Affinage

SMYD5

Protein-lysine N-trimethyltransferase SMYD5 · UniProt Q6GMV2

Length
418 aa
Mass
47.3 kDa
Annotated
2026-04-28
21 papers in source corpus 14 papers cited in narrative 14 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SMYD5 is a SET-domain lysine methyltransferase that acts on both histone and non-histone substrates to regulate chromatin silencing, gene expression, and translation. At chromatin, SMYD5 trimethylates H4K20 at heterochromatin to silence endogenous retroelements and maintain genome stability in embryonic stem cells (PMID:28250819, PMID:28951459), and trimethylates H3K36 at gene promoters through RNA Polymerase II-dependent recruitment requiring its C-terminal glutamic acid-rich domain (PMID:35680905). The principal non-histone substrate of SMYD5 is the ribosomal protein RPL40, which it trimethylates at lysine 22 via a KXY recognition motif; loss of this modification causes ribosome collisions and reduced translation elongation (PMID:39048817, PMID:39103523, PMID:40184250). SMYD5 also methylates non-histone proteins PGC-1α and FoxO1, promoting their ubiquitin-dependent degradation to suppress mitochondrial biogenesis and modulate synoviocyte proliferation, respectively (PMID:35643234, PMID:40165083).

Mechanistic history

Synthesis pass · year-by-year structured walk · 7 steps
  1. 2016 Medium

    Establishing a developmental role: loss of Smyd5 in zebrafish expanded hematopoietic progenitor populations without affecting gross morphology, revealing that SMYD5 normally restrains hematopoiesis.

    Evidence Morpholino knockdown and CRISPR/Cas9 knockout in zebrafish with in situ hybridization for hematopoietic markers

    PMID:27377701

    Open questions at the time
    • Mechanism linking SMYD5 methyltransferase activity to hematopoietic gene repression not identified
    • Mammalian hematopoietic phenotype not tested
  2. 2017 High

    Identifying the first histone substrate: SMYD5 was shown to mediate H4K20me3 at heterochromatin in ES cells, and its depletion caused retroelement de-repression, chromosomal aberrations, and loss of self-renewal, establishing SMYD5 as a guardian of heterochromatin integrity.

    Evidence shRNA knockdown with ChIP-seq, western blot, cytogenetic analysis, and gene expression profiling in mouse ES cells

    PMID:28250819 PMID:28951459

    Open questions at the time
    • In vitro reconstitution of H4K20 methyltransferase activity by recombinant SMYD5 not demonstrated in these studies
    • Whether SMYD5 acts directly or recruits another methyltransferase for H4K20me3 was unresolved
  3. 2022 High

    Revealing a second histone mark: SMYD5 was found to catalyze H3K36me3 specifically at gene promoters (distinct from SETD2 at gene bodies), recruited by RNA Pol II and dependent on its C-terminal glutamic acid-rich domain, thereby expanding the substrate repertoire beyond H4K20.

    Evidence ChIP-seq, SMYD5 knockout cells with domain-truncation rescue, in vitro methyltransferase assay

    PMID:35680905

    Open questions at the time
    • Whether promoter H3K36me3 and heterochromatic H4K20me3 are regulated by the same or different SMYD5 complexes remains unclear
    • Structural basis for C-terminal domain requirement not determined
  4. 2022 High

    First non-histone substrate identified: SMYD5 methylates PGC-1α, promoting its ubiquitination and degradation, thereby attenuating mitochondrial biogenesis in intestinal epithelial cells — establishing SMYD5 as a regulator of metabolic programs through non-histone methylation.

    Evidence Co-immunoprecipitation, in vitro methylation with MS site identification, cycloheximide chase, conditional KO mouse, Seahorse respirometry

    PMID:35643234

    Open questions at the time
    • Specific lysine sites on PGC-1α and the E3 ligase mediating downstream ubiquitination not fully characterized
    • Whether this mechanism operates outside intestinal epithelium is unknown
  5. 2023 Medium

    Linking SMYD5 to viral transcription: SMYD5 binds HIV-1 TAR RNA and Tat protein, methylates Tat, and is required for HIV-1 transcription; reciprocally, Tat stabilizes SMYD5 via USP11, revealing a host-virus feedback loop.

