Microorganism Gene Screening via Genomic Library Segmentation
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Solution Overview
Problem
Current methods for identifying genes involved in the production of bioactive molecules by microorganisms are time-consuming and inefficient, often requiring extensive characterization of multiple products to determine which chemical structures or proteins are responsible for observed activities.
Innovation Solution
A method involving culturing microorganisms under different conditions, sequencing proteins and RNA, and grouping sequences based on genomic location or open reading frames to rapidly identify genes correlated with product levels, allowing for the transfer of these genes to other hosts for scalable production.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional methods are used to identify genes involved in product production, then comprehensive characterization of multiple products is achieved, but the process becomes extremely time-consuming
Solution Approach 1:
The patent segments the genome into multiple libraries of DNA fragments, allowing parallel processing and analysis of different genomic regions. This segmentation enables simultaneous screening of multiple gene candidates across different libraries, dramatically reducing the time required for comprehensive gene identification while maintaining accuracy through systematic coverage of the entire genome.
Solution Approach 2:
The patent performs preliminary actions by constructing comprehensive genomic libraries and pre-screening them under various culture conditions before final gene identification. Expressible sequence tags are generated and stored in libraries in advance, allowing rapid querying and identification when a specific product activity is observed, thus avoiding time-consuming characterization later.
2Measurement precision
If extensive product characterization is performed to determine responsible chemical structures, then accurate identification of active molecules is achieved, but the complexity of the process increases
Solution Approach 1:
The patent implements feedback mechanisms where expressible sequence tags from genomic libraries are screened against observed product activities. The results feed back into identifying candidate genes, which are then validated and used to guide further screening. This feedback loop systematically narrows down candidates without requiring exhaustive characterization of all possible products, reducing process complexity while maintaining accuracy.
Solution Approach 2:
The patent introduces expressible sequence tags as intermediaries between the genome and the product activity observation. These tags serve as mediators that link genomic information to phenotypic expression, allowing indirect identification of responsible genes without direct complex characterization of all chemical structures. The tags act as proxies that simplify the identification process.
3Measurement precision
If multiple culture conditions are screened to identify product production, then comprehensive gene identification is achieved, but the number of required sequences increases
Solution Approach 1:
The patent merges information from multiple culture conditions by integrating data from screens conducted under different conditions into a unified genomic library system. Expressible sequence tags from various conditions are combined and analyzed together, allowing identification of genes that show consistent expression patterns across conditions. This merging approach maintains comprehensive identification while managing data volume through integrated analysis.
Solution Approach 2:
The patent creates universal genomic libraries that can be used across multiple culture conditions and for multiple product types. The same library infrastructure and screening methodology can identify genes for different products by simply changing the screening conditions, eliminating the need for separate comprehensive analyses for each condition. This multi-functionality reduces the effective quantity of unique sequence data that must be processed.
Data Source
AI summary
In one aspect the disclosure relations to means and methods for identifying a protein or a DNA encoding the protein, involved in the production of a product by a micro-organism. In the methods the micro-organism is cultured under different culture conditions each of which exhibit a different level of the product that is produced by the micro-organism. The genetic expression of the genes of the micro-organism is compared with the level of the product, and groups of DNAs are identified that are involved in the production of the product by the micro-organism.