Algologia 2016, 26(1): 3–17 https://doi.org/10.15407/alg26.01.003General Problems of Algology
Evolution of the circadian clock system in cyanobacteria: a genomic perspective
V.Ya. Dvornyk- College of Science and General Studies, Alfaisal University,
- Al Maather, Riyadh, Kingdom of Saudi Arabia,
- e-mail: vdvornyk@alfaisal.edu
Abstract
Cyanobacteria are the first prokaryotes shown to have an endogenous circadian clock, an ability to sustain life processes with an approximate daily periodicity. During its long and complex evolutionary history, the circadian system of cyanobacteria has underwent several major changes, which resulted in its structural diversification. Three main types of the system, which possess different sets of elements, have been identified so far. There is evidence that these differences may be associated with some functional modifications. Macroevolution of the circadian system has been governed by many factors, including multiple duplications, gene recruitment and de novo gene origin, domain accretion and fusion, and selection. Rapid accumulation of genomic data provides new possibilities for comprehensive comparative analyses and more accurate reconstruction of an evolutionary scenario for this finely tuned regulatory mechanism of cyanobacteria.
Keywords: cyanobacteria, circadian system, evolution, genomics
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References
- Axmann I.M., Duhring U., Seeliger L., Arnold A., Vanselow J.T., Kramer A., and Wilde A., J. Bacteriol., 2009, 191(17):5342-5347.
- Axmann I.M., Hertel S., Wiegard A., Dorrich A.K, and Wilde A., Mar. Genom., 2014, 14:3-16.
- Baca I., Sprockett D., and Dvornyk V., J. Mol. Evol., 2010, 70(5):453-465.
- Crosthwaite S.K., Loros J.J., and Dunlap J.C., Cell., 1995, 81(7):1003-1012.
- DiRuggiero J., Brown J.R., Bogert A.P., and Robb F.T., J. Mol. Evol., 1999, 49(4):474-484.
- Ditty J.L., Williams S.B., and Golden S.S., Annu. Rev. Genet., 2003, 37:513-543.
- Dunlap J.C., Loros J.J., and DeCoursey P.J., Chronobiology: Biological Timekeeping, Sinauer Assoc. Inc., Sunderland, MA, 2004.
- Dvornyk V., J. Mol. Evol., 2005, 60(1):105-112.
- Dvornyk V., Microbiology, 2006, 152(Pt 1):75-84.
- Dvornyk V., The Circadian Clock Gear in Cyanobacteria: Assembled by Evolution in Bacterial Circadian Programs, Springer-Verlag, Berlin; Heidelberg, 2009, pp. 241-258.
- Dvornyk V., Deng, H.W., and Nevo E., Mol. Biol. Evol., 2004, 21(8):1468-1476.
- Dvornyk V. and Jahan A.S., Mol. Biol. Evol., 2012, 29(12):3899-3907.
- Dvornyk V. and Knudsen B., Genetica, 2005, 124(2, 3):247-254.
- Dvornyk V. and Nevo E., J. Mol. Evol., 2004, 58(3):341-347.
- Dvornyk V., Vinogradova O., and Nevo E., Proc. Natl. Acad. Sci, USA, 2002, 99(4):2082-2087.http://dx.doi.org/10.1073/pnas.261699498
- Dvornyk V., Vinogradova O., and Nevo E., Proc. Natl. Acad. Sci, USA, 2003, 100(5):2495-2500.http://dx.doi.org/10.1073/pnas.0130099100
- Espinosa J., Boyd J.S., Cantos R., Salinas P., Golden S.S., and Contreras A., Proc. Natl. Acad. Sci. USA, 2015, 112(7):2198-2203.http://dx.doi.org/10.1073/pnas.1424632112
- Gu X., Mol. Biol. Evol., 1999, 16(12):1664-1674.
- Gu X., Mol. Biol. Evol., 2001, 18(4):453-464.
- Hanaoka M., Takai N., Hosokawa N., Fujiwara M., Akimoto Y., Kobori N., Iwasaki H., Kondo T., and Tanaka K., J. Biol. Chem., 2012, 287(31):26321-26327.
- Holtman C.K., Chen Y., Sandoval P., Gonzales A., Nalty M.S., Thomas T.L., Youderian P., and Golden S.S., DNA Res., 2005, 12(2):103-115.
- Hosokawa N., Kushige H., and Iwasaki H., Proc. Natl. Acad. Sci. USA, 2013, 110(35):14486-14491.http://dx.doi.org/10.1073/pnas.1302243110
- Ishiura M., Kutsuna S., Aoki S., Iwasaki H., Andersson C.R., Tanabe A., Golden S.S., Johnson C.H., and Kondo T., Science, 1998, 281(5382):1519-1523.http://dx.doi.org/10.1126/science.281.5382.1519
- Ivleva N.B., Bramlett M.R., Lindahl P.A., and Golden S.S., EMBO J., 2005, 24(6):1202-1210.
- Iwasaki H., Williams S.B., Kitayama Y., Ishiura M., Golden S.S., and Kondo T., Cell., 2000, 101(2):223-233.
- Johnson C.H. and Golden S.S., Annu. Rev. Microbiol., 1999, 53:389-409.
