New features on the environmental regulation of metabolism revealed by modeling the cellular proteomic adaptations induced by light, carbon and inorganic nitrogen in Chlamydomonas reinhardtii
[en] Microalgae are currently emerging to be very promising organisms for the production of biofuels and high-added value compounds. Understanding the influence of environmental alterations on their metabolism is a crucial issue. Light, carbon and nitrogen availability have been reported to induce important metabolic adaptations. So far, the influence of these variables has essentially been studied while varying only one or two environmental factors at the same time. The goal of the present work was to model the cellular proteomic adaptations of the green microalga Chlamydomonas reinhardtii upon the simultaneous changes of light intensity, carbon concentrations (CO2 and acetate) and inorganic nitrogen concentrations (nitrate and ammonium) in the culture medium. Statistical design of experiments (DOE) enabled to define 32 culture conditions to be tested experimentally. Relative protein abundance was quantified by two dimensional differential in-gel electrophoresis (2D-DIGE). Additional assays for respiration, photosynthesis, and lipid and pigment concentrations were also carried out. A hierarchical clustering survey enabled to partition biological variables (proteins + assays) into eight co-regulated clusters. In most cases, the biological variables partitioned in the same cluster had already been reported to participate to common biological functions (acetate assimilation, bioenergetic processes, light harvesting, Calvin cycle and protein metabolism). The environmental regulation within each cluster was further characterized by a series of multivariate methods including principal component analysis and multiple linear regressions. This metadata analysis enabled to highlight the existence of a clear regulatory pattern for every cluster and to mathematically simulate the effects of light, carbon and nitrogen. The influence of these environmental variables on cellular metabolism is described in details and thoroughly discussed. This work provides an overview of the metabolic adaptations contributing to maintain cellular homeostasis upon extensive environmental changes. Some of the results presented here could be used as starting points for more specific fundamental or applied investigations.
New features on the environmental regulation of metabolism revealed by modeling the cellular proteomic adaptations induced by light, carbon and inorganic nitrogen in Chlamydomonas reinhardtii
Publication date :
2016
Journal title :
Frontiers in Plant Science
eISSN :
1664-462X
Publisher :
Frontiers Research Foundation, Lausanne, Switzerland
Allen, R., Trelease, R., and Thomas, T. (1988). Regulation of isocitrate lyase gene expression in sunflower. Plant Physiol. 86, 527-532. doi: 10.1104/pp.86.2.527
Badger, M., von Caemmerer, S., Ruuska, S., and Nakano, H. (2000). Electron flow to oxygen in higher plants and algae: rates and control of direct photoreduction (Mehler reaction) and rubisco oxygenase. Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci. 355, 1433-1446. doi: 10.1098/rstb.2000.0704
Bligh, E., and Dyer, W. (1959). A rapid method of total lipid extraction and purification. Can. J. Biochem. Physiol. 37, 911-917. doi: 10.1139/o59-099
Borkhsenious, O., Mason, C., and Moroney, J. (1998). The intracellular localization of ribulose-1,5-bisphosphate carboxylase/oxygenase in Chlamydomonas reinhardtii. Plant Physiol. 116, 1585-1591. doi: 10.1104/pp.116.4.1585
Boyle, N., and Morgan, J. (2009). Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii. BMC Syst. Biol. 3:4. doi: 10.1186/1752-0509-3-4
Brooks, A., Portis, A., and Sharkey, T. (1988). Effects of irradiance and methyl viologen treatment on ATP, ADP, and activation of ribulose bisphosphate carboxylase in spinach leaves. Plant Physiol. 88, 850-853. doi: 10.1104/pp.88.3.850
Browse, J., McCourt, P., and Somerville, C. (1986). Fatty acid composition of leaf lipids determined after combined digestion and fatty acid methyl ester formation from fresh tissue. Anal. Biochem. 152, 141-145. doi: 10.1016/0003- 2697(86)90132-6
Burnham, K., and Anderson, D. (2004). Multimodel inference. Understanding AIC and BIC in model selection. Sociol. Methods Res. 33, 261-304. doi: 10.1177/0049124104268644
Carpentier, S., Witters, E., Laukens, K., Deckers, P., Swennen, R., and Panis, B. (2005). Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two−dimensional gel electrophoresis analysis. Proteomics 5, 2497-2507. doi: 10.1002/pmic.200401222
Chen, F., and Johns, M. (1994). Substrate inhibition of Chlamydomonas reinhardtii by acetate in heterotrophic culture. Process Biochem. 29, 245-252. doi: 10.1016/0032-9592(94)80064-2
Chen, F., and Johns, M. (1996). Heterotrophic growth of Chlamydomonas reinhardtii on acetate in chemostat culture. Process Biochem. 31, 601-604. doi: 10.1016/S0032-9592(96)00006-4
Collos, Y., and Harrison, P. (2014). Acclimation and toxicity of high ammonium concentrations to unicellular algae. Mar. Pollut. Bull. 80, 8-23. doi: 10.1016/j.marpolbul.2014.01.006
Durnford, D., Price, J., McKim, S., and Sarchfield, M. (2003). Light-harvesting complex gene expression is controlled by both transcriptional and post-transcriptional mechanisms during photoacclimation in Chlamydomonas reinhardtii. Physiol. Plant. 118, 193-205. doi: 10.1034/j.1399-3054.2003.00078.x
Falkowski, P., and LaRoche, J. (1991). Acclimation to spectral irradiance in algae. J. Phycol. 27, 8-14. doi: 10.1111/j.0022-3646.1991.00008.x
Falkowski, P., and Raven, J. (2013). Aquatic Photosynthesis. Princeton, NJ: Princeton University Press.
