ArticleBMC genomics2010
An inventory of the Aspergillus niger secretome by combining in silico predictions with shotgun proteomics data.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 83 citations in OpenAlex.
- FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes.Database : the journal of biological databases and curation · 2023Article
- Genomic and proteomic analysis of Tausonia pullulans reveals a key role for a GH15 glucoamylase in starch hydrolysis.Applied microbiology and biotechnology · 2022Article
- Protein expression and secretion by filamentous fungi.Journal of biosciences · 2021Review
- Unconventional Secretion of Nigerolysins A fromMicroorganisms · 2020Article
- Evolution and functional characterization of pectate lyase PEL12, a member of a highly expanded Clonostachys rosea polysaccharide lyase 1 family.BMC microbiology · 2018Article
- Genomic and exoproteomic diversity in plant biomass degradation approaches among Aspergilli.Studies in mycology · 2018Article
- Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species.Scientific reports · 2018Article
- A community-driven reconstruction of theFungal biology and biotechnology · 2018Article
- PApplied and environmental microbiology · 2017Article
- Expression ofBiotechnology for biofuels · 2017Article
- The amyR-deletion strain of Aspergillus niger CICC2462 is a suitable host strain to express secreted protein with a low background.Microbial cell factories · 2016Article
- Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization.Scientific reports · 2015Article
- Methodologies and perspectives of proteomics applied to filamentous fungi: from sample preparation to secretome analysis.International journal of molecular sciences · 2015Review
- Comparative Secretome Analysis of Trichoderma reesei and Aspergillus niger during Growth on Sugarcane Biomass.PloS one · 2015Article
- The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer.Genome biology and evolution · 2014Article
- Comparative genome analysis of entomopathogenic fungi reveals a complex set of secreted proteins.BMC genomics · 2014Article
- Targeted lipid analysis of haemolytic mycelial extracts of Aspergillus niger.Molecules (Basel, Switzerland) · 2014Article
- A genomic survey of proteases in Aspergilli.BMC genomics · 2014Article
- A comparative systems analysis of polysaccharide-elicited responses in Neurospora crassa reveals carbon source-specific cellular adaptations.Molecular microbiology · 2014Article
- How many signal peptides are there in bacteria?Environmental microbiology · 2013Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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 in silico prediction methods suffer from gene-model errors introduced during genome annotation.
resultsA 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.
conclusionsWe 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.
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