
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.
action: ACCEPT
reason: Well-supported ISS annotation based on clear orthology to yeast
NIP7, which has direct experimental evidence (IDA/IMP) for this process.
supported_by:
- reference_id: PMID:9271378
supporting_text: 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
- reference_id: PMID:9891085
supporting_text: Rrp43p and a second essential protein, Nop8p, were
identified in a two-hybrid screen as Nip7p-interacting proteins
# ================== rRNA BINDING (NEW) ==================
- term:
id: GO:0019843
label: rRNA binding
evidence_type: ISS
original_reference_id: PMID:18001138
review:
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.
action: NEW
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.
supported_by:
- reference_id: PMID:18001138
supporting_text: Both proteins can bind specifically to polyuridine, and
RNA interaction requires specific residues of the PUA domain
- reference_id: PMID:9271378
supporting_text: A fraction of Nip7p cosedimented through sucrose
gradients with free 60S ribosomal subunits but not with 80S monosomes or
polysomal ribosomes
core_functions:
- description: nip7 functions as a nucleolar trans-acting factor in 60S
ribosomal subunit biogenesis. Its PUA domain binds pre-rRNA (with
polyuridine preference) while the N-terminal pre-PUA domain mediates
interactions with other assembly factors. The protein associates transiently
with pre-60S ribosomal particles during 27S pre-rRNA processing and
dissociates as the subunit matures.
molecular_function:
id: GO:0019843
label: rRNA binding
directly_involved_in:
- id: GO:0042273
label: ribosomal large subunit biogenesis
locations:
- id: GO:0005730
label: nucleolus
supported_by:
- reference_id: PMID:18001138
supporting_text: 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
- reference_id: PMID:9271378
supporting_text: A fraction of Nip7p cosedimented through sucrose gradients
with free 60S ribosomal subunits but not with 80S monosomes or polysomal
ribosomes
- reference_id: PMID:9891085
supporting_text: Rrp43p and a second essential protein, Nop8p, were
identified in a two-hybrid screen as Nip7p-interacting proteins
in_complex:
id: GO:0030687
label: preribosome, large subunit precursor
suggested_questions:
- question: 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.
- question: 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)?
suggested_experiments:
- description: 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.
experiment_type: gene knockout / conditional knockdown
- description: 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.
experiment_type: fluorescence microscopy