Affinage

RPL31

Large ribosomal subunit protein eL31 · UniProt P62899

Length
125 aa
Mass
14.5 kDa
Annotated
2026-06-10
42 papers in source corpus 8 papers cited in narrative 8 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 4/4 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RPL31 (eL31/L31) is a structural protein of the 60S large ribosomal subunit, first purified from native ribosomes (PMID:863909) and shown by cDNA cloning to be a ~14 kDa, 124-residue protein homologous to yeast ribosomal protein L34 (PMID:3816785). Within the ribosome it occupies the polypeptide tunnel exit, where it serves as a contact point for the ribosome-associated chaperone complex RAC (Zuo1/Ssz1); loss of Rpl31 produces translational fidelity defects and aminoglycoside sensitivity, and Rpl31 acts in a function shared with Rpl39 such that combined loss is lethal (PMID:18829863). Nucleolar and nuclear targeting of RPL31 depends on a C-terminal RLSRKR motif, with the tetrapeptide RLSR being the minimal critical determinant (PMID:8907615). Beyond its ribosomal role, RPL31 has extraribosomal, pro-proliferative activity: its depletion in prostate cancer cells stabilizes p53 and induces p21 and MDM2, arresting growth, with proliferation partly restored by concurrent p53 knockdown (PMID:25285958), and in colorectal cancer it drives proliferation, migration, and tumor growth through the downstream effector DEPDC1 (PMID:36309731).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1977 Medium

    Established RPL31 as a discrete physical constituent of the large ribosomal subunit rather than a co-purifying contaminant, defining the protein's basic identity.

    Evidence Biochemical purification from rat liver 60S subunits with SDS-PAGE and amino acid composition analysis

    PMID:863909

    Open questions at the time
    • No sequence or gene identity at this stage
    • Position within the subunit not defined
    • No functional assignment
  2. 1987 Medium

    Defined the primary structure and evolutionary relationship of the protein, providing the molecular basis to recognize it across species.

    Evidence cDNA cloning, nucleotide sequencing, and hybrid-selected translation of rat L31

    PMID:3816785

    Open questions at the time
    • Sequence alone does not establish function
    • No structural placement within the ribosome
    • Homology to yeast L34 inferred from sequence only
  3. 1996 High

    Resolved how RPL31 reaches its site of action by mapping a discrete C-terminal targeting motif required for nucleolar and nuclear localization.

    Evidence Immunocytochemistry of RPL31–β-galactosidase fusions with deletion and substitution mutants in COS-1 cells

    PMID:8907615

    Open questions at the time
    • Trans-acting import machinery recognizing RLSR not identified
    • Does not address ribosome-assembly role of nucleolar targeting
  4. 2008 High

    Placed RPL31 functionally at the polypeptide tunnel exit and tied it to translational fidelity and chaperone recruitment, moving from structural component to mechanistic player.

    Evidence Yeast genetics with double/triple deletions, epistasis, multicopy suppressor screen, aminoglycoside sensitivity, and translational fidelity assays

    PMID:18829863

    Open questions at the time
    • Molecular basis of the RAC contact not structurally resolved in this study
    • Relationship between Rpl31 and Rpl39 shared function mechanistically undefined
    • Conservation of tunnel-exit role to human RPL31 not directly tested here
  5. 2014 Medium

    Revealed an extraribosomal function by linking RPL31 to suppression of the p53 pathway and to cancer cell proliferation.

    Evidence shRNA/siRNA knockdown in prostate cancer cells with p53/p21/MDM2 western blots and a p53 co-knockdown rescue

    PMID:25285958

    Open questions at the time
    • Partial rescue indicates additional p53-independent effectors
    • Direct molecular mechanism of p53 destabilization not defined
    • Single cell-type context
  6. 2022 Medium

    Identified a downstream effector, placing RPL31 upstream of DEPDC1 in driving tumor growth.

    Evidence Knockdown/overexpression with proliferation/migration/apoptosis assays, xenografts, and double-knockdown epistasis in colorectal cancer cells

    PMID:36309731

    Open questions at the time
    • Mechanism by which RPL31 controls DEPDC1 expression unknown
    • Connection to ribosomal vs extraribosomal activity unresolved
  7. 2022 Low

    Linked RPL31 to RAS/MEK/ERK signaling in a regenerative context and identified miR-483-5p as an upstream regulator.

