Affinage

KTI12

Protein KTI12 homolog · UniProt Q96EK9

Length
354 aa
Mass
38.6 kDa
Annotated
2026-04-28
26 papers in source corpus 14 papers cited in narrative 14 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

KTI12 encodes a conserved tRNA-dependent ATPase that functions as an essential regulatory cofactor of the Elongator complex, required for wobble uridine (U34) anticodon modification of tRNAs. Structurally resembling O-phosphoseryl-tRNA kinase (PSTK), KTI12 contains an N-terminal ATPase domain with a functionally critical P-loop motif and a C-terminal tRNA-binding domain; its C-terminal domain recruits tRNA and delivers it to Elongator for anticodon modification, while ATP hydrolysis by the N-terminal domain is essential for this function (PMID:30916349, PMID:40226916). KTI12 physically associates with Elongator as a regulatory rather than structural subunit and modulates the phosphorylation state of the Elongator subunit Elp1 through antagonistic interplay between casein kinase Hrr25 and the Sit4 phosphatase, with Elp1 phosphorylation at Ser-1198/Ser-1202 in turn regulating Kti12–Elongator interaction (PMID:14718557, PMID:19656297, PMID:25569479). This tRNA-dependent ATPase activity and Elongator association are conserved from yeast to humans (PMID:33417976).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 1994 Medium

    Identification of KTI12 as a gene required for sensitivity to K. lactis zymocin placed it in the intracellular pathway of the toxin's target, establishing its genetic existence and linkage to a defined cellular process.

    Evidence Screen for toxin-resistant mutants with complementation analysis and gene disruption in S. cerevisiae

    PMID:8065362

    Open questions at the time
    • Molecular function and protein product unknown
    • Relationship to Elongator not yet established
    • Single lab identification without independent replication at the time
  2. 2001 High

    The discovery that KTI12 physically associates with the Elongator complex and that its deletion phenocopies Elongator mutants established KTI12 as an Elongator-associated factor rather than an independent toxin-resistance gene.

    Evidence Co-immunoprecipitation, transposon tagging, and phenotypic analysis in S. cerevisiae

    PMID:11296232

    Open questions at the time
    • Whether Kti12 is a structural or regulatory Elongator subunit
    • Enzymatic activity of Kti12 unknown
  3. 2002 High

    Characterization of Kti12 as a regulatory rather than structural Elongator subunit, with an essential P-loop motif, established that Kti12 modulates Elongator function without being required for complex assembly.

    Evidence Reciprocal Co-IP, cell fractionation, P-loop mutagenesis, two-hybrid assays in S. cerevisiae

    PMID:11929532 PMID:12139626

    Open questions at the time
    • Nature of Kti12's enzymatic activity unknown despite P-loop identification
    • Mechanism by which Kti12 regulates Elongator unclear
  4. 2004 High

    Demonstration that Kti12 controls Elp1 phosphorylation state — with overproduction intensifying and absence abolishing phosphorylation — revealed a specific regulatory mechanism linking Kti12 to Elongator activity via the Sit4 phosphatase.

    Evidence Co-fractionation, phosphorylation analysis, genetic epistasis, and overexpression/deletion studies in S. cerevisiae

    PMID:14718557

    Open questions at the time
    • Identity of the kinase responsible for Elp1 phosphorylation not yet known
    • Whether Kti12 directly affects Sit4 or acts indirectly
  5. 2005 High

    Biochemical purification showed Kti12 is a monomeric protein forming a fragile complex with Elongator, and genome-wide ChIP revealed Elongator-independent chromatin association, separating Kti12's chromatin binding from its Elongator regulatory role.

    Evidence Purification to homogeneity, co-depletion, in vitro HAT assay (negative), genome-wide ChIP in S. cerevisiae

    PMID:15772087

    Open questions at the time
    • Functional significance of Elongator-independent chromatin binding unresolved
    • Direct enzymatic activity still unidentified
  6. 2008 High

    Identification that the FeS cluster in Elp3 is required for Kti12 binding to Elongator revealed a structural prerequisite for the Kti12–Elongator interaction at the molecular level.

    Evidence FeS cluster mutagenesis combined with TAP and Co-IP in S. cerevisiae

    PMID:18986986

    Open questions at the time
    • Whether Kti12 contacts Elp3 directly or the FeS cluster induces a conformational change
    • Structural basis of the interaction unknown
  7. 2009 High

    Discovery that casein kinase Hrr25 binds Elongator in a Kti12-dependent manner and mediates Elp1 phosphorylation completed the kinase-phosphatase circuit (Hrr25/Sit4/Kti12) controlling Elongator function.

