Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation

Jaeger D, Winkler A, Mussgnug JH, Kalinowski J, Goesmann A, Kruse O (2017)
Biotechnology for Biofuels 10: 197.

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Background Oleaginous microalgae are promising production hosts for the sustainable generation of lipid-based bioproducts and as bioenergy carriers such as biodiesel. Transcriptomics of the lipid accumulation phase, triggered efficiently by nitrogen starvation, is a valuable approach for the identification of gene targets for metabolic engineering. Results An explorative analysis of the detailed transcriptional response to different stages of nitrogen availability was performed in the oleaginous green alga Monoraphidium neglectum. Transcript data were correlated with metabolic data for cellular contents of starch and of different lipid fractions. A pronounced transcriptional down-regulation of photosynthesis became apparent in response to nitrogen starvation, whereas glucose catabolism was found to be up-regulated. An in-depth reconstruction and analysis of the pathways for glycerolipid, central carbon, and starch metabolism revealed that distinct transcriptional changes were generally found only for specific steps within a metabolic pathway. In addition to pathway analyses, the transcript data were also used to refine the current genome annotation. The transcriptome data were integrated into a database and complemented with data for other microalgae which were also subjected to nitrogen starvation. It is available at https://tdbmn.cebitec.uni-bielefeld.de. Conclusions Based on the transcriptional responses to different stages of nitrogen availability, a model for triacylglycerol and lipid hyperaccumulation is proposed, which involves transcriptional induction of thioesterases, differential regulation of lipases, and a re-routing of the central carbon metabolism. Over-expression of distinct thioesterases was identified to be a potential strategy to increase the oleaginous phenotype of M. neglectum, and furthermore specific lipases were identified as potential targets for future metabolic engineering approaches.
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Biotechnology for Biofuels
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Jaeger D, Winkler A, Mussgnug JH, Kalinowski J, Goesmann A, Kruse O. Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. Biotechnology for Biofuels. 2017;10: 197.
Jaeger, D., Winkler, A., Mussgnug, J. H., Kalinowski, J., Goesmann, A., & Kruse, O. (2017). Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. Biotechnology for Biofuels, 10, 197. doi:10.1186/s13068-017-0882-1
Jaeger, D., Winkler, A., Mussgnug, J. H., Kalinowski, J., Goesmann, A., and Kruse, O. (2017). Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. Biotechnology for Biofuels 10:197.
Jaeger, D., et al., 2017. Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. Biotechnology for Biofuels, 10: 197.
D. Jaeger, et al., “Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation”, Biotechnology for Biofuels, vol. 10, 2017, : 197.
Jaeger, D., Winkler, A., Mussgnug, J.H., Kalinowski, J., Goesmann, A., Kruse, O.: Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. Biotechnology for Biofuels. 10, : 197 (2017).
Jaeger, Daniel, Winkler, Anika, Mussgnug, Jan H., Kalinowski, Jörn, Goesmann, Alexander, and Kruse, Olaf. “Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation”. Biotechnology for Biofuels 10 (2017): 197.
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154 References

Daten bereitgestellt von Europe PubMed Central.

