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 ฮฑ
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
|
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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NCGR_LOCUS1765 (UniProt A0A811M5M6) is annotated (UniProt) as nuclear cap-binding protein subunit 1 (NCBP1; also called CBP80), a conserved eukaryotic scaffold subunit of the nuclear cap-binding complex (CBC). Direct, gene-specific functional literature in Miscanthus lutarioriparius was not identified in the retrieved corpus; therefore, the most defensible functional annotation is orthology-based inference from well-characterized CBC/NCBP1 biology in eukaryotes and plants (notably Arabidopsis thaliana), combined with recent (2024) mechanistic/structural work on CBC interaction networks. (daszkowskagolec2018emergingrolesof pages 1-4, kataoka2024thenuclearcapbinding pages 1-2, dubiez2024structuralbasisfor pages 1-5)
Eukaryotic RNA polymerase II transcripts acquire a 5โฒ m7G cap. In the nucleus, this cap is recognized by the CBC, classically a heterodimer of NCBP1 (CBP80) and NCBP2 (CBP20). (kataoka2024thenuclearcapbinding pages 1-2, kataoka2024thenuclearcapbinding pages 2-4)
A key mechanistic point is that both subunits are required for stable cap binding: the cap-binding pocket is in NCBP2, and NCBP1 induces a conformational change that yields high-affinity cap recognition. (kataoka2024thenuclearcapbinding pages 1-2)
Definition for annotation: NCBP1/CBP80 is not an enzyme/transporter; it is best described as a cap-associated RNA-processing scaffold/adaptor that recruits and coordinates multiple RNA biogenesis, export, and surveillance activities on newly capped nuclear transcripts. (kataoka2024thenuclearcapbinding pages 2-4, kataoka2024thenuclearcapbinding pages 5-6)
The 2024 CBC review notes that NCBP1 contains an N-terminal bipartite nuclear localization signal (NLS) that binds importin-ฮฑ, supporting predominantly nuclear localization. (kataoka2024thenuclearcapbinding pages 1-2, kataoka2024thenuclearcapbinding pages 2-4)
In plants, CBC subunits are described as structurally/functionally analogous (in an evolutionary sense) to cytoplasmic cap-binding factors: plant CBP80 shows domain similarity to eIF4G (HEAT/MIF4G-like features), consistent with a major role as an interaction scaffold in translation-coupled processes. (daszkowskagolec2018emergingrolesof pages 9-11, daszkowskagolec2018emergingrolesof pages 6-9)
A plant-focused synthesis describes the plant nuclear CBC (nCBC) as a CBP20โCBP80 heterodimer that binds the m7G cap, protects transcripts, and participates in transcription-coupled processing, splicing, miRNA biogenesis, nuclear export, and the pioneer round of translation/NMD, with demonstrated connections to ABA/ethylene signaling and abiotic stress phenotypes (salt, drought). (daszkowskagolec2018emergingrolesof pages 1-4, daszkowskagolec2018emergingrolesof pages 9-11)
Most likely molecular function: NCGR_LOCUS1765 encodes an NCBP1/CBP80 ortholog that forms the CBC with NCBP2/CBP20 and acts as a cap-dependent RNP assembly platform that connects 5โฒ-capping to downstream RNA-processing steps by recruiting factors. (kataoka2024thenuclearcapbinding pages 1-2, kataoka2024thenuclearcapbinding pages 2-4)
In plants specifically, CBP80 stabilizes CBP20 and enables cap binding; CBP80 is described as a stabilizing subunit whose presence is required for robust cap-binding by the complex. (daszkowskagolec2018emergingrolesof pages 1-4)
