Functional diversification of yeast telomere associated protein, Rif1, in higher eukaryotes

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Sreesankar, Easwaran ^a   Senthilkumar, Ramamoorthy ^b   Bharathi, Vellaichamy ^b   Mishra, Rakesh K ^b   Mishra, Krishnaveni ^a  

^a UNIVERSITY OF HYDERABAD   (India)

^b CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DROSOPHILA PROTEIN; FUNGAL PROTEIN; PHOSPHOPROTEIN PHOSPHATASE 1; RAP1 INTERACTING FACTOR 1 PROTEIN; TELOMERASE; UNCLASSIFIED DRUG; REPRESSOR PROTEIN; RIF1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; SMALL INTERFERING RNA; TELOMERE BINDING PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CELL NUCLEUS; CONTROLLED STUDY; DNA DAMAGE; DROSOPHILA MELANOGASTER; ENZYME LOCALIZATION; EUKARYOTE; GENETIC CONSERVATION; GENETIC VARIABILITY; HELA CELL; HETEROCHROMATIN; MOLECULAR DOCKING; NONHUMAN; PHYLOGENY; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN EXPRESSION; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN MOTIF; SEQUENCE HOMOLOGY; TELOMERE; VERTEBRATE; YEAST; ANIMAL; BIOLOGY; CHEMISTRY; CLASSIFICATION; DRUG ANTAGONISM; GENETICS; HUMAN; METABOLISM; MOLECULAR EVOLUTION; PROTEIN BINDING; RETROPOSON; RNA INTERFERENCE; SACCHAROMYCES CEREVISIAE;

DROSOPHILA MELANOGASTER; EUKARYOTA; MAMMALIA; VERTEBRATA;

ANIMALS; COMPUTATIONAL BIOLOGY; DNA DAMAGE; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; HELA CELLS; HUMANS; PHYLOGENY; PROTEIN BINDING; PROTEIN PHOSPHATASE 1; REPRESSOR PROTEINS; RETROELEMENTS; RNA INTERFERENCE; RNA, SMALL INTERFERING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TELOMERE; TELOMERE-BINDING PROTEINS;

EID: 84862277336     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-255     Document Type: Article

References (43)