Valuable products from biotechnology of microalgae.
Pulz O, Gross W., Appl. Microbiol. Biotechnol. 65(6), 2004
PMID: 15300417
Algae biofuels: versatility for the future of bioenergy.
Jones CS, Mayfield SP., Curr. Opin. Biotechnol. 23(3), 2011
PMID: 22104720
Exploiting diversity and synthetic biology for the production of algal biofuels.
Georgianna DR, Mayfield SP., Nature 488(7411), 2012
PMID: 22895338
Biofuels from algae: challenges and potential.
Hannon M, Gimpel J, Tran M, Rasala B, Mayfield S., Biofuels 1(5), 2010
PMID: 21833344
The promise and challenges of microalgal-derived biofuels
Pienkos PT, Darzins A., 2009
Advances in microalgae engineering and synthetic biology applications for biofuel production.
Gimpel JA, Specht EA, Georgianna DR, Mayfield SP., Curr Opin Chem Biol 17(3), 2013
PMID: 23684717
Genetic tools and techniques for Chlamydomonas reinhardtii.
Mussgnug JH., Appl. Microbiol. Biotechnol. 99(13), 2015
PMID: 26025017
Metabolism of acyl-lipids in Chlamydomonas reinhardtii.
Li-Beisson Y, Beisson F, Riekhof W., Plant J. 82(3), 2015
PMID: 25660108
Microalgae for oil: strain selection, induction of lipid synthesis and outdoor mass cultivation in a low-cost photobioreactor.
Rodolfi L, Chini Zittelli G, Bassi N, Padovani G, Biondi N, Bonini G, Tredici MR., Biotechnol. Bioeng. 102(1), 2009
PMID: 18683258
Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism.
Miller R, Wu G, Deshpande RR, Vieler A, Gartner K, Li X, Moellering ER, Zauner S, Cornish AJ, Liu B, Bullard B, Sears BB, Kuo MH, Hegg EL, Shachar-Hill Y, Shiu SH, Benning C., Plant Physiol. 154(4), 2010
PMID: 20935180
Nitrogen-Sparing Mechanisms in Chlamydomonas Affect the Transcriptome, the Proteome, and Photosynthetic Metabolism.
Schmollinger S, Muhlhaus T, Boyle NR, Blaby IK, Casero D, Mettler T, Moseley JL, Kropat J, Sommer F, Strenkert D, Hemme D, Pellegrini M, Grossman AR, Stitt M, Schroda M, Merchant SS., Plant Cell 26(4), 2014
PMID: 24748044
Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas.
Boyle NR, Page MD, Liu B, Blaby IK, Casero D, Kropat J, Cokus SJ, Hong-Hermesdorf A, Shaw J, Karpowicz SJ, Gallaher SD, Johnson S, Benning C, Pellegrini M, Grossman A, Merchant SS., J. Biol. Chem. 287(19), 2012
PMID: 22403401
The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii.
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., Eukaryotic Cell 13(5), 2014
PMID: 24585881
Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant.
Blaby IK, Glaesener AG, Mettler T, Fitz-Gibbon ST, Gallaher SD, Liu B, Boyle NR, Kropat J, Stitt M, Johnson S, Benning C, Pellegrini M, Casero D, Merchant SS., Plant Cell 25(11), 2013
PMID: 24280389
Transcriptome analysis of Chlamydomonas reinhardtii during the process of lipid accumulation.
Lv H, Qu G, Qi X, Lu L, Tian C, Ma Y., Genomics 101(4), 2013
PMID: 23396177
Comparative transcriptome analysis reveals a potential photosynthate partitioning mechanism between lipid and starch biosynthetic pathways in green microalgae
Chang WC, Zheng HQ, Chen cNN., 2016
Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation.
Yang ZK, Niu YF, Ma YH, Xue J, Zhang MH, Yang WD, Liu JS, Lu SH, Guan Y, Li HY., Biotechnol Biofuels 6(1), 2013
PMID: 23642220
Choreography of Transcriptomes and Lipidomes of Nannochloropsis Reveals the Mechanisms of Oil Synthesis in Microalgae.
Li J, Han D, Wang D, Ning K, Jia J, Wei L, Jing X, Huang S, Chen J, Li Y, Hu Q, Xu J., Plant Cell 26(4), 2014
PMID: 24692423
Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropis gaditana.
Radakovits R, Jinkerson RE, Fuerstenberg SI, Tae H, Settlage RE, Boore JL, Posewitz MC., Nat Commun 3(), 2012
PMID: 22353717
The response of Chlamydomonas reinhardtii to nitrogen deprivation: a systems biology analysis.
Park JJ, Wang H, Gargouri M, Deshpande RR, Skepper JN, Holguin FO, Juergens MT, Shachar-Hill Y, Hicks LM, Gang DR., Plant J. 81(4), 2015
PMID: 25515814
The protein Compromised Hydrolysis of Triacylglycerols 7 (CHT7) acts as a repressor of cellular quiescence in Chlamydomonas.
Tsai CH, Warakanont J, Takeuchi T, Sears BB, Moellering ER, Benning C., Proc. Natl. Acad. Sci. U.S.A. 111(44), 2014
PMID: 25313078
A forward genetic approach in Chlamydomonas reinhardtii as a strategy for exploring starch catabolism.
Tuncay H, Findinier J, Duchene T, Cogez V, Cousin C, Peltier G, Ball SG, Dauvillee D., PLoS ONE 8(9), 2013
PMID: 24019981
Chlamydomonas as a model for biofuels and bio-products production.
Scranton MA, Ostrand JT, Fields FJ, Mayfield SP., Plant J. 82(3), 2015
PMID: 25641390
Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production.
Bogen C, Al-Dilaimi A, Albersmeier A, Wichmann J, Grundmann M, Rupp O, Lauersen KJ, Blifernez-Klassen O, Kalinowski J, Goesmann A, Mussgnug JH, Kruse O., BMC Genomics 14(), 2013
PMID: 24373495
Label-free in vivo analysis of intracellular lipid droplets in the oleaginous microalga Monoraphidium neglectum by coherent Raman scattering microscopy.
Jaeger D, Pilger C, Hachmeister H, Oberlander E, Wordenweber R, Wichmann J, Mussgnug JH, Huser T, Kruse O., Sci Rep 6(), 2016
PMID: 27767024
Nuclear transformation and functional gene expression in the oleaginous microalga Monoraphidium neglectum.
Jaeger D, Hubner W, Huser T, Mussgnug JH, Kruse O., J. Biotechnol. 249(), 2017
PMID: 28302588
Dynamics of protein and polar lipid recruitment during lipid droplet assembly in Chlamydomonas reinhardtii.
Tsai CH, Zienkiewicz K, Amstutz CL, Brink BG, Warakanont J, Roston R, Benning C., Plant J. 83(4), 2015
PMID: 26096381

