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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.

Carvalho ND, Jørgensen TR, Arentshorst M, Nitsche BM, van den Hondel CA, Archer DB, Ram AF - BMC Genomics (2012)

Bottom Line: In addition to the well known HacA targets such as the ER resident foldases and chaperones, GO enrichment analysis revealed up-regulation of genes involved in protein glycosylation, phospholipid biosynthesis, intracellular protein transport, exocytosis and protein complex assembly in the HacACA mutant.Biological processes over-represented in the down-regulated genes include those belonging to central metabolic pathways, translation and transcription.The results indicate that the constitutive activation of the HacA leads to a coordinated regulation of the folding and secretion capacity of the cell, but with consequences on growth and fungal physiology to reduce secretion stress.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biology Leiden, Leiden University, Molecular Microbiology and Biotechnology, BE Leiden, The Netherlands.

ABSTRACT

Background: HacA/Xbp1 is a conserved bZIP transcription factor in eukaryotic cells which regulates gene expression in response to various forms of secretion stress and as part of secretory cell differentiation. In the present study, we replaced the endogenous hacA gene of an Aspergillus niger strain with a gene encoding a constitutively active form of the HacA transcription factor (HacACA). The impact of constitutive HacA activity during exponential growth was explored in bioreactor controlled cultures using transcriptomic analysis to identify affected genes and processes.

Results: Transcription profiles for the wild-type strain (HacAWT) and the HacACA strain were obtained using Affymetrix GeneChip analysis of three replicate batch cultures of each strain. In addition to the well known HacA targets such as the ER resident foldases and chaperones, GO enrichment analysis revealed up-regulation of genes involved in protein glycosylation, phospholipid biosynthesis, intracellular protein transport, exocytosis and protein complex assembly in the HacACA mutant. Biological processes over-represented in the down-regulated genes include those belonging to central metabolic pathways, translation and transcription. A remarkable transcriptional response in the HacACA strain was the down-regulation of the AmyR transcription factor and its target genes.

Conclusions: The results indicate that the constitutive activation of the HacA leads to a coordinated regulation of the folding and secretion capacity of the cell, but with consequences on growth and fungal physiology to reduce secretion stress.

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Related in: MedlinePlus

Analysis of differentially expressed genes in HacACA at all three time points in comparison to HacAWT . Venn diagrams of the number of overlapping and non-overlapping induced (A) or repressed (B) genes on A. niger  HacACA mutant strain at different time points in comparison to HacAWT strain
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Figure 3: Analysis of differentially expressed genes in HacACA at all three time points in comparison to HacAWT . Venn diagrams of the number of overlapping and non-overlapping induced (A) or repressed (B) genes on A. niger HacACA mutant strain at different time points in comparison to HacAWT strain

Mentions: The number of differentially-expressed genes (FDR <0.005) in a pair-wise comparison are given in Table 1. In response to constitutive activation of hacA at time point 1 (HacACA-1), 1235 genes were differentially expressed. The number of differentially expressed genes increased when comparing the later time points (HacACA-2 and HacACA-3) to the wild-type strain to give a total number of 1698 and 1978 differentially expressed genes. Table 1 also shows that the transcriptomic differences between the different time points of the constitutive HacA strain were relatively minor (48 and 179 differentially expressed genes comparing HacACA-2 vs. HacACA-1 and HacACA-3 vs. HacACA-1 respectively). Comparison of HacACA-2 with HacACA-3 revealed very similar transcriptomes and with the stringent FDR of <0.005, no differentially expressed genes were detected. As a start to analyse the expression data, Venn diagrams were made to identify genes that were differentially expressed in HacACA at all three time points when compared to the wild-type strain. As shown in Figure 3A, 616 genes were up-regulated in the constitutive HacA strain at all three time points and 433 genes were down-regulated (Figure 3B). A complete list of all expression data and the FDR-values for the pair-wise comparison of the different strains and time points is given in [Additional file 3].


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.

