CF-targeter

CF-targeter selects optimal microbial chassis and designs heterologous biosynthetic pathways to enable production of target chemicals by integrating symbolic reaction repositories, genome-scale metabolic models (GEMs), and high-throughput pathway search.

Key Features:

• Extensive chassis selection: Evaluates over 70 candidate microorganisms for their potential to produce more than 6,000 target molecules.
• Pathway search algorithm: Performs up to 1,400,000 searches per target compound using symbolic reaction repositories and genome-scale metabolic models (GEMs) to design heterologous pathways.
• High-throughput computation: Computes nearly 50 million biosynthetic pathways over a month-long period by harnessing supercomputing resources.
• Yield and thermodynamic assessment: Provides real-time calculations of maximum theoretical yields and thermodynamic feasibility under customized growth conditions and physiological states.
• Biosynthetic optimization: Identifies experimentally validated pathways and suggests alternative solutions with fewer heterologous steps or higher potential yields via engineering of alternative organism hosts.

Scientific Applications:

• Chassis selection for biosynthesis: Guides selection of suitable host organisms for production of specific target molecules.
• Heterologous pathway design: Designs candidate heterologous biosynthetic routes tailored to chosen chassis using symbolic reactions and GEMs.
• Pathway evaluation and ranking: Assesses pathway thermodynamic feasibility and maximum theoretical yields to compare candidate routes.
• Cell factory optimization: Suggests chassis- and pathway-level engineering options to reduce heterologous steps or improve yields for sustainable bioproduction.

Methodology:

CF-targeter couples symbolic reaction repositories with a pathway search algorithm integrated with various genome-scale metabolic models (GEMs), performs up to 1,400,000 searches per target compound, and uses supercomputing resources to compute nearly 50 million candidate biosynthetic pathways and calculate maximum theoretical yields and thermodynamic feasibility.