MOESM1 of Biomarkers allow detection of nutrient limitations and respective supplementation for elimination in Pichia pastoris fed-batch cultures

Additional file 1: Figure S1. Mean expression values (microarray data) of the carboxypeptidase B gene during the methanol and glucose fed-batch process. Table S2. Description of biological function of marker genes adapted from Saccharomyces Genome Database (SGD). Table S3. qPCR primer sequences. Figure S4. Principal component analysis (variable factor map; F2 vs. F1) of the methanol fed-batch (1 h, 15 h, 27 h, 41 h, 53 h and 67 h after starting the methanol fed-batch) referred to the glycerol fed-batch (log2 fold change). Figure S5. Principal component analysis (variable factor map; F3 vs. F2) of the methanol fed-batch (1 h, 15 h, 27 h, 41 h, 53 h and 67 h after starting the methanol fed-batch) referred to the glycerol fed-batch (log2 fold change). Figure S6. Principal component analysis (variable factor map; F2 vs. F1) of the glucose fed-batch (1 h, 15 h, 27 h, 41 h, 53 h and 67 h after starting the glucose fed-batch) referred to the glycerol fed-batch (log2 fold change). Figure S7. Principal component analysis (variable factor map; F3 vs. F2) of the glucose fed-batch (1 h, 15 h, 27 h, 41 h, 53 h and 67 h after starting the glucose fed-batch) referred to the glycerol fed-batch (log2 fold change)

Monitoring of transcriptional regulation in under protein production conditions-4

<p><b>Copyright information:</b></p><p>Taken from "Monitoring of transcriptional regulation in under protein production conditions"</p><p>http://www.biomedcentral.com/1471-2164/8/179</p><p>BMC Genomics 2007;8():179-179.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1919374.</p><p></p>steady state; Blue bars: 20 °C steady state. BiP: intracellular signals for the UPR marker BiP/Kar2p (detected with anti-Grp78/BiP specific IgG). HC: intracellular signals for Fab heavy chain (obtained with anti-h-Fab specific IgG); LC: intracellular signals for light chain (analyzed with anti-kappa light chain IgG)

Monitoring of transcriptional regulation in under protein production conditions-1

<p><b>Copyright information:</b></p><p>Taken from "Monitoring of transcriptional regulation in under protein production conditions"</p><p>http://www.biomedcentral.com/1471-2164/8/179</p><p>BMC Genomics 2007;8():179-179.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1919374.</p><p></p>ndend up- or downregulatated genes are highlighted; B: Logratio of cultures producing 2F5 Fab under control of the GAP promoter compared to the wild type, in the same order as A. Red bars: change in transcript up > 2-fold; yellow bars: up > 1.5 fold; white bars: unchanged; blue bars: down > 1.5 fold

Monitoring of transcriptional regulation in under protein production conditions-0

<p><b>Copyright information:</b></p><p>Taken from "Monitoring of transcriptional regulation in under protein production conditions"</p><p>http://www.biomedcentral.com/1471-2164/8/179</p><p>BMC Genomics 2007;8():179-179.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1919374.</p><p></p>mparison to the wild type. Data from were taken from [21], where UPR was induced with DTT or tunicamycin. ScD60 (treatment with DTT after 60 min); ScD120 (treatment with DTT after 120 min); ScT60 (treatment with tunicamycin after 60 min), all compared to a non-treated culture. Cluster analysis was made using EPClust [], Euklidian distance with complete linkage. Subclusters are shown for the following: A: genes induced in both yeasts; B: upregulated in , down-regulated in ; C: down-regulated to unchanged in , upregulated in ; D: reduced in both yeasts. Subclusters of genes that are unchanged in both organisms are not displayed. The brightest colouring corresponds to the logregulation ≥ ± 2

Monitoring of transcriptional regulation in under protein production conditions-2

<p><b>Copyright information:</b></p><p>Taken from "Monitoring of transcriptional regulation in under protein production conditions"</p><p>http://www.biomedcentral.com/1471-2164/8/179</p><p>BMC Genomics 2007;8():179-179.</p><p>Published online 19 Jun 2007</p><p>PMCID:PMC1919374.</p><p></p>ts control strain (containing only the Fab expression cassette). B: 2F5 Fab producing SMD1168 co-expressing compared to the control strain. Both diagrams are ordered from the lowest to the highest logratio. Colour legend as in figure 2

Additional file 2: of GoldenPiCS: a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris

GoldenPiCS modules and plasmids. Modules and plasmids are listed with corresponding cloning- and fusion sites and full sequences. DNA orientation is 5’to 3′. All plasmids are available at Addgene. (XLSX 33 kb

MOESM2 of Functional inclusion bodies produced in the yeast Pichia pastoris

Additional file 2. Raw experimental data

MOESM1 of Functional inclusion bodies produced in the yeast Pichia pastoris

Additional file 1. VP1GFP gene and protein sequences

Additional file 1: of Systems-level organization of yeast methylotrophic lifestyle

Transcriptomic, proteomic, and metabolomic regulation of P. pastoris during methylotrophic growth. Containing the following eight sheets: Summary Omics Data: number of significantly regulated genes, proteins or metabolites (e.g. “up” refers to up-regulation in methanol/glycerol compared to glucose). Transcriptomics and proteomics: Average fold changes and P values of transcriptomics and proteomics comparing P. pastoris cultivated with methanol/glycerol or glucose as carbon source in chemostat. Average values derive from three biological replicates per condition. Metabolomics: Average fold changes and P values of metabolomics measurements comparing P. pastoris cultivated with methanol/glycerol or glucose as carbon source in chemostat cultivations. Average values derive from three biological replicates per condition. Co-regulation (related to Fig. 1 in the text): Regulation of the 575 gene-protein pairs with transcriptomics and proteomics data available and assignment to regulatory groups. Central carbon metabolism (related to Fig. 4 in the text): Average fold changes and P values of transcriptomics, proteomics, and metabolomics measurement depicted in Fig. 4. Amino acid metabolism (related to Fig. 6 in the text): Average fold changes and P values of transcriptomics, proteomics, and metabolomics measurement depicted in Fig. 6. Vitamin biosynthesis (related to Fig. 7 in the text): Average fold changes and P values of transcriptomics, proteomics, and metabolomics measurement depicted in Fig. 7. Peroxisomal gene regulation: Average fold changes and P values of transcriptomics and proteomics for all mentioned peroxisomal genes. Average values derive from three biological replicates per condition. (XLSX 2348 kb

Additional file 4: of Systems-level organization of yeast methylotrophic lifestyle

Proteomic identification and quantification of methanol metabolic enzymes and control proteins in peroxisomal fractions and homogenates of P. pastoris cells grown on methanol. Containing the following three sheets: Protein hits: contains all identified proteins that met the threshold in at least one sample, with their respective MASCOT scores, number of peptides, and percent sequence coverage. Peptide hits: list of all identified peptides, their MASCOT scores, mass and charge values, and intensities. Peptides used for quant + areas: lists all peptides of the proteins in Table 3 that were used for quantification, and their respective peak areas in the different samples. (XLSX 879 kb