Affinage

RTCB

RNA-splicing ligase RTCB · UniProt Q9Y3I0

Round 2 corrected
Length
505 aa
Mass
55.2 kDa
Annotated
2026-04-28
82 papers in source corpus 30 papers cited in narrative 30 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RTCB is the sole 3ʹ–5ʹ RNA ligase in metazoan cells, serving as the catalytic subunit of the tRNA ligase complex that joins RNA ends bearing 2ʹ,3ʹ-cyclic phosphate (or 3ʹ-phosphate) to 5ʹ-OH termini through a GTP- and Mn²⁺-dependent three-step mechanism: covalent guanylylation of an active-site histidine, transfer of GMP to the RNA 3ʹ-phosphate, and nucleophilic attack by the 5ʹ-OH to seal the backbone (PMID:22474365, PMID:22949672). This activity is essential both for maturation of intron-containing pre-tRNAs and for unconventional splicing of XBP1 mRNA during the ER-stress unfolded protein response, with nuclear versus cytoplasmic partitioning of RTCB—governed by Ashwin/FAM98B-containing versus FAM98A/C-containing complexes—directing these two functions, respectively (PMID:21311021, PMID:25087875, PMID:25378478). The cofactor Archease activates RTCB for multiple-turnover catalysis by reaching into the active site to coordinate GTP and metal ions during enzyme guanylylation (PMID:24435797, PMID:38493148), while c-Abl–mediated tyrosine phosphorylation at Y306 attenuates RTCB interaction with IRE1α and XBP1 splicing, with PTP1B acting as the opposing phosphatase (PMID:35193953). Beyond tRNA and XBP1 substrates, RTCB repairs stress-induced tRNA fragments (tiRNAs), re-ligates MazF-cleaved 16S rRNA in bacteria to restore ribosome function, inhibits axon regeneration in C. elegans neurons independently of the UPR, and protects dopaminergic neurons from α-synuclein toxicity through XBP1 splicing (PMID:36361884, PMID:27789694, PMID:26100902, PMID:25429148).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 2011 High

    Identification of RTCB as the long-sought metazoan tRNA splicing ligase resolved a decades-old gap: activity-guided purification from HeLa extracts and RNAi depletion established that HSPC117/RTCB is required for pre-tRNA maturation, while parallel work on E. coli RtcB showed it seals 2ʹ,3ʹ-cyclic phosphate and 5ʹ-OH RNA ends.

    Evidence Biochemical purification from HeLa extracts with RNAi validation (human); in vitro ligation assays with purified E. coli RtcB

    PMID:21224389 PMID:21311021

    Open questions at the time
    • Subunit composition and stoichiometry of the human tRNA ligase complex were unknown
    • Catalytic mechanism beyond end-joining specificity had not been elucidated
  2. 2011 High

    Dissection of the catalytic pathway revealed that RtcB first hydrolyzes 2ʹ,3ʹ-cyclic phosphate via intrinsic phosphodiesterase activity, then forms a covalent enzyme–GMP intermediate to join 3ʹ-phosphate to 5ʹ-OH, and that this activity can functionally replace yeast Trl1 for both tRNA and HAC1 mRNA splicing.

    Evidence Biochemical intermediate trapping with GTP analogs and mutagenesis (E. coli RtcB); genetic complementation of yeast trl1Δ

    PMID:21757685 PMID:22045815

    Open questions at the time
    • Identity of the guanylylated residue was not yet determined
    • Mammalian UPR ligase identity was inferred from yeast complementation, not directly shown
  3. 2012 High

    The complete three-step ligation mechanism was established—histidine guanylylation, guanylyl transfer to 3ʹ-phosphate RNA, and strand sealing—while high-resolution crystal structures of archaeal RtcB revealed the two-metal active site and geometry of the His404–GMP intermediate.

    Evidence Mass spectrometry of covalent intermediates and mutagenesis of His337 (E. coli); X-ray crystallography at 1.6 Å and 2.3 Å (P. horikoshii RtcB–Mn²⁺ and RtcB–GMP complexes)

    PMID:22474365 PMID:22730297 PMID:22949672

    Open questions at the time
    • How the 5ʹ-OH RNA strand is recognized and positioned was structurally unresolved
    • The convergent two-metal mechanism with classical ligases raised questions about evolutionary origin
  4. 2013 High

    Three crystallographic snapshots along the guanylylation coordinate—pre-GTP, GTPαS-bound, and His404–GMP states—demonstrated that a second Mn²⁺ ion is recruited upon GTP binding and positions the α-phosphorus for in-line nucleophilic attack, establishing a two-metal catalytic paradigm convergent with ATP-dependent ligases.

