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Jasper Koehorst

About Jasper Koehorst:
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SEEK ID: https://hub.ibisba.eu/people/107

Location:  Netherlands

Expertise: Data Management, Software Engineering, Genetics, Microbiology, Molecular Biology, Bioinformatics

Tools: R, Python, Java, Computational and theoretical biology, Genetic analysis

ORCID: https://orcid.org/0000-0001-8172-8981

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An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually requires the presence of a N- terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted.
However, prediction of a SP does not guarantee that the protein is actually secreted and current
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Start date: 1st Jul 2019

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An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data

Abstract (Expand)

Background The ecological niche occupied by a fungal species, its pathogenicity and its usefulness as a microbial cell factory to a large degree depends on its secretome. Protein secretion usually …y requires the presence of a N-terminal signal peptide (SP) and by scanning for this feature using available highly accurate SP-prediction tools, the fraction of potentially secreted proteins can be directly predicted. However, prediction of a SP does not guarantee that the protein is actually secreted and current in silico prediction methods suffer from gene-model errors introduced during genome annotation. Results A majority rule based classifier that also evaluates signal peptide predictions from the best homologs of three neighbouring Aspergillus species was developed to create an improved list of potential signal peptide containing proteins encoded by the Aspergillus niger genome. As a complement to these in silico predictions, the secretome associated with growth and upon carbon source depletion was determined using a shotgun proteomics approach. Overall, some 200 proteins with a predicted signal peptide were identified to be secreted proteins. Concordant changes in the secretome state were observed as a response to changes in growth/culture conditions. Additionally, two proteins secreted via a non-classical route operating in A. niger were identified. Conclusions We were able to improve the in silico inventory of A. niger secretory proteins by combining different gene-model predictions from neighbouring Aspergilli and thereby avoiding prediction conflicts associated with inaccurate gene-models. The expected accuracy of signal peptide prediction for proteins that lack homologous sequences in the proteomes of related species is 85%. An experimental validation of the predicted proteome confirmed in silico predictions.

Authors: Machtelt Braaksma, Elena S Martens-Uzunova, Peter J Punt, Peter J Schaap

Date Published: 1st Dec 2010

Publication Type: Journal

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