Primary site of action: the nucleus, associated with nascent or newly capped Pol II transcripts, consistent with NCBP1โs NLS/importin interaction and CBCโs co-transcriptional engagement. (kataoka2024thenuclearcapbinding pages 1-2, kataoka2024thenuclearcapbinding pages 2-4)
Extended lifecycle: CBC can remain bound through export and support the pioneer round of translation, after which it is exchanged for eIF4E/eIF4F for steady-state cytoplasmic translation. (kataoka2024thenuclearcapbinding pages 4-5)
Because Miscanthus-specific experiments were not retrieved, processes below are inferred from orthologous plant/eukaryotic CBC biology:
NCBP1/CBP80 is not a catalyst. Its โsubstrateโ is best defined as m7G-capped RNA polymerase II transcripts in the context of an RNA-protein complex (CBC), where it supports high-affinity cap engagement and recruitment of processing/export/surveillance factors. (kataoka2024thenuclearcapbinding pages 1-2, kataoka2024thenuclearcapbinding pages 2-4)
A 2024 review summarizes CBC as a multitasking binding partner of Pol II transcripts, emphasizing that CBC binds co-transcriptionally and coordinates mRNA processing, export, and the pioneer translation step. It also highlights the canonical subunit definitions (NCBP1/NCBP2) and an alternative cap-associated partner (NCBP3) forming a lower-affinity complex with NCBP1, indicating compositional flexibility. (kataoka2024thenuclearcapbinding pages 1-2, kataoka2024thenuclearcapbinding pages 5-6)
URL / publication date: Kataoka N. 2024-10. Journal of Biochemistry 175:9โ15. https://doi.org/10.1093/jb/mvad081 (kataoka2024thenuclearcapbinding pages 1-2)
A 2024 structural/mechanistic study (bioRxiv preprint; originally posted 2023-07-25, version cited in Nov 2024 listing) details how CBC and its cofactor ARS2 assemble with mutually exclusive โeffectorsโ that bias transcripts toward productive fates (processing/export) or degradative fates (exosome-linked decay). Productive factors include PHAX, NCBP3, ALYREF, and degradative linkers include ZC3H18/ZFC3H1, which connect to exosome adaptor pathways (NEXT/PAXT). (dubiez2024structuralbasisfor pages 1-5)
This work provides quantitative binding/competition details: e.g., a NCBP3 W581 helix binds a CBP80 Trp pocket; for NELF-E, a W345E mutation weakened CBC affinity (reported Kd shift from 113 nM to 1.3 ฮผM), and PHAX binding to CBC is reported in the ~125 nM range. (dubiez2024structuralbasisfor pages 8-11)
URL / posting date: Dubiez E. et al. posted 2023-07-25; cited as 2024-11 in retrieved metadata. bioRxiv. https://doi.org/10.1101/2023.07.25.550453 (dubiez2024structuralbasisfor pages 1-5)
Because CBC influences splicing, miRNA biogenesis, and RNA decay pathways that shape hormone and stress outputs in Arabidopsis, orthologs such as Miscanthus NCGR_LOCUS1765 are plausible leverage points for engineering or selecting stress-tolerance phenotypes in crops/biomass grasses (e.g., drought/salt tolerance), but this remains a hypothesis unless validated in Miscanthus. (daszkowskagolec2018emergingrolesof pages 9-11, daszkowskagolec2018emergingrolesof pages 1-4)
A 2024 Miscanthus transcriptomic/physiological study (not gene-specific for NCGR_LOCUS1765 in the accessible text) underscores that M. lutarioriparia/lutarioriparius is used in phytoremediation and has strong tolerance to heavy metals, with large-scale transcriptional remodeling under Cd stress (tens of thousands of DEGs). While this does not directly annotate NCGR_LOCUS1765, it illustrates the practical context in which RNA-processing regulators could be relevant for resilience traits. (Note: no NCGR_LOCUS1765/NCBP1 mention was extractable from this text for direct evidence.)