    Evidence X-ray crystallography of three P. horikoshii RtcB complexes including a GTPαS analog

    PMID:23560983

    Open questions at the time
    • Structural basis for RNA substrate binding remained unresolved
    • No human RtcB structure was available
  5. 2014 High

    RTCB was directly established as the mammalian UPR RNA ligase: knockout cells fail to splice XBP1 mRNA, and conditional deletion in mouse plasma cells abolishes XBP1s expression, ER expansion, and antibody secretion, while C. elegans studies confirmed roles in both xbp-1 splicing and neuroprotection against α-synuclein toxicity.

    Evidence RTCB KO and conditional KO mouse models with in vitro/in vivo XBP1 splicing assays; C. elegans genetic models with lifespan, UPR, and neurodegeneration readouts

    PMID:25087875 PMID:25366321 PMID:25378478 PMID:25429148

    Open questions at the time
    • Mechanism of RTCB recruitment to IRE1α-cleaved XBP1 exons was unknown
    • Whether RTCB has substrates beyond tRNA and XBP1 in mammals was unclear
  6. 2014 High

    Archease was identified as the essential cofactor that converts RtcB from a single-turnover to a multiple-turnover enzyme by accelerating guanylylation and broadening NTP specificity, and the shuttling complex architecture (RTCB–DDX1–hCLE–FAM98B) was defined.

    Evidence Biochemical reconstitution of Archease activation with kinetics; 1.4 Å Archease crystal structure; co-IP and fractionation of the nuclear–cytoplasmic shuttling complex

    PMID:24435797 PMID:24608264

    Open questions at the time
    • How Archease contacts the RtcB active site was structurally unknown
    • Functional roles of DDX1 and hCLE within the complex were undefined
  7. 2015 High

    A UPR- and tRNA-independent function of RtcB was discovered: in C. elegans neurons, RtcB inhibits axon regeneration after injury via a mechanism requiring its ligase activity but not Archease or XBP-1, revealing an unknown RNA substrate.

    Evidence C. elegans axon injury/regeneration assays with epistasis analysis against xbp-1, archease, and tRNA pathway mutants

    PMID:26100902

    Open questions at the time
    • The RNA substrate ligated by RtcB during axon regeneration is unidentified
    • Whether this function is conserved in mammals is untested
  8. 2016 High

    Systematic alanine-scanning mutagenesis of E. coli RtcB assigned individual metal-coordinating and RNA-contact residues to specific catalytic steps, revealing that Cys78 is universally required, Asp75 discriminates cyclic phosphodiesterase from guanylylation, and Arg189 specifically coordinates the 5ʹ-OH end.

    Evidence Step-specific substrate assays (cyclic phosphate, 3ʹ-phosphate, pre-guanylylated) with alanine mutants

    PMID:26858100

    Open questions at the time
    • Structural visualization of the complete RNA-bound active site was still lacking
    • Human-specific residue contributions were untested
  9. 2017 High

    Bacterial RtcB was shown to repair MazF-cleaved 16S rRNA in specialized ribosomes, restoring canonical translation capacity and establishing rRNA as a physiological RtcB substrate beyond tRNA.

    Evidence In vitro RtcB ligation of 16S rRNA fragments and in vivo complementation after MazF stress in E. coli

    PMID:27789694

    Open questions at the time
    • Whether mammalian RTCB repairs rRNA damage is untested
    • Generalizability to other ribotoxin-induced rRNA breaks was unknown
  10. 2021 High

    A crystal structure of RtcB bound to a 5ʹ-OH DNA oligonucleotide revealed the contacts that position the nucleophilic strand (Asn202, Arg238, Arg190), and identified active-site Cys98 oxidation to sulfonic acid, suggesting redox sensitivity of RtcB catalysis.

    Evidence 2.7 Å X-ray crystallography of P. horikoshii RtcB–DNA complex

    PMID:33619169

    Open questions at the time
    • Structure used DNA rather than RNA; RNA-specific contacts may differ
    • Physiological relevance of Cys oxidation-based regulation was not demonstrated in cells
  11. 2022 High

    Multiple advances broadened RTCB biology: crystallographic analysis of permissive versus inhibitory metals explained Mn²⁺ selectivity via M2 coordination geometry; a specialized bacterial RtcB2 was found to repair only rRNA (not tRNA) in the ribosome decoding center; RTCB was shown to repair angiogenin-generated tiRNAs; and c-Abl/PTP1B-mediated phosphorylation at Y306 was established as a regulatory switch governing RTCB–IRE1α interaction and XBP1 splicing versus RIDD fate decisions.