    Evidence Co-immunoprecipitation, in vitro methylation, ChIP at HIV-1 promoter, shRNA knockdown in primary CD4+ T cells

    PMID:36897778

    Open questions at the time
    • Tat methylation site(s) and their functional consequence for Tat activity not determined
    • Whether SMYD5's role in HIV-1 transcription depends on its methyltransferase activity versus a scaffolding function is unresolved
    • Single-lab finding
  6. 2024 High

    Defining the principal non-histone substrate: three independent studies converged on RPL40 K22 as the primary SMYD5 substrate, showing that SMYD5-mediated RPL40K22me3 promotes translation elongation and that SMYD5 loss causes ribosome collisions and reduced polysome levels — repositioning SMYD5 as a central translational regulator.

    Evidence Biochemical proteomics, reconstituted in vitro methyltransferase assays with active-site mutagenesis, KO in K562 cells and mouse models, ribosome profiling, polysome profiling, KXY motif analysis

    PMID:39048817 PMID:39103523 PMID:40184250

    Open questions at the time
    • How RPL40K22me3 mechanistically prevents ribosome collisions at the structural level is unknown
    • Whether SMYD5 methylates additional ribosomal proteins or translation factors via the KXY motif is unexplored
    • Discrepancy between robust in vitro histone methylation in some studies and absence in others remains unresolved
  7. 2024 Medium

    Expanding non-histone substrates: SMYD5 methylates FoxO1, promoting its degradation and driving synoviocyte proliferation and inflammatory signaling in rheumatoid arthritis, paralleling the PGC-1α degradation mechanism.

    Evidence Co-immunoprecipitation, in vitro methylation, gain/loss-of-function in fibroblast-like synoviocytes, AAV-mediated knockdown in CIA mouse model

    PMID:40165083

    Open questions at the time
    • FoxO1 methylation site(s) not mapped
    • The E3 ligase linking FoxO1 methylation to ubiquitination is unidentified
    • Single-lab finding

Open questions

Synthesis pass · forward-looking unresolved questions
  • The central unresolved question is how SMYD5 partitions its activity between histone substrates (H4K20, H3K36) and non-histone substrates (RPL40, PGC-1α, FoxO1): whether these reflect distinct subcellular pools, regulatory states, or complex-dependent targeting remains unknown.
  • No structural model of SMYD5 with any substrate exists
  • Relative physiological contribution of histone versus RPL40 methylation to SMYD5-null phenotypes not dissected
  • No crystal structure of SMYD5-RPL40 complex to explain KXY motif recognition

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016740 transferase activity 9
Localization
GO:0005634 nucleus 5 GO:0005694 chromosome 2
Pathway
R-HSA-392499 Metabolism of proteins 5 R-HSA-4839726 Chromatin organization 4 R-HSA-74160 Gene expression (Transcription) 2
Partners
FOXO1PGC-1ΑRPL40USP11

