TYW1B is a human paralogue of the tRNA 4-demethylwyosine synthase TYW1. The two proteins are about 96% identical, and TYW1B is encoded on chromosome 7. TYW1B shares TYW1's domain layout: an N-terminal flavodoxin-like domain and a C-terminal radical S-adenosyl-L-methionine (SAM) domain with an intact CX3CX2C [4Fe-4S]-binding motif. In TYW1 and its yeast and archaeal orthologues, these domains catalyse the pyruvate-dependent conversion of N1-methylguanosine 37 in tRNA(Phe) into 4-demethylwyosine, the second step of wybutosine biosynthesis. Canonical TYW1B differs from TYW1 at the cofactor sites. It lacks the flavodoxin phosphate-binding loop that binds FMN in TYW1. In place of the segment with two of the three cysteines that coordinate the auxiliary, pyruvate-binding [4Fe-4S] cluster, it has an alternative sequence. No experimental study of TYW1B activity, localisation or physiological role has been reported. Whether TYW1B makes any contribution to wybutosine synthesis, or is a catalytically impaired copy of TYW1, is unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the radical SAM domain (IPR007197). TYW1B keeps the radical SAM fold and its CX3CX2C cluster-binding triad, so a generic catalytic capacity is plausible. No reaction has been shown for TYW1B. Reason: Project rule: MODIFY GO:0003824 to the specific reaction MF the gene carries or is shown to have, and KEEP_AS_NON_CORE when no reaction is known. The only candidate reaction, GO:0102521, is transferred from yeast Tyw1, and here it is UNDECIDED. Canonical TYW1B lacks two of the three auxiliary-cluster cysteines that the TYW1 reaction needs (file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md). The root term is therefore as precise as the evidence allows, and is not core. Supporting Evidence: file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md Radical SAM cluster: the CX3CX2C cysteines (TYW1 C416/C420/C423) are retained in TYW1B (C352/C356/C359). |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: A binary interaction with the bitter-taste receptor TAS2R19 (P59542), detected in the HuRI proteome-scale yeast two-hybrid map. Reason: Generic protein binding from a high-throughput Y2H screen carries no functional information. No more informative MF can be drawn from an interaction with a taste GPCR, which has no known link to tRNA modification. Removing the annotation does not mean the reported interaction is false. Supporting Evidence: file:human/TYW1B/TYW1B-uniprot.txt Q6NUM6; P59542: TAS2R19; NbExp=3 |
| GO:0008033 tRNA processing | IEA GO_REF:0000002 | UNDECIDED | Summary: InterPro2GO mapping from the TYW1 family signature (IPR034556). For TYW1 this stands for wybutosine synthesis. For TYW1B, no tRNA modification activity has been shown. Reason: Family membership alone gives this term. Its specific meaning, wybutosine biosynthetic process (GO:0031591), is UNDECIDED for TYW1B, because canonical TYW1B has lost key cofactor-binding residues and there is no TYW1B-specific experimental evidence. The same action is used here for consistency. Supporting Evidence: file:human/TYW1B/TYW1B-uniprot.txt Belongs to the TYW1 family. file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md canonical TYW1B is not expected to have the full tRNA 4-demethylwyosine synthase activity of TYW1 |
| GO:0010181 FMN binding | IEA GO_REF:0000002 | UNDECIDED | Summary: InterPro2GO mapping from the flavodoxin-like domain signatures. Canonical TYW1B lacks the segment matching TYW1 residues 46-91. That segment includes the flavodoxin phosphate-binding loop (TYW1 SQTGT 85-89), which UniProt annotates as FMN-binding in TYW1. The second FMN-contact region (TYW1 176-208) is kept with one substitution. Reason: In the eukaryotic enzyme the flavodoxin domain binds FMN (PMID:34184886). Without the phosphate-binding loop it is uncertain that TYW1B binds FMN. The UniProt TYW1B FMN feature at 43-47 is a ProRule projection, and it does not align with the TYW1 loop (file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md). FMN binding by TYW1B has not been tested. Supporting Evidence: file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md fall inside the TYW1 segment 46-91 that is absent from canonical TYW1B PMID:34184886 eukaryal homologues contain a flavin binding domain in addition to the radical SAM domain shared with archaeal homologues |