The 2024 review explicitly frames CBC as a โmultitaskingโ binding partner of Pol II transcripts and emphasizes its coordinating role across gene expression stepsโproviding a strong expert consensus lens for annotating NCBP1/CBP80 family proteins as central coordinators of RNA maturation and fate, not single-pathway factors. (kataoka2024thenuclearcapbinding pages 1-2, kataoka2024thenuclearcapbinding pages 5-6)
The 2024 structural work advances an expert-level, mechanistic view that CBC-ARS2 is an effector recruitment hub, with competitive binding among factors that promote export/processing vs nuclear degradationโan important conceptual update beyond the classical โexport factorโ view of CBC. (dubiez2024structuralbasisfor pages 1-5, dubiez2024structuralbasisfor pages 8-11)
In Arabidopsis CBC mutants:
- Genome-wide analyses reported 518 intron retention events in Atcbp80/abh1 and 931 in Atcbp20, with 298 shared events. (daszkowskagolec2018emergingrolesof pages 4-6)
- An RT-PCR alternative splicing panel covering 435 events found CBC-influenced splicing changes in 101 genes, with ~50% of affected events occurring at the first intron and preferential impact at the 5โฒ splice site; CBP80 showed a stronger effect than CBP20, consistent with a scaffold role. (daszkowskagolec2018emergingrolesof pages 4-6)
A plant-focused review reports that co-translational RNA decay was decreased to approximately 50% in Atcbp80/abh1 mutants, and affected transcripts were enriched for stress/temperature response functions (as summarized). (daszkowskagolec2018emergingrolesof pages 9-11)
The following schematic summarizes the 2024 competitive binding model and multiple CBC binding sites.
(dubiez2024structuralbasisfor media 80a1309a)
NCGR_LOCUS1765 (A0A811M5M6) encodes an NCBP1/CBP80 family protein predicted to localize to the nucleus via an NLS/importin system and to function as the large subunit of the nuclear cap-binding complex with NCBP2/CBP20. It likely binds (indirectly, via CBC) m7G-capped Pol II transcripts and acts as a scaffold/adaptor coordinating cap-proximal splicing, miRNA biogenesis, mRNA 3โฒ processing, nuclear export, pioneer translation, and RNA surveillance/decay (including NMD/co-translational decay). Plant ortholog studies link CBC to ABA/abiotic stress response phenotypes, suggesting relevance to stress resilience in Miscanthus, but Miscanthus gene-specific validation is currently lacking in the retrieved literature. (daszkowskagolec2018emergingrolesof pages 1-4, daszkowskagolec2018emergingrolesof pages 4-6, daszkowskagolec2018emergingrolesof pages 9-11, kataoka2024thenuclearcapbinding pages 4-5)
| Aspect | Evidence summary | Key citations (with year and URL) |
|---|---|---|
| Identity/domains | Target verification: UniProt A0A811M5M6 is annotated as nuclear cap-binding protein subunit 1 from Miscanthus lutarioriparius (gene/ORF NCGR_LOCUS1765) and assigned to the NCBP1/CBP80 family with ARM-type fold / CBP80 / MIF4G-like domains. Literature caveat: no Miscanthus paper retrieved here directly names NCGR_LOCUS1765 or reports gene-specific experiments, so functional annotation is inferred from orthology to plant/eukaryotic NCBP1/CBP80. Across eukaryotes, CBC is a heterodimer of NCBP1 (CBP80) and NCBP2 (CBP20); NCBP1 contains an N-terminal bipartite NLS and promotes the high-affinity cap-binding conformation of NCBP2. In plants, CBP80 is the larger scaffold-like subunit, consistent with the UniProt domain architecture. (kataoka2024thenuclearcapbinding pages 1-2, daszkowskagolec2018emergingrolesof pages 1-4) | Kataoka 2024, J. Biochem. https://doi.org/10.1093/jb/mvad081; Daszkowska-Golec 2018, Plant Physiol. https://doi.org/10.1104/pp.17.01017 |
