Genomically Recoded Organisms Resisting Horizontal Gene Transfer
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Solution Overview
Problem
Organisms engineered for specific functions are vulnerable to horizontal gene transfer (HGT) from conjugative plasmids and viruses, which can destabilize their functions and pose economic and health risks, highlighting the need for molecular mechanisms to resist such transfers.
Innovation Solution
Genomically recoded organisms (GROs) with eliminated codons and recombinant expression constructs for ribosomal rescue pathways, such as tmRNA-SmpB, ArfA, or ArfB, are developed to resist HGT by reassigning codons and incorporating orthogonal translation systems, preventing the transfer and expression of horizontally transferred genetic elements.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If organisms use the standard genetic code, then faithful translation of proteins across living organisms is enabled, but vulnerability to horizontal gene transfer and exploitation by viruses and plasmids increases
Solution Approach 1:
The patent applies parameter changes by systematically altering the genetic code parameters - specifically reassigning stop codons (UAA, UAG, UGA) to encode amino acids and introducing non-canonical amino acids with altered codon assignments. This fundamental parameter change in the genetic code creates a translational barrier that prevents exploitation by standard viruses and plasmids while maintaining faithful protein synthesis through the engineered orthogonal translation system
Solution Approach 2:
The patent introduces an intermediary orthogonal translation system comprising engineered aminoacyl-tRNA synthetases and tRNAs that mediate between the altered genetic code and protein synthesis. This intermediary system allows the organism to read and translate the modified codons correctly while creating a language barrier that standard horizontal gene transfer elements cannot overcome
2Object-affected harmful factors
If codon reassignment is implemented to resist HGT, then resistance to horizontally transferred genetic elements is improved, but complexity of the translation system increases
Solution Approach 1:
The patent segments the translation system into orthogonal components - separate aminoacyl-tRNA synthetases for canonical and non-canonical amino acids, distinct tRNA populations with specific anticodons, and modular genetic code assignments. This segmentation allows independent optimization and control of different translation functions, managing complexity through systematic organization of the engineered components
Solution Approach 2:
The engineered orthogonal translation system performs multiple functions: it decodes reassigned stop codons, incorporates non-canonical amino acids, maintains resistance to HGT, and ensures faithful protein synthesis. This multi-functional design consolidates several protective and translational capabilities into a unified system, reducing overall complexity despite the fundamental code alterations
3Stability of the object's composition
If genomic recoding is performed to eliminate codons, then functional stability against viral exploitation is enhanced, but difficulty of detecting and measuring resistance increases
Solution Approach 1:
The patent employs reporter genes that produce detectable signals (fluorescence, color changes, or other measurable outputs) to indicate successful resistance against horizontal gene transfer. These phenotypic markers provide visual or instrumental detection methods that simplify monitoring of resistance characteristics despite the complex underlying genomic recoding
Solution Approach 2:
The patent creates measurable copies or proxies of the resistance function through reporter systems and selectable markers that replicate the protective effect of codon reassignment in a detectable form. These proxy systems allow indirect measurement of resistance without requiring direct analysis of the complex recoded genome or translation machinery
Data Source
AI summary
Organisms resistant to horizontal gene transfer (HGT), and compositions and methods of use thereof are provided. The organisms are typically genomically recoded organisms (GRO), typically cells, having a genome in which at least one endogenous codon has been eliminated by reassignment of the codon to a synonymous or non-synonymous codon. The GRO typically include a recombinant expression construct for expression of at least one element of a ribosomal rescue pathway, typically lacking the eliminated codon. Typically, the disclosed cells are resistant to completed transfer and/or expression of a horizontally transferred genetic element (HTGE) from another organism compared a corresponding cell having a genome wherein the eliminated codon has not been eliminated. In some embodiments, the organism from which the HTGE is being transferred is a bacterium or a virus.