    Evidence Multiple crystal structures with different metals; cryo-EM of PrfH–ribosome complex at 2.55 Å with RtcB2 repair assays; tiRNA northern blots with RTCB knockdown; phosphoproteomics with kinase/phosphatase assays and phosphomutant XBP1 splicing readouts

    PMID:35193953 PMID:35858322 PMID:36130078 PMID:36361884

    Open questions at the time
    • How Y306 phosphorylation structurally disrupts RTCB–IRE1α interaction is unresolved
    • Whether tiRNA repair by RTCB has downstream physiological consequences is unclear
    • RtcB2 substrate discrimination mechanism at the molecular level is incomplete
  12. 2024 High

    Cryo-EM and X-ray structures of the human RTCB–Archease complex revealed how Archease reaches into the RTCB active site to coordinate GTP and metals for guanylylation while simultaneously occluding premature RNA substrate binding, resolving a decade-old question about the cofactor's activation mechanism.

    Evidence Cryo-EM/X-ray structures of human RTCB–Archease in pre- and post-activation states with mutagenesis and guanylylation assays

    PMID:38493148

    Open questions at the time
    • Full human tRNA-LC pentameric complex structure was not yet available
    • How Archease dissociates to allow RNA substrate access is kinetically uncharacterized
  13. 2025 Medium

    USP45 was identified as a deubiquitinase that stabilizes RTCB by removing polyubiquitin chains, with RTCB serving as a hierarchical platform for USP45-mediated DDX1 deubiquitination, linking RTCB protein turnover to cell proliferation.

    Evidence Co-IP, ubiquitination assays, siRNA knockdown, and murine tumor models

    PMID:41468936

    Open questions at the time
    • The E3 ubiquitin ligase targeting RTCB for degradation is unidentified
    • Whether USP45-mediated stabilization affects XBP1 splicing or tRNA maturation is untested
    • Single-lab finding awaits independent confirmation

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include the identity of the RNA substrate through which RTCB inhibits axon regeneration, the structural basis of full human pentameric tRNA-LC engagement with RNA, whether RTCB-mediated tiRNA repair has physiological consequences, and whether the recently proposed SOS splicing/transposon excision function is a conserved RTCB activity.
  • Axon regeneration RNA substrate unidentified
  • No structure of RNA-bound human tRNA-LC pentamer
  • Physiological impact of tiRNA repair unknown
  • SOS splicing function awaits peer-reviewed confirmation

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016874 ligase activity 5 GO:0140098 catalytic activity, acting on RNA 5 GO:0003723 RNA binding 3
Localization
GO:0005829 cytosol 3 GO:0005634 nucleus 2
Pathway
R-HSA-8953854 Metabolism of RNA 4 R-HSA-8953897 Cellular responses to stimuli 3 R-HSA-392499 Metabolism of proteins 2
Partners
CGI-99DDX1FAM98AFAM98BRTRAFUSP45ZBTB8OS
Complex memberships
tRNA ligase complex (tRNA-LC)