| Molecular function | Primary function (orthology-based): NCBP1/CBP80 is a non-enzymatic RNA-binding complex subunit/scaffold in the nuclear cap-binding complex (CBC). CBC binds the 5โฒ m7G cap of RNA polymerase II transcripts; the cap pocket is in NCBP2/CBP20, while NCBP1 induces/stabilizes the cap-bound state and recruits downstream processing factors. Thus NCGR_LOCUS1765 is best annotated as a cap-associated adaptor/scaffold that chaperones newly capped RNAs through processing, export, surveillance, and pioneer translation, not as a catalyst or transporter. (kataoka2024thenuclearcapbinding pages 1-2, kataoka2024thenuclearcapbinding pages 2-4, daszkowskagolec2018emergingrolesof pages 1-4) | Kataoka 2024, https://doi.org/10.1093/jb/mvad081; Daszkowska-Golec 2018, https://doi.org/10.1104/pp.17.01017 |
| Localization | Expected localization: predominantly nuclear, associated with nascent Pol II transcripts near transcription sites; after export, CBC can remain on mRNA during the pioneer round of translation before being replaced by eIF4E. NCBP1 contains a bipartite NLS that binds importin-ฮฑ, supporting nuclear import/localization. For a Miscanthus ortholog, the most likely cellular site of action is the nucleoplasm / co-transcriptional mRNP assembly environment, with transient persistence on exported transcripts. (kataoka2024thenuclearcapbinding pages 1-2, kataoka2024thenuclearcapbinding pages 4-5, kataoka2024thenuclearcapbinding pages 5-6) | Kataoka 2024, https://doi.org/10.1093/jb/mvad081; Kataoka 2024, https://doi.org/10.1093/jb/mvad081 |
| Key pathways/processes | Conserved CBC-linked processes likely relevant to NCGR_LOCUS1765: (1) co-transcriptional splicing, especially efficient removal of cap-proximal/first introns via U1 snRNP/spliceosome support; (2) 3โฒ end processing/polyadenylation; (3) nuclear export of capped RNAs via adaptors such as PHAX for snRNAs or TREX/Aly/REF/TAP/NXF1-like routes for mRNAs; (4) miRNA biogenesis in plants through cooperation with SERRATE/SE, DCL1, HYL1, D-bodies, and pri-miRNA stabilization/processing; (5) pioneer translation and nonsense-mediated decay (NMD)/co-translational RNA decay; and (6) coupling to chromatin-linked RNA processing in plants (e.g., COMPASS-like and EFS-linked regulation at FLC). These roles are established in Arabidopsis/eukaryotes and provide the strongest current annotation framework for the Miscanthus protein. (kataoka2024thenuclearcapbinding pages 2-4, kataoka2024thenuclearcapbinding pages 4-5, daszkowskagolec2018emergingrolesof pages 6-9, daszkowskagolec2018emergingrolesof pages 9-11, daszkowskagolec2018emergingrolesof pages 4-6) | Kataoka 2024, https://doi.org/10.1093/jb/mvad081; Daszkowska-Golec 2018, https://doi.org/10.1104/pp.17.01017; Laubinger et al. 2008, https://doi.org/10.1073/pnas.0802493105; Kim et al. 2008, https://doi.org/10.1093/pcp/pcn146; Raczynska et al. 2010, https://doi.org/10.1093/nar/gkp869 |
| Plant-specific phenotypes | No direct Miscanthus phenotype found for NCGR_LOCUS1765. By orthology to Arabidopsis CBP80/ABH1, loss of CBC function is associated with ABA hypersensitivity, altered salt/osmotic/drought responses, changes in miRNA accumulation, altered flowering-related splicing (e.g., FLC), and broad alternative-splicing defects. These phenotypes support annotation of the Miscanthus ortholog as a regulator of RNA processing tied to abiotic stress signaling, but this remains an inference until gene-specific Miscanthus experiments are available. (daszkowskagolec2018emergingrolesof pages 1-4, daszkowskagolec2018emergingrolesof pages 9-11, daszkowskagolec2018emergingrolesof pages 24-32, daszkowskagolec2018emergingrolesof pages 4-6) | Daszkowska-Golec 2018, https://doi.org/10.1104/pp.17.01017; Laubinger et al. 2008, https://doi.org/10.1073/pnas.0802493105; Kim et al. 2008, https://doi.org/10.1093/pcp/pcn146; Raczynska et al. 2010, https://doi.org/10.1093/nar/gkp869 |