Fernandez, E., Galvan, A., and Quesada, A. (2004). "Nitrogen assimilation and its regulation," in The Molecular Biology of Chloroplasts and Mitochondria in Chlamydomonas, eds J.-D. Rochaix, M. Goldschmidt-Clermont, and S. Merchant (Boston, MA: Springer), 637-659.
Finazzi, G., Johnson, G., Dall’Osto, L., Zito, F., Bonente, G., Bassi, R., et al. (2006). Nonphotochemical quenching of chlorophyll fluorescence in Chlamydomonas reinhardtii. Biochemistry 45, 1490-1498. doi: 10.1021/bi0521588
Foyer, C., and Noctor, G. (2003). Redox sensing and signalling associated with reactive oxygen in chloroplasts, peroxisomes and mitochondria. Physiol. Plant. 119, 355-364. doi: 10.1034/j.1399-3054.2003.00223.x
Foyer, C., Noctor, G., and Hodges, M. (2011). Respiration and nitrogen assimilation: targeting mitochondria-associated metabolism as a means to enhance nitrogen use efficiency. J. Exp. Bot. 62, 1467-1482. doi: 10.1093/jxb/erq453
Fukushima, A., Kusano, M., Redestig, H., Arita, M., and Saito, K. (2009). Integrated omics approaches in plant systems biology. Curr. Opin. Chem. Biol. 13, 532-538. doi: 10.1016/j.cbpa.2009.09.022
Gérin, S., Mathy, G., Blomme, A., Franck, F., and Sluse, F. (2010). Plasticity of the mitoproteome to nitrogen sources (nitrate and ammonium) in Chlamydomonas reinhardtii: the logic of Aox1 gene localization. Biochim. Biophys. Acta Bioener. 1797, 994-1003. doi: 10.1016/j.bbabio.2010.02.034
Gérin, S., Mathy, G., and Franck, F. (2014). Modeling the dependence of respiration and photosynthesis upon light, acetate, carbon dioxide, nitrate and ammonium in Chlamydomonas reinhardtii using design of experiments and multiple regression. BMC Syst. Biol. 8:96. doi: 10.1186/s12918-014-0096-0
Graham, I., Denby, K., and Leaver, C. (1994). Carbon catabolite repression regulates glyoxylate cycle gene expression in cucumber. Plant Cell 6, 761-772. doi: 10.1105/tpc.6.5.761
Greenbaum, D., Colangelo, C., Williams, K., and Gerstein, M. (2003). Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4:117. doi: 10.1186/gb-2003-4-9-117
Hahn, D., Kaltenbach, C., and Kück, U. (1998). The Calvin cycle enzyme sedoheptulose-1,7-bisphosphatase is encoded by a light-regulated gene in Chlamydomonas reinhardtii. Plant Mol. Biol. 36, 929-934. doi: 10.1023/A:1005911022601
Harris, E. (2001). Chlamydomonas as a model organism. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52, 363-406. doi: 10.1146/annurev.arplant.52.1.363
Hauser, T., Popilka, L., Hartl, F., and Hayer-Hartl, M. (2015). Role of auxiliary proteins in Rubisco biogenesis and function. Nat. Plants 1:15065. doi: 10.1038/nplants.2015.65
Höhner, R., Barth, J., Magneschi, L., Jaeger, D., Niehues, A., Bald, T., et al. (2013). The metabolic status drives acclimation of iron deficiency responses in Chlamydomonas reinhardtii as revealed by proteomics based hierarchical clustering and reverse genetics. Mol. Cell. Proteomics 12, 2774-2790. doi: 10.1074/mcp.M113.029991
Huppe, H., and Turpin, D. (1994). Integration of carbon and nitrogen metabolism in plant and algal cells. Annu. Rev. Plant Physiol. Plant Mol. Biol. 45, 577-607. doi: 10.1146/annurev.pp.45.060194.003045
