[en] Nitrogen stress is a common strategy employed to stimulate lipid accumulation in microalgae, a biofuel feedstock of topical interest. Although widely investigated, the underlying mechanism of this strategy is still poorly understood. We examined the proteome response of lipid accumulation in the model diatom, Phaeodactylum tricornutum (CCAP 1055/1), at an earlier stage of exposure to selective nitrogen exclusion than previously investigated, and at a time point when changes would reflect lipid accumulation more than carbohydrate accumulation. In total 1043 proteins were confidently identified (≥ 2 unique peptides) with 645 significant (p < 0.05) changes observed, in the LC-MS/MS based iTRAQ investigation. Analysis of significant changes in KEGG pathways and individual proteins showed that under nitrogen starvation P. tricornutum reorganizes its proteome in favour of nitrogen scavenging and reduced lipid degradation whilst rearranging the central energy metabolism that deprioritizes photosynthetic pathways. By doing this, this species appears to increase nitrogen availability inside the cell and limit its use to the pathways where it is needed most. Compared to previously published proteomic analysis of nitrogen starvation in Chlamydomonas reinhardtii, central energy metabolism and photosynthesis appear to be affected more in the diatom, whilst the green algae appears to invest its energy in reorganizing respiration and the cellular organization pathways.
Disciplines :
Biotechnology
Author, co-author :
LONGWORTH, Joseph ; ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
Wu, Danying; ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
Huete-Ortega, María; ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
Wright, Phillip C; ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
Vaidyanathan, Seetharaman; ChELSI Institute, Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
External co-authors :
yes
Language :
English
Title :
Proteome response of Phaeodactylum tricornutum, during lipid accumulation induced by nitrogen depletion.
Brennan L., Owende P. Biofuels from microalgae-a review of technologies for production, processing, and extractions of biofuels and co-products. Renew. Sust. Energ. Rev. 2010, 14:557-577. 10.1016/j.rser.2009.10.009.
Demirbas A., Fatih Demirbas M. Importance of algae oil as a source of biodiesel. Energy Convers. Manag. 2011, 52:163-170. 10.1016/j.enconman.2010.06.055.
Mata T.M., Martins A.A., Caetano N.S. Microalgae for biodiesel production and other applications: a review. Renew. Sust. Energ. Rev. 2010, 14:217-232. 10.1016/j.rser.2009.07.020.
Griffiths M.J., Harrison S.T.L. Lipid productivity as a key characteristic for choosing algal species for biodiesel production. J. Appl. Phycol. 2009, 21:493-507. 10.1007/s10811-008-9392-7.
Lee D.Y., Park J.-J., Barupal D.K., Fiehn O. System response of metabolic networks in Chlamydomonas reinhardtii to total available ammonium. Mol. Cell. Proteomics 2012, 11:973-988. 10.1074/mcp.M111.016733.
Longworth J., Noirel J., Pandhal J., Wright P.C., Vaidyanathan S. HILIC- and SCX-based quantitative proteomics of Chlamydomonas reinhardtii during nitrogen starvation induced lipid and carbohydrate accumulation. J. Proteome Res. 2012, 11:5959-5971. 10.1021/pr300692t.
Nguyen H.M., Baudet M., Cuiné S., Adriano J.-M., Barthe D., Billon E., Bruley C., Beisson F., Peltier G., Ferro M., Li-Beisson Y. Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: with focus on proteins involved in lipid metabolism. Proteomics 2011, 11:4266-4273. 10.1002/pmic.201100114.
Wang H., Alvarez S., Hicks L.M. Comprehensive comparison of iTRAQ and label-free LC-based quantitative proteomics approaches using two Chlamydomonas reinhardtii strains of interest for biofuels engineering. J. Proteome Res. 2011, 11:487-501. 10.1021/pr2008225.
Wase N., Black P.N., Stanley B.A., DiRusso C.C. Integrated quantitative analysis of nitrogen stress response in Chlamydomonas reinhardtii using metabolite and protein profiling. J. Proteome Res. 2014, 13:1373-1396. 10.1021/pr400952z.
Gimpel J.A., Specht E.A., Georgianna D.R., Mayfield S.P. Advances in microalgae engineering and synthetic biology applications for biofuel production. Curr. Opin. Chem. Biol. 2013, 17:489-495. 10.1016/j.cbpa.2013.03.038.
