Algal omics: Unlocking bioproduct diversity in algae cell factories

Photosynthesis Research

Volumn 123, Issue 3, 2015, Pages 255-263

  Guarnieri, Michael T ^a   Pienkos, Philip T ^a  

^a NATIONAL RENEWABLE ENERGY LABORATORY   (United States)

Author keywords

Algae; Biofuels; Biotechnology; Cell factory; Omics

Indexed keywords

BIOFUEL; DRUG;

BIOREACTOR; DIET SUPPLEMENTATION; GENETICS; GENOMICS; GREEN ALGA; METABOLIC ENGINEERING; METABOLISM; METABOLOMICS; MICROALGA; PROCEDURES;

BIOFUELS; BIOREACTORS; CHLOROPHYTA; DIETARY SUPPLEMENTS; GENOMICS; METABOLIC ENGINEERING; METABOLOMICS; MICROALGAE; PHARMACEUTICAL PREPARATIONS;

EID: 84895853399     PISSN: 01668595     EISSN: 15735079     Source Type: Journal    
DOI: 10.1007/s11120-014-9989-4     Document Type: Article

References (76)

1. Adarme-Vega TC et al (2012) Microalgal biofactories: a promising approach towards sustainable omega-3 fatty acid production. Microb Cell Fact 11:96
2. Apt KE, Behrens PW (1999) Commercial developments in microalgal biotechnology. J Phycol 35:215
3. Baba M, Ioki M, Nakajima N, Shiraiwa Y, Watanabe MM (2012) Transcriptome analysis of an oil-rich race A strain of Botryococcus braunii (BOT-88-2) by de novo assembly of pyrosequencing cDNA reads. Bioresour Technol 109:282
4. Boyle NR et al (2012) Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J Biol Chem 287:15811
5. Boynton JE et al (1988) Chloroplast transformation in Chlamydomonas with high velocity microprojectiles. Science 240:1534
6. Cordero BF, Couso I, Leon R, Rodriguez H, Vargas MA (2011) Enhancement of carotenoids biosynthesis in Chlamydomonas reinhardtii by nuclear transformation using a phytoene synthase gene isolated from Chlorella zofingiensis. Appl Microbiol Biotechnol 91:341
7. Couso I, Vila M, Rodriguez H, Vargas MA, Leon R (2011) Overexpression of an exogenous phytoene synthase gene in the unicellular alga Chlamydomonas reinhardtii leads to an increase in the content of carotenoids. Biotechnol Prog 27:54
8. Dennis J, Stephenson AL, Howe CJ, Scott SA, Smith AG (2010) Influence of nitrogen-limitation regime on the production by Chlorella vulgaris of lipids for biodiesel feedstocks. Biofuels 1:47
9. Dong Z, Chen Y (2013) Transcriptomics: advances and approaches. Sci China Life Sci 56:960
10. Eisenberg D, Marcotte EM, Xenarios I, Yeates TO (2000) Protein function in the post-genomic era. Nature 405:823
11. Eom H, Lee CG, Jin E (2006) Gene expression profile analysis in astaxanthin-induced Haematococcus pluvialis using a cDNA microarray. Planta 223:1231
12. Fan J, Andre C, Xu C (2011) A chloroplast pathway for the de novo biosynthesis of triacylglycerol in Chlamydomonas reinhardtii. FEBS Lett 585:1985
13. Gaffron H, Rubin J (1942) Fermentative and photochemical production of hydrogen in algae. J Gen Physiol 26:219
14. Ghirardi ML et al (2007) Hydrogenases and hydrogen photoproduction in oxygenic photosynthetic organisms. Annu Rev Plant Biol 58:71
15. Gillet S, Decottignies P, Chardonnet S, Le Marechal P (2006) Cadmium response and redoxin targets in Chlamydomonas reinhardtii: a proteomic approach. Photosynth Res 89:201
16. Golueke CG, Oswald WJ (1959) Biological conversion of light energy to the chemical energy of methane. Appl Microbiol 7:219
17. Gregory JA, Topol AB, Doerner DZ, Mayfield S (2013) Alga-produced cholera toxin-Pfs25 fusion proteins as oral vaccines. Appl Environ Microbiol 79:3917
18. Grossman AR (2005) Paths toward algal genomics. Plant Physiol 137:410
19. Grossman AR et al (2007) Novel metabolism in Chlamydomonas through the lens of genomics. Curr Opin Plant Biol 10:190
20. Guarnieri MT (2013) Comparative proteomics lends insight into genotype-specific pathogenicity. Proteomics 13:2544
21. Guarnieri MT et al (2011) Examination of triacylglycerol biosynthetic pathways via de novo transcriptomic and proteomic analyses in an unsequenced microalga. PLoS One 6:e25851
22. Guarnieri MT, Nag A, Yang S, Pienkos PT (2013) Proteomic analysis of Chlorella vulgaris: potential targets for enhanced lipid accumulation. J Proteomics 93:245
