Functional Proteomics: A Promising Approach to Find Novel Components of the Circadian System

References

• Akimoto H., Wu C., Kinumi T., Ohmiya Y. Biological rhythmicity in expressed proteins of the marine dinoflagellate Lingulodinium polyedrum demonstrated by chronological proteomics. Biochem. Biophys. Res. Commun. 2004; 315: 306–312
   PubMed Web of Science ®Google Scholar
• Bachvaroff T. R., Concepcion G. T., Rogers G. T., Herman E. M., Delwiche C. F. Dinoflagellate expressed sequence tag data indicate massive transfer of chloroplast genes to the nuclear genome. Protist. 2004; 155: 65–78
   PubMed Web of Science ®Google Scholar
• Boudreau E., Nickelsen J., Lemaire S. D., Ossenbuhl F., Rochaix J. D. The Nac2 gene of Chlamydomonas encodes a chloroplast TPR‐like protein involved in psbD mRNA stability. EMBO J. 2000; 19: 3366–3376
   PubMed Web of Science ®Google Scholar
• Bruce V. G. The biological clock in Chlamydomonas reinhardtii. J. Protozool. 1970; 17: 328–334
   Google Scholar
• Bruce V. G. Mutants of the biological clock in Chlamydomonas reinhardtii. Genetics 1972; 70: 537–548
   PubMed Web of Science ®Google Scholar
• Byrne T. E., Wells M. R., Johnson C. H. Circadian rhythms of chemotaxis to ammonium and methylammonium uptake in Chlamydomonas. Plant Physiol. 1992; 98: 879–886
   PubMed Web of Science ®Google Scholar
• Chen S., Prapapanich V., Rimerman R. A., Honore B., Smith D. F. Interactions of p60, a mediator of progesterone receptor assembly, with heat shock proteins hsp90 and hsp70. Mol. Endocrinol. 1996; 10: 682–693
   PubMedGoogle Scholar
• Danon A., Mayfield S. P. ADP‐dependent phosphorylation regulates RNA‐binding in vitro: implications in light‐modulated translation. EMBO J. 1994; 13: 2227–2235
   PubMed Web of Science ®Google Scholar
• Denison C., Rudner A. D., Gerber S. A., Bakalarski C. E., Moazed D., Gygi S. P. A proteomic strategy for gaining insights into protein sumoylation in yeast. Mol. Cell Proteomics 2005; 4: 246–254
   PubMed Web of Science ®Google Scholar
• Doran P., Dowling P., Lohan J., McDonnell K., Poetsch S., Ohlendieck K. Subproteomics analysis of Ca2+‐binding proteins demonstrates decreased calsequestrin expression in dystrophic mouse skeletal muscle. Eur. J. Biochem. 2004; 271: 3943–3952
   PubMedGoogle Scholar
• Dunlap J. P., Loros J. J. The Neurospora circadian system. J. Biol. Rhythms 2004; 19: 414–424
   PubMed Web of Science ®Google Scholar
• Eng J., McCormack A. L., Yates J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994; 5: 976–989
   PubMed Web of Science ®Google Scholar
• Fagan T., Morse D., Hastings J. W. Circadian synthesis of a nuclear‐encoded chloroplast glyceraldehyde‐3‐phosphate dehydrogenase in the dinoflagellate Gonyaulax polyedra is translationally controlled. Biochem. 1999; 38: 7689–695
   PubMed Web of Science ®Google Scholar
• Freedman R. B., Hirst T. R., Tuite M. F. Protein disulphide isomerase: building bridges in protein folding. Trends Biochem. Sci. 1994; 19: 331–336
   PubMed Web of Science ®Google Scholar
• Goto K., Johnson C. H. Is the cell division cycle gated by a circadian clock? The case of Chlamydomonas reinhardtii. J. Cell Biol. 1995; 129: 1061–1069
   PubMed Web of Science ®Google Scholar
• Grossman A. R. Paths toward algal genomics. Plant Physiol. 2005; 137: 410–427
   PubMed Web of Science ®Google Scholar
• Grossman A. R., Harris E. E., Hauser C., Lefebvre P. A., Martinez D., Rokhsar D., Shrager J., Silflow C. D., Stern D., Vallon O., Zhang Z. Chlamydomonas reinhardtii at the crossroads of genomics. Eukaryot. Cell 2003; 2: 1137–1150
   PubMed Web of Science ®Google Scholar
• Harmer S. L., Hogenesch J. B., Straume M., Chang H. S., Han B., Zhu T., Wang X., Kreps J. A., Kay S. A. Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 2000; 290: 2110–2113
   PubMed Web of Science ®Google Scholar
• Harmer S. L., Panda S., Kay S. A. Molecular bases of circadian rhythms. Annu. Rev. Cell Dev. Biol. 2001; 17: 215–253
   PubMed Web of Science ®Google Scholar
• Harris E. H. Chlamydomonas as a model organism. Annu. Rev. Plant Physiol. Plant Mol. Biol. 2001; 52: 363–406
   PubMed Web of Science ®Google Scholar
• Hastings J. W., Sweeney B. M. A persistent diurnal rhythm of luminescence in Gonyaulax polyedra. Biol. Bull. 1958; 115: 440–458
