Gene Design for Vaccine Vector Expression Stability
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Solution Overview
Problem
Existing vaccine vector development faces challenges with poor foreign protein expression, inefficient post-translational processing, and gene insert instability, often due to the foreign gene being nonessential for vector propagation and causing negative effects on replicative fitness.
Innovation Solution
A gene design approach that modifies protein sequences to reduce interference with vector propagation and stabilizes nucleotide sequences by using a codon bias similar to the vector, removing mutation-prone elements, and replacing domains with analogous operable elements from other polypeptides to enhance expression and compatibility.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If foreign gene sequences are introduced into vaccine vectors to express immunogenic proteins, then protein expression is improved, but vector propagation and genetic stability deteriorate
Solution Approach 1:
The patent applies parameter changes by modifying the nucleotide sequence of foreign genes to match the codon usage bias, GC content, and nucleotide composition of the vector genome. This includes optimizing codon frequency, adjusting GC content to match the vector, and eliminating mutation-prone sequences while maintaining the encoded protein sequence, thereby improving both expression and stability
Solution Approach 2:
The patent applies local quality by making specific modifications to particular regions of the foreign gene sequence. This includes targeting mutation-prone areas for stabilization, optimizing local codon usage in different gene regions, and selectively modifying nucleotide sequences to match vector characteristics while preserving essential protein-coding regions
2Productivity
If gene optimization procedures are used to increase protein expression, then expression levels are improved, but gene insert stability and vector compatibility deteriorate
Solution Approach 1:
The patent applies parameter changes by systematically modifying multiple parameters of the gene sequence simultaneously: codon usage frequency, GC content, nucleotide composition, and elimination of unstable sequences. This multi-parameter optimization approach achieves both high expression and stability, unlike traditional single-parameter optimization
Solution Approach 2:
The patent converts potentially harmful foreign gene sequences into beneficial stable inserts by identifying and eliminating mutation-prone elements, optimizing codon usage to match vector preferences, and adjusting nucleotide composition to reduce immunogenicity and improve replication compatibility, thereby transforming the foreign gene from a liability into an asset
3Productivity
If synthetic coding sequences are designed with characteristics of highly expressed cellular mRNAs, then translation efficiency is improved, but vector replication compatibility deteriorates
Solution Approach 1:
The patent applies parameter changes by shifting the optimization reference from cellular mRNA characteristics to vector genome characteristics. This includes matching codon usage to the vector's preferred codons, adjusting GC content to match the vector's genomic composition, and optimizing nucleotide sequences for vector replication machinery recognition rather than cellular translation machinery
Solution Approach 2:
The patent inverts the traditional optimization approach by instead of optimizing for cellular expression systems, optimizing the foreign gene to match the vector's own genomic characteristics. This inversion ensures that the gene behaves like a native vector gene, improving replication compatibility while maintaining expression efficiency
Data Source
AI summary
The present invention relates to methods of developing gene inserts that are more compatible with the host vectors by modifying a protein sequence to lessen potential interference with vector propagation while ensuring that the protein is expressed and processed efficiently and maintains desired structural features, and designing a gene with a nucleotide sequence that resembles the base composition of the host vector genome.