Source 1primary paper2021Nature Communications
Toolkit/photo-crosslinking
photo-crosslinking
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Photo-crosslinking in this context is an application of genetic code expansion in Bacillus subtilis that enables light-triggered covalent capture of molecular interactions. The reported system was part of a broader noncanonical amino acid incorporation platform used for photo-crosslinking, click-labelling, and translational titration.
Usefulness & Problems
Why this is useful
This approach is useful for probing protein interactions and cell-division biology in vivo in Bacillus subtilis using genetically encoded, light-responsive chemistry. The source study indicates that the underlying genetic code expansion platform enabled interrogation of bacterial cytokinesis by precise modulation of cell division dynamics.
Source:
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Source:
we demonstrate broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons
Problem solved
It addresses the problem of introducing photo-reactive chemical functionality into proteins in Bacillus subtilis, where efficient genetic code expansion had been limited. This enables covalent trapping of interactions under light control within a bacterial system.
Source:
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Problem links
Need precise spatiotemporal control with light input
DerivedPhoto-crosslinking is an application enabled by genetic code expansion systems in Bacillus subtilis, where light-responsive noncanonical amino acid incorporation is used to support covalent capture of molecular interactions. In the cited study, these systems were used alongside click-labeling and translational titration and were applied to interrogate bacterial cell division and validate a predicted protein-protein binding interface.
Need tighter control over protein production
DerivedPhoto-crosslinking is an application enabled by genetic code expansion systems in Bacillus subtilis, where light-responsive noncanonical amino acid incorporation is used to support covalent capture of molecular interactions. In the cited study, these systems were used alongside click-labeling and translational titration and were applied to interrogate bacterial cell division and validate a predicted protein-protein binding interface.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A reusable architecture pattern for arranging parts into an engineered system.
Mechanisms
genetic code expansiongenetic code expansionphoto-crosslinkingphoto-crosslinkingtranslation controltranslation controlTranslation ControlTechniques
No technique tags yet.
Target processes
translationInput: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationimplementation constraint: spectral hardware requirementoperating role: builder
Implementation depends on a genetic code expansion system in Bacillus subtilis capable of incorporating noncanonical amino acids, and the study reports use of three system families and two codon choices. The supplied evidence does not provide construct architecture, orthogonal synthetase/tRNA identities, or optical exposure parameters for the photo-crosslinking application.
The provided evidence does not specify the photo-crosslinking amino acid, illumination wavelength, crosslinking efficiency, or target proteins. Validation described here is limited to a single 2021 study in Bacillus subtilis, with no independent replication provided.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Observations
successBacteriaapplication demoBacillus subtilis
Inferred from claim c2 during normalization. The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration. Derived from claim c2. Quoted text: We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Source:
successBacteriaapplication demoBacillus subtilis
Inferred from claim c2 during normalization. The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration. Derived from claim c2. Quoted text: We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Source:
successBacteriaapplication demoBacillus subtilis
Inferred from claim c2 during normalization. The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration. Derived from claim c2. Quoted text: We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Source:
successBacteriaapplication demoBacillus subtilis
Inferred from claim c2 during normalization. The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration. Derived from claim c2. Quoted text: We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Source:
successBacteriaapplication demoBacillus subtilis
Inferred from claim c2 during normalization. The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration. Derived from claim c2. Quoted text: We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Source:
successBacteriaapplication demoBacillus subtilis
Inferred from claim c2 during normalization. The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration. Derived from claim c2. Quoted text: We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Source:
successBacteriaapplication demoBacillus subtilis
Inferred from claim c2 during normalization. The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration. Derived from claim c2. Quoted text: We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Source:
Supporting Sources
Ranked Claims
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo.
begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
The authors demonstrate broad and efficient genetic code expansion in Bacillus subtilis using 3 families of genetic code expansion systems and 2 codon choices.
we demonstrate broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons
codon choices 2distinct non-standard amino acids incorporated 20genetic code expansion system families 3
The authors demonstrate broad and efficient genetic code expansion in Bacillus subtilis using 3 families of genetic code expansion systems and 2 codon choices.
we demonstrate broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons
codon choices 2distinct non-standard amino acids incorporated 20genetic code expansion system families 3
The authors demonstrate broad and efficient genetic code expansion in Bacillus subtilis using 3 families of genetic code expansion systems and 2 codon choices.
we demonstrate broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons
codon choices 2distinct non-standard amino acids incorporated 20genetic code expansion system families 3
The authors demonstrate broad and efficient genetic code expansion in Bacillus subtilis using 3 families of genetic code expansion systems and 2 codon choices.
we demonstrate broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons
codon choices 2distinct non-standard amino acids incorporated 20genetic code expansion system families 3
The authors demonstrate broad and efficient genetic code expansion in Bacillus subtilis using 3 families of genetic code expansion systems and 2 codon choices.
we demonstrate broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons
codon choices 2distinct non-standard amino acids incorporated 20genetic code expansion system families 3
These tools allowed the authors to demonstrate differences between E. coli and Bacillus subtilis stop codon suppression.
These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression
These tools allowed the authors to demonstrate differences between E. coli and Bacillus subtilis stop codon suppression.
These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression
These tools allowed the authors to demonstrate differences between E. coli and Bacillus subtilis stop codon suppression.
These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression
These tools allowed the authors to demonstrate differences between E. coli and Bacillus subtilis stop codon suppression.
These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression
These tools allowed the authors to demonstrate differences between E. coli and Bacillus subtilis stop codon suppression.
These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression
The paper concerns designing efficient genetic code expansion in Bacillus subtilis to gain biological insights.
Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights
Section: title
The paper concerns designing efficient genetic code expansion in Bacillus subtilis to gain biological insights.
Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights
Section: title
The paper concerns designing efficient genetic code expansion in Bacillus subtilis to gain biological insights.
Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights
Section: title
The paper concerns designing efficient genetic code expansion in Bacillus subtilis to gain biological insights.
Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights
Section: title
The paper concerns designing efficient genetic code expansion in Bacillus subtilis to gain biological insights.
Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights
Section: title
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
Approval Evidence
1 source2 linked approval claimsfirst-pass slug photo-crosslinking
We use these systems to achieve ... photo-crosslinking
Source:
applicationsupports
The genetic code expansion systems were used to achieve click-labelling, photo-crosslinking, and translational titration.
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Source:
validation usesupports
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
Source:
Comparisons
Source-backed strengths
The source study reports broad and efficient genetic code expansion in Bacillus subtilis using three families of systems and two codon choices, providing the foundation for photo-crosslinking applications. Photo-crosslinking was demonstrated as one of several enabled downstream uses of this platform.
Source:
These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression
Compared with click-labelling
photo-crosslinking and click-labelling address a similar problem space because they share translation.
Shared frame: same top-level item type; shared target processes: translation; shared mechanisms: genetic code expansion, translation control, translation_control; same primary input modality: light
Compared with genetic code expansion in Bacillus subtilis
photo-crosslinking and genetic code expansion in Bacillus subtilis address a similar problem space because they share translation.
Shared frame: same top-level item type; shared target processes: translation; shared mechanisms: translation control, translation_control; same primary input modality: light
Relative tradeoffs: looks easier to implement in practice.
Compared with translational titration
photo-crosslinking and translational titration address a similar problem space because they share translation.
Shared frame: same top-level item type; shared target processes: translation; shared mechanisms: genetic code expansion, translation control, translation_control; same primary input modality: light
Relative tradeoffs: looks easier to implement in practice.
Ranked Citations
- 1.