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Journal of Applied Phycology

, Volume 31, Issue 5, pp 2895–2910 | Cite as

Comparative transcriptome analysis of wild type and an oleaginous mutant strain of Desmodesmus sp. reveals a unique reprogramming of lipid metabolism under high light

  • Meilin He
  • Hong Song
  • Wu Chen
  • Yi Zhang
  • Tong Wang
  • Changhai WangEmail author
  • Weijie Du
Article

Abstract

A mutant generated via ethylmethane sulfonate mutagenesis, Desmodesmus sp. G3, exhibited greater biomass and neutral lipid production over the wild type (WT) strain Desmodesmus sp. G41 in our previous study (Zhang et al., Bioresour Technol 207:268–275, 2016). G3 possessed a higher growth rate and lipid production than WT, with a biomass yield and total lipid content of 1302.86 mg L−1 and 48.58% respectively, which was promoted by 20.50% and 18.84%, compared to WT. Comparative transcriptome analysis was performed to elucidate the mechanism supporting enhanced biomass and lipid production in G3. A total of 1488 differentially expressed genes (DEGs) was identified comparing G3 and WT sequencing datasets, of which 753 and 735 genes were upregulated and downregulated respectively in G3. Pathway enrichment analysis indicated that ‘photosynthesis,’ ‘starch and sucrose metabolism,’ ‘fatty acid elongation,’ and ‘pyruvate metabolism’ were the notable represented DEGs-enriched pathways that might affect cell growth and lipid metabolism. Light harvesting capture was enhanced in G3. To protect PSII from photodamage, light harvesting complex-dependent non-photochemical quenching and state transitions was employed as the photoprotective strategy. De novo fatty acids (FAs) synthesis in chloroplast was downregulated in G3 while mitochondrion localized FAs elongation was enhanced to recycle carbon skeletons for lipid biosynthesis. Pyruvate mechanism was activated in G3 to generate acetyl-CoA through a pyruvate dehydrogenase bypass pathway, as the predominant pathway to provide precursor for lipids biosynthesis.

Keywords

Desmodesmus sp. Chlorophycae High light Mutant RNA-seq Lipid metabolism Pyruvate metabolism 

Notes

Acknowledgements

The authors appreciate the assistance from Novogene Bioinformatics Technology (Beijing, China) for sequencing, sequence assembly and analysis. The authors are grateful for the financial support from the Fundamental Research Funds for the Central Universities, the National Natural Science Foundation of China (No. 31770436 and No. 31500318), Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Co-Innovation Center for Jiangsu Marine Bio-Industry Technology.

Supplementary material

10811_2019_1821_MOESM1_ESM.docx (129 kb)
ESM 1 (DOCX 128 kb)
10811_2019_1821_MOESM2_ESM.xls (105 kb)
ESM 2 (XLS 105 kb)

