Profusion of G-quadruplexes on both subunits of metazoan ribosomes


Autoři: Santi Mestre-Fos aff001;  Petar I. Penev aff001;  John Colin Richards aff001;  William L. Dean aff004;  Robert D. Gray aff004;  Jonathan B. Chaires aff004;  Loren Dean Williams aff001
Působiště autorů: Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, United States of America aff001;  School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America aff002;  School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America aff003;  James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America aff004
Vyšlo v časopise: PLoS ONE 14(12)
Kategorie: Research Article
doi: 10.1371/journal.pone.0226177

Souhrn

Mammalian and bird ribosomes are nearly twice the mass of prokaryotic ribosomes in part because of their extraordinarily long rRNA tentacles. Human rRNA tentacles are not fully observable in current three-dimensional structures and their conformations remain to be fully resolved. In previous work we identified sequences that favor G-quadruplexes in silico and in vitro in rRNA tentacles of the human large ribosomal subunit. We demonstrated by experiment that these sequences form G-quadruplexes in vitro. Here, using a more recent motif definition, we report additional G-quadruplex sequences on surfaces of both subunits of the human ribosome. The revised sequence definition reveals expansive arrays of potential G-quadruplex sequences on LSU tentacles. In addition, we demonstrate by a variety of experimental methods that fragments of the small subunit rRNA form G-quadruplexes in vitro. Prior to this report rRNA sequences that form G-quadruplexes were confined to the large ribosomal subunit. Our combined results indicate that the surface of the assembled human ribosome contains numerous sequences capable of forming G-quadruplexes on both ribosomal subunits. The data suggest conversion between duplexes and G-quadruplexes in response to association with proteins, ions, or other RNAs. In some systems it seems likely that the integrated population of RNA G-quadruplexes may be dominated by rRNA, which is the most abundant cellular RNA.

Klíčová slova:

Multiple alignment calculation – Oligomers – Ribosomal RNA – Ribosomes – RNA annealing – Sequence alignment – Sequence motif analysis – Chordata


Zdroje

1. Mestre-Fos S, Penev PI, Suttapitugsakul S, Hu M, Ito C, Petrov AS, Wartell RM, Wu R, Williams LD. G-quadruplexes in human ribosomal RNA. J Mol Biol. 2019;431(10):1940–55. doi: 10.1016/j.jmb.2019.03.010 30885721

2. Millevoi S, Moine H, Vagner S. G‐quadruplexes in RNA biology. Wiley Interdisciplinary Reviews: RNA. 2012;3(4):495–507. doi: 10.1002/wrna.1113 22488917

3. Fay MM, Lyons SM, Ivanov P. RNA G-quadruplexes in biology: Principles and molecular mechanisms. J Mol Biol. 2017;429(14):2127–47. doi: 10.1016/j.jmb.2017.05.017 28554731

4. Lightfoot HL, Hagen T, Clery A, Allain FH-T, Hall J. Control of the polyamine biosynthesis pathway by G2-quadruplexes. eLife. 2018;7:e36362. doi: 10.7554/eLife.36362 30063205

5. Jodoin R, Bauer L, Garant J-M, Laaref AM, Phaneuf F, Perreault J-P. The folding of 5′-UTR human G-quadruplexes possessing a long central loop. RNA. 2014;20(7):1129–41. doi: 10.1261/rna.044578.114 24865610

6. Martadinata H, Phan AT. Formation of a stacked dimeric G-quadruplex containing bulges by the 5′-terminal region of human telomerase RNA (hTERC). Biochemistry. 2014;53(10):1595–600. doi: 10.1021/bi4015727 24601523

7. Pandey S, Agarwala P, Maiti S. Effect of loops and G-quartets on the stability of RNA G-quadruplexes. J Phys Chem B. 2013;117(23):6896–905. doi: 10.1021/jp401739m 23683360

8. Qin M, Chen Z, Luo Q, Wen Y, Zhang N, Jiang H, Yang H. Two-quartet G-quadruplexes formed by DNA sequences containing four contiguous GG runs. J Phys Chem B. 2015;119(9):3706–13. doi: 10.1021/jp512914t 25689673

9. Kwok CK, Marsico G, Sahakyan AB, Chambers VS, Balasubramanian S. Rg4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome. Nat Methods. 2016;13(10):841. doi: 10.1038/nmeth.3965 27571552

10. Milo R, Phillips R. Cell biology by the numbers: Garland Science; 2015.

11. Rudra D, Zhao Y, Warner JR. Central role of ifh1p–Fhl1p interaction in the synthesis of yeast ribosomal proteins. EMBO J. 2005;24(3):533–42. doi: 10.1038/sj.emboj.7600553 15692568

12. Singh YH, Andrabi M, Kahali B, Ghosh TC, Mizuguchi K, Kochetov AV, Ahmad S. On nucleotide solvent accessibility in RNA structure. Gene. 2010;463(1–2):41–8. Epub 2010/05/18. doi: 10.1016/j.gene.2010.05.001 20470873.

13. Kikin O, D’Antonio L, Bagga PS. QGRS mapper: A web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 2006;34(suppl_2):W676–W82.

