Yeast KEOPS complex regulates telomere length independently of its t6A modification function

Ying-Ying Liu; Ming-Hong He; Jia-Cheng Liu; Yi-Si Lu; Jing Peng; Jin-Qiu Zhou

doi:10.1016/j.jgg.2018.03.004

Volume 45 Issue 5

May 2018

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2018 > 45(5): 247-257

PDF( 2699 KB)

Yeast KEOPS complex regulates telomere length independently of its t6A modification function

doi: 10.1016/j.jgg.2018.03.004

a
CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
b
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China

More Information

Corresponding author: E-mail address: jqzhou@sibcb.ac.cn (Jin-Qiu Zhou)
Received Date: 2018-01-30
Accepted Date: 2018-03-23
Rev Recd Date: 2018-03-15

Available Online: 2018-05-04

Publish Date: 2018-05-20

Abstract

Abstract

In Saccharomyces cerevisiae, the highly conserved Sua5 and KEOPS complex (including five subunits Kae1, Bud32, Cgi121, Pcc1 and Gon7) catalyze a universal tRNA modification, namely N⁶-threonylcarbamoyladenosine (t⁶A), and regulate telomere replication and recombination. However, whether telomere regulation function of Sua5 and KEOPS complex depends on the t⁶A modification activity remains unclear. Here we show that Sua5 and KEOPS regulate telomere length in the same genetic pathway. Interestingly, the telomere length regulation by KEOPS is independent of its t⁶A biosynthesis activity. Cytoplasmic overexpression of Qri7, a functional counterpart of KEOPS in mitochondria, restores cytosolic tRNA t⁶A modification and cell growth, but is not sufficient to rescue telomere length in the KEOPS mutant kae1Δ cells, indicating that a t⁶A modification-independent function is responsible for the telomere regulation. The results of our in vitro biochemical and in vivo genetic assays suggest that telomerase RNA TLC1 might not be modified by Sua5 and KEOPS. Moreover, deletion of KEOPS subunits results in a dramatic reduction of telomeric G-overhang, suggesting that KEOPS regulates telomere length by promoting G-overhang generation. These findings support a model in which KEOPS regulates telomere replication independently of its function on tRNA modification.
- Telomere,
- KEOPS complex,
- Sua5,
- G-overhang

FullText(HTML)

References(66)

