Using natural selection to explore the adaptive potential of Chlamydomonas reinhardtii

PLoS ONE

Volumn 9, Issue 3, 2014, Pages

  Perrineau, Marie Mathilde ^a   Gross, Jeferson ^a   Zelzion, Ehud ^a   Price, Dana C ^a   Levitan, Orly ^a   Boyd, Jeffrey ^a   Bhattacharya, Debashish ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; NITROGEN; ORGANIC CARBON; TRANSCRIPTOME;

ALGAL CELL CULTURE; AMINO ACID SUBSTITUTION; ARTICLE; CARBON SOURCE; CELL CYCLE; CELL GROWTH; CELL RESPIRATION; CHLAMYDOMONAS REINHARDTII; CONTROLLED STUDY; DEPLETION; DILUTION; DNA POLYMORPHISM; DNA REPAIR; DOWN REGULATION; EVOLUTIONARY ADAPTATION; GENE CONTROL; GENE SEQUENCE; GENETIC STRAIN; GENOME; GROWTH RATE; LIGHT EXPOSURE; LIPID STORAGE; LIQUID CULTURE; NATURAL SELECTION; NITROGEN DEPLETION; NONHUMAN; PHOTOSYNTHESIS; PROTEIN SYNTHESIS; SINGLE NUCLEOTIDE POLYMORPHISM; STEM CELL; STRAIN IMPROVEMENT; UPREGULATION; ADAPTATION; GENETIC SELECTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM;

ADAPTATION, PHYSIOLOGICAL; CHLAMYDOMONAS REINHARDTII; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC;

EID: 84899085300     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0092533     Document Type: Article

References (55)