- Kageyama H., Kondo T., and Iwasaki H., J. Biol. Chem., 2003, 278(4):2388-2395.
- Katayama M., Kondo T., Xiong J., and Golden S.S., J. Bacteriol., 2003, 185(4):1415-1422.
- Katayama M., Tsinoremas N.F., Kondo T., and Golden S.S., J. Bacteriol., 1999, 181(11):3516-3524.
- Kimura M., The Neutral Theory of Molecular Evolution, Cambridge Univ. Press, Cambridge, 1983.
- Komárek J., Kaštovský J., Mareš J., and Johansen J.R., Preslia, 2014, 86(4):295-235.
- Kondo T., Mori T., Lebedeva N.V., Aoki S., Ishiura M., and Golden S.S., Science, 1997, 275(5297):224-227.http://dx.doi.org/10.1126/science.275.5297.224
- Kucho K., Okamoto K., Tsuchiya Y., Nomura S., Nango M., Kanehisa M., and Ishiura M., J. Bacteriol., 2005, 187(6):2190-2199.
- Kutsuna S., Kondo T., Aoki S., and Ishiura M., J. Bacteriol., 1998, 180(8):2167-2174.
- Kutsuna S., Kondo T., Ikegami H., Uzumaki T., Katayama M., and Ishiura M., J. Bacteriol., 2007, 189(21):7690-7696.
- Leipe D.D., Aravind L., Grishin N.V., and Koonin E.V., Genome Res., 2000, 10(1):5-16.
- Meyer E., Leonard N.J., Bhat B., Stubbe J., and Smith J.M., Biochemistry, 1992, 31(21):5022-5032.http://dx.doi.org/10.1021/bi00136a016
- Mutsuda M., Michel K.P., Zhang X., Montgomery B.L., and Golden S.S., J. Biol. Chem., 2003, 278(21):19102-19110.
- Nair U., Ditty J.L., Min H., and Golden S.S., J. Bacteriol., 2002, 184(13):3530-3538.
- Nakamura Y., Kaneko T., Sato S., Mimuro M., Miyashita H., Tsuchiya T., Sasamoto S., Watanabe A., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Nakazaki N., Shimpo S., Takeuchi C., Yamada M., and Tabata S., DNA Res., 2003, 10(4):137-145.
- Ng K.W., Pointing S.B., and Dvornyk V., Appl. Environ. Microbiol., 2013, 79(5):1516-1522.
- Pattanayek R., Williams D.R., Pattanayek S., Xu Y., Mori T., Johnson C.H., Stewart P.L., and Egli M., EMBO J., 2006, 25(9):2017-2028.
- Pattanayek R., Yadagiri K.K., Ohi M.D., and Egli M., Cell Cycle, 2013, 12(5):810-817.http://dx.doi.org/10.4161/cc.23757
- Pittendrigh C.S., Annu. Rev. Physiol., 1993, 55:16-54.
- Roca A.I. and Cox M.M., Crit. Rev. Biochem. Mol. Biol., 1990, 25(6):415-456.
- Schmitz O., Katayama M., Williams S.B., Kondo T., and Golden S.S., Science, 2000, 289(5480):765-768.http://dx.doi.org/10.1126/science.289.5480.765
- Schopf J.W. and Packer B.M., Science, 1987, 237:70-73.
- Shalapyonok A., Olson R.J., and Shalapyonok L.S., Appl. Environ. Microbiol., 1998, 64(3):1066-1069.
- Takai N., Nakajima M., Oyama T., Kito R., Sugita C., Sugita M., Kondo T., and Iwasaki H., Proc. Natl. Acad. Sci. USA, 2006, 103(32):12109-12114.http://dx.doi.org/10.1073/pnas.0602955103
- Taniguchi Y., Yamaguchi A., Hijikata A., Iwasaki H., Kamagata K., Ishiura M., Go M., and Kondo T., FEBS Lett., 2001, 496(2, 3):86-90.
- Tomita J., Nakajima M., Kondo T., and Iwasaki H., Science, 2005, 307(5707):251-254.http://dx.doi.org/10.1126/science.1102540
- Tomitani A., Knoll A.H., Cavanaugh C.M., and Ohno T., Proc. Natl. Acad. Sci. USA, 2006, 103(14):5442-5447.http://dx.doi.org/10.1073/pnas.0600999103
- Tsinoremas N.F., Ishiura M., Kondo T., Tanaka K., Takahashi H., and Johnson C.H., EMBO J., 1996, 15:2488-2495.
- Vakonakis I. and LiWang A.C., Proc. Natl. Acad. Sci. USA, 2004, 101(30):10925-10930.
- Watanabe W., Sampei G., Aiba A., and Mizobuchi K., J. Bacteriol., 1989, 171(1):198-204.
- Whitton B.A., Survival and Dormancy of Algae in Survival and Dormancy of Microorganisms, John Wiley, New York, 1987, pp. 109-167.
- Wiegard A., Dorrich A.K., Deinzer H.T., Beck C., Wilde A., Holtzendorff J., and Axmann I.M., Microbiology, 2013, 159(Pt 5):948-958.
- Woelfle M.A., Ouyang Y., Phanvijhitsiri K., and Johnson C.H., Curr. Biol., 2004, 14(16): 1481-1486.