Identification of growth phenotype-related genes in Aspergillus oryzae by heterologous macroarray and suppression subtractive hybridization

Environmental cues that induce the physiology of solid medium: a study on lovastatin production by Aspergillus terreus

AIMS

The aim of this work was to identify the main environmental factors that induce the special physiology displayed by fungi growing in solid culture-that is, higher secondary metabolite (SM) production-compared with those in submerged culture.

METHODS AND RESULTS

Lovastatin-specific production (SP) was used as an indicator of the physiological status, and different model culture systems were used to evaluate the impact of potential solid-state fermentation (SSF) environmental stimuli. Direct contact with air was identified as an important stimulus. Cultures with two or more hours of exposure to air showed typical SSF lovastatin SP (1462% higher than cultures exposed for 0·08 h). Intermediate times of exposure generated intermediate physiological states. Support-related stimuli also induced higher lovastatin SP, even in a liquid environment (679% increase).

CONCLUSIONS

Direct contact with air, as well as support-related stimuli, are major environmental cues that induce the physiology of solid medium.

SIGNIFICANCE AND IMPACT OF THE STUDY

This knowledge is the starting point to investigate how these environmental cues are sensed and transduced, impacting SM and enzyme production. These results have important applied potential in new strategies to generate overproducing strains, as well as application in the design of novel production systems.

Scientific Advances with Aspergillus Species that Are Used for Food and Biotech Applications

Yeast and filamentous fungi have been used for centuries in diverse biotechnological processes. Fungal fermentation technology is traditionally used in relation to food production, such as for bread, beer, cheese, sake and soy sauce. Last century, the industrial application of yeast and filamentous fungi expanded rapidly, with excellent examples such as purified enzymes and secondary metabolites (e.g. antibiotics), which are used in a wide range of food as well as non-food industries. Research on protein and/or metabolite secretion by fungal species has focused on identifying bottlenecks in (post-) transcriptional regulation of protein production, metabolic rerouting, morphology and the transit of proteins through the secretion pathway. In past years, genome sequencing of some fungi (e.g. Aspergillus oryzae, Aspergillus niger) has been completed. The available genome sequences have enabled identification of genes and functionally important regions of the genome. This has directed research to focus on a post-genomics era in which transcriptomics, proteomics and metabolomics methodologies will help to explore the scientific relevance and industrial application of fungal genome sequences.

The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available, web-based resource for researchers studying fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD curators have now completed comprehensive review of the entire published literature about Aspergillus nidulans and Aspergillus fumigatus, and this annotation is provided with streamlined, ortholog-based navigation of the multispecies information. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. AspGD also provides resources to foster interaction and dissemination of community information and resources. We welcome and encourage feedback at aspergillus-curator@lists.stanford.edu.

Phylogeny of fungal hemoglobins and expression analysis of the Aspergillus oryzae flavohemoglobin gene fhbA during hyphal growth

The fhbA genes encoding putative flavohemoglobins (FHb) from Aspergillus niger and Aspergillus oryzae were isolated. Comparison of the deduced amino acid sequence of the A. niger fhbA gene and other putative filamentous fungal FHb-encoding genes to that of Ralstonia eutropha shows an overall conserved gene structure and completely conserved catalytic amino acids. Several yeasts and filamentous fungi, including both Aspergillus species have been found to contain a small FHb gene family mostly consisting of two family members. Based on these sequences the evolutionary history of the fungal FHb family was reconstructed. The isolated fhbA genes from A. oryzae and A. niger belong to a phylogenetic group, which exclusively contains Aspergillus genes. Different experimental approaches show that fhbA transcript levels appear during active hyphal growth. Moreover, in a pclA-disrupted strain with a hyperbranching growth phenotype, the transcript levels of the fhbA gene were 2–5 times higher compared to the wild-type. These results suggest that FHb from filamentous fungi have a function that is correlated to the hyphal growth phenotype.

Cross-species hybridization with Fusarium verticillioides microarrays reveals new insights into Fusarium fujikuroi nitrogen regulation and the role of AreA and NMR

In filamentous fungi, the GATA-type transcription factor AreA plays a major role in the transcriptional activation of genes needed to utilize poor nitrogen sources. In Fusarium fujikuroi, AreA also controls genes involved in the biosynthesis of gibberellins, a family of diterpenoid plant hormones. To identify more genes responding to nitrogen limitation or sufficiency in an AreA-dependent or -independent manner, we examined changes in gene expression of F. fujikuroi wild-type and DeltaareA strains by use of a Fusarium verticillioides microarray representing approximately 9,300 genes. Analysis of the array data revealed sets of genes significantly down- and upregulated in the areA mutant under both N starvation and N-sufficient conditions. Among the downregulated genes are those involved in nitrogen metabolism, e.g., those encoding glutamine synthetase and nitrogen permeases, but also those involved in secondary metabolism. Besides AreA-dependent genes, we found an even larger set of genes responding to N starvation and N-sufficient conditions in an AreA-independent manner. To study the impact of NMR on AreA activity, we examined the expression of several AreA target genes in the wild type and in areA and nmr deletion and overexpression mutants. We show that NMR interacts with AreA as expected but affects gene expression only in early growth stages. This is the first report on genome-wide expression studies examining the influence of AreA on nitrogen-responsive gene expression in a genome-wide manner in filamentous fungi.

TPR domain of Ser/Thr phosphatase of Aspergillus oryzae shows no auto-inhibitory effect on the dephosphorylation activity

A Ser/Thr phosphatase gene cloned from Aspergillus oryzae, aoppt, revealed that the tetratricopeptide repeat (TPR) and catalytic domains of the full-length AoPPT are located at the N- and C-terminal regions, respectively, similar to those of human Ser/Thr phosphatase 5 (PP5) and yeast Ppt1. Four different regions of AoPPT, namely, a full-length polypeptide, the catalytic domain, the catalytic domain plus C-terminal 15 amino-acid residues and the TPR domain were expressed in Escherichia coli and their roles in dephosphorylation activity were examined, using p-nitrophenyl phosphate as the substrate. The full-length AoPPT showed the highest dephosphorylation activity while the catalytic domain had the lowest activity. The activity of the catalytic domain was not inhibited by the presence of the TPR domain and arachidonic acid did not increase the activity of the full-length enzyme. These findings suggest that the integrity of the entire enzyme would be necessary for its full activity to be expressed.

Identification of genes from Aspergillus oryzae that are preferentially expressed in membrane-surface liquid culture

We identified 22 genes from Aspergillus oryzae that are preferentially expressed in membrane-surface liquid culture (MSLC), among which Ser/Thr protein kinase (aopk1) and phosphatase (aoppt) genes were cloned. We also revealed that aopk1 encodes a protein with an N-terminal sequence 150 amino acid residues longer than that predicted from the registered sequence in GenBank.

Heterologous protein expression in filamentous fungi

Filamentous fungi are commonly used in the fermentation industry for the large-scale production of proteins--mainly industrial enzymes. Recent advances in fungal genomics and related experimental technologies such as gene arrays and proteomics are rapidly changing the approaches to the development and use of filamentous fungi as hosts for the production of both homologous and heterologous gene products. The emphasis is moving towards sourcing new genes of interest through database mining and unravelling the circuits related to fungal gene regulation, applying, for example, transcriptomics. However, although heterologous fungal proteins are efficiently expressed, expression of gene products from other organisms is subject to several bottlenecks that reduce yield. Current approaches emphasize the study of pathways involved in protein modification and degradation in general rather than gene-by-gene approaches.