Abstract
The unicellular green alga Chlamydomonas reinhardtii has two flagella and a primitive visual system, the eyespot apparatus, which allows the cell to phototax. About 40 years ago, it was shown that the circadian clock controls its phototactic movement. Since then, several circadian rhythms such as chemotaxis, cell division, UV sensitivity, adherence to glass, or starch metabolism have been characterized. The availability of its entire genome sequence along with homology studies and the analysis of several sub-proteomes render C. reinhardtii as an excellent eukaryotic model organism to study its circadian clock at different levels of organization. Previous studies point to several potential photoreceptors that may be involved in forwarding light information to entrain its clock. However, experimental data are still missing toward this end. In the past years, several components have been functionally characterized that are likely to be part of the oscillatory machinery of C. reinhardtii since alterations in their expression levels or insertional mutagenesis of the genes resulted in defects in phase, period, or amplitude of at least two independent measured rhythms. These include several RHYTHM OF CHLOROPLAST (ROC) proteins, a CONSTANS protein (CrCO) that is involved in parallel in photoperiodic control, as well as the two subunits of the circadian RNA-binding protein CHLAMY1. The latter is also tightly connected to circadian output processes. Several candidates including a significant number of ROCs, CrCO, and CASEIN KINASE1 whose alterations of expression affect the circadian clock have in parallel severe effects on the release of daughter cells, flagellar formation, and/or movement, indicating that these processes are interconnected in C. reinhardtii. The challenging task for the future will be to get insights into the clock network and to find out how the clock-related factors are functionally connected. In this respect, system biology approaches will certainly contribute in the future to improve our understanding of the C. reinhardtii clock machinery.
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Abbreviations
- arg7 :
-
Encoding ASL
- ASL:
-
ARGININO SUCCINATE LYASE
- BP:
-
BINDING PROTEIN
- C (1, 3):
-
C (1, 3) subunit of CHLAMY1
- CAB:
-
CHLOROPHYLL a/b BINDING PROTEIN
- CCA1:
-
CIRCADIAN CLOCK-ASSOCIATED 1
- CCT:
-
CO-COL-TOC1
- CDKB1:
-
CYCLIN-DEPENDENT KINASE B1
- CO:
-
CONSTANS
- COL:
-
CONSTANS-like
- ChR (1, 2):
-
CHANNELRHODOPSIN-(1, 2)
- CK (1, 2):
-
CASEIN KINASE (1, 2)
- CrCO:
-
CONSTANS of C. reinhardtii
- CRY (a, p):
-
CRYPTOCHROME (animal-like, plant-like)
- CT:
-
Circadian time
- CYCA1:
-
CYCLIN A1
- DREB1A:
-
Dehydration response element binding1A
- EST:
-
Expressed sequence tag
- FMRP:
-
FRAGILE X MENTAL RETARDATION PROTEIN
- FRQ:
-
FREQUENCY
- GBSSI:
-
GRANULE-BOUND STARCH SYNTHASE
- GRP (7, 8):
-
GLYCINE-RICH RNA-BINDING PROTEIN
- GS2:
-
GLUTAMINE SYNTHETASE 2
- HBP:
-
HEME-BINDING PROTEIN
- LD:
-
Long day
- LHY:
-
LATE ELONGATED HYPOCOTYL
- NII1:
-
NITRITE REDUCTASE 1
- NPAS2:
-
NEURONAL PAS DOMAIN PROTEIN 2
- Ox:
-
Overexpressing
- PAS:
-
PER-ARNT-SIM
- PER:
-
PERIOD
- PHOT:
-
PHOTOTROPIN
- PHY:
-
PHYTOCHROME
- PP (1, 2A):
-
PROTEIN PHOSPHATASE (1, 2A)
- RNAi:
-
RNA interference
- ROC:
-
RHYTHM OF CHLOROPLAST
