Affinage

MAK16

Protein MAK16 homolog · UniProt Q9BXY0

Length
300 aa
Mass
35.4 kDa
Annotated
2026-06-10
25 papers in source corpus 8 papers cited in narrative 8 extracted findings
Cross-family judge faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

MAK16 is an essential, conserved nucleolar protein required for biogenesis of the large (60S) ribosomal subunit (PMID:7739558, PMID:10838225). Within early nucleolar pre-60S intermediates it acts as a component of the Nsa1-Rrp1-Rpf1-Mak16 module that stabilizes the solvent face of the assembling subunit, with cryo-EM placing it at defined states of the sequential rRNA folding pathway (PMID:29245012); an equivalent human pre-ribosomal module (WDR74-RPF1-MAK16-RRP1) couples to the RNA helicase MTR4 and is collectively required for accurate pre-rRNA cleavage during 60S biogenesis (PMID:39706051). Functionally, Mak16 is needed for stability of the 27SB pre-rRNA and hence for maturation of mature 25S and 5.8S rRNAs, and its proper release from the pre-60S particle is governed by upstream factors such as eIF4G1 (PMID:16710831, PMID:35615984). Mak16 harbors a redox-active [4Fe-4S]2+/1+ cluster (midpoint potential below -500 mV) that is essential for its stability and for its interaction with the partner Rpf1; oxidative stress converts it to a [3Fe-4S]1+ form, destabilizes the protein, disrupts the Mak16-Rpf1 complex, and reduces 25S rRNA, linking 60S assembly to cellular redox status (PMID:41231949). Loss of MAK16 function causes G1 cell cycle arrest, consistent with the dependence of proliferation on adequate 60S subunit supply (PMID:3045810, PMID:7739558).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1988 Medium

    Established that MAK16 encodes a nuclear protein whose loss blocks cell cycle progression, first linking the gene to proliferation control.

    Evidence Subcellular fractionation of MAK16-LacZ fusions and G1-arrest phenotyping of a temperature-sensitive mak16-1 mutant in yeast

    PMID:3045810

    Open questions at the time
    • Molecular basis of the G1 arrest not defined
    • Nuclear localization shown but sub-nuclear (nucleolar) targeting not yet resolved
  2. 1995 Medium

    Connected the cell cycle phenotype to a concrete molecular defect by showing MAK16 is required for the supply of free 60S ribosomal subunits.

    Evidence Sucrose gradient polysome profiling of mak16 mutants with genetic complementation in yeast

    PMID:7739558

    Open questions at the time
    • Step in 60S biogenesis affected not identified
    • Direct molecular role of the protein unknown
  3. 2000 Medium

    Refined the localization to the nucleolus and showed this targeting is conserved across species, consistent with a ribosome biogenesis role.

    Evidence GFP-fusion imaging of MAK16 homologs in COS-7 cells plus in vitro CK2 phosphorylation assay

    PMID:10838225

    Open questions at the time
    • Functional significance of CK2 phosphorylation untested in vivo
    • Mechanism of nucleolar function not addressed
  4. 2006 Medium

    Pinpointed the rRNA-processing step by showing Mak16 is required for 27SB pre-rRNA stability and downstream 25S/5.8S maturation, and that mere pre-ribosome association is insufficient for function.

    Evidence Northern blot of rRNA intermediates and gradient fractionation in temperature-sensitive mak16-1 yeast

    PMID:16710831

    Open questions at the time
    • How Mak16 promotes 27SB stability mechanistically unresolved
    • Direct partners within the pre-60S particle not defined
  5. 2017 High

    Provided the structural framework by placing Mak16 in the Nsa1-Rrp1-Rpf1-Mak16 module stabilizing the solvent face of early nucleolar pre-60S intermediates.

    Evidence Cryo-EM of purified early 60S biogenesis intermediates at 3.3-4.5 A from S. cerevisiae

    PMID:29245012

    Open questions at the time
    • Dynamics of module assembly/release not captured
    • Functional consequence of contacts not perturbed in structures
  6. 2022 Medium

    Positioned Mak16 within an ordered maturation pathway by showing eIF4G1 loss causes aberrant retention of Mak16 on pre-60S and impairs PET maturation and 27S processing.

    Evidence Mass spectrometry of purified pre-60S complexes from eIF4G1-deletion yeast with genetic interaction analysis

    PMID:35615984

    Open questions at the time
    • Direct vs. indirect role of eIF4G1 in Mak16 release unclear
    • Mechanism coupling Mak16 retention to PET defects not defined
  7. 2024 Medium

    Demonstrated conservation of the module in human cells and its functional coupling to the MTR4 helicase, with mutual interdependence of WDR74-RPF1-MAK16-RRP1 for pre-rRNA cleavage.