| GO:0031591 wybutosine biosynthetic process | IBA GO_REF:0000033 | UNDECIDED | Summary: PAINT IBA from PTN000358104, grounded in yeast Tyw1. TYW1B is a very recent duplicate of TYW1, so it falls inside the clade that inherited the function. However, there is TYW1B-specific sequence divergence at the catalytic cofactor sites. Reason: The node placement is sound for TYW1, and TYW1B is phylogenetically inside it. An IBA can still be challenged where there is target-specific evidence of divergence. Here, canonical TYW1B has lost two of the three auxiliary [4Fe-4S]-cluster cysteines (TYW1 C381 and C394, which align to the Pyrococcus abyssi ligands). In the archaeal enzyme that cluster binds the pyruvate cosubstrate (PMID:23043105). TYW1B has also lost the flavodoxin phosphate-binding loop. No TYW1B activity or knockout data exist. In TYW1-knockout human ES cells OHyW is undetectable (PMID:38706838), so TYW1B does not make up for TYW1 loss in those cells, if the knockout was paralogue-specific. The sequence and genetic evidence argue against participation without disproving it, so the row is UNDECIDED rather than REMOVE. Propagation Review Root cause: UNRESOLVED Failure modes: PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN000358104 SUPPORTS SOURCE BUT NOT TARGET The TYW1-family ancestral node is well placed, with yeast Tyw1 experimentally required for yW. TYW1B descends from it through a recent duplication of TYW1. In canonical TYW1B, the auxiliary-cluster cysteines (TYW1 C381/C394) and the flavodoxin phosphate-binding loop are replaced, so possible loss of activity is specific to the target. The divergence is inferred from sequence and has not been tested. SGD:S000006128 · TYW1 SUPPORTS SOURCE BUT NOT TARGET Yeast Tyw1 is the experimental donor. It keeps all the cofactor motifs that canonical TYW1B lacks. Supporting Evidence: file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md In TYW1B, C381 aligns to P325 and C394 has no counterpart; only C407 (TYW1B C343) is retained. PMID:23043105 these additional cysteines are involved in the coordination of a second [4Fe-4S] cluster displaying a free coordination site that interacts with pyruvate, the second substrate of the reaction PMID:38706838 OHyW was completely undetectable in TYW1-knockout hESCs |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO mapping from the radical SAM domain. TYW1B keeps the CX3CX2C motif that binds the radical SAM [4Fe-4S] cluster in this family. Reason: Project rule for generic radical SAM rows: MODIFY GO:0051536 to its descendant GO:0051539, which the gene already carries. The cluster bound by the retained radical SAM triad is a [4Fe-4S] cluster. Proposed replacements: 4 iron, 4 sulfur cluster binding Supporting Evidence: file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md Radical SAM cluster: the CX3CX2C cysteines (TYW1 C416/C420/C423) are retained in TYW1B (C352/C356/C359). |
| GO:0051539 4 iron, 4 sulfur cluster binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO mapping from the TYW1 family signature. TYW1B keeps the radical SAM cysteine triad (C352, C356, C359), so it can probably bind the radical SAM [4Fe-4S] cluster. Two of the three auxiliary-cluster ligands are missing, so the second cluster found in TYW1 is probably not bound. Reason: Project rule: GO:0051539 is ACCEPT for active radical SAM enzymes, and KEEP_AS_NON_CORE where catalysis is not established. Catalysis by TYW1B has not been shown and is doubtful on sequence grounds, but binding of the radical SAM cluster is well supported by the conserved ligands. Supporting Evidence: file:human/TYW1B/TYW1B-uniprot.txt /ligand_note="4Fe-4S-S-AdoMet" file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md Radical SAM cluster: the CX3CX2C cysteines (TYW1 C416/C420/C423) are retained in TYW1B (C352/C356/C359). |
