Source 1primary paper2023Journal of Cell Science
Toolkit/CIB1
CIB1
Also known as: calcium- and integrin-binding protein 1, CIB, cryptochrome-interacting bHLH
Taxonomy: Mechanism Branch / Component. Workflows sit above the mechanism and technique branches rather than replacing them.
Assembly Hierarchy
Part of
- CRY2/CIB1multi component switch← this item is a component
Summary
As a tool component, CIB1 is most directly supported as the cryptochrome-interacting bHLH partner used with CRY2 to create blue-light-controlled protein association systems. In these systems, CIB1 is typically fused to localization, transcriptional, or enzymatic modules so that blue light drives CRY2–CIB1 binding and light withdrawal reverses the interaction.
Usefulness & Problems
Why this is useful
CIB1 is useful because it provides the binding partner that converts CRY2 photoexcitation into controllable recruitment, localization, and transcriptional outputs. The supplied evidence supports its use in split-enzyme reconstitution and optogenetic two-hybrid architectures, including split-TurboID activation and TALE-based light-inducible transcriptional regulation.
Source:
Overexpression of the HBI1-related bHLHs brassinosteroid enhanced expression2 (BEE2) and cryptochrome-interacting bHLH (CIB1) partially inhibits immunity, indicating that BEE2 and CIB1 may act redundantly with HBI1.
Source:
Here we describe the development of light-inducible transcriptional effectors (LITEs), an optogenetic two-hybrid system integrating the customizable TALE DNA-binding domain with the light-sensitive cryptochrome 2 protein and its interacting partner CIB1 from Arabidopsis thaliana.
Problem solved
CIB1 helps solve the problem of achieving reversible, light-gated control over protein proximity in cells. Specifically, it enables blue-light-triggered recruitment of CRY2-tagged proteins to CIB1-tagged targets or compartments, allowing temporal control of signaling, localization, and transcription-related functions.
Source:
Here we describe the development of light-inducible transcriptional effectors (LITEs), an optogenetic two-hybrid system integrating the customizable TALE DNA-binding domain with the light-sensitive cryptochrome 2 protein and its interacting partner CIB1 from Arabidopsis thaliana.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Component: A low-level protein part used inside a larger architecture that realizes a mechanism.
Mechanisms
Heterodimerizationlight-induced heterodimerizationOligomerizationprotein recruitment/localization controlreversible dissociation after light withdrawalsplit-enzyme reconstitutionTechniques
Structural CharacterizationTarget processes
localizationsignalingtranscriptionInput: Chemical
Implementation Constraints
Reported implementations fuse CIB1 to functional modules such as one half of split-TurboID, membrane anchors, or components of a TALE-based transcriptional system, while CRY2 is fused to the complementary module. Blue light is the activating input in the cited optogenetic systems, and turning off illumination causes CRY2–CIB1 dissociation. The evidence most directly supports CIB1 as a fusion-compatible recruitment handle rather than as a standalone effector domain.
The supplied evidence also shows that the name CIB1 is ambiguous, referring both to the plant cryptochrome-interacting bHLH used in optogenetics and to a vertebrate calcium- and integrin-binding protein 1 with distinct biology. For the optogenetic use case, the evidence does not provide quantitative kinetics, binding affinities, spectral details beyond blue light, or broad cross-system benchmarking. CIB1 fusion proteins can alter CRY2 homo-oligomerization, indicating context dependence that may complicate interpretation or optimization.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Observations
successMammalian Cell Linemechanistic demo
Inferred from claim claim_3 during normalization. Upon blue light illumination, CRY2 and CIB1 dimerize, reconstitute split-TurboID, and initiate biotinylation. Derived from claim claim_3. Quoted text: upon illumination with blue light, CRY2 and CIB1 dimerize, reconstitute split-TurboID and initiate biotinylation
Source:
Supporting Sources
Source 2primary paper2004Journal of Biological Chemistry
Source 3primary paper2011Journal of Biological Chemistry
Source 4primary paper2009Protein Science
Source 5primary paper2015ACS Synthetic Biology
Source 6primary paper2014PLANT PHYSIOLOGY
Source 7primary paper2013Nature
Ranked Claims
LAB fuses the two halves of split-TurboID to the photodimeric proteins CRY2 and CIB1.
Our technology, called light-activated BioID (LAB), fuses the two halves of the split-TurboID proximity labeling enzyme to the photodimeric proteins CRY2 and CIB1.
Upon blue light illumination, CRY2 and CIB1 dimerize, reconstitute split-TurboID, and initiate biotinylation.
upon illumination with blue light, CRY2 and CIB1 dimerize, reconstitute split-TurboID and initiate biotinylation
Turning off the light causes CRY2 and CIB1 to dissociate and halts biotinylation.
