Number of Aspergillus omics articles published over the

Aspergillus as a multi-purpose cell factory: current status and perspectives. Meyer V, Wu B, Ram AF - Biotechnol. Lett. (2010) Bottom Line: Aspergilli have a long history in biotechnology as expression platforms for the production of food ingredients, pharmaceuticals and enzymes.The achievements made during the last years, however, have the potential to revolutionize Aspergillus biotechnology and to assure Aspergillus a dominant place among microbial cell factories.New trends and concepts related to Aspergillus genomics and systems biology will be discussed as well as the challenges that have to be met to integrate omics data with metabolic engineering attempts. View Article: PubMed Central - PubMed Affiliation: Department of Molecular Microbiology and Biotechnology, Leiden University, Institute of Biology Leiden, Sylviusweg 72, 2333 BE, Leiden, The Netherlands. v.meyer@biology.leidenuniv.nl ABSTRACT Aspergilli have a long history in biotechnology as expression platforms for the production of food ingredients, pharmaceuticals and enzymes. The achievements made during the last years, however, have the potential to revolutionize Aspergillus biotechnology and to assure Aspergillus a dominant place among microbial cell factories. This mini-review will highlight most recent breakthroughs in fundamental and applied Aspergillus research with a focus on new molecular tools, techniques and products. New trends and concepts related to Aspergillus genomics and systems biology will be discussed as well as the challenges that have to be met to integrate omics data with metabolic engineering attempts. Show MeSH Major Aspergillus/genetics/metabolism Biotechnology/methods* Genetic Engineering/methods* Systems Biology/methods* Minor Genomics/methods	© Copyright Policy Related In: Results - Collection Show All Figures getmorefigures.php?uid=PMC3040820&req=5 Fig1: Number of Aspergillus omics articles published over the last years in Pubmed (by October 2010) Mentions: The sequencing of fungal genomes led Aspergillus research into a new era referred to as systems biology. Instead of studying one gene or protein at a time, the complete set of genes, proteins and/or metabolites are studied simultaneously, aiming at a comprehensive understanding of the robustness, viability and productivity of industrial Aspergillus strains and at the identification of factors important for pathogenicity of medical Aspergilli. For each of the omics subdisciplines (transcriptomics, proteomics, metabolomics) a dedicated set of equipment, techniques and software tools has to be developed, a process which is still on-going for many Aspergillus species. For the whole genus, only about 30 omics studies appear yearly in Pubmed (Fig. 1), illustrating that Aspergillus systems biology is still in its infancy. Among these, the following publications on industrially used Aspergilli are worth highlighting: (i) a metabolic network was established for A. niger and A. oryzae based on genomic databases and extensive literature surveys (Andersen et al. 2008; Vongsangnak et al. 2008). (Note that a web-based pathway viewer has recently been launched for A. fumigatus (Tuckwell et al. 2010.) (ii) The starch-, pectin- and inulin-degrading enzyme network of A. niger was identified using a combined database mining and transcriptomic approach (Martens-Uzunova et al. 2006; Yuan et al. 2006, 2008; Martens-Uzunova and Schaap 2009). (iii) An integrated transcriptomics and proteomics approach identified new leads for improved protein secretion of A. niger (Guillemette et al. 2007; Levin et al. 2007; Jacobs et al. 2009). (iv) A transcriptomics and genetic study predicted regulatory networks important for the morphological control of A. niger growth (Meyer et al. 2009). (v) A transcriptomics and metabolomics study disclosed regulatory genes involved in lovastatin biosynthesis in A. terreus (Askenazi et al. 2003). (vi) A transcriptome analysis identified genes important for high-yield solid-phase fermentations in A. oryzae (Tamano et al. 2008).Fig. 1

Aspergillus as a multi-purpose cell factory: current status and perspectives.

Meyer V, Wu B, Ram AF - Biotechnol. Lett. (2010)

Bottom Line: Aspergilli have a long history in biotechnology as expression platforms for the production of food ingredients, pharmaceuticals and enzymes.The achievements made during the last years, however, have the potential to revolutionize Aspergillus biotechnology and to assure Aspergillus a dominant place among microbial cell factories.New trends and concepts related to Aspergillus genomics and systems biology will be discussed as well as the challenges that have to be met to integrate omics data with metabolic engineering attempts.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Microbiology and Biotechnology, Leiden University, Institute of Biology Leiden, Sylviusweg 72, 2333 BE, Leiden, The Netherlands. v.meyer@biology.leidenuniv.nl

ABSTRACT

Aspergilli have a long history in biotechnology as expression platforms for the production of food ingredients, pharmaceuticals and enzymes. The achievements made during the last years, however, have the potential to revolutionize Aspergillus biotechnology and to assure Aspergillus a dominant place among microbial cell factories. This mini-review will highlight most recent breakthroughs in fundamental and applied Aspergillus research with a focus on new molecular tools, techniques and products. New trends and concepts related to Aspergillus genomics and systems biology will be discussed as well as the challenges that have to be met to integrate omics data with metabolic engineering attempts.

Show MeSH

Number of Aspergillus omics articles published over the last years in Pubmed (by October 2010)

Related In: Results - Collection

Show All Figures

getmorefigures.php?uid=PMC3040820&req=5

Fig1: Number of Aspergillus omics articles published over the last years in Pubmed (by October 2010)

Mentions: The sequencing of fungal genomes led Aspergillus research into a new era referred to as systems biology. Instead of studying one gene or protein at a time, the complete set of genes, proteins and/or metabolites are studied simultaneously, aiming at a comprehensive understanding of the robustness, viability and productivity of industrial Aspergillus strains and at the identification of factors important for pathogenicity of medical Aspergilli. For each of the omics subdisciplines (transcriptomics, proteomics, metabolomics) a dedicated set of equipment, techniques and software tools has to be developed, a process which is still on-going for many Aspergillus species. For the whole genus, only about 30 omics studies appear yearly in Pubmed (Fig. 1), illustrating that Aspergillus systems biology is still in its infancy. Among these, the following publications on industrially used Aspergilli are worth highlighting: (i) a metabolic network was established for A. niger and A. oryzae based on genomic databases and extensive literature surveys (Andersen et al. 2008; Vongsangnak et al. 2008). (Note that a web-based pathway viewer has recently been launched for A. fumigatus (Tuckwell et al. 2010.) (ii) The starch-, pectin- and inulin-degrading enzyme network of A. niger was identified using a combined database mining and transcriptomic approach (Martens-Uzunova et al. 2006; Yuan et al. 2006, 2008; Martens-Uzunova and Schaap 2009). (iii) An integrated transcriptomics and proteomics approach identified new leads for improved protein secretion of A. niger (Guillemette et al. 2007; Levin et al. 2007; Jacobs et al. 2009). (iv) A transcriptomics and genetic study predicted regulatory networks important for the morphological control of A. niger growth (Meyer et al. 2009). (v) A transcriptomics and metabolomics study disclosed regulatory genes involved in lovastatin biosynthesis in A. terreus (Askenazi et al. 2003). (vi) A transcriptome analysis identified genes important for high-yield solid-phase fermentations in A. oryzae (Tamano et al. 2008).Fig. 1