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Materials and methods
- Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans


The strain used in this study was the strain Aspergillus nidulans A187 (pabaA1 yA2; obtained from the Fungal Genetics Stock Center, Kansas City, KA, USA).

Growth medium

The medium used in all batch cultivations was a chemically defined medium as described by Agger and coworkers [53], with the following modifications: NH4Cl was used as the nitrogen source, at a concentration of 12.2 g/l, and three different carbon sources were tested, namely glucose, glycerol, and ethanol (10 g/l). Yeast extract was added to the fermenter at a concentration of 3 mg/l in order to encourage the germination of spores. Furthermore, the nutritional supplement p-aminobenzoic acid (PABA) was added to the medium at a concentration of 1 mg/l, as well as the antifoam agent 204 (Sigma, Brøndby, Denmark)) at a concentration of 0.05 ml/l.

Propagation of spores

The fermenters were inoculated with spores of A. nidulans A187 previously propagated on solid minimal medium [54] containing PABA (10 mg/l). The same stock of spores of A. nidulans was used to inoculate all the plates. The spores were cultivated at 37°C, during 3 to 4 days, and harvested by adding distilled water. For the fermentations performed in replicates, the fermenters were inoculated with the same solution of spores, to a final concentration of 5 × 109 spores/l. High concentrations of spores in the inoculum were employed because they favor dispersed filamentous growth. The spore solutions were vortex mixed before introduction into the fermenters, in order to prevent agglomeration of spores and thus pellet formation.

Batch cultivations

All aerobic batch cultivations were performed in 3 L-Braun fermenters with a working volume of 2 l. The bioreactors were equipped with two Rushton four-blade disc turbines and no baffles (thereby reducing the surface available for wall growth). Air was used to sparge the bioreactor. The concentrations of oxygen and carbon dioxide in the exhaust gas were monitored using an acoustic gas analyzer (Brüel & Kjær, Nærum, Denmark). Temperature, pH, agitation, and aeration rate were controlled throughout the cultivations. The temperature was maintained at 30°C. The pH was controlled by automatic addition of 2 N NaOH and 2 N HCl. For the cultivations on glucose and glycerol, the pH was initially set to 3.0 to prevent spore aggregation; only when the spores started to germinate was the pH gradually increased to 6.0. Because pellet formation is unlikely to occur during growth on ethanol, the pH was set to 6.0 from the start, in the cultivations performed with this carbon source. Similarly, the stirrer speed was initially set to 100 rpm and the aeration rate to 0.01 vvm, and only after the spores started to germinate were these parameters progressively increased to 700 rpm and 1 vvm, respectively.


For quantification of cell mass and extracellular metabolites, the fermentation broth was withdrawn from the fermenter vessel and filtered through nitrocellulose filters (pore size 0.45 μm; Pall Corporation, East Hills, NY, USA). The filter cakes were immediately processed for determination of cell mass, whereas the filtrates were stored at -20°C until they were analyzed for determination of extracellular metabolites (substrates and metabolic byproducts).

For gene expression analysis, the mycelia were harvested and processed within half a minute. The mycelia were filtered using Miracloth (Calbiochem, San Diego, CA, USA) and washed with phosphate-buffered saline (PBS) solution (137 mmol/l NaCl, 2.7 mmol/l KCl, 10 mmol/l Na2HPO4, and 0.24 mmol/l KH2PO4; pH 7.4). After removal of excess PBS solution, the mycelia were frozen in liquid nitrogen and stored at -80°C until further analysis.

Cell mass determination

Cell dry weight was determined using nitrocellulose filters (pore size 0.45 μm; Pall Corporation). The filters were predried in a microwave oven at 150 W for 10 minutes and subsequently weighed. A known volume of cell culture was filtered and the filter cake was washed with 0.9% NaCl and dried on the filter for 15 minutes in a microwave oven at 150 W. The filter was weighed again to determine the cell mass concentration.

Analysis of extracellular metabolites

The concentrations of sugars, organic acids, and polyols in the filtrates (thawed on ice) were determined using high-pressure liquid-chromatography on an Aminex HPX-87Hm column (Bio-Rad, Hercules, CA, USA). The column was kept at 65°C and eluted at 0.6 ml/minute with 5 mmol/l H2SO4. The compounds were detected refractometrically (410 Differential Refractometer, Waters Corporation, Milford, MA, USA).

Extraction of total RNA

Total RNA was isolated using the Qiagen RNeasy Mini Kit (QIAGEN Nordic, Ballerup, Denmark), according to the protocol for isolation of total RNA from animal tissues. For this purpose, approximately 20 to 30 mg frozen mycelium was placed in a 2 ml Eppendorf tube, precooled in liquid nitrogen, containing three RNase-treated steel balls (two balls with a diameter of 2 mm and one ball with a diameter of 5 mm). The tubes were then shaken in a Retsch Mixer Mill, at 3°C, for 6 to 8 minutes, until the mycelia were ground to powder and thus ready for extraction of total RNA. The quality and quantity of the total RNA extracted were determined by spectrophotometric analysis and by gel electrophoresis. The total RNA was stored at -80°C until further processing.

