Source 1primary paper2024MED
Toolkit/cdiGEBS
cdiGEBS
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
Here, we developed a genetically encoded biosensor, cdiGEBS, based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH.
Usefulness & Problems
Why this is useful
cdiGEBS is a genetically encoded fluorescent biosensor for monitoring cellular c-di-GMP levels in Escherichia coli. The abstract states that it detects both low and high c-di-GMP levels and reports a 23-fold fluorescence dynamic change.; detecting cellular c-di-GMP levels in Escherichia coli; distinguishing low and high c-di-GMP states; detecting subtle c-di-GMP changes caused by altered synthesis or degradation enzyme expression; identifying new diguanylate cyclases; evaluating chemicals that modulate c-di-GMP levels; high-throughput screening of inhibitors of c-di-GMP synthesis enzymes
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cdiGEBS is a genetically encoded fluorescent biosensor for monitoring cellular c-di-GMP levels in Escherichia coli. The abstract states that it detects both low and high c-di-GMP levels and reports a 23-fold fluorescence dynamic change.
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detecting cellular c-di-GMP levels in Escherichia coli
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distinguishing low and high c-di-GMP states
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detecting subtle c-di-GMP changes caused by altered synthesis or degradation enzyme expression
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identifying new diguanylate cyclases
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evaluating chemicals that modulate c-di-GMP levels
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high-throughput screening of inhibitors of c-di-GMP synthesis enzymes
Problem solved
It addresses the need to sensitively monitor cellular c-di-GMP levels for studying c-di-GMP-regulated behaviors and for screening modulators of c-di-GMP signaling or synthesis.; provides a genetically encoded fluorescent readout of cellular c-di-GMP levels; enables sensitive detection across a broad range of c-di-GMP levels
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It addresses the need to sensitively monitor cellular c-di-GMP levels for studying c-di-GMP-regulated behaviors and for screening modulators of c-di-GMP signaling or synthesis.
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provides a genetically encoded fluorescent readout of cellular c-di-GMP levels
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enables sensitive detection across a broad range of c-di-GMP levels
Problem links
enables sensitive detection across a broad range of c-di-GMP levels
LiteratureIt addresses the need to sensitively monitor cellular c-di-GMP levels for studying c-di-GMP-regulated behaviors and for screening modulators of c-di-GMP signaling or synthesis.
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It addresses the need to sensitively monitor cellular c-di-GMP levels for studying c-di-GMP-regulated behaviors and for screening modulators of c-di-GMP signaling or synthesis.
provides a genetically encoded fluorescent readout of cellular c-di-GMP levels
LiteratureIt addresses the need to sensitively monitor cellular c-di-GMP levels for studying c-di-GMP-regulated behaviors and for screening modulators of c-di-GMP signaling or synthesis.
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It addresses the need to sensitively monitor cellular c-di-GMP levels for studying c-di-GMP-regulated behaviors and for screening modulators of c-di-GMP signaling or synthesis.
Published Workflows
Objective: Develop a genetically encoded fluorescent biosensor that sensitively reports cellular c-di-GMP levels in Escherichia coli and supports downstream discovery of diguanylate cyclases and chemical modulators.
Why it works: The workflow is based on coupling fluorescence output to the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH, so changes in cellular c-di-GMP are converted into a measurable fluorescent signal.
c-di-GMP-responsive transcriptional activity mediated by MrkHgenetically encoded fluorescent biosensinghigh-throughput screening
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A reusable architecture pattern for arranging parts into an engineered system.
Target processes
degradationrecombinationselectiontranscriptionInput: Chemical
Implementation Constraints
cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: sensor
The sensor is genetically encoded and is based on the c-di-GMP-responsive transcription factor MrkH, so it requires expression of the biosensor system in cells. Its output is fluorescence.; genetically encoded biosensor format implies cellular expression of the biosensor construct; sensor mechanism is based on the c-di-GMP-responsive transcription factor MrkH
The abstract does not show that cdiGEBS directly identifies molecular targets or mechanisms of candidate chemicals beyond reporting modulation of c-di-GMP levels. It also does not establish performance outside the reported E. coli context.; abstract evidence limits demonstrated use context to Escherichia coli
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
cdiGEBS can be applied to identify new diguanylate cyclases and evaluate chemicals that modulate c-di-GMP levels.
These capabilities allow us to apply cdiGEBS for identifying new diguanylate cyclases and evaluating chemicals that modulate c-di-GMP levels
cdiGEBS can distinguish different c-di-GMP synthesis activities among WspR mutants.
can distinguish different synthesis activities among WspR mutants
cdiGEBS is based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH.
cdiGEBS, based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH
cdiGEBS can detect both low and high cellular c-di-GMP levels.
cdiGEBS can detect both low and high cellular c-di-GMP levels
cdiGEBS shows a 23-fold fluorescence dynamic change.
with a high fluorescence dynamic change of 23-fold
fluorescence dynamic change 23 fold
cdiGEBS has potential as a high-throughput tool for screening inhibitors of c-di-GMP synthesis enzymes.
highlighting its potential as a high-throughput tool for screening inhibitors of c-di-GMP synthesis enzymes
cdiGEBS can detect subtle changes in c-di-GMP concentrations caused by variation in expression of c-di-GMP synthesis or degradation enzymes.
it can detect subtle changes in c-di-GMP concentrations due to variations in the expression of c-di-GMP synthesis or degradation enzymes
The study developed cdiGEBS, a genetically encoded fluorescent biosensor for cellular c-di-GMP detection in Escherichia coli.