Tirichine L., Bowler C. Decoding algal genomes: tracing back the history of photosynthetic life on earth. Plant J. 2011, 66:45-57. 10.1111/j.1365-313X.2011.04540.x.
Maheswari U., Jabbari K., Petit J.-L., Porcel B.M., Allen A.E., Cadoret J.-P., De Martino A., Heijde M., Kaas R., La Roche J., Lopez P.J., Martin-Jézéquel V., Meichenin A., Mock T., Schnitzler Parker M., Vardi A., Armbrust E.V., Weissenbach J., Katinka M., Bowler C. Digital expression profiling of novel diatom transcripts provides insight into their biological functions. Genome Biol. 2010, 11. 10.1186/gb-2010-11-8-r85.
Wilson J.H. The food value of Phaeodactylum tricornutum Bohlin to the larvae of Ostrea edulis L. and Crassostrea gigas Thunberg. Aquaculture 1978, 13:313-323. 10.1016/0044-8486(78)90178-3.
Bowler C., De Martino A., Falciatore A. Diatom cell division in an environmental context. Curr. Opin. Plant Biol. 2010, 13:623-630. 10.1016/j.pbi.2010.09.014.
Gleick P.H., Palaniappan M. Peak water limits to freshwater withdrawal and use. PNAS 2010, 107:11155-11162. 10.1073/pnas.1004812107.
Song M., Pei H., Hu W., Ma G. Evaluation of the potential of 10 microalgal strains for biodiesel production. Bioresour. Technol. 2013, 141:245-251. 10.1016/j.biortech.2013.02.024.
Armbrust E.V., Berges J.A., Bowler C., Green B.R., Martinez D., Putnam N.H., Zhou S., Allen A.E., Apt K.E., Bechner M., Brzezinski M.A., Chaal B.K., Chiovitti A., Davis A.K., Demarest M.S., Detter J.C., Glavina T., Goodstein D., Hadi M.Z., Hellsten U., Hildebrand M., Jenkins B.D., Jurka J., Kapitonov V.V., Kroger N., Lau W.W.Y., Lane T.W., Larimer F.W., Lippmeier J.C., Lucas S., Medina M., Montsant A., Obornik M., Parker M.S., Palenik B., Pazour G.J., Richardson P.M., Rynearson T.A., Saito M.A., Schwartz D.C., Thamatrakoln K., Valentin K., Vardi A., Wilkerson F.P., Rokhsar D.S. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 2004, 306:79-86. 10.1126/science.1101156.
Hildebrand M., Davis A.K., Smith S.R., Traller J.C., Abbriano R. The place of diatoms in the biofuels industry. Biofuels 2012, 3:221-240. 10.4155/bfs.11.157.
Osborn H.L., Hook S.E. Using transcriptomic profiles in the diatom Phaeodactylum tricornutum to identify and prioritize stressors. Aquat. Toxicol. 2013, 138-139:12-25. 10.1016/j.aquatox.2013.04.002.
Yang Z.-K., Niu Y.-F., Ma Y.-H., Xue J., Zhang M.-H., Yang W.-D., Liu J.-S., Lu S.-H., Guan Y., Li H.-Y. Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation. Biotechnol. Biofuels 2013, 6. 10.1186/1754-6834-6-67.
Valenzuela J., Mazurie A., Carlson R.P., Gerlach R., Cooksey K.E., Peyton B.M., Fields M.W. Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum. Biotechnol. Biofuels 2012, 5:40. 10.1186/1754-6834-5-40.
Levitan O., Dinamarca J., Zelzion E., Lun D.S., Guerra L.T., Kim M.K., Kim J., Van Mooy B.A.S., Bhattacharya D., Falkowski P.G. Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress. Proc. Natl. Acad. Sci. U. S. A. 2015, 112:412-417. 10.1073/pnas.1419818112.
Schwanhäusser B., Busse D., Li N., Dittmar G., Schuchhardt J., Wolf J., Chen W., Selbach M. Global quantification of mammalian gene expression control. Nature 2011, 473:337-342. 10.1038/nature10098.
Foss E.J., Radulovic D., Shaffer S.A., Goodlett D.R., Kruglyak L., Bedalov A. Genetic variation shapes protein networks mainly through non-transcriptional mechanisms. PLoS Biol. 2011, 9:e1001144. 10.1371/journal.pbio.1001144.