- RRM:
-
RNA recognition motif
- SD:
-
Short day
- SOUL3:
-
SOUL-HEME-BINDING-PROTEIN3
- TIM:
-
TIMELESS
- TOC1:
-
TIMING OF CAB EXPRESSION1
References
Agarwal PK, Agarwal P, Reddy MK, Sopory SK (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25:1263–1274. doi:10.1007/s00299-006-0204-8
Barreau C, Paillard L, Méreau A, Osborne HB (2006) Mammalian CELF/Bruno-like RNA-binding proteins: molecular characteristics and biological functions. Biochimie 88:515–525. doi:10.1016/j.biochi.2005.10.011
Boesger J, Wagner V, Weisheit W, Mittag M (2009) Analysis of flagellar phosphoproteins from Chlamydomonas reinhardtii. Eukaryot Cell 8:922–932. doi:10.1128/EC.00067-09
Breton G, Kay SA (2006) Circadian rhythms lit up in Chlamydomonas. Genome Biol 7:215. doi:10.1186/gb-2006-7-4-215
Bruce VG (1970) The biological clock in Chlamydomonas reinhardtii. J Protozool 17:328–334
Bruce VG (1972) Mutants of the biological clock in Chlamydomonas reinhardtii. Genetics 70:537–548
Bruce VG (1974) Recombinants between clock mutants of Chlamydomonas reinhardtii. Genetics 77:221–230
Byrne TE, Wells MR, Johnson CH (1992) Circadian rhythms of chemotaxis to ammonium and methylammonium uptake in Chlamydomonas. Plant Physiol 98:879–886
Corellou F, Schwartz C, Motta J-P, Djouani-Tahri EB, Samchez F, Bouget F-Y (2009) Clocks in the green lineage: comparative functional analysis of the circadian architecture of the picoeukaryote Ostreococcus. Plant Cell 21:3436–3449. doi:10.1105/tpc.109.068825
DeBruyne JP, Weaver DR, Reppert SM (2007) Peripheral circadian oscillators require CLOCK. Curr Biol 17:R538–9. doi:10.1016/j.cub.2007.05.067
Fernandez E, Galvan A (2008) Nitrate assimilation in Chlamydomonas. Eukaryot Cell 4:555–559. doi:10.1128/EC.00431-07
Garbarino-Pico E, Green CB (2007) Posttranscriptional regulation of mammalian circadian clock output. Cold Spring Harb Symp Quant Biol 72:145–156. doi:10.1101/sqb.2007.72.022
Goldman BD (2001) Mammalian photoperiodic system: formal properties and neuroendocrine mechanisms of photoperiodic time measurement. J Biol Rhythms 16:283–301. doi:10.1177/074873001129001980
Goodwin BC (1965) Oscillatory behavior in enzymatic control processes. Adv Enzyme Regul 3:425–438
Goto K, Johnson CH (1995) Is the cell division cycle gated by a circadian clock? The case of Chlamydomonas reinhardtii. J Cell Biol 129:1061–1069
Grossman AR, Harris EE, Hauser C, Lefebvre PA, Martinez D, Rokhsar D, Shrager J, Silflow CD, Stern D, Vallon O, Zhang Z (2003) Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryot Cell 2:1137–1150. doi:10.1128/EC.2.6.1137-1150.2003
Hanai S, Hamasaka Y, Ishida N (2008) Circadian entrainment to red light in Drosophila: requirement of Rhodopsin 1 and Rhodopsin 6. Neuroreport 19:1441–1444. doi:10.1097/WNR.0b013e32830e4961
Harmer SL (2009) The circadian system in higher plants. Annu Rev Plant Biol 60:357–377. doi:10.1146/annurev.arplant.043008.092054
Harris EH (2001) Chlamydomonas as a model organism. Annu Rev Plant Physiol Plant Mol Biol 52:363–406. doi:10.1146/annurev.arplant.52.1.363
Hegemann P (2008) Algal sensory photoreceptors. Annu Rev Plant Biol 59:167–189. doi:10.1146/annurev.arplant.59.032607.092847
Heitzer M, Eckert A, Fuhrmann M, Griesbeck C (2007) Influence of codon bias on the expression of foreign genes in microalgae. Adv Exp Med Biol 616:46–53. doi:10.1007/978-0-387-75532-8_5
