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A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Computer-aided synthesis of biochemical pathways.

M L Mavrovouniotis¹, G Stephanopoulos, G Stephanopoulos

¹Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

Biotechnology and Bioengineering

|December 20, 1990

Summary

This study presents an algorithm for synthesizing biochemical pathways that meet specific constraints. The method successfully identified new lysine synthesis routes and revealed essential intermediates and yield limitations.

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Area of Science:

Biochemistry
Metabolic Engineering
Systems Biology

Background:

Biochemical pathways are fundamental to cellular function.
Understanding and designing metabolic pathways is crucial for biotechnology and synthetic biology.
Stoichiometric constraints are critical in defining feasible biochemical transformations.

Purpose of the Study:

To develop and present an algorithm for the systematic synthesis of biochemical pathways that satisfy stoichiometric constraints.
To apply this algorithm to discover novel pathways for lysine synthesis from glucose and ammonia.
To uncover fundamental metabolic constraints and limitations through pathway synthesis.

Main Methods:

Development of a recursive algorithm to transform a base-set of pathways.
Application of the algorithm to enforce constraints on reactants, products, and intermediates.
Analysis of pathway feasibility and identification of necessary intermediates and yield limits.

Main Results:

The algorithm successfully generated known and novel biochemical pathways for lysine synthesis.
Alternative pathways bypassing key enzymes like malate dehydrogenase were identified.
The study confirmed oxaloacetate as a necessary intermediate for lysine synthesis from glucose.
A maximum theoretical yield of 67% for lysine from glucose was determined.

Conclusions:

The developed algorithm provides a systematic approach for biochemical pathway synthesis.
This method can uncover novel metabolic routes and reveal inherent biological constraints.
The findings have implications for optimizing metabolic engineering strategies and understanding cellular metabolism.