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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
BMC Genomics. 2009; 10: 75.
Published online Feb 10, 2009. doi:  10.1186/1471-2164-10-75
PMCID: PMC2657799
Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production
Diana M Harris,1,2 Zita A van der Krogt,1,2 Paul Klaassen,3 Leonie M Raamsdonk,3 Susanne Hage,3 Marco A van den Berg,3 Roel AL Bovenberg,3 Jack T Pronk,1,2 and Jean-Marc Darancorresponding author1,2
1Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
2Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
3DSM Anti-Infectives, DAI/INNO (624-0270), Postbus 425, 2600 AK, Delft, The Netherlands
corresponding authorCorresponding author.
Diana M Harris: DHarris/at/; Zita A van der Krogt: Z.A.vanderKrogt/at/; Paul Klaassen: Paul.Klaassen/at/DSM.COM; Leonie M Raamsdonk: Leonie.raamsdonk/at/; Susanne Hage: sussane.hage/at/; Marco A van den Berg: Marco.Berg-van-den/at/; Roel AL Bovenberg: roel.bovenberg/at/; Jack T Pronk: j.t.pronk/at/; Jean-Marc Daran: j.g.daran/at/
Received September 2, 2008; Accepted February 10, 2009.
Since the discovery of the antibacterial activity of penicillin by Fleming 80 years ago, improvements of penicillin titer were essentially achieved by classical strain improvement through mutagenesis and screening. The recent sequencing of Penicillium chrysogenum strain Wisconsin1255-54 and the availability of genomics tools such as DNA-microarray offer new perspective.
In studies on β-lactam production by P. chrysogenum, addition and omission of a side-chain precursor is commonly used to generate producing and non-producing scenarios. To dissect effects of penicillinG production and of its side-chain precursor phenylacetic acid (PAA), a derivative of a penicillinG high-producing strain without a functional penicillin-biosynthesis gene cluster was constructed. In glucose-limited chemostat cultures of the high-producing and cluster-free strains, PAA addition caused a small reduction of the biomass yield, consistent with PAA acting as a weak-organic-acid uncoupler. Microarray-based analysis on chemostat cultures of the high-producing and cluster-free strains, grown in the presence and absence of PAA, showed that: (i) Absence of a penicillin gene cluster resulted in transcriptional upregulation of a gene cluster putatively involved in production of the secondary metabolite aristolochene and its derivatives, (ii) The homogentisate pathway for PAA catabolism is strongly transcriptionally upregulated in PAA-supplemented cultures (iii) Several genes involved in nitrogen and sulfur metabolism were transcriptionally upregulated under penicillinG producing conditions only, suggesting a drain of amino-acid precursor pools. Furthermore, the number of candidate genes for penicillin transporters was strongly reduced, thus enabling a focusing of functional analysis studies.
This study demonstrates the usefulness of combinatorial transcriptome analysis in chemostat cultures to dissect effects of biological and process parameters on gene expression regulation. This study provides for the first time clear-cut target genes for metabolic engineering, beyond the three genes of the β-lactam pathway.
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