AUTHOR UNKNOWN, 0
Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production.
Hildebrand M, Abbriano RM, Polle JE, Traller JC, Trentacoste EM, Smith SR, Davis AK., Curr Opin Chem Biol 17(3), 2013
PMID: 23538202
Oil accumulation in the model green alga Chlamydomonas reinhardtii: characterization, variability between common laboratory strains and relationship with starch reserves.
Siaut M, Cuine S, Cagnon C, Fessler B, Nguyen M, Carrier P, Beyly A, Beisson F, Triantaphylides C, Li-Beisson Y, Peltier G., BMC Biotechnol. 11(), 2011
PMID: 21255402
Metabolic changes of starch and lipid triggered by nitrogen starvation in the microalga Chlorella zofingiensis.
Zhu S, Huang W, Xu J, Wang Z, Xu J, Yuan Z., Bioresour. Technol. 152(), 2013
PMID: 24308944
TAG, you're it! Chlamydomonas as a reference organism for understanding algal triacylglycerol accumulation.
Merchant SS, Kropat J, Liu B, Shaw J, Warakanont J., Curr. Opin. Biotechnol. 23(3), 2011
PMID: 22209109
The impact of nitrogen starvation on the dynamics of triacylglycerol accumulation in nine microalgae strains.
Breuer G, Lamers PP, Martens DE, Draaisma RB, Wijffels RH., Bioresour. Technol. 124(), 2012
PMID: 22995162
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y., Genome Res. 18(9), 2008
PMID: 18550803
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.
Wang L, Feng Z, Wang X, Wang X, Zhang X., Bioinformatics 26(1), 2009
PMID: 19855105
The Intraperitoneal Transcriptome of the Opportunistic Pathogen Enterococcus faecalis in Mice.
Muller C, Cacaci M, Sauvageot N, Sanguinetti M, Rattei T, Eder T, Giard JC, Kalinowski J, Hain T, Hartke A., PLoS ONE 10(5), 2015
PMID: 25978463
Genomic Foundation of Starch-to-Lipid Switch in Oleaginous Chlorella spp.
Fan J, Ning K, Zeng X, Luo Y, Wang D, Hu J, Li J, Xu H, Huang J, Wan M, Wang W, Zhang D, Shen G, Run C, Liao J, Fang L, Huang S, Jing X, Su X, Wang A, Bai L, Hu Z, Xu J, Li Y., Plant Physiol. 169(4), 2015
PMID: 26486592
New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics.
Toepel J, Illmer-Kephalides M, Jaenicke S, Straube J, May P, Goesmann A, Kruse O., Plant Biotechnol. J. 11(6), 2013
PMID: 23551401
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L., Nat Protoc 7(3), 2012
PMID: 22383036
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL., Genome Biol. 14(4), 2013
PMID: 23618408
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L., Nat. Biotechnol. 28(5), 2010
PMID: 20436464
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M., Bioinformatics 32(5), 2015
PMID: 26559507
Use of a cDNA microarray to analyse gene expression patterns in human cancer.
DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM., Nat. Genet. 14(4), 1996
PMID: 8944026
Parallel human genome analysis: microarray-based expression monitoring of 1000 genes.
Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW., Proc. Natl. Acad. Sci. U.S.A. 93(20), 1996
PMID: 8855227
Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica.
Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J., NPJ Syst Biol Appl 2(), 2016
PMID: 28725468
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.
Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A., Nat Protoc 8(8), 2013
PMID: 23845962
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Love MI, Huber W, Anders S., Genome Biol. 15(12), 2014
PMID: 25516281
Differential expression analysis for sequence count data.
Anders S, Huber W., Genome Biol. 11(10), 2010
PMID: 20979621
Comparative analysis of leaf-type ferredoxin-NADP oxidoreductase isoforms in Arabidopsis thaliana.
Lintala M, Allahverdiyeva Y, Kangasjarvi S, Lehtimaki N, Keranen M, Rintamaki E, Aro EM, Mulo P., Plant J. 57(6), 2008
PMID: 19054362
Cyclic electron flow around photosystem I is essential for photosynthesis.
Munekage Y, Hashimoto M, Miyake C, Tomizawa K, Endo T, Tasaka M, Shikanai T., Nature 429(6991), 2004
PMID: 15175756
Ca(2+)-regulated cyclic electron flow supplies ATP for nitrogen starvation-induced lipid biosynthesis in green alga.
Chen H, Hu J, Qiao Y, Chen W, Rong J, Zhang Y, He C, Wang Q., Sci Rep 5(), 2015
PMID: 26450399

