Compressed Biosynthetic Pathways for Nonribosomal Peptide Diversity
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Solution Overview
Problem
There is a challenge in expanding the chemical diversity of nonribosomal peptides, as many niches and species have been tapped for their natural molecules, making it difficult to find new clinically relevant compounds, and existing methods struggle with heterologous expression and pathway engineering for producing new molecules.
Innovation Solution
A compressed biosynthetic pathway is created by combining ancestral homologous genes from different organisms, such as Escherichia coli and Vibrio cholerae, to produce new nonribosomal peptides, including iron chelators like serratiochelins, by expressing these genes in modified bacterial cells and supplementing with various amine or polyamine linker precursors.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If traditional methods are used to find new nonribosomal peptides from natural sources, then existing molecules can be obtained, but chemical diversity is limited because many niches and species have already been tapped
Solution Approach 1:
The patent applies preliminary action by pre-assembling compressed biosynthetic pathways containing genes from multiple organisms (e.g., E. coli and V. cholerae) into engineered bacterial cells before exposure to precursor molecules. This preparatory genetic engineering enables the cells to immediately produce diverse nonribosomal peptides when supplied with different amine or polyamine precursors, rather than requiring sequential discovery and engineering efforts
Solution Approach 2:
The engineered bacterial cells achieve universality by incorporating compressed pathways that can process multiple types of precursor molecules (various amines and polyamines) through the same enzymatic machinery. The same engineered cell strain can produce different nonribosomal peptide variants by simply changing the precursor substrate, making the system multi-functional for generating chemical diversity
2Productivity
If existing biosynthetic pathways are engineered for heterologous expression, then new molecules can be produced, but the process is complex and difficult to implement
Solution Approach 1:
The patent segments complex natural biosynthetic pathways into compressed versions containing only the essential genes needed for nonribosomal peptide production. By isolating and combining specific functional genes from different organisms into streamlined pathways, the engineering complexity is reduced while maintaining the ability to produce diverse molecules
Solution Approach 2:
The patent merges genes from multiple different organisms (e.g., E. coli and V. cholerae) into single compressed biosynthetic pathways within engineered bacterial cells. This combining of heterogeneous genetic elements creates functional pathways that can produce molecules not found in any single natural source, achieving productivity through synergistic integration
3Adaptability or versatility
If ancestral homologs from different organisms are combined in a single cell, then over 30 new molecules can be produced, but the genetic engineering required is challenging
Solution Approach 1:
The patent performs preliminary genetic engineering to assemble compressed pathways containing ancestral homologs from different organisms before exposing the cells to precursor diversity. The genetic framework is prepared in advance with all necessary enzymes and regulatory elements, enabling subsequent production of structurally diverse molecules without requiring further complex engineering
Solution Approach 2:
The engineered bacterial cell serves as an intermediary system that hosts compressed pathways from multiple organisms. This cellular intermediary integrates the genetic elements and coordinates their expression to produce diverse nonribosomal peptides, mediating between the disparate genetic sources and the final diverse molecular products
Data Source
AI summary
Provided herein are synthetic pathways from Escherichia coli and Vibrio cholerae genes for the production of new, synthetic nonribosomal peptides, and methods and compositions comprising the same. Some aspects of the present disclosure are directed to modified bacterial cells comprising a compressed biosynthetic pathway that comprises (a) biosynthetic genes obtained from one species encoding enzymes active in the bioassembly of a nonribosomal molecule, (b) biosynthetic genes obtained from another species encoding enzymes active in the bioassembly of a nonribosomal molecule that is different from the nonribosomal molecule of (a). In some embodiments, the biosynthetic genes of (a) are Escherichia coli biosynthetic genes and may include entD gene, an entC gene, an entE gene, an entB gene and an entA gene. In some embodiments, the biosynthetic genes of (b) are Vibrio cholera biosynthetic genes and may include a vibH gene and a vibF gene.