Engineered Plant Microbes for Species-Specific Pathogen Killing
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Solution Overview
Problem
Current agricultural treatments for bacterial diseases in plants, such as antibiotics and heavy metals, disrupt the phyto- and rhizo-microbiomes and lead to treatment-resistant bacteria, causing significant yield losses and environmental contamination.
Innovation Solution
Modified bacteria are engineered with expression vectors containing endonucleases and guide nucleic acids to target specific plant-associated bacteria, using a low copy origin of replication, enabling species-specific killing without disrupting the broader microbiome.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If broad spectrum bactericidal treatments (antibiotics and heavy metals) are used to treat bacterial diseases in plants, then disease treatment effectiveness is improved, but the phyto- and rhizo-microbiomes are disrupted and treatment-resistant bacteria develop
Solution Approach 1:
The patent segments the bacterial population into target pathogens and beneficial microbiome members by using CRISPR-Cas systems with guide RNAs that specifically recognize and destroy only pathogenic bacterial DNA sequences, leaving beneficial bacteria untouched. This segmentation allows selective elimination of harmful bacteria while preserving the microbiome structure.
Solution Approach 2:
The patent applies local quality by making the bactericidal action specific to certain bacterial species through engineered guide RNAs that target unique genomic sequences of pathogens. The treatment has different effects on different bacteria: destructive to targets, neutral to non-targets, thereby creating localized specificity in an otherwise complex microbiome environment.
2Measurement precision
If modified bacteria with conjugation machinery are introduced to transfer CRISPR-Cas systems to target pathogens, then species-specific pathogen killing is achieved, but the complexity of the bacterial system increases
Solution Approach 1:
The patent uses modified bacteria as intermediary carriers that hold and transfer the CRISPR-Cas genetic system to target pathogens through natural conjugation machinery. These intermediary bacteria facilitate the delivery of precision-targeting components without themselves being the final therapeutic agent, simplifying the overall delivery mechanism.
Solution Approach 2:
The patent exploits the bacteria's own natural conjugation machinery to perform the gene transfer function. Rather than introducing artificial delivery systems, the modified bacteria use their endogenous ability to transfer DNA to other bacteria, allowing the system to self-assemble and self-deliver the CRISPR components to target pathogens.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The modified bacteria effectively kill targeted pathogens while preserving the plant microbiome, reducing disease pressure and increasing plant growth and yield, with high specificity and minimal environmental impact.
Implementation Method 1
the first exogenous nucleic acid comprises: a sequence encoding for an endonuclease; and a sequence encoding for at least one guide nucleic acid, wherein the at least one guide nucleic acid targets a sequence in a genome of one or more species of plant-associated bacteria
Implementation Method 2
the second exogenous nucleic acid encodes for a bacterial conjugation machinery
Data Source
AI summary
Provided herein are compositions and methods for use in challenging pathogenic bacteria on plants. Optional features include modification of a donor bacteria to include exogenous nucleic acids encoding for conjugation machinery and gene modification components, such as guide sequence for use in CRISPR. The compositions and methods provided herein can be used for delivery to a wide variety of crops and for targeting one or more pathogens.