AUTHOR UNKNOWN, 0
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
CDD: NCBI's conserved domain database.
Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH., Nucleic Acids Res. 43(Database issue), 2014
PMID: 25414356
The Chlamydomonas genome reveals the evolution of key animal and plant functions.
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR., Science 318(5848), 2007
PMID: 17932292
Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779.
Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya , Simpson JP, Terbush A, Warakanont J, Zauner S, Farre EM, Hegg EL, Jiang N, Kuo MH, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu SH, Benning C., PLoS Genet. 8(11), 2012
PMID: 23166516
The Phaeodactylum genome reveals the evolutionary history of diatom genomes.
Bowler C, Allen AE, Badger JH, Grimwood J, Jabbari K, Kuo A, Maheswari U, Martens C, Maumus F, Otillar RP, Rayko E, Salamov A, Vandepoele K, Beszteri B, Gruber A, Heijde M, Katinka M, Mock T, Valentin K, Verret F, Berges JA, Brownlee C, Cadoret JP, Chiovitti A, Choi CJ, Coesel S, De Martino A, Detter JC, Durkin C, Falciatore A, Fournet J, Haruta M, Huysman MJ, Jenkins BD, Jiroutova K, Jorgensen RE, Joubert Y, Kaplan A, Kroger N, Kroth PG, La Roche J, Lindquist E, Lommer M, Martin-Jezequel V, Lopez PJ, Lucas S, Mangogna M, McGinnis K, Medlin LK, Montsant A, Oudot-Le Secq MP, Napoli C, Obornik M, Parker MS, Petit JL, Porcel BM, Poulsen N, Robison M, Rychlewski L, Rynearson TA, Schmutz J, Shapiro H, Siaut M, Stanley M, Sussman MR, Taylor AR, Vardi A, von Dassow P, Vyverman W, Willis A, Wyrwicz LS, Rokhsar DS, Weissenbach J, Armbrust EV, Green BR, Van de Peer Y, Grigoriev IV., Nature 456(7219), 2008
PMID: 18923393
A distinct DGAT with sn-3 acetyltransferase activity that synthesizes unusual, reduced-viscosity oils in Euonymus and transgenic seeds.
Durrett TP, McClosky DD, Tumaney AW, Elzinga DA, Ohlrogge J, Pollard M., Proc. Natl. Acad. Sci. U.S.A. 107(20), 2010
PMID: 20439724
PredAlgo: a new subcellular localization prediction tool dedicated to green algae.
Tardif M, Atteia A, Specht M, Cogne G, Rolland N, Brugiere S, Hippler M, Ferro M, Bruley C, Peltier G, Vallon O, Cournac L., Mol. Biol. Evol. 29(12), 2012
PMID: 22826458

