Analysis of sensitive CO2 pathways and genes related to carbon uptake and accumulation in chlamydomonas reinhardtii through genomic scale modeling and experimental validation

Frontiers in Plant Science

Volumn 7, Issue FEB2016, 2016, Pages

  Winck, Flavia V ^a,c   Páez Melo, David O ^a   Riaño Pachón, Diego M ^a,b   Martins, Marina C M ^b   Caldana, Camila ^b   González Barrios, Andrés F ^a  

^a UNIVERSIDAD DE LOS ANDES   (Colombia)

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

^c UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Bioenergy; Biomass; Biotechnology; Carbon uptake; Chlamydomonas; Flux balance analysis; Microalgae; Systems biology

Indexed keywords

EID: 84958568194     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2016.00043     Document Type: Article

References (41)

1. Araújo, W. L., Nunes-Nesi, A., and Fernie, A. R. (2014). On the role of plant mitochondrial metabolism and its impact on photosynthesis in both optimal and sub-optimal growth conditions. Photosyn. Res. 119, 141-156. doi: 10.1007/s11120-013-9807-4.
2. Badger, M. R., Kaplan, A., and Berry, J. A. (1980). Internal inorganic carbon pool ofChlamydomonas reinhardtii: evidence for a carbon dioxide-concentrating mechanism. Plant Physiol. 66, 407-413. doi: 10.1104/pp.66.3.407.
3. Behera, S., Singh, R., Arora, R., Sharma, N. K., Shukla, M., and Kumar, S. (2014). Scope of algae as third generation biofuels. Front. Bioeng. Biotechnol. 2:90. doi: 10.3389/fbioe.2014.00090.
4. Boyle, N. R., and Morgan, J. A. (2009). Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii. BMC Syst. Biol. 3:4. doi: 10.1186/1752-0509-3-4.
5. Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254. doi: 10.1016/0003-2697(76)90527-3.
6. 2deprivation coincides with massive transcriptional restructuring in Chlamydomonas reinhardtii. Plant Cell 24, 1860-1875. doi: 10.1105/tpc.111.093435.
7. Carvalho, A. P., Meireles, L. A., and Malcata, F. X. (2006). Microalgal reactors: a review of enclosed system designs and performances. Biotechnol. Prog. 22, 1490-1506. doi: 10.1002/bp060065r.
8. Chang, R. L., Ghamsari, L., Manichaikul, A., Hom, E. F., Balaji, S., Fu, W., et al. (2011). Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism. Mol. Syst. Biol. 7, 518. doi: 10.1038/msb.2011.52.
9. Cuadros-Inostroza, A., Caldana, C., Redestig, H., Kusano, M., Lisec, J., Peña-Cortés, H., et al. (2009). TargetSearch-a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinformatics 10:428. doi: 10.1186/1471-2105-10-428.
10. Dishisha, T., Pereyra, L. P., Pyo, S. H., Britton, R. A., and Hatti-Kaul, R. (2014). Flux analysis of the Lactobacillus reuteri propanediol-utilization pathway for production of 3-hydroxypropionaldehyde, 3-hydroxypropionic acid and 1, 3-propanediol from glycerol. Microb. Cell Fact. 13:76. doi: 10.1186/1475-2859-13-76.
11. Edwards, J. S., Covert, M., and Palsson, B. (2002). Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol. 4, 133-140. doi: 10.1046/j.1462-2920.2002.00282.x.
12. 2-concentrating mechanism regulator CIA5/CCM1. Plant Cell 24, 1876-1893. doi: 10.1105/tpc.112.097949.
13. Giavalisco, P., Li, Y., Matthes, A., Eckhardt, A., Hubberten, H. M., Hesse, H., et al. (2011). Elemental formula annotation of polar and lipophilic metabolites using (13) C, (15) N and (34) S isotope labelling, in combination with high-resolution mass spectrometry. Plant J. 68, 364-376. doi: 10.1111/j.1365-313X.2011.04682.x.
14. Harris, E. H. (2001). Chlamydomonas as a model organism. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52, 363-406. doi: 10.1146/annurev.arplant.52.1.363.
15. Henriques, M., Silva, A., and Rocha, J. (2007). "Extraction and quantification of pigments from a marine microalga: a simple and reproducible method," inCommunicating Current Research and Educational Topics and Trends in Applied Microbiology, Vol. 2, ed A. Méndez-Vilas (Badajoz: Formatex), 586-593.
16. Hoegh-Guldberg, O., and Bruno, J. F. (2010). The impact of climate change on the world's marine ecosystems. Science 328, 1523-1528. doi: 10.1126/science.1189930.
17. Kanehisa, M., and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes.Nucleic Acids Res. 28, 27-30. doi: 10.1093/nar/28.1.27.