Huang K, Beck CF (2003) Phototropin is the blue-light receptor that controls multiple steps in the sexual life cycle of the green alga Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 100:6269–6274. doi:10.1073/pnas.0931459100
Hubbard KE, Robertson FC, Dalchau N, Webb AA (2010) Systems analyses of circadian networks. Mol Biosyst. doi: 10.1039/b907714f
Hwang S, Kawazoe R, Herrin DL (1996) Transcription of tufA and other chloroplast-encoded genes is controlled by a circadian clock in Chlamydomonas. Proc Natl Acad Sci 93:996–1000
Iliev D, Voytsekh O, Schmidt EM, Fiedler M, Nykytenko A, Mittag M (2006a) A heteromeric RNA-binding protein is involved in maintaining acrophase and period of the circadian clock. Plant Physiol 142:797–806. doi:10.1104/pp. 106.085944
Iliev D, Voytsekh O, Mittag M (2006b) The circadian system of Chlamydomonas reinhardtii. Biol Rhythms Res 37:323–333
Immeln D, Schlesinger R, Heberle J, Kottke T (2007) Blue light induces radical formation and autophosphorylation in the light-sensitive domain of Chlamydomonas cryptochrome. J Biol Chem 282:21720–21728. doi:10.1074/jbc.M700849200
Jacobshagen S, Kessler B, Rinehart CA (2008) At least four distinct circadian regulatory mechanisms are required for all phases of rhythms in mRNA amount. J Biol Rhythms 23:511–524. doi:10.1177/0748730408325753
Johnson CH, Kondo T, Hastings JW (1991) Action spectrum for resetting the circadian phototaxis rhythm in the CW15 strain of Chlamydomonas. II. Illuminated cells. Plant Physiol 97:1122–1129
Johnson CH, Kondo T, Goto K (1992) Circadian rhythms in Chlamydomonas. In: Honma K, Honma S, Hiroshige T (eds) Circadian clocks from cell to human: Proceedings of the Fourth Sapporo Symposium on Biological Rhythms. Hokkaido University Press, Sapporo, pp 139–155
Kiaulehn S, Voytsekh O, Fuhrmann M, Mittag M (2007) The presence of UG-repeat sequences in the 3′-UTRs of reporter luciferase mRNAs mediates circadian expression and can determine acrophase in Chlamydomonas reinhardtii. J Biol Rhythms 22:275–277. doi:10.1177/0748730407301053
Kitanishi K, Igarashi J, Havasaka K, Hikage N, Saiful I, Yamauchi S, Uchida T, Ishimori K, Shimizu T (2008) Heme-binding characteristics of the isolated PAS-A domain of mouse Per2, a transcriptional regulatory factor associated with circadian rhythms. Biochemistry 47:6157–6168. doi:10.1021/bi7023892
Kondo T, Johnson CH, Hastings JW (1991) Action spectrum for resetting the circadian phototaxis rhythm in the CW15 strain of Chlamydomonas. I. Cells in darkness. Plant Physiol 95:197–205
Kottke T, Hegemann P, Dick B, Heberle J (2006) The photochemistry of the light-, oxygen-, and voltage-sensitive domains in the algal blue light receptor phot. Biopolymers 82:373–378. doi:10.1002/bip.20510
Kucho K, Okamoto K, Tabata S, Fukuzawa H, Ishiura M (2005) Identification of novel clock-controlled genes by cDNA macroarray analysis in Chlamydomonas reinhardtii. Plant Mol Biol 57:889–906. doi:10.1007/s11103-005-3248-1
Manichaikul A, Ghamsari L, Hom EFY, Lin Ch, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK, Thiele I, Yang X, Fan Ch, Mello E, Hill DE, Vidal M, Salehi-Ashtiani K, Papin JA (2009) Metabolic network analysis integrated with transcript verification for sequenced genomes. Nature Methods 6:589–592. doi:10.1038/nmeth.1348