    Evidence miRNA overexpression with RPL31, p-MEK, p-ERK western blots and osteogenic differentiation assays in hBMSCs

    PMID:35248705

    Open questions at the time
    • No RPL31 rescue or mutagenesis confirming the RAS/MEK/ERK link is RPL31-specific
    • Correlative pathway readout only
    • Single lab
  8. 2023 Low

    Extended the pro-tumorigenic loss-of-function phenotype to gastric cancer with a tentative pathway assignment.

    Evidence Lentiviral shRNA knockdown with proliferation/apoptosis/migration assays and xenografts in gastric cancer lines

    PMID:36816257

    Open questions at the time
    • JAK-STAT placement described as preliminary analysis only
    • No mechanistic validation of the pathway link
    • Single lab

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RPL31's ribosomal tunnel-exit/RAC function mechanistically connects to its extraribosomal control of p53, DEPDC1, and downstream signaling remains unresolved.
  • No structural model of human RPL31 within the ribosome in the corpus
  • Direct biochemical mechanism for p53 destabilization undefined
  • Whether oncogenic effects depend on translation or are truly extraribosomal is untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 2
Localization
GO:0005840 ribosome 2 GO:0005634 nucleus 1 GO:0005730 nucleolus 1
Partners
RACRPL39
Complex memberships
60S large ribosomal subunit

Evidence

Reading pass · 8 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1977 RPL31 (L31) was purified as a protein component of the 60S large ribosomal subunit from rat liver ribosomes, with its molecular weight estimated by SDS-PAGE and amino acid composition determined. Ion exchange chromatography (carboxymethylcellulose), Sephadex gel filtration, SDS-PAGE, amino acid composition analysis The Journal of biological chemistry Medium 863909
1987 The primary structure of rat ribosomal protein L31 was determined from cloned cDNA: 124 amino acids, molecular mass ~14,331 Da, showing marked homology with yeast ribosomal protein L34. cDNA cloning, nucleotide sequencing, hybrid-selected translation European journal of biochemistry Medium 3816785
1996 Nucleolar localization of rat RPL31 is mediated by the amino acid sequence RLSRKR (residues 87–92) near the C-terminus; mutations at R87 prevented nucleolar localization, while mutations including R90 prevented both nuclear and nucleolar localization. The minimal critical sequence is the tetrapeptide RLSR. Immunocytochemistry of RPL31-β-galactosidase fusion proteins with deletion and substitution mutants transiently expressed in COS-1 cells European journal of cell biology High 8907615
2008 Yeast Rpl31 (encoded by RPL31a and RPL31b) is a contact point of the Ribosome-Associated Complex (RAC, consisting of Zuo1/Ssz1) at the polypeptide tunnel exit of the large ribosomal subunit. Loss of Rpl31 causes translational fidelity defects and sensitivity to aminoglycoside antibiotics. Rpl31 and RAC are functionally interdependent, whereas Rpl31 and Rpl39 independently affect a common ribosome function; combined deletion of RPL31a/b and RPL39 is lethal. RPL39 overexpression suppresses Δrpl31a/b growth defects but RAC overexpression does not. Yeast genetics (double and triple deletion mutants), growth assays, epistasis analysis, multicopy suppressor screen, aminoglycoside sensitivity assays, translational fidelity assays Molecular biology of the cell High 18829863
2014 RPL31 knockdown in human prostate cancer cells (LNCaP and bicalutamide-resistant BicR) increases p53 protein levels and its targets p21 and MDM2, decreases p53 degradation, and suppresses cell proliferation and cell-cycle progression. Partial rescue by p53 siRNA co-treatment indicates RPL31 promotes cancer cell growth at least partly via suppression of the p53 pathway. shRNA functional screen, siRNA knockdown, western blot (p53, p21, MDM2), cell proliferation and cell-cycle assays, p53 co-knockdown rescue experiment PloS one Medium 25285958
2022 Silencing of eL31 (RPL31) in colorectal cancer cells restricts proliferation, migration, and colony formation while enhancing apoptosis in vitro and impairs tumor growth in vivo (xenograft). DEPDC1 was identified as a downstream target of eL31; DEPDC1 depletion phenocopies eL31 knockdown, and DEPDC1 depletion reverses the pro-proliferative effects of eL31 overexpression, placing eL31 upstream of DEPDC1 in this pathway. siRNA/shRNA knockdown, overexpression, cell proliferation/migration/apoptosis assays, xenograft mouse model, epistasis by double knockdown rescue Journal of translational medicine Medium 36309731
2022 miR-483-5p inhibits osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) by directly targeting RPL31, reducing its expression. RPL31 activates the RAS/MEK/ERK signaling pathway; miR-483-5p overexpression reduces phosphorylated MEK and ERK levels, and this effect is mediated through RPL31 suppression. miRNA overexpression, western blot (RPL31, p-MEK, p-ERK), osteogenic differentiation assays, bioinformatics target prediction validated by cell experiments Cellular signalling Low 35248705
2023 RPL31 knockdown in gastric cancer cell lines (AGS and MGC-803) inhibits proliferation and migration and promotes apoptosis in vitro, and suppresses xenograft tumor growth in vivo. Preliminary analysis indicated RPL31 functions through the JAK-STAT signaling pathway. Lentiviral shRNA knockdown, cell proliferation/apoptosis/migration assays, xenograft mouse model, pathway analysis (JAK-STAT) Heliyon Low 36816257

