Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: A systems biological analysis

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 3, 2009, Pages 847-852

  Luo, Ruoyu ^a,b,c   Wei, Haibin ^c   Ye, Lin ^c   Wang, Kankan ^d   Chen, Fan ^e   Luo, Lijun ^f   Liu, Lei ^a,b   Li, Yuanyuan ^b   Crabbe, M James C ^g   Jin, Li ^c   Li, Yixue ^a,b   Zhong, Yang ^b,c,f  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

^c FUDAN UNIVERSITY   (China)

^d SHANGHAI SECOND MEDICAL UNIVERSITY   (China)

^e INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^f SHANGHAI AGROBIOLOGICAL GENE CENTER   (China)

^g UNIVERSITY OF BEDFORDSHIRE   (United Kingdom)

Author keywords

Climate extremes; Environmental stress; Flux balance; Metabolic control; Metabolomics

Indexed keywords

CARBON DIOXIDE; 3 PHOSPHOGLYCERIC ACID; 3-PHOSPHOGLYCERATE; GLYCERIC ACID;

ARTICLE; BIOASSAY; BIOLOGY; C3 PLANT; CARBON DIOXIDE CONCENTRATING MECHANISM; CHLOROPLAST; CLIMATE CHANGE; COMPLEX FORMATION; DROUGHT STRESS; ENVIRONMENTAL CHANGE; ENVIRONMENTAL STRESS; FLUCTUATING ASYMMETRY; METABOLIC REGULATION; METABOLITE; METABOLOMICS; MOLECULAR DYNAMICS; NONHUMAN; PHOTOSYNTHESIS; PLANT METABOLISM; PRIORITY JOURNAL; DROUGHT; METABOLISM; METHODOLOGY; PLANT; SYSTEMS BIOLOGY; THEORETICAL MODEL;

CARBON DIOXIDE; CHLOROPLASTS; DROUGHTS; GLYCERIC ACIDS; MODELS, THEORETICAL; PHOTOSYNTHESIS; PLANTS; SYSTEMS BIOLOGY;

EID: 58849110784     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0810731105     Document Type: Article

References (34)

1. Palsson B (2000) The challenges of in silico biology. Nat Biotechnol 18:1147-1150.
2. Schilling CH, Schuster S, Palsson BO, Heinrich R (1999) Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era. Biotechnol Prog 15:296-303.
3. Varma A, Palsson BO (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 60:3724-3731.
4. Edwards JS, Palsson BO (2000) Robustness analysis of the Escherichia coli metabolic network. Biotechnol Prog 16:927-939.
5. Segre D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99:15112-15117.
6. Edwards JS, Palsson BO (2000) The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97:5528-5533.
7. Deutscher D, Meilijson I, Kupiec M, Ruppin E (2006) Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat Genet 38:993-998.
8. Kauffman KJ, Prakash P, Edwards JS (2003) Advances in flux balance analysis. Curr Opin Biotechnol 14:491-496.
9. Stephanopoulos G, Alper H, Moxley J (2004) Exploiting biological complexity for strain improvement through systems biology. Nat Biotechnol 22:1261-1267.
10. Mahadevan R, Edwards JS, Doyle FJ, III (2002) Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys J 83:1331-1340.
11. Luo RY, et al. (2006) Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Mol Syst Biol 2:2006.0031.
12. Raamsdonk LM, et al. (2001) A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol 19:45-50.
13. Stelling J, Sauer U, Szallasi Z, Doyle FJ, III, Doyle J (2004) Robustness of cellular functions. Cell 118:675-685.
14. Kitano H (2004) Biological robustness. Nat Rev Genet 5:826-837.
15. Csete M, Doyle J (2004) Bow ties, metabolism, and disease. Trends Biotechnol 22:446-450.
16. Hasty J, McMillen D, Collins JJ (2002) Engineered gene circuits. Nature 420:224-230.
17. Carlson JM, Doyle J (1999) Highly optimized tolerance: A mechanism for power laws in designed systems. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Top 60:1412-1427.
18. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:C47-C52.
19. Hartman JLT, Garvik B, Hartwell L (2001) Cell biology: Principles for the buffering of genetic variation. Science 291:1001-1004.
20. Kitano H (2007) Towards a theory of biological robustness. Mol Syst Biol 3:137.
21. Pettersson G, Ryde-Pettersson U (1988) A mathematical model of the Calvin photosynthesis cycle. Eur J Biochem 175:661-672.
22. 3 photosynthesis in silico. Photosynth Res 90:45-66.
23. Wingler A, Lea PJ, Quick WP, Leegood RC (2000) Photorespiration: Metabolic pathways and their role in stress protection. Philos Trans R Soc London Ser B 355:1517-1529.
24. 2 on the expression of ribulose-1,5-bisphosphate carboxylase/oxygenase genes and carbohydrate accumulation in leaves of Arabidopsis thaliana (L) Heynh. Plant Physiol 116:715-723.
25. 2 supply on the biochemistry and physiology of photosynthesis in sunflower. J Exp Bot 53:1781-1791.
26. 2 enrichment. Plant Physiol 82:528-533.
27. Shimizu H, Haken H (1983) Cooperative dynamics in organelles. J Theor Biol 104:261-273.
28. Vo TD, Greenberg HJ, Palsson BO (2004) Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J Biol Chem 279:39532-39540.
29. Seki M, et al. (2002) Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J 31:279-292.
30. Prigogine I, Nicolis G, Babloyantz A (1974) Nonequilibrium problems in biological phenomena. Ann NY Acad Sci 231:99-105.
31. Tcherkez GGB, Farquhar GD, Andrews TJ (2006) Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized. Proc Natl Acad Sci USA 103:7246-7251.
32. Kaern M, Elston TC, Blake WJ, Collins JJ (2005) Stochasticity in gene expression: From theories to phenotypes. Nat Rev Genet 6:451-464.
33. Kaufmann BB, van Oudenaarden A (2007) Stochastic gene expression: From single molecules to the proteome. Curr Opin Genet Dev 17:107-112.
34. Basso K, et al. (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 37:382-390.