References

  1. Alonso AP, Goffman FD, Ohlrogge JB, Shachar-Hill Y (2007) Carbon conversion efficiency and central metabolic fluxes in developing sunflower (Helianthus annuus L.) embryos. Plant J 52:296–308PubMedGoogle Scholar
  2. Avidan O, Pick U (2015) Acetyl-CoA synthetase is activated as part of the PDH-bypass in the oleaginous green alga Chlorella desiccata. J Exp Bot 66:7287–7298PubMedPubMedCentralGoogle Scholar
  3. Ballottari M, Girardon J, Betterle N, Morosinotto T, Bassi R (2010) Identification of the chromophores involved in aggregation-dependent energy quenching of the monomeric photosystem II antenna protein Lhcb5. J Biol Chem 285:28309–28321PubMedPubMedCentralGoogle Scholar
  4. Bourgis F, Kilaru A, Cao X, Ngando-Ebongue G-F, Drira N, Ohlrogge JB, Arondel V (2011) Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning. Proc Natl Acad Sci U S A 108:12527–12532PubMedPubMedCentralGoogle Scholar
  5. Bulté L, Gans P, Rebéillé F, Wollman FA (1990) ATP control on state transitions in vivo in Chlamydomonas reinhardtii. BBA-Bioenergetics 1020:72–80Google Scholar
  6. Carrier G, Garnier M, Le Cunff L, Bougaran G, Probert I, De Vargas C, Corre E, Cadoret J-P, Saint-Jean B (2014) Comparative transcriptome of wild type and selected strains of the microalgae Tisochrysis lutea provides insights into the genetic basis, lipid metabolism and the life cycle. PLoS One 9:e86889PubMedPubMedCentralGoogle Scholar
  7. Cheng RL, Feng J, Zhang BX, Huang Y, Cheng J, Zhang CX (2014) Transcriptome and gene expression analysis of an oleaginous diatom under different salinity conditions. Bioenerg Res 7:192–205Google Scholar
  8. Chisti Y (2007) Biodiesel from microalgae. Biotechnol Adv 25:294–306Google Scholar
  9. de Bianchi S, Betterle N, Kouril R, Cazzaniga S, Boekema E, Bassi R, Dall’Osto L (2011) Arabidopsis mutants deleted in the light-harvesting protein Lhcb4 have a disrupted photosystem II macrostructure and are defective in photoprotection. Plant Cell 23:2659–2679PubMedPubMedCentralGoogle Scholar
  10. de Mooij T, Janssen M, Cerezo-Chinarro O, Mussgnug JH, Kruse O, Ballottari M, Bassi R, Bujaldon S, Wollman F-A, Wijffels RH (2015) Antenna size reduction as a strategy to increase biomass productivity: a great potential not yet realized. J Appl Phycol 27:1063–1077Google Scholar
  11. Fan J, Andre C, Xu C (2011) A chloroplast pathway for the de novo biosynthesis of triacylglycerol in Chlamydomonas reinhardtii. FEBS Lett 585:1985–1991PubMedGoogle Scholar
  12. Fan J, Cui Y, Wan M, Wang W, Li Y (2014) Lipid accumulation and biosynthesis genes response of the oleaginous Chlorella pyrenoidosa under three nutrition stressors. Biotechnol Biofuels 7:17PubMedPubMedCentralGoogle Scholar
  13. Ferrell J, Sarisky-Reed V (2010) National algal biofuels technology roadmap. EERE Publication and Product Library,Google Scholar
  14. Gavilanes J, Lizarbe M, Municio A, Oñaderra M (1982) Effects of palmitoyl-CoA on the structure-function of the fatty acid synthetase complex from Ceratitis capitata. Int J Biochem Cell Biol 14:1061–1066Google Scholar
  15. Goodenough U, Blaby I, Casero D, Gallaher SD, Goodson C, Johnson S, Lee JH, Merchant SS, Pellegrini M, Roth R, Rusch J, Singh M, Umen JG, Weiss TL, Wulan T (2014) The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. Eukaryot Cell 13:591–613PubMedPubMedCentralGoogle Scholar
  16. Goodson C, Roth R, Wang ZT, Goodenough U (2011) Structural correlates of cytoplasmic and chloroplast lipid body synthesis in Chlamydomonas reinhardtii and stimulation of lipid body production with acetate boost. Eukaryot Cell 10:1592–1606PubMedPubMedCentralGoogle Scholar
  17. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652PubMedPubMedCentralGoogle Scholar
  18. Ho SH, Chen CY, Chang JS (2012) Effect of light intensity and nitrogen starvation on CO2 fixation and lipid/carbohydrate production of an indigenous microalga Scenedesmus obliquus CNW-N. Bioresour Technol 113:244–252PubMedGoogle Scholar