Marshall WF (2008) The cell biological basis of ciliary disease. J Cell Biol 180:17–21. doi:10.1083/jcb.200710085
Matsuo T, Okamoto K, Onai K, Niwa Y, Shimogawara K, Ishiura M (2008) A systematic forward genetic analysis identified components of the Chlamydomonas circadian system. Genes Dev 22:918–930. doi:10.1101/gad.1650408
May P, Christian JO, Kempa S, Walther D (2009) ChlamyCyc: an integrative systems biology database and webportal for Chlamydomonas reinhardtii. BMC Genomics 10:209. doi:10.1186/1471-2164-10-209
Mehra A, Baker CL, Loros JJ, Dunlap JC (2009) Post-translational modifications in circadian rhythms. Trends Biochem Sci 34:483–490. doi:10.1016/j.tibs.2009.06.006
Meng OJ, McMaster A, Beesley S, Lu WQ, Gibbs J, Parks D, Collins J, Farrow S, Donn R, Ray D, Loudon A (2008) Ligand modulation of REV-ERBalpha fuction resets the peripheral circadian clock in a phasic manner. J Cell Sci 121:3629–3635. doi:10.1242/10.1242/jcs.035048
Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Maréchal-Drouard L et al (2007) The evolution of key animal and plant functions is revealed by analysis of the Chlamydomonas genome. Science 318:245–250. doi:10.1126/science.1143609
Mergenhagen D (1984) Circadian clock: genetic characterization of a short period mutant of Chlamydomonas reinhardii. Eur J Cell Biol 33:13–18
Mergenhagen D, Schweiger HG (1975) The effect of different inhibitors of transcription and translation on the expression and control of circadian rhythm in individual cells of Acetabularia. Exp Cell Res 94:321–326
Mergenhagen D, Mergenhagen E (1987) The biological clock of Chlamydomonas reinhardii in space. Eur J Cell Biol 43:203–207
Mittag M (1996) Conserved circadian elements in phylogenetically diverse algae. Proc Natl Acad Sci USA 93:14401–14404
Mittag M, Wagner V (2003) The circadian clock of the unicellular eukaryotic model organism Chlamydomonas reinhardtii. Biol Chem 384:689–695. doi:10.1515/BC.2003.077
Mittag M, Kiaulehn S, Johnson CH (2005) The circadian clock in Chlamydomonas reinhardtii. What is for? What is similar to? Plant Physiol 137:399–409. doi:10.1104/pp.104.052415
Nagel G, Szellas T, Huhn W, Kateriya S, Adeishvili N, Berthold P, Ollig D, Hegemann P, Bamberg E (2003) Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc Natl Acad Sci USA 100:13940–13945. doi:10.1073/pnas.1936192100
Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, Kondo T (2005) Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science 308:414–415. doi:10.1126/science.1108451
Nikaido SS, Johnson CH (2000) Daily and circadian variation in survival from ultraviolet radiation in Chlamydomonas reinhardtii. Photochem Photobiol 71:758–765. doi:10.1562/0031-8655(2000)0710758DACVIS2.0.CO2
Pajuelo E, Pajuelo P, Clemente MT, Marquez AJ (1995) Regulation of the expression of ferredoxin-nitrite reductase in synchronous cultures of Chlamydomonas reinhardtii. Biochim Biophys Acta 1249:72–78
Pazour GJ, Agrin N, Leszyk J, Witman GB (2005) Proteomic analysis of a eukaryotic cilium. J Cell Biol 170:103–113. doi:10.1083/jcb.200504008
Ral JP, Colleoni C, Wattebled F, Dauvillée D, Nempont C, Deschamps P, Li Z, Morell MK, Chibbar R, Purton S, d’Hulst C, Ball SG (2006) Circadian clock regulation of starch metabolism establishes GBSSI as a major contributor to amylopectin synthesis in Chlamydomonas reinhardtii. Plant Physiol 142:305–317. doi:10.1104/pp.106.081885
