Affinage

NIFK

MKI67 FHA domain-interacting nucleolar phosphoprotein · UniProt Q9BYG3

Length
293 aa
Mass
34.2 kDa
Annotated
2026-06-10
21 papers in source corpus 7 papers cited in narrative 7 extracted findings
Cross-family judge faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

NIFK is a nucleolar RRM-containing protein that bridges ribosome biogenesis and cell proliferation, originally defined by its mitosis-specific, phosphorylation-dependent association with the FHA domain of the proliferation marker Ki-67 (PMID:11342549). This interaction is recognized through a phosphothreonine determinant in NIFK (pThr234-Pro235), with binding controlled by the phosphothreonine, its +1 to +3 residues, and an extended surface beyond the canonical FHA recognition motif (PMID:14659764); a fraction of NIFK co-localizes with phosphorylated Ki-67 at the periphery of mitotic chromosomes (PMID:11342549). In interphase, NIFK functions in rRNA maturation: its RRM binds the 5' region of ITS2 rRNA in a sequence- and structure-dependent manner to drive ITS1 cleavage and 28S/5.8S rRNA maturation, and loss of this activity triggers reversible p53-dependent G1 arrest via RPL5/RPL11-mediated nucleolar stress (PMID:25826659). Structural work on the yeast ortholog Nop15 shows that a flexible C-terminal α-helical region occludes the RRM RNA-binding surface in the free protein and, upon incorporation into the pre-ribosome, rearranges to expose that surface for stem-loop RNA contact while extending into new protein interactions (PMID:27789691). In cancer, NIFK supports Ki-67-dependent proliferation and promotes metastasis by downregulating CK1α through the transcription factor RUNX1, thereby activating pro-metastatic TCF4/β-catenin signaling (PMID:26984280), and supports colorectal cancer growth, lipogenesis, and survival through the c-MYC pathway (PMID:37950567).

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 2001 High

    Established NIFK as a physiological partner of the proliferation marker Ki-67, answering whether Ki-67's FHA domain has a defined cell-cycle-regulated ligand.

    Evidence In vitro binding from mitotic cells, yeast two-hybrid domain mapping, Xenopus egg extract binding, and immunofluorescence co-localization

    PMID:11342549

    Open questions at the time
    • Functional consequence of the Ki-67 interaction was not defined
    • Did not resolve the exact phospho-residue or kinase responsible
  2. 2004 High

    Defined the structural and chemical basis of Ki-67 FHA recognition of NIFK, refining the determinants beyond a simple phosphothreonine motif.

    Evidence NMR solution structure of the Ki-67 FHA domain and HSQC mapping of binding to an ~44-residue NIFK fragment

    PMID:14659764

    Open questions at the time
    • Used a short peptide fragment rather than full-length proteins
    • Kinase generating pThr234 not identified
  3. 2015 High

    Assigned NIFK a direct molecular role in ribosome biogenesis, showing its RRM is required for ITS2-dependent pre-rRNA processing and that its loss imposes a p53-dependent cell-cycle checkpoint.

    Evidence siRNA knockdown, RRM mutant complementation, rRNA processing and RNA-binding assays, cell cycle and p53 pathway analysis

    PMID:25826659

    Open questions at the time
    • Did not resolve how RRM engagement is coordinated within the assembling pre-ribosome
    • Relationship between rRNA function and the Ki-67 interaction unclear
  4. 2016 High

    Placed NIFK in a pro-tumorigenic signaling axis, showing it drives proliferation and metastasis by repressing CK1α via RUNX1 to release TCF4/β-catenin signaling.

    Evidence siRNA knockdown with CK1α double-knockdown epistasis rescue, migration/invasion assays, in vivo metastasis assay, transcriptional reporters

    PMID:26984280

    Open questions at the time
    • Mechanism connecting nucleolar/RRM function to CK1α regulation not established
    • Direct vs indirect control of RUNX1/CSNK1A1 not resolved
  5. 2017 High

    Revealed the conformational mechanism by which the ortholog Nop15 RRM is autoinhibited and activated within the pre-ribosome, explaining how RNA-binding is gated.

    Evidence X-ray crystallography (2.0 Å), SAXS, NMR, RNA-binding assays, and cryo-EM comparison of yeast Nop15

    PMID:27789691

    Open questions at the time
    • Conformational model derived from yeast ortholog, not human NIFK
    • Does not address regulation by the Ki-67 interaction
  6. 2023 Medium

    Extended NIFK's oncogenic role to colorectal cancer, linking its proliferative and lipogenic functions to the c-MYC pathway.

