NCGR_LOCUS1765 encodes the large subunit (CBP80/NCBP1) of the nuclear cap-binding complex (CBC) in Miscanthus lutarioriparius. The CBC is a heterodimer of NCBP1 and NCBP2 (CBP20) that recognizes the m7G cap structure on RNA polymerase II transcripts. NCBP1 does not directly contact the cap but induces a conformational change in NCBP2 that enables high-affinity cap recognition. As a scaffold/adaptor protein containing MIF4G-like domains and an ARM-type fold, NCBP1 recruits and coordinates multiple downstream RNA processing factors. The CBC participates in co-transcriptional splicing (especially cap-proximal first intron removal), miRNA biogenesis, mRNA 3-prime end processing, nuclear mRNA export, the pioneer round of translation, and nonsense-mediated mRNA decay. In plants, the Arabidopsis ortholog ABH1/CBP80 has been shown to regulate alternative splicing genome-wide and to modulate ABA signaling and abiotic stress responses. No Miscanthus-specific experimental data exist for this gene; functional annotation is based on orthology to well-characterized plant and metazoan NCBP1 proteins.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000339 RNA cap binding | IEA GO_REF:0000120 | ACCEPT | Summary: RNA cap binding is the core molecular function of the CBC complex of which NCBP1/CBP80 is a subunit. While the actual cap-binding pocket resides in NCBP2/CBP20, NCBP1 induces the conformational change in NCBP2 required for high-affinity m7G cap recognition. As an essential subunit of the cap-binding complex, annotating NCBP1 with this term is appropriate since it enables the function. Supporting Evidence: PMID:37830942 NCBP1 triggers a conformational change of NCBP2, which results in high-affinity binding to m7G cap PMID:37830942 Both proteins are required for stable binding to the cap structure, neither subunit alone has a strong affinity for it |
| GO:0003723 RNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: This broad annotation derives from the MIF4G-like domain (IPR003890). NCBP1 interacts with RNA as part of the CBC complex. While technically correct as a parent of more specific terms already annotated, it is uninformative. Reason: RNA binding is accurate but very general. The more specific RNA cap binding (GO:0000339) and mRNA binding (GO:0003729) annotations already capture the relevant molecular functions more precisely. Supporting Evidence: PMID:37830942 Although NCBP1 and NCBP2 bind to the cap structure synergistically, both proteins can associate with RNA directly |
| GO:0003729 mRNA binding | IEA GO_REF:0000118 | ACCEPT | Summary: As part of the CBC, NCBP1 binds capped mRNA transcripts and remains associated with them through processing, export, and the pioneer round of translation. mRNA binding is a core function of the CBC complex. Supporting Evidence: PMID:19864257 CBP proteins remain bound to the mRNA during the pioneer round of translation playing an essential role in mRNA quality control |
| GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | IEA GO_REF:0000118 | ACCEPT | Summary: CBC supports the pioneer round of translation, which is the translation event that triggers NMD for transcripts containing premature termination codons. In mammalian cells, CBP80 recruits the NMD factor Upf1. Supporting Evidence: PMID:19864257 CBP proteins remain bound to the mRNA during the pioneer round of translation playing an essential role in mRNA quality control PMID:19864257 in mammalian cells, CBP80 recruits the NMD factor Upf1 and promotes the interaction of Upf1 with the NMD factor Upf2 |
| GO:0006406 mRNA export from nucleus | IEA GO_REF:0000002 | ACCEPT | Summary: CBC plays a direct role in mRNA nuclear export. The cap and the CBC have multiple functions in mRNA biogenesis including nuclear export. Supporting Evidence: PMID:19864257 The cap and the CBC have multiple functions in mRNA biogenesis including splicing file:9POAL/NCGR_LOCUS1765/NCGR_LOCUS1765-deep-research-falcon.md nuclear export of capped RNAs via adaptors such as PHAX for snRNAs or TREX/Aly/REF/TAP/NXF1-like routes for mRNAs |
| GO:0016070 RNA metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: This is a very broad parent term derived from the MIF4G-like domains (IPR015172, IPR015174). While correct, it is subsumed by more specific process annotations already present (NMD, mRNA export). Reason: The term is accurate but uninformative. The specific processes annotated (NMD, mRNA export, RNA splicing) provide more precise functional description. Supporting Evidence: PMID:29142023 Plant nuclear CBC consisted of two subunits (CBP20 and CBP80) is involved in both conserved processes related to RNA metabolism |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: NCBP1 contains a bipartite nuclear localization signal (NLS) that binds importin alpha, supporting