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  A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana

Sajitz-Hermstein, M., & Nikoloski, Z. (2010). A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana. Bioinformatics, 26(18), i582-i588. doi:10.1093/bioinformatics/btq390.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-2355-A Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0019-BC35-2
Genre: Journal Article

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 Creators:
Sajitz-Hermstein, M.1, 2, Author              
Nikoloski, Z.1, Author              
Affiliations:
1Mathematical Modelling and Systems Biology - Nikoloski, Cooperative Research Groups, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753310              
2System Regulation, Department Stitt, Max Planck Institute of Molecular Plant Physiology, Max Planck Society, ou_1753327              

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Free keywords: amino-acid usage escherichia-coli metabolism nitrogen balance evolution selection networks growth sugars
 Abstract: Motivation: 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.

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Language(s): eng - English
 Dates: 2010-09-092010
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: ISI:000281714100026
DOI: 10.1093/bioinformatics/btq390
ISSN: 1367-4811 (Electronic)1367-4803 (Linking)
URI: ://000281714100026http://bioinformatics.oxfordjournals.org/content/26/18/i582.full.pdf
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Title: Bioinformatics
Source Genre: Journal
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Publ. Info: Oxford : Oxford University Press
Pages: - Volume / Issue: 26 (18) Sequence Number: - Start / End Page: i582 - i588 Identifier: ISSN: 1367-4803
CoNE: https://pure.mpg.de/cone/journals/resource/954926969991