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Improving functional annotation for industrial microbes: a case study with Pichia pastoris.


Type

Article

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Authors

Rutherford, Kim M 
McDowall, Mark D 
Oliver, Stephen G 

Abstract

The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial microbes that are used widely in biotechnology. In this Opinion piece, we use Pichia (Komagataella) pastoris to illustrate the limitations of the available annotation. We consider the resources that can be implemented in the short term both to improve Gene Ontology (GO) annotation coverage based on annotation transfer, and to establish curation pipelines for the literature corpus of this organism.

Description

Keywords

Komagataella pastoris, Pichia pastoris, functional annotation, industrial microbes, recombinant protein production, Biotechnology, Fungal Proteins, Industrial Microbiology, Molecular Sequence Annotation, Pichia

Journal Title

Trends Biotechnol

Conference Name

Journal ISSN

0167-7799
1879-3096

Volume Title

Publisher

Elsevier BV
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/K011138/1)
Wellcome Trust (090548/Z/09/Z)
European Commission (289126)
We gratefully acknowledge funding from the Wellcome Trust (PomBase and Canto; WT090548MA to SGO), and the EU 7th Framework Programme (BIOLEDGE Contract No: 289126 to SGO).