Toolkit/DNA array technology

DNA array technology

Assay Method·Research·Since 2006

Also known as: DNA array

Taxonomy: Technique Branch / Method. Workflows sit above the mechanism and technique branches rather than replacing them.

Summary

We used DNA array technology to decipher the interplay between these responses in P. putida KT2440 subjected to a short challenge (15 min) with toluene.

Usefulness & Problems

Why this is useful

DNA array technology was used to profile transcriptional responses in P. putida KT2440 after short aromatic-compound exposure. In this paper it serves as the main readout for comparing stress and metabolic programs.; measuring transcriptional response profiles after aromatic compound exposure; comparing expression programs across toluene, o-xylene, and 3-methylbenzoate conditions

Source:

DNA array technology was used to profile transcriptional responses in P. putida KT2440 after short aromatic-compound exposure. In this paper it serves as the main readout for comparing stress and metabolic programs.

Source:

measuring transcriptional response profiles after aromatic compound exposure

Source:

comparing expression programs across toluene, o-xylene, and 3-methylbenzoate conditions

Problem solved

It enables system-level comparison of how many genes shift toward stress tolerance versus aromatic metabolism under toluene challenge.; deciphering interplay between metabolic and stress-response transcriptional programs

Source:

It enables system-level comparison of how many genes shift toward stress tolerance versus aromatic metabolism under toluene challenge.

Source:

deciphering interplay between metabolic and stress-response transcriptional programs

Problem links

deciphering interplay between metabolic and stress-response transcriptional programs

Literature

It enables system-level comparison of how many genes shift toward stress tolerance versus aromatic metabolism under toluene challenge.

Source:

It enables system-level comparison of how many genes shift toward stress tolerance versus aromatic metabolism under toluene challenge.

Published Workflows

Transcriptional Tradeoff between Metabolic and Stress-response Programs in Pseudomonas putida KT2440 Cells Exposed to Toluene

2006

Objective: Use DNA array profiling to compare how Pseudomonas putida KT2440 reallocates transcriptional capacity between aromatic-compound metabolism and stress-response programs after short exposure to toluene and related compounds.

Why it works: The workflow compares expression profiles after a short toluene challenge with profiles from o-xylene and 3-methylbenzoate exposure so that shared and distinct transcriptional programs can be interpreted in terms of stress versus metabolic induction.

tradeoff between stress-response and aromatic metabolism programsinduction of TOL pathway by aromatic compoundsstress-associated inhibition of motility functionsDNA array technologycomparative exposure profiling

Stages

  1. 1.
    Short aromatic challenge and transcriptome measurement(broad_screen)

    This stage generates the primary expression profile used to assess how cells respond to toluene.

    Selection: Measure genome-scale transcriptional responses after a short toluene challenge.

  2. 2.
    Comparative profiling against related aromatic exposures(secondary_characterization)

    Comparator exposures help distinguish responses linked to aromatic toxicity from those linked to specific catabolic pathway induction.

    Selection: Compare toluene-induced expression profiles with those from o-xylene and 3-methylbenzoate exposure.

Steps

  1. 1.
    Expose Pseudomonas putida KT2440 cells to toluene for 15 minutes

    Create an acute toluene-response condition for transcriptional profiling.

    The short challenge precedes expression measurement because the study aims to capture immediate transcriptional interplay after toluene exposure.

  2. 2.
    Measure gene expression using DNA array technologyassay method

    Obtain transcriptional profiles from challenged cells.

    Expression measurement follows exposure because the array readout is used to decode the response induced by the challenge.

  3. 3.
    Compare the toluene expression profile with profiles from o-xylene and 3-methylbenzoate exposure

    Disentangle general aromatic stress responses from pathway-specific metabolic induction patterns.

    Comparator analysis is done after obtaining the toluene profile so the authors can interpret which responses are shared with a non-biodegradable aromatic and which are associated with a specific lower-pathway substrate.