| Recent 2024 structural insights | 2024 update: structural work refined CBC as a dynamic interaction platform with multiple overlapping effector-binding surfaces on CBP80/CBP20. Productive and degradative effectors such as PHAX, NCBP3, NELF-E, ZC3H18, and ARS2 compete for CBC/CBCA binding. A conserved CBP80 tryptophan-binding pocket engages Trp-containing helices from several effectors; ARS2 can initially recruit effectors but also block direct CBC binding, helping determine whether a transcript proceeds toward processing/export or nuclear degradation. These insights support annotating NCGR_LOCUS1765 as a decision-making hub in cap-proximal RNP assembly, not merely a passive cap-associated factor. (dubiez2024structuralbasisfor pages 1-5, dubiez2024structuralbasisfor pages 29-34, dubiez2024structuralbasisfor pages 8-11, dubiez2024structuralbasisfor media 80a1309a) | Dubiez et al. 2024, bioRxiv https://doi.org/10.1101/2023.07.25.550453; Kataoka 2024, https://doi.org/10.1093/jb/mvad081 |
| Quantitative stats | Quantitative evidence from plant ortholog studies: in Arabidopsis, an RT-PCR panel of 435 alternative-splicing events found CBC-dependent changes in 101 genes, with ~50% of affected events at the first intron; genome-wide analyses reported 518 intron-retention events in Atcbp80/abh1, 931 in Atcbp20, with 298 shared. A cotranslational RNA-decay/NMD analysis found decay reduced to ~50% of wild type in Atcbp80/abh1. Structural biochemistry in 2024 reported binding affinities consistent with competitive CBC engagement, including NELF-E W345E weakening affinity from 113 nM to 1.3 ยตM, and PHAX full-length binding near 125 nM. Miscanthus-specific quantitative data for NCGR_LOCUS1765 were not found in the retrieved literature. (daszkowskagolec2018emergingrolesof pages 4-6, daszkowskagolec2018emergingrolesof pages 9-11, dubiez2024structuralbasisfor pages 8-11) | Daszkowska-Golec 2018, https://doi.org/10.1104/pp.17.01017; Raczynska et al. 2010, https://doi.org/10.1093/nar/gkp869; Dubiez et al. 2024, https://doi.org/10.1101/2023.07.25.550453 |
Table: This table summarizes a cautious functional annotation of Miscanthus lutarioriparius NCGR_LOCUS1765 (UniProt A0A811M5M6) based on verified membership in the NCBP1/CBP80 family. It distinguishes direct evidence from orthology-based inference and highlights both classic plant findings and 2024 structural advances on the nuclear cap-binding complex.
References
(daszkowskagolec2018emergingrolesof pages 1-4): Agata Daszkowska-Golec. Emerging roles of the nuclear cap-binding complex in abiotic stress responses1[open]. Plant Physiology, 176:242-253, Nov 2018. URL: https://doi.org/10.1104/pp.17.01017, doi:10.1104/pp.17.01017. This article has 21 citations and is from a highest quality peer-reviewed journal.
(kataoka2024thenuclearcapbinding pages 1-2): Naoyuki Kataoka. The nuclear cap-binding complex, a multitasking binding partner of rna polymerase ii transcripts. Journal of Biochemistry, 175:9-15, Oct 2024. URL: https://doi.org/10.1093/jb/mvad081, doi:10.1093/jb/mvad081. This article has 24 citations and is from a peer-reviewed journal.
(dubiez2024structuralbasisfor pages 1-5): Etienne Dubiez, Erika Pellegrini, Maja Finderup Brask, William Garland, Anne-Emmanuelle Foucher, Karine Huard, Torben Heick Jensen, Stephen Cusack, and Jan Kadlec. Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex. bioRxiv, Nov 2024. URL: https://doi.org/10.1101/2023.07.25.550453, doi:10.1101/2023.07.25.550453. This article has 20 citations.
(kataoka2024thenuclearcapbinding pages 2-4): Naoyuki Kataoka. The nuclear cap-binding complex, a multitasking binding partner of rna polymerase ii transcripts. Journal of Biochemistry, 175:9-15, Oct 2024. URL: https://doi.org/10.1093/jb/mvad081, doi:10.1093/jb/mvad081. This article has 24 citations and is from a peer-reviewed journal.
