Toolkit/SRTS-OPRTS

SRTS-OPRTS

RNA Element·Research·Since 2025

Also known as: artificial TA pairs, synthetic RNA devices

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

Summary

we reconstructed artificial TA pairs termed SRTS-OPRTS. A platform for generating orthogonal SRTS-OPRTS pairs with cross-species application ... was developed

Usefulness & Problems

Why this is useful

SRTS-OPRTS are artificial RNA regulator pairs reconstructed from type I toxin-antitoxin cores to control gene expression post-transcriptionally. The abstract states they can function as portable and orthogonal regulatory devices.; post-transcriptional gene regulation; building orthogonal RNA regulator pairs; cross-species deployment in bacteria; constructing dynamic genetic circuits

Source:

SRTS-OPRTS are artificial RNA regulator pairs reconstructed from type I toxin-antitoxin cores to control gene expression post-transcriptionally. The abstract states they can function as portable and orthogonal regulatory devices.

Source:

post-transcriptional gene regulation

Source:

building orthogonal RNA regulator pairs

Source:

cross-species deployment in bacteria

Source:

constructing dynamic genetic circuits

Problem solved

The system provides a way to build portable, orthogonal RNA-based regulators for quantitative gene control and dynamic circuit construction across multiple bacterial hosts.; repurposes native type I toxin-antitoxin logic into portable synthetic RNA regulators; enables orthogonal post-transcriptional control across multiple bacterial species

Source:

The system provides a way to build portable, orthogonal RNA-based regulators for quantitative gene control and dynamic circuit construction across multiple bacterial hosts.

Source:

repurposes native type I toxin-antitoxin logic into portable synthetic RNA regulators

Source:

enables orthogonal post-transcriptional control across multiple bacterial species

Problem links

enables orthogonal post-transcriptional control across multiple bacterial species

Literature

The system provides a way to build portable, orthogonal RNA-based regulators for quantitative gene control and dynamic circuit construction across multiple bacterial hosts.

Source:

The system provides a way to build portable, orthogonal RNA-based regulators for quantitative gene control and dynamic circuit construction across multiple bacterial hosts.

repurposes native type I toxin-antitoxin logic into portable synthetic RNA regulators

Literature

The system provides a way to build portable, orthogonal RNA-based regulators for quantitative gene control and dynamic circuit construction across multiple bacterial hosts.

Source:

The system provides a way to build portable, orthogonal RNA-based regulators for quantitative gene control and dynamic circuit construction across multiple bacterial hosts.

Published Workflows

Design of orthogonal and portable RNA devices for post-transcriptional regulation by reverse engineering type I toxin-antitoxin systems.

2025

Objective: Reverse engineer type I toxin-antitoxin systems into orthogonal and portable RNA devices for post-transcriptional regulation and downstream circuit construction.

Why it works: The abstract states that type I toxin-antitoxin systems are evolutionarily optimized regulatory modules with rapid kinetics and modular architectures, motivating their reuse as synthetic RNA devices.

antitoxin RNA interference with cognate toxin mRNA translationpost-transcriptional RNA-RNA regulationreverse engineeringcore isolationconstraint-based design using structure and energy constraints

Stages

  1. 1.
    Core isolation from native type I TA pairs(library_design)

    This stage extracts the reusable core architecture from native systems before artificial pair reconstruction.

    Selection: Isolation of the core of type I TA pairs for reuse as synthetic regulatory modules.

  2. 2.
    Artificial pair reconstruction(library_build)

    This stage converts isolated native cores into engineered RNA device pairs.

    Selection: Reconstruction of artificial TA-derived RNA regulator pairs.

  3. 3.
    Constraint-based generation of orthogonal portable pairs(library_design)

    The stage exists to produce orthogonal and portable regulator pairs rather than only reconstructed native-like pairs.

    Selection: Introduce structure and energy constraints to generate orthogonal SRTS-OPRTS pairs with cross-species application.

  4. 4.
    Functional characterization in gene regulation and circuit applications(functional_characterization)

    This stage demonstrates that the designed RNA devices work as practical regulatory tools and support downstream circuit behaviors.

    Selection: Test quantitative regulation, mutually inhibitory switch construction, and selective enrichment applications.

Steps

  1. 1.
    Isolate the core of type I toxin-antitoxin pairs

    Extract the minimal reusable regulatory core from native type I TA systems.

    The abstract presents core isolation as the first step before artificial pair reconstruction.

  2. 2.
    Demonstrate independence between structure and repression function

    Establish that the reusable design can separate structural features from repression function for engineering.

    The abstract places this demonstration immediately after core isolation and before reconstruction of artificial pairs, implying it justifies the engineering step.

  3. 3.
    Reconstruct artificial TA-derived RNA pairs as SRTS-OPRTSengineered RNA regulator pair

    Create synthetic post-transcriptional regulatory devices from the validated TA core logic.

    Artificial reconstruction follows core isolation and structure-function analysis in the abstract's reported order.

  4. 4.
    Introduce structure and energy constraints to generate orthogonal cross-species pairsdesigned RNA regulator pair set

    Generate orthogonal SRTS-OPRTS pairs that remain portable across multiple bacterial species.

    Constraint-based design is applied after artificial pair reconstruction to improve orthogonality and portability.

  5. 5.
    Test quantitative gene regulation using SRTS with cognate 3' UTR OPRTSengineered regulatory RNA elements

    Validate that the designed RNA elements can quantitatively regulate target genes.

    Functional regulation testing follows design and pair generation to confirm practical activity.

  6. 6.
    Construct dynamic mutually inhibitory switches from tagged genesRNA-enabled circuit construct

    Use portability of the RNA devices to build reciprocal regulatory circuits.