    Evidence siRNA knockdown with c-MYC overexpression rescue, gene set enrichment analysis, western blot

    PMID:37950567

    Open questions at the time
    • Direct molecular link between NIFK and c-MYC not defined
    • Whether lipogenic effects depend on rRNA function untested

Open questions

Synthesis pass · forward-looking unresolved questions
  • How NIFK's nucleolar rRNA-processing activity is mechanistically coupled to its mitotic Ki-67 interaction and to its downstream control of CK1α/β-catenin and c-MYC signaling remains unresolved.
  • No mechanism unifying ribosome biogenesis with cancer signaling outputs
  • Kinase generating pThr234 unidentified
  • No structure of human NIFK within the human pre-ribosome

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 2 GO:0140098 catalytic activity, acting on RNA 1
Localization
GO:0005694 chromosome 1 GO:0005730 nucleolus 1
Pathway
R-HSA-1640170 Cell Cycle 2 R-HSA-8953854 Metabolism of RNA 2
Partners
MKI67
Complex memberships
pre-ribosome

Evidence

Reading pass · 7 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2001 NIFK (hNIFK) was identified as a binding partner of the FHA domain of Ki-67 (pKi-67). The interaction is mitosis-specific and phosphorylation-dependent, requiring two threonine residues within residues 226–269 of hNIFK (Thr-234 and Thr-238). A moiety of hNIFK co-localizes with pKi-67 at the peripheral region of mitotic chromosomes. In vitro binding assay with mitotically arrested cells, yeast two-hybrid domain mapping, Xenopus egg extract binding assay, immunofluorescence co-localization The Journal of biological chemistry High 11342549
2004 NMR solution structure of the Ki-67 FHA domain was determined and its binding to an ~44-residue fragment of hNIFK was characterized. The pThr site recognized by Ki-67 FHA is pThr234-Pro235 of hNIFK. Three factors control the interaction: the phosphothreonine residue, +1 to +3 residues, and an extended binding surface beyond the canonical pTXX(D/I/L) motif. NMR solution structure determination, HSQC NMR binding surface mapping, structural analysis of FHA domain–hNIFK fragment complex Journal of molecular biology High 14659764
2015 NIFK is required for rRNA maturation via its RNA recognition motif (RRM). Silencing NIFK impairs cleavage of internal transcribed spacer (ITS) 1, leading to defective 28S and 5.8S rRNA maturation. The RRM of NIFK preferentially binds the 5'-region of ITS2 rRNA in a sequence- and secondary structure-dependent manner. NIFK knockdown causes reversible p53-dependent G1 arrest, possibly through RPL5/RPL11-mediated nucleolar stress. RNA-binding-deficient RRM mutants fail to rescue pre-rRNA processing or G1 progression. siRNA knockdown, RRM mutant complementation, rRNA processing assay, RNA-binding assay, cell cycle analysis, p53 pathway analysis RNA biology High 25826659
2016 NIFK promotes lung cancer cell proliferation in a Ki-67-dependent manner and promotes metastasis by downregulating casein kinase 1α (CK1α), a suppressor of pro-metastatic TCF4/β-catenin signaling. NIFK knockdown upregulates CK1α; silencing CK1α in NIFK-knockdown cells restores TCF4/β-catenin transcriptional activity, cell migration, and metastasis. RUNX1 was identified as a transcription factor of CSNK1A1 (CK1α) that is negatively regulated by NIFK. siRNA knockdown, rescue experiments (CK1α silencing in NIFK-knockdown cells), in vitro migration/invasion assays, in vivo metastasis assay, transcriptional reporter assays eLife High 26984280
2017 Crystal structure of yeast Nop15 (ortholog of human NIFK) at 2.0 Å reveals a C-terminal α-helical region that occludes the canonical RNA-binding surface of the RRM. SAXS and NMR show the C-terminal residues are highly flexible but essential for tight RNA binding. In the pre-ribosome (cryo-EM structure), dramatic rearrangement of the C-terminal region exposes the RNA-binding surface to contact the base of a stem-loop RNA target and forms a newly extended α-helix that makes additional protein interactions. X-ray crystallography (2.0 Å), SAXS, NMR, RNA-binding assays, cryo-EM comparison Nucleic acids research High 27789691
2003 The nifk gene is widely expressed in adult mouse tissues beyond proliferating cells, and its mRNA is up-regulated in denervated hind limb skeletal muscle, suggesting functions beyond Ki-67 interaction. Differential display cloning, RT-PCR expression analysis in multiple tissues and denervated vs. innervated muscle Cell biology international Low 12798774
2023 NIFK silencing in colorectal cancer cells inhibits cell growth, reduces metastasis, promotes apoptosis, and decreases lipid accumulation and fatty acid synthesis via downregulation of lipogenic enzymes. These effects are mediated through the MYC pathway, as c-MYC overexpression rescues the phenotypes caused by NIFK silencing. siRNA knockdown, c-MYC overexpression rescue, gene set enrichment analysis, western blot Bioscience, biotechnology, and biochemistry Medium 37950567