Evidence

Reading pass · 30 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2011 HSPC117 (RtcB) was identified as the essential catalytic subunit of a human tRNA splicing ligase complex in HeLa cells. Activity-guided purification of tRNA ligase from HeLa cell extracts identified HSPC117 as required for maturation of intron-containing pre-tRNA both in vitro and in living cells via RNA interference-mediated depletion. Activity-guided biochemical purification from HeLa extracts, RNA interference knockdown, in vitro tRNA maturation assays Science High 21311021
2011 E. coli RtcB was identified as an RNA ligase that seals broken tRNA-like stem-loop structures with 2',3'-cyclic phosphate and 5'-OH ends to form a splice junction with a 2'-OH, 3',5'-phosphodiester, functioning as part of an RNA repair operon with RNA cyclase RtcA. In vitro RNA ligase activity assays with purified E. coli RtcB on tRNA substrates Journal of Biological Chemistry High 21224389
2011 RtcB executes a two-step RNA repair pathway: it first hydrolyzes 2',3'-cyclic phosphate ends to 3'-monophosphate via intrinsic 2',3'-cyclic phosphodiesterase activity, then joins 3'-phosphate to 5'-OH ends using GTP, forming a covalent RtcB-guanylate adduct (phosphoramidate bond) as an intermediate. Both activities require manganese and are abolished by active-site mutations. In vitro biochemical assays, active-site mutagenesis, GTP-binding assays, chemical sensitivity tests (acid/hydroxylamine/alkali) Journal of Biological Chemistry High 22045815
2011 E. coli RtcB can substitute for yeast tRNA ligase Trl1 in vivo to catalyze tRNA splicing and HAC1 mRNA splicing during the unfolded protein response, demonstrating RtcB as a bona fide RNA repair enzyme with broad physiological actions including UPR mRNA splicing. Genetic complementation of yeast trl1Δ cells with E. coli RtcB, in vivo tRNA splicing and HAC1 mRNA splicing assays Journal of Biological Chemistry High 21757685
2012 RtcB executes a three-step ligation mechanism: (i) His337 reacts with GTP to form a covalent RtcB-(histidinyl-N)-GMP intermediate; (ii) guanylate is transferred to the RNA 3'-phosphate to form a polynucleotide-(3')pp(5')G intermediate; (iii) 5'-OH attacks the activated 3' end to form the splice junction with release of GMP. Mass spectrometry identification of covalent intermediates, biochemical assays with substrate analogs, mutagenesis of His337 Proceedings of the National Academy of Sciences High 22474365
2012 The 2',3'-cyclic phosphodiesterase step of RtcB requires GTP and formation of the RtcB-GMP adduct prior to cyclic phosphate hydrolysis, and the sealing of 2',3'-cyclic phosphate ends by RtcB involves a kinetically valid RNA(3')pp(5')G intermediate, supporting a mechanism in which cyclic phosphate is first hydrolyzed to 3'-monophosphate before guanylylation and ligation. Kinetic biochemical assays with GTP analogs, isotope-labeled substrates, intermediate trapping Nucleic Acids Research High 22730297
2012 Crystal structures of Pyrococcus horikoshii RtcB in complex with Mn2+ alone (1.6 Å) and with covalently bound GMP (2.3 Å) revealed two Mn2+ ions at the active site, the geometry of histidine-404 guanylylation, and the binding sites for GMP and RNA phosphate backbone (via sulfate ions). Extensive mutagenesis validated key residues for each step of ligation. X-ray crystallography (1.6 Å and 2.3 Å crystal structures), site-directed mutagenesis, biochemical activity assays Proceedings of the National Academy of Sciences High 22949672
2013 Three crystal structures of P. horikoshii RtcB captured snapshots along the guanylylation pathway: pre-GTP state (single Mn1), GTPαS-bound state (two Mn2+ ions, His404-Nε poised for in-line attack on α-phosphorus), and the histidine-GMP intermediate. The two-metal mechanism for nucleotidylated enzyme intermediate formation is convergent with classical ATP/Mg-dependent ligases. X-ray crystallography of three RtcB complexes including GTPαS analog, structural analysis of in-line attack geometry Biochemistry High 23560983
2014 RtcB was identified as the mammalian UPR RNA ligase responsible for ligation of the two XBP1 exons after IRE1α cleavage. RtcB knockout cells show defective XBP1 mRNA splicing during ER stress; genetic rescue and in vitro splicing demonstrate that RNA ligase activity of RtcB is directly required. Synthetic biology XBP1 splicing circuit screen, RtcB knockout cells, genetic rescue with wild-type vs. catalytic-dead RtcB, in vitro splicing assays Molecular Cell High 25087875
2014 Archease, a 16-kDa protein co-encoded with RtcB in a tRNA splicing operon, functions as a cofactor that activates RtcB by accelerating both the RNA 3'-phosphate guanylylation and ligation steps, alters NTP specificity from GTP-exclusive to accepting ATP, dGTP, or ITP, and can rescue RtcB variants with inactivating substitutions in the guanine-binding pocket. A 1.4 Å crystal structure of P. horikoshii Archease revealed a metal-binding site of conserved carboxylates required for RtcB activation. Biochemical activity assays, NTP specificity testing, mutagenesis of Archease metal-binding residues, 1.4 Å crystal structure of Archease Nucleic Acids Research High 24435797