Rogers S., Girolami M., Kolch W., Waters K.M., Liu T., Thrall B., Wiley S.H. Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models. Bioinformatics 2008, 24:2894-2900.
Dyhrman S.T., Jenkins B.D., Rynearson T.A., Saito M.A., Mercier M.L., Alexander H., Whitney L.P., Drzewianowski A., Bulygin V.V., Bertrand E.M., Wu Z., Benitez-Nelson C., Heithoff A. The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response. PLoS One 2012, 7:e33768. 10.1371/journal.pone.0033768.
Guarnieri M.T., Nag A., Yang S., Pienkos P.T. Proteomic analysis of Chlorella vulgaris: potential targets for enhanced lipid accumulation. J. Proteome 2013, 93:245-253. 10.1016/j.jprot.2013.05.025.
Guarnieri M.T., Nag A., Smolinski S.L., Darzins A., Seibert M., Pienkos P.T. Examination of triacylglycerol biosynthetic pathways via de novo transcriptomic and proteomic analyses in an unsequenced microalga. PLoS One 2011, 6:e25851. 10.1371/journal.pone.0025851.
Jamers A., Blust R., De Coen W. Omics in algae: paving the way for a systems biological understanding of algal stress phenomena?. Aquat. Toxicol. 2009, 92:114-121. 10.1016/j.aquatox.2009.02.012.
Lee B., Choi G.-G., Choi Y.-E., Sung M., Park M.S., Yang J.-W. Enhancement of lipid productivity by ethyl methane sulfonate-mediated random mutagenesis and proteomic analysis in Chlamydomonas reinhardtii. Korean J. Chem. Eng. 2014, 31:1036-1042. 10.1007/s11814-014-0007-5.
Li Y., Mu J., Chen D., Han F., Xu H., Kong F., Xie F., Feng B. Production of biomass and lipid by the microalgae Chlorella protothecoides with heterotrophic-Cu(II) stressed (HCuS) coupling cultivation. Bioresour. Technol. 2013, 148:283-292. 10.1016/j.biortech.2013.08.153.
Rolland N., Atteia A., Decottignies P., Garin J., Hippler M., Kreimer G., Lemaire S.D., Mittag M., Wagner V. Chlamydomonas proteomics. Curr. Opin. Microbiol. 2009, 12:285-291. 10.1016/j.mib.2009.04.001.
Park J.-J., Wang H., Gargouri M., Deshpande R.R., Skepper J.N., Holguin F.O., Juergens M.T., Shachar-Hill Y., Hicks L.M., Gang D.R. The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis. Plant J. 2015, 81:611-624. 10.1111/tpj.12747.
Carvalho R., Lettieri T. Proteomic analysis of the marine diatom Thalassiosira pseudonana upon exposure to benzo(a)pyrene. BMC Genomics 2011, 12:159. 10.1186/1471-2164-12-159.
Frigeri L.G., Radabaugh T.R., Haynes P.A., Hildebrand M. Identification of proteins from a cell wall fraction of the diatom Thalassiosira pseudonana: insights into silica structure formation. Mol. Cell. Proteomics 2006, 5:182-193. 10.1074/mcp.M500174-MCP200.
Grouneva I., Rokka A., Aro E.-M. The thylakoid membrane proteome of two marine diatoms outlines both diatom-specific and species-specific features of the photosynthetic machinery. J. Proteome Res. 2011, 10:5338-5353. 10.1021/pr200600f.
Hockin N.L., Mock T., Mulholland F., Kopriva S., Malin G. The response of diatom central carbon metabolism to nitrogen starvation is different from that of green algae and higher plants. Plant Physiol. 2012, 158:299-312. 10.1104/pp.111.184333.
Kettles N.L., Kopriva S., Malin G. Insights into the regulation of DMSP synthesis in the diatom Thalassiosira pseudonana through APR activity, proteomics and gene expression analyses on cells acclimating to changes in salinity, light and nitrogen. PLoS One 2014, 9:e94795. 10.1371/journal.pone.0094795.
Lobanov A.V., Fomenko D.E., Zhang Y., Sengupta A., Hatfield D.L., Gladyshev V.N. Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol. 2007, 8:R198. 10.1186/gb-2007-8-9-r198.
