Evolution and Regulation of Cellular Periodic Processes: a Role for Paralogues

Overview

Journal EMBO Rep

Specialty Molecular Biology

Date 2010 Feb 20

PMID 20168326

Citations 3

Authors

Kalliopi Trachana

Lars Juhl Jensen

Peer Bork

Affiliations

Soon will be listed here.

Abstract

Several cyclic processes take place within a single organism. For example, the cell cycle is coordinated with the 24 h diurnal rhythm in animals and plants, and with the 40 min ultradian rhythm in budding yeast. To examine the evolution of periodic gene expression during these processes, we performed the first systematic comparison in three organisms (Homo sapiens, Arabidopsis thaliana and Saccharomyces cerevisiae) by using public microarray data. We observed that although diurnal-regulated and ultradian-regulated genes are not generally cell-cycle-regulated, they tend to have cell-cycle-regulated paralogues. Thus, diverged temporal expression of paralogues seems to facilitate cellular orchestration under different periodic stimuli. Lineage-specific functional repertoires of periodic-associated paralogues imply that this mode of regulation might have evolved independently in several organisms.

Citing Articles

Genetic Variability of the Functional Domains of Chromodomains Helicase DNA-Binding (CHD) Proteins.

Cardoso A, Lopes-Marques M, Oliveira M, Amorim A, Prata M, Azevedo L Genes (Basel). 2021; 12(11).

PMID: 34828433 PMC: 8623811. DOI: 10.3390/genes12111827.

Three-Locus Sequence Identification and Differential Tebuconazole Sensitivity Suggest Novel Haplotype from Trinidad.

Villafana R, Rampersad S Pathogens. 2020; 9(3).

PMID: 32121520 PMC: 7157627. DOI: 10.3390/pathogens9030175.

Evolution of Daily Gene Co-expression Patterns from Algae to Plants.

de Los Reyes P, Romero-Campero F, Ruiz M, Romero J, Valverde F Front Plant Sci. 2017; 8:1217.

PMID: 28751903 PMC: 5508029. DOI: 10.3389/fpls.2017.01217.

References

Rowicka M, Kudlicki A, Tu B, Otwinowski Z . High-resolution timing of cell cycle-regulated gene expression. Proc Natl Acad Sci U S A. 2007; 104(43):16892-7. PMC: 2040468. DOI: 10.1073/pnas.0706022104. View

Letunic I, Yamada T, Kanehisa M, Bork P . iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci. 2008; 33(3):101-3. DOI: 10.1016/j.tibs.2008.01.001. View

Wolfe K, Shields D . Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 1997; 387(6634):708-13. DOI: 10.1038/42711. View

Delaunay F, Laudet V . Circadian clock and microarrays: mammalian genome gets rhythm. Trends Genet. 2002; 18(12):595-7. DOI: 10.1016/s0168-9525(02)02794-4. View

Odom D, Dowell R, Jacobsen E, Gordon W, Danford T, MacIsaac K . Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet. 2007; 39(6):730-2. PMC: 3797512. DOI: 10.1038/ng2047. View

Wagner A . Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol. 2002; 19(10):1760-8. DOI: 10.1093/oxfordjournals.molbev.a003998. View

Dallman P, Spirito R, Siimes M . Diurnal patterns of DNA synthesis in the rat: modification by diet and feeding schedule. J Nutr. 1974; 104(10):1234-41. DOI: 10.1093/jn/104.10.1234. View

Verwaal R, Paalman J, Hogenkamp A, Verkleij A, Verrips C, Boonstra J . HXT5 expression is determined by growth rates in Saccharomyces cerevisiae. Yeast. 2002; 19(12):1029-38. DOI: 10.1002/yea.895. View

Smith A, Zeeman S, Smith S . Starch degradation. Annu Rev Plant Biol. 2005; 56:73-98. DOI: 10.1146/annurev.arplant.56.032604.144257. View

10.

Hittinger C, Carroll S . Gene duplication and the adaptive evolution of a classic genetic switch. Nature. 2007; 449(7163):677-81. DOI: 10.1038/nature06151. View

11.

Ozcan S, Johnston M . Function and regulation of yeast hexose transporters. Microbiol Mol Biol Rev. 1999; 63(3):554-69. PMC: 103746. DOI: 10.1128/MMBR.63.3.554-569.1999. View

12.

de Lichtenberg U, Jensen L, Fausboll A, Jensen T, Bork P, Brunak S . Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics. 2004; 21(7):1164-71. DOI: 10.1093/bioinformatics/bti093. View

13.

Maere S, de Bodt S, Raes J, Casneuf T, Van Montagu M, Kuiper M . Modeling gene and genome duplications in eukaryotes. Proc Natl Acad Sci U S A. 2005; 102(15):5454-9. PMC: 556253. DOI: 10.1073/pnas.0501102102. View

14.

Byrne K, Wolfe K . The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res. 2005; 15(10):1456-61. PMC: 1240090. DOI: 10.1101/gr.3672305. View

15.

Merritt T, Quattro J . Negative charge correlates with neural expression in vertebrate aldolase isozymes. J Mol Evol. 2002; 55(6):674-83. DOI: 10.1007/s00239-002-2363-8. View

16.

Harmer S, Hogenesch J, Straume M, Chang H, Han B, Zhu T . Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science. 2000; 290(5499):2110-3. DOI: 10.1126/science.290.5499.2110. View

17.

Kleinjan D, Bancewicz R, Gautier P, Dahm R, Schonthaler H, Damante G . Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence. PLoS Genet. 2008; 4(2):e29. PMC: 2242813. DOI: 10.1371/journal.pgen.0040029. View

18.

Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E . The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003; 4:41. PMC: 222959. DOI: 10.1186/1471-2105-4-41. View

19.

Lloyd D, Murray D . Redox rhythmicity: clocks at the core of temporal coherence. Bioessays. 2007; 29(5):465-73. DOI: 10.1002/bies.20575. View

20.

Borisjuk L, Rolletschek H, Radchuk R, Weschke W, Wobus U, Weber H . Seed development and differentiation: a role for metabolic regulation. Plant Biol (Stuttg). 2004; 6(4):375-86. DOI: 10.1055/s-2004-817908. View