Source 1primary paper2006Photochemical & Photobiological Sciences
Toolkit/YtvA
YtvA
Also known as: LOV photoreceptor YtvA of Bacillus subtilis, LOV-STAS protein, YtvA
Taxonomy: Mechanism Branch / Component. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
YtvA is a blue-light-sensing LOV-STAS photoreceptor from Bacillus subtilis whose LOV domain has been structurally analyzed for LOV-LOV dimerization and interdomain interactions. Homologous mutations in a conserved LOV hydrophobic pocket alter activation-state kinetics, supporting YtvA as a tunable LOV sensor domain relevant to optogenetic design.
Usefulness & Problems
Why this is useful
YtvA is useful as a model LOV photoreceptor for understanding how blue-light sensing, dimerization interfaces, and interdomain coupling shape signaling-state behavior. Evidence that homologous pocket mutations alter dark-recovery and photo-adduct lifetimes indicates utility for tuning on/off kinetics in LOV-based optogenetic tools.
Source:
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
Source:
LOV photoreceptors are widely distributed throughout all kingdoms of life, and have in recent years, due to their modular nature, been broadly used as sensor domains for the construction of optogenetic tools.
Problem solved
YtvA helps address the problem of how to rationally tune LOV photoreceptor signaling kinetics, especially dark recovery and steady-state on/off equilibria. The cited work links conserved hydrophobic-pocket mutations to altered activation-state lifetimes, providing an engineering principle for kinetic control.
Source:
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Component: A low-level protein part used inside a larger architecture that realizes a mechanism.
Mechanisms
conformational uncagingConformational UncagingHeterodimerizationinterdomain conformational couplinglov-lov dimerizationphoto-adduct lifetime tuningTechniques
Structural CharacterizationTarget processes
No target processes tagged yet.
Input: Light
Implementation Constraints
YtvA is a LOV-STAS protein from Bacillus subtilis and functions as a blue-light-sensing photoreceptor. Practical engineering guidance from the supplied evidence centers on introducing homologous mutations within a conserved LOV hydrophobic pocket to tune dark-recovery kinetics, but specific construct architectures and expression conditions are not described.
The supplied evidence supports YtvA primarily as a mechanistic and engineering-relevant sensor domain, but does not document a specific deployed optogenetic construct or application outcome. Quantitative performance metrics, illumination parameters, and validation in diverse cellular systems are not provided in the supplied evidence.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Source 2primary paper2022Photochemical & Photobiological Sciences
Source 3primary paper2017Biochemistry
Ranked Claims
The identified conserved-pocket mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors.
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
The identified conserved-pocket mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors.
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
The identified conserved-pocket mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors.
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
The identified conserved-pocket mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors.
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
The identified conserved-pocket mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors.
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
The identified conserved-pocket mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors.
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
The identified conserved-pocket mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors.
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
Additional pocket mutations in PpSB1-LOV and homologous mutations in YtvA and the Avena sativa LOV2 domain produce similarly altered kinetics.
Additional mutations within the pocket of PpSB1-LOV and the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis and the Avena sativa LOV2 domain result in similarly altered kinetics.
Additional pocket mutations in PpSB1-LOV and homologous mutations in YtvA and the Avena sativa LOV2 domain produce similarly altered kinetics.
Additional mutations within the pocket of PpSB1-LOV and the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis and the Avena sativa LOV2 domain result in similarly altered kinetics.
Additional pocket mutations in PpSB1-LOV and homologous mutations in YtvA and the Avena sativa LOV2 domain produce similarly altered kinetics.
Additional mutations within the pocket of PpSB1-LOV and the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis and the Avena sativa LOV2 domain result in similarly altered kinetics.
Additional pocket mutations in PpSB1-LOV and homologous mutations in YtvA and the Avena sativa LOV2 domain produce similarly altered kinetics.
Additional mutations within the pocket of PpSB1-LOV and the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis and the Avena sativa LOV2 domain result in similarly altered kinetics.
Additional pocket mutations in PpSB1-LOV and homologous mutations in YtvA and the Avena sativa LOV2 domain produce similarly altered kinetics.
Additional mutations within the pocket of PpSB1-LOV and the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis and the Avena sativa LOV2 domain result in similarly altered kinetics.
Additional pocket mutations in PpSB1-LOV and homologous mutations in YtvA and the Avena sativa LOV2 domain produce similarly altered kinetics.
Additional mutations within the pocket of PpSB1-LOV and the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis and the Avena sativa LOV2 domain result in similarly altered kinetics.
Additional pocket mutations in PpSB1-LOV and homologous mutations in YtvA and the Avena sativa LOV2 domain produce similarly altered kinetics.