Carvalho ND, Jørgensen TR, Arentshorst M, Nitsche BM, van den Hondel CA, Archer DB, Ram AF - BMC Genomics (2012)

Analysis of differentially expressed genes in HacACA at all three time points in comparison to HacAWT . Venn diagrams of the number of overlapping and non-overlapping induced (A) or repressed (B) genes on A. niger  HacACA mutant strain at different time points in comparison to HacAWT strain
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472299&req=5

Figure 3: Analysis of differentially expressed genes in HacACA at all three time points in comparison to HacAWT . Venn diagrams of the number of overlapping and non-overlapping induced (A) or repressed (B) genes on A. niger HacACA mutant strain at different time points in comparison to HacAWT strain
Mentions: The number of differentially-expressed genes (FDR <0.005) in a pair-wise comparison are given in Table 1. In response to constitutive activation of hacA at time point 1 (HacACA-1), 1235 genes were differentially expressed. The number of differentially expressed genes increased when comparing the later time points (HacACA-2 and HacACA-3) to the wild-type strain to give a total number of 1698 and 1978 differentially expressed genes. Table 1 also shows that the transcriptomic differences between the different time points of the constitutive HacA strain were relatively minor (48 and 179 differentially expressed genes comparing HacACA-2 vs. HacACA-1 and HacACA-3 vs. HacACA-1 respectively). Comparison of HacACA-2 with HacACA-3 revealed very similar transcriptomes and with the stringent FDR of <0.005, no differentially expressed genes were detected. As a start to analyse the expression data, Venn diagrams were made to identify genes that were differentially expressed in HacACA at all three time points when compared to the wild-type strain. As shown in Figure 3A, 616 genes were up-regulated in the constitutive HacA strain at all three time points and 433 genes were down-regulated (Figure 3B). A complete list of all expression data and the FDR-values for the pair-wise comparison of the different strains and time points is given in [Additional file 3].

Bottom Line: In addition to the well known HacA targets such as the ER resident foldases and chaperones, GO enrichment analysis revealed up-regulation of genes involved in protein glycosylation, phospholipid biosynthesis, intracellular protein transport, exocytosis and protein complex assembly in the HacACA mutant.Biological processes over-represented in the down-regulated genes include those belonging to central metabolic pathways, translation and transcription.The results indicate that the constitutive activation of the HacA leads to a coordinated regulation of the folding and secretion capacity of the cell, but with consequences on growth and fungal physiology to reduce secretion stress.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Biology Leiden, Leiden University, Molecular Microbiology and Biotechnology, BE Leiden, The Netherlands.

ABSTRACT

Background: HacA/Xbp1 is a conserved bZIP transcription factor in eukaryotic cells which regulates gene expression in response to various forms of secretion stress and as part of secretory cell differentiation. In the present study, we replaced the endogenous hacA gene of an Aspergillus niger strain with a gene encoding a constitutively active form of the HacA transcription factor (HacACA). The impact of constitutive HacA activity during exponential growth was explored in bioreactor controlled cultures using transcriptomic analysis to identify affected genes and processes.

Results: Transcription profiles for the wild-type strain (HacAWT) and the HacACA strain were obtained using Affymetrix GeneChip analysis of three replicate batch cultures of each strain. In addition to the well known HacA targets such as the ER resident foldases and chaperones, GO enrichment analysis revealed up-regulation of genes involved in protein glycosylation, phospholipid biosynthesis, intracellular protein transport, exocytosis and protein complex assembly in the HacACA mutant. Biological processes over-represented in the down-regulated genes include those belonging to central metabolic pathways, translation and transcription. A remarkable transcriptional response in the HacACA strain was the down-regulation of the AmyR transcription factor and its target genes.

Conclusions: The results indicate that the constitutive activation of the HacA leads to a coordinated regulation of the folding and secretion capacity of the cell, but with consequences on growth and fungal physiology to reduce secretion stress.

Show MeSH
Related in: MedlinePlus