Genomics of protein folding in the endoplasmic reticulum, secretion stress and glycosylation in the aspergilli

Geysens, Steven; Whyteside, Graham; Archer, David B.

doi:10.1016/j.fgb.2008.07.016

Cited by 30 publications

(26 citation statements)

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“…The aim of ERAD is to direct misfolded proteins to the cytosol where they become degraded by the proteasome. In addition, another cellular protein quality system, the unfolded protein response (UPR), is induced, which aims at proper refolding of misfolded proteins via induced expression of chaperones and foldases [5,16]. For this purpose, the UPR transcription factor HacA becomes activated via splicing of an unconventional 20-nt intron out of the hacA mRNA.…”

Section: Introductionmentioning

confidence: 99%

The transcriptomic fingerprint of glucoamylase over-expression in Aspergillus niger

et al. 2012

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BackgroundFilamentous fungi such as Aspergillus niger are well known for their exceptionally high capacity for secretion of proteins, organic acids, and secondary metabolites and they are therefore used in biotechnology as versatile microbial production platforms. However, system-wide insights into their metabolic and secretory capacities are sparse and rational strain improvement approaches are therefore limited. In order to gain a genome-wide view on the transcriptional regulation of the protein secretory pathway of A. niger, we investigated the transcriptome of A. niger when it was forced to overexpression the glaA gene (encoding glucoamylase, GlaA) and secrete GlaA to high level.ResultsAn A. niger wild-type strain and a GlaA over-expressing strain, containing multiple copies of the glaA gene, were cultivated under maltose-limited chemostat conditions (specific growth rate 0.1 h-1). Elevated glaA mRNA and extracellular GlaA levels in the over-expressing strain were accompanied by elevated transcript levels from 772 genes and lowered transcript levels from 815 genes when compared to the wild-type strain. Using GO term enrichment analysis, four higher-order categories were identified in the up-regulated gene set: i) endoplasmic reticulum (ER) membrane translocation, ii) protein glycosylation, iii) vesicle transport, and iv) ion homeostasis. Among these, about 130 genes had predicted functions for the passage of proteins through the ER and those genes included target genes of the HacA transcription factor that mediates the unfolded protein response (UPR), e.g. bipA, clxA, prpA, tigA and pdiA. In order to identify those genes that are important for high-level secretion of proteins by A. niger, we compared the transcriptome of the GlaA overexpression strain of A. niger with six other relevant transcriptomes of A. niger. Overall, 40 genes were found to have either elevated (from 36 genes) or lowered (from 4 genes) transcript levels under all conditions that were examined, thus defining the core set of genes important for ensuring high protein traffic through the secretory pathway.ConclusionWe have defined the A. niger genes that respond to elevated secretion of GlaA and, furthermore, we have defined a core set of genes that appear to be involved more generally in the intensified traffic of proteins through the secretory pathway of A. niger. The consistent up-regulation of a gene encoding the acetyl-coenzyme A transporter suggests a possible role for transient acetylation to ensure correct folding of secreted proteins.

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Section: Introductionmentioning

confidence: 99%

The transcriptomic fingerprint of glucoamylase over-expression in Aspergillus niger

et al. 2012

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“…Proteins predicted to play a role in secretion were grouped in functional annotation groups guided by previously published functional classification schemes (16), the Functional Catalogue (FunCat) annotation scheme, and the predicted molecular function as provided with the A. niger CBS531.88 genome annotation (42). Proteins considered to be involved in secretion were used for a BLAST search (NCBI) against Saccharomyces cerevisiae and Homo sapiens protein databases.…”