(kataoka2024thenuclearcapbinding pages 5-6): Naoyuki Kataoka. The nuclear cap-binding complex, a multitasking binding partner of rna polymerase ii transcripts. Journal of Biochemistry, 175:9-15, Oct 2024. URL: https://doi.org/10.1093/jb/mvad081, doi:10.1093/jb/mvad081. This article has 24 citations and is from a peer-reviewed journal.
(daszkowskagolec2018emergingrolesof pages 9-11): Agata Daszkowska-Golec. Emerging roles of the nuclear cap-binding complex in abiotic stress responses1[open]. Plant Physiology, 176:242-253, Nov 2018. URL: https://doi.org/10.1104/pp.17.01017, doi:10.1104/pp.17.01017. This article has 21 citations and is from a highest quality peer-reviewed journal.
(daszkowskagolec2018emergingrolesof pages 6-9): Agata Daszkowska-Golec. Emerging roles of the nuclear cap-binding complex in abiotic stress responses1[open]. Plant Physiology, 176:242-253, Nov 2018. URL: https://doi.org/10.1104/pp.17.01017, doi:10.1104/pp.17.01017. This article has 21 citations and is from a highest quality peer-reviewed journal.
(kataoka2024thenuclearcapbinding pages 4-5): Naoyuki Kataoka. The nuclear cap-binding complex, a multitasking binding partner of rna polymerase ii transcripts. Journal of Biochemistry, 175:9-15, Oct 2024. URL: https://doi.org/10.1093/jb/mvad081, doi:10.1093/jb/mvad081. This article has 24 citations and is from a peer-reviewed journal.
(daszkowskagolec2018emergingrolesof pages 4-6): Agata Daszkowska-Golec. Emerging roles of the nuclear cap-binding complex in abiotic stress responses1[open]. Plant Physiology, 176:242-253, Nov 2018. URL: https://doi.org/10.1104/pp.17.01017, doi:10.1104/pp.17.01017. This article has 21 citations and is from a highest quality peer-reviewed journal.
(dubiez2024structuralbasisfor pages 8-11): Etienne Dubiez, Erika Pellegrini, Maja Finderup Brask, William Garland, Anne-Emmanuelle Foucher, Karine Huard, Torben Heick Jensen, Stephen Cusack, and Jan Kadlec. Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex. bioRxiv, Nov 2024. URL: https://doi.org/10.1101/2023.07.25.550453, doi:10.1101/2023.07.25.550453. This article has 20 citations.
(dubiez2024structuralbasisfor media 80a1309a): Etienne Dubiez, Erika Pellegrini, Maja Finderup Brask, William Garland, Anne-Emmanuelle Foucher, Karine Huard, Torben Heick Jensen, Stephen Cusack, and Jan Kadlec. Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex. bioRxiv, Nov 2024. URL: https://doi.org/10.1101/2023.07.25.550453, doi:10.1101/2023.07.25.550453. This article has 20 citations.
(daszkowskagolec2018emergingrolesof pages 24-32): Agata Daszkowska-Golec. Emerging roles of the nuclear cap-binding complex in abiotic stress responses1[open]. Plant Physiology, 176:242-253, Nov 2018. URL: https://doi.org/10.1104/pp.17.01017, doi:10.1104/pp.17.01017. This article has 21 citations and is from a highest quality peer-reviewed journal.
(dubiez2024structuralbasisfor pages 29-34): Etienne Dubiez, Erika Pellegrini, Maja Finderup Brask, William Garland, Anne-Emmanuelle Foucher, Karine Huard, Torben Heick Jensen, Stephen Cusack, and Jan Kadlec. Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex. bioRxiv, Nov 2024. URL: https://doi.org/10.1101/2023.07.25.550453, doi:10.1101/2023.07.25.550453. This article has 20 citations.
id: A0A811M5M6
gene_symbol: NCGR_LOCUS1765
aliases:
- CBP80
- NCBP1
taxon:
id: NCBITaxon:422564
label: Miscanthus lutarioriparius
description: 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.
