Development of a Chlamydomonas reinhardtii metabolic network dynamic model to describe distinct phenotypes occurring at different CO2 levels

PeerJ

Volumn 2018, Issue 9, 2018, Pages

  Salguero, Daniela Alejandra Mora ^a   Fernández Niño, Miguel ^a   Serrano Bermúdez, Luis Miguel ^b   Melo, David O Páez ^a   Winck, Flavia V ^c   Caldana, Camila ^d   Barrios, Andrés Fernando González ^a  

^a UNIVERSIDAD DE LOS ANDES   (Colombia)

^b UNIVERSIDAD NACIONAL DE COLOMBIA   (Colombia)

^c UNIVERSITY OF SÃO PAULO   (Brazil)

^d BRAZILIAN CENTER FOR RESEARCH IN ENERGY AND MATERIALS CNPEM   (Brazil)

Author keywords

Biomass; Biotechnology; Chlamydomonas reinhardtii; CO2 fixation; Dynamic model; Metabolic network; Metabolomics; Transcriptomics

Indexed keywords

NITROGEN;

ARTICLE; BIOMASS PRODUCTION; CARBON DIOXIDE FIXATION; CELL GROWTH; CHLAMYDOMONAS REINHARDTII; ENVIRONMENTAL CHANGE; ESCHERICHIA COLI; GENE EXPRESSION; HETEROTROPH; INHIBITION CONSTANT; MATHEMATICAL MODEL; METABOLITE; METABOLOMICS; MICROBIAL GENETICS; MIXOTROPH; NONHUMAN; PH; PHOTOAUTOTROPH; TRANSCRIPTOMICS;

EID: 85052855651     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.5528     Document Type: Article

References (45)

