Open Access Research article

The impact of oxygen on the transcriptome of recombinant S. cerevisiae and P. pastoris - a comparative analysis

Kristin Baumann1, Laura Dato2, Alexandra B Graf34, Gianni Frascotti2, Martin Dragosits36, Danilo Porro2, Diethard Mattanovich35, Pau Ferrer1* and Paola Branduardi2

Author Affiliations

1 Department of Chemical Engineering, Autonomous University of Barcelona, Spain

2 Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy

3 Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria

4 School of Bioengineering, University of Applied Sciences, FH Campus Vienna, Austria

5 Austrian Centre of Industrial Biotechnology (ACIB GmbH), Vienna, Austria

6 Department of Computer Science, UC Davis Genome Center, University of California, Davis, USA

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BMC Genomics 2011, 12:218  doi:10.1186/1471-2164-12-218

Published: 9 May 2011

Additional files

Additional file 1:

List of orthologues. List of the orthologues (2891 gene IDs) between S. cerevisiae and P. pastoris used for the direct comparison of the results of the transcriptional analysis. Orthology was determined using a reciprocal best hit strategy based on protein BLASTs (E-value cut-off < 10-5 and filtering for at least one high scoring segment > 50 amino acids with a similarity > 40%). 388 gene IDs passing the filters were excluded since they were missing either on the S. cerevisiae or on the P. pastoris microarrays.

Column A, P. pastoris gene IDs used in microarrays; column B, S. cerevisiae systematic names; column C, S. cerevisiae short gene names (corresponding to the protein names); column D, number of S. cerevisiae genes for which the P. pastoris protein was the best hit.

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Additional file 2:

MetaCyc Data Saccharomyces cerevisiae. Regulated S. cerevisiae pathways in hypoxia vs. normoxia. Individual S. cerevisiae (recombinant strain) pathways that were transcriptionally regulated (i e. exceeding the log2 FC threshold of 0.59) in the comparison hypoxic vs. normoxic conditions, as resulting from the MetaCyc analysis presented in Figure 3 http://pathway.yeastgenome.org webcite. Pathway numbers in the first column are referred to Figure 3. Pathway diagrams show all the intermediates of each pathways; reaction lines and the corresponding genes are colour-coded (three colour bins) according to the fold change threshold: red for upregulated, yellow for downregulated and blue for unregulated; log2 FC for each gene are also shown in colour. Last column contains the extended enzyme names corresponding to each gene of the pathway.

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Additional file 3:

MetaCyc data Pichia pastoris. Regulated P. pastoris pathways in hypoxia vs. normoxia. Individual P. pastoris (recombinant strain) pathways that were transcriptionally regulated (i e. exceeding the log2 FC threshold of 0.59) in the comparison hypoxic vs. normoxic conditions, as resulting from the MetaCyc analysis presented in Figure 3 http://pathway.yeastgenome.org webcite. Pathway numbers in the first column are referred to Figure 3. Pathway diagrams show all the intermediates of each pathways; reaction lines and the corresponding genes are colour-coded (three colour bins) according to the fold change threshold: red for upregulated, yellow for downregulated and blue for unregulated; log2 FC for each gene are also shown in colour. Last column contains the extended enzyme names corresponding to each gene of the pathway.

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Additional file 4:

Metabolic pathways. List of metabolic pathways that correspond to the numbers indicated on the cellular overview chart depicted in Figure 3.

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Additional file 5:

Gene list of single clusters. Lists of genes corresponding to each of the cluster resulting from the k-means clustering (k = 10) depicted in Figure 4B (obtained by Expression Profiler analysis; http://www.ebi.ac.uk/expressionprofiler webcite). Each column contains a single cluster. Column names indicate cluster number and, in brackets, the total number of genes present in each cluster.

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