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2017 SMYD5 mediates trimethylation of histone H4 lysine 20 (H4K20me3) at heterochromatin regions in embryonic stem cells; knockdown of SMYD5 leads to global decrease of H4K20me3 levels, redistribution of H3K9me3/2, G9a, and HP1α, and de-repression of endogenous retroelements, compromising ES cell self-renewal. shRNA knockdown, ChIP-seq, quantitative western blot, immunofluorescence Epigenetics & chromatin High 28250819
2017 SMYD5 maintains chromosome integrity by regulating H4K20me3 and H3K9me3 at heterochromatin; depletion of SMYD5 during ES cell differentiation causes chromosomal aberrations, de-repression of LTR and LINE repetitive elements, and formation of transformed cells with cancer-like expression signatures. shRNA knockdown, ChIP-seq, cytogenetic analysis, gene expression profiling Cancer research High 28951459
2022 SMYD5 catalyzes H3K36me3 at gene promoters (distinct from SETD2-mediated H3K36me3 at gene bodies); SMYD5 is recruited to chromatin by RNA Polymerase II, and its enzymatic activity requires its C-terminal glutamic acid-rich domain, as C-terminal truncation abolishes H3K36me3 restoration at promoters. ChIP-seq, SMYD5 knockout cells, domain-truncation overexpression rescue, in vitro methyltransferase assay Nature communications High 35680905
2022 SMYD5 physically interacts with PGC-1α (co-immunoprecipitation), mediates lysine methylation of PGC-1α (in vitro methylation assay + mass spectrometry identification of methylated lysines), and this methylation facilitates PGC-1α ubiquitination and proteasomal degradation, attenuating mitochondrial biogenesis and respiration in intestinal epithelial cells. Co-immunoprecipitation, in vitro methylation assay, mass spectrometry, cycloheximide chase assay, conditional knockout mouse model, Seahorse respirometry Cellular and molecular gastroenterology and hepatology High 35643234
2024 SMYD5 is the principal methyltransferase that trimethylates ribosomal protein RPL40 at lysine 22 (rpL40K22me3); this modification regulates mRNA translation output and ribosome elongation, as SMYD5 loss leads to increased ribosome collisions and reduced translation; identified by biochemical-proteomics strategy across diverse samples. Biochemical proteomics, in vitro methyltransferase assay, ribosome profiling, SMYD5 ablation in cell lines and mouse models, patient-derived xenograft Nature High 39048817
2024 SMYD5 catalyzes RPL40 K22me3 in vitro and in cells; loss of SMYD5 reduces translation output and causes ribosome elongation defects (increased ribosome collisions) and decreased polysome levels; SMYD5 requires a KXY motif for substrate recognition, and does not methylate histones in vitro. In vitro methyltransferase assay with recombinant SMYD5, active-site mutagenesis, SMYD5 knockout (K562 cells), mass spectrometry, polysome profiling, systematic motif analysis Cell research High 39103523
2025 SMYD5 trimethylates RPL40/eL40 at lysine 22 through recognition of a KXY motif; active-site mutations ablate this activity; SMYD5 KO causes complete loss of RPL40 K22me3 and decreased polysome levels; SMYD5 does not methylate histones in vitro, explaining its substrate specificity divergence from other SMYD family members. In vitro methyltransferase assay with recombinant SMYD5 and synthetic RPL40, active-site mutagenesis, SMYD5 KO (K562 cells), mass spectrometry, systematic motif scanning, polysome profiling Cell reports High 40184250
2023 SMYD5 binds the HIV-1 TAR element RNA and Tat protein, methylates Tat in vitro, associates with the HIV-1 promoter in vivo, and is required for HIV-1 transcription in CD4+ T cells; Tat expression increases SMYD5 protein levels via USP11-dependent stabilization. Co-immunoprecipitation, in vitro methylation assay, chromatin immunoprecipitation (ChIP), shRNA knockdown in cell lines and primary T cells, flow cytometry Cell reports Medium 36897778
2024 SMYD5 represses the MHR gene SP1 at euthermia; this repression correlates with temperature-dependent H3K36me3 levels at the SP1 locus; CRISPR screen identified SMYD5 as regulator of 37+ temperature-dependent genes, suggesting SMYD5-mediated H3K36me3 integrates temperature cues into gene expression. Forward CRISPR-Cas9 mutagenesis screen, ChIP-seq (H3K36me3), gene expression analysis Cell reports Medium 39083378
2016 Loss-of-function of Smyd5 in zebrafish (morpholino and CRISPR/Cas9) leads to increased expression of primitive and definitive hematopoietic markers (pu.1, mpx, l-plastin, cmyb), demonstrating a role for Smyd5 in hematopoiesis without affecting gross morphology, heart, or skeletal muscle development. Morpholino knockdown, CRISPR/Cas9 knockout in zebrafish, in situ hybridization for hematopoietic markers Scientific reports Medium 27377701
2021 SMYD5 physically interacts with protamine (a sperm chromatin-condensing protein); the C-terminal poly-glutamic acid tract and a 30-residue insertion in the MYND domain regulate SMYD5 structural stability, but protamine binding dominates stability and overrides these effects; interaction is SMYD5-specific (SMYD2 is destabilized by protamine). Thermal shift assay, machine learning stability screening (Silver Bullets Bio library), orthogonal partial least squares regression, biochemical binding assay Biochemical and biophysical research communications Low 33676231
2024 SMYD5 mediates methylation of FoxO1, leading to its ubiquitination and accelerated degradation, thereby promoting fibroblast-like synoviocyte (FLS) proliferation; SMYD5 also upregulates HK2 expression to promote lactate release and NF-κB activation in FLS, driving inflammatory responses in rheumatoid arthritis. Co-immunoprecipitation, in vitro methylation assay, loss-of-function/gain-of-function experiments in FLS, AAV-mediated knockdown in CIA mouse model, proteomic screening Cellular & molecular biology letters Medium 40165083
2024 SMYD5 knockdown in lung cancer cells increases SH2B3 expression by decreasing H4K20me3 levels at the SH2B3 locus, thereby inhibiting epithelial-mesenchymal transition, cell migration, and invasion. shRNA knockdown, ChIP (H4K20me3), cell migration/invasion assays, EMT marker analysis Molecules and cells Low 38723947
2025 SMYD5 interacts with BRD4 in hepatocellular carcinoma cells; knockdown of SMYD5 inhibits HCC cell proliferation and increases apoptosis, and the SMYD5-BRD4 interaction axis is proposed as a therapeutic target. Co-immunoprecipitation (SMYD5-BRD4 interaction), functional knockdown assays, bioinformatics analysis Pharmaceuticals (Basel, Switzerland) Low 40872497

