Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803

Biotechnology Journal

Volumn 6, Issue 3, 2011, Pages 330-342

  Montagud, Arnau ^a,b   Zelezniak, Aleksej ^b,c   Navarro, Emilio ^d   de Córdoba, Pedro Fernández ^a   Urchueguía, Javier F ^a   Patil, Kiran Raosaheb ^b  

^a UNIVERSITAT POLITÈCNICA DE VALÈNCIA   (Spain)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^d UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

Cyanobacteria; Flux coupling analysis; Metabolic engineering; Photanol

Indexed keywords

AUTOTROPHY; BUILDING BLOCKES; CARBON SOURCE; CYANOBACTERIA; CYANOBACTERIUM; ETHANOL PRODUCTION; FLUX ACTIVITY; FLUX COUPLING; FLUX COUPLING ANALYSIS; GAIN INSIGHT; GENOME-SCALE METABOLIC MODELS; GROWTH CONDITIONS; HETEROTROPHY; HOT SPOT; METABOLIC ENGINEERING; METABOLIC NETWORK; METABOLIC SHIFT; MIXOTROPHY; PHOTANOL; PHOTOSYNTHETIC BACTERIAS; POTENTIAL PRODUCTION; SOCIO-ECONOMICS; STRUCTURAL ORGANIZATION; SYNECHOCYSTIS; SYNECHOCYSTIS SP; TRANSCRIPTIONAL REGULATION;

BACTERIA; DRILLING PLATFORMS; ECOLOGY; ETHANOL; GENES; PRODUCTION PLATFORMS;

METABOLISM;

ALCOHOL; CARBON; HYDROGEN;

ARTICLE; AUTOTROPHY; CATABOLISM; HETEROTROPHY; MIXOTROPHY; NONHUMAN; PHOTOSYNTHESIS; PRIORITY JOURNAL; SYNECHOCYSTIS; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS;

CARBON CYCLE; ETHANOL; HYDROGEN; METABOLIC NETWORKS AND PATHWAYS; PHOTOSYNTHESIS; SYNECHOCYSTIS; TRANSCRIPTION, GENETIC;

CYANOBACTERIA; PHOTOBACTERIA; SYNECHOCYSTIS; SYNECHOCYSTIS SP.;

EID: 79952126110     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201000109     Document Type: Article

References (27)

1. Tamagnini, P., Leitao, E., Oliveira, P., Ferreira, D. et al., Cyanobacterial hydrogenases: diversity, regulation and applications. FEMS Microbiol. Rev. 2007, 31, 692-720.
2. Angermayr, S. A., Hellingwerf, K. J., Lindblad, P., Teixeira de Mattos, M. J., Energy biotechnology with cyanobacteria. Curr. Opin. Biotechnol. 2009, 20, 257-263.
3. Kufryk, G. I., Sachet, M., Schmetterer, G., Vermaas, W. F., Transformation of the cyanobacterium Synechocystis sp. PCC 6803 as a tool for genetic mapping: optimization of efficiency. FEMS Microbiol. Lett. 2002, 206, 215-219.
4. Kaneko, T., Sato, S., Kotani, H., Tanaka, A. et al., Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 1996, 3, 109-136.
5. Gutthann, F., Egert, M., Marques, A., Appel, J., Inhibition of respiration and nitrate assimilation enhances photohydrogen evolution under low oxygen concentrations in Synechocystis sp. PCC 6803. Biochim. Biophys. Acta 2007, 1767, 161-169.
6. Lindberg, P., Park, S., Melis, A., Engineering a platform for photosynthetic isoprene production in cyanobacteria, using Synechocystis as the model organism. Metab. Eng. 2010, 12, 70-79.
7. Wu, G. F., Wu, Q. Y., Shen, Z. Y., Accumulation of poly-beta-hydroxybutyrate in cyanobacterium Synechocystis sp. PCC6803. Bioresour. Technol. 2001, 76, 85-90.
8. Liu, X., Brune, D., Vermaas, W., Curtiss, R. 3rd, Production and secretion of fatty acids in genetically engineered cyanobacteria. Proc. Natl. Acad. Sci. U S A 2010.
9. Patil, K. R., Akesson, M., Nielsen, J., Use of genome-scale microbial models for metabolic engineering. Curr. Opin. Biotechnol. 2004, 15, 64-69.
10. Barrett, C. L., Kim, T. Y., Kim, H. U., Palsson, B. O., Lee, S. Y., Systems biology as a foundation for genome-scale synthetic biology. Curr. Opin. Biotechnol. 2006, 17, 488-492.
11. Morange, M., A new revolution? The place of systems biology and synthetic biology in the history of biology. EMBO Rep. 2009, 10, 1 S. 50-53.
12. Shastri, A. A., Morgan, J. A., Flux balance analysis of photoautotrophic metabolism. Biotechnol. Prog. 2005, 21, 1617-1626.
13. Navarro, E., Montagud, A., Fernández de Córdoba, P., Urchueguía, J. F., Metabolic flux analysis of the hydrogen production potential in Synechocystis sp. PCC6803. Int. J. Hydrogen Energy 2009, 34, 8828-8838.
14. Montagud, A., Navarro, E., Fernández de Córdoba, P., Urchueguía, J. F. et al., Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium. BMC System Biology 2010, 4, 156.
15. Burgard, A. P., Nikolaev, E. V., Schilling, C. H., Maranas, C. D., Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 2004, 14, 301-312.
16. Notebaart, R. A., Teusink, B., Siezen, R. J., Papp, B., Co-regulation of metabolic genes is better explained by flux coupling than by network distance. PLoS Comput. Biol. 2008, 4, e26.
17. Suthers, P. F., Chang, Y. J., Maranas, C. D., Improved computational performance of MFA using elementary metabolite units and flux coupling. Metab. Eng. 2010, 12, 123-128.
18. Oliveira, A. P., Patil, K. R., Nielsen, J., Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. BMC Syst. Biol. 2008, 2, 17.
19. Patil, K. R., Nielsen, J., Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Natl. Acad. Sci. U S A 2005, 102, 2685-2689.
20. Karp, P. D., Paley, S. M., Krummenacker, M., Latendresse, M. et al., Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform 2010, 11, 40-79.
21. Cvijovic, M., Olivares-Hernandez, R., Agren, R., Dahr, N. et al., BioMet Toolbox: genome-wide analysis of metabolism. Nucleic Acids Res. 2010. 38, W144-W149.
22. Gill, R. T., Katsoulakis, E., Schmitt, W., Taroncher-Oldenburg, G. et al., Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp. strain PCC 6803. J. Bacteriol. 2002, 184, 3671-3681.
23. Edwards, J. S., Palsson, B. O., Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 2000, 1, 1.
24. Forster, J., Famili, I., Fu, P., Palsson, B. O., Nielsen, J., Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 2003, 13, 244-253.
25. Bader, G. D., Hogue, C. W., An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4, 2.
26. Csete, M., Doyle, J., Bow ties, metabolism and disease. Trends Biotechnol. 2004, 22, 446-450.
27. Whitton, B. A., Potts, M., The ecology of cyanobacteria: their diversity in time and space, Kluwer Academic, Boston 2000.