Source 1primary paper2021Nature Communications
Toolkit/genetic code expansion in Bacillus subtilis
genetic code expansion in Bacillus subtilis
Also known as: chemical biology system in B. subtilis, genetic code expansion
Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Genetic code expansion in Bacillus subtilis is a translation-engineering method for site-specific incorporation of non-standard amino acids into proteins in vivo. The reported system achieved broad and efficient incorporation of 20 distinct non-standard amino acids in B. subtilis using three families of genetic code expansion systems and two codon choices.
Usefulness & Problems
Why this is useful
This method enables chemical biology manipulations in B. subtilis that require precise installation of non-standard amino acids during translation. Reported uses include click-labelling, photo-crosslinking, translational titration, validation of a predicted protein-protein binding interface, and interrogation of bacterial cytokinesis by modulating cell division dynamics in vivo.
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We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
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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 need for efficient, broad genetic code expansion directly in Bacillus subtilis rather than relying on systems optimized in other bacteria. The work also enabled comparison of stop codon suppression behavior between E. coli and B. subtilis, highlighting host-specific differences relevant to translation engineering.
Source:
We use these systems to achieve click-labelling, photo-crosslinking, and translational titration.
Problem links
Need precise spatiotemporal control with light input
DerivedGenetic code expansion in Bacillus subtilis is a translation-engineering method for site-specific incorporation of non-standard amino acids into proteins in vivo. The reported system achieved broad and efficient incorporation of 20 distinct non-standard amino acids in B. subtilis using three families of genetic code expansion systems and two codon choices.
Need tighter control over protein production
DerivedGenetic code expansion in Bacillus subtilis is a translation-engineering method for site-specific incorporation of non-standard amino acids into proteins in vivo. The reported system achieved broad and efficient incorporation of 20 distinct non-standard amino acids in B. subtilis using three families of genetic code expansion systems and two codon choices.
Taxonomy & Function
Primary hierarchy
Technique Branch
Method: A concrete method used to build, optimize, or evolve an engineered system.
Techniques
No technique tags yet.
Target processes
translationInput: Light
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: spectral hardware requirementoperating role: builder
Implementation in B. subtilis involved three families of genetic code expansion systems and two codon choices for non-standard amino acid incorporation. The evidence supports use for translational titration, click chemistry-based labeling, and photo-crosslinking, but does not provide construct architecture, expression conditions, or non-standard amino acid delivery details.
The supplied evidence does not specify the identities of the orthogonal synthetase/tRNA systems, the exact codons used, or quantitative incorporation efficiencies. Independent replication is not provided in the evidence, and validation is described from a single source study.
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Observations
successBacteriaapplication demoBacillus subtilis
Inferred from claim c1 during normalization. The authors demonstrate broad and efficient genetic code expansion in Bacillus subtilis using 3 families of genetic code expansion systems and 2 codon choices. Derived from claim c1. Quoted text: 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
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codon choices2distinct non-standard amino acids incorporated20genetic code expansion system families3
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.
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successBacteriaapplication demo
Inferred from claim c5 during normalization. These tools were used to begin interrogating properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. Derived from claim c5. Quoted text: begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo
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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.
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
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 were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
Approval Evidence
1 source5 linked approval claimsfirst-pass slug genetic-code-expansion-in-bacillus-subtilis
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
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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.
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biological applicationsupports
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
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capabilitysupports
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
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comparative observationsupports
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
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validation usesupports
These tools were used to validate a predicted protein-protein binding interface.
validate a predicted protein-protein binding interface
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Comparisons
Source-backed strengths
The system was reported to support broad and efficient incorporation of 20 distinct non-standard amino acids. It used three families of genetic code expansion systems and two codon choices, and it was applied across multiple functional assays including click-labelling, photo-crosslinking, translational titration, and interface validation.
Source:
These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression
Compared with brain stimulation
genetic code expansion in Bacillus subtilis and brain stimulation address a similar problem space because they share translation.
Shared frame: same top-level item type; shared target processes: translation; shared mechanisms: translation_control; same primary input modality: light
Strengths here: looks easier to implement in practice.
Compared with click-labelling
genetic code expansion in Bacillus subtilis 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: translation control, translation_control; same primary input modality: light
Strengths here: looks easier to implement in practice.
Compared with thermal sonogenetics
genetic code expansion in Bacillus subtilis and thermal sonogenetics address a similar problem space because they share translation.
Shared frame: same top-level item type; shared target processes: translation; shared mechanisms: translation_control; same primary input modality: light
Strengths here: looks easier to implement in practice.
Ranked Citations
- 1.