Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: May 14, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Comparative transcriptome analysis for metabolic engineering.

Shuobo Shi¹, Tao Chen, Xueming Zhao

¹Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China. shuobos@chalmers.se

Methods in Molecular Biology (Clifton, N.J.)

|February 19, 2013

Summary

This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Engineering Rhodotorula toruloides as a platform organism for de novo synthesis of fatty-acid esters.

Nature communications·2026

Same author

Editorial for the Special Issue "Advances in Metabolic Engineering of Industrial Microorganisms".

Microorganisms·2026

Same author

MRPAND: A one-tube multiplex ago-mediated nucleic acid detection platform for visualized EGFR genotyping in point-of-care settings.

Talanta·2026

Same author

Development of microbial chassis for production of fungal natural products.

Critical reviews in biotechnology·2026

Same author

Innovative tools for customized yeast cell factory.

Biodesign research·2025

Same author

Engineering metabolism of Saccharomyces cerevisiae for production of chemicals.

Current opinion in biotechnology·2025

Same journal

Isolation of Mesenchymal Stem Cell-Derived Extracellular Vesicles.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Modeling Melanoma Immune Surveillance by CAR-T Cells in Human Skin Organoids.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Stepwise Optimization of a Matrigel-Based In Vitro Angiogenesis Assay for Reproducible and Quantifiable 2D-Tube Formation Using HUVECs.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Quantifying Mechanical Properties of Fresh Ovarian Tissue with Optical Brillouin Microscopy.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

3D Chromatin Architecture During Early Development: New Methods and New Findings.

Methods in molecular biology (Clifton, N.J.)·2026

Same journal

Metabolic Plasticity in Embryogenesis Throughout the Lens of NAD<sup></sup>.

Methods in molecular biology (Clifton, N.J.)·2026

See all related articles

Comparative transcriptome profiling of Bacillus subtilis identified new targets for metabolic engineering. This approach enhanced riboflavin production by 32%.

Area of Science:

Microbiology
Metabolic Engineering
Systems Biology

Background:

Transcriptome profiling offers a comprehensive view of gene expression, crucial for understanding cellular physiology and regulatory networks.
Transcriptomics is a sensitive and tractable 'omic' technique that significantly advances metabolic engineering by enabling system-level analysis of cellular metabolism.
Identifying specific genetic targets is key to optimizing microbial production strains.

Purpose of the Study:

To rationally identify novel engineering targets for enhancing riboflavin production in Bacillus subtilis.
To demonstrate the utility of comparative transcriptome analysis in guiding metabolic engineering strategies.
To provide detailed experimental protocols for target prediction using transcriptomics.

Main Methods:

More Related Videos

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics

Published on: February 18, 2009

Related Experiment Videos

Last Updated: May 14, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

High-Throughput Metabolic Profiling for Model Refinements of Microalgae

Published on: December 4, 2021

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics

Published on: February 18, 2009

Comparative transcriptome profiling was conducted between a high-yielding riboflavin-producing Bacillus subtilis strain (RH33) and the wild-type strain (B. subtilis 168).
Differential gene expression analysis was used to identify genes and pathways involved in enhanced riboflavin synthesis.
The identified targets were then utilized to engineer the microbial strain.

Main Results:

The comparative transcriptome analysis successfully identified potential targets for metabolic engineering.
Engineering strategies guided by transcriptomic data resulted in a significant improvement in riboflavin titer.
The riboflavin titer was improved by 32 ± 3% using the transcriptome analysis-guided method.

Conclusions:

Comparative transcriptome profiling is an effective strategy for discovering engineering targets in microbial systems.
This transcriptomics-guided approach significantly enhances the efficiency of metabolic engineering for improved product yields.
The study provides a reproducible protocol for leveraging transcriptomic data to optimize industrial microbial strains.