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Open Access Research

Systemic analysis of the response of Aspergillus niger to ambient pH

Mikael R Andersen1, Linda Lehmann1 and Jens Nielsen12*

Author Affiliations

1 Center for Microbial Biotechnology, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark

2 Current address: Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden

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Genome Biology 2009, 10:R47  doi:10.1186/gb-2009-10-5-r47

Published: 1 May 2009

Additional files

Additional file 1:

Figure containing an overview of modeled acid production as a function of pH maximizing for growth coupled with acid (proton) production.

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Additional file 2:

Figure containing an overview of modeled acid production as a function of pH, maximizing for proton production with fixed growth.

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Additional file 3:

For each of the three ontologies (metabolic function, biologic process, and cellular component) is shown the significant terms (p.elim < 0.05).

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Additional file 4:

Cluster D is not shown, as it contains only one gene. The clusters are grouped based on statistical significance in pairwise comparisons of transcriptome data at pH values of 2.5, 4.5, and 6.0. Each cluster has nine values. The first three are biologic replicates at pH 2.5; the middle three are at pH 4.5; and the last three are from pH 6.0. The genes are clustered by using Matlab and the ClustreLustre algorithm [58].

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Additional file 5:

The HiLo, MeLo, and HiMe columns are log2 ratios of gene-expression indices in comparisons of pH 6.0 (Hi), pH 4.5 (Me), and pH 2.5 (Lo). Negative values mean that the index was higher in the second condition. If the comparison was not significant, a N/A is shown. Annotations are manually extracted from the Joint Genome Institute (JGI) website [62] and are the manual annotation (if that was present), or a general Interpro or GO-term prediction (if no manual annotation was present). A '-' means that no putative function could be assigned. The Colocalized column: Genes with the same number are colocalized. The Sec Metabolites column: Genes that are believed to be in a colocalized, co-regulated secondary metabolite cluster are marked with numbers.

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Additional file 6:

Table of the proton-creating reactions of the acid-production model that were added to the previously described genome-scale stoichiometric model of A. niger [7].

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