2014 The mammalian tRNA ligase complex containing RTCB as the catalytic subunit mediates XBP1 mRNA splicing in vitro and in vivo. Conditional depletion of RTCB in plasma cells prevents XBP1s expression, resulting in reduced/disorganized ER and severe defects in antibody secretion, establishing RTCB's role in plasma cell differentiation. Conditional knockout mouse model (Rtcbfl/fl Cd23-Cre), in vitro splicing assay, electron microscopy of ER structure, antibody secretion assays EMBO Journal High 25378478
2014 In C. elegans, RtcB ligates xbp-1 mRNA during the IRE-1 branch of the unfolded protein response and ligates endogenous pre-tRNA halves. Loss of RtcB causes accumulation of unligated xbp-1 mRNA fragments, defective UPR, and decreased lifespan. Growth/lifespan defects from absent tRNA ligation can be bypassed by pre-spliced tRNAs, demonstrating that RtcB has additional functions independent of tRNA maturation and UPR. C. elegans genetic model, RNA analysis of xbp-1 splicing intermediates, lifespan assays, rescue with pre-spliced tRNA transgenes EMBO Reports High 25366321
2014 In C. elegans, RTCB-1 (worm ortholog of HSPC117) protects dopaminergic neurons from α-synuclein-induced neurodegeneration. The RNA ligase activity of RTCB-1 is required for its neuroprotective function, which is mediated through XBP-1 splicing in the UPR pathway; a ligase-dead RTCB-1 mutant fails to provide neuroprotection. C. elegans genetics, RNAi depletion of rtcb-1, neuronal-specific expression of RNA ligase-dead mutant, 6-OHDA neurotoxin assays, xbp-1 mRNA splicing analysis Journal of Neuroscience High 25429148
2014 hCLE/C14orf166 associates with HSPC117 (RtcB), DDX1, and FAM98B forming a shuttling complex present in both nucleus and cytoplasm. Silencing of hCLE downregulates nuclear and cytoplasmic accumulation of DDX1, HSPC117, and FAM98B. Nuclear import of this complex requires active transcription. Nuclear/cytoplasmic fractionation with AP-MS, photoactivatable GFP imaging, siRNA knockdown, co-immunoprecipitation PLoS One Medium 24608264
2015 RtcB activity in neurons inhibits axon regeneration after nerve injury in C. elegans. This function is independent of tRNA ligation, UPR/XBP1 splicing, and the RtcB cofactor archease. RtcB is enriched at axon termini after nerve injury. C. elegans genetic model, axon injury/regeneration assays, epistasis with xbp-1 and tRNA pathway mutants, archease mutant analysis, subcellular localization after injury Proceedings of the National Academy of Sciences High 26100902
2015 Archease evolved to support multiple-turnover activity of RtcB. RtcB from Thermus thermophilus is a single-turnover enzyme that requires Archease from P. horikoshii for multiple turnovers, whereas RtcB from Thermobifida fusca cannot be activated by either Archease, demonstrating that coevolution of the two proteins is necessary for a functional interaction. Biochemical turnover assays with heterologous Archease-RtcB pairs, kinetic analysis RNA High 26385509
2016 Alanine-scanning mutagenesis of E. coli RtcB revealed distinct roles for metal-coordinating residues: Cys78 is required for all steps; Asp75 (Mn2 coordination) allows cyclic phosphodiester hydrolysis but cripples 3'-phosphate guanylylation; His281 (Mn1 coordination) impairs overall ligation but permits sealing of preguanylylated substrate; Arg189 specifically coordinates the 5'-OH RNA end, with R189A slowing the RNAppG/5'-OH sealing step ~200-fold. Site-directed alanine mutagenesis, multi-step substrate assays (cyclic phosphate, 3'-phosphate, preguanylylated substrates), kinetic analysis Journal of Bacteriology High 26858100
2017 The RNA ligase RtcB catalyzes re-ligation of the truncated 16S rRNA in MazF-generated specialized ribosomes in E. coli, restoring their ability to translate canonical mRNAs, establishing a physiological function for bacterial RtcB in ribosome repair and reversal of ribosome heterogeneity. In vitro RtcB ligation of 16S rRNA fragments, in vivo complementation after MazF stress-induced rRNA cleavage, translation assays Nucleic Acids Research High 27789694
2019 hCLE/RTRAF, DDX1, HSPC117 (RTCB), and FAM98B form a cap-binding complex in the cytoplasm. All four proteins bind cap analog-containing resins independently of eIF4E. hCLE silencing reduces accumulation of its interacting proteins and decreases mRNA translation. The complex associates with RNAs involved in mRNA translation. Cap-analog resin pulldown, co-immunoprecipitation, siRNA silencing, polysome/translation assays, RNA-seq of associated RNAs Frontiers in Physiology Medium 30833903
2021 Crystal structure of Pyrococcus horikoshii RtcB in complex with a 5'-OH DNA oligonucleotide (2.7 Å) revealed that Asn202 contacts the terminal 5'-OH nucleophile; Arg238 contacts A1pT2 and T2pG3 phosphates; Arg190 and Gln194 contact the T2pG3 phosphate; and Arg190 makes a π-cation interaction with the G3 nucleobase. Active-site Cys98 was oxidized to cysteine sulfonic acid, suggesting RtcB activity may be sensitive to oxidative stress. X-ray crystallography (2.7 Å), structural analysis of enzyme-substrate contacts RNA High 33619169
2022 The RTCB ligase complex (RTCB-LC) negatively regulates stress-induced tiRNA production by repairing tRNA halves generated by angiogenin cleavage. Knockdown of RTCB significantly increases stress-induced tiRNA production; gel-purified tiRNAs are repaired to full-length tRNAs by RtcB in vitro. Oxidative stress inhibits RTCB-LC, boosting tiRNA production. RTCB knockdown, in vitro repair assay of gel-purified tiRNAs, northern blotting for tiRNAs under H2O2 stress International Journal of Molecular Sciences Medium 36361884