Dörmann P., 2001
A galactoglycerolipid lipase is required for triacylglycerol accumulation and survival following nitrogen deprivation in Chlamydomonas reinhardtii.
Li X, Moellering ER, Liu B, Johnny C, Fedewa M, Sears BB, Kuo MH, Benning C., Plant Cell 24(11), 2012
PMID: 23161887
Algorithms for hierarchical clustering: an overview
Murtagh F, Contreras P., 2012
Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
Rousseeuw PJ., 1987
Computational cluster validation in post-genomic data analysis.
Handl J, Knowles J, Kell DB., Bioinformatics 21(15), 2005
PMID: 15914541
Oil accumulation is controlled by carbon precursor supply for fatty acid synthesis in Chlamydomonas reinhardtii.
Fan J, Yan C, Andre C, Shanklin J, Schwender J, Xu C., Plant Cell Physiol. 53(8), 2012
PMID: 22642988
Functional integration of the HUP1 hexose symporter gene into the genome of C. reinhardtii: Impacts on biological H(2) production.
Doebbe A, Rupprecht J, Beckmann J, Mussgnug JH, Hallmann A, Hankamer B, Kruse O., J. Biotechnol. 131(1), 2007
PMID: 17624461
Functional analysis of hydrogen photoproduction in respiratory-deficient mutants of Chlamydomonas reinhardtii
Lecler R, Godaux D, Vigeolas H, Hiligsmann S, Thonart P, Franck F, Cardol P, Remacle C., 2011
C(4) photosynthesis: discovery and resolution.
Hatch MD., Photosyn. Res. 73(1-3), 2002
PMID: 16245128
Biodiesel from microalgae.
Chisti Y., Biotechnol. Adv. 25(3), 2007
PMID: 17350212
Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition.
Morey JS, Monroe EA, Kinney AL, Beal M, Johnson JG, Hitchcock GL, Van Dolah FM., BMC Genomics 12(), 2011
PMID: 21729317
The regulation of photosynthetic structure and function during nitrogen deprivation in Chlamydomonas reinhardtii.
Juergens MT, Deshpande RR, Lucker BF, Park JJ, Wang H, Gargouri M, Holguin FO, Disbrow B, Schaub T, Skepper JN, Kramer DM, Gang DR, Hicks LM, Shachar-Hill Y., Plant Physiol. 167(2), 2014
PMID: 25489023
Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica.
Qiao K, Imam Abidi SH, Liu H, Zhang H, Chakraborty S, Watson N, Kumaran Ajikumar P, Stephanopoulos G., Metab. Eng. 29(), 2015
PMID: 25732624
Acyl-lipid metabolism.
Li-Beisson Y, Shorrosh B, Beisson F, Andersson MX, Arondel V, Bates PD, Baud S, Bird D, Debono A, Durrett TP, Franke RB, Graham IA, Katayama K, Kelly AA, Larson T, Markham JE, Miquel M, Molina I, Nishida I, Rowland O, Samuels L, Schmid KM, Wada H, Welti R, Xu C, Zallot R, Ohlrogge J., Arabidopsis Book 8(), 2010
PMID: 22303259
Analysis of acyl fluxes through multiple pathways of triacylglycerol synthesis in developing soybean embryos.
Bates PD, Durrett TP, Ohlrogge JB, Pollard M., Plant Physiol. 150(1), 2009
PMID: 19329563
Molecular mechanisms for photosynthetic carbon partitioning into storage neutral lipids in Nannochloropsis oceanica under nitrogen-depletion conditions
Jia J, Han D, Gerken HG, Li Y, Sommerfeld M, Hu Q, Xu J., 2015
Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli.
Yao Z, Davis RM, Kishony R, Kahne D, Ruiz N., Proc. Natl. Acad. Sci. U.S.A. 109(38), 2012
PMID: 22908292
Feedback inhibition of fatty acid synthesis in tobacco suspension cells
Shintani DK, Ohlrogge JB., 1995
Overexpression of stearoyl-ACP desaturase enhances accumulations of oleic acid in the green alga Chlamydomonas reinhardtii
Hwangbo K, Ahn J-W, Lim J-M, Park Y-I, Liu JR, Jeong W-J., 2014
An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii.
Li X, Zhang R, Patena W, Gang SS, Blum SR, Ivanova N, Yue R, Robertson JM, Lefebvre PA, Fitz-Gibbon ST, Grossman AR, Jonikas MC., Plant Cell 28(2), 2016
PMID: 26764374
Functional analysis of three type-2 DGAT homologue genes for triacylglycerol production in the green microalga Chlamydomonas reinhardtii.
La Russa M, Bogen C, Uhmeyer A, Doebbe A, Filippone E, Kruse O, Mussgnug JH., J. Biotechnol. 162(1), 2012
PMID: 22542934
The complex architecture of oxygenic photosynthesis.
Nelson N, Ben-Shem A., Nat. Rev. Mol. Cell Biol. 5(12), 2004
PMID: 15573135
Environmental control of glycerolipid metabolism in microalgae: commercial implications and future research directions
Roessler PG., 1990
Glycerol and neutral lipid production in the oleaginous marine diatom Phaeodactylum tricornutum promoted by overexpression of glycerol-3-phosphate dehydrogenase
Yao Y, Lu Y, Peng K-T, Huang T, Niu Y-F, Xie W-H, Yang W-D, Liu J-S, Li H-Y., 2014
Enhancement of glycerol metabolism in the oleaginous marine diatom Fistulifera solaris JPCC DA0580 to improve triacylglycerol productivity.
Muto M, Tanaka M, Liang Y, Yoshino T, Matsumoto M, Tanaka T., Biotechnol Biofuels 8(1), 2015
PMID: 25632299
Malic enzyme is a major source of NADPH for lipid accumulation by Aspergillus nidulans
Wynn JP, Ratledge C., 1997
Possible regulatory roles of ATP: citrate lyase, malic enzyme, and AMP deaminase in lipid accumulation by Rhodosporidium toruloides CBS 14
Evans CT, Ratledge C., 1985
Genetic improvement of the microalga Phaeodactylum tricornutum for boosting neutral lipid accumulation.
Xue J, Niu YF, Huang T, Yang WD, Liu JS, Li HY., Metab. Eng. 27(), 2014
PMID: 25447640
The pivotal role of malic enzyme in enhancing oil accumulation in green microalga Chlorella pyrenoidosa.
Xue J, Wang L, Zhang L, Balamurugan S, Li DW, Zeng H, Yang WD, Liu JS, Li HY., Microb. Cell Fact. 15(1), 2016
PMID: 27387324
Carbon partitioning in green algae (chlorophyta) and the enolase enzyme.
Polle JE, Neofotis P, Huang A, Chang W, Sury K, Wiech EM., Metabolites 4(3), 2014
PMID: 25093929
Chloroplast lipid transfer processes in Chlamydomonas reinhardtii involving a TRIGALACTOSYLDIACYLGLYCEROL 2 (TGD2) orthologue.
Warakanont J, Tsai CH, Michel EJ, Murphy GR 3rd, Hsueh PY, Roston RL, Sears BB, Benning C., Plant J. 84(5), 2015
PMID: 26496373
Characterization of a novel thioesterase (PtTE) from Phaeodactylum tricornutum.
Gong Y, Guo X, Wan X, Liang Z, Jiang M., J. Basic Microbiol. 51(6), 2011
PMID: 21656819
Fatty acid production in genetically modified cyanobacteria.
Liu X, Sheng J, Curtiss R 3rd., Proc. Natl. Acad. Sci. U.S.A. 108(17), 2011
PMID: 21482809
Metabolic engineering of lipid catabolism increases microalgal lipid accumulation without compromising growth.
Trentacoste EM, Shrestha RP, Smith SR, Gle C, Hartmann AC, Hildebrand M, Gerwick WH., Proc. Natl. Acad. Sci. U.S.A. 110(49), 2013
PMID: 24248374
Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production.
Blazeck J, Hill A, Liu L, Knight R, Miller J, Pan A, Otoupal P, Alper HS., Nat Commun 5(), 2014
PMID: 24445655
Starchless mutants of Chlamydomonas reinhardtii lack the small subunit of a heterotetrameric ADP-glucose pyrophosphorylase.
Zabawinski C, Van Den Koornhuyse N, D'Hulst C, Schlichting R, Giersch C, Delrue B, Lacroix JM, Preiss J, Ball S., J. Bacteriol. 183(3), 2001
PMID: 11208806
Metabolic and photosynthetic consequences of blocking starch biosynthesis in the green alga Chlamydomonas reinhardtii sta6 mutant.
Krishnan A, Kumaraswamy GK, Vinyard DJ, Gu H, Ananyev G, Posewitz MC, Dismukes GC., Plant J. 81(6), 2015
PMID: 25645872
Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae.
Ngan CY, Wong CH, Choi C, Yoshinaga Y, Louie K, Jia J, Chen C, Bowen B, Cheng H, Leonelli L, Kuo R, Baran R, Garcia-Cerdan JG, Pratap A, Wang M, Lim J, Tice H, Daum C, Xu J, Northen T, Visel A, Bristow J, Niyogi KK, Wei CL., Nat Plants 1(), 2015
PMID: 27250540