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confidence: 99%

Shotgun Proteomics of Aspergillus niger Microsomes upon d -Xylose Induction

Oliveira

Passel

Schaap

et al. 2010

Appl Environ Microbiol

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Protein secretion plays an eminent role in cell maintenance and adaptation to the extracellular environment of microorganisms. Although protein secretion is an extremely efficient process in filamentous fungi, the mechanisms underlying protein secretion have remained largely uncharacterized in these organisms. In this study, we analyzed the effects of the D-xylose induction of cellulase and hemicellulase enzyme secretion on the protein composition of secretory organelles in Aspergillus niger. We aimed to systematically identify the components involved in the secretion of these enzymes via mass spectrometry of enriched subcellular microsomal fractions. Under each condition, fractions enriched for secretory organelles were processed for tandem mass spectrometry, resulting in the identification of peptides that originate from 1,081 proteins, 254 of which-many of them hypothetical proteins-were predicted to play direct roles in the secretory pathway. D-Xylose induction led to an increase in specific small GTPases known to be associated with polarized growth, exocytosis, and endocytosis. Moreover, the endoplasmic-reticulum-associated degradation (ERAD) components Cdc48 and all 14 of the 20S proteasomal subunits were recruited to the secretory organelles. In conclusion, induction of extracellular enzymes results in specific changes in the secretory subproteome of A. niger, and the most prominent change found in this study was the recruitment of the 20S proteasomal subunits to the secretory organelles.Aspergillus niger is a soil-dwelling filamentous fungus with a high capacity for decomposing plant materials. Many of the secreted depolymerizing enzymes have important biotechnological applications, e.g., to modify plant-derived food products. Homologous protein secretion in filamentous fungi may yield up to 20 g per liter of extracellular medium (14). For this reason, A. niger has been used intensively as a cell factory for enzyme production (3,14,32). In contrast to this, yields are much lower for heterologous protein secretion, with exceptions (11,18,35,59).The secretory potential of A. niger is not well understood, and only a limited number of functional studies have been performed to investigate the major components of the fungal secretion pathway. These studies have addressed overall transcriptional and translational responses in A. niger by studying the impact of secretion stress-inducing chemicals, temperature shifts, protein overproduction, or growth on carbon sources that induce changes in secretory states (20,23,26).In recent years, high-throughput shotgun proteomics has been used to study cell organelle makeup and function. Through the combined use of liquid chromatography and tandem mass spectrometry (LC-MS/MS), various studies have identified many organelle-specific proteins, including proteins related to protein secretion (18,24,29,51,51). In the case of aspergilli, such studies have focused mainly on the secretome and not on the actual components of the secretory pathway (34,36,55).In a previous study, we...

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“…This event leads to the accumulation of unfolded proteins within the ER resulting in ER stress. To maintain homeostasis of ER functions, the cell reacts to the accumulation of unfolded proteins in the ER by inducing a pathway known as the UPR (Geysens et al, 2009). The UPR pathway has been studied in A. oryzae (Ye and Pan, 2008) and four key components of this pathway are: (1) the Hac1 protein is a transcription activator that up‐regulates the transcription of various target‐genes of the UPR pathway; (2) the Bip protein is a chaperone of the HSP70 class that plays an important role in the UPR; (3) the Pdi is a luminal ER enzyme that catalyses the mechanism of disulfide bond formation; (4) the Ppi is an enzyme of catalyzing the cis‐trans isomerization of a peptide bond on the N‐terminal side of proline residues in polypeptides (Ye and Pan, 2008).…”

Section: Resultsmentioning

confidence: 99%

Integrated analysis of the global transcriptional response to α‐amylase over‐production by Aspergillus oryzae

Vongsangnak

Hansen

Nielsen

2010

Biotech & Bioengineering

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The filamentous fungus Aspergillus oryzae is an important microbial cell factory for industrial production of many enzymes, such as α-amylase. In order to optimize the industrial enzyme production process, there is a need to understand fundamental processes underlying enzyme production, here under how enzyme production links to metabolism through global regulation. Through a genome-scale metabolic network for integrated analysis of transcriptome data and flux calculation, we identified key players (genes, enzymes, proteins, and metabolites) involved in the processes of enzyme synthesis and secretion, nucleotide metabolism, and amino acid metabolism that can be the potential targets for improving industrial enzyme production.

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Genomics of protein folding in the endoplasmic reticulum, secretion stress and glycosylation in the aspergilli

Cited by 30 publications

References 262 publications

The transcriptomic fingerprint of glucoamylase over-expression in Aspergillus niger

The transcriptomic fingerprint of glucoamylase over-expression in Aspergillus niger

Shotgun Proteomics of Aspergillus niger Microsomes upon d -Xylose Induction

Integrated analysis of the global transcriptional response to α‐amylase over‐production by Aspergillus oryzae

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