    Evidence Co-IP, phosphorylation analysis, genetic epistasis, overexpression studies in S. cerevisiae

    PMID:19656297

    Open questions at the time
    • Whether Kti12 directly recruits Hrr25 or alters Elongator conformation to enable Hrr25 binding
    • Direct phosphorylation sites on Elp1 not yet mapped
  8. 2015 High

    Mapping of Hrr25 phosphosites on Elp1 (Ser-1198, Ser-1202) and showing that these sites regulate Kti12–Elongator interaction provided the first site-specific mechanism linking Elp1 phosphorylation to tRNA modification and Kti12 binding.

    Evidence In vivo phosphosite mapping, phosphomimetic/non-phosphorylatable mutagenesis, tRNA modification and Co-IP assays

    PMID:25569479

    Open questions at the time
    • How phosphorylation state mechanistically alters Kti12 binding affinity
    • Whether additional Elp1 phosphosites contribute
  9. 2019 High

    Crystal structure determination revealed Kti12 is a tRNA-dependent ATPase structurally homologous to PSTK, resolving the long-standing question of its enzymatic activity and establishing that ATP hydrolysis is required for Elongator-mediated tRNA modification.

    Evidence Crystal structure; in vitro ATPase assay; tRNA binding assays; Co-IP; in vivo tRNA modification assay; mutagenesis in S. cerevisiae

    PMID:30916349

    Open questions at the time
    • Substrate of ATP hydrolysis product unclear — whether Kti12 phosphotransfers or uses ATP hydrolysis conformationally
    • Structural basis of Kti12–Elongator interaction not resolved
  10. 2021 High

    Demonstration that human KTI12 interacts with Elongator as its primary partner and exhibits tRNA-dependent ATPase activity established functional conservation from yeast to humans and distinguished KTI12 from its structural homolog PSTK.

    Evidence Co-IP, BioID2 proximity labeling, in vitro ATPase assay in human cells

    PMID:33417976

    Open questions at the time
    • Whether human KTI12 regulates ELP1 phosphorylation analogously to yeast
    • Precise tRNA substrate specificity in human cells not fully defined
  11. 2025 High

    Mutagenesis of the C-terminal domain established that tRNA binding by this domain is essential for Kti12 recruitment to Elongator and for tRNA modification, supporting a model in which Kti12 acts as a tRNA carrier that delivers substrate tRNAs to the Elongator active site.

    Evidence Site-directed mutagenesis of conserved basic residues; in vitro tRNA binding; LC-MS tRNA modification assay; Co-IP; zymocin resistance in S. cerevisiae

    PMID:40226916

    Open questions at the time
    • Whether Kti12 discriminates among tRNA species or delivers all Elongator substrates equally
    • Structural model of the Kti12–tRNA–Elongator ternary complex not yet available

Open questions

Synthesis pass · forward-looking unresolved questions
  • The precise mechanistic role of ATP hydrolysis by Kti12 — whether it drives a phosphotransfer reaction, a conformational change for tRNA release, or another catalytic step — remains unknown, as does the structure of the Kti12–Elongator–tRNA ternary complex.
  • No structural model of the Kti12–Elongator–tRNA ternary complex
  • Product of ATP hydrolysis (ADP vs. phosphotransfer) not determined
  • Whether Kti12 has substrates beyond tRNA in vivo is untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 4 GO:0003723 RNA binding 3 GO:0140657 ATP-dependent activity 3
Localization
GO:0005634 nucleus 2 GO:0005694 chromosome 2
Pathway
R-HSA-8953854 Metabolism of RNA 3
Partners
ELP1ELP2ELP3HRR25KTI11SIT4
Complex memberships
Elongator complex (regulatory/accessory association)