14. Martadinata H, Phan AT. Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution. J Am Chem Soc. 2009;131(7):2570–8. doi: 10.1021/ja806592z 19183046

15. Xiao C-D, Shibata T, Yamamoto Y, Xu Y. An intramolecular antiparallel G-quadruplex formed by human telomere RNA. Chemical Communications. 2018;54(32):3944–6. doi: 10.1039/c8cc01427b 29610814

16. del Villar‐Guerra R, Trent JO, Chaires JB. G‐quadruplex secondary structure obtained from circular dichroism spectroscopy. Angew Chem Int Ed. 2018;57(24):7171–5.

17. Kypr J, Kejnovská I, Renčiuk D, Vorlíčková M. Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res. 2009;37(6):1713–25. doi: 10.1093/nar/gkp026 19190094

18. Ratliff RL, Liu JJ, Vaughan MR, Gray DM. Sequence‐dependence of the CD of synthetic double‐stranded RNAs containing inosinate instead of guanylate subunits. Biopolymers. 1986;25(9):1735–50. doi: 10.1002/bip.360250914 3021250

19. Renaud de la Faverie A, Guedin A, Bedrat A, Yatsunyk LA, Mergny J-L. Thioflavin T as a fluorescence light-up probe for G4 formation. Nucleic Acids Res. 2014;42(8):e65–e. doi: 10.1093/nar/gku111 24510097

20. Zhang S, Sun H, Chen H, Li Q, Guan A, Wang L, Shi Y, Xu S, Liu M, Tang Y. Direct visualization of nucleolar G-quadruplexes in live cells by using a fluorescent light-up probe. Biochim Biophys Acta. 2018;1862(5):1101–6.

21. Dean WL, Gray RD, Monsen RC, DeLeeuw L, Chaires JB. Putting a new spin of G4 structure and binding by analytical ultracentrifugation. bioRxiv. 2018:359356.

22. Renard I, Grandmougin M, Roux A, Yang SY, Lejault P, Pirrotta M, Wong JM, Monchaud D. Small-molecule affinity capture of DNA/RNA quadruplexes and their identification in vitro and in vivo through the G4RP protocol. Nucleic Acids Res. 2019;47(11):5502–10. doi: 10.1093/nar/gkz215 30949698

23. Yang SY, Lejault P., Chevrier S., Boidot R., Robertson A.G., Wong M.Y., Monchaud D. Transcriptome-wide identification of transient RNA G-quadruplexes in human cells. Nat Commun. 2018;9(4730):1–11. doi: 10.1038/s41467-018-07224-8 30413703

24. Maharana S, Wang J, Papadopoulos DK, Richter D, Pozniakovsky A, Poser I, Bickle M, Rizk S, Guillén-Boixet J, Franzmann TM, Jahnel M, Marrone L, Chang Y-T, Sterneckert J, et al. RNA buffers the phase separation behavior of prion-like RNA binding proteins. Science. 2018;360(6391):918–21. doi: 10.1126/science.aar7366 29650702

25. Dormann D, Haass C. Fused in sarcoma (fus): An oncogene goes awry in neurodegeneration. Mol Cell Neurosci. 2013;56:475–86. doi: 10.1016/j.mcn.2013.03.006 23557964

26. Jain A, Vale RD. RNA phase transitions in repeat expansion disorders. Nature. 2017;546(7657):243. doi: 10.1038/nature22386 28562589

27. Fujii K, Susanto TT, Saurabh S, Barna M. Decoding the function of expansion segments in ribosomes. Mol Cell. 2018;72(6):1013–20. e6. doi: 10.1016/j.molcel.2018.11.023 30576652

28. Knorr AG, Schmidt C, Tesina P, Berninghausen O, Becker T, Beatrix B, Beckmann R. Ribosome-nata architecture reveals that rRNA expansion segments coordinate N-terminal acetylation. Nat Struct Mol Biol. 2019;26:35–9. doi: 10.1038/s41594-018-0165-y 30559462

29. Schuck P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys J. 2000;78(3):1606–19. doi: 10.1016/S0006-3495(00)76713-0 10692345

30. Bernier CR, Petrov AS, Kovacs NA, Penev PI, Williams LD. Translation: The universal structural core of life. Mol Biol Evol. 2018;35(8):2065–76. doi: 10.1093/molbev/msy101 29788252

31. Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000;7(1–2):203–14. Epub 2000/07/13. doi: 10.1089/10665270050081478 10890397.

32. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2018;46(D1):D8–d13. Epub 2017/11/16. doi: 10.1093/nar/gkx1095 29140470

33. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80. doi: 10.1093/molbev/mst010 23329690

34. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25(9):1189–91. doi: 10.1093/bioinformatics/btp033 19151095

35. Kumar S, Stecher G, Suleski M, Hedges SB. Timetree: A resource for timelines, timetrees, and divergence times. Mol Biol Evol. 2017;34(7):1812–9. doi: 10.1093/molbev/msx116 28387841

36. Khatter H, Myasnikov AG, Natchiar SK, Klaholz BP. Structure of the human 80S ribosome. Nature. 2015;520:640. doi: 10.1038/nature14427 25901680

37. Bernier CR, Petrov AS, Waterbury CC, Jett J, Li F, Freil LE, Xiong X, Wang L, Migliozzi BLR, Hershkovits E, Xue Y, Hsiao C, Bowman JC, Harvey SC, et al. Ribovision suite for visualization and analysis of ribosomes. Faraday Discuss. 2014;169(0):195–207. doi: 10.1039/C3FD00126A 25340471


Článek vyšel v časopise

PLOS One


2019 Číslo 12