REL1 (TbMP52, KREL1) is the mitochondrial RNA-editing ligase 1 of Trypanosoma brucei, an ATP-dependent RNA ligase of the RNA ligase 2 (Rnl2) family within the nucleotidyltransferase superfamily. Imported into the single mitochondrion via an N-terminal transit peptide, it is a core subunit of the ~1.6 MDa RNA editing complex (editosome) that inserts and deletes uridylates in maxicircle-encoded pre-mRNAs as directed by guide RNAs. REL1 forms a covalent enzyme-AMP intermediate on Lys87 and seals the nicked mRNA after endonucleolytic cleavage and U removal, acting in the deletion subcomplex together with the 3'-exouridylylase and the zinc-finger protein MP63, whereas its paralog REL2 serves the insertion subcomplex. Its 1.2 A crystal structure with ATP and Mg2+ reveals an editing-ligase-specific adenine pocket. REL1 is essential for editing and for viability of both bloodstream and procyclic forms and has no close human homolog.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003972 RNA ligase (ATP) activity | IEA GO_REF:0000120 | ACCEPT | Summary: RNA ligase (ATP) activity (EC 6.5.1.3) assigned from the Rnl2 family signature and the EC number. Recombinant/purified REL1 has experimentally demonstrated RNA ligase activity and is adenylatable. Reason: The electronic assignment is directly confirmed by biochemistry (adenylation and RNA ligation by TbMP52) and by the ATP-bound crystal structure. This is the core molecular function of REL1. Supporting Evidence: PMID:11251122 The TbMP52 protein is shown to be a component of this complex, to have RNA ligase activity, and to be one of two adenylatable proteins in the complex. PMID:15465048 We report here the crystal structure of the catalytic domain of TbREL1 at 1.2 A resolution, in complex with ATP and magnesium. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: ATP binding inferred from the Rnl2 domain; the crystal structure shows ATP bound in the active site. Reason: Correct (structurally demonstrated) but ATP binding is a mechanistic part of the ATP-dependent ligase reaction rather than a separate function; retained as non-core. Supporting Evidence: PMID:15465048 ATP makes extensive direct and indirect interactions with the ligase via essentially all its atoms while extending its base into a deep pocket. |
| GO:0005737 cytoplasm | IDA GO_REF:0000109 | MODIFY | Summary: TrypTag genome-wide fluorescent tagging call of cytoplasm. Reason: In GO, cytoplasm includes the mitochondrion, so the call is not wrong but is far less specific than the established location. REL1 has a mitochondrial transit peptide and the editosome is purified from mitochondria; a diffuse cytosolic signal from a high-throughput tag (e.g. N-terminal tag masking the transit peptide) is not evidence of a cytosolic pool. Replace with mitochondrion, which the gene already carries. Proposed replacements: mitochondrion Supporting Evidence: PMID:11134327 was enriched from Trypanosoma brucei mitochondria by sequential ion-exchange and gel filtration chromatography, followed by glycerol gradient sedimentation. |
| GO:0005739 mitochondrion | IDA PMID:11134327 Association of two novel proteins, TbMP52 and TbMP48, with t... | ACCEPT | Summary: TbMP52 was identified by monoclonal antibody and mass spectrometry in the editing complex enriched from purified T. brucei mitochondria. Reason: Mitochondrial localization is supported by co-purification with the mitochondrial editosome and by the N-terminal mitochondrial transit peptide. Supporting Evidence: PMID:11134327 A multiprotein complex that contains these activities and catalyzes deletion editing in vitro was enriched from Trypanosoma brucei mitochondria by sequential ion-exchange and gel filtration chromatography, followed by glycerol gradient sedimentation. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: Mapped from the UniProt subcellular location (Mitochondrion). Reason: Consistent with experimental mitochondrial co-purification and the transit peptide. Supporting Evidence: PMID:11134327 was enriched from Trypanosoma brucei mitochondria by sequential ion-exchange and gel filtration chromatography, followed by glycerol gradient sedimentation. |
| GO:0005739 mitochondrion | ISS GO_REF:0000024 | ACCEPT | Summary: Transferred from the near-identical REL1 entry of another T. brucei strain (P86926). Reason: Same protein in a different strain; consistent with direct evidence. |
| GO:0005739 mitochondrion | RCA PMID:20660476 The Trypanosoma brucei MitoCarta and its regulation and spli... | ACCEPT | Summary: Predicted mitochondrial by the T. brucei MitoCarta SVM classifier. Reason: Computational prediction agrees with experimental evidence for mitochondrial localization. Supporting Evidence: PMID:20660476 We present a novel computational method for genome-wide prediction of mitochondrial proteins using a support vector machine-based classifier with ∼90% prediction accuracy. |
