Abstract
The heterotrophic microalga Crypthecodinium cohnii is well known for its lipid accumulation, with a high proportion of docosahexaenoic acid (DHA). In this study, we report a novel screening approach to obtain mutants of C. cohnii with high growth and lipid content using the acetyl-CoA carboxylase (ACCase) inhibitor sethoxydim. C. cohnii mutants were generated using atmospheric and room-temperature plasma (ARTP) and then screened for two rounds in media supplemented with sethoxydim. These efforts led to the identification of mutant M-1-2, which had 24.32% higher growth and 7.05% higher lipid content than the wild type, demonstrating the effectiveness of the sethoxydim-based screening. Consistently, the M-1-2 mutant displayed a 16.15% increase in ACCase enzymatic activity and 1.53-fold upregulation of its ACCase-encoding gene based on comparative ACCase activity analysis and transcriptomic analysis, respectively. In addition, transcriptomic analysis showed that transcripts involved in fatty acid biosynthesis, energy, central carbohydrate, and amino acid metabolism were upregulated in the mutant compared to the wild type.
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De Swaaf ME, Sijtsma L, Pronk JT (2003) High-cell-density fed-batch cultivation of the docosahexaenoic acid producing marine alga Crypthecodinium cohnii. Biotechnol Bioeng 81(6):666–672. doi:10.1002/bit.10513
Dotray PA, DiTomaso JM, Gronwald JW, Wyse DL, Kochian LV (1993) Effects of acetyl-coenzyme A carboxylase inhibitors on root cell transmembrane electric potentials in graminicide-tolerant and -susceptible corn (Zea mays L.) Plant Physiol 103(3):919–924. doi:10.1104/pp.103.3.919
Dunahay TG, Jarvis EE, Dais SS, Roessler PG (1996) Manipulation of microalgal lipid production using genetic engineering. Appl Biochem Biotech 57–58(1):223–231. doi:10.1007/BF02941703
Dunahay TG, Jarvis EE, Roessler PG (1995) Genetic transformation of the diatoms Cyclotella cryptica and Navicula saprophila. J Phycol 31(6):1004–1012. doi:10.1111/j.0022-3646.1995.01004.x
Fatland BL, Nikolau BJ, Wurtele ES (2005) Reverse genetic characterization of cytosolic acetyl-CoA generation by ATP-citrate lyase in Arabidopsis. Plant Cell 17(1):182–203. doi:10.1105/tpc.104.026211
Gao M, Song X, Feng Y, Li W, Cui Q (2013) Isolation and characterization of Aurantiochytrium species: high docosahexaenoic acid (DHA) production by the newly isolated microalga, Aurantiochytrium sp. SD116. J Oleo Sci 62(3):143–151. doi:10.5650/jos.62.143
Glaser C, Lattka E, Rzehak P, Steer C, Koletzko B (2011) Genetic variation in polyunsaturated fatty acid metabolism and its potential relevance for human development and health. Matern Child Nut 7(Suppl 2):27–40. doi:10.1111/j.1740-8709.2011.00319.x
Greenspan P, Mayer EP, Fowler SD (1985) Nile red: a selective fluorescent stain for intracellular lipid droplets. J Cell Biol 100(100):965–973. doi:10.1083/jcb.100.3.965
Guo T, Tang Y, Xi YL, He AY, Sun BJ, Wu H, Liang DF, Jiang M, Ouyang P-K (2011) Clostridium beijerinckii mutant obtained by atmospheric pressure glow discharge producing high proportions of butanol and solvent yields. Biotechnol Lett 33(12):2379–2383. doi:10.1007/s10529-011-0702-9
Guruvaiah M, Narra M, Dixit G, Karawadia P, Shah D (2015) Isolation, screening and optimization of estuary region (Khambhat, Gujarat) microalgae for lipid/oil production. Int J Appl Sci Biotechnol 3(2):197–201. doi:10.3126/ijasbt.v3i2.12534