1. Bianchi A, Negrini S, Shore D. Delivery of yeast telomerase to a DNA break depends on the recruitment functions of Cdc13 and Est1. Mol Cell 2004, 16(1):139-146. 10.1016/j.molcel.2004.09.009, 15469829.
2. Osterhage JL, Friedman KL. Chromosome end maintenance by telomerase. J Biol Chem 2009, 284(24):16061-16065. 10.1074/jbc.R900011200, 2713563, 19286666.
3. O'Sullivan RJ, Karlseder J. Telomeres: protecting chromosomes against genome instability. Nat Rev Mol Cell Biol 2010, 11(3):171-181. 2842081, 20125188.
4. Smogorzewska A, de Lange T. Regulation of telomerase by telomeric proteins. Annu Rev Biochem 2004, 73:177-208. 10.1146/annurev.biochem.73.071403.160049, 15189140.
5. Hardy CF, Sussel L, Shore D. A RAP1-interacting protein involved in transcriptional silencing and telomere length regulation. Genes Dev 1992, 6(5):801-814. 10.1101/gad.6.5.801, 1577274.
6. Wotton D, Shore D. A novel Rap1p-interacting factor, Rif2p, cooperates with Rif1p to regulate telomere length in Saccharomyces cerevisiae. Genes Dev 1997, 11(6):748-760. 10.1101/gad.11.6.748, 9087429.
7. Hirano Y, Fukunaga K, Sugimoto K. Rif1 and rif2 inhibit localization of tel1 to DNA ends. Mol Cell 2009, 33(3):312-322. 10.1016/j.molcel.2008.12.027, 2662776, 19217405.
8. Teng SC, Chang J, McCowan B, Zakian VA. Telomerase-independent lengthening of yeast telomeres occurs by an abrupt Rad50p-dependent, Rif-inhibited recombinational process. Mol Cell 2000, 6(4):947-952. 10.1016/S1097-2765(05)00094-8, 11090632.
9. Mishra K, Shore D. Yeast Ku protein plays a direct role in telomeric silencing and counteracts inhibition by rif proteins. Curr Biol 1999, 9(19):1123-1126. 10.1016/S0960-9822(99)80483-7, 10531008.
10. Bourns BD, Alexander MK, Smith AM, Zakian VA. Sir proteins, Rif proteins, and Cdc13p bind Saccharomyces telomeres in vivo. Mol Cell Biol 1998, 18(9):5600-5608. 109144, 9710643.
11. Smith CD, Smith DL, DeRisi JL, Blackburn EH. Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae. Mol Biol Cell 2003, 14(2):556-570. 10.1091/mbc.E02-08-0457, 149992, 12589054.
12. Kanoh J, Ishikawa F. spRap1 and spRif1, recruited to telomeres by Taz1, are essential for telomere function in fission yeast. Curr Biol 2001, 11(20):1624-1630. 10.1016/S0960-9822(01)00503-6, 11676925.
13. Miller KM, Ferreira MG, Cooper JP. Taz1, Rap1 and Rif1 act both interdependently and independently to maintain telomeres. EMBO J 2005, 24(17):3128-3135. 10.1038/sj.emboj.7600779, 1201358, 16096639.
14. Ramirez-Zavaleta CY, Salas-Delgado GE, De Las Penas A, Castano I. Subtelomeric silencing of the MTL3 locus of Candida glabrata requires yKu70, yKu80, and Rif1 proteins. Eukaryot Cell 2010, 9(10):1602-1611. 10.1128/EC.00129-10, 2950432, 20675581.
15. Adams IR, McLaren A. Identification and characterisation of mRif1: a mouse telomere-associated protein highly expressed in germ cells and embryo-derived pluripotent stem cells. Dev Dyn 2004, 229(4):733-744. 10.1002/dvdy.10471, 15042697.
16. Silverman J, Takai H, Buonomo SB, Eisenhaber F, de Lange T. Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint. Genes Dev 2004, 18(17):2108-2119. 10.1101/gad.1216004, 515289, 15342490.
17. Xu L, Blackburn EH. Human Rif1 protein binds aberrant telomeres and aligns along anaphase midzone microtubules. J Cell Biol 2004, 167(5):819-830. 10.1083/jcb.200408181, 2172464, 15583028.
18. Buonomo SB, Wu Y, Ferguson D, de Lange T. Mammalian Rif1 contributes to replication stress survival and homology-directed repair. J Cell Biol 2009, 187(3):385-398. 10.1083/jcb.200902039, 2779251, 19948482.
19. Wang H, Zhao A, Chen L, Zhong X, Liao J, Gao M, Cai M, Lee DH, Li J, Chowdhury D, et al. Human RIF1 encodes an anti-apoptotic factor required for DNA repair. Carcinogenesis 2009, 30(8):1314-1319. 10.1093/carcin/bgp136, 2718077, 19483192.
20. Xu D, Muniandy P, Leo E, Yin J, Thangavel S, Shen X, Ii M, Agama K, Guo R, Fox D, et al. Rif1 provides a new DNA-binding interface for the Bloom syndrome complex to maintain normal replication. EMBO J 2010, 29(18):3140-3155. 10.1038/emboj.2010.186, 2944062, 20711169.
21. Mason JM, Frydrychova RC, Biessmann H. Drosophila telomeres: an exception providing new insights. Bioessays 2008, 30(1):25-37. 10.1002/bies.20688, 2804870, 18081009.