| GO:0009451 RNA modification | IDA PMID:11134327 Association of two novel proteins, TbMP52 and TbMP48, with t... | MODIFY | Summary: Based on association of TbMP52 with the complex that catalyzes in vitro deletion editing; GO merged "RNA editing" into RNA modification. Reason: The process is correct but very general. REL1 ligates mRNA during U-insertion/ deletion editing of mitochondrial mRNAs, which is captured by mitochondrial mRNA modification (GO:0080156, a descendant of RNA modification). Repression of REL1 blocks editing in vivo and the REL1 subcomplex catalyzes deletion editing, so REL1 directly performs a step (ligation) of the process. Proposed replacements: mitochondrial mRNA modification Supporting Evidence: PMID:11134327 These results suggest that TbMP52 and TbMP48 are components of the RNA editing complex. PMID:11251122 Regulated repression of TbMP52 blocks editing, which shows that it is a functional component of the editing complex. |
| GO:0009451 RNA modification | IEA GO_REF:0000117 | MODIFY | Summary: ARBA machine-learning assignment of RNA modification. Reason: As for the IDA row, the specific supported process is mitochondrial mRNA modification (U-insertion/deletion editing). Proposed replacements: mitochondrial mRNA modification Supporting Evidence: PMID:14536071 A purified TbREL1 subcomplex catalyzed precleaved deletion editing in vitro, while a purified TbREL2 subcomplex catalyzed precleaved insertion editing in vitro. |
| GO:0016874 ligase activity | IEA GO_REF:0000002 | MODIFY | Summary: Generic ligase activity from the InterPro family. Reason: Correct but uninformative; the specific activity, RNA ligase (ATP) activity (GO:0003972), is experimentally supported and already annotated. Proposed replacements: RNA ligase (ATP) activity Supporting Evidence: PMID:11251122 to have RNA ligase activity, and to be one of two adenylatable proteins in the complex. |
| GO:0020023 kinetoplast | IDA GO_REF:0000109 | KEEP AS NON CORE | Summary: TrypTag fluorescent-tagging call of kinetoplast. Reason: The kinetoplast is a genuine kinetoplastid sub-mitochondrial structure, and an enrichment of editosome signal near the kDNA (source of maxicircle transcripts and guide RNAs) is plausible. The core site of editing is the mitochondrial matrix (editosome), so this is kept as a valid but non-core location. |
| GO:0020023 kinetoplast | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA electronic assignment of kinetoplast. Reason: Consistent with the TrypTag kinetoplast call; kept non-core as for the IDA row. |
| GO:0031019 mitochondrial mRNA editing complex | IDA PMID:11134327 Association of two novel proteins, TbMP52 and TbMP48, with t... | ACCEPT | Summary: TbMP52 identified as a component of the purified ~1,600 kDa editing complex; the monoclonal antibody against TbMP52 immunoprecipitates deletion editing activity. Reason: Core location. REL1 is a stable editosome subunit, confirmed by tagged-REL1 purification of a deletion subcomplex. Supporting Evidence: PMID:11134327 specifically immunoprecipitates in vitro deletion RNA editing activity. PMID:14536071 purification of complexes via tagged editing ligases TbREL1 and TbREL2, comprehensive yeast two-hybrid analysis, and coimmunoprecipitation of recombinant proteins. |
| GO:0031019 mitochondrial mRNA editing complex | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA electronic assignment to the editosome. Reason: Agrees with direct experimental evidence. Supporting Evidence: PMID:11251122 The TbMP52 protein is shown to be a component of this complex, to have RNA ligase activity, and to be one of two adenylatable proteins in the complex. |
| GO:0031019 mitochondrial mRNA editing complex | RCA PMID:26991453 A Protein Complex Map of Trypanosoma brucei. | ACCEPT | Summary: Co-fractionation protein complex map of T. brucei, with REL1 used as a pulldown bait, places REL1 with core editosome proteins. Reason: Consistent with direct experimental evidence. Supporting Evidence: PMID:26991453 17 are known to be involved in the core editosome complex [72], while 21 function in the MRB1 complex [73]. |
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Download this section (compressed HTML)Q: Is REL1 strictly specific to deletion-site ligation in vivo, or can it contribute to ligation at insertion sites, given that tagged REL1 and REL2 purify functionally distinct deletion and insertion subcomplexes?
Q: Does GO need a specific process term for guide RNA-directed uridine insertion/deletion mRNA editing, distinct from generic mitochondrial mRNA modification?
Experiment: Replace endogenous REL1 with catalytic (K87A) and adenine-pocket mutants and measure editing at deletion versus insertion sites by high-throughput sequencing of edited transcripts.
Hypothesis: REL1 ligation is required specifically at deletion sites, and loss of its activity cannot be rescued by REL2.
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