Hüttemann, M., Lee, I., Samavati, L., Yu, H., and Doan, J. (2007). Regulation of mitochondrial oxidative phosphorylation through cell signaling. Biochim. Biophys. Acta Mol. Cell Res. 1773, 1701-1720. doi: 10.1016/j.bbamcr.2007.10.001
Hyams, J., and Davies, D. (1972). The induction and characterization of cell wall mutants of Chlamydomonas reinhardi. Mutat. Res. 14, 381-389. doi: 10.1016/0027-5107(72)90135-2
Jezek, P., Engstova, H., Zackova, M., Vercesi, A., Costa, A., Arruda, P., et al. (1998). Fatty acid cycling mechanism and mitochondrial uncoupling proteins. Biochim. Biophys. Acta Bioener. 1365, 319-327. doi: 10.1016/S0005-2728(98)00 084-X
Johnson, X., and Alric, J. (2012). Interactions between starch breakdown, acetate assimilation and cyclic electron flow in Chlamydomonas reinhardtii. J. Biol. Chem. 287, 26445-26452. doi: 10.1074/jbc.M112.370205
Kupriyanova, E., Sinetova, M., Cho, S., Park, Y., Los, D., and Pronina, N. (2013). CO2-concentrating mechanism in cyanobacterial photosynthesis: organization, physiological role, and evolutionary origin. Photosyn. Res. 117, 133-146. doi: 10.1007/s11120-013-9860-z
Lamb, R., Bonuccelli, G., Ozsvari, B., Peiris-Pages, M., Fiorillo, M., Smith, D., et al. (2015). Mitochondrial mass, a new metabolic biomarker for stem-like cancer cells: Understanding WNT/FGF-driven anabolic signaling. Oncotarget 6, 30453. doi: 10.18632/oncotarget.5852
Lee, D., Park, J., Barupal, D., and Fiehn, O. (2012). System response of metabolic networks in Chlamydomonas reinhardtii to total available ammonium. Mol. Cell. Proteomics 11, 973-988. doi: 10.1074/mcp.M111.0 16733
Lemaire, S., Guillon, B., Le Maréchal, P., Keryer, E., Miginiac-Maslow, M., and Decottignies, P. (2004). New thioredoxin targets in the unicellular photosynthetic eurkaryote Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. U.S.A. 101, 7475-7480. doi: 10.1073/pnas.0402221101
Lichtenthaler, H., and Wellburn, A. (1983). Determinations of total carotenoids and chlorophyll a and b in leaf extracts in different solvents. Biochem. Soc. Trans. 11, 591-592. doi: 10.1042/bst0110591
Lowry, O., Rosebrough, N., Farr, A., and Randall, R. (1951). Protein measurement with the Folin phenol reagent. J. Biol. Chem. 193, 165-175.
Marouga, R., David, S., and Hawkins, E. (2005). The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal. Bioanal. Chem. 382, 669-678. doi: 10.1007/s00216-005-3126-3
Mathy, G., Cardol, P., Dinant, M., Blomme, A., Gérin, S., Cloes, M., et al. (2010). Proteomic and functional characterization of a Chlamydomonas reinhardtii mutant lacking the mitochondrial alternative oxidase 1. J. Proteome Res. 9, 2825-2838. doi: 10.1021/pr900866e
Mathy, G., and Sluse, F. (2008). Mitochondrial comparative proteomics: strengths and pitfalls. Biochim. Biophys. Acta Bioener. 1777, 1072-1077. doi: 10.1016/j.bbabio.2008.04.042
May, C., Brosseron, F., Chartowski, P., Meyer, H., and Marcus, K. (2012). "Differential proteome analysis using 2D-DIGE," in Methods in Molecular Biology, ed K. Marcus (Clifton, NJ: Humana Press), 75-82.
