title: The cultural divide: exponential growth in classical 2D and metabolic equilibrium in 3D environments.
abstract: BACKGROUND
  Cellular metabolism can be considered to have two extremes: one is characterized by exponential growth (in 2D cultures) and the other by a dynamic equilibrium (in 3D cultures). We have analyzed the proteome and cellular architecture at these two extremes and found that they are dramatically different.
  
  
  RESULTS
  Structurally, actin organization is changed, microtubules are increased and keratins 8 and 18 decreased. Metabolically, glycolysis, fatty acid metabolism and the pentose phosphate shunt are increased while TCA cycle and oxidative phosphorylation is unchanged. Enzymes involved in cholesterol and urea synthesis are increased consistent with the attainment of cholesterol and urea production rates seen in vivo. DNA repair enzymes are increased even though cells are predominantly in Go. Transport around the cell--along the microtubules, through the nuclear pore and in various types of vesicles has been prioritized. There are numerous coherent changes in transcription, splicing, translation, protein folding and degradation. The amount of individual proteins within complexes is shown to be highly coordinated. Typically subunits which initiate a particular function are present in increased amounts compared to other subunits of the same complex.
  
  
  CONCLUSIONS
  We have previously demonstrated that cells at dynamic equilibrium can match the physiological performance of cells in tissues in vivo. Here we describe the multitude of protein changes necessary to achieve this performance.
authors.affiliation: Tissue Culture Engineering Laboratory, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Wrzesinski
authors.affiliation: Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Adelina
authors.initials: A
authors.lastname: Rogowska-Wrzesinska
authors.affiliation: Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Rattiyaporn
authors.initials: R
authors.lastname: Kanlaya
authors.affiliation: Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Kamil
authors.initials: K
authors.lastname: Borkowski
authors.affiliation: Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Veit
authors.initials: V
authors.lastname: Schwämmle
authors.affiliation: Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Jie
authors.initials: J
authors.lastname: Dai
authors.affiliation: Tissue Culture Engineering Laboratory, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Kira Eyd
authors.initials: KE
authors.lastname: Joensen
authors.affiliation: Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Wojdyla
authors.affiliation: Tissue Culture Engineering Laboratory, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Vasco Botelho
authors.initials: VB
authors.lastname: Carvalho
authors.affiliation: Tissue Culture Engineering Laboratory, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Fey
mesh_terms: D000199:Actins / Q000378:metabolism; D002450:Cell Communication; D018929:Cell Culture Techniques; D002468:Cell Physiological Phenomena; D049109:Cell Proliferation; D002478:Cells, Cultured; D002853:Chromatography, Liquid; D056945:Hep G2 Cells; D006801:Humans; D055442:Metabolome; D008870:Microtubules / Q000378:metabolism / Q000648:ultrastructure; D020543:Proteome; D053719:Tandem Mass Spectrometry
chemical_list: D000199:Actins; D020543:Proteome