  19. Ho SH, Nakanishi A, Kato Y, Yamasaki H, Chang JS, Misawa N, Hirose Y, Minagawa J, Hasunuma T, Kondo A (2017) Dynamic metabolic profiling together with transcription analysis reveals salinity-induced starch-to-lipid biosynthesis in alga Chlamydomonas sp. JSC4. Sci Rep 7:45471Google Scholar
  20. Hoffmeister M, Piotrowski M, Nowitzki U, Martin W (2005) Mitochondrial trans-2-enoyl-CoA reductase of wax ester fermentation from Euglena gracilis defines a new family of enzymes involved in lipid synthesis. J Biol Chem 280:4329–4338PubMedGoogle Scholar
  21. Holthuis JC, Menon AK (2014) Lipid landscapes and pipelines in membrane homeostasis. Nature 510:48–57PubMedGoogle Scholar
  22. 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 54:621–639Google Scholar
  23. Kamalanathan M, Pierangelini M, Shearman LA, Gleadow R, Beardall J (2016) Impacts of nitrogen and phosphorus starvation on the physiology of Chlamydomonas reinhardtii. J Appl Phycol 28:1509–1520Google Scholar
  24. Kenny P, Flynn KJ (2017) Physiology limits commercially viable photoautotrophic production of microalgal biofuels. J Appl Phycol 29:2713–2727PubMedPubMedCentralGoogle Scholar
  25. Korithoski B, Lévesque CM, Cvitkovitch DG (2007) Involvement of the detoxifying enzyme lactoylglutathione lyase in Streptococcus mutans aciduricity. J Bacteriol 189:7586–7592PubMedPubMedCentralGoogle Scholar
  26. Larkum AW (2016) Photosynthesis and light harvesting in algae. In: Borowitzka MA, Beardall J, Raven J (eds) The physiology of microalgae. Springer, Cham, pp 67–87Google Scholar
  27. Lenka SK, Carbonaro N, Park R, Miller SM, Thorpe I, Li Y (2016) Current advances in molecular, biochemical, and computational modeling analysis of microalgal triacylglycerol biosynthesis. Biotechnol Adv 34:1046–1063PubMedGoogle Scholar
  28. Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformat 12:323Google Scholar
  29. Li Y, Han D, Hu G, Sommerfeld M, Hu Q (2010) Inhibition of starch synthesis results in overproduction of lipids in Chlamydomonas reinhardtii. Biotechnol Bioeng 107:258–268PubMedGoogle Scholar
  30. Li X, Moellering ER, Liu B, Johnny C, Fedewa M, Sears BB, Kuo M-H, Benning C (2012) A galactoglycerolipid lipase is required for triacylglycerol accumulation and survival following nitrogen deprivation in Chlamydomonas reinhardtii. Plant Cell 24:4670–4686PubMedPubMedCentralGoogle Scholar
  31. Li J, Han D, Wang D, Ning K, Jia J, Wei L, Jing X, Huang S, Chen J, Li Y (2014) Choreography of transcriptomes and lipidomes of Nannochloropsis reveals the mechanisms of oil synthesis in microalgae. Plant Cell 26:1645–1665PubMedPubMedCentralGoogle Scholar
  32. Li K, Cheng J, Lu HX, Yang WJ, Zhou JH, Cen KF (2017) Transcriptome-based analysis on carbon metabolism of Haematococcus pluvialis mutant under 15% CO2. Bioresour Technol 233:313–321PubMedGoogle Scholar
  33. Liu JH, Yuan C, Hu GR, Li FL (2012) Effects of light intensity on the growth and lipid accumulation of microalga Scenedesmus sp. 11-1 under nitrogen limitation. Appl Biochem Biotechnol 166:2127–2137PubMedGoogle Scholar
  34. Ma YH, Wang X, Niu YF, Yang ZK, Zhang MH, Wang ZM, Yang WD, Liu JS, Li HY (2014) Antisense knockdown of pyruvate dehydrogenase kinase promotes the neutral lipid accumulation in the diatom Phaeodactylum tricornutum. Microb Cell Factories 13:100Google Scholar
  35. Mashek DG, Li LO, Coleman RA (2007) Long-chain acyl-CoA synthetases and fatty acid channeling. Futur Lipidol 2:465–476Google Scholar
  36. Miller R, Wu G, Deshpande RR, Vieler A, Gärtner K, Li X, Moellering ER, Zauner S, Cornish A, Liu B (2010) Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen-deprivation predict diversion of metabolism. Plant Physiol 154:1737–1752PubMedPubMedCentralGoogle Scholar
  37. Pan YY, Wang ST, Chuang LT, Chang YW, Chen CNN (2011) Isolation of thermo-tolerant and high lipid content green microalgae: oil accumulation is predominantly controlled by photosystem efficiency during stress treatments in Desmodesmus. Bioresour Technol 102:10510–10517PubMedGoogle Scholar
  38. Polle JE, Kanakagiri SD, Melis A (2003) tla1, a DNA insertional transformant of the green alga Chlamydomonas reinhardtii with a truncated light-harvesting chlorophyll antenna size. Planta 217:49–59PubMedGoogle Scholar