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. doi:10.1104/pp.103.031930
Reiter RJ (1993) The melatonin rhythm: both a clock and a calendar. Experientia 49:654–664. doi:10.1007/BF01923947
Rensing L, Ruoff P (2002) Temperature effect on entrainment, phase shifting, and amplitude of circadian clocks and its molecular bases. Chronobiol Int 19:807–864. doi:10.1081/CBI-120014569
Robson F, Costa MM, Hepworth S, Vizir I, Pineiro M, Reeves PH, Putterill J, Coupland G (2001) Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. Plant J 28:619–631. doi:10.1046/j.1365-313x.2001.01163.x
Rockwell NC, Su Y-S, Lagarias JC (2006) Phytochrome structure and signaling mechanisms. Annu Rev Plant Biol 75:837–858. doi:10.1146/annurev.arplant.56.032604.144208
Rolland N, Atteia A, Decottignies P, Garin J, Hippler M, Kreimer G, Lemaire SD, Mittag M, Wagner V (2009) Chlamydomonas proteomics. Curr Opin Microbiol 12:285–291. doi:10.16/j.mib.2009.04.001
Romero JM, Valverde F (2009) Evolutionarily conserved photoperiodic mechanisms in plants. Plant Signaling & Behavior 4:642–644. doi:10.1016/j.cub.2009.01.044
Rupprecht J (2009) From systems biology to fuel—Chlamydomonas reinhardtii as a model for a systems biology approach to improve biohydrogen production. J Biotechnol 142:10–20. doi:10.1016/j.jbiotec.2009.02.008
Salvador ML, Klein U, Bogorad L (1998) Endogenous fluctuations of DNA topology in the chloroplast of Chlamydomonas reinhardtii. Mol Cell Biol 18:7235–7242
Sato E, Sagami I, Uchida T, Sato A, Kitagawa T, Igarashi J, Shimizu T (2004) SOUL in mouse eyes is a new hexameric heme-binding protein with characteristic optical absorption, resonance Raman spectral and heme-binding properties. Biochemistry 43:14189–14198. doi:10.1021/bi048742i
Schmidt M, Gessner G, Luff M, Heiland I, Wagner V, Kaminski M, Geimer S, Eitzinger N, Reissenweber T, Voytsekh O et al (2006) Proteomic analysis of the eyespot of Chlamydomonas reinhardtii provides novel insights into its components and tactic movements. Plant Cell 18:1908–1930. doi:10.1105/tpc.106.041749
Schöning JC, Streitner C, Meyer IM, Gao Y, Staiger D (2008) Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis. Nucleic Acids Res 36:6977–6987. doi:10.1093/nar/gkn847
Serrano G, Herrera-Palau R, Romero JM, Serrano A, Coupland G, Valverde F (2009) Chlamydomonas CONSTANS and the evolution of plant photoperiodic signaling. Curr Biol 19:359–368. doi:10.1016/j.cub.2009.01.044
Silflow CD, Lefebvre PA (2001) Assembly and motility of eukaryotic cilia and flagella. Lessons from Chlamydomonas reinhardtii. Plant Physiol 127:1500–1507. doi:10.1104/pp.010807
Sofola O, Sundram V, Ng F, Kleyner Y, Morales J, Botas J, Jackson FR, Nelson DL (2008) The Drosophila FMRP and LARK RNA-binding proteins function together to regulate eye development and circadian behavior. Neurosci 28:10200–10205. doi:10.1523/JNEUROSCI.2786-08.2008
Straley SC, Bruce VG (1979) Stickiness to glass: circadian changes in the cell surface of Chlamydomonas reinhardtii. Plant Physiol 63:1175–1181
Suzuki L, Johnson CH (2002) Photoperiodic control of germination in the unicell Chlamydomonas. Naturwissenschaften 89:214–220. doi:10.1007/s00114-002-0302-6