18. Li, Y., Han, D., Hu, G., Dauvillee, D., Sommerfeld, M., Ball, S., et al. (2010). Chlamydomonas starchless mutant defective in ADP-glucose pyrophosphorylase hyper-accumulates triacylglycerol. Metab. Eng. 12, 387-391. doi: 10.1016/j.ymben.2010.02.002.
19. Lisec, J., Schauer, N., Kopka, J., Willmitzer, L., and Fernie, A. R. (2006). Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat. Protoc. 1, 387-396. doi: 10.1038/nprot.2006.59.
20. Matsumoto, M., Yokouchi, H., Suzuki, N., Ohata, H., and Matsunaga, T. (2003). Saccharification of marine microalgae using marine bacteria for ethanol production.Appl. Biochem. Biotechnol. 105-108, 247-254. doi: 10.1385/ABAB:105:1-3:247.
21. Mavrovouniotis, M. L. (1990). Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution. Biotechnol. Bioeng. 36, 1070-1082. doi: 10.1002/bit.260361013.
22. 2 levels for Chlamydomonas reinhardtii utilizing a flux balance analysis approach," in Advances in Computational Biology, eds L. F. Castillo, M. Cristancho, G. Isaza, A. Pinzón, and J. M. C. Rodríguez (Springer International Publishing), 279-285.
23. O'Neill, B. C., and Oppenheimer, M. (2002). Climate change: dangerous climate impacts and the Kyoto protocol. Science 296, 1971-1972. doi: 10.1126/science.1071238.
24. Orth, J. D., Thiele, I., and Palsson, B. Ø. (2010). What is flux balance analysis? Nat. Biotechnol. 28, 245-248. doi: 10.1038/nbt.1614.
25. Packer, A., Li, Y., Andersen, T., Hu, Q., Kuang, Y., and Sommerfeld, M. (2011). Growth and neutral lipid synthesis in green microalgae: a mathematical model.Bioresour. Technol. 102, 111-117. doi: 10.1016/j.biortech.2010.06.029.
26. Perez-Garcia, O., Villas-Boas, S. G., Swift, S., Chandran, K., and Singhal, N. (2014). Clarifying the regulation of NO/N2O production in Nitrosomonas europaea during anoxic-oxic transition via flux balance analysis of a metabolic network model. Water Res. 60, 267-277. doi: 10.1016/j.watres.2014.04.049.
27. Petersen, T. N., Brunak, S., von Heijne, G., and Nielsen, H. (2011). SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785-786. doi: 10.1038/nmeth.1701.
28. Pfaffl, M. W. (2001). A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29:e45. doi: 10.1093/nar/29.9.e45.
29. Rosenberg, J. N., Oyler, G. A., Wilkinson, L., and Betenbaugh, M. J. (2008). A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution.Curr. Opin. Biotechnol. 19, 430-436. doi: 10.1016/j.copbio.2008.07.008.
30. Rutledge, R. G. (2011). A Java program for LRE-based real-time qPCR that enables large-scale absolute quantification. PLoS ONE 6:e17636. doi: 10.1371/journal.pone.0017636.
31. Rutledge, R. G., and Stewart, D. (2008). A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR. BMC Biotechnol. 8:47. doi: 10.1186/1472-6750-8-47.
32. Savage, N. (2011). Algae: the scum solution. Nature 474, S15-S16. doi: 10.1038/ 474S015a.
33. Sayers, E. W., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., et al. (2009). Database resources of the national center for biotechnology information.Nucleic Acids Res. 37, D5-D15. doi: 10.1093/nar/gkp382.
34. Scranton, M. A., Ostrand, J. T., Fields, F. J., and Mayfield, S. P. (2015). Chlamydomonas as a model for biofuels and bio-products production. Plant J. 82, 523-531. doi: 10.1111/tpj.12780.
35. Singh, A., and Olsen, S. I. (2011). A critical review of biochemical conversion, sustainability and life cycle assessment of algal biofuels. Appl. Energy 88, 3548-3555. doi: 10.1016/j.apenergy.2010.12.012.
36. Singh, A., Olsen, S. I., and Nigam, P. S. (2011). A viable technology to generate third-generation biofuel. J. Chem. Technol. Biotechnol. 86, 1349-1353. doi: 10.1002/jctb.2666.
37. Sorokin, C., and Krauss, R. W. (1958). The effects of light intensity on the growth rates of green algae. Plant Physiol. 33, 109-113. doi: 10.1104/pp.33.2.109.
38. Stitt, M., Lilley, R. M., Gerhardt, R., and Heldt, H. W. (1989). Metabolite levels in specific cells and subcellular compartments of plant leaves. Methods Enzymol. 174, 518-552.
39. 2recapture. Photosyn. Res. 109, 115-122. doi: 10.1007/s11120-011-9643-3.
40. Weckwerth, W., Wenzel, K., and Fiehn, O. (2004). Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics 4, 78-83. doi: 10.1002/pmic.200200500.
41. Winck, F. V., Arvidsson, S., Riaño-Pachón, D. M., Hempel, S., Koseska, A., Nikoloski, Z., et al. (2013). Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation. PLoS ONE 8:e79909. doi: 10.1371/journal.pone.0079909.