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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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Functional classification of differentially expressed genes in HacACA. Representation of the main significant induced and repressed biological processes in the HacACA mutant strain in comparison to HacAWT strain.
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Figure 4: Functional classification of differentially expressed genes in HacACA. Representation of the main significant induced and repressed biological processes in the HacACA mutant strain in comparison to HacAWT strain.

Mentions: To obtain an overview of the processes affected at the transcriptional level between the HacAWT and the HacACA-1 mutant, overrepresented GO-terms among differentially expressed genes were identified. For this analysis, we used the Fisher's exact test Gene Ontology annotation tool (FetGOat) [50]. Network maps of related GO-terms (Biological Processes), over- or under-represented in the HacACA strain, are given in Additional file 6 and Additional file 7. In Additional file 8 and Additional file 9, the results of the GO-enrichment analysis are given. To analyse the results, two complementary approaches were taken. Firstly, we rationally defined GO-terms of higher order that include several GO-terms. Secondly, we looked specifically at GO-terms that are terminal in the network, as these annotations are the most detailed (see Additional file 6). These approaches enabled us to identify four major categories of genes to describe the most relevant up-regulated biological processes in the HacACA strain (Figure 4). The four main categories of genes included those related to I) ER translocation and protein folding [Additional file 10, II) intracellular vesicle trafficking [Additional file 11, III) protein glycosylation [Additional file 12 and IV) lipid metabolism [Additional file 13. These four main categories are further described in the following section.


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)

Functional classification of differentially expressed genes in HacACA. Representation of the main significant induced and repressed biological processes in the HacACA mutant strain in comparison to HacAWT strain.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Functional classification of differentially expressed genes in HacACA. Representation of the main significant induced and repressed biological processes in the HacACA mutant strain in comparison to HacAWT strain.
Mentions: To obtain an overview of the processes affected at the transcriptional level between the HacAWT and the HacACA-1 mutant, overrepresented GO-terms among differentially expressed genes were identified. For this analysis, we used the Fisher's exact test Gene Ontology annotation tool (FetGOat) [50]. Network maps of related GO-terms (Biological Processes), over- or under-represented in the HacACA strain, are given in Additional file 6 and Additional file 7. In Additional file 8 and Additional file 9, the results of the GO-enrichment analysis are given. To analyse the results, two complementary approaches were taken. Firstly, we rationally defined GO-terms of higher order that include several GO-terms. Secondly, we looked specifically at GO-terms that are terminal in the network, as these annotations are the most detailed (see Additional file 6). These approaches enabled us to identify four major categories of genes to describe the most relevant up-regulated biological processes in the HacACA strain (Figure 4). The four main categories of genes included those related to I) ER translocation and protein folding [Additional file 10, II) intracellular vesicle trafficking [Additional file 11, III) protein glycosylation [Additional file 12 and IV) lipid metabolism [Additional file 13. These four main categories are further described in the following section.

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