| GO:0102521 tRNA-4-demethylwyosine synthase activity | IEA GO_REF:0000120 | UNDECIDED | Summary: Combined IEA from the UniProt EC 4.1.3.44 / RHEA:36347 assignment. That assignment is itself by similarity to yeast Tyw1 (ECO:0000250). No experimental activity has been reported for TYW1B. Reason: The reaction needs pyruvate bound at the auxiliary [4Fe-4S] cluster (PMID:23043105, PMID:36326713). Canonical TYW1B lacks two of that cluster's three cysteine ligands and the FMN phosphate-binding loop (file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md). Loss of TYW1 alone abolishes OHyW in human ES cells (PMID:38706838). Together these make full activity unlikely, but none of it is a direct test of TYW1B. With no experiment either way, the row is UNDECIDED rather than ACCEPT (which would rest on transfer by similarity alone) or REMOVE (which would rest on inference alone). Supporting Evidence: file:human/TYW1B/TYW1B-uniprot.txt Evidence={ECO:0000250|UniProtKB:Q08960}; file:human/TYW1B/TYW1B-bioinformatics/RESULTS.md canonical TYW1B is not expected to have the full tRNA 4-demethylwyosine synthase activity of TYW1 PMID:36326713 a new role for the auxiliary cluster in catalyzing the oxidative cleavage |
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Download this section (compressed HTML)Q: Is a TYW1B protein, distinguishable from TYW1 by unique peptides, detectable in any human tissue? Do any TYW1B transcripts keep the TYW1-like exons that encode the FMN loop and the auxiliary-cluster cysteines?
Q: Did the TYW1 knockout in hESCs (PMID:38706838) leave TYW1B intact? If so, does TYW1B lack activity, or is it simply not expressed in ES cells?
Q: Is TYW1B conserved as a separate gene outside great apes, or is it a recent duplication that is decaying?
Experiment: Anaerobically reconstitute recombinant TYW1B and TYW1 side by side. Measure iron, sulfide and FMN content, and do EPR for cluster number. Assay pyruvate-dependent imG-14 formation on m1G37-tRNA(Phe) by LC-MS. Include TYW1B with the TYW1 auxiliary-cluster segment restored as a gain-of-function control.
Hypothesis: Canonical TYW1B cannot form imG-14 because it lacks auxiliary-cluster ligands.
Type: in vitro enzymology
Experiment: Express TYW1B or TYW1 cDNA in TYW1-knockout cells that have been checked for an intact TYW1B locus. Quantify OHyW and imG-14 in tRNA(Phe) by LC-MS/MS.
Hypothesis: TYW1B does not restore wybutosine synthesis in TYW1-null human cells.
Type: genetic complementation
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: It is unknown whether TYW1B is made as a stable protein with any tRNA 4-demethylwyosine synthase activity, or whether it is a catalytically impaired copy of TYW1 with no role in wybutosine biosynthesis.
OPEN BIOLOGY WHOLLY_DARK
What is known: TYW1B is about 96% identical to TYW1 and keeps the radical SAM cysteine triad. Canonical TYW1B lacks the flavodoxin FMN phosphate-binding loop and two of the three auxiliary-cluster cysteines. In human ES cells, knockout of TYW1 alone abolishes hydroxywybutosine. No biochemical or genetic study of TYW1B exists, and its catalytic activity is annotated only by similarity to yeast Tyw1.
Significance: This decides whether TYW1B is a second human wybutosine enzyme, possibly redundant with TYW1 in some tissues, or a non-functional paralogue. That in turn affects how TYW1 deficiency and TYW1B variants found in genomic studies should be interpreted.
What would resolve it: Detect TYW1B-specific peptides in human tissue. Express and reconstitute recombinant TYW1B and assay imG-14 formation on m1G37-tRNA(Phe). Complement TYW1-null human cells with TYW1B and measure OHyW by LC-MS.
Provenance (the field's own admissions):
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