May, P., Christian, J., Kempa, S., and Walther, D. (2009). ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics 10:209. doi: 10.1186/1471-2164-10-209
Merchant, S., Prochnik, S., Vallon, O., Harris, E., Karpowicz, S., Witman, G., et al. (2007). The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318, 245-250. doi: 10.1126/science.11 43609
Miller, R., Wu, G., Deshpande, R., Vieler, A., Gärtner, K., Li, X., et al. (2010). Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism. Plant Physiol. 154, 1737-1752. doi: 10.1104/pp.110.165159
Mitchell, M., Meyer, M., and Griffiths, H. (2014). Dynamics of carbon-concentrating mechanism induction and protein relocalization during the dark-to-light transition in synchronized Chlamydomonas reinhardtii. Plant Physiol. 166, 1073-1082. doi: 10.1104/pp.114.246918
Mochida, K., and Shinozaki, K. (2011). Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol. 52, 2017-2038. doi: 10.1093/pcp/pcr153
Moroney, J., Ma, Y., Frey, W., Fusilier, K., Pham, T., Simms, T., et al. (2011). The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles. Photosyn. Res. 109, 133-149. doi: 10.1007/s11120-011-9635-3
Murphy, D. (1986). The molecular organization and function of the photosynthetic membranes of higher plants. Biochim. Biophys. Acta Rev. Biomembranes 864, 33-94. doi: 10.1016/0304-4157(86)90015-8
Neale, P., and Melis, A. (1986). Algal photosynthetic membrane complexes and the photosynthesis-irradiance curve: a comparison of light adaptation responsesin Chlamydomonas reinhardtii (Chlorophyta). J. Phycol. 22, 531-538. doi: 10.1111/j.1529-8817.1986.tb02497.x
Nield, J., Redding, K., and Hippler, M. (2004). Remodeling of light-harvesting protein complexes in Chlamydomonas in response to environmental changes. Eukaryotic Cell 3, 1370-1380. doi: 10.1128/EC.3.6.1370-1380.2004
Nogales, J., Guijo, M., Quesada, A., and Merchan, F. (2004). Functional analysis and regulation of the malate synthase from Chlamydomonas reinhardtii. Planta 219, 325-331. doi: 10.1007/s00425-004-1223-8
Perchorowicz, J., Raynes, D., and Jensen, R. (1981). Light limitation of photosynthesis and cativation of ribulose bisphosphate carboxylase in wheat seedlings. Proc. Natl. Acad. Sci. U.S.A. 78, 2985-2989. doi: 10.1073/pnas.78.5.2985
Perez-Garcia, O., Escalante, F., de-Bashan, L., and Bashan, Y. (2011). Heterotrophic cultures of microalgae: metabolism and potential products. Water Res. 45, 11-36. doi: 10.1016/j.watres.2010.08.037
Petridou, S., Foster, K., and Kindle, K. (1997). Light induces accumulation of isocitrate lyase mRNA in a carotenoid-deficient mutant of Chlamydomonas reinhardtii. Plant Mol. Biol. 33, 381-392. doi: 10.1023/A:1005728411921
Plumley, F., and Schmidt, G. (1989). Nitrogen-dependent regulation of photosynthetic gene expression. Proc. Natl. Acad. Sci. U.S.A. 86, 2678-2682. doi: 10.1073/pnas.86.8.2678
Raines, C. (2003). The Calvin cycle revisited. Photosyn. Res. 75, 1-10. doi: 10.1023/A:1022421515027
Rajaram, H., and Apte, S. (2008). Nitrogen status and heat-stress-dependent differential expression of the cpn60 chaperonin gene influences thermotolerance in the cyanobacterium Anabaena. Microbiology 154, 317-325. doi: 10.1099/mic.0.2007/011064-0
Roberts, M. (2003). 14-3-3 proteins find new partners in plant cell signalling. Trends Plant Sci. 8, 218-223. doi: 10.1016/S1360-1385(03)00056-6
Sager, R., and Granick, S. (1953). Nutritional studies with Chlamydomonas reinhardi. Ann. N.Y. Acad. Sci. 56, 831-838. doi: 10.1111/j.1749- 6632.1953.tb30261.x
SAS (2012). JMP 10 Modeling and Multivariate Methods. Cary, NC: SAS Institute. SAS (2013). JMP 11 Multivariate Methods. Cary, NC: SAS Institute.