Hao G, Chen H, Wang L, Gu Z, Song Y, Zhang H, Chen W, Chen YQ (2014) Role of malic enzyme during fatty acid synthesis in the oleaginous fungus Mortierella alpina. Appl Environ Microbiol 80(9):2672–2678. doi:10.1128/AEM.00140-14
He LW, Zhang XJ, Wang G (2013) Expression analysis of phosphoenolpyruvate carboxykinase in Porphyra haitanensis (Rhodophyta) sporophytes and gametophytes. Phycol Res 61(3):172–179. doi:10.1111/pre.12005
Hsieh CH, Wu WT (2009) Cultivation of microalgae for oil production with a cultivation strategy of urea limitation. Bioresour Technol 100(17):3921–3926. doi:10.1016/j.biortech.2009.03.019
Hu Q, Sommerfeld M, Jarvis E, Ghirardi M, Posewitz M, Seibert M, Darzins A (2008) Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J 54(4):621–639. doi:10.1111/j.1365-313X.2008.03492.x
Huang GH, Chen F, Dong W, Zhang XW, Chen G (2010) Biodiesel production by microalgal biotechnology. Appl Energ 87(1):38–46. doi:10.1016/j.apenergy.2009.06.016
Humburg NE, Colby SR, Hill ER, Kitchen LM, Lym RG, McAvoy WJ, Prasad R (1989) Herbicide handbook of the Weed Science Society of America, ed 6 edn. Weed Science Society of America, Champaign-Urbana
Hynes MJ, Murray SL (2010) ATP-citrate lyase is required for production of cytosolic acetyl coenzyme A and development in Aspergillus nidulans. Eukaryot Cell 9(7):1039–1048. doi:10.1128/EC.00080-10
Jiang Y, Chen F (1999) Effects of salinity on cell growth and docosahexaenoic acid content of the heterotrophic marine microalga Crypthecodinium cohnii. J Ind Microbiol Biot 23(6):508–513. doi:10.1038/sj.jim.2900759
Jiang Y, Chen F, Liang SZ (1999) Production potential of docosahexaenoic acid by the heterotrophic marine dinoflagellate Crypthecodinium cohnii. Process Biochem 34(6–7):633–637. doi:10.1016/S0032-9592(98)00134-4
Klaus D, Ohlrogge JB, Neuhaus HE, Dormann P (2004) Increased fatty acid production in potato by engineering of acetyl-CoA carboxylase. Planta 219(3):389–396. doi:10.1007/s00425-004-1236-3
Kuratko CN, Salem N (2013) Docosahexaenoic acid from algal oil. Eur J Lipid Sci Tech 115(9):965–976. doi:10.1002/ejlt.201300060
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359. doi:10.1038/nmeth.1923
Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics 12(1):93–99. doi:10.1186/1471-2105-12-323
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079. doi:10.1093/bioinformatics/btp352
Li J, Niu X, Pei G, Sui X, Zhang X, Chen L, Zhang W (2015) Identification and metabolomic analysis of chemical modulators for lipid accumulation in Crypthecodinium cohnii. Bioresour Technol 191:362–368. doi:10.1016/j.biortech.2015.03.068
Li Z, Sun H, Mo X, Li X, Xu B, Tian P (2013) Overexpression of malic enzyme (ME) of Mucor circinelloides improved lipid accumulation in engineered Rhodotorula glutinis. Appl Microbiol Biotechnol 97(11):4927–4936. doi:10.1007/s00253-012-4571-5
Liu B, Sun Z, Ma X, Yang B, Jiang Y, Wei D, Chen F (2015a) Mutation breeding of extracellular polysaccharide-producing microalga Crypthecodinium cohnii by a novel mutagenesis with atmospheric and room temperature plasma. Int J Mol Sci 16(4):8201–8212. doi:10.3390/ijms16048201
Liu C, Zhang X, Rao ZM, Shao ML, Zhang LL, Wu D, Xu ZH, Li H (2015b) Mutation breeding of high 4-androstene-3,17-dione-producing Mycobacterium neoaurum ZADF-4 by atmospheric and room temperature plasma treatment. J Zhejiang Univ Sci B 16(4):286–295. doi:10.1631/jzus.B1400274