2022 Crystal structures of Pyrococcus horikoshii RtcB with permissive metals (Mn, Co, Ni) or inhibitory metals (Zn, Cu) bound to GTP revealed that inhibitory metals adopt tetrahedral M2 coordination contacting only γ-phosphate, whereas permissive metals adopt pentahedral M2 coordination contacting β- and γ-phosphates. The His404-Nε-Pα-O angle is closer to apical in permissive metals, explaining differential catalytic competency. X-ray crystallography with multiple metal ion substitutions, guanylylation activity assays with different metals RNA High 36130078
2022 A subset of bacterial RtcB (RtcB2) specifically repairs ribosomal damage in the decoding center of 30S subunits but not damaged tRNAs. Repair requires prior dismantling of the damaged 70S ribosome by PrfH, which selectively recognizes cleaved 3'-terminal nucleotides. A 2.55 Å cryo-EM structure of PrfH-damaged ribosome complex revealed the discrimination mechanism; RtcB2 efficiently repairs the freed damaged 30S but not tRNA substrates. Cryo-EM (2.55 Å), in vitro peptide-release and RNA repair assays, cell-based ribotoxin resistance assays Proceedings of the National Academy of Sciences High 35858322
2022 RtcB is tyrosine-phosphorylated by c-Abl kinase at Y306 and dephosphorylated by PTP1B phosphatase. Phosphorylation at Y306 perturbs RtcB interaction with IRE1α, attenuating XBP1 mRNA splicing. The balance of c-Abl/PTP1B activity on RtcB determines whether IRE1α signaling produces adaptive (XBP1 splicing) or pro-death (RIDD) outputs. Phosphoproteomics, kinase/phosphatase in vitro assays, co-immunoprecipitation of RtcB-IRE1α interaction, XBP1 splicing assays with phosphomimetic/phospho-dead mutants Life Science Alliance High 35193953
2024 Biochemical and structural analysis of the human RTCB-Archease complex revealed that Archease reaches into the active site of RTCB to promote covalent RTCB-GMP intermediate formation by coordinating GTP and metal ions, while simultaneously preventing futile RNA substrate binding to RTCB during the activation reaction. Monomer structures of Archease and RTCB defined additional states within the RNA ligation mechanism. Cryo-EM/X-ray crystallography of human RTCB-Archease in pre- and post-activation states, biochemical guanylylation assays, mutagenesis Nature Communications High 38493148
2025 The deubiquitinase USP45 interacts and co-localizes with RTCB and DDX1, directly removing polyubiquitin chains from both proteins to stabilize them. USP45-mediated DDX1 deubiquitination requires RTCB (asymmetric hierarchy), whereas RTCB deubiquitination is DDX1-independent. USP45 cooperates with RTCB to promote cell proliferation via RTCB-dependent DDX1 deubiquitination. Co-immunoprecipitation, ubiquitination assays, siRNA knockdown, murine tumor models, substrate-specific deubiquitination assays International Journal of Biological Macromolecules Medium 41468936
2023 RTCB was found to compete with DDX21 for binding to RNA helicase DDX1, attenuating the DDX21-DDX1 association. This RTCB-DDX1 interaction suppresses type I and III interferon expression and downstream interferon-stimulated gene expression, thereby facilitating influenza A virus replication. Co-immunoprecipitation, RTCB knockout cells, overexpression studies, IFN/cytokine quantification, competitive binding assays Journal of Immunology Medium 37556111
2025 Cryo-EM structure of the human tRNA ligase complex (tRNA-LC) revealed that CGI-99, DDX1, and FAM98B form an alpha-helical bundle contacting RTCB on the opposite side from the ligase active site; FAM98B and CGI-99 form an intricately co-folded heterodimer that clamps Ashwin in a pincer-like structure; DDX1 is tethered to tRNA-LC via its C-terminal helix. The paralogous FAM98A and FAM98C underpin assembly of compositionally distinct RTCB-containing complexes lacking Ashwin. Cryo-EM, structure-based mutagenesis of complex interfaces, interaction analysis bioRxivpreprint High bio_10.1101_2025.08.01.668197
2025 Ashwin (ASW), a vertebrate-specific tRNA-LC subunit, acts as the nuclear import factor of the tRNA-LC via a dual nuclear localization signal (NLS). Disruption of the NLS retains the tRNA-LC in the cytoplasm, impairing pre-tRNA splicing and causing accumulation of 5' tRNA fragments. ASW interacts exclusively with the FAM98B-containing RTCB complex, enabling nuclear tRNA biogenesis, while FAM98A/C-containing complexes retain RTCB in the cytoplasm for XBP1 splicing during UPR. NLS mutagenesis, subcellular fractionation, pre-tRNA splicing assays, NLS-RTCB rescue in ASW-depleted cells, FAM98 paralog-specific immunoprecipitation bioRxivpreprint High bio_10.1101_2025.08.01.668163
2025 RTCB participates in a novel 'SOS splicing' system that excises DNA transposons from host mRNAs in C. elegans and human cells, independently of the spliceosome. CAAP1 bridges RTCB and AKAP17A (which binds TE-containing mRNAs), allowing RTCB to ligate mRNA fragments generated by TE excision. This system is triggered by base-pairing of inverted terminal repeat elements. Genetic screens in C. elegans and human cells, RNA-seq, co-immunoprecipitation of RTCB-CAAP1-AKAP17A, in vivo TE excision assays bioRxivpreprint Medium bio_10.1101_2025.02.14.638102