1. Harris JM (2013) Population, resources, and energy in the global economy: A vindication of Herman Daly's vision. Working Paper - Global Development and Environment Institute, Tufts University. 20 p.
2. Sheehan J, Dunahay T, Benemann J, Roessler P (1998) Look back at the U.S. department of energy's aquatic species program: biodiesel from algae; close-out report. NREL Report Number TP-580-24190. 325 p.
3. Huesemann MH, Hausmann TS, Bartha R, Aksoy M, Weissman JC, et al. (2009) Biomass productivities in wild type and pigment mutant of Cyclotella sp. (Diatom). Appl Biochem Biotechnol 157: 507-526.
4. Hannon M, Gimpel J, Tran M, Rasala B, Mayfield S (2010) Biofuels from algae: Challenges and potential. Biofuels 1: 763-784.
5. Demirbas A, Demirbas MF (2011) Importance of algae oil as a source of biodiesel. Energy Conver Manage 52: 163-170.
6. Russell GE (1978) Plant breeding for pest and disease resistance. Butterworths. 485 p.
7. Acquaah G (2007) Principles of plant genetics and breeding. Blackwell. 584 p.
8. Snow AA, Smith VH (2012) Genetically engineered algae for biofuels: a key role for ecologists. BioScience 62: 765-768.
9. Lenski RE, Rose MR, Simpson SC, Tadler SC (1991) Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. Am Nat 138: 1315-1341.
10. Elena SF, Lenski RE (2003) Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4: 457-469. (Pubitemid 36648145)
11. Bell G (2012) Experimental evolution of heterotrophy in a green alga. Evolution 67: 468-476.
12. Kawecki TJ, Lenski RE, Ebert D, Hollis B, Olivieri I, et al. (2012) Experimental evolution. Trends Ecol Evol 27: 547-560.
13. Blount ZD, Barrick JE, Davidson CJ, Lenski RE (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489: 513-518.
14. Lohbeck KT, Riebesell U, Collins S, Reusch TBH (2013) Functional genetic divergence in high co2 adapted Emiliania huxleyi populations. Evolution 67: 1892-1900.
15. Brueggeman AJ, Gangadharaiah DS, Cserhati MF, Casero D, Weeks DP, et al. (2012) Activation of the carbon concentrating mechanism by CO2 deprivation coincides with massive transcriptional restructuring in Chlamydomonas reinhardtii. Plant Cell 24: 1860-1875.
16. Fang W, Si Y, Douglass S, Casero D, Merchant SS, et al. (2012) Transcriptomewide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell 24: 1876-1893.
17. González-Ballester D, Casero D, Cokus S, Pellegrini M, Merchant SS, et al. (2010) RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell 22: 2058-2084.
18. Collins S (2011) Many possible worlds: expanding the ecological scenarios in experimental evolution. Evol Biol 38: 3-14.
19. Gu Z, Oliver S (2009) Yeasts as models in evolutionary biology. Genome Biol 10: 304-306.
20. Collins S, Bell G (2004) Phenotypic consequences of 1,000 generations of selection at elevated CO2 in a green alga. Nature 431: 566-569. (Pubitemid 39336336)
21. Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, et al. (2007) The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 318: 245-250.
22. Gorman DS, Levine RP (1965) Cytochrome f and plastocyanin: their sequence in the photosynthetic electron transport chain of Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 54: 1665-1669.
23. Govender T, Ramanna L, Rawat I, Bux F (2012) BODIPY staining, an alternative to the Nile Red fluorescence method for the evaluation of intracellular lipids in microalgae. Bioresour Technol 114: 507-511.
24. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25: 402-408. (Pubitemid 34164012)
25. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106.
26. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Stat Soc Ser B 57: 289-300.
27. Sung W, Ackerman MS, Miller SF, Doak TG, Lynch M (2012) Drift-barrier hypothesis and mutation-rate evolution. Proc Natl Acad Sci USA 109: 18488-18492.
28. Castruita M, Casero D, Karpowicz SJ, Kropat J, Vieler A, et al. (2011) Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. Plant Cell 23: 1273-1292.
29. Marañón E, Cermeño P, López-Sandoval DC, Rodríguez-Ramos T, Sobrino C, et al. (2013) Unimodal size scaling of phytoplankton growth and the size dependence of nutrient uptake and use. Ecology Lett 16: 371-379.
30. Bec B, Collos Y, Vaquer A (2008) Growth rate peaks at intermediate cell size in marine photosynthetic picoeukaryotes. Limnol Oceanogr 53: 863-867. (Pubitemid 351705433)
31. Lee K, Lee C-G (2001) Effect of light/dark cycles on wastewater treatments by microalgae. Biotechnol Bioprocess Eng 6: 194-199. (Pubitemid 33811603)
32. Ness RW, Morgan AD, Colegrave N, Keightley PD (2012) Estimate of the spontaneous mutation rate in Chlamydomonas reinhardtii. Genetics 192: 1447-1454.