Turning off the light leads to the dissociation of CRY2 and CIB1 and halts biotinylation.
Photoexcited CRY2 can undergo both homo-oligomerization and heterodimerization with CIB1 under blue light.
the photoexcited CRY2 can both undergo homo-oligomerization and heterodimerization by binding to its dimerization partner CIB1
Certain CIB1 fusion proteins can suppress CRY2 homo-oligomerization.
the presence of certain CIB1 fusion proteins can suppress CRY2 homo-oligomerization
Recruitment of cytoplasmic CRY2 to the membrane via interaction with membrane-bound CIB1 significantly intensifies CRY2 homo-oligomerization.
the homo-oligomerization of cytoplasmic CRY2 can be significantly intensified by its recruitment to the membrane via interaction with the membrane-bound CIB1
BEE2 and CIB1 partially inhibit immunity and may act redundantly with HBI1.
Overexpression of the HBI1-related bHLHs brassinosteroid enhanced expression2 (BEE2) and cryptochrome-interacting bHLH (CIB1) partially inhibits immunity, indicating that BEE2 and CIB1 may act redundantly with HBI1.
The paper describes development of LITEs, an optogenetic two-hybrid system integrating a TALE DNA-binding domain with cryptochrome 2 and CIB1.
Here we describe the development of light-inducible transcriptional effectors (LITEs), an optogenetic two-hybrid system integrating the customizable TALE DNA-binding domain with the light-sensitive cryptochrome 2 protein and its interacting partner CIB1 from Arabidopsis thaliana.
CIB1 is a specific binding partner for the platelet integrin αIIb cytoplasmic domain.
The calcium- and integrin-binding protein 1 (CIB1) is a ubiquitous Ca(2+)-binding protein and a specific binding partner for the platelet integrin αIIb cytoplasmic domain
EF-hand III of both Ca2+-CIB1 and Mg2+-CIB1 is directly involved in the interaction of CIB1 with αIIb.
The EF-hand III of both Ca(2+)-CIB1 and Mg(2+)-CIB1 was identified to be directly involved in the interaction of CIB1 with αIIb.
CIB1 behaves differently from related EF-hand regulatory calcium-binding proteins such as calmodulin or neuronal calcium sensor proteins.
Together, these data illustrate that CIB1 behaves quite differently from related EF-hand regulatory calcium-binding proteins, such as calmodulin or neuronal calcium sensor proteins.
The C-terminal helix of Ca2+-CIB1 is displaced upon αIIb binding.
NMR measurements of backbone amide proton slow motion (microsecond to millisecond) dynamics confirmed that the C-terminal helix of Ca(2+)-CIB1 is displaced upon αIIb binding.
Ca2+-CIB1 and Mg2+-CIB1 have similar structures, but the N-lobe of Mg2+-CIB1 is slightly more opened than that of Ca2+-CIB1.
Ca(2+)-CIB1 and Mg(2+)-CIB1 have similar structures, but the N-lobe of Mg(2+)-CIB1 is slightly more opened than that of Ca(2+)-CIB1.
The solution structure of Ca2+-CIB1 has smaller opened EF-hands in its C-domain than available crystal structures.
The solution structure of Ca(2+)-CIB1 possesses smaller opened EF-hands in its C-domain compared with available crystal structures.
CIB1 exhibits low-affinity Ca2+ binding events with Kd about 10^-2 M.
our data identify low affinity ( K d , 10 −2 M ) Ca 2+ binding events
Kd 10^-2 M
Low-affinity Ca2+ binding events should be considered when analyzing and interpreting protein crystallographic structures determined in the presence of very high Ca2+ concentrations.
the impact of low affinity Ca 2+ binding events should be considered when analyzing and interpreting protein crystallographic structures determined in the presence of very high Ca 2+ concentrations
Biophysical and biochemical experiments failed to detect phosphatase activity for CIB1 under several solution conditions.
Biophysical and biochemical experiments failed to detect ... phosphatase activity for CIB1 under several solution conditions
Biophysical and biochemical experiments failed to detect glutathione binding for CIB1 under several solution conditions.
Biophysical and biochemical experiments failed to detect glutathione binding
Biophysical and biochemical experiments failed to detect protein dimerization for CIB1 under several solution conditions.
Biophysical and biochemical experiments failed to detect ... protein dimerization
Low-affinity Ca2+ binding events influence the structures of the N- and C-terminal extensions of CIB1 under high Ca2+ crystallization conditions.
low affinity ... Ca 2+ binding events that influence the structures of the N‐ and C‐terminal extensions of CIB1 under high (300 m M ) Ca 2+ crystallization conditions
Ca2+ concentration 300 mM
CIB1 binds multiple effector proteins, including platelet alphaIIbbeta3 integrin and several serine/threonine kinases.