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 The response regulator RRG-1 functions upstream of a mitogen-activated protein kinase pathway impacting asexual development, female fertility, osmotic stress, and fungicide resistance in Neurospora crassa. Molecular biology of the cell 80 17392518
2017 SMYD5 regulates H4K20me3-marked heterochromatin to safeguard ES cell self-renewal and prevent spurious differentiation. Epigenetics & chromatin 55 28250819
2022 SMYD5 catalyzes histone H3 lysine 36 trimethylation at promoters. Nature communications 37 35680905
2024 SMYD5 methylation of rpL40 links ribosomal output to gastric cancer. Nature 30 39048817
2017 SMYD5 Controls Heterochromatin and Chromosome Integrity during Embryonic Stem Cell Differentiation. Cancer research 30 28951459
2016 Smyd5 plays pivotal roles in both primitive and definitive hematopoiesis during zebrafish embryogenesis. Scientific reports 29 27377701
2022 Epithelial SMYD5 Exaggerates IBD by Down-regulating Mitochondrial Functions via Post-Translational Control of PGC-1α Stability. Cellular and molecular gastroenterology and hepatology 17 35643234
2023 The lysine methyltransferase SMYD5 amplifies HIV-1 transcription and is post-transcriptionally upregulated by Tat and USP11. Cell reports 14 36897778
2024 SMYD5 is a ribosomal methyltransferase that catalyzes RPL40 lysine methylation to enhance translation output and promote hepatocellular carcinoma. Cell research 13 39103523
2022 Unique SMYD5 Structure Revealed by AlphaFold Correlates with Its Functional Divergence. Biomolecules 11 35740908
2022 SMYD5 acts as a potential biomarker for hepatocellular carcinoma. Experimental cell research 9 35218722
2002 Glucose-inducible expression of rrg1+ in Schizosaccharomyces pombe: post-transcriptional regulation of mRNA stability mediated by the downstream region of the poly(A) site. Nucleic acids research 6 11861905
2024 Negative regulation of SH2B3 by SMYD5 controls epithelial-mesenchymal transition in lung cancer. Molecules and cells 5 38723947
2021 Sperm chromatin-condensing protamine enhances SMYD5 thermal stability. Biochemical and biophysical research communications 5 33676231
2024 SMYD5 is a regulator of the mild hypothermia response. Cell reports 2 39083378
2025 Novel regulation mechanism of histone methyltransferase SMYD5 in rheumatoid arthritis. Cellular & molecular biology letters 1 40165083
2023 A flow cytometry-based assay to investigate HIV-1 expression in SMYD5 shRNA containing primary CD4+ T cells. STAR protocols 1 37925635
2025 SMYD5 is a ribosomal methyltransferase that trimethylates RPL40 lysine 22 through recognition of a KXY motif. Cell reports 0 40184250
2025 SMYD5-BRD4 Interaction Drives Hepatocellular Carcinoma Progression: A Combined in Silico and Experimental Analysis. Pharmaceuticals (Basel, Switzerland) 0 40872497
2024 SMYD5 is a regulator of the mild hypothermia response. bioRxiv : the preprint server for biology 0 37333301
2002 A glucose-inducible gene in Schizosaccharomyces pombe, rrg1+, is involved in negative regulation of G2/M progression. Molecules and cells 0 12442907