Hyde1 Gene Product and T6SS Delivery for Plant Pathogen Control
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Solution Overview
Problem
The understanding of molecular mechanisms governing plant-microbe interactions is limited, hindering the ability to combat plant diseases and harness beneficial bacterial functions for agriculture, and there is a need to identify and characterize bacterial genes that help microbes thrive in the plant environment.
Innovation Solution
Utilization of a purified or isolated Hyde1 gene product, or a functional fragment thereof, and a modified host cell capable of expressing a Type VI secretion system (T6SS), Hyde1, to inhibit the growth of pathogenic bacteria by introducing a non-pathogenic bacterial strain expressing Hyde1 or Hyde2, which can limit or reduce the growth of pathogenic bacteria in environments.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Adaptability or versatility
If cultivation-independent methods (metagenome sequencing) are used to study plant-associated bacteria, then the ability to capture DNA of uncultivated organisms is improved, but the ability to perform functional validation of in silico predictions deteriorates
Solution Approach 1:
The research approach is segmented into two distinct phases: (1) cultivation-independent metagenome sequencing to discover and identify bacterial genes and functions in the plant environment, and (2) cultivation-dependent isolate-based methods to perform functional validation of the in silico predictions. This segmentation allows each method to excel at its specific task without compromise.
Solution Approach 2:
The patent uses cultivated bacterial isolates as an intermediary between the initial metagenomic discovery phase and the functional validation phase. These isolates serve as a bridge that connects the in silico predictions from metagenomics with experimental functional validation, enabling the translation of computational predictions into verified biological knowledge.
2Reliability
If cultivated bacterial isolates are used for functional validation, then the ability to perform functional validation is improved, but the coverage of rare uncultivated organisms deteriorates
Solution Approach 1:
The research methodology is divided into sequential segments where metagenomics first identifies genes and functions from the total bacterial community including rare uncultivated organisms, and then cultivated isolates are used to functionally validate specific predictions. This segmentation ensures both broad coverage and deep validation.
Solution Approach 2:
Metagenome sequencing is performed as a preliminary action before isolate-based functional validation. This preliminary step identifies candidate genes and functions in the plant environment, which then guide subsequent targeted functional validation using cultivated isolates, ensuring that validation efforts focus on the most relevant discoveries.
3Device complexity
If limited sequencing depth is used in metagenomics, then the cost and complexity are reduced, but the ability to access genomes of rare organisms deteriorates
Solution Approach 1:
The patent applies partial sequencing depth to the metagenomic analysis, focusing on capturing sufficient data to identify common and dominant bacterial genes and functions in the plant environment. Rather than attempting to sequence every rare organism completely, the method performs partial action that is sufficient for discovery purposes, with the understanding that cultivated isolates will provide complete genomic information for validation.
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 Hyde1 gene product effectively kills a broad array of plant pathogenic bacterial species, and modified bacterial cells can be used as biocontrol agents to treat plant diseases and reduce pathogenic bacterial growth in environments, such as intensive care units, by expressing Hyde1 or Hyde2 through the Type VI secretion system.
Implementation Method 1
a modified host cell comprises one or more genes encoding, and/or capable of expressing, a Type VI secretion system (T6SS), Hyde1, and/or Hyde2
Data Source
AI summary
The present invention provides for a composition comprising a purified or isolated Hyde1 gene product, or a functional fragment thereof; a modified host cell capable of expressing a Type VI secretion system (T6SS), Hyde1, and/or Hyde2, or a functional fragment thereof; a method of treating a disease caused all or in part by a bacterial cell, comprising administering a composition of the present invention to a subject in need thereof; and a method to limit or reduce growth of a pathogenic bacteria in an environment, comprising: introducing a non-pathogenic bacterial capable of expressing a Type VI secretion system (T6SS), Hyde1, and/or Hyde2, or functional fragment thereof, to an environment.