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Methanol Independent Expression by Pichia Pastoris Employing De-repression Technologies
Published on: January 23, 2019
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Improving functional annotation for industrial microbes: a case study with Pichia pastoris.
Duygu Dikicioglu1, Valerie Wood1, Kim M Rutherford1
1Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
Trends in Biotechnology
|June 16, 2014
Summary
Industrial microbes like Pichia pastoris lack comprehensive functional gene annotation. This research proposes short-term solutions to improve annotation using Pichia pastoris as a model for better biotechnology applications.
Area of Science:
- Microbiology
- Biotechnology
- Bioinformatics
Background:
- Model organism databases provide extensive functional annotation for research microbes like Escherichia coli and Saccharomyces cerevisiae.
- Industrial microbes, widely used in biotechnology, often lack sufficient functional annotation, hindering research and development.
- Pichia (Komagataella) pastoris serves as a key example illustrating these annotation limitations.
Purpose of the Study:
- To highlight the limitations in functional gene annotation for industrial microbes using Pichia pastoris as a case study.
- To propose short-term strategies for enhancing Gene Ontology (GO) annotation coverage for under-annotated industrial microbes.
- To outline the establishment of curation pipelines for the scientific literature of industrial organisms.
Main Methods:
- Utilizing annotation transfer methods to improve Gene Ontology (GO) coverage.
- Analyzing the current state of functional annotation for Pichia pastoris.
- Considering the development of literature curation pipelines.
Main Results:
- Identified significant gaps in functional annotation for the industrial yeast Pichia pastoris.
- Demonstrated the feasibility of improving annotation through transfer from well-annotated organisms.
- Outlined a strategic approach for establishing robust curation processes.
Conclusions:
- There is a critical need to improve functional annotation for industrial microbes to support biotechnology advancements.
- Annotation transfer and dedicated curation pipelines are viable short-term solutions.
- Enhancing annotation resources for organisms like Pichia pastoris will accelerate their application in biotechnology.
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