AUTHOR UNKNOWN, 0
Efficient phototrophic production of a high-value sesquiterpenoid from the eukaryotic microalga Chlamydomonas reinhardtii.
Lauersen KJ, Baier T, Wichmann J, Wordenweber R, Mussgnug JH, Hubner W, Huser T, Kruse O., Metab. Eng. 38(), 2016
PMID: 27474353
Phosphoketolase pathway contributes to carbon metabolism in cyanobacteria.
Xiong W, Lee TC, Rommelfanger S, Gjersing E, Cano M, Maness PC, Ghirardi M, Yu J., Nat Plants 2(), 2015
PMID: 27250745
The metabolic blueprint of Phaeodactylum tricornutum reveals a eukaryotic Entner-Doudoroff glycolytic pathway.
Fabris M, Matthijs M, Rombauts S, Vyverman W, Goossens A, Baart GJ., Plant J. 70(6), 2012
PMID: 22332784
Bacterial and eukaryotic phosphoketolases: phylogeny, distribution and evolution.
Sanchez B, Zuniga M, Gonzalez-Candelas F, de los Reyes-Gavilan CG, Margolles A., J. Mol. Microbiol. Biotechnol. 18(1), 2010
PMID: 20068356
Engineering Yarrowia lipolytica as a platform for synthesis of drop-in transportation fuels and oleochemicals.
Xu P, Qiao K, Ahn WS, Stephanopoulos G., Proc. Natl. Acad. Sci. U.S.A. 113(39), 2016
PMID: 27621436
The development of artificial media for marine algae.
PROVASOLI L, MCLAUGHLIN JJ, DROOP MR., Arch Mikrobiol 25(4), 1957
PMID: 13403656

