title: A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana.
abstract: BACKGROUND
  Comprehensive understanding of cellular processes requires development of approaches which consider the energetic balances in the cell. The existing approaches that address this problem are based on defining energy-equivalent costs which do not include the effects of a changing environment. By incorporating these effects, one could provide a framework for integrating 'omics' data from various levels of the system in order to provide interpretations with respect to the energy state and to elicit conclusions about putative global energy-related response mechanisms in the cell.
  
  
  RESULTS
  Here we define a cost measure for amino acid synthesis based on flux balance analysis of a genome-scale metabolic network, and develop methods for its integration with proteomics and metabolomics data. This is a first measure which accounts for the effect of different environmental conditions. We applied this approach to a genome-scale network of Arabidopsis thaliana and calculated the costs for all amino acids and proteins present in the network under light and dark conditions. Integration of function and process ontology terms in the analysis of protein abundances and their costs indicates that, during the night, the cell favors cheaper proteins compared with the light environment. However, this does not imply that there is squandering of resources during the day. The results from the association analysis between the costs, levels and well-defined expenses of amino acid synthesis, indicate that our approach not only captures the adjustment made at the switch of conditions, but also could explain the anticipation of resource usage via a global energy-related regulatory mechanism of amino acid and protein synthesis.
authors.affiliation: Max-Planck Institute of Molecular Plant Physiology, University of Postdam, Potsdam, Germany.
authors.forename: Max
authors.initials: M
authors.lastname: Sajitz-Hermstein
authors.forename: Zoran
authors.initials: Z
authors.lastname: Nikoloski
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis*; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D003624:Darkness; D004734:Energy Metabolism; D004777:Environment; D018745:Genome, Plant; D008027:Light; D055432:Metabolomics / Q000379:methods; D008954:Models, Biological; D040901:Proteomics / Q000379:methods*
chemical_list: D000596:Amino Acids; D029681:Arabidopsis Proteins
references.citation: Nature. 1989 Sep 21;341(6239):245-8
references.pmid: 2506452
references.citation: J Theor Biol. 2008 Jun 7;252(3):497-504
references.pmid: 18249414
references.citation: Plant Physiol. 2004 Sep;136(1):2483-99
references.pmid: 15375205
references.citation: J Exp Bot. 2003 Jan;54(382):585-93
references.pmid: 12508069
references.citation: Genome Biol. 2004;5(2):R10
references.pmid: 14759260
references.citation: Plant Physiol. 2004 Jun;135(2):745-55
references.pmid: 15173566
references.citation: J Mol Evol. 2007 May;64(5):558-71
references.pmid: 17476453
references.citation: Nat Biotechnol. 2008 Sep;26(9):1003-10
references.pmid: 18711341
references.citation: Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3695-700
references.pmid: 11904428
references.citation: Mol Biol Evol. 1998 Jun;15(6):774-6
references.pmid: 9615459
references.citation: Plant Physiol. 2009 Nov;151(3):1570-81
references.pmid: 19755544
references.citation: Plant Physiol. 2009 Jan;149(1):585-98
references.pmid: 18987214
references.citation: Trends Biochem Sci. 1999 Nov;24(11):437-40
references.pmid: 10542411
references.citation: Planta. 1998 Dec;207(1):27-41
references.pmid: 9951717
references.citation: Mol Syst Biol. 2007;3:119
references.pmid: 17625511
references.citation: Plant Physiol. 2007 Nov;145(3):640-52
references.pmid: 17885087
references.citation: Proc Biol Sci. 2006 May 22;273(1591):1293-300
references.pmid: 16720405
references.citation: Appl Environ Microbiol. 1993 Aug;59(8):2465-73
references.pmid: 8368835
references.citation: J Mol Evol. 2003 Feb;56(2):151-61
references.pmid: 12574861
references.citation: Proc Natl Acad Sci U S A. 2000 May 9;97(10):5528-33
references.pmid: 10805808
references.citation: J Exp Bot. 2002 Apr;53(370):959-70
references.pmid: 11912238
references.citation: Annu Rev Physiol. 1996;58:539-63
references.pmid: 8815808
references.citation: Science. 2001 Jul 13;293(5528):297-300
references.pmid: 11452124
references.citation: Mol Biol Evol. 2006 Sep;23(9):1670-80
references.pmid: 16754641
references.citation: J Exp Bot. 2002 Apr;53(370):939-45
references.pmid: 11912236
references.citation: J Theor Biol. 1997 Jul 21;187(2):165-73
references.pmid: 9237887
references.citation: J Exp Zool B Mol Dev Evol. 2007 May 15;308(3):322-4
references.pmid: 17262826
references.citation: Genome Biol. 2006;7(8):R76
references.pmid: 16916443
references.citation: Plant Physiol. 2010 Mar;152(3):1251-62
references.pmid: 20107023
references.citation: Mol Cell Proteomics. 2005 Sep;4(9):1265-72
references.pmid: 15958392
references.citation: Bioinformatics. 2007 May 15;23(10):1258-64
references.pmid: 17344237
references.citation: BMC Syst Biol. 2007 Jan 08;1:2
references.pmid: 17408509
references.citation: Physiol Mol Biol Plants. 2009 Jan;15(1):23-30
references.pmid: 23572909