title: Systems-level organization of yeast methylotrophic lifestyle.
abstract: BACKGROUND
  Some yeasts have evolved a methylotrophic lifestyle enabling them to utilize the single carbon compound methanol as a carbon and energy source. Among them, Pichia pastoris (syn. Komagataella sp.) is frequently used for the production of heterologous proteins and also serves as a model organism for organelle research. Our current knowledge of methylotrophic lifestyle mainly derives from sophisticated biochemical studies which identified many key methanol utilization enzymes such as alcohol oxidase and dihydroxyacetone synthase and their localization to the peroxisomes. C1 assimilation is supposed to involve the pentose phosphate pathway, but details of these reactions are not known to date.
  
  
  RESULTS
  In this work we analyzed the regulation patterns of 5,354 genes, 575 proteins, 141 metabolites, and fluxes through 39 reactions of P. pastoris comparing growth on glucose and on a methanol/glycerol mixed medium, respectively. Contrary to previous assumptions, we found that the entire methanol assimilation pathway is localized to peroxisomes rather than employing part of the cytosolic pentose phosphate pathway for xylulose-5-phosphate regeneration. For this purpose, P. pastoris (and presumably also other methylotrophic yeasts) have evolved a duplicated methanol inducible enzyme set targeted to peroxisomes. This compartmentalized cyclic C1 assimilation process termed xylose-monophosphate cycle resembles the principle of the Calvin cycle and uses sedoheptulose-1,7-bisphosphate as intermediate. The strong induction of alcohol oxidase, dihydroxyacetone synthase, formaldehyde and formate dehydrogenase, and catalase leads to high demand of their cofactors riboflavin, thiamine, nicotinamide, and heme, respectively, which is reflected in strong up-regulation of the respective synthesis pathways on methanol. Methanol-grown cells have a higher protein but lower free amino acid content, which can be attributed to the high drain towards methanol metabolic enzymes and their cofactors. In context with up-regulation of many amino acid biosynthesis genes or proteins, this visualizes an increased flux towards amino acid and protein synthesis which is reflected also in increased levels of transcripts and/or proteins related to ribosome biogenesis and translation.
  
  
  CONCLUSIONS
  Taken together, our work illustrates how concerted interpretation of multiple levels of systems biology data can contribute to elucidation of yet unknown cellular pathways and revolutionize our understanding of cellular biology.
authors.affiliation: Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.|Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.
authors.forename: Hannes
authors.initials: H
authors.lastname: Rußmayer
authors.affiliation: Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.|Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.
authors.forename: Markus
authors.initials: M
authors.lastname: Buchetics
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
authors.forename: Clemens
authors.initials: C
authors.lastname: Gruber
authors.affiliation: Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.|Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.
authors.forename: Minoska
authors.initials: M
authors.lastname: Valli
authors.affiliation: Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria.|Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria.
authors.forename: Karlheinz
authors.initials: K
authors.lastname: Grillitsch
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|School of Bioengineering, University of Applied Sciences FH Campus, A-1190 Vienna, Austria.
authors.forename: Gerda
authors.initials: G
authors.lastname: Modarres
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.|Present addresses: Sandoz GmbH, A-6250 Kundl, Austria.
authors.forename: Raffaele
authors.initials: R
authors.lastname: Guerrasio
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.|Present addresses: BIOCRATES Life Sciences AG, A-6020 Innsbruck, Austria.
authors.forename: Kristaps
authors.initials: K
authors.lastname: Klavins
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.|University of Tübingen, D-72076 Tübingen, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Neubauer
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
authors.forename: Hedda
authors.initials: H
authors.lastname: Drexler
authors.affiliation: Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.|Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.
authors.forename: Matthias
authors.initials: M
authors.lastname: Steiger
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
authors.forename: Christina
authors.initials: C
authors.lastname: Troyer
authors.affiliation: BIOCRATES Life Sciences AG, A-6020 Innsbruck, Austria.
authors.forename: Ali
authors.initials: A
authors.lastname: Al Chalabi
authors.affiliation: BIOCRATES Life Sciences AG, A-6020 Innsbruck, Austria.
authors.forename: Guido
authors.initials: G
authors.lastname: Krebiehl
authors.affiliation: BIOCRATES Life Sciences AG, A-6020 Innsbruck, Austria.
authors.forename: Denise
authors.initials: D
authors.lastname: Sonntag
authors.affiliation: Institute of Plant Sciences, NAWI Graz, University of Graz, A-8010 Graz, Austria.
authors.forename: Günther
authors.initials: G
authors.lastname: Zellnig
authors.affiliation: Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria.|Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria.
authors.forename: Günther
authors.initials: G
authors.lastname: Daum
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria.
authors.forename: Alexandra B
authors.initials: AB
authors.lastname: Graf
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
authors.forename: Friedrich
authors.initials: F
authors.lastname: Altmann
authors.affiliation: Institute of Analytical Chemistry, University of Vienna, A-1090 Vienna, Austria.
authors.forename: Gunda
authors.initials: G
authors.lastname: Koellensperger
authors.affiliation: Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.|Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
authors.forename: Stephan
authors.initials: S
authors.lastname: Hann
authors.affiliation: Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.|Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Sauer
authors.affiliation: Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. diethard.mattanovich@boku.ac.at.|Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria. diethard.mattanovich@boku.ac.at.
authors.forename: Diethard
authors.initials: D
authors.lastname: Mattanovich
authors.affiliation: Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.|Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Gasser
mesh_terms: D005656:Fungal Proteins / Q000235:genetics* / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D005947:Glucose / Q000378:metabolism*; D005990:Glycerol / Q000378:metabolism*; D000432:Methanol / Q000378:metabolism*; D010843:Pichia / Q000235:genetics* / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D005947:Glucose; D005990:Glycerol; D000432:Methanol