Systems-level organization of yeast methylotrophic lifestyle

BMC Biology

Research Article

Alexandra B. Graf¹  Christina Troyer²  Hedda Drexler²  Clemens Gruber²  Stephan Hann²  Friedrich Altmann²  Kristaps Klavins³  Raffaele Guerrasio⁴  Stefan Neubauer⁵  Gerda Modarres⁶  Ali Al Chalabi⁷  Guido Krebiehl⁷  Denise Sonntag⁷  Hannes Rußmayer⁸  Brigitte Gasser⁸  Markus Buchetics⁸  Minoska Valli⁸  Michael Sauer⁸  Diethard Mattanovich⁸  Matthias Steiger⁸  Gunda Koellensperger⁹  Karlheinz Grillitsch^1,10  Günther Daum^1,10  Günther Zellnig^1,11 

[1] Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria;Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria;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;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;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;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;Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria;School of Bioengineering, University of Applied Sciences FH Campus, A-1190 Vienna, Austria;BIOCRATES Life Sciences AG, A-6020 Innsbruck, Austria;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;Institute of Analytical Chemistry, University of Vienna, A-1090 Vienna, Austria;Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria;Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria;Institute of Plant Sciences, NAWI Graz, University of Graz, A-8010 Graz, Austria;

关键词: Metabolome;    Methanol;    Peroxisome;    Pichia pastoris;    Proteome;    Transcriptome;    Xylulose-monophosphate cycle;   

DOI  :  10.1186/s12915-015-0186-5

 received in 2015-09-02, accepted in 2015-09-03,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundSome 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.ResultsIn 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.ConclusionsTaken 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.

【 授权许可】

CC BY   
© Rußmayer et al. 2015