AUTHOR UNKNOWN, 0
Improving RNA-Seq expression estimates by correcting for fragment bias.
Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L., Genome Biol. 12(3), 2011
PMID: 21410973
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M., Bioinformatics 21(18), 2005
PMID: 16081474
Phytozome: a comparative platform for green plant genomics.
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22110026
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome.
Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E., Genesis 53(8), 2015
PMID: 26201819

AUTHOR UNKNOWN, 2016

AUTHOR UNKNOWN, 0
Starch metabolism in Arabidopsis
Streb S, Zeeman SC., 2012
Starch degradation.
Smith AM, Zeeman SC, Smith SM., Annu Rev Plant Biol 56(), 2005
PMID: 15862090
Chapter 1-starch metabolism A2-Harris, Elizabeth H
Ball SG, Deschamps P., 2009
Genetic engineering of algae for enhanced biofuel production.
Radakovits R, Jinkerson RE, Darzins A, Posewitz MC., Eukaryotic Cell 9(4), 2010
PMID: 20139239

AUTHOR UNKNOWN, 0
How does gene expression clustering work?
D'haeseleer P., Nat. Biotechnol. 23(12), 2005
PMID: 16333293

AUTHOR UNKNOWN, 0
Manipulating fatty acid biosynthesis in microalgae for biofuel through protein-protein interactions.
Blatti JL, Beld J, Behnke CA, Mendez M, Mayfield SP, Burkart MD., PLoS ONE 7(9), 2012
PMID: 23028438

AUTHOR UNKNOWN, 0
Efficient foreign gene expression in Chlamydomonas reinhardtii mediated by an endogenous intron
Lumbreras V, Stevens DR, Purton S., 1998
The bacterial phleomycin resistance geneble as a dominant selectable marker in Chlamydomonas
Stevens DR, Purton S, Rochaix J-D., 1996

AUTHOR UNKNOWN, 0
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