Deciphering nutritional stress responses via knowledge-enriched transcriptomics for microbial engineering

Area of Science:

• Microbial Physiology
• Systems Biology
• Biotechnology

Background:

• Bacterial nutrition and stress responses are crucial for microbial research and biotechnology.
• Understanding Vibrio natriegens' metabolic flexibility is key for optimizing its use in engineered systems.

Purpose of the Study:

• To decipher Vibrio natriegens' complex stress responses to various nutrient conditions using knowledge-enriched transcriptomic analytics.
• To provide a quantitative basis for transcriptome dynamics across diverse nutrient environments.
• To identify novel nutrient transporters and understand trace element effects on metabolism.

Main Methods:

• Employed knowledge-enriched transcriptomic analytics on a comprehensive dataset.
• Computed 64 independently modulated gene sets to analyze transcriptome dynamics.
• Investigated nutrient-induced stress responses including osmotic stress and proteostasis.

Main Results:

• Identified novel transporter systems for diverse substrates.
• Detailed the impact of trace elements on bacterial metabolism and growth.
• Characterized nutrient-induced stress responses like osmotic stress and altered protein expression.
• Clarified the role of the acetate-associated regulon in carbon source selection.

Conclusions:

• The study provides deep insights into the transcriptional landscape of bacterial nutrition.
• Findings underscore the significance of nutritional understanding for tailoring strain engineering strategies.
• Facilitates the development of more efficient and robust microbial systems for biotechnological applications.