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25(4):402–408. doi:10.1006/meth.2001.1262
Lopes da Silva T, Reis A (2008) The use of multi-parameter flow cytometry to study the impact of n-dodecane additions to marine dinoflagellate microalga Crypthecodinium cohnii batch fermentations and DHA production. J Ind Microbiol Biotechnol 35(8):875–887. doi:10.1007/s10295-008-0360-7
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15(12):550. doi:10.1186/s13059-014-0550-8
Mühlroth A, Li K, Røkke G, Winge P, Olsen Y, Hohmann-Marriott MF, Vadstein O, Bones AM (2013) Pathways of lipid metabolism in marine algae, co-expression network, bottlenecks and candidate genes for enhanced production of EPA and DHA in species of Chromista. Mar Drugs 11(11):4662–4697. doi:10.3309/md11114662
Ma Y, Yang H, Chen X, Sun B, Du G, Zhou Z, Song J, Fan Y, Shen W (2015a) Significantly improving the yield of recombinant proteins in Bacillus subtilis by a novel powerful mutagenesis tool (ARTP): alkaline α-amylase as a case study. Protein Expres Purif 114:82–88. doi:10.1016/j.pep.2015.06.016
Ma Z, Tan Y, Cui G, Feng Y, Cui Q, Song X (2015b) Transcriptome and gene expression analysis of DHA producer Aurantiochytrium under low temperature conditions. Sci Rep 5:14446. doi:10.1038/srep14446
Pleissner D, Eriksen NT (2012) Effects of phosphorous, nitrogen, and carbon limitation on biomass composition in batch and continuous flow cultures of the heterotrophic dinoflagellate Crypthecodinium cohnii. Biotechnol Bioeng 109(8):2005–2016. doi:10.1002/bit.24470
Pora B, Zhou J (2012) Methods of mutagenesis of Schizochytrium sp. and variant strains produced thereof, WO, WO/2012/175027 A1
Qi F, Zhang M, Chen Y, Jiang X, Lin J, Cao X, Huang J (2016) A lignocellulosic hydrolysate-tolerant Aurantiochytrium sp. mutant strain for docosahexaenoic acid production. Bioresour Technol 227:221–226. doi:10.1016/j.biortech.2016.12.011
Qiang W, Ling-ran F, Luo W, Han-guang L, Lin W, Ya Z, Xiao-bin Y (2014) Mutation breeding of lycopene-producing strain Blakeslea trispora by a novel atmospheric and room temperature plasma (ARTP). Appl Biochem Biotechnol 174(1):452–460. doi:10.1007/s12010-014-0998-8
Reiskind JB, Bowes G (1991) The role of phosphoenolpyruvate carboxykinase in a marine macroalga with C4-like photosynthetic characteristics. Proc Natl Acad Sci U S A 88(7):2883–2887. doi:10.1073/pnas.88.7.2883
Robinson DG, Storey JD (2014) subSeq: determining appropriate sequencing depth through efficient read subsampling. Bioinformatics 30(23):3424–3426. doi:10.1093/bioinformatics/btu552
Santin-Montanya I, Sandin-Espana P, Garcia Baudin JM, Coll-Morales J (2007) Optimal growth of Dunaliella primolecta in axenic conditions to assay herbicides. Chemosphere 66(7):1315–1322. doi:10.1016/j.chemosphere.2006.07.019
Santos-Sánchez NF, Valadez-Blanco R, Hernández-Carlos B, Torres-Ariño A, Guadarrama-Mendoza PC, Salas-Coronado R (2016) Lipids rich in ω-3 polyunsaturated fatty acids from microalgae. Appl Microbiol Biotechnol 100(20):8667–8884. doi:10.1007/s00253-016-7818-8
Sasaki Y, Nagano Y (2004) Plant acetyl-CoA carboxylase: structure, biosynthesis, regulation, and gene manipulation for plant breeding. Biosci Biotechnol Biochem 68(6):1175–1184. doi:10.1271/bbb.68.1175