23. Hildebrand M et al (2013) Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production. Curr Opin Chem Biol 17:506
24. Hu Q et al (2008) Microalgal triacylglycerols as feedstocks for biofuel production: perspectives and advances. Plant J 54:621
25. Ioki M et al (2012a) Modes of hydrocarbon oil biosynthesis revealed by comparative gene expression analysis for race A and race B strains of Botryococcus braunii. Bioresour Technol 109:271
26. Ioki M, Baba M, Nakajima N, Shiraiwa Y, Watanabe MM (2012b) Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-70) by de novo assembly of 5′-end sequences of full-length cDNA clones. Bioresour Technol 109:277
27. Ioki M, Baba M, Nakajima N, Shiraiwa Y, Watanabe MM (2012c) Transcriptome analysis of an oil-rich race B strain of Botryococcus braunii (BOT-22) by de novo assembly of pyrosequencing cDNA reads. Bioresour Technol 109:292
28. Jamers A, Blust R, De Coen W (2009) Omics in algae: paving the way for a systems biological understanding of algal stress phenomena? Aquat Toxicol 92:114
29. Jones CS, Mayfield SP (2012) Algae biofuels: versatility for the future of bioenergy. Curr Opin Biotechnol 23:346
30. Karpowicz SJ, Prochnik SE, Grossman AR, Merchant SS (2011) The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. J Biol Chem 286:21427
31. Knoshaug EP, Shi B, Shannon TG, Mleziva MM, Pienkos PT (2013) The potential of photosynthetic aquatic species as sources of useful cellulose fibers - a review. J Appl Phycol 25:1123
32. Lee do Y, Park JJ, Barupal DK, Fiehn O (2012) System response of metabolic networks in Chlamydomonas reinhardtii to total available ammonium. Mol Cell Proteomics 11:973
33. Leon-Banares R, Gonzalez-Ballester D, Galvan A, Fernandez E (2004) Transgenic microalgae as green cell-factories. Trends Biotechnol 22:45
34. Liu GN, Zhu YH, Jiang JG (2009) The metabolomics of carotenoids in engineered cell factory. Appl Microbiol Biotechnol 83:989
35. Lohr M, Im CS, Grossman AR (2005) Genome-based examination of chlorophyll and carotenoid biosynthesis in Chlamydomonas reinhardtii. Plant Physiol 138:490
36. Lohr M, Schwender J, Polle JE (2012) Isoprenoid biosynthesis in eukaryotic phototrophs: a spotlight on algae. Plant Sci 185-186:9
37. Lopez D, Casero D, Cokus SJ, Merchant SS, Pellegrini M (2011) Algal functional annotation tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. BMC Bioinform 12:282
38. Lu Y, Oyler GA (2009) Green algae as a platform to express therapeutic proteins. Discov Med 8:28
39. Lv H et al (2013) Transcriptome analysis of Chlamydomonas reinhardtii during the process of lipid accumulation. Genomics 101:229
40. Matsushima D et al (2012) The single cellular green microalga Botryococcus braunii, race B possesses three distinct 1-deoxy-d-xylulose 5-phosphate synthases. Plant Sci 185-186:309
41. Mayfield SP, Kindle KL (1990) Stable nuclear transformation of Chlamydomonas reinhardtii by using a C. reinhardtii gene as the selectable marker. Proc Natl Acad Sci USA 87:2087
42. Mayfield SP, Franklin SE, Lerner RA (2003) Expression and assembly of a fully active antibody in algae. Proc Natl Acad Sci USA 100:438
43. Merchant SS et al (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318:245
44. Miller R et al (2010) Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism. Plant Physiol 154:1737
45. Moellering ER, Benning C (2010) RNA interference silencing of a major lipid droplet protein affects lipid droplet size in Chlamydomonas reinhardtii. Eukaryot Cell 9:97
46. Molnar I et al (2012) Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa). BMC Genom 13:576
47. Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255
48. Msanne J et al (2012) Metabolic and gene expression changes triggered by nitrogen deprivation in the photoautotrophically grown microalgae Chlamydomonas reinhardtii and Coccomyxa sp. C-169. Phytochemistry 75:50
49. Murphy CD (2012) The microbial cell factory. Org Biomol Chem 10:1949