33. Jeong B, Wu-Scharf D, Zhang C, Cerutti H (2002) Suppressors of transcriptional transgenic silencing in Chlamydomonas are sensitive to DNA-damaging agents and reactivate transposable elements. Proc Natl Acad Sci USA 99: 1076-1081. (Pubitemid 34106638)
34. Luck M, Mathes T, Bruun S, Fudim R, Hagedorn R, et al. (2012) A photochromic histidine kinase rhodopsin (HKR1) that is bimodally switched by ultraviolet and blue light. J Biol Chem 287: 40083-40090.
35. Dittami SM, Gravot A, Goulitquer S, Rousvoal S, Peters AF, Bouchereau A, Boyen C, Tonon T (2012) Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae). Plant J 71: 366-377.
36. Rudra D, Warner JR (2004) What better measure than ribosome synthesis? Genes Develop 18: 2431-2436. (Pubitemid 39362886)
37. Bailis JM, Luche DD, Hunter T, Forsburg SL (2008) Minichromosome maintenance proteins interact with checkpoint and recombination proteins to promote s-phase genome stability. Mol Cell Biol 28: 1724-1738.
38. Santosa V, Martha S, Hirose N, Tanaka K (2013) The fission yeast minichromosome maintenance (MCM)-binding protein (MCM-BP), Mcb1, regulates MCM function during prereplicative complex formation in DNA replication. J Biol Chem 288: 6864-6880.
39. Liang DT, Hodson JA, Forsburg SL (1999) Reduced dosage of a single fission yeast MCM protein causes genetic instability and S phase delay. J Cell Sci 112: 559-567. (Pubitemid 29106202)
40. Maki K, Inoue T, Onaka A, Hashizume H, Somete N, et al. (2011) An abundance of pre-replicative complexes (pre-RCs) facilitates recombinational repair under replication stress in fission yeast. J Biol Chem 286: 41701-41710.
41. Andersen SL, Sekelsky J (2010) Meiotic versus mitotic recombination: two different routes for double-strand break repair. Bioessays 32: 1058-1066.
42. Mittag M, Kiaulehn S, Johnson CH (2005) The circadian clock in Chlamydomonas reinhardtii . What is it for? What is it similar to? Plant Physiol 137: 399-409. (Pubitemid 43126674)
43. Niwa Y, Matsuo T, Onai K, Kato D, Tachikawa M, Ishiura M (2013) Phase-resetting mechanism of the circadian clock in Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 110: 13666-13671.
44. Nishihama R, Kohchi T (2013) Evolutionary insights into photoregulation of the cell cycle in the green lineage. Curr Opin Plant Biol 16:630-637.
45. Reisdorph NA, Small GD (2004) The CPH1 gene of Chlamydomonas reinhardtii encodes two forms of cryptochrome whose levels are controlled by light-induced proteolysis. Plant Physiol 134: 1546-1554. (Pubitemid 38527364)
46. Gokhale A, Wirschell M, Sale WS (2009) Regulation of dynein-driven microtubule sliding by the axonemal protein kinase CK1 in Chlamydomonas flagella. J Cell Biol 186: 817-824.
47. Vlcek D, Sevcovicová A, Sviezená B, Gálová E, Miadoková E (2008) Chlamydomonas reinhardtii: a convenient model system for the study of DNA repair in photoautotrophic eukaryotes. Curr Genet 53: 1-22. (Pubitemid 50002018)
48. Heifetz PB, Förster B, Osmond CB, Giles LJ, Boynton JE (2000) Effects of acetate on facultative autotrophy in Chlamydomonas reinhardtii assessed by photosynthetic measurements and stable isotope analyses. Plant Physiol 122: 1439-1445. (Pubitemid 30221423)
49. Johnson X, Alric J (2013) Central carbon metabolism and electron transport in Chlamydomonas reinhardtii, metabolic constraints for carbon partitioning between oil and starch. Eukaryot cell 12: 776-793.
50. Zhila NO, Kalacheva GS, Volova TG, Botryococcus A, Ippas K (2005) Effect of nitrogen limitation on the growth and lipid composition of the green alga Botryococcus braunii Kütz IPPAS H-252. Russ J Plant Physiol 52: 357-365.
51. Miller R, Wu G, Deshpande RR, Vieler A, Gärtner K, et al. (2010) Changes in transcript abundance in Chlamydomonas reinhardtii following nitrogen deprivation predict diversion of metabolism. Plant Physiol 154: 1737-1752.
52. Fett JP, Coleman JR (1994) Regulation of periplasmic carbonic anhydrase expression in Chlamydomonas reinhardtii by acetate and pH. Plant Physiol 106: 103-108.
53. Matsuo M, Endo T, Asada K (1998) Properties of the respiratory NAD(P)H dehydrogenase isolated from the cyanobacterium Synechocystis PCC6803. Plant Cell Physiol 39: 263-267. (Pubitemid 28186890)
54. Page MD, Allen MD, Kropat J, Urzica EI, Karpowicz SJ, et al. (2012) Fe sparing and Fe recycling contribute to increased superoxide dismutase capacity in iron-starved Chlamydomonas reinhardtii. Plant Cell 24: 2649-2665.
55. Griffiths MJ, Harrison STL (2009) Lipid productivity as a key characteristic for choosing algal species for biodiesel production. J Appl Phycol 21: 493-507.