    Evidence Co-immunoprecipitation/mass spectrometry and functional knockdown with pre-rRNA processing readout in human cells

    PMID:39706051

    Open questions at the time
    • Architecture of the human module relative to yeast not structurally resolved
    • Direct vs. bridged contacts with MTR4 not mapped
  8. 2025 High

    Revealed a chemical cofactor basis for Mak16 function: a redox-active [4Fe-4S] cluster required for protein stability and Rpf1 binding, providing a mechanism linking ribosome assembly to redox state.

    Evidence EPR/electrochemistry of reconstituted cluster, in vivo H2O2 treatment, coordination-residue mutagenesis, Mak16-Rpf1 co-IP, and Northern blot for 25S in yeast and human Mak16

    PMID:41231949

    Open questions at the time
    • Physiological redox conditions that toggle the cluster in vivo not defined
    • Whether cluster loss is reversible/regulated remains open
    • Structural basis of cluster-dependent Rpf1 interaction not resolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How redox-driven Mak16 cluster status is integrated with the broader pre-60S maturation timeline to regulate ribosome output under stress remains unresolved.
  • No quantitative link between cluster oxidation and cell-cycle/proliferation phenotypes
  • Upstream Fe/S assembly machinery for Mak16 not identified in the corpus

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 2
Localization
GO:0005634 nucleus 1 GO:0005730 nucleolus 1
Pathway
R-HSA-8953854 Metabolism of RNA 3 R-HSA-1852241 Organelle biogenesis and maintenance 1
Partners
MTR4NSA1RPF1RRP1WDR74
Complex memberships
66S/pre-60S pre-ribosomal particleNsa1-Rrp1-Rpf1-Mak16 pre-60S moduleWDR74-RPF1-MAK16-RRP1 module

Evidence

Reading pass · 8 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1988 MAK16 encodes a 306-amino acid nuclear protein (Mr 35,694) with two nuclear localization signal sequences; MAK16-LacZ fusion proteins containing one NLS entered the nucleus as determined by subcellular fractionation, while unfused beta-galactosidase did not. Loss-of-function (mak16-1) causes G1 arrest at non-permissive temperature, with cells remaining mating competent, placing MAK16 function in G1 cell cycle progression. Subcellular fractionation of MAK16-LacZ fusion proteins; cell cycle staging by mating competence assay; DNA sequencing to identify NLS motifs Proceedings of the National Academy of Sciences of the United States of America Medium 3045810
1995 mak16 mutants have decreased free 60S ribosomal subunits, as shown by polysome profile analysis; supplying the normal MAK16 gene restored free 60S subunit levels, L-A copy number, and L-A coat protein to wild-type levels, establishing that MAK16 function is required for 60S ribosomal subunit supply. Sucrose gradient polysome profiling; complementation with single-copy MAK16 gene Molecular and cellular biology Medium 7739558
2000 The Schistosoma mansoni MAK16 homolog (SmMAK16) is phosphorylated in vitro by human protein kinase CK2. GFP fusions of SmMAK16 localize exclusively to nucleoli (not nuclei) in COS-7 cells, and the yeast and C. elegans homologs similarly direct nucleolar accumulation, establishing nucleolar targeting as a conserved feature of MAK16 family proteins and suggesting a role in 60S subunit biogenesis. In vitro phosphorylation assay with recombinant CK2; transient transfection of GFP fusion constructs in COS-7 cells; fluorescence microscopy Molecular and biochemical parasitology Medium 10838225
2006 Mak16p is required for the stability of the 27SB precursor rRNA in S. cerevisiae: at non-permissive temperature, mak16-1 cells show a dramatic decrease in 27SB pre-rRNA levels, leading to loss of mature 25S and 5.8S rRNAs, while 18S and 5S are only moderately affected. The mutant Mak16-1p protein was still associated with the 66S pre-ribosomal complex, indicating that mere association with the 66S pre-RNP is insufficient for function. Northern blot analysis of rRNA processing intermediates in temperature-sensitive mak16-1 yeast; sucrose density gradient fractionation Yeast (Chichester, England) Medium 16710831
2017 Cryo-EM structures of early nucleolar 60S biogenesis intermediates at 3.3–4.5 Å resolution reveal that Mak16 functions as part of the Nsa1-Rrp1-Rpf1-Mak16 module, which stabilizes the solvent side of the 60S subunit during early nucleolar pre-60S assembly. The structural snapshots show Mak16 mapped to specific assembly states in the sequential folding pathway. Cryo-electron microscopy (cryo-EM) of purified early 60S biogenesis intermediates from S. cerevisiae; structural modeling at 3.3–4.5 Å resolution Cell High 29245012
2022 Deletion of eIF4G1 in S. cerevisiae causes abnormal retention of Mak16 (along with Ssf1, Rrp15, Rrp14) on the pre-60S complex, impairing polypeptide exit tunnel (PET) maturation and 27S processing, placing Mak16 in a pathway downstream of eIF4G1 during pre-60S maturation. Mass spectrometry of purified pre-60S complexes from eIF4G1 deletion yeast; genetic interaction analysis Journal of cell science Medium 35615984
2024 In human cells, MAK16 functions as part of a pre-ribosomal WDR74 module (comprising WDR74, RPF1, MAK16, and RRP1) identified by co-immunoprecipitation coupled with mass spectrometry. Each component of this module is mutually required for interaction of other members with the RNA helicase MTR4, and all components are required for accurate cleavage of pre-rRNA during 60S biogenesis. Co-immunoprecipitation combined with mass spectrometry; functional knockdown experiments monitoring pre-rRNA processing Biochemical and biophysical research communications Medium 39706051
2025 Mak16 (yeast and human) contains a redox-active [4Fe-4S]2+/1+ cluster with midpoint potential below -500 mV, identified by both in vivo and in vitro methods. Oxidative stress (H2O2) causes [3Fe-4S]1+ cluster formation, destabilizes Mak16, and disrupts its interaction with Rpf1 in vivo. Disruption of Fe/S cluster coordination by mutagenesis destabilized Mak16, impaired Mak16-Rpf1 complex formation, and decreased 25S rRNA levels, establishing the Fe/S cluster as essential for Mak16 function in 60S ribosome biogenesis and as a potential sensor for redox imbalance. In vitro Fe/S cluster characterization (EPR spectroscopy, electrochemistry); in vivo H2O2 treatment; mutagenesis of Fe/S cluster coordination residues; co-immunoprecipitation of Mak16-Rpf1 complex; Northern blot for 25S rRNA levels Proceedings of the National Academy of Sciences of the United States of America High 41231949