22. Andrade MA, Petosa C, O'Donoghue SI, Muller CW, Bork P. Comparison of ARM and HEAT protein repeats. J Mol Biol 2001, 309(1):1-18. 10.1006/jmbi.2001.4624, 11491282.
23. Hendrickx A, Beullens M, Ceulemans H, Den Abt T, Van Eynde A, Nicolaescu E, Lesage B, Bollen M. Docking motif-guided mapping of the interactome of protein phosphatase-1. Chem Biol 2009, 16(4):365-371. 10.1016/j.chembiol.2009.02.012, 19389623.
24. Egloff MP, Johnson DF, Moorhead G, Cohen PT, Cohen P, Barford D. Structural basis for the recognition of regulatory subunits by the catalytic subunit of protein phosphatase 1. EMBO J 1997, 16(8):1876-1887. 10.1093/emboj/16.8.1876, 1169791, 9155014.
25. Liu D, Vleugel M, Backer CB, Hori T, Fukagawa T, Cheeseman IM, Lampson MA. Regulated targeting of protein phosphatase 1 to the outer kinetochore by KNL1 opposes Aurora B kinase. J Cell Biol 2010, 188(6):809-820. 10.1083/jcb.201001006, 2845083, 20231380.
26. Moorhead GB, Trinkle-Mulcahy L, Nimick M, De Wever V, Campbell DG, Gourlay R, Lam YW, Lamond AI. Displacement affinity chromatography of protein phosphatase one (PP1) complexes. BMC Biochem 2008, 9:28. 10.1186/1471-2091-9-28, 2587467, 19000314.
27. Greenwood J, Cooper JP. Non-coding telomeric and subtelomeric transcripts are differentially regulated by telomeric and heterochromatin assembly factors in fission yeast. Nucleic Acids Res 2011, 40(7):2956-2963. 3326310, 22139922.
28. Iglesias N, Redon S, Pfeiffer V, Dees M, Lingner J, Luke B. Subtelomeric repetitive elements determine TERRA regulation by Rap1/Rif and Rap1/Sir complexes in yeast. EMBO Rep 2011, 12(6):587-593. 10.1038/embor.2011.73, 3128280, 21525956.
29. Capkova Frydrychova R, Biessmann H, Mason JM. Regulation of telomere length in Drosophila. Cytogenet Genome Res 2008, 122(3-4):356-364. 2637470, 19188706.
30. Torok T, Benitez C, Takacs S, Biessmann H. The protein encoded by the gene proliferation disrupter (prod) is associated with the telomeric retrotransposon array in Drosophila melanogaster. Chromosoma 2007, 116(2):185-195. 10.1007/s00412-006-0090-4, 17186256.
31. Darst RP, Garcia SN, Koch MR, Pillus L. Slx5 promotes transcriptional silencing and is required for robust growth in the absence of Sir2. Mol Cell Biol 2008, 28(4):1361-1372. 10.1128/MCB.01291-07, 2258744, 18086879.
32. Martin SG, Laroche T, Suka N, Grunstein M, Gasser SM. Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell 1999, 97(5):621-633. 10.1016/S0092-8674(00)80773-4, 10367891.
33. Kennedy BK, Gotta M, Sinclair DA, Mills K, McNabb DS, Murthy M, Pak SM, Laroche T, Gasser SM, Guarente L. Redistribution of silencing proteins from telomeres to the nucleolus is associated with extension of life span in S. cerevisiae. Cell 1997, 89(3):381-391. 10.1016/S0092-8674(00)80219-6, 9150138.
34. Park S, Patterson EE, Cobb J, Audhya A, Gartenberg MR, Fox CA. Palmitoylation controls the dynamics of budding-yeast heterochromatin via the telomere-binding protein Rif1. Proc Natl Acad Sci U S A 2011, 108(35):14572-14577. 10.1073/pnas.1105262108, 3167557, 21844336.
35. Villasante A, Abad JP, Planello R, Mendez-Lago M, Celniker SE, de Pablos B. Drosophila telomeric retrotransposons derived from an ancestral element that was recruited to replace telomerase. Genome Res 2007, 17(12):1909-1918. 10.1101/gr.6365107, 2099598, 17989257.
36. Anbalagan S, Bonetti D, Lucchini G, Longhese MP. Rif1 supports the function of the CST complex in yeast telomere capping. PLoS Genet 2011, 7(3):e1002024. 10.1371/journal.pgen.1002024, 3060071, 21437267.
37. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
38. Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34(Web Server issue):W369-W373. 1538909, 16845028.
39. Eddy SR. Profile hidden Markov models. Bioinformatics 1998, 14(9):755. 10.1093/bioinformatics/14.9.755, 9918945.
40. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25(24):4876. 10.1093/nar/25.24.4876, 147148, 9396791.
41. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673. 10.1093/nar/22.22.4673, 308517, 7984417.
42. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. 2007, 24(8).
43. Walter MF, Biessmann MR, Benitez C, Torok T, Mason JM, Biessmann H. Effects of telomere length in Drosophila melanogaster on life span, fecundity, and fertility. Chromosoma 2007, 116(1):41-51. 10.1007/s00412-006-0081-5, 2254661, 17089138.