  39. Rylott EL, Rogers CA, Gilday AD, Edgell T, Larson TR, Graham IA (2003) Arabidopsis mutants in short-and medium-chain acyl-CoA oxidase activities accumulate acyl-CoAs and reveal that fatty acid β-oxidation is essential for embryo development. J Biol Chem 278:21370–21377PubMedGoogle Scholar
  40. Scheller HV, Jensen PE, Haldrup A, Lunde C, Knoetzel J (2001) Role of subunits in eukaryotic photosystem I. Biochim Biophys Acta 1507:41–60PubMedGoogle Scholar
  41. Schenk P, Thomas-Hall S, Stephens E, Marx U, Mussgnug J, Posten C, Kruse O, Hankamer B (2008) Second generation biofuels: high-efficiency microalgae for biodiesel production. Bioenerg Res 1:20–43Google Scholar
  42. Schmittgen TD, Livak KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3:1101–1108Google Scholar
  43. Shapiguzov A, Ingelsson B, Samol I, Andres C, Kessler F, Rochaix JD, Vener AV, Goldschmidt-Clermont M (2010) The PPH1 phosphatase is specifically involved in LHCII dephosphorylation and state transitions in Arabidopsis. Proc Natl Acad Sci U S A 107:4782–4787PubMedPubMedCentralGoogle Scholar
  44. Sharma KK, Schuhmann H, Schenk PM (2012) High lipid induction in microalgae for biodiesel production. Energies 5:1532–1553Google Scholar
  45. Shtaida N, Khozin-Goldberg I, Solovchenko A, Chekanov K, Didi-Cohen S, Leu S, Cohen Z, Boussiba S (2014) Downregulation of a putative plastid PDC E1α subunit impairs photosynthetic activity and triacylglycerol accumulation in nitrogen-starved photoautotrophic Chlamydomonas reinhardtii. J Exp Bot 65:6563–6576PubMedPubMedCentralGoogle Scholar
  46. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100:9440–9445PubMedPubMedCentralGoogle Scholar
  47. Tan KWM, Lee YK (2016) The dilemma for lipid productivity in green microalgae: importance of substrate provision in improving oil yield without sacrificing growth. Biotechnol Biofuels 9:255PubMedPubMedCentralGoogle Scholar
  48. Tovar-Mendez A, Miernyk JA, Randall DD (2003) Regulation of pyruvate dehydrogenase complex activity in plant cells. Eur J Biochem 270:1043–1049PubMedGoogle Scholar
  49. Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63PubMedPubMedCentralGoogle Scholar
  50. Xin L, Hu HY, Ke G, Sun YX (2010) Effects of different nitrogen and phosphorus concentrations on the growth, nutrient uptake, and lipid accumulation of a freshwater microalga Scenedesmus sp. Bioresour Technol 101:5494–5500Google Scholar
  51. Xing G, Yuan H, Yang J, Li J, Gao Q, Li W, Wang E (2018) Integrated analyses of transcriptome, proteome and fatty acid profilings of the oleaginous microalga Auxenochlorella protothecoides UTEX 2341 reveal differential reprogramming of fatty acid metabolism in response to low and high temperatures. Algal Res 33:16–27Google Scholar
  52. Yeh KL, Chang JS (2011) Nitrogen starvation strategies and photobioreactor design for enhancing lipid content and lipid production of a newly isolated microalga Chlorella vulgaris ESP-31: implications for biofuels. Biotechnol J 6:1358–1366PubMedGoogle Scholar
  53. Yoon K, Han D, Li Y, Sommerfeld M, Hu Q (2012) Phospholipid: diacylglycerol acyltransferase is a multifunctional enzyme involved in membrane lipid turnover and degradation while synthesizing triacylglycerol in the unicellular green microalga Chlamydomonas reinhardtii. Plant Cell 24:3708–3724PubMedPubMedCentralGoogle Scholar
  54. Zhang Y, He M, Zou S, Fei C, Yan Y, Zheng S, Rajper AA, Wang C (2016) Breeding of high biomass and lipid producing Desmodesmus sp. by ethylmethane sulfonate-induced mutation. Bioresour Technol 207:268–275PubMedGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Meilin He
    • 1
  • Hong Song
    • 1
  • Wu Chen
    • 1
  • Yi Zhang
    • 1
    • 2
  • Tong Wang
    • 1
  • Changhai Wang
    • 1
    Email author
  • Weijie Du
    • 1
  1. 1.Jiangsu Key Laboratory of Marine Biology, College of Resources and Environmental ScienceNanjing Agricultural UniversityNanjingChina
  2. 2.Inner Mongolia Environmental Monitoring CenterHohhotChina

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