References

[1]	Agari, Y., Sato, S., Wakamatsu, T. et al. Proteins, 70 (2008),pp. 1108-1111
[2]	Azzalin, C.M., Lingner, J. Trends Cell Biol., 25 (2015),pp. 29-36
[3]	Ben-Aroya, S., Coombes, C., Kwok, T. et al. Mol. Cell, 30 (2008),pp. 248-258
[4]	Bryan, T.M., Reddel, R.R. Eur. J. Cancer, 33 (1997),pp. 767-773
[5]	Chan, P.P., Lowe, T.M. GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes Nucleic Acids Res., 44 (2016),pp. D184-D189
[6]	Collinet, B., Friberg, A., Brooks, M.A. et al. Strategies for the structural analysis of multi-protein complexes: lessons from the 3D-Repertoire project J. Struct. Biol., 175 (2011),pp. 147-158
[7]	Costessi, A., Mahrour, N., Sharma, V. et al. The human EKC/KEOPS complex is recruited to Cullin2 ubiquitin ligases by the human tumour antigen PRAME PLoS One, 7 (2012)
[8]	Dandjinou, A.T., Levesque, N., Larose, S. et al. A phylogenetically based secondary structure for the yeast telomerase RNA Curr. Biol., 14 (2004),pp. 1148-1158
[9]	Daugeron, M.C., Lenstra, T.L., Frizzarin, M. et al. Nucleic Acids Res., 39 (2011),pp. 6148-6160
[10]	de Lange, T. How telomeres solve the end-protection problem Science, 326 (2009),pp. 948-952
[11]	Deutsch, C., El Yacoubi, B., de Crecy-Lagard, V. et al. J. Biol. Chem., 287 (2012),pp. 13666-13673
[12]	Diede, S.J., Gottschling, D.E. Curr. Biol., 11 (2001),pp. 1336-1340
[13]	Downey, M., Houlsworth, R., Maringele, L. et al. A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator Cell, 124 (2006),pp. 1155-1168
[14]	Dzikowska, A., Grzelak, A., Gawlik, J. et al. Gene, 573 (2015),pp. 310-320
[15]	El Yacoubi, B., Hatin, I., Deutsch, C. et al. A role for the universal Kae1/Qri7/YgjD (COG0533) family in tRNA modification EMBO J., 30 (2011),pp. 882-893
[16]	El Yacoubi, B., Lyons, B., Cruz, Y. et al. The universal YrdC/Sua5 family is required for the formation of threonylcarbamoyladenosine in tRNA Nucleic Acids Res., 37 (2009),pp. 2894-2909
[17]	Evans, S.K., Lundblad, V. Est1 and Cdc13 as comediators of telomerase access Science, 286 (1999),pp. 117-120
[18]	Faure, V., Coulon, S., Hardy, J. et al. Cdc13 and telomerase bind through different mechanisms at the lagging- and leading-strand telomeres Mol. Cell, 38 (2010),pp. 842-852
[19]	Galperin, M.Y., Koonin, E.V. ‘Conserved hypothetical’ proteins: prioritization of targets for experimental study Nucleic Acids Res., 32 (2004),pp. 5452-5463
[20]	Goudsouzian, L.K., Tuzon, C.T., Zakian, V.A. Mol. Cell, 24 (2006),pp. 603-610
[21]	Gustilo, E.M., Vendeix, F.A., Agris, P.F. tRNA's modifications bring order to gene expression Curr. Opin. Microbiol., 11 (2008),pp. 134-140
[22]	Hieter, R.S.S.a.P. Genetics, 122 (1989),pp. 19-27
[23]	Hu, Y., Tang, H.B., Liu, N.N. et al. Telomerase-null survivor screening identifies novel telomere recombination regulators PLoS Genet., 9 (2013)
[24]	Hurley, J.H. The sugar kinase/heat shock protein 70/actin super family: implications of conserved structure for mechanism Annu. Rev. Biophys. Biomol. Struct., 25 (1996),pp. 137-162
[25]	Juhling, F., Morl, M., Hartmann, R.K. et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes Nucleic Acids Res., 37 (2009),pp. D159-D162
[26]	Kato, Y., Kawasaki, H., Ohyama, Y. et al. Genetics, 188 (2011),pp. 871-882
[27]	Kisseleva-Romanova, E., Lopreiato, R., Baudin-Baillieu, A. et al. Yeast homolog of a cancer-testis antigen defines a new transcription complex EMBO J., 25 (2006),pp. 3576-3585
[28]	Kristoffersen, P., Jensen, G.B., Gerdes, K. et al. Bacterial toxin-antitoxin gene system as containment control in yeast cells Appl. Environ. Microbiol., 66 (2000),pp. 5524-5526
[29]	Kuratani, M., Kasai, T., Akasaka, R. et al. Proteins, 79 (2011),pp. 2065-2075
[30]	Kyriakou, D., Stavrou, E., Demosthenous, P. et al. BMC Biol., 14 (2016),p. 106
[31]	Larrivee, M., LeBel, C., Wellinger, R.J. The generation of proper constitutive G-tails on yeast telomeres is dependent on the MRX complex Genes Dev., 18 (2004),pp. 1391-1396
[32]	Lauhon, C.T. Biochemistry, 51 (2012),pp. 8950-8963
[33]	Le, S., Moore, J.K., Haber, J.E. et al. RAD50 and RAD51 define two pathways that collaborate to maintain telomeres in the absence of telomerase Genetics, 152 (1999),pp. 143-152
[34]	Lemieux, B., Laterreur, N., Perederina, A. et al. Active yeast telomerase shares subunits with ribonucleoproteins RNase P and RNase MRP Cell, 165 (2016),pp. 1171-1181