Source papers

Stage 0 corpus · 25 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2017 Visualizing the Assembly Pathway of Nucleolar Pre-60S Ribosomes. Cell 157 29245012
1996 Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription. Molecular and cellular biology 122 8552095
1995 Yeast virus propagation depends critically on free 60S ribosomal subunit concentration. Molecular and cellular biology 94 7739558
1980 "Superkiller" mutations suppress chromosomal mutations affecting double-stranded RNA killer plasmid replication in saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 64 6987655
2005 Glutathione transferase-like proteins encoded in genomes of yeasts and fungi: insights into evolution of a multifunctional protein superfamily. FEMS microbiology letters 57 15621414
1987 Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: isolation of the MAK16 gene and analysis of an adjacent gene essential for growth at low temperatures. Yeast (Chichester, England) 57 3332963
1979 Mak mutants of yeast: mapping and characterization. Journal of bacteriology 55 387719
1984 Temperature-sensitive lethal mutations on yeast chromosome I appear to define only a small number of genes. Genetics 52 6383953
1994 Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: analysis of the genes in the FUN38-MAK16-SPO7 region. Journal of bacteriology 35 8144453
1988 Host function of MAK16: G1 arrest by a mak16 mutant of Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences of the United States of America 32 3045810
2020 Integrated analysis of RNA-binding proteins in human colorectal cancer. World journal of surgical oncology 26 32828126
2019 Adaptation to Extreme Environments in an Admixed Human Population from the Atacama Desert. Genome biology and evolution 15 31384924
2006 Mak16p is required for the maturation of 25S and 5.8S rRNAs in the yeast Saccharomyces cerevisiae. Yeast (Chichester, England) 13 16710831
2000 SmMAK16, the Schistosoma mansoni homologue of MAK16 from yeast, targets protein transport to the nucleolus. Molecular and biochemical parasitology 12 10838225
2024 Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals. iScience 4 38433915
2024 Pre-ribosomal WDR74 module coordinates the early and late pre-rRNA processing stages for the NVL2-mediated regulation of 60S ribosome biogenesis. Biochemical and biophysical research communications 3 39706051
2022 Translation initiation factor eIF4G1 modulates assembly of the polypeptide exit tunnel region in yeast ribosome biogenesis. Journal of cell science 3 35615984
2016 Bacterial versus human sphingosine-1-phosphate lyase (S1PL) in the design of potential S1PL inhibitors. Bioorganic & medicinal chemistry 3 27475537
2014 The MAK16 gene of Entamoeba histolytica and its identification in isolates from patients. The Korean journal of parasitology 3 25246723
1986 Molecular characterization of chromosomal genes affecting double-stranded RNA replication in Saccharomyces cerevisiae. Basic life sciences 2 3551912
2026 Translational hub ribosomal protein S5 promotes glioblastoma progression by affecting translation patterns. International journal of biological macromolecules 0 42103131
2025 Multi-Omics and Clinical Validation Identify Key Glycolysis- and Immune-Related Genes in Sepsis. International journal of general medicine 0 40927774
2025 Combined bioinformatics and experimental validation identifies m1A-modified genes as potential diagnostic biomarkers in periodontitis and diabetes. Archives of oral biology 0 41106306
2025 The function of Mak16 in ribosome biogenesis depends on its [4Fe-4S] cluster. Proceedings of the National Academy of Sciences of the United States of America 0 41231949
2024 Identification of two transcription factors that work coordinately to regulate early development in Entamoeba. mBio 0 39540742

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