Nunn B.L., Ting Y.S., Malmström L., Tsai Y.S., Squier A., Goodlett D.R., Harvey H.R. The path to preservation: using proteomics to decipher the fate of diatom proteins during microbial degradation. Limnol. Oceanogr. 2010, 55:1790-1804. 10.4319/lo.2010.55.4.1790.
Ge F., Huang W., Chen Z., Zhang C., Xiong Q., Bowler C., Yang J., Xu J., Hu H. Methylcrotonyl-CoA carboxylase regulates triacylglycerol accumulation in the model diatom Phaeodactylum tricornutum. Plant Cell 2014, (tpc.114.124982). 10.1105/tpc.114.124982.
Chen Z., Yang M., Li C., Wang Y., Zhang J., Wang D., Zhang X., Ge F. Phosphoproteomic analysis provides novel insights into stress responses in Phaeodactylum tricornutum, a model diatom. J. Proteome Res. 2014, 13:2511-2523. 10.1021/pr401290u.
Rosenwasser S., van Creveld S.G., Schatz D., Malitsky S., Tzfadia O., Aharoni A., Levin Y., Gabashvili A., Feldmesser E., Vardi A. Mapping the diatom redox-sensitive proteome provides insight into response to nitrogen stress in the marine environment. PNAS 2014, 201319773. 10.1073/pnas.1319773111.
Yang Z.-K., Ma Y.-H., Zheng J.-W., Yang W.-D., Liu J.-S., Li H.-Y. Proteomics to reveal metabolic network shifts towards lipid accumulation following nitrogen deprivation in the diatom Phaeodactylum tricornutum. J. Appl. Phycol. 2014, 26:73-82. 10.1007/s10811-013-0050-3.
Evans C., Noirel J., Ow S.Y., Salim M., Pereira-Medrano A.G., Couto N., Pandhal J., Smith D., Pham T.K., Karunakaran E., Zou X., Biggs C.A., Wright P.C. An insight into iTRAQ: where do we stand now?. Anal. Bioanal. Chem. 2012, 404:1011-1027. 10.1007/s00216-012-5918-6.
Ow S.Y., Salim M., Noirel J., Evans C., Rehman I., Wright P.C. iTRAQ underestimation in simple and complex mixtures: "the good, the bad and the ugly,". J. Proteome Res. 2009, 8:5347-5355. 10.1021/pr900634c.
Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., Khainovski N., Pillai S., Dey S., Daniels S., Purkayastha S., Juhasz P., Martin S., Bartlet-Jones M., He F., Jacobson A., Pappin D.J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3:1154-1169.
Frada M.J., Burrows E.H., Wyman K.D., Falkowski P.G. Quantum requirements for growth and fatty acid biosynthesis in the marine diatom Phaeodactylum tricornutum (Bacillariophyceae) in nitrogen replete and limited conditions. J. Phycol. 2013, 49:381-388. 10.1111/jpy.12046.
Wellburn R.W. The spectral determination of chlorophylls a and b, as well as total carotenoids, using various solvents with spectrophotometers of different resolution. J. Plant Physiol. 1994, 144:307-313.
Gerhardt P., Murray R.G.E., Wood W.A., Krieg N.R. Methods for General and Molecular Bacteriology 1994, American Society for Microbiology.
Chen W., Zhang C., Song L., Sommerfeld M., Hu Q. A high throughput Nile red method for quantitative measurement of neutral lipids in microalgae. J. Microbiol. Methods 2009, 77:41-47. 10.1016/j.mimet.2009.01.001.
DAVID: Functional Annotation Result Summary, (n.d.). (accessed July 17, 2013). http://david.abcc.ncifcrf.gov/summary.jsp.
Huang D.W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2008, 4:44-57. 10.1038/nprot.2008.211.
Schmollinger S., Mühlhaus T., Boyle N.R., Blaby I.K., Casero D., Mettler T., Moseley J.L., Kropat J., Sommer F., Strenkert D., Hemme D., Pellegrini M., Grossman A.R., Stitt M., Schroda M., Merchant S.S. Nitrogen-sparing mechanisms in Chlamydomonas affect the transcriptome, the proteome, and photosynthetic metabolism. Plant Cell 2014, 26:1410-1435. 10.1105/tpc.113.122523.
