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Open Access Research article

Genomic analysis of the secretion stress response in the enzyme-producing cell factory Aspergillus niger

Thomas Guillemette16, Noël NME van Peij2, Theo Goosen3, Karin Lanthaler4, Geoffrey D Robson4, Cees AMJJ van den Hondel5, Hein Stam2 and David B Archer1*

Author Affiliations

1 School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, UK

2 DSM Food Specialties, P.O. Box 1, 2600 MA Delft, The Netherlands

3 Biocentre, HAN University, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands

4 Faculty of Life Sciences, Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK

5 Clusius Laboratory, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands

6 Laboratoire de Microbiologie, UMR 77 Pathologie Végétale, Université d'Angers, 2 bd Lavoisier, 49045 Angers cedex, France

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BMC Genomics 2007, 8:158  doi:10.1186/1471-2164-8-158

Published: 11 June 2007

Abstract

Background

Filamentous fungi such as Aspergillus niger have a high capacity secretory system and are therefore widely exploited for the industrial production of native and heterologous proteins. However, in most cases the yields of non-fungal proteins are significantly lower than those obtained for fungal proteins. One well-studied bottleneck appears to be the result of mis-folding of heterologous proteins in the ER during early stages of secretion, with related stress responses in the host, including the unfolded protein response (UPR). This study aims at uncovering transcriptional and translational responses occurring in A. niger exposed to secretion stress.

Results

A genome-wide transcriptional analysis of protein secretion-related stress responses was determined using Affymetrix DNA GeneChips and independent verification for selected genes. Endoplasmic reticulum (ER)-associated stress was induced either by chemical treatment of the wild-type cells with dithiothreitol (DTT) or tunicamycin, or by expressing a human protein, tissue plasminogen activator (t-PA). All of these treatments triggered the UPR, as shown by the expression levels of several well-known UPR target genes. The predicted proteins encoded by most of the up-regulated genes function as part of the secretory system including chaperones, foldases, glycosylation enzymes, vesicle transport proteins, and ER-associated degradation proteins. Several genes were down-regulated under stress conditions and these included several genes that encode secreted enzymes. Moreover, translational regulation under ER stress was investigated by polysomal fractionation. This analysis confirmed the post-transcriptional control of hacA expression and highlighted that differential translation also occurs during ER stress, in particular for some genes encoding secreted proteins or proteins involved in ribosomal biogenesis and assembly.

Conclusion

This is first genome-wide analysis of both transcriptional and translational events following protein secretion stress. Insight has been gained into the molecular basis of protein secretion and secretion-related stress in an effective protein-secreting fungus, and provides an opportunity to identify target genes for manipulation in strain improvement strategies.