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1987 Products of the iron-molybdenum cofactor-specific biosynthetic genes, nifE and nifN, are structurally homologous to the products of the nitrogenase molybdenum-iron protein genes, nifD and nifK. Journal of bacteriology 126 3470285
2018 Long non-coding RNA NIFK-AS1 inhibits M2 polarization of macrophages in endometrial cancer through targeting miR-146a. The international journal of biochemistry & cell biology 99 30176290
2000 Molecular evolution of nitrogen fixation: the evolutionary history of the nifD, nifK, nifE, and nifN genes. Journal of molecular evolution 96 10903367
2001 A novel nucleolar protein, NIFK, interacts with the forkhead associated domain of Ki-67 antigen in mitosis. The Journal of biological chemistry 63 11342549
2021 Upregulation of lncRNA NIFK-AS1 in hepatocellular carcinoma by m6A methylation promotes disease progression and sorafenib resistance. Human cell 62 34374933
2016 The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501. Proceedings of the National Academy of Sciences of the United States of America 48 27407147
2004 Structure of human Ki67 FHA domain and its binding to a phosphoprotein fragment from hNIFK reveal unique recognition sites and new views to the structural basis of FHA domain functions. Journal of molecular biology 45 14659764
2016 The nucleolar protein NIFK promotes cancer progression via CK1α/β-catenin in metastasis and Ki-67-dependent cell proliferation. eLife 39 26984280
1995 Assessing horizontal transfer of nifHDK genes in eubacteria: nucleotide sequence of nifK from Frankia strain HFPCcI3. Molecular biology and evolution 33 7877490
1987 Rhizobium meliloti nifN (fixF) gene is part of an operon regulated by a nifA-dependent promoter and codes for a polypeptide homologous to the nifK gene product. Journal of bacteriology 31 3316182
1992 Electrophoretic studies on the assembly of the nitrogenase molybdenum-iron protein from the Klebsiella pneumoniae nifD and nifK gene products. The Journal of biological chemistry 29 1429737
2010 Inferring the evolutionary history of Mo-dependent nitrogen fixation from phylogenetic studies of nifK and nifDK. Journal of molecular evolution 23 20640414
2015 The RNA recognition motif of NIFK is required for rRNA maturation during cell cycle progression. RNA biology 21 25826659
1987 A quantitative approach to sequence comparisons of nitrogenase MoFe protein alpha- and beta-subunits including the newly sequenced nifK gene from Klebsiella pneumoniae. The Biochemical journal 18 3322261
1998 Cloning and transcriptional analysis of the nifUHDK genes of Trichodesmium sp. IMS101 reveals stable nifD, nifDK and nifK transcripts. Microbiology (Reading, England) 11 9884228
2017 Structural analysis reveals the flexible C-terminus of Nop15 undergoes rearrangement to recognize a pre-ribosomal RNA folding intermediate. Nucleic acids research 9 27789691
2012 Increased transcription of NOP15, involved in ribosome biogenesis in Saccharomyces cerevisiae, enhances the production yield of RNA as a source of nucleotide seasoning. Journal of bioscience and bioengineering 9 22608550
1990 Analysis of Azotobacter vinelandii strains containing defined deletions in the nifD and nifK genes. Journal of bacteriology 5 2120192
2022 A novel biomarker NIFK-AS1 promotes hepatocellular carcinoma cell cycle progression through interaction with SRSF10. Journal of gastrointestinal oncology 4 36092356
2003 The nifk gene is widely expressed in mouse tissues and is up-regulated in denervated hind limb muscle. Cell biology international 3 12798774
2023 The nucleolar protein NIFK accelerates the progression of colorectal cancer via activating MYC pathway. Bioscience, biotechnology, and biochemistry 2 37950567

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