1. Anderson RA. 2005. Algal culturing techniques. 1st edition. Amsterdam: Elsevier, 589
2. 3-fluxes in cyanobacteria and microalgae during steady-state photosynthesis. Physiologia Plantarum 90(3):529-536 DOI 10.1111/j.1399-3054.1994.tb08811.x
3. BioCyc Database Collection. 2016. Summary of Chlamydomonas reinhardtii. Version 20. 1. Available at https:// biocyc.org/ organism-summary?object=CHLAMY
4. Blazier AS, Papin JA. 2012. Integration of expression data in genome-scale metabolic network reconstructions. Frontiers in Physiology 3:Article 299 DOI 10.3389/fphys.2012.00299
5. Boyle N, Morgan J. 2009. Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii. BMC Systems Biology 3(1):4 DOI 10.1186/1752-0509-3-4
6. 2 deprivation coincides with massive transcriptional restructuring in Chlamydomonas reinhardtii. The Plant Cell 24:1860-1875 DOI 10.1105/tpc.111.093435
7. Chaiboonchoe A, Ghamsari L, Dohai B, Ng P, Khraiwesh B, Jaiswal A, Jijakli K, Koussa J, Nelson DR, Cai H, Yang X, Chang RL, Papin J, Yu H, Balaji S, Salehi-Ashtiani K. 2016. Systems level analysis of the Chlamydomonas reinhardtii metabolic network reveals variability in evolutionary co-conservation. Molecular BioSystems 12:2394-2407 DOI 10.1039/c6mb00237d
8. Chang RL, Ghamsari L, Manichaikul A, Hom EF, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K, Papin JA. 2011. Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Molecular Systems Biology 7(518):Article 518 DOI 10.1038/msb.2011.52
9. Chen Q, Wang Z, Wei DQ. 2010. Progress in the applications of flux analysis of metabolic networks. Chinese Science Bulletin 55(22):2315-2322 DOI 10.1007/s11434-010-3022-x
10. ChlamyCyc 5.0. 2015. Plant metabolic network. Available at http:// www.plantcyc.org/ databases/ chlamycyc/ 5.0
11. 2-concentrating mechanism regulator CIA5/CCM1. The Plant Cell 24(5):1876-1893 DOI 10.1105/tpc.112.097949
12. Gianchandani EP, Chavali AK, Papin JA. 2010. The application of flux balance analysis in systems biology. Wiley Interdisciplinary Reviews: Systems Biology and Medicine 2(3):372-382 DOI 10.1002/wsbm.60
13. Harris EH. 2001. Chlamydomonas as a model organism. Annual Review of Plant Physiology and Plant Molecular Biology 52(1):363-406 DOI 10.1146/annurev.arplant.52.1.363
14. Ideker T, Krogan NJ. 2012. Differential network biology. Molecular Systems Biology 8:565 DOI 10.1038/msb.2011.99
15. Imam S, Schäuble S, Valenzuela J, Lõpez García De Lomana A, Carter W, Price NE, Baliga NS. 2015. A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. The Plant Journal 84(6):1239-1256 DOI 10.1111/tpj.13059
16. Kanehisa Laboratories. 2016. KEGG: Kyoto Encyclopedia of Genes and Genomes. Available at http://www.genome.jp/kegg/pathway.html?sess=2764b8338258d6286de91bbebe 6faf46
17. Kauffman KJ, Prakash P, Edwards JS. 2003. Advances in flux balance analysis. Current Opinion in Biotechnology 14(5):491-496 DOI 10.1016/j.copbio.2003.08.001
18. Kebeish R, Niessen M, Thiruveedhi K, Bari R, Hirsch H, Rosenkranz R, Stäbler N, Schönfeld B, Kreuzaler F, Peterhänsel C. 2007. Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana. Nature Biotechnology 25:593-599 DOI 10.1038/nbt1299
19. Kliphuis AMJ, Klok AJ, Martens DE, Lamers PP, Janssen M, Wijffels RH. 2012. Metabolic modeling of Chlamydomonas reinhardtii: energy requirements for photoautotrophic growth and maintenance. Journal of Applied Phycology 24(2):253-266 DOI 10.1007/s10811-011-9674-3
20. Kumar VS, Dasika M, Maranas CD. 2007. Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8:212 DOI 10.1016/j.sbi.2004.04.004
21. Lee E, Jalalizadeh M, Zhang Q. 2015. Growth kinetic models for microalgae cultivation: a review. Algal Res 12:497-512 DOI 10.1016/j.algal.2015.10.004
22. Mahadevan R, Edwards JS, Doyle FJ. 2002. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophysical Journal 83(3):1331-1340 DOI 10.1016/S0006-3495(02)73903-9
23. Mahadevan R, Schilling CH. 2003. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metabolic Engineering 5(4):264-276 DOI 10.1016/j.ymben.2003.09.002
24. Maranas C, Zomorrodi A. 2016. Optimization methods in metabolic networks. Hoboken: Wiley
25. Mavrovouniotis ML. 1990. Group contributions for estimating standard Gibbs energies of formation of biochemical compounds in aqueous solution. Biotechnology and Bioengineering 36(10):1070-1082 DOI 10.1002/bit.260361013
26. ModelSEED. 2015. Model seed genome-scale metabolic models. Available at http:// modelseed.org/
27. Moon M, Kim CW, Park WK, Yoo G, Choi YE, Yang JW. 2013. MixotrophicGrowth with acetate or volatile fatty acids maximizes growth and lipid production in Chlamydomonas reinhardtii. Algal Research 2(4):352-357 DOI 10.1016/j.algal.2013.09.003
28. 2 to increase the efficiency of photosynthetic carbon fixation? Plant Physiology 119(1):9-16 DOI 10.1104/pp.119.1.9
29. Moroney JV, Ynalvez RA. 2007. Proposed carbon dioxide concentrating mechanism in Chlamydomonas reinhardtii. Eukaryotic Cell 6(8):1251-1259 DOI 10.1128/EC.00064-07
30. Petersen TN, Brunak S, Von Heijne G, Nielsen H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods 8(10):785-786 DOI 10.1038/nmeth.1701
31. Rosenberg JN, Oyler GA, Wilkinson L, Betenbaugh MJ. 2008. A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution. Current Opinion in Biotechnology 19(5):430-436 DOI 10.1016/j.copbio.2008.07.008
32. Rupprecht J. 2009. From systems biology to fuel-Chlamydomonas reinhardtii as a model for a systems biology approach to improve biohydrogen production. Journal of Biotechnology 142(1):10-20 DOI 10.1016/j.jbiotec.2009.02.008
33. Sayre R. 2010. Microalgae: the potential for carbon capture. BioScience 60(9):722-727 DOI 10.1525/bio.2010.60.9.9
34. Schellenberger J, Lewis NE, Palsson BO. 2011. Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophysical Journal 100:544-553 DOI 10.1016/j.bpj.2010.12.3707
35. Schmidt BJ, Lin-Schmidt X, Chamberlin A, Salehi-Ashtiani K, Papin JA. 2010. Metabolic systems analysis to advance algal biotechnology. Biotechnol. J 5(7):660-670 DOI 10.1002/biot.201000129
36. Schmittgen TD, Livak KJ. 2008. Analyzing real-time PCR data by the comparative CT method. Nature Protocols 3(6):1101-1108 DOI 10.1038/nprot.2008.73
37. Scranton MA, Ostrand JT, Fields FJ, Mayfield SP. 2015. Chlamydomonas as a model for biofuels and bio-products production. The Plant Journal 82(3):523-531 DOI 10.1111/tpj.12780
38. Senger RS, Papoutsakis ET. 2008. Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. Biotechnology and Bioengineering 101(5):1036-1052 DOI 10.1002/bit.22010
39. Serrano-Bermúdez LM. 2016. Análisis de balance de flujo dinámico de la producción de 1, 3-propanodiol a partir de Clostridium sp. Bogota: Universidad Nacional de Colombia
40. Serrano-Bermúdez LM, González Barrios AF, Maranas CD, Montoya D. 2017. Clostridium butyricum maximizes growth while minimizing enzyme usage and atp production: metabolic flux distribution of a strain cultured in glycerol. BMC Systems Biology 11(1):58 DOI 10.1186/s12918-017-0434-0
41. Tebbani S, Titica M, Caraman S, Boillereaux L. 2013. Estimation of Chlamydomonas reinhardtii growth in a torus photobioreactor. In: 12th IFAC symposium on computer applications in biotechnology, 16-18, December 2013. The International Federation of Automatic Control: Mumbai
42. Winck FV, Páez Melo DO, González Barrios AF. 2013. Carbon acquisition and accumulation in microalgae Chlamydomonas: insights from 'omics' approaches. Journal of Proteomics 94:207-218 DOI 10.1016/j.jprot.2013.09.016
43. 2 pathways and genes related to carbon uptake and accumulation in Chlamydomonas reinhardtii through genomic scale modeling and experimental validation. Frontiers in Plant Science 7:1-12 DOI 10.3389/fpls.2016.00043
44. Yamano T, Fukuzawa H. 2009. Carbon-concentrating mechanism in a green alga, Chlamydomonas reinhardtii, revealed by transcriptome analyses. Journal of Basic Microbiology 49(1):42-51 DOI 10.1002/jobm.200800352
45. Zhang X-W, Chen F, Johns MR. 1999. Kinetic models for heterotrophic growth of Chlamydomonas reinhardtii in batch and fed-batch cultures. Process Biochemistry 35(3-4):385-389 DOI 10.1016/S0032-9592(99)00082-5