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Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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Related Experiment Video

Updated: Jan 15, 2026

A High-Yield Streptomyces Transcription-Translation Toolkit for Synthetic Biology and Natural Product Applications

A High-Yield Streptomyces Transcription-Translation Toolkit for Synthetic Biology and Natural Product Applications

Published on: September 10, 2021

StreptoCAD: An Open-Source Software Toolbox Automating Genome Engineering Workflows in Streptomycetes.

Lucas Levassor^1,2, Christopher M Whitford¹, Søren D Petersen²

¹Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby 2800, Denmark.

ACS Synthetic Biology

|October 14, 2025

Summary

StreptoCAD is a new open-source software that automates genome engineering in Streptomyces, accelerating the discovery of novel bioactive molecules for medicine and agriculture. This tool simplifies complex genetic tasks, making advanced manipulations more accessible.

Keywords:

CRISPR-Cas systems FAIR principles genome engineering overexpression libraries streptomyces synthetic biology

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Area of Science:

* Microbiology
* Molecular Biology
* Bioinformatics

Background:

* Streptomyces bacteria are crucial for discovering novel bioactive molecules.
* Current genetic engineering methods for Streptomyces are manual, complex, and slow, hindering high-throughput exploration.
* Automation is needed to streamline genome engineering in Streptomyces.

Purpose of the Study:

* To introduce StreptoCAD, an open-source software toolbox for automating Streptomyces genome engineering.
* To support various CRISPR-based and gene overexpression strategies.
* To accelerate the discovery of novel bioactive molecules from Streptomyces.

Main Methods:

* StreptoCAD automates the design of DNA primers and CRISPR guide sequences.
* The software simulates plasmid assemblies and genomic modifications.
* It provides standardized outputs for laboratory implementation and documentation, adhering to FAIR principles.

Main Results:

* StreptoCAD offers six design workflows, including overexpression libraries, base-editing, and CRISPR-based genome engineering (Cas9, Cas3, CRISPRi).
* Experimental validation demonstrated the tool's efficiency in creating gene overexpression and CRISPRi knockdown strains in Streptomyces Gö40/10.
* The software ensures reproducibility and simplifies data management.

Conclusions:

* StreptoCAD significantly simplifies complex Streptomyces genetic engineering tasks.
* The tool promotes collaboration through standardized workflows and design parameters.
* StreptoCAD is poised to revolutionize Streptomyces genome engineering, accelerating natural product discovery.