[35]	Lin, C.A., Ellis, S.R., True, H.L. The Sua5 protein is essential for normal translational regulation in yeast Mol. Cell. Biol., 30 (2010),pp. 354-363
[36]	Lopreiato, R., Facchin, S., Sartori, G. et al. Biochem. J., 377 (2004),pp. 395-405
[37]	Lundblad, V., Blackburn, E.H. An alternative pathway for yeast telomere maintenance rescues Est1-senescence Cell, 73 (1993),pp. 347-360
[38]	Maicher, A., Lockhart, A., Luke, B. Breaking new ground: digging into TERRA function Biochim. Biophys. Acta, 1839 (2014),pp. 387-394
[39]	Mao, D.Y., Neculai, D., Downey, M. et al. Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine Mol. Cell, 32 (2008),pp. 259-275
[40]	McEachern, M.J., Haber, J.E. Break-induced replication and recombinational telomere elongation in yeast Annu. Rev. Biochem., 75 (2006),pp. 111-135
[41]	Meng, F.L., Chen, X.F., Hu, Y. et al. Cell Res., 20 (2010),pp. 495-498
[42]	Meng, F.L., Hu, Y., Shen, N. et al. Sua5p a single-stranded telomeric DNA-binding protein facilitates telomere replication EMBO J., 28 (2009),pp. 1466-1478
[43]	Nichols, C.E., Lamb, H.K., Thompson, P. et al. Protein Sci., 22 (2013),pp. 628-640
[44]	Oberto, J., Breuil, N., Hecker, A. et al. Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance Nucleic Acids Res., 37 (2009),pp. 5343-5352
[45]	Pardo, B., Marcand, P. Rap1 prevents telomere fusions by nonhomologous end joining EMBO J., 24 (2005),pp. 3117-3127
[46]	Peng, J., He, M.H., Duan, Y.M. et al. Inhibition of telomere recombination by inactivation of KEOPS subunit Cgi121 promotes cell longevity PLoS Genet., 11 (2015)
[47]	Perrochia, L., Crozat, E., Hecker, A. et al. Nucleic Acids Res., 41 (2013),pp. 1953-1964
[48]	Perrochia, L., Guetta, D., Hecker, A. et al. Nucleic Acids Res., 41 (2013),pp. 9484-9499
[49]	Pfeiffer, V., Lingner, J. Replication of telomeres and the regulation of telomerase Cold Spring Harb. Perspect. Biol., 5 (2013)
[50]	Podlevsky, J.D., Bley, C.J., Omana, R.V. et al. The telomerase database Nucleic Acids Res., 36 (2008),pp. D339-D343
[51]	Ribeyre, C., Shore, D. Anticheckpoint pathways at telomeres in yeast Nat. Struct. Mol. Biol., 19 (2012),pp. 307-313
[52]	Singer, M.S., Gottschling, D.E. Science, 266 (1994),pp. 404-409
[53]	Srinivasan, M., Mehta, P., Yu, Y. et al. The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A EMBO J., 30 (2011),pp. 873-881
[54]	Takata, H., Tanaka, Y., Matsuura, A. Mol. Cell, 17 (2005),pp. 573-583
[55]	Thiaville, P.C., El Yacoubi, B., Perrochia, L. et al. Cross kingdom functional conservation of the core universally conserved threonylcarbamoyladenosine tRNA synthesis enzymes Eukaryot. Cell, 13 (2014),pp. 1222-1231
[56]	Thiaville, P.C., Legendre, R., Rojas-Benitez, D. et al. Microb. Cell, 3 (2016),pp. 29-45
[57]	Tsang, T.H., Buck, M., Ames, B.N. Sequence specificity of tRNA-modifying enzymes: an analysis of 258 tRNA sequences Biochim. Biophys. Acta, 741 (1983),pp. 180-196
[58]	Wan, L.C., Maisonneuve, P., Szilard, R.K. et al. Proteomic analysis of the human KEOPS complex identifies C14ORF142 as a core subunit homologous to yeast Gon7 Nucleic Acids Res., 45 (2017),pp. 805-817
[59]	Wan, L.C., Mao, D.Y., Neculai, D. et al. Reconstitution and characterization of eukaryotic N6-threonylcarbamoylation of tRNA using a minimal enzyme system Nucleic Acids Res., 41 (2013),pp. 6332-6346
[60]	Wellinger, R.J., Zakian, V.A. Genetics, 191 (2012),pp. 1073-1105
[61]	Wu, Y., Zakian, V.A. Proc. Natl. Acad. Sci. U. S. A., 108 (2011),pp. 20362-20369
[62]	Wu, Z., Liu, J., Zhang, Q.D. et al. Rad6-Bre1-mediated H2B ubiquitination regulates telomere replication by promoting telomere-end resection Nucleic Acids Res., 45 (2017),pp. 3308-3322
[63]	Yarian, C., Townsend, H., Czestkowski, W. et al. Accurate translation of the genetic code depends on tRNA modified nucleosides J. Biol. Chem., 277 (2002),pp. 16391-16395
[64]	Zappulla, D.C., Cech, T.R. Yeast telomerase RNA: a flexible scaffold for protein subunits Proc. Natl. Acad. Sci. U.S.A., 101 (2004),pp. 10024-10029
[65]	Zhang, W., Collinet, B., Graille, M. et al. Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex Nucleic Acids Res., 43 (2015),pp. 3358-3372
[66]	Zhou, X.-L., Ruan, Z.-R., Huang, Q. et al. Translational fidelity maintenance preventing Ser mis-incorporation at Thr codon in protein from eukaryote Nucleic Acids Res., 41 (2013),pp. 302-314