   Google Scholar
• Hastings J. W., Astrachan L., Sweeney B. M. A persistent diurnal rhythm in photosynthesis. J. Gen. Physiol. 1961; 45: 69–76
   PubMed Web of Science ®Google Scholar
• He Q., Cheng P., Yang Y., He Q., Yu H., Liu Y. FWD1‐mediated degradation of FREQUENCY in Neurospora establishes a conserved mechanism for circadian clock regulation. EMBO J. 2003; 22: 4421–4430
   PubMed Web of Science ®Google Scholar
• Hirano H., Islam N., Kawasaki H. Technical aspects of functional proteomics in plants. Phytochem. 2004; 65: 1487–498
   PubMed Web of Science ®Google Scholar
• Hogenesh J. B., Panda S., Kay S., Takahashi J. S. Circadian transcriptional output in the SCN and liver of the mouse. Novartis Found. Symp. 2003; 253: 171–180
   PubMedGoogle Scholar
• Johnson C. H. Precise circadian clocks in prokaryotic cyanobacteria. Curr. Issues Mol. Biol. 2004; 6: 103–110
   PubMed Web of Science ®Google Scholar
• Johnson C. H., Kondo T., Goto K. Circadian rhythms in Chlamydomonas. Circadian Clocks from Cell to Human. Proceedings of the Fourth Sapporo Symposium on Biological Rhythms, T. Hiroshige, K. Honma. Hokkaido University Press. 1992; 139–155
   Google Scholar
• Kim J., Mayfield S. P. Protein disulfide isomerase as a regulator of chloroplast translational activation. Science 1997; 278: 1954–1957
   PubMed Web of Science ®Google Scholar
• Kim S. Y., Chudapongse N., Lee S. M., Levin M. C., Oh J. T., Park H. J., Ho I. K. Proteomic analysis of phosphotyrosyl proteins in the rat brain: effect of butorphanol dependence. J. Neurosci. Res. 2004; 77: 867–877
   PubMed Web of Science ®Google Scholar
• Kleffmann T., Russenberger D., von Zychlinski A., Christopher W., Sjolander K., Gruissem W., Baginsky S. The Arabidopsis thaliana chloroplast proteome reveals pathway abundance and novel protein functions. Curr. Biol. 2004; 14: 354–362
   PubMed Web of Science ®Google Scholar
• Ko H. W., Jiang J., Edery I. Role for Slimb in the degradation of Drosophila Period protein phosphorylated by Doubletime. Nature 2002; 420: 673–678
   PubMed Web of Science ®Google Scholar
• Lacombe E., Doorselaere J. V., Boerjan W., Boudet A. M., Grima‐Pettenati J. Characterization of cis‐elements required for vascular expression of the cinnamoyl CoA reductase gene and for protein‐DNA complex formation. Plant J. 2000; 23: 663–676
   PubMed Web of Science ®Google Scholar
• Liu J., Shen X., Nguyen V. A., Kunos G., Gao B. Alpha(1) adrenergic agonist induction of p21(waf1/cip1) mRNA stability in transfected HepG2 cells correlates with the increased binding of an AU‐rich element binding factor. J. Biol. Chem. 2000; 275: 11846–11851
   PubMed Web of Science ®Google Scholar
• Marcovic P., Roenneberg T., Morse D. Phased protein synthesis at several circadian times does not change protein levels in Gonyaulax. J. Biol. Rhythms 1996; 11: 57–67
   PubMed Web of Science ®Google Scholar
• Mergenhagen D. Circadian clock: genetic characterization of a short period mutant of Chlamydomonas reinhardtii. Eur. J. Cell Biol. 1984; 33: 13–18
   Web of Science ®Google Scholar
• Milos P., Morse D., Hastings J. W. Circadian control over synthesis of many Gonyaulax proteins is at a translational level. Naturwissenschaften. 1990; 77: 87–89
   PubMed Web of Science ®Google Scholar
• Mittag M. Circadian rhythms in microalgae. Int. Rev. Cytol. 2001; 206: 213–247
   PubMedGoogle Scholar
• Mittag M., Wagner V. The circadian clock of the unicellular eukaryotic model organism Chlamydomonas reinhardtii. Biol. Chem. 2003; 384: 689–95
   Web of Science ®Google Scholar
• Mittag M., Li L. M., Hastings J. W. The mRNA level of the circadian regulated Gonyaulax luciferase remains constant over the cycle. Chronobiol. Int. 1998; 15: 93–98
   PubMed Web of Science ®Google Scholar
• Mittag M., Kiaulehn S., Johnson C. H. The circadian clock in Chlamydomonas reinhardtii: What is it for? What is it similar to?. Plant Physiol. 2005; 137: 399–409
   PubMed Web of Science ®Google Scholar
• Morse D., Milos P. M., Roux E., Hastings J. W. Circadian regulation of the synthesis of substrate binding protein in the Gonyaulax bioluminescent system involves translational control. Proc. Natl. Acad. Sci. USA. 1989; 86: 172–176
