Synthetic Genetic Elements for Cross-Kingdom Expression
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Solution Overview
Problem
Current methods for heterologous expression of biosynthetic gene clusters (BGCs) in diverse microorganisms face challenges due to strain-specific expression, protein folding issues, metabolic differences, and instability of genetic elements, limiting the functional mobility and characterization of complex biosynthetic pathways.
Innovation Solution
A computational strategy for recoding nucleic acid sequences, including codon selection, N-terminal bias, hybrid regulatory elements, and screening for internal ribosome binding sites and terminators, combined with inducible expression circuits and landing pads, to facilitate stable and versatile expression of synthetic genetic elements across various microbial taxa.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If heterologous expression of BGCs is performed in diverse microorganisms using conventional methods, then expression can be achieved in some hosts, but strain-specific expression bottlenecks occur due to metabolic differences, protein folding issues, and genetic instability
Solution Approach 1:
The patent applies parameter changes by systematically optimizing codon usage to match host-specific codon preferences, adjusting regulatory element sequences to match host recognition patterns, and modifying protein sequence parameters to improve folding stability. These parameter optimizations enable reliable expression across diverse microbial hosts by adapting the genetic elements to each host's biological characteristics.
Solution Approach 2:
The patent creates universal genetic elements that can function across multiple host types. By designing regulatory elements with broad recognition patterns and using consensus sequence approaches, the invention enables a single set of optimized genetic elements to achieve reliable expression in Gram-negative bacteria, Gram-positive bacteria, and yeast, thus achieving multi-functionality across diverse hosts.
2Adaptability or versatility
If codon optimization and regulatory element redesign are performed to improve expression across hosts, then host range increases, but the complexity of genetic element design and validation increases
Solution Approach 1:
The patent uses computational methods to systematically change sequence parameters such as codon usage frequency, GC content, and regulatory motif sequences. These parameter optimizations are performed using bioinformatics tools that automatically analyze host genome data and generate optimized sequences, reducing manual design complexity while achieving broad host compatibility.
Solution Approach 2:
The patent performs preliminary computational optimization of genetic elements before experimental validation. By using in silico methods to predict and optimize codon usage, regulatory element functionality, and potential secondary structures, the invention reduces the complexity of subsequent experimental work by pre-resolving many design issues through computational analysis.
Data Source
AI summary
Computational strategies and compositions and methods of use thereof and formed therefrom are provided. Included are hybrid transcriptional expression signals for both prokaryotes and eukaryotes, and compositions and methods of introducing and mobilizing SGEs into multiple kingdoms. The strategies are particularly advantageous for hierarchically redesigning multigene biological pathways for mobilization, expression, and characterization in versatile organisms. Orphan biosynthetic gene clusters (BGCs) can be computationally redesigned into synthetic genetic elements (SGEs) and functionalized for expression across diverse hosts.