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 KTI12 was identified as a gene whose loss-of-function or elevated copy number both confer resistance to K. lactis toxin (zymocin), placing KTI12 in the pathway of the toxin's intracellular target in S. cerevisiae. Comprehensive screen for toxin-resistant mutants; complementation analysis; gene disruption Molecular and cellular biology Medium 8065362
2001 KTI12 (TOT4) was identified as a component that physically associates with the Elongator complex of RNA polymerase II holoenzyme, and loss of KTI12 confers resistance to K. lactis zymocin and phenocopies Elongator deletion phenotypes (caffeine and Calcofluor White sensitivity, G1 delay). mTn3 transposon tagging; co-immunoprecipitation; phenotypic analysis The EMBO journal High 11296232
2002 Tot4p/Kti12p co-immunoprecipitates with Elongator and co-migrates with RNA polymerase II and Elongator in cell fractionation; its deletion or overexpression does not disrupt Elongator subunit interactions, indicating Kti12 is a regulatory rather than structural Elongator subunit. A conserved P-loop motif is required for biological activity. Co-immunoprecipitation; cell fractionation; P-loop deletion mutagenesis; overexpression from GAL10 promoter Molecular microbiology High 11929532
2002 Kti12p (Tot4p) interacts with Elongator subunits Tot2 and Tot3 (Elp2, Elp3) in two-hybrid assays, and also interacts with Cdc19p (pyruvate kinase), suggesting a role in coordinating cell growth with carbon metabolism. Kti12p can be chromatin-immunoprecipitated at the ADH1 promoter. Two-hybrid analysis; chromatin immunoprecipitation Molecular microbiology Medium 12139626
2004 Kti12 (Tot4) regulates phosphorylation of Elongator's largest subunit Elp1 (Tot1): overproduction of Kti12 intensifies Elp1 phosphorylation, while its absence abolishes it. Kti12, Sit4 phosphatase, and Elp1 co-fractionate, and Sit4 and Kti12 physically compete to control Elp1 de-/phosphorylation, which is required for toxin-target (G1 block) capacity. Co-fractionation; phosphorylation analysis; genetic epistasis; overexpression and deletion studies Molecular biology of the cell High 14718557
2005 Native Kti12 purified to homogeneity is a single polypeptide that forms a fragile complex with Elongator under physiological salt conditions; depletion of Kti12 from yeast extract co-depletes Elongator. Purified Kti12 does not affect Elongator histone acetyltransferase activity in vitro. Kti12 associates with chromatin genome-wide even in non-transcribed regions and in the absence of Elongator. Biochemical purification; co-depletion; in vitro HAT assay; chromatin immunoprecipitation; RNA immunoprecipitation The Journal of biological chemistry High 15772087
2008 A functional iron-sulfur (FeS) cluster in Elongator subunit Elp3 is required for the association of the complex with its accessory factors Kti11 and Kti12; FeS cluster mutations disrupt Kti12 binding to Elongator without affecting Elongator-RNA polymerase II chromatin association. Tandem affinity purification; FeS cluster mutagenesis; co-immunoprecipitation The Journal of biological chemistry High 18986986
2009 Casein kinase Hrr25 binds to Elongator in a manner dependent on Kti12; Hrr25 binding to Elongator is enhanced in kti12 overexpression conditions. Kti12 overexpression triggers Elp1 hyperphosphorylation, an effect blocked by hrr25 mutations. This indicates Kti12 indirectly affects Elp1 phosphorylation through controlling Sit4-dependent dephosphorylation. Co-immunoprecipitation; phosphorylation analysis; genetic epistasis; overexpression studies Molecular microbiology High 19656297
2015 Phosphorylation of Elp1 by Hrr25 at Ser-1198 and Ser-1202 plays a positive role in Elongator tRNA modification function and regulates the interaction of Elongator with its accessory protein Kti12, as shown by phosphomimetic and non-phosphorylatable substitutions. In vivo phosphosite mapping; alanine/phosphomimetic substitution; tRNA modification assay; co-immunoprecipitation PLoS genetics High 25569479
2017 Kti12 motifs including the P-loop (nucleotide-binding) and conserved regions are directly required for Elongator interaction and for tRNA modification activity (wobble U34); mutations in these motifs that disrupt Elongator interaction correlate with loss of U34 modification and phenotypes identical to Elongator loss. Zymocin resistance screen; site-directed mutagenesis; tRNA modification assays (nonsense/missense suppression); co-immunoprecipitation Toxins High 28872616
2019 Kti12 is a tRNA-dependent ATPase with a crystal structure revealing striking similarity to O-phosphoseryl-tRNA kinase (PSTK); it employs a similar mechanism of tRNA binding and shows tRNASec-dependent ATPase activity. Kti12 binds directly to Elongator, and ATP hydrolysis by Kti12 is crucial for Elongator to maintain proper tRNA anticodon modification (wobble U34) in vivo. Crystal structure determination; in vitro ATPase assay; tRNA-binding assays; Co-IP; in vivo tRNA modification assay; mutagenesis Nucleic acids research High 30916349
2020 Fungal Kti12 proteins contain an N-terminal ATPase domain and a C-terminal tRNA-binding domain connected by a flexible linker. A naturally occurring K14L substitution in the Walker A motif lowers ATP affinity but does not abolish catalytic activity at high ATP concentrations, demonstrating that the Walker A motif is functionally flexible. In vitro ATPase assay; complementation assay in yeast; sequence analysis Current genetics Medium 32236652
2021 Human KTI12 protein interacts with Elongator as its main partner in human cells, with additional interactions identified with proteins involved in vesicular transport, RNA metabolism, and deubiquitination. Human KTI12 and PSTK do not share interactors and do not influence each other's biological functions. Human KTI12 shows tRNA-dependent ATPase activity similar to yeast Kti12. Co-IP; BioID2 proximity labeling; in vitro ATPase assay with tRNA substrates; functional assays in human cells Biochimica et biophysica acta. Molecular cell research High 33417976
2025 The C-terminal domain of Kti12 is essential for tRNA binding in vitro; mutations of conserved basic residues in this domain progressively abolish tRNA binding, drastically reduce Elongator-dependent tRNA anticodon modifications in vivo, and reduce Kti12's ability to interact with Elongator. Elongator-unbound pools of Kti12 can be distinguished from Elongator-bound pools in a tRNA-dependent manner, suggesting Kti12 acts as a tRNA carrier that recruits tRNA to Elongator for anticodon modification. Site-directed mutagenesis; in vitro tRNA binding assay; in vivo tRNA modification assay (LC-MS); co-immunoprecipitation; zymocin resistance assay Nucleic acids research High 40226916