   PubMed Web of Science ®Google Scholar
• Nikaido S. S., Johnson C. H. Daily and circadian variation in survival from ultraviolet radiation in Chlamydomonas reinhardtii. Photochem. Photobiol. 2000; 71: 758–765
   PubMed Web of Science ®Google Scholar
• Okamoto T., Higuchi K., Shinkawa T., Isobe T., Lorz H., Koshiba T., Kranz E. Identification of major proteins in maize egg cells. Plant Cell Physiol. 2004; 45: 1406–1412
   PubMed Web of Science ®Google Scholar
• Panda S., Antoch M. P., Miller B. H., Si A. I., Schook A. B., Straume M., Schultz P. G., Kay S. A., Takahashi J. S., Hogenesch J. B. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 2002a; 109: 307–320
   PubMed Web of Science ®Google Scholar
• Panda S., Hogenesch J. B., Kay S. A. Circadian rhythms from flies to human. Nature 2002b; 417: 329–335
   PubMed Web of Science ®Google Scholar
• Peltier J. B., Ytterberg A. J., Sun Q., van Wijk K. J. New functions of the thylakoid membrane proteome of Arabidopsis thaliana revealed by a simple, fast, and versatile fractionation strategy. J. Biol. Chem. 2004; 279: 49367–49383
   PubMed Web of Science ®Google Scholar
• Prinz T., Muller J., Kuhn K., Schafer J., Thompson A., Schwarz J., Hamon C. Characterization of low abundant membrane protein using the protein sequence tag technology. J. Proteome Res. 2004; 3: 1073–1081
   PubMed Web of Science ®Google Scholar
• Reinders J., Lewandrowski U., Moebius J., Wagner Y., Sickmann A. Challenges in mass spectrometry‐based proteomics. Proteomics 2004; 4: 3686–36703
   PubMed Web of Science ®Google Scholar
• Reppert S. M., Weaver D. R. Coordination of circadian timing in mammals. Nature 2002; 418: 935–941
   PubMed Web of Science ®Google Scholar
• Roenneberg T., Hastings J. W. Cell movement and pattern formation in Gonyaulax polyedra. Oscillations and Morphogenesis, L. Rensing. Marcel Dekker, New York 1992; 399–412
   Google Scholar
• Schramm A., Apostolov O., Sitek B., Pfeiffer K., Struhler K., Meyer H. E., Havers W., Eggert A. Proteomics: techniques and applications in cancer research. Klin. Padiatr. 2003; 215: 293–297
   PubMed Web of Science ®Google Scholar
• Stauber E. J., Hippler M. Chlamydomonas reinhardtii proteomics. Plant Physiol. Biochem. 2004; 42: 989–1001
   PubMed Web of Science ®Google Scholar
• Straley S. C., Bruce V. G. Stickiness to glass: circadian changes in the cell surface of Chlamydomonas reinhardtii. Plant Physiol. 1979; 63: 1175–81
   PubMed Web of Science ®Google Scholar
• Sweeney B. M., Hastings J. W. Rhythmic cell division in populations of Gonyaulax polyedra. J. Protozool. 1958; 5: 217–224
   Google Scholar
• Taylor R. S., Wu C. C., Hays L. G., Eng J. K., Yates J. R., Howell K. E. Proteomics of rat liver Golgi complex: minor proteins are identified through sequential fractionation. Electrophoresis 2000; 21: 3441–3459
   PubMed Web of Science ®Google Scholar
• Trebitsh T., Meiri E., Ostersetzer O., Adam Z., Danon A. The protein disulfide isomerase‐like RB60 is partitioned between stroma and thylakoids in Chlamydomonas reinhardtii chloroplasts. J. Biol. Chem. 2001; 276: 4564–4569
   PubMed Web of Science ®Google Scholar
• Vaistij F. E., Boudreau E., Lemaire S. D., Goldschmidt‐Clermont M., Rochaix J. D. Characterization of Mbb1, a nucleus‐encoded tetratricopeptide‐like repeat protein required for expression of the chloroplast psbB/psbT/psbH gene cluster in Chlamydomonas reinhardtii. Proc. Natl. Acad. Sci. USA. 2000; 97: 14813–14818
   PubMed Web of Science ®Google Scholar
• Van der Voorn L., Ploegh H. L. The WD‐40 repeat. FEBS Lett. 1992; 307: 131–134
   PubMed Web of Science ®Google Scholar
• Wagner V., Fiedler M., Markert C., Hippler M., Mittag M. Functional proteomics of circadian expressed proteins from Chlamydomonas reinhardtii. FEBS Lett. 2004; 559: 129–135
   PubMed Web of Science ®Google Scholar
• Werner R. Chlamydomonas reinhardtii as a unicellular model for circadian rhythm analysis. Chronobiol. Int. 2002; 19: 325–343
   PubMed Web of Science ®Google Scholar
• Zhang Z., Quick M. K., Kanelakis K. C., Gijzen M., Krishna P. Characterization of a plant homolog of hop, a cochaperone of hsp90. Plant Physiol. 2003; 131: 525–535
   PubMed Web of Science ®Google Scholar