CIB1 (CIB) is an EF-hand-containing protein that binds multiple effector proteins, including the platelet alphaIIbbeta3 integrin and several serine/threonine kinases
Differences in structure, oligomeric state, and phylogeny define a new family of CIB1-related proteins extending from arthropods to humans.
Differences in structure, oligomeric state, and phylogeny define a new family of CIB1-related proteins that extends from arthropods to humans
Ca2+-bound CIB1 is largely monomeric both when bound to a relevant peptide ligand and when ligand-free.
Ca(2+)-bound CIB1 is largely monomeric whether bound to a relevant peptide ligand or ligand-free
The crystal structure of Ca2+-bound CIB1 was determined at 2.0 A resolution.
The crystal structure for Ca(2+)-bound CIB1 has been determined at 2.0 A resolution
crystal structure resolution 2 A
Ca2+-bound CIB1 is a compact alpha-helical protein containing four EF-hands, with the last two binding calcium ions in the standard EF-hand fashion.
reveals a compact alpha-helical protein containing four EF-hands, the last two of which bind calcium ions in the standard fashion seen in many other EF-hand proteins
CIB1 contains a hydrophobic pocket implicated in ligand binding.
CIB1 contains a hydrophobic pocket that has been implicated in ligand binding by previous mutational analysis
CIB1 shares high structural similarity with calcineurin B and the neuronal calcium sensor family of EF-hand-containing proteins.
CIB1 shares high structural similarity with calcineurin B and the neuronal calcium sensor (NCS) family of EF-hand-containing proteins
Approval Evidence
20 sources104 linked approval claimsfirst-pass slug cib1
USP14 directly interacts with and stabilizes calcium- and integrin-binding protein 1 (CIB1) by reversing K48-linked proteolytic ubiquitination at K24.
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to the photodimeric proteins CRY2 and CIB1
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CIB1 gene encoding calcium-and integrin-binding protein-1 (CIB1).
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the UPR regulator Cib1
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we used yeast-two-hybrid screening to identify cytosolic Ca2+ and integrin-binding protein 1 (CIB1), as its interacting partner.
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binding to its dimerization partner CIB1
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Overexpression of the HBI1-related bHLHs ... cryptochrome-interacting bHLH (CIB1)
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the role of CIB1 (calcium and integrin binding protein-1) associated with integrin signaling was analyzed
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the soybean basic helix-loop-helix transcription activator CIB1 (for cryptochrome-interacting bHLH1)
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The unusual C-terminal extension of the U. maydis Hac1 homolog, Cib1 (for Clp1 interacting bZIP1), mediates direct interaction with Clp1.
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the transcription factor CRYPTOCHROME-INTERACTING basic helix-loop-helix 1 (CIB1)
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its interacting partner CIB1 from Arabidopsis thaliana
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gain of function effectsupports
In vivo AAV9-mediated transduction of CIB1 promotes lenvatinib resistance in patient-derived xenografts.
in vivo adeno-associated virus 9 mediated transduction of CIB1 promoted lenvatinib resistance in PDXs
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loss of function effectsupports
CIB1 knockdown resensitizes patient-derived xenografts to lenvatinib.
whereas CIB1 knockdown resensitized the response of PDXs to lenvatinib
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mechanistic interactionsupports
USP14 directly interacts with and stabilizes CIB1 by reversing K48-linked proteolytic ubiquitination at K24.
USP14 directly interacts with and stabilizes calcium- and integrin-binding protein 1 (CIB1) by reversing K48-linked proteolytic ubiquitination at K24
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pathway facilitationsupports
USP14-mediated stabilization of CIB1 facilitates the PAK1-ERK1/2 signaling axis.
thus facilitating the P21-activated kinase 1 (PAK1)-ERK1/2 signaling axis
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therapeutic implicationsupports
Targeting CIB1 and its pathways may be a novel pharmaceutical intervention for lenvatinib-resistant hepatocellular carcinoma.
Targeting CIB1 and its pathways may be a novel pharmaceutical intervention for the treatment of lenvatinib-resistant HCC.
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construct architecturesupports
LAB fuses the two halves of split-TurboID to the photodimeric proteins CRY2 and CIB1.
Our technology, called light-activated BioID (LAB), fuses the two halves of the split-TurboID proximity labeling enzyme to the photodimeric proteins CRY2 and CIB1.
Source:
mechanism of actionsupports
Upon blue light illumination, CRY2 and CIB1 dimerize, reconstitute split-TurboID, and initiate biotinylation.
upon illumination with blue light, CRY2 and CIB1 dimerize, reconstitute split-TurboID and initiate biotinylation
Source:
reversibilitysupports
Turning off the light causes CRY2 and CIB1 to dissociate and halts biotinylation.