references:
- id: file:9POAL/NCGR_LOCUS1765/NCGR_LOCUS1765-deep-research-falcon.md
title: Falcon deep research on NCGR_LOCUS1765 function based on orthology to NCBP1/CBP80 family
- id: PMID:29142023
title: Emerging Roles of the Nuclear Cap-Binding Complex in Abiotic Stress Responses
- id: PMID:37830942
title: The Nuclear Cap-Binding Complex, a multitasking binding partner of RNA polymerase II transcripts
- id: PMID:18550839
title: Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing
in Arabidopsis thaliana
- id: PMID:19864257
title: Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana
- id: GO_REF:0000120
title: Phylogenomic annotation based on UniProt, InterPro and PANTHER
- id: GO_REF:0000002
title: Gene Ontology annotation through InterPro
- id: GO_REF:0000118
title: TreeGrafter annotation based on PANTHER
- id: GO_REF:0000044
title: Gene Ontology annotation through UniProt keyword mapping
existing_annotations:
- term:
id: GO:0000339
label: RNA cap binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
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.
action: ACCEPT
supported_by:
- reference_id: PMID:37830942
supporting_text: NCBP1 triggers a conformational change of NCBP2, which results in high-affinity binding
to m7G cap
- reference_id: PMID:37830942
supporting_text: Both proteins are required for stable binding to the cap structure, neither subunit
alone has a strong affinity for it
- term:
id: GO:0003723
label: RNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: KEEP_AS_NON_CORE
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.
supported_by:
- reference_id: PMID:37830942
supporting_text: Although NCBP1 and NCBP2 bind to the cap structure synergistically, both proteins
can associate with RNA directly
- term:
id: GO:0003729
label: mRNA binding
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
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.
action: ACCEPT
supported_by:
- reference_id: PMID:19864257
supporting_text: CBP proteins remain bound to the mRNA during the pioneer round of translation playing
an essential role in mRNA quality control
- term:
id: GO:0000184
label: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
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.
action: ACCEPT
supported_by:
- reference_id: PMID:19864257
supporting_text: CBP proteins remain bound to the mRNA during the pioneer round of translation playing
an essential role in mRNA quality control
- reference_id: PMID:19864257
supporting_text: in mammalian cells, CBP80 recruits the NMD factor Upf1 and promotes the interaction
of Upf1 with the NMD factor Upf2
- term:
id: GO:0006406
label: mRNA export from nucleus
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: CBC plays a direct role in mRNA nuclear export. The cap and the CBC have multiple functions
in mRNA biogenesis including nuclear export.
action: ACCEPT
supported_by:
- reference_id: PMID:19864257
supporting_text: The cap and the CBC have multiple functions in mRNA biogenesis including splicing
- reference_id: file:9POAL/NCGR_LOCUS1765/NCGR_LOCUS1765-deep-research-falcon.md
supporting_text: nuclear export of capped RNAs via adaptors such as PHAX for snRNAs or TREX/Aly/REF/TAP/NXF1-like
routes for mRNAs
- term:
id: GO:0016070
label: RNA metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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).
action: KEEP_AS_NON_CORE
reason: The term is accurate but uninformative. The specific processes annotated (NMD, mRNA export, RNA
splicing) provide more precise functional description.
supported_by:
- reference_id: PMID:29142023
supporting_text: Plant nuclear CBC consisted of two subunits (CBP20 and CBP80) is involved in both
conserved processes related to RNA metabolism
- term:
id: GO:0005634
label: nucleus
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
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.
action: ACCEPT
supported_by:
- reference_id: PMID:37830942
supporting_text: NCBP1 harbours a bipartite-type nuclear localization signal at the amino-terminus
that binds to importin ฮฑ
- reference_id: PMID:37830942
supporting_text: At the steady state, CBC is localized in the nucleus
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
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.
action: KEEP_AS_NON_CORE
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.
supported_by:
- reference_id: PMID:19864257
supporting_text: CBP proteins remain bound to the mRNA during the pioneer round of translation playing
an essential role in mRNA quality control
- term:
id: GO:0005846
label: nuclear cap binding complex
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
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.