Here, we developed a genetically encoded biosensor, cdiGEBS
Approval Evidence
1 source8 linked approval claimsfirst-pass slug cdigebs
Here, we developed a genetically encoded biosensor, cdiGEBS, based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH.
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applicationsupports
cdiGEBS can be applied to identify new diguanylate cyclases and evaluate chemicals that modulate c-di-GMP levels.
These capabilities allow us to apply cdiGEBS for identifying new diguanylate cyclases and evaluating chemicals that modulate c-di-GMP levels
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discriminationsupports
cdiGEBS can distinguish different c-di-GMP synthesis activities among WspR mutants.
can distinguish different synthesis activities among WspR mutants
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mechanismsupports
cdiGEBS is based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH.
cdiGEBS, based on the transcriptional activity of the c-di-GMP-responsive transcription factor MrkH
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performancesupports
cdiGEBS can detect both low and high cellular c-di-GMP levels.
cdiGEBS can detect both low and high cellular c-di-GMP levels
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performancesupports
cdiGEBS shows a 23-fold fluorescence dynamic change.
with a high fluorescence dynamic change of 23-fold
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screening positioningsupports
cdiGEBS has potential as a high-throughput tool for screening inhibitors of c-di-GMP synthesis enzymes.
highlighting its potential as a high-throughput tool for screening inhibitors of c-di-GMP synthesis enzymes
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sensitivitysupports
cdiGEBS can detect subtle changes in c-di-GMP concentrations caused by variation in expression of c-di-GMP synthesis or degradation enzymes.
it can detect subtle changes in c-di-GMP concentrations due to variations in the expression of c-di-GMP synthesis or degradation enzymes
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tool developmentsupports
The study developed cdiGEBS, a genetically encoded fluorescent biosensor for cellular c-di-GMP detection in Escherichia coli.
Here, we developed a genetically encoded biosensor, cdiGEBS
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Comparisons
Source-stated alternatives
Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
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Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Source-backed strengths
23-fold fluorescence dynamic change; detects both low and high cellular c-di-GMP levels; can resolve subtle changes in c-di-GMP concentrations; can distinguish different synthesis activities among WspR mutants; positioned as a high-throughput screening tool
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23-fold fluorescence dynamic change
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detects both low and high cellular c-di-GMP levels
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can resolve subtle changes in c-di-GMP concentrations
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can distinguish different synthesis activities among WspR mutants
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positioned as a high-throughput screening tool
Compared with biosensors
Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Shared frame: source-stated alternative in extracted literature
Strengths here: 23-fold fluorescence dynamic change; detects both low and high cellular c-di-GMP levels; can resolve subtle changes in c-di-GMP concentrations.
Relative tradeoffs: abstract evidence limits demonstrated use context to Escherichia coli.
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Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Compared with biosensors for active Rho detection
Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Shared frame: source-stated alternative in extracted literature
Strengths here: 23-fold fluorescence dynamic change; detects both low and high cellular c-di-GMP levels; can resolve subtle changes in c-di-GMP concentrations.
Relative tradeoffs: abstract evidence limits demonstrated use context to Escherichia coli.
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Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Compared with fluorescent protein based reporters and biosensors
Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Shared frame: source-stated alternative in extracted literature
Strengths here: 23-fold fluorescence dynamic change; detects both low and high cellular c-di-GMP levels; can resolve subtle changes in c-di-GMP concentrations.
Relative tradeoffs: abstract evidence limits demonstrated use context to Escherichia coli.
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Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Compared with genetically engineered biosensors
Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Shared frame: source-stated alternative in extracted literature
Strengths here: 23-fold fluorescence dynamic change; detects both low and high cellular c-di-GMP levels; can resolve subtle changes in c-di-GMP concentrations.
Relative tradeoffs: abstract evidence limits demonstrated use context to Escherichia coli.
Source:
Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Compared with in vivo bimolecular fluorescence complementation
Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Shared frame: source-stated alternative in extracted literature
Strengths here: 23-fold fluorescence dynamic change; detects both low and high cellular c-di-GMP levels; can resolve subtle changes in c-di-GMP concentrations.
Relative tradeoffs: abstract evidence limits demonstrated use context to Escherichia coli.
Source:
Upstream source discovery notes that the full text contrasts cdiGEBS with prior c-di-GMP biosensors including a MrkH insertion-based fluorescent sensor and the BldD-based BiFC sensor CensYBL.
Ranked Citations
- 1.