Schroda, M., Vallon, O., Wollman, F., and Beck, C. (1999). A chloroplast-targeted protein 70 (HSP70) contributes to the photoprotection and repair of photosystem II during and after photoinhibition. Plant Cell 11, 1165-1178. doi: 10.1105/tpc.11.6.1165
Schuster, G., Timberg, R., and Ohad, I. (1988). Turnover of thylakoid photosystem II proteins during photoinhibition of Chlamydomonas reinhardtii. Eur. J. Biochem. 177, 403-410. doi: 10.1111/j.1432-1033.1988.tb14389.x
Shevchenko, A., Henrik Tomas, J., Olsen, J., and Mann, M. (1996). In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 1, 2856-2860. doi: 10.1038/nprot.2006.468
Singh, A., Elvitigala, T., Bhattacharyya-Pakrasi, M., Aurora, R., Ghosh, B., and Pakrasi, H. (2008). Integration of carbon and nitrogen metabolism with energy production is crucial to energy acclimation in the cyanobacterium Synechocystis. Plant Physiol. 148, 467-478. doi: 10.1104/pp.108.123489
Smirnoff, N. (2011). Vitamin C: the metabolism and functions of ascorbic acid in plants. Adv. Bot. Res. 59, 107-177. doi: 10.1016/B978-0-12-385853-5.00003-9
Spalding, M. (2009). "The CO2-concentrating mechanism and carbon assimilation," in The Chlamydomonas Sourcebook. Organellar and Metabolic Processes, 2 Edn. ed D. Stern (Boston, MA: Elsevier Academic Press), 257-301.
Spalding, M., Van, K., Wang, Y., and Nakamura, Y. (2002). Acclimation of Chlamydomonas to changing carbon availability. Funct. Plant Biol. 29, 221-230. doi: 10.1071/PP01182
Sueltemeyer, D., Klug, K., and Fock, H. (1986). Effect of photon fluence rate on oxygen evolution and uptake by Chlamydomonas reinhardtii suspensions grown in ambient and CO2-enriched air. Plant Physiol. 81, 372-375. doi: 10.1104/pp.81.2.372
Teramoto, H., Nakamori, A., Minagawa, J., and Ono, T. (2002). Light-intensity-dependent expression of Lhc gene family encoding light-harvesting chlorophyll-a/b proteins of photosystem II in Chlamydomonas reinhardtii. Plant Physiol. 130, 325-333. doi: 10.1104/pp.004622
Tobin, E., and Silverthorne, J. (1985). Light regulation of gene expression in higher plants. Annu. Rev. Plant Physiol. 36, 569-593. doi: 10.1146/annurev.pp.36.060185.003033
Trebst, A. (2003). Function of β-carotene and tocopherol in photosystem II. Zeitschrift fur Naturforschung C J. Biosci. 58, 609-620. doi: 10.1515/znc-2003-9-1001
Turpin, D. (1991). Effects of inorganic N availability on algal photosynthesis and carbon metabolism. J. Phycol. 27, 14-20. doi: 10.1111/j.0022-3646.1991.00014.x
Vance, P., and Spalding, M. (2005). Growth, photosynthesis, and gene expression in Chlamydomonas over a range of CO2 concentrations and CO2/O2 ratios: CO2 regulates multiple acclimation states. Can. J. Bot. 83, 796-809. doi: 10.1139/b05-064
Von Gromoff, E., Treier, U., and Beck, C. (1989). Three light-inducible heat shock genes of Chlamydomonas reinhardtii. Mol. Cell. Biol. 9, 3911-3918. doi: 10.1128/MCB.9.9.3911
Wang, Y., Duanmu, D., and Spalding, M. (2011). Carbon dioxide concentrating mechanism in Chlamydomonas reinhardtii: inorganic carbon transport and CO2 recapture. Photosyn. Res. 109, 115-122. doi: 10.1007/s11120-011-9643-3
Ward, J. Jr. (1963). Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc. 58, 236-244. doi: 10.1080/01621459.1963.10500845
White, A., and Critchley, C. (1999). Rapid light curves: a new fluorescence method to assess the state of the photosynthetic apparatus. Photosyn. Res. 59, 63-72. doi: 10.1023/A:1006188004189
Work, V., D’Adamo, S., Radakovits, R., Jinkerson, R., and Posewitz, M. (2012). Improving photosynthesis and metabolic networks for the competitive production of phototroph-derived biofuels. Curr. Opin. Biotechnol. 23, 290-297. doi: 10.1016/j.copbio.2011.11.022
Xue, X., Gauthier, D., Turpin, D., and Weger, H. (1996). Interactions between photosynthesis and respiration in the green alga Chlamydomonas reinhardtii. Characterization of light-enhanced dark respiration. Plant Physiol. 112, 1005-1014.
Yang, Y., and Gao, K. (2003). Effects of CO2 concentrations on the freshwater microalgae, Chlamydomonas reinhardtii, Chlorella pyrenoidosa and Scenedesmus obliquus (Chlorophyta). J. Appl. Phycol. 15, 379-389. doi: 10.1023/A:1026021021774