action: ACCEPT
supported_by:
- reference_id: PMID:37830942
supporting_text: CBC consists of two polypeptides, whose molecular masses are 20 and 80 kDa
- reference_id: PMID:19864257
supporting_text: 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
- term:
id: GO:0008380
label: RNA splicing
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
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.
action: NEW
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.
supported_by:
- reference_id: PMID:19864257
supporting_text: Significant changes in the ratios of alternative splicing isoforms were found in
101 genes
- reference_id: PMID:19864257
supporting_text: CBP80 plays a more significant role in alternative splicing than CBP20, probably being
a platform for interactions with other splicing factors
- reference_id: PMID:18550839
supporting_text: se, abh1/cbp80, and cbp20 mutants also share similar splicing defects, leading to
the accumulation of many partially spliced transcripts
- term:
id: GO:0035196
label: miRNA processing
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: NEW
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.
supported_by:
- reference_id: PMID:18550839
supporting_text: Inactivation of either ABH1/CBP80 or CBP20 results in decreased levels of mature
miRNAs accompanied by apparent stabilization of pri-miRNAs
- reference_id: PMID:19864257
supporting_text: CBP20 and CBP80 are suggested to bind to capped pri-miRNA transcripts and play role
in their processing
core_functions:
- description: Forms the large scaffold subunit of the nuclear cap-binding complex (CBC) with NCBP2/CBP20,
enabling high-affinity recognition of the m7G cap on RNA polymerase II transcripts and recruitment of
downstream RNA processing factors
supported_by:
- reference_id: PMID:37830942
supporting_text: NCBP1 triggers a conformational change of NCBP2, which results in high-affinity binding
to m7G cap
- reference_id: PMID:37830942
supporting_text: Both proteins are required for stable binding to the cap structure, neither subunit
alone has a strong affinity for it
molecular_function:
id: GO:0000339
label: RNA cap binding
directly_involved_in:
- id: GO:0006397
label: mRNA processing
locations:
- id: GO:0005634
label: nucleus
- description: Coordinates co-transcriptional pre-mRNA splicing, particularly efficient removal of cap-proximal
first introns, and modulates alternative splicing patterns genome-wide
supported_by:
- reference_id: PMID:19864257
supporting_text: Significant changes in the ratios of alternative splicing isoforms were found in 101
genes
- reference_id: PMID:19864257
supporting_text: CBP80 plays a more significant role in alternative splicing than CBP20, probably being
a platform for interactions with other splicing factors
molecular_function:
id: GO:0000339
label: RNA cap binding
directly_involved_in:
- id: GO:0008380
label: RNA splicing
locations:
- id: GO:0005634
label: nucleus
- description: Supports miRNA biogenesis in plants by binding pri-miRNAs and facilitating their processing
through cooperation with SERRATE and the DCL1 complex
supported_by:
- reference_id: PMID:18550839
supporting_text: Inactivation of either ABH1/CBP80 or CBP20 results in decreased levels of mature miRNAs
accompanied by apparent stabilization of pri-miRNAs
- reference_id: PMID:19864257
supporting_text: CBP20 and CBP80 are suggested to bind to capped pri-miRNA transcripts and play role
in their processing
molecular_function:
id: GO:0000339
label: RNA cap binding
directly_involved_in:
- id: GO:0035196
label: miRNA processing
locations:
- id: GO:0005634
label: nucleus
suggested_questions:
- question: Does NCGR_LOCUS1765 in Miscanthus lutarioriparius functionally complement the Arabidopsis abh1/cbp80
mutant phenotypes, including ABA hypersensitivity and altered miRNA biogenesis?
experts:
- Plant RNA biology researchers
- Miscanthus geneticists
- question: Are there Miscanthus-specific alternative splicing events regulated by CBC that differ from those
observed in Arabidopsis or other grasses?
experts:
- Plant splicing biology researchers
- Grass genomics specialists
suggested_experiments:
- hypothesis: NCGR_LOCUS1765 functions as a canonical NCBP1/CBP80 ortholog with conserved roles in splicing
regulation and miRNA biogenesis in Miscanthus
description: 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: CBC function in Miscanthus contributes to abiotic stress tolerance relevant to its use as a
bioenergy crop
description: 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.