Turning off the light leads to the dissociation of CRY2 and CIB1 and halts biotinylation.
Source:
complex formationsupports
CIB1 forms a complex with EVER1 and EVER2.
CIB1 forms a complex with EVER1 and EVER2
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dependency relationshipsupports
CIB1 protein is not expressed in EVER1-deficient or EVER2-deficient cells.
CIB1 proteins are not expressed in EVER1-or EVER2-deficient cells.
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disease associationsupports
Homozygous null mutations of CIB1 are described in patients with epidermodysplasia verruciformis.
We describe EV patients homozygous for null mutations of the CIB1 gene encoding calcium-and integrin-binding protein-1 (CIB1).
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expression observationsupports
CIB1 is strongly expressed in skin and cultured keratinocytes of controls but not in those of patients.
CIB1 is strongly expressed in the skin and cultured keratinocytes of controls but not in those of patients.
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functional independencesupports
Known functions of EVER1 and EVER2 in human keratinocytes are not dependent on CIB1.
The known functions of EVER1 and EVER2 in human keratinocytes are not dependent on CIB1
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mechanistic hypothesissupports
CIB1 likely acts as a restriction factor against HPVs.
suggesting that this protein acts as a restriction factor against HPVs
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negative phenotypesupports
CIB1 deficiency does not impair keratinocyte adhesion or migration.
CIB1 deficiency does not impair keratinocyte adhesion or migration.
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protein interactionsupports
In keratinocytes, CIB1 interacts with HPV E5 and E8 proteins encoded by α-HPV16 and γ-HPV4, respectively.
In keratinocytes, the CIB1 protein interacts with the HPV E5 and E8 proteins encoded by α-HPV16 and γ-HPV4, respectively
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protein interactionsupports
Crosstalk between the unfolded protein response and pathogenic development pathways is mediated by protein-protein interactions between Cib1 and Clp1.
Crosstalk between the UPR and pathways controlling pathogenic development is mediated by protein-protein interactions between the UPR regulator Cib1 and the developmental regulator Clp1.
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regulatory associationsupports
Increased ER stress resistance is connected to Clp1-dependent alterations of Cib1 phosphorylation, protein stability, and UPR gene expression.
We show that increased ER stress resistance is connected to Clp1-dependent alterations of Cib1 phosphorylation, protein stability and UPR gene expression.
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regulatory effectsupports
Cib1/Clp1 complex formation aligns fungal proliferation in planta, efficient effector secretion, increased ER stress tolerance, and long-term UPR activation in planta.
Cib1/Clp1 complex formation results in mutual modification of the connected regulatory networks thereby aligning fungal proliferation in planta, efficient effector secretion with increased ER stress tolerance and long-term UPR activation in planta.
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correlationsupports
Cellular cADPR levels correlate directly with CIB1 levels after CIB1 knockdown or knockout.
Using shRNA to knock down and Cas9/guide RNA to knock out CIB1, a direct correlation between the cellular cADPR and CIB1 levels was demonstrated.
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Comparisons
Source-backed strengths
The CRY2–CIB1 interaction is directly supported to occur upon blue light illumination and to reverse after light withdrawal, providing an externally controllable and reversible dimerization module. CIB1 has been validated in multiple tool contexts in the supplied evidence, including split-TurboID reconstitution and LITE transcriptional control systems. Additional evidence indicates that CIB1 fusion context can modulate CRY2 homo-oligomerization, which may be advantageous for tuning system behavior.
Source:
Together, these data illustrate that CIB1 behaves quite differently from related EF-hand regulatory calcium-binding proteins, such as calmodulin or neuronal calcium sensor proteins.
Ranked Citations
- 1.
Derived from 3 linked claims and 1 validation observations. Example evidence: Our technology, called light-activated BioID (LAB), fuses the two halves of the split-TurboID proximity labeling enzyme to the photodimeric proteins CRY2 and CIB1.
- 2.
- 3.
- 4.
- 5.
- 6.
Derived from 1 linked claims. Example evidence: Overexpression of the HBI1-related bHLHs brassinosteroid enhanced expression2 (BEE2) and cryptochrome-interacting bHLH (CIB1) partially inhibits immunity, indicating that BEE2 and CIB1 may act redundantly with HBI1.
- 7.
Derived from 1 linked claims. Example evidence: Here we describe the development of light-inducible transcriptional effectors (LITEs), an optogenetic two-hybrid system integrating the customizable TALE DNA-binding domain with the light-sensitive cryptochrome 2 protein and its interacting partner CIB1 from Arabidopsis thaliana.