Source papers

Stage 0 corpus · 82 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
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2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2016 ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure. Cell 1233 26777405
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2012 The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Molecular cell 973 22681889
1999 The DNA sequence of human chromosome 22. Nature 808 10591208
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
2017 Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Science (New York, N.Y.) 533 28302793
2021 Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature 532 33845483
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2010 Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell 318 21145461
2016 Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics. Cell reports 306 27342126
2013 Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. PLoS genetics 292 23382691
2018 Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation. Cell reports 274 30110629
2012 A high-throughput approach for measuring temporal changes in the interactome. Nature methods 273 22863883
2017 A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis. Molecular cell 248 28431233
2017 Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nature communications 221 28524877
2004 RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers. Cell 214 15163412
2016 An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nature communications 211 27173435
2009 Proteomic analysis of integrin-associated complexes identifies RCC2 as a dual regulator of Rac1 and Arf6. Science signaling 207 19738201
2014 A synthetic biology approach identifies the mammalian UPR RNA ligase RtcB. Molecular cell 206 25087875
2011 HSPC117 is the essential subunit of a human tRNA splicing ligase complex. Science (New York, N.Y.) 204 21311021
2015 A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. eLife 198 26673895
2014 The mammalian tRNA ligase complex mediates splicing of XBP1 mRNA and controls antibody secretion in plasma cells. The EMBO journal 170 25378478
2020 UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Nature cell biology 168 32807901
2019 H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature cell biology 162 30804502
2011 RtcB is the RNA ligase component of an Escherichia coli RNA repair operon. The Journal of biological chemistry 133 21224389
2014 The RtcB RNA ligase is an essential component of the metazoan unfolded protein response. EMBO reports 131 25366321
2012 RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-(histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates. Proceedings of the National Academy of Sciences of the United States of America 93 22474365
2011 Novel mechanism of RNA repair by RtcB via sequential 2',3'-cyclic phosphodiesterase and 3'-Phosphate/5'-hydroxyl ligation reactions. The Journal of biological chemistry 92 22045815
2011 RtcB, a novel RNA ligase, can catalyze tRNA splicing and HAC1 mRNA splicing in vivo. The Journal of biological chemistry 91 21757685
2017 Nanoparticle Delivery of miR-34a Eradicates Long-term-cultured Breast Cancer Stem Cells via Targeting C22ORF28 Directly. Theranostics 52 29187905
2014 hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex. PloS one 52 24608264
2012 Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH. Proceedings of the National Academy of Sciences of the United States of America 51 22949672
2017 The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli. Nucleic acids research 50 27789694
2020 Soy Isoflavone Genistein Impedes Cancer Stemness and Mesenchymal Transition in Head and Neck Cancer through Activating miR-34a/RTCB Axis. Nutrients 46 32610494
2014 RTCB-1 mediates neuroprotection via XBP-1 mRNA splicing in the unfolded protein response pathway. The Journal of neuroscience : the official journal of the Society for Neuroscience 45 25429148
2012 The sequential 2',3'-cyclic phosphodiesterase and 3'-phosphate/5'-OH ligation steps of the RtcB RNA splicing pathway are GTP-dependent. Nucleic acids research 45 22730297
2013 Structures of the noncanonical RNA ligase RtcB reveal the mechanism of histidine guanylylation. Biochemistry 43 23560983
2014 A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation. Nucleic acids research 42 24435797
2013 2'-Phosphate cyclase activity of RtcA: a potential rationale for the operon organization of RtcA with an RNA repair ligase RtcB in Escherichia coli and other bacterial taxa. RNA (New York, N.Y.) 36 23945037
2015 RNA ligation in neurons by RtcB inhibits axon regeneration. Proceedings of the National Academy of Sciences of the United States of America 29 26100902