Microarray manufacturing and design

The microarrays used for the analysis of the transcriptome of A. nidulans were custom-made NimbleExpress™ arrays (NimbleGen Systems Inc., Madison, WI, USA), which were acquired through Affymetrix (Santa Clara, CA, USA). NimbleExpress™ arrays are manufactured using a Maskless Array Synthesizer system, which makes use of a Digital Micromirror Device. This device consists of a system of miniature aluminum mirrors, which are individually controlled, enabling the synthesis of oligomers in a similar way to the photolithographic process used in the manufacture of Affymetrix® GeneChip arrays. The NimbleExpress™ arrays are packaged in an Affymetrix® GeneChip cartridge (49 format), and can be used with GeneChip reagents and processed on the GeneChip® Instrument System (for more information, see [55]).

The selection of the probes for interrogating the ORFs within the genome of A. nidulans was performed by the Affymetrix Chip Design Group, who used the same algorithms employed in the design of standard Affymetrix® GeneChip arrays. The arrays contain only perfect match (PM) probes. Of the 9,541 putative genes identified in the genome of A. nidulans (Aspergillus nidulans Database [9], release 3.1; Broad Institute), 9,444 were represented in the microarray (CBS01CMBA530008N). Each ORF was interrogated with one (8,628), two (815), or three probe sets (1), and each of these probe sets were composed of 11 probes (whenever possible) of 25 oligomers. Different types of probe sets were represented on the array, namely type 1 (if all probes in the set hybridized exclusively with the target sequence), type 2 (if all probes in the set hybridized with the target sequence and cross-hybridized with other sequences), and type 3 (mixed probe set). In the data analysis, only probe sets of type 1 (or, rather, probes that did not cross-hybridize with genes other than the target) were considered, which brought the number of putative genes investigated down to 9,371.

Preparation of biotin-labeled cRNA and microarray processing

Biotin-labeled cRNA was prepared from approximately 10 μg of total RNA, according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual (2004) [56]. An additional cleanup step was performed before fragmentation, using the Qiagen RNeasy Mini Kit (protocol for RNA Cleanup), in order to guarantee good-quality cRNA samples for subsequent processing. The cRNA was quantified in a spectrophotometer (Amersham Pharmacia Biotech, GE Healthcare Bio-Sciences AB, Uppsala, Sweden) and its quality was assessed by gel electrophoresis and using a bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA). The biotin-labeled cRNA was then fragmented and approximately 13 μg of fragmented cRNA was hybridized to the custom-made NimbleExpress™ array (CBS01CMBA530008N), as described in the Affymetrix GeneChip® Expression Analysis Technical Manual (2004) [56]. The array was further processed on a GeneChip® Fluidics Station FS-400 (fluidics protocol EukGE-WS2v4) and on an Agilent GeneArray® Scanner. The scanned probe array images (.DAT files) were converted into .CEL files using the GeneChip® Operating Software (Affymetrix).

Reconstruction of the metabolic network and gene annotation

The metabolic network of A. nidulans was reconstructed by employing a pathway-driven approach described elsewhere [57] and comparative genomics tools based on sequence similarity. The metabolism of A. nidulans was reconstructed using as templates detailed metabolic reconstructions previously developed for A. niger [20], Saccharomyces cerevisiae [21], and Mus musculus [22]. Pathway prediction in A. nidulans was supported by available information on its genetics, biochemistry, and physiology. Thereby, it was possible to identify metabolic functions without a gene associated in the genome of A. nidulans, and thus candidate ORFs for encoding those functions, by employing similarity-based tools of comparative genomic analysis (BLAST [Basic Local Alignment Search Tool]) and using public (nonredundant) databases of genes and proteins of established function [58].

Analysis of transcriptome data

Raw probe intensities were preprocessed by applying the RMA (robust multiarray average) method for background correction (based on PM probe information) [59], and were subsequently normalized using the qspline method [60]. Gene expression index values were calculated using the method developed by Li and Wong [61], using the PM-only model. Normalized gene expression data was deposited at the GEO database [62], with accession numbers GPL3604 (platform), GSM102371-GSM102379 (samples), and GSE4578 (series).

Statistical analysis was applied to determine differentially expressed genes between the categories of replicated experiments. For all of the possible pair-wise comparisons within the three different categories, the logit-t method [63] was employed, whereas ANOVA was used to compare gene expression levels among all categories. The genes whose expression was found to be significantly changed using the ANOVA test were further arranged into clusters, by applying ClusterLustre, a Bayesian consensus clustering method recently developed and available in the Matlab application [19].

Furthermore, reporter metabolites (metabolites around which the most significant changes in transcription occur) and highly correlated metabolic subnetworks (sets of connected genes with significant and coordinated transcriptional response to a perturbation) were identified for each of the pair-wise comparisons possible within the three categories, as described by Patil and Nielsen [23]. For this purpose, information on the topology of the reconstructed metabolic network of A. nidulans was used in combination with the P values from the logit-t test performed for each of the pair-wise comparisons of expression data.

Data deposition

Normalized gene expression data were deposited at the GEO database [62], with accession numbers GPL3604 (platform), GSM102371-GSM102379 (samples), and GSE4578 (series).

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