Source papers

Stage 0 corpus · 42 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2004 Zinc is a key factor in controlling alternation of two types of L31 protein in the Bacillus subtilis ribosome. Molecular microbiology 118 15049826
2008 Ribosome-associated complex binds to ribosomes in close proximity of Rpl31 at the exit of the polypeptide tunnel in yeast. Molecular biology of the cell 71 18829863
1977 Isolation of eukaryotic ribosomal proteins. Purification and characterization of 60 S ribosomal subunit proteins L3, L6, L7', L8, L10, L15, L17, L18, L19, L23', L25, L27', L28, L29, L31, L32, L34, L35, L36, L36', and L37'. The Journal of biological chemistry 68 863909
2006 Liberation of zinc-containing L31 (RpmE) from ribosomes by its paralogous gene product, YtiA, in Bacillus subtilis. Journal of bacteriology 62 16547061
1989 Comparative analysis of proteins induced by heat shock, salinity, and osmotic stress in the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31. Journal of bacteriology 46 2504700
2008 Effects of redox potential and Ca2+ on the inositol 1,4,5-trisphosphate receptor L3-1 loop region: implications for receptor regulation. The Journal of biological chemistry 39 18635540
2011 Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli. Journal of inorganic biochemistry 35 22196016
2014 Short hairpin RNA library-based functional screening identified ribosomal protein L31 that modulates prostate cancer cell growth via p53 pathway. PloS one 31 25285958
1988 Complete amino acid sequences of the ribosomal proteins L25, L29 and L31 from the archaebacterium Halobacterium marismortui. European journal of biochemistry 30 3350019
1987 Nucleotide sequence of cloned cDNA specific for rat ribosomal protein L31. European journal of biochemistry 28 3816785
1978 Primary structure of Escherichia coli ribosomal protein L31. Biochemistry 28 339950
2014 Synthesis of ZnO nanoparticles using the cell extract of the cyanobacterium, Anabaena strain L31 and its conjugation with UV-B absorbing compound shinorine. Journal of photochemistry and photobiology. B, Biology 27 24911272
1996 Sequence requirement for nucleolar localization of rat ribosomal protein L31. European journal of cell biology 26 8907615
1999 Characterization of Escherichia coli 50S ribosomal protein L31. FEMS microbiology letters 24 10556732
2017 Ribosomal protein L31 in Escherichia coli contributes to ribosome subunit association and translation, whereas short L31 cleaved by protease 7 reduces both activities. Genes to cells : devoted to molecular & cellular mechanisms 22 28397381
2002 Differential expression of ribosomal L31, Zis, gas-5 and mitochondrial mRNAs following oxidant induction of proliferative vascular smooth muscle cell phenotypes. Atherosclerosis 21 11849648
1994 Phorbol ester induction of differentiation and apoptosis in the K562 cell line is accompanied by marked decreases in the stability of globin mRNAs and decreases in the steady state level of mRNAs encoding for ribosomal proteins L35, L31, L27, and L21. Cellular & molecular biology research 20 7804323
2020 YkgM and YkgO maintain translation by replacing their paralogs, zinc-binding ribosomal proteins L31 and L36, with identical activities. Genes to cells : devoted to molecular & cellular mechanisms 19 32559334
2005 Differential expression of the two kdp operons in the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31. Applied and environmental microbiology 18 16151117
2006 Proteomic study of the Bacillus subtilis ribosome: Finding of zinc-dependent replacement for ribosomal protein L31 paralogues. The Journal of general and applied microbiology 14 17310068