Source papers

Stage 0 corpus · 26 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2001 Saccharomyces cerevisiae Elongator mutations confer resistance to the Kluyveromyces lactis zymocin. The EMBO journal 373 11296232
1994 Two Saccharomyces cerevisiae genes which control sensitivity to G1 arrest induced by Kluyveromyces lactis toxin. Molecular and cellular biology 73 8065362
2003 DRL1, a homolog of the yeast TOT4/KTI12 protein, has a function in meristem activity and organ growth in plants. The Plant cell 68 12615938
2002 Molecular analysis of KTI12/TOT4, a Saccharomyces cerevisiae gene required for Kluyveromyces lactis zymocin action. Molecular microbiology 55 11929532
2004 The yeast elongator histone acetylase requires Sit4-dependent dephosphorylation for toxin-target capacity. Molecular biology of the cell 53 14718557
2009 Elongator function depends on antagonistic regulation by casein kinase Hrr25 and protein phosphatase Sit4. Molecular microbiology 49 19656297
2008 An iron-sulfur cluster domain in Elp3 important for the structural integrity of elongator. The Journal of biological chemistry 47 18986986
2015 Phosphorylation of Elp1 by Hrr25 is required for elongator-dependent tRNA modification in yeast. PLoS genetics 41 25569479
1989 Soybean Seed Protein Genes Are Regulated Spatially during Embryogenesis. The Plant cell 41 12359887
2002 Protein interactions within Saccharomyces cerevisiae Elongator, a complex essential for Kluyveromyces lactis zymocicity. Molecular microbiology 32 12139626
2005 Physical and functional interaction between Elongator and the chromatin-associated Kti12 protein. The Journal of biological chemistry 31 15772087
2014 Loss of wobble uridine modification in tRNA anticodons interferes with TOR pathway signaling. Microbial cell (Graz, Austria) 27 28357221
2019 Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator. Nucleic acids research 24 30916349
2017 Use of a Yeast tRNase Killer Toxin to Diagnose Kti12 Motifs Required for tRNA Modification by Elongator. Toxins 17 28872616
2014 Comparative analysis of the conserved functions of Arabidopsis DRL1 and yeast KTI12. Molecules and cells 9 25518926
2022 Overexpression of GhKTI12 Enhances Seed Yield and Biomass Production in Nicotiana Tabacum. Genes 8 35327981
2020 PtKTI12 genes influence wobble uridine modifications and drought stress tolerance in hybrid poplar. Tree physiology 8 32705117
2020 Identification of Novel Potential Type 2 Diabetes Genes Mediating β-Cell Loss and Hyperglycemia Using Positional Cloning. Frontiers in genetics 8 33133152
2013 A novel Sit4 phosphatase complex is involved in the response to ceramide stress in yeast. Oxidative medicine and cellular longevity 6 24082981
2022 AtELP4 a subunit of the Elongator complex in Arabidopsis, mediates cell proliferation and dorsoventral polarity during leaf morphogenesis. Frontiers in plant science 5 36340367
2017 The Elongator complex-associated protein DRL1 plays a positive role in immune responses against necrotrophic fungal pathogens in Arabidopsis. Molecular plant pathology 5 27868335
2020 Fungal Kti12 proteins display unusual linker regions and unique ATPase p-loops. Current genetics 4 32236652
2014 Inflammatory markers, oxidative stress, and antioxidant capacity in healthy allo-HSCT donors during hematopoietic stem cell mobilization. Journal of clinical apheresis 4 25270291
2021 Same but different - Molecular comparison of human KTI12 and PSTK. Biochimica et biophysica acta. Molecular cell research 3 33417976
2025 tRNA binding to Kti12 is crucial for wobble uridine modification by Elongator. Nucleic acids research 2 40226916
2026 ZmDRL1 regulates maize leaf angle via phytohormone signaling. Plant cell reports 0 42012545