A genomic survey of proteases in Aspergilli

Abstract

BackgroundProteases can hydrolyze peptides in aqueous environments. This property has made proteases the most important industrial enzymes by taking up about 60% of the total enzyme market. Microorganisms are the main sources for industrial protease production due to their high yield and a wide range of biochemical properties. Several Aspergilli have the ability to produce a variety of proteases, but no comprehensive comparative study has been carried out on protease productivity in this genus so far.ResultsWe have performed a combined analysis of comparative genomics, proteomics and enzymology tests on seven Aspergillus species grown on wheat bran and sugar beet pulp. Putative proteases were identified by homology search and Pfam domains. These genes were then clusters based on orthology and extracellular proteases were identified by protein subcellular localization prediction. Proteomics was used to identify the secreted enzymes in the cultures, while protease essays with and without inhibitors were performed to determine the overall protease activity per protease class. All this data was then integrated to compare the protease productivities in Aspergilli.ConclusionsGenomes of Aspergillus species contain a similar proportion of protease encoding genes. According to comparative genomics, proteomics and enzymatic experiments serine proteases make up the largest group in the protease spectrum across the species. In general wheat bran gives higher induction of proteases than sugar beet pulp. Interesting differences of protease activity, extracellular enzyme spectrum composition, protein occurrence and abundance were identified for species. By combining in silico and wet-lab experiments, we present the intriguing variety of protease productivity in Aspergilli.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-523) contains supplementary material, which is available to authorized users.

Spatial differentiation of gene expression in Aspergillus niger colony grown for sugar beet pulp utilization

“…Sixty-two (putative) extracellular proteases were predicted by orthology search with the data from Budak et al 29 (see Supplementary Table 4 online). Thirty genes were evenly expressed across the colony and eighteen genes were not significantly expressed.…”

Enabling Low Cost Biopharmaceuticals: A Systematic Approach to Delete Proteases from a Well-Known Protein Production Host Trichoderma reesei

“…reesei we have achieved a 96% reduction with only 7 deletions. Protease genes have been surveyed in the Aspergilli genomes and there were typically over 300 putative genes per species [ 48 ]. In A .…”

Closely related fungi employ diverse enzymatic strategies to degrade plant biomass

“…Proteins from 3 ml of culture filtrate were precipitated with cold TCA/acetone and the amount of protein recovered was determined using the RCDC kit assay (BioRad, Mississauga, ON, Canada). Five micrograms of protein were digested with trypsin and an aliquot analyzed by LC–MS/MS as previously described [ 60 ] on a Velos LTQ-Orbitrap mass spectrometer (Thermo-Fisher, San Jose, CA, USA). MS/MS data were processed using Proteome Discoverer Quant 1.3 (Thermo-Fisher) and spectral data were searched against Aspergillus protein databases downloaded from the Aspergillus Genome Database (AspGD).…”