Improving functional annotation for industrial microbes: a case study with Pichia pastoris.
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Authors
Dikicioglu, Duygu https://orcid.org/0000-0002-3018-4790
Wood, Valerie https://orcid.org/0000-0001-6330-7526
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
1879-3096
Volume Title
Publisher
Elsevier BV
Publisher DOI
Sponsorship
Biotechnology and Biological Sciences Research Council (BB/K011138/1)
Wellcome Trust (090548/Z/09/Z)
European Commission (289126)
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).