Sweeney BM, Haxo FT (1961) Persistence of a photosynthetic rhythm in enucleated Acetabularia. Science 134:1361–1363
Tsuda K, Kuwasako K, Takahashi M, Someya T, Inoue M, Tereda T, Kobayashi N, Shirouzu M, Kigawa T, Tanaka A et al (2009) Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3. Nucleic Acids Res 37:5151–5166. doi:10.1093/nar/gkp546
Voytsekh O, Seitz SB, Iliev D, Mittag M (2008) Both subunits of the circadian RNA-binding protein CHLAMY1 can integrate temperature information. Plant Physiol 147:2179–2193. doi:10.1104/pp.108.118570
Wagner V, Fiedler M, Markert C, Hippler M, Mittag M (2004) Functional proteomics of circadian expressed proteins from Chlamydomonas reinhardtii. FEBS Lett 559:129–135. doi:10.1016/S0014-5793(04)00051-1
Wagner V, Ullmann K, Mollwo A, Kaminski M, Mittag M, Kreimer G (2008) The phosphoproteome of a Chlamydomonas reinhardtii eyespot fraction includes key proteins of the light signaling pathway. Plant Physiol 146:772–788. doi:10.1104/pp.107.109645
Wagner V, Boesger J, Mittag M (2009) Sub-proteome analysis in the green flagellate alga Chlamydomonas reinhardtii. J Basic Microbiol 49:32–41. doi:10.1002/jobm.200800292
Waltenberger H, Schneid C, Grosch JO, Bareiss A, Mittag M (2001) Identification of target mRNAs for the clock-controlled RNA-binding protein Chlamy1 from C. reinhardtii. Mol Genet Genomics 265:180–188. doi:10.1007/s004380000406
Wijnen H, Young MW (2006) Interplay of circadian clocks and metabolic rhythms. Annu Rev Genet 40:409–448. doi:10.1146/annurev.genet.40.110405.090603
Woelfle MA, Xu Y, Qin X, Johnson CH (2007) Circadian rhythms of superhelical status of DNA in cyanobacteria. Proc Natl Acad Sci USA 104:18819–18824. doi:10.1073/pnas.0705069104
Yang J, Kim KD, Lucas A, Drahos KE, Santos CS, Mury SP, Capelluto DG, Finkielstein CV (2008) A novel heme-regulatory motif mediates heme-dependent degradation of the circadian factor period 2. Mol Cell Biol 28:4697–4711. doi:10.128/MCB.00236-08
Zhao B, Schneid C, Iliev D, Schmidt EM, Wagner V, Wollnik F, Mittag M (2004) The circadian RNA-binding protein CHLAMY1 represents a novel type heteromer of RNA recognition motif and lysine homology-containing subunits. Eukaryot Cell 3:815–825. doi:10.1128/EC.3.3.815-825.2004
Zylka MJ, Reppert SM (1999) Discovery of a putative heme-binding protein family (SOUL/HBP) by two-tissue suppression subtractive hybridization and database searches. Brain Res Mol Brain Res 74:175–181. doi:10.1016/S0169-328X(99)00277-6
Acknowledgments
We thank Georg Kreimer, Takuya Matsuo, Stefanie Seitz, Federico Valverde, and Olga Voytsekh for helpful comments on the manuscript. Our work was supported by the Deutsche Forschungsgemeinschaft (grant no. Mi 373 to MM) and the BMBF (Project GoFORSYS, grant no. 0315260A, work package 1 to MM). TS has a fellowship in the Jena School for Microbial Communication that is supported by DFG.
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Thomas Schulze and Katja Prager contributed equally.
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Schulze, T., Prager, K., Dathe, H. et al. How the green alga Chlamydomonas reinhardtii keeps time. Protoplasma 244, 3–14 (2010). https://doi.org/10.1007/s00709-010-0113-0
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DOI: https://doi.org/10.1007/s00709-010-0113-0