Article thumbnail

Predicting the Physiological Role of Circadian Metabolic Regulation in the Green Alga Chlamydomonas reinhardtii

By Sascha Schäuble, Ines Heiland, Olga Voytsekh, Maria Mittag and Stefan Schuster

Abstract

Although the number of reconstructed metabolic networks is steadily growing, experimental data integration into these networks is still challenging. Based on elementary flux mode analysis, we combine sequence information with metabolic pathway analysis and include, as a novel aspect, circadian regulation. While minimizing the need of assumptions, we are able to predict changes in the metabolic state and can hypothesise on the physiological role of circadian control in nitrogen metabolism of the green alga Chlamydomonas reinhardtii

Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:3161734
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles

Citations

  1. (2000). A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks.
  2. (2006). A heteromeric RNAbinding protein is involved in maintaining acrophase and period of the circadian clock.
  3. (2010). A note on the complexity of finding and enumerating elementary modes.
  4. (2005). Adenine and adenosine salvage pathways in erythrocytes and the role of S-adenosylhomocysteine hydrolase. A theoretical study using elementary ux modes.
  5. (1999). Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology John Wiley & Sons, 1st edition 1999 edition.
  6. (2009). Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary ux patterns.
  7. (2010). CASOP: a computational approach for strain optimization aiming at high productivity.
  8. (2009). ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.
  9. (1996). Conserved circadian elements in phylogenetically diverse algae.
  10. (2009). Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism.
  11. (2002). Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth.
  12. (2004). Ferna ´ndez E
  13. (2007). Ferna ´ndez E, Galva ´n A
  14. (2005). Functional genomics of the regulation of the nitrate assimilation pathway in Chlamydomonas.
  15. (2005). Identi_cation of novel clockcontrolled genes by cDNA macroarray analysis in Chlamydomonas reinhardtii.
  16. (2001). Identification of target mRNAs for the clock-controlled RNA-binding protein Chlamy 1 from Chlamydomonas reinhardtii.
  17. (2001). In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.
  18. (2007). Integrated network reconstruction, visualization and analysis using YANAsquare.
  19. (2004). Integrating high-throughput and computational data elucidates bacterial networks.
  20. (2008). Is maximization of molar yield in metabolic networks favoured by evolution?
  21. (2008). KEGG for linking genomes to life and the environment.
  22. (2008). Large-scale computation of elementary ux modes with bit pattern trees.
  23. (2009). Metabolic engineering of Escherichia coli for efficient conversion of glycerol to ethanol.
  24. (2002). Metabolic network structure determines key aspects of functionality and regulation.
  25. (2006). Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum.
  26. (2002). Metabolic pathway analysis of a recombinant yeast for rational strain development.
  27. (2010). Metabolic reconstruction, constraintbased analysis and game theory to probe genomescale metabolic networks.
  28. (2008). Networkbased prediction of human tissue-specific metabolism.
  29. (1998). Nitrate transport: a key step in nitrate assimilation.
  30. (2007). Observing metabolic functions at the genome scale.
  31. (1994). On elementary ux modes in biochemical reaction systems at steady state.
  32. (2009). Reconstruction of biochemical networks in microorganisms.
  33. (2001). Regulation of gene expression in ux balance models of metabolism.
  34. (2009). Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis.
  35. (2004). Rubisco without the Calvin cycle improves the carbon efficiency of developing green seeds.
  36. (2003). Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genomescale reconstructed metabolic network.
  37. (2006). Steinbu ¨chel A
  38. (1994). Stoichiometric ux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
  39. (2008). Structural robustness of metabolic networks with respect to multiple knockouts.
  40. (2010). The biomass objective function.
  41. (2007). The Chlamydomonas genome reveals the evolution of key animal and plant functions.
  42. (2004). The circadian RNA-binding protein CHLAMY 1 represents a novel type heteromer of RNA recognition motif and lysine homology domain-containing subunits.
  43. (2006). The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies.
  44. (2007). The Presence of UGrepeat sequences in the 39-UTRs of reporter luciferase mRNAs mediates circadian expression and can determine acrophase in Chlamydomonas reinhardtii.
  45. (2010). The Universal Protein Resource (UniProt) in 2010.
  46. (2010). Theoretical study of lipid biosynthesis in wild-type Escherichia coli and in a protoplast-type L-form using elementary ux mode analysis.