predominantly nuclear localization. The CBC functions primarily in the nucleus where it associates with nascent Pol II transcripts. Supporting Evidence: PMID:37830942 NCBP1 harbours a bipartite-type nuclear localization signal at the amino-terminus that binds to importin Ξ± PMID:37830942 At the steady state, CBC is localized in the nucleus |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: CBC accompanies exported mRNA into the cytoplasm during the pioneer round of translation before being replaced by eIF4E. Cytoplasmic localization is transient and associated with this specific phase of mRNA metabolism. Reason: While NCBP1 does transit through the cytoplasm during the pioneer round of translation, the primary site of function is the nucleus. Cytoplasmic presence is transient rather than representing a major site of action. Supporting Evidence: PMID:19864257 CBP proteins remain bound to the mRNA during the pioneer round of translation playing an essential role in mRNA quality control |
| GO:0005846 nuclear cap binding complex | IEA GO_REF:0000120 | ACCEPT | Summary: NCBP1/CBP80 is one of the two subunits that compose the nuclear cap-binding complex (CBC), along with NCBP2/CBP20. This is the defining complex membership for this protein. Supporting Evidence: PMID:37830942 CBC consists of two polypeptides, whose molecular masses are 20 and 80 kDa PMID:19864257 The eukaryotic nuclear cap-binding complex (CBC) consists of two subunits (CBP20 and CBP80) that, as a complex, bind to the cap structure of RNA polymerase II transcripts |
| GO:0008380 RNA splicing | IEA GO_REF:0000120 | NEW | Summary: CBC is directly involved in co-transcriptional splicing, particularly supporting efficient removal of cap-proximal first introns via U1 snRNP interaction at the 5-prime splice site. In Arabidopsis, an RT-PCR panel found CBC-dependent splicing changes in 101 genes with CBP80 playing a more significant role than CBP20. Reason: RNA splicing is a well-documented CBC function present in the UniProt record but absent from the QuickGO annotations. CBC promotes spliceosome assembly on the first intron through U1 snRNP recruitment in both plants and animals. Supporting Evidence: PMID:19864257 Significant changes in the ratios of alternative splicing isoforms were found in 101 genes PMID:19864257 CBP80 plays a more significant role in alternative splicing than CBP20, probably being a platform for interactions with other splicing factors PMID:18550839 se, abh1/cbp80, and cbp20 mutants also share similar splicing defects, leading to the accumulation of many partially spliced transcripts |
| GO:0035196 miRNA processing | IEA GO_REF:0000002 | NEW | Summary: In plants, CBC binds pri-miRNAs and supports their processing through cooperation with SERRATE and the DCL1 complex. Arabidopsis cbp80/abh1 mutants have reduced miRNA levels and increased pri-miRNA levels. Reason: miRNA biogenesis is a major documented function of CBC in plants but is not captured by the existing GOA annotations. The Arabidopsis ortholog ABH1/CBP80 has been experimentally shown to be required for efficient miRNA processing. Supporting Evidence: PMID:18550839 Inactivation of either ABH1/CBP80 or CBP20 results in decreased levels of mature miRNAs accompanied by apparent stabilization of pri-miRNAs PMID:19864257 CBP20 and CBP80 are suggested to bind to capped pri-miRNA transcripts and play role in their processing |
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Download this section (compressed HTML)Q: Does NCGR_LOCUS1765 in Miscanthus lutarioriparius functionally complement the Arabidopsis abh1/cbp80 mutant phenotypes, including ABA hypersensitivity and altered miRNA biogenesis?
Suggested experts: Plant RNA biology researchers, Miscanthus geneticists
Q: Are there Miscanthus-specific alternative splicing events regulated by CBC that differ from those observed in Arabidopsis or other grasses?
Suggested experts: Plant splicing biology researchers, Grass genomics specialists
Experiment: Generate CRISPR knockout or knockdown lines of NCGR_LOCUS1765 in Miscanthus and assess phenotypes including ABA sensitivity, miRNA profiles via small RNA-seq, and alternative splicing changes via RNA-seq compared to wild-type plants.
Hypothesis: NCGR_LOCUS1765 functions as a canonical NCBP1/CBP80 ortholog with conserved roles in splicing regulation and miRNA biogenesis in Miscanthus
Experiment: Compare NCGR_LOCUS1765 expression under drought, salt, and heavy metal stress conditions in Miscanthus lutarioriparius. Correlate with changes in splicing patterns and miRNA abundance to determine if CBC-mediated RNA processing contributes to stress resilience.
Hypothesis: CBC function in Miscanthus contributes to abiotic stress tolerance relevant to its use as a bioenergy crop
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