Binns D., Dimmer E., Huntley R., Barrell D., O'Donovan C., Apweiler R. QuickGO: a web-based tool for gene ontology searching. Bioinformatics 2009, 25:3045-3046. 10.1093/bioinformatics/btp536.
Allen A.E., Vardi A., Bowler C. An ecological and evolutionary context for integrated nitrogen metabolism and related signaling pathways in marine diatoms. Curr. Opin. Plant Biol. 2006, 9:264-273. 10.1016/j.pbi.2006.03.013.
Allen A.E., Dupont C.L., Oborník M., Horák A., Nunes-Nesi A., McCrow J.P., Zheng H., Johnson D.A., Hu H., Fernie A.R., Bowler C. Evolution and metabolic significance of the urea cycle in photosynthetic diatoms. Nature 2011, 473:203-207. 10.1038/nature10074.
Le Bihan T., Martin S.F., Chirnside E.S., van Ooijen G., Barrios-Llerena M.E., O'Neill J.S., Shliaha P.V., Kerr L.E., Millar A.J. Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri. J. Proteome 2011, 74:2060-2070. 10.1016/j.jprot.2011.05.028.
Carvalho W.F., Granéli E. Contribution of phagotrophy versus autotrophy to Prymnesium parvum growth under nitrogen and phosphorus sufficiency and deficiency. Harmful Algae 2010, 9:105-115. 10.1016/j.hal.2009.08.007.
Lamb C.A., Dooley H.C., Tooze S.A. Endocytosis and autophagy: shared machinery for degradation. BioEssays 2013, 35:34-45. 10.1002/bies.201200130.
Shui W., Sheu L., Liu J., Smart B., Petzold C.J., Hsieh T., Pitcher A., Keasling J.D., Bertozzi C.R. Membrane proteomics of phagosomes suggests a connection to autophagy. PNAS 2008, 105:16952-16957. 10.1073/pnas.0809218105.
Rismani-Yazdi H., Haznedaroglu B.Z., Hsin C., Peccia J. Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation. Biotechnol. Biofuels 2012, 5:74. 10.1186/1754-6834-5-74.
Trentacoste E.M., Shrestha R.P., Smith S.R., Glé C., Hartmann A.C., Hildebrand M., Gerwick W.H. Metabolic engineering of lipid catabolism increases microalgal lipid accumulation without compromising growth. PNAS 2013, 110:19748-19753. 10.1073/pnas.1309299110.
Burrows E.H., Bennette N.B., Carrieri D., Dixon J.L., Brinker A., Frada M., Baldassano S.N., Falkowski P.G., Dismukes G.C. Dynamics of lipid biosynthesis and redistribution in the marine diatom Phaeodactylum tricornutum under nitrate deprivation. BioEnergy Res. 2012, 5:876-885. 10.1007/s12155-012-9201-7.
Tolonen A.C., Aach J., Lindell D., Johnson Z.I., Rector T., Steen R., Church G.M., Chisholm S.W. Global gene expression of Prochlorococcus ecotypes in response to changes in nitrogen availability. Mol. Syst. Biol. 2006, 2:53. 10.1038/msb4100087.
Candan N., Tarhan L. The correlation between antioxidant enzyme activities and lipid peroxidation levels in Mentha pulegium organs grown in Ca2+, Mg2+, Cu2+, Zn2+ and Mn2+ stress conditions. Plant Sci. 2003, 165:769-776. 10.1016/S0168-9452(03)00269-3.
McKew B.A., Lefebvre S.C., Achterberg E.P., Metodieva G., Raines C.A., Metodiev M.V., Geider R.J. Plasticity in the proteome of Emiliania huxleyi CCMP 1516 to extremes of light is highly targeted. New Phytol. 2013, 200:61-73. 10.1111/nph.12352.
Naumann B., Stauber E.J., Busch A., Sommer F., Hippler M. N-terminal processing of Lhca3 is a key step in remodeling of the photosystem I-light-harvesting complex under iron deficiency in Chlamydomonas reinhardtii. J. Biol. Chem. 2005, 280:20431-20441. 10.1074/jbc.M414486200.
Abe J., Kubo T., Takagi Y., Saito T., Miura K., Fukuzawa H., Matsuda Y. The transcriptional program of synchronous gametogenesis in Chlamydomonas reinhardtii. Curr. Genet. 2004, 46:304-315. 10.1007/s00294-004-0526-4.