Additional mutations within the pocket of PpSB1-LOV and the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis and the Avena sativa LOV2 domain result in similarly altered kinetics.
Mutations that alter the lifetime of the photo-adduct signaling state can tune LOV sensor on/off kinetics and steady-state on/off equilibria.
Mutations that alter the lifetime of the photo-adduct signaling state represent a convenient handle to tune LOV sensor on/off kinetics and, thus, steady-state on/off equilibria of the photoreceptor (or optogenetic switch).
LOV photoreceptors have been broadly used as sensor domains for the construction of optogenetic tools.
LOV photoreceptors are widely distributed throughout all kingdoms of life, and have in recent years, due to their modular nature, been broadly used as sensor domains for the construction of optogenetic tools.
In PpSB1-LOV, the I48T mutation accelerates adduct rupture and is structurally and mechanistically benign, with unaltered light-induced structural changes by NMR spectroscopy and X-ray crystallography.
Using the slow cycling bacterial short LOV photoreceptor PpSB1-LOV, we show that the I48T mutation within this pocket, which accelerates adduct rupture, is otherwise structurally and mechanistically benign, i.e., light-induced structural changes, as probed by NMR spectroscopy and X-ray crystallography, are not altered in the variant.
In PpSB1-LOV, the I48T mutation accelerates adduct rupture and is structurally and mechanistically benign, with unaltered light-induced structural changes by NMR spectroscopy and X-ray crystallography.
Using the slow cycling bacterial short LOV photoreceptor PpSB1-LOV, we show that the I48T mutation within this pocket, which accelerates adduct rupture, is otherwise structurally and mechanistically benign, i.e., light-induced structural changes, as probed by NMR spectroscopy and X-ray crystallography, are not altered in the variant.
In PpSB1-LOV, the I48T mutation accelerates adduct rupture and is structurally and mechanistically benign, with unaltered light-induced structural changes by NMR spectroscopy and X-ray crystallography.
Using the slow cycling bacterial short LOV photoreceptor PpSB1-LOV, we show that the I48T mutation within this pocket, which accelerates adduct rupture, is otherwise structurally and mechanistically benign, i.e., light-induced structural changes, as probed by NMR spectroscopy and X-ray crystallography, are not altered in the variant.
In PpSB1-LOV, the I48T mutation accelerates adduct rupture and is structurally and mechanistically benign, with unaltered light-induced structural changes by NMR spectroscopy and X-ray crystallography.
Using the slow cycling bacterial short LOV photoreceptor PpSB1-LOV, we show that the I48T mutation within this pocket, which accelerates adduct rupture, is otherwise structurally and mechanistically benign, i.e., light-induced structural changes, as probed by NMR spectroscopy and X-ray crystallography, are not altered in the variant.
In PpSB1-LOV, the I48T mutation accelerates adduct rupture and is structurally and mechanistically benign, with unaltered light-induced structural changes by NMR spectroscopy and X-ray crystallography.
Using the slow cycling bacterial short LOV photoreceptor PpSB1-LOV, we show that the I48T mutation within this pocket, which accelerates adduct rupture, is otherwise structurally and mechanistically benign, i.e., light-induced structural changes, as probed by NMR spectroscopy and X-ray crystallography, are not altered in the variant.
In PpSB1-LOV, the I48T mutation accelerates adduct rupture and is structurally and mechanistically benign, with unaltered light-induced structural changes by NMR spectroscopy and X-ray crystallography.
Using the slow cycling bacterial short LOV photoreceptor PpSB1-LOV, we show that the I48T mutation within this pocket, which accelerates adduct rupture, is otherwise structurally and mechanistically benign, i.e., light-induced structural changes, as probed by NMR spectroscopy and X-ray crystallography, are not altered in the variant.
In PpSB1-LOV, the I48T mutation accelerates adduct rupture and is structurally and mechanistically benign, with unaltered light-induced structural changes by NMR spectroscopy and X-ray crystallography.
Using the slow cycling bacterial short LOV photoreceptor PpSB1-LOV, we show that the I48T mutation within this pocket, which accelerates adduct rupture, is otherwise structurally and mechanistically benign, i.e., light-induced structural changes, as probed by NMR spectroscopy and X-ray crystallography, are not altered in the variant.