    The abstract states that portability enabled this downstream circuit construction after regulatory function was established.

  7. 7.
    Construct a selective lethal system to enrich high-fluorescent mutantsselection-linked application construct

    Apply the RNA-device framework to phenotype enrichment.

    The abstract describes this as a further application leveraging the established approach after regulation and portability were demonstrated.

Taxonomy & Function

Primary hierarchy

Mechanism Branch

Component: A low-level RNA part used inside a larger architecture that realizes a mechanism.

Target processes

No target processes tagged yet.

Implementation Constraints

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

Use requires engineered cognate SRTS and OPRTS elements and host expression in bacterial species named in the abstract. The design process also depends on structure and energy constraints.; requires introduction of structure and energy constraints during design; requires cognate pairing between SRTS and 3' UTR OPRTS

The abstract does not show applicability outside the listed bacterial species or define limits on host factors, sequence scope, or off-target behavior.; evidence in the provided abstract is limited to prokaryotic hosts; exact sequence design rules and performance boundaries are not given in the provided text

Validation

Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication

Supporting Sources

Ranked Claims

Claim 1applicationsupports2025Source 1needs review

Portability of the RNA devices enabled construction of dynamic mutually inhibitory switches in which genes tagged by SRTS and OPRTS regulate each other.

Such portability enabled convenient construction of dynamic mutually inhibitory switches, where genes tagged by SRTS and OPRTS could regulate each other.
Claim 2application performancesupports2025Source 1needs review

A selective lethal system built using the approach enriched high-fluorescent mutants and produced up to 11.32-fold enhancement in mean fluorescence intensity.

a selective lethal system was further constructed to enrich high-fluorescent mutants, resulting in up to 11.32-fold enhancement in mean fluorescence intensity
mean fluorescence intensity enhancement 11.32 fold
Claim 3engineering outcomesupports2025Source 1needs review

The authors reconstructed artificial type I toxin-antitoxin-derived RNA regulator pairs termed SRTS-OPRTS.

we reconstructed artificial TA pairs termed SRTS-OPRTS
Claim 4functional performancesupports2025Source 1needs review

SRTS achieved quantitative regulation of genes when paired with cognate 3' UTR OPRTS.

SRTS achieved quantitative regulation of the gene with 3' UTR cognate OPRTS
Claim 5platform capabilitysupports2025Source 1needs review

A design platform generated orthogonal SRTS-OPRTS pairs with cross-species application in Bacillus subtilis, Escherichia coli, and Corynebacterium glutamicum by introducing structure and energy constraints.

A platform for generating orthogonal SRTS-OPRTS pairs with cross-species application (Bacillus subtilis, Escherichia coli, and Corynebacterium glutamicum) was developed by introducing structure and energy constraints.

Approval Evidence

1 source5 linked approval claimsfirst-pass slug srts-oprts
we reconstructed artificial TA pairs termed SRTS-OPRTS. A platform for generating orthogonal SRTS-OPRTS pairs with cross-species application ... was developed

Source:

applicationsupports

Portability of the RNA devices enabled construction of dynamic mutually inhibitory switches in which genes tagged by SRTS and OPRTS regulate each other.

Such portability enabled convenient construction of dynamic mutually inhibitory switches, where genes tagged by SRTS and OPRTS could regulate each other.

Source:

application performancesupports

A selective lethal system built using the approach enriched high-fluorescent mutants and produced up to 11.32-fold enhancement in mean fluorescence intensity.

a selective lethal system was further constructed to enrich high-fluorescent mutants, resulting in up to 11.32-fold enhancement in mean fluorescence intensity

Source:

engineering outcomesupports

The authors reconstructed artificial type I toxin-antitoxin-derived RNA regulator pairs termed SRTS-OPRTS.

we reconstructed artificial TA pairs termed SRTS-OPRTS

Source:

functional performancesupports

SRTS achieved quantitative regulation of genes when paired with cognate 3' UTR OPRTS.

SRTS achieved quantitative regulation of the gene with 3' UTR cognate OPRTS

Source:

platform capabilitysupports

A design platform generated orthogonal SRTS-OPRTS pairs with cross-species application in Bacillus subtilis, Escherichia coli, and Corynebacterium glutamicum by introducing structure and energy constraints.

A platform for generating orthogonal SRTS-OPRTS pairs with cross-species application (Bacillus subtilis, Escherichia coli, and Corynebacterium glutamicum) was developed by introducing structure and energy constraints.

Source:

Comparisons

Source-stated alternatives

The source contrasts these engineered devices with native type I toxin-antitoxin systems, which serve as the design template rather than the final portable tool.

Source:

The source contrasts these engineered devices with native type I toxin-antitoxin systems, which serve as the design template rather than the final portable tool.

Source-backed strengths

orthogonal pair generation is explicitly described; portable across Bacillus subtilis, Escherichia coli, and Corynebacterium glutamicum; supports quantitative regulation and circuit construction

Source:

orthogonal pair generation is explicitly described

Source:

portable across Bacillus subtilis, Escherichia coli, and Corynebacterium glutamicum

Source:

supports quantitative regulation and circuit construction

Compared with caged guide RNA

SRTS-OPRTS and caged guide RNA address a similar problem space.

Shared frame: same top-level item type

Strengths here: looks easier to implement in practice.

Compared with Cas6 binding site

SRTS-OPRTS and Cas6 binding site address a similar problem space.

Shared frame: same top-level item type

Compared with RhVI1 promoter

SRTS-OPRTS and RhVI1 promoter address a similar problem space.

Shared frame: same top-level item type

Strengths here: looks easier to implement in practice.

Ranked Citations

  1. 1.
    StructuralSource 1MED2025Claim 1Claim 2Claim 3

    Extracted from this source document.