2004 MrpL36p, a highly diverged L31 ribosomal protein homolog with additional functional domains in Saccharomyces cerevisiae mitochondria. Genetics 12 15166137
2022 MicroRNA-483-5p inhibits osteogenic differentiation of human bone marrow mesenchymal stem cells by targeting the RPL31-mediated RAS/MEK/ERK signaling pathway. Cellular signalling 11 35248705
2022 Silencing eL31 suppresses the progression of colorectal cancer via targeting DEPDC1. Journal of translational medicine 11 36309731
2012 Expression, purification, and evaluation for anticancer activity of ribosomal protein L31 gene (RPL31) from the giant panda (Ailuropoda melanoleuca). Molecular biology reports 10 22714919
2022 Zur and zinc increase expression of E. coli ribosomal protein L31 through RNA-mediated repression of the repressor L31p. Nucleic acids research 9 36533433
2015 Induction and differential expression of certain novel proteins in Anabaena L31 under UV-B radiation stress. Frontiers in microbiology 9 25759687
1981 The gene for ribosomal protein L31, rpmE, is located at 88.5 minutes on the Escherichia coli chromosomal linkage map. Journal of bacteriology 8 7026537
2020 Autogenous regulation in vivo of the rpmE gene encoding ribosomal protein L31 (bL31), a key component of the protein-protein intersubunit bridge B1b. RNA (New York, N.Y.) 7 32209634
2005 An atypical KdpD homologue from the cyanobacterium Anabaena sp. strain L-31: cloning, in vivo expression, and interaction with Escherichia coli KdpD-CTD. Journal of bacteriology 7 15995207
2015 GroEL of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31 exhibits GroES and ATP-independent refolding activity. Journal of biochemistry 6 26449235
2014 Draft genome sequences and description of Lactobacillus rhamnosus strains L31, L34, and L35. Standards in genomic sciences 6 25197459
2008 Characterization of a response regulator protein that binds to Anabaena sp. strain L-31 kdp-promoter region. Archives of biochemistry and biophysics 6 18328254
1994 Mosquito ribosomal protein rpL31 resembles rat rpL34: cDNA and deduced amino acid sequence. Biochimica et biophysica acta 6 8049275
1980 Regulation of glutamine synthetase in the blue-green alga Anabaena L-31. Biochimica et biophysica acta 6 6108785
2023 Ribosomal protein L31 (RPL31) inhibits the proliferation and migration of gastric cancer cells. Heliyon 5 36816257
1994 A role for osmotic stress-induced proteins in the osmotolerance of a nitrogen-fixing cyanobacterium, Anabaena sp. strain L-31. Journal of bacteriology 5 8083182
2020 Comparison of transcriptional change of B. melitensis M5-90 after macrophage infection highlights the role of ribosome gene L31 in virulence. Veterinary microbiology 4 33373884
2019 Role of NS5A-L31/Y93 Double Wild-type in Failure of Glecaprevir/Pibrentasvir Double Therapy in Two Patients with a History of Direct-acting Antiviral Agent Failure: An Ultra-deep Sequencing Analysis. Internal medicine (Tokyo, Japan) 4 31178495
1993 Cloning and nucleotide sequence of the gene for dinitrogenase reductase (nifH) from the heterocyst-forming cyanobacterium Anabaena sp. L31. Biochimica et biophysica acta 4 8424961
1985 Modification of Escherichia coli ribosomes with the fluorescent reagent N-[[(iodoacetyl)amino]ethyl]-5-naphthylamine-1-sulfonic acid. Identification of derivatized L31' and studies on its intraribosomal properties. Biochemistry 4 3910100
2014 Antifibrotic activity of conjugates based on amphiphilic pluronic F68 and hydrophobic pluronic L31 with hyaluronate-endo-β-N-acetylhexosaminidase in pulmonary fibrosis. Bulletin of experimental biology and medicine 2 24906958
2024 [Structure and Evolution of DNA Transposons of the L31 Superfamily in Bivalves]. Molekuliarnaia biologiia 0 38943580

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