A conserved hydrophobic pocket has mutations with strong impact on adduct-state lifetime across different LOV photoreceptor families.
we identify a conserved hydrophobic pocket for which mutations have a strong impact on the adduct-state lifetime across different LOV photoreceptor families
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
adduct formation rate variation 3.6 fold
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
structural change timescale micro- to submillisecondvariation magnitude orders of magnitude
The study reports a competitive interface involving LOV-LOV dimerization and interdomain interactions in YtvA.
reveals a competitive interface for LOV—LOV dimerization and interdomain interactions
The study reports a competitive interface involving LOV-LOV dimerization and interdomain interactions in YtvA.
reveals a competitive interface for LOV—LOV dimerization and interdomain interactions
The study reports a competitive interface involving LOV-LOV dimerization and interdomain interactions in YtvA.
reveals a competitive interface for LOV—LOV dimerization and interdomain interactions
The study reports a competitive interface involving LOV-LOV dimerization and interdomain interactions in YtvA.
reveals a competitive interface for LOV—LOV dimerization and interdomain interactions
The study reports a competitive interface involving LOV-LOV dimerization and interdomain interactions in YtvA.
reveals a competitive interface for LOV—LOV dimerization and interdomain interactions
The study reports a competitive interface involving LOV-LOV dimerization and interdomain interactions in YtvA.
reveals a competitive interface for LOV—LOV dimerization and interdomain interactions
The study reports a competitive interface involving LOV-LOV dimerization and interdomain interactions in YtvA.
reveals a competitive interface for LOV—LOV dimerization and interdomain interactions
YtvA is a blue-light sensing protein.
Conformational analysis of the blue-light sensing protein YtvA
YtvA is a blue-light sensing protein.
Conformational analysis of the blue-light sensing protein YtvA
YtvA is a blue-light sensing protein.
Conformational analysis of the blue-light sensing protein YtvA
YtvA is a blue-light sensing protein.
Conformational analysis of the blue-light sensing protein YtvA
YtvA is a blue-light sensing protein.
Conformational analysis of the blue-light sensing protein YtvA
YtvA is a blue-light sensing protein.
Conformational analysis of the blue-light sensing protein YtvA
YtvA is a blue-light sensing protein.
Conformational analysis of the blue-light sensing protein YtvA
Approval Evidence
3 sources8 linked approval claimsfirst-pass slug ytva
the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis
Source:
the LOV-STAS protein, YtvA
Source:
Conformational analysis of the blue-light sensing protein YtvA reveals a competitive interface for LOV—LOV dimerization and interdomain interactions
Source:
application potentialsupports
The identified conserved-pocket mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors.
Given the conserved nature of the corresponding structural region, the here identified mutations should find application in dark-recovery tuning of optogenetic tools and LOV photoreceptors, alike.
Source:
cross family generalizationsupports
Additional pocket mutations in PpSB1-LOV and homologous mutations in YtvA and the Avena sativa LOV2 domain produce similarly altered kinetics.
Additional mutations within the pocket of PpSB1-LOV and the introduction of homologous mutations in the LOV photoreceptor YtvA of Bacillus subtilis and the Avena sativa LOV2 domain result in similarly altered kinetics.
Source:
mechanistic conservationsupports
Across AsLOV2, YtvA, EL222, and LovK, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved despite differences in tertiary structure.
Despite differences in tertiary structure, the overall pathway leading to cysteine adduct formation from the FMN triplet state is highly conserved, although there are slight variations in rate.
Source:
post adduct kinetic divergencesupports
After adduct formation, vibrational spectra and kinetics differ significantly among the full-length LOV photoreceptors and are directly linked to the specific output function of the LOV domain.
However, significant differences are observed in the vibrational spectra and kinetics after adduct formation, which are directly linked to the specific output function of the LOV domain.
Source:
rate variationsupports
The rate of adduct formation varies by only 3.6-fold among the studied LOV proteins.
While the rate of adduct formation varies by only 3.6-fold among the proteins
Source:
structural change timescalesupports
Large-scale structural changes in the full-length LOV photoreceptors occur over micro- to submillisecond time scales and vary by orders of magnitude depending on output function.
the subsequent large-scale structural changes in the full-length LOV photoreceptors occur over the micro- to submillisecond time scales and vary by orders of magnitude depending on the different output function of each LOV domain.
Source:
structural mechanistic claimsupports
The study reports a competitive interface involving LOV-LOV dimerization and interdomain interactions in YtvA.
reveals a competitive interface for LOV—LOV dimerization and interdomain interactions
Source:
structural mechanistic claimsupports
YtvA is a blue-light sensing protein.
Conformational analysis of the blue-light sensing protein YtvA
Source:
Comparisons
Source-backed strengths
YtvA has direct structural evidence for a competitive interface involving LOV-LOV dimerization and interdomain interactions, which informs mechanistic understanding of signal propagation. Homologous mutations in YtvA were reported to produce altered kinetics consistent with effects seen in other LOV-family proteins, supporting cross-family relevance of the tuning principle.
Source:
Mutations that alter the lifetime of the photo-adduct signaling state represent a convenient handle to tune LOV sensor on/off kinetics and, thus, steady-state on/off equilibria of the photoreceptor (or optogenetic switch).
Ranked Citations
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