Taxonomy & Function

Primary hierarchy

Technique Branch

Method: A concrete measurement method used to characterize an engineered system.

Target processes

degradationtranscription

Implementation Constraints

cofactor dependency: cofactor requirement unknownencoding mode: genetically encodedimplementation constraint: context specific validationoperating role: sensor

The abstract supports a need for P. putida KT2440 cells, aromatic exposure conditions, and DNA array-based expression measurement. It does not specify platform or downstream validation assays.; requires exposed P. putida KT2440 samples and gene expression profiling workflow

The abstract does not show that the array alone establishes mechanism, protein activity, or causal regulation.; abstract does not report specific array design, probe content, or validation details

Validation

Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication

Supporting Sources

Ranked Claims

Claim 1motility inhibitionsupports2006Source 1needs review

Toluene, and to a lesser extent o-xylene, inhibit motility functions in Pseudomonas putida KT2440 as a response to aromatic toxicity.

In addition, toluene (and to a lesser extent o-xylene) inhibit motility functions as an unequivocal response to aromatic toxicity.
Claim 2stress response interpretationsupports2006Source 1needs review

Toluene is sensed by Pseudomonas putida KT2440 more as a stressor than as a nutrient.

We argue that toluene is sensed by P. putida KT2440 as a stressor rather than as a nutrient
Claim 3transcriptional tradeoffsupports2006Source 1needs review

In Pseudomonas putida KT2440 exposed to toluene, most available transcriptional machinery is reassigned to general stress responses while only a small share is redirected to aromatic compound degradation.

The resulting expression profiles suggest that the bulk of the available transcriptional machinery is reassigned to endure general stress, whereas only a small share of the available machinery is redirected to the degradation of the aromatic compounds.

Approval Evidence

1 source3 linked approval claimsfirst-pass slug dna-array-technology
We used DNA array technology to decipher the interplay between these responses in P. putida KT2440 subjected to a short challenge (15 min) with toluene.

Source:

motility inhibitionsupports

Toluene, and to a lesser extent o-xylene, inhibit motility functions in Pseudomonas putida KT2440 as a response to aromatic toxicity.

In addition, toluene (and to a lesser extent o-xylene) inhibit motility functions as an unequivocal response to aromatic toxicity.

Source:

stress response interpretationsupports

Toluene is sensed by Pseudomonas putida KT2440 more as a stressor than as a nutrient.

We argue that toluene is sensed by P. putida KT2440 as a stressor rather than as a nutrient

Source:

transcriptional tradeoffsupports

In Pseudomonas putida KT2440 exposed to toluene, most available transcriptional machinery is reassigned to general stress responses while only a small share is redirected to aromatic compound degradation.

The resulting expression profiles suggest that the bulk of the available transcriptional machinery is reassigned to endure general stress, whereas only a small share of the available machinery is redirected to the degradation of the aromatic compounds.

Source:

Comparisons

Source-stated alternatives

The source does not explicitly name alternative transcriptomic methods.

Source:

The source does not explicitly name alternative transcriptomic methods.

Source-backed strengths

supports parallel expression profiling across many genes

Source:

supports parallel expression profiling across many genes

Compared with blue light-responsive Cas13b mRNA knockdown system

DNA array technology and blue light-responsive Cas13b mRNA knockdown system address a similar problem space because they share degradation, transcription.

Shared frame: shared target processes: degradation, transcription; shared mechanisms: degradation

Strengths here: looks easier to implement in practice.

Compared with cdiGEBS

DNA array technology and cdiGEBS address a similar problem space because they share degradation, transcription.

Shared frame: shared target processes: degradation, transcription; shared mechanisms: degradation

Compared with tools and sensors for imaging

DNA array technology and tools and sensors for imaging address a similar problem space because they share degradation.

Shared frame: same top-level item type; shared target processes: degradation; shared mechanisms: degradation

Ranked Citations

  1. 1.
    StructuralSource 1Journal of Biological Chemistry2006Claim 1Claim 2Claim 3

    Extracted from this source document.