50. Mus F, Dubini A, Seibert M, Posewitz MC, Grossman AR (2007) Anaerobic acclimation in Chlamydomonas reinhardtii: anoxic gene expression, hydrogenase induction, and metabolic pathways. J Biol Chem 282:25475
51. Nguyen AV et al (2008) Transcriptome for photobiological hydrogen production induced by sulfur deprivation in the green alga Chlamydomonas reinhardtii. Eukaryot Cell 7:1965
52. Nguyen HM et al (2011) Proteomic profiling of oil bodies isolated from the unicellular green microalga Chlamydomonas reinhardtii: with focus on proteins involved in lipid metabolism. Proteomics 11:4266
53. Niehaus TD et al (2011) Identification of unique mechanisms for triterpene biosynthesis in Botryococcus braunii. Proc Natl Acad Sci USA 108:12260
54. Niehaus TD et al (2012) Functional identification of triterpene methyltransferases from Botryococcus braunii race B. J Biol Chem 287:8163
55. Okazaki Y, Saito K (2012) Recent advances of metabolomics in plant biotechnology. Plant Biotechnol Rep 6:1
56. Patel N et al (2004) Differential gene expression of Chlamydomonas reinhardtii in response to 2,4,6-trinitrotoluene (TNT) using microarray analysis. Plant Sci 167:1109
57. Patel VJ et al (2009) A comparison of labeling and label-free mass spectrometry-based proteomics approaches. J Proteome Res 8:3752
58. Radakovits R, Jinkerson RE, Darzins A, Posewitz MC (2010) Genetic engineering of algae for enhanced biofuel production. Eukaryot Cell 9:486
59. Ramos AA et al (2009) Molecular and functional characterization of a cDNA encoding 4-hydroxy-3-methylbut-2-enyl diphosphate reductase from Dunaliella salina. J Plant Physiol 166:968
60. Rasala BA et al (2012) Robust expression and secretion of Xylanase1 in Chlamydomonas reinhardtii by fusion to a selection gene and processing with the FMDV 2A peptide. PLoS One 7:e43349
61. Rismani-Yazdi H, Haznedaroglu BZ, Hsin C, Peccia J (2012) Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation. Biotechnol Biofuels 5:74
62. Rosenberg JN, Oyler GA, Wilkinson L, Betenbaugh MJ (2008) A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution. Curr Opin Biotechnol 19:430
63. Sheehan J, Dunahay T, Bennemann J, Roessler P (1998) "DOE aquatic species program closeout report. www.nrel.gov/docs/legosti/fy98/24190.pdf "
64. Shrestha RP et al (2012) Whole transcriptome analysis of the silicon response of the diatom Thalassiosira pseudonana. BMC Genom 13:499
65. Simon DF, Descombes P, Zerges W, Wilkinson KJ (2008) Global expression profiling of Chlamydomonas reinhardtii exposed to trace levels of free cadmium. Environ Toxicol Chem 27:1668
66. Specht E, Miyake-Stoner S, Mayfield S (2010) Micro-algae come of age as a platform for recombinant protein production. Biotechnol Lett 32:1373
67. Sun TH et al (2010) Coordinated regulation of gene expression for carotenoid metabolism in Chlamydomonas reinhardtii. J Integr Plant Biol 52:868
68. Takaichi S (2011) Carotenoids in algae: distributions, biosyntheses and functions. Mar Drugs 9:1101
69. Toepel J et al (2013) New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. Plant Biotechnol J 11:717
70. Tran M et al (2013a) Production of anti-cancer immunotoxins in algae: ribosome inactivating proteins as fusion partners. Biotechnol Bioeng 110:2826
71. Tran M et al (2013b) Production of unique immunotoxin cancer therapeutics in algal chloroplasts. Proc Natl Acad Sci USA 110:E15
72. Vanderschuren H, Lentz E, Zainuddin I, Gruissem W (2013) Proteomics of model and crop plant species: status, current limitations and strategic advances for crop improvement. J Proteomics 93:5
73. Wu Q, Yuan H, Zhang L, Zhang Y (2012) Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis - a review. Anal Chim Acta 731:1
74. Yang S, Guarnieri MT, Smolinski S, Ghirardi M, Pienkos PT (2013) De novo transcriptomic analysis of hydrogen production in the green alga Chlamydomonas moewusii through RNA-Seq. Biotechnol Biofuels 6:118
75. Yohn C, Mendez M, Behnke C, Brand A (2011) Stress-induced lipid trigger. Patent No WO/2011 97261:11
76. Yu Y et al (2013) Development of Synechocystis sp. PCC 6803 as a phototrophic cell factory. Mar Drugs 11:2894