2022 RTCB Complex Regulates Stress-Induced tRNA Cleavage. International journal of molecular sciences 22 36361884
2019 hCLE/RTRAF-HSPC117-DDX1-FAM98B: A New Cap-Binding Complex That Activates mRNA Translation. Frontiers in physiology 20 30833903
2015 Coevolution of RtcB and Archease created a multiple-turnover RNA ligase. RNA (New York, N.Y.) 19 26385509
2017 Site-Selective RNA Splicing Nanozyme: DNAzyme and RtcB Conjugates on a Gold Nanoparticle. ACS chemical biology 16 29155548
2022 Stress-induced tyrosine phosphorylation of RtcB modulates IRE1 activity and signaling outputs. Life science alliance 15 35193953
2020 lncRNA NEAT1 Facilitates Cell Proliferation, Invasion and Migration by Regulating CBX7 and RTCB in Breast Cancer. OncoTargets and therapy 15 32273717
2021 Structure of 3'-PO4/5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide. RNA (New York, N.Y.) 14 33619169
2016 Distinct Contributions of Enzymic Functional Groups to the 2',3'-Cyclic Phosphodiesterase, 3'-Phosphate Guanylylation, and 3'-ppG/5'-OH Ligation Steps of the Escherichia coli RtcB Nucleic Acid Splicing Pathway. Journal of bacteriology 14 26858100
2010 HSPC117 deficiency in cloned embryos causes placental abnormality and fetal death. Biochemical and biophysical research communications 14 20510672
2022 Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB. Proceedings of the National Academy of Sciences of the United States of America 13 35858322
2021 Protein Aggregation Patterns Inform about Breast Cancer Response to Antiestrogens and Reveal the RNA Ligase RTCB as Mediator of Acquired Tamoxifen Resistance. Cancers 13 34206811
2019 The bacterial RNA ligase RtcB accelerates the repair process of fragmented rRNA upon releasing the antibiotic stress. Science China. Life sciences 13 31250189
2017 Homology model of the human tRNA splicing ligase RtcB. Proteins 13 28707320
2021 Putative RNA Ligase RtcB Affects the Switch between T6SS and T3SS in Pseudomonas aeruginosa. International journal of molecular sciences 10 34830443
2008 FAAP, a novel murine protein, is involved in cell adhesion through regulating vinculin-paxillin association. Frontiers in bioscience : a journal and virtual library 10 18508721
2017 Physical interaction between the strawberry allergen Fra a 1 and an associated partner FaAP: Interaction of Fra a 1 proteins and FaAP. Proteins 8 28656626
2014 Making ends meet: a role of RNA ligase RTCB in unfolded protein response. The EMBO journal 8 25404664
2022 Structures of RNA ligase RtcB in complexes with divalent cations and GTP. RNA (New York, N.Y.) 7 36130078
2010 Expression and regulation of FAAP in the mouse epididymis. Endocrine 7 21046479
2024 Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease. Nature communications 6 38493148
2024 Multiscale In Silico Study of the Mechanism of Activation of the RtcB Ligase by the PTP1B Phosphatase. Journal of chemical information and modeling 5 38282538
2023 Insights into the structure and function of the RNA ligase RtcB. Cellular and molecular life sciences : CMLS 5 37935993
2021 YY1 and RTCB in mouse uterine decidualization and embryo implantation. Reproduction (Cambridge, England) 5 34591784
2023 The RNA-Splicing Ligase RTCB Promotes Influenza A Virus Replication by Suppressing Innate Immunity via Interaction with RNA Helicase DDX1. Journal of immunology (Baltimore, Md. : 1950) 4 37556111
2019 Expression and subcellular localization of HSPC117 in min pig tissues and the PK15 cell line. Technology and health care : official journal of the European Society for Engineering and Medicine 3 31045548
2014 HSPC117 is regulated by epigenetic modification and is involved in the migration of JEG-3 cells. International journal of molecular sciences 3 24941254
2022 High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage. RNA biology 2 36369947
2020 lncRNA NEAT1 Facilitates Cell Proliferation, Invasion and Migration by Regulating CBX7 and RTCB in Breast Cancer [Retraction]. OncoTargets and therapy 2 32848416
2025 Deubiquitinase USP45 stabilizes RTCB and DDX1, promoting tumorigenesis and chemoresistance. International journal of biological macromolecules 1 41468936
2024 RTCB deficiency triggers colitis in mice by influencing the NF-κB and Wnt/β-catenin signaling pathways. Acta biochimica et biophysica Sinica 1 38425245
2021 Biomimetic amphiphilic FAAP NPs nanoparticles: Synthesis, characterization and antivirus activity. International immunopharmacology 1 34619499
2026 RTCB is essential for early mouse embryogenesis. Biology of reproduction 0 41524728
2022 Application of RtcB ligase to monitor self-cleaving ribozyme activity by RNA-seq. Biological chemistry 0 35025187
2019 Purification and enzymatic characterization of the RNA ligase RTCB from Thermus thermophilus. Biotechnology letters 0 31280403