Schneider DA, Gourse RL (2004) Relationship between growth rate and ATP concentration in Escherichia coli: a bioassay for available cellular ATP. J Biol Chem 279(9):8262. doi:10.1074/jbc.M311996200
Sui X, Niu X, Shi M, Pei G, Li J, Chen L, Wang J, Zhang W (2014) Metabolomic analysis reveals mechanism of antioxidant butylated hydroxyanisole on lipid accumulation in Crypthecodinium cohnii. J Agr Food Chem 62(51):12477–12484. doi:10.1021/jf503671m
Wan M, Liu P, Xia J, Rosenberg JN, Oyler GA, Betenbaugh MJ, Nie Z, Qiu Q (2011) The effect of mixotrophy on microalgal growth, lipid content, and expression levels of three pathway genes in Chlorella sorokiniana. Appl Microbiol Biotechnol 91(3):835–844. doi:10.1007/s00253-011-3399-8
Wang X, Lu M, Wang S, Fang Y, Wang D, Ren W, Zhao G (2014) The atmospheric and room-temperature plasma (ARTP) method on the dextranase activity and structure. Int J Biol Macromol 70:284–291. doi:10.1016/j.ijbiomac.2014.07.006
Wang Y, Tao S, Gao X, Shi M, Wu L, Lei C, Zhang W (2015) Biosynthesis of platform chemical 3-hydroxypropionic acid (3-HP) directly from CO2 in cyanobacterium Synechocystis sp. PCC 6803. Metab Eng 34:60–70. doi:10.1016/j.ymben.2015.10.008
Xiong W, Li X, Xiang J, Wu Q (2008) High-density fermentation of microalga Chlorella protothecoides in bioreactor for microbio-diesel production. Appl Microbiol Biotechnol 78(1):29–36. doi:10.1007/s00253-007-1285-1
Xue J, Wang L, Zhang L, Balamurugan S, Li DW, Zeng H, Yang WD, Liu JS, Li HY (2016) The pivotal role of malic enzyme in enhancing oil accumulation in green microalga Chlorella pyrenoidosa. Microb Cell Factories 15(1):120. doi:10.1186/s12934-016-0519-2
Yaakob Z, Ali E, Zainal A, Mohamad M, Takriff MS (2014) An overview: biomolecules from microalgae for animal feed and aquaculture. J Biol Res-Thessalon 21(1):6. doi:10.1186/2241-5793-21-6
Yang S, Lu SH, Yuan YJ (2009) Cerium elicitor-induced phosphatidic acid triggers apoptotic signaling development in Taxus cuspidata cell suspension cultures. Chem Phys Lipids 159(1):13–20. doi:10.1016/j.chemphyslip.2009.02.004
Yongmanitchai W, Ward OP (1989) Omega-3 fatty acids: alternative sources of production. Process Biochem 24(12):117–125
Zhang X, Zhang XF, Li HP, Wang LY, Zhang C, Xing XH, Bao CY (2014) Atmospheric and room temperature plasma (ARTP) as a new powerful mutagenesis tool. Appl Microbiol Biotechnol 98(12):5387–5396. doi:10.1007/s00253-014-5755-y
Acknowledgments
The authors would like to thank Prof. Hao Song for the help with the ARTP experiments. This study was funded by grants from the National High-tech R&D Program (“863” program, project No. 2012AA02A707), the National Basic Research Program of China (“973” program, project No. 2014CB745101), the Doctoral Program of Higher Education of China (Nos. 20120032110020 and 20130032120022), the National Natural Science Foundation of China (No. 21621004), the Tianjin Municipal Science and Technology Commission (No. 15JCZDJC32500), and Zaoneng Biotechnology Inc.
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Liu, J., Pei, G., Diao, J. et al. Screening and transcriptomic analysis of Crypthecodinium cohnii mutants with high growth and lipid content using the acetyl-CoA carboxylase inhibitor sethoxydim. Appl Microbiol Biotechnol 101, 6179–6191 (2017). https://doi.org/10.1007/s00253-017-8397-z
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DOI: https://doi.org/10.1007/s00253-017-8397-z