Open Access Research article

Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress

Neuza DSP Carvalho12, Thomas R Jørgensen124, Mark Arentshorst1, Benjamin M Nitsche15, Cees AMJJ van den Hondel12, David B Archer3 and Arthur FJ Ram12*

Author Affiliations

1 Institute of Biology Leiden, Leiden University, Molecular Microbiology and Biotechnology, Sylviusweg 72, 2333, BE Leiden, The Netherlands

2 Kluyver Centre for Genomics of Industrial Fermentation, P.O box 5057, 2600, GA Delft, The Netherlands

3 School of Biology, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom

4 Present address: Protein Expression, Novo Nordisk, Novo Nordisk Park, 2760, Måløv, Denmark

5 Present address: Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355, Berlin, Germany

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BMC Genomics 2012, 13:350  doi:10.1186/1471-2164-13-350

Published: 30 July 2012

Additional files

Additional file 1:

Construction plasmids and confirmation of a reference strain and a strain only expressing the hacA induced form. Schematic representation of the plasmids pHAC (A) and pConstHac (B) (Note: fragment sizes are not on scale). (C) Sequence alignment of pHAC and pConstHAC showing the absence of the 20 nt intron on pConstHac. (D) PCR amplification of gDNA of HacAWT (NC1.1) and HacACA (NC2.1) transformants. Primers were designed about 100 bp upstream and 100 bp downstream of the hacA intron region, giving rise to a band of 200 bp for HacACA and 220 bp for HacAWT. Sizes of the DNA Marker (M) are indicated.

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Additional file 2:

Growth profiles ofA. niger HacAWT (A, B, C) and HacACA (D, E, F) triplicate batch cultures. Dry weight biomass concentration (gDWkg-1) as a function of time (h) illustrates the growth of the cultures. The maximum specific growth rate for each culture was determined from the slope (α) of the ln transformation of biomass (Cbiomass) (lnX) in the exponential growth phase as a function of time (h), as well from log transformation of alkali addition as a function of time (h). Dash-line represents the end of the exponential growth phase (depletion of glucose).

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Additional file 3:

Complete list of all differentially expressed genes in HacACA. Expression data and the FDR-values for the pair wise comparison of the different strains and time points.

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Additional file 4:

Overview of the 616 HacACA up-regulated genes in the 3 time points. Subset of all differentially expressed genes (Additional file 3).

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Additional file 5:

HacACA up-regulated genes that contain at least one UPRE sequence. Subset of all differentially expressed genes (Additional file 3).

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Additional file 6:

Network maps of related up-regulated GO-terms. Results of the GO-enrichment analysis of biological processes of all differentially expressed genes in HacACA-1/HacAWT.

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Additional file 7:

Network maps of related down-regulated GO-terms. Results of the GO-enrichment analysis of biological processes of all differentially expressed genes in HacACA-1/HacAWT.

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Additional file 8:

GO analysis of biological processes enriched in the up-regulated set of genes in HacACA. Subset of all differentially expressed genes (Additional file 3).

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Additional file 9:

GO analysis of biological processes enriched in the down-regulated set of genes in HacACA. Subset of all differentially expressed genes (Additional file 3).

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Additional file 10:

Expression values of selected genes related to enriched GO terms of ER associated processes. Subset of all differentially expressed genes (Additional file 3).

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Additional file 11:

Expression values of selected genes related to enriched GO terms associated with vesicle transport within the cell. Subset of all differentially expressed genes (Additional file 3).

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Additional file 12:

Expression values of selected genes related to enriched GO terms associated with glycosylation processes. Subset of all differentially expressed genes (Additional file 3)

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Additional file 13:

Expression values of selected genes related to enriched GO terms associated with lipid metabolic processes. Subset of all differentially expressed genes (Additional file 3).

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Additional file 14:

Expression values of selected genes related to the GO terms “hydrolase activity”, “glutathione catabolic processes” and “vacuolar acidification”. Subset of all differentially expressed genes (Additional file 3).

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Additional file 15:

Expression values of selected down-regulated genes related to enriched GO terms. Subset of all differentially expressed genes (Additional file 3).

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Additional file 16:

Commonly induced and repressed genes in the HacACA strain and A. niger strains treated with DTT and Tunicamycin and expressing tPA. Subset of all differentially expressed genes (Additional file 3) and Guillemette’ study [37].

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Additional file 17:

Expression values of genes related to extracellular proteases production.

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