RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri

Nucleic Acids Research

Volumn 41, Issue 12, 2013, Pages 6250-6258

  Su, Andreas A H ^a   Tripp, Vanessa ^a,b   Randau, Lennart ^a,b  

^a MAX PLANCK INSTITUTE FOR TERRESTRIAL MICROBIOLOGY   (Germany)

^b PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; METHANOPYRUS KANDLERI; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; RNA METABOLISM; RNA PROCESSING; RNA SEQUENCE; RNA STABILITY; SEQUENCE ANALYSIS; TEMPERATURE DEPENDENCE;

EURYARCHAEOTA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOT TEMPERATURE; INVERTED REPEAT SEQUENCES; RNA EDITING; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, ARCHAEAL; RNA, GUIDE; RNA, SMALL UNTRANSLATED; RNA, TRANSFER; SEQUENCE ANALYSIS, RNA;

EID: 84880213700     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt317     Document Type: Article

References (41)

1. Slesarev, A.I., Mezhevaya, K.V., Makarova, K.S., Polushin, N.N., Shcherbinina, O.V., Shakhova, V.V., Belova, G.I., Aravind, L., Natale, D.A., Rogozin, I.B. et al. (2002) The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl Acad. Sci. USA, 99, 4644-4649.
2. Huber, R., Kurr, M., Jannasch, H.W. and Stetter, K.O. (1989) A novel group of abyssal methanogenic archaebacteria (Methanopyrus) growing at 110°C. Nature, 342, 833-834.
3. Takai, K., Nakamura, K., Toki, T., Tsunogai, U., Miyazaki, M., Miyazaki, J., Hirayama, H., Nakagawa, S., Nunoura, T. and Horikoshi, K. (2008) Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. Proc. Natl Acad. Sci. USA, 105, 10949-10954.
4. Shima, S., Herault, D.A., Berkessel, A. and Thauer, R.K. (1998) Activation and thermostabilization effects of cyclic 2, 3-diphosphoglycerate on enzymes from the hyperthermophilic Methanopyrus kandleri. Arch. Microbiol., 170, 469-472.
5. Breitung, J., Borner, G., Scholz, S., Linder, D., Stetter, K.O. and Thauer, R.K. (1992) Salt dependence, kinetic properties and catalytic mechanism of N-formylmethanofuran: tetrahydromethanopterin formyltransferase from the extreme thermophile Methanopyrus kandleri. Eur. J. Biochem., 210, 971-981.
6. Slesarev, A.I., Stetter, K.O., Lake, J.A., Gellert, M., Krah, R. and Kozyavkin, SA. (1993) DNA topoisomerase V is a relative of eukaryotic topoisomerase I from a hyperthermophilic prokaryote. Nature, 364, 735-737.
7. Krah, R., Kozyavkin, SA., Slesarev, A.I. and Gellert, M. (1996) A two-subunit type I DNA topoisomerase (reverse gyrase) from an extreme hyperthermophile. Proc. Natl Acad. Sci. USA, 93, 106-110.
8. Randau, L., Stanley, B.J., Kohlway, A., Mechta, S., Xiong, Y. and Soll, D. (2009) A cytidine deaminase edits C to U in transfer RNAs in Archaea. Science, 324, 657-659.
9. Forterre, P. (2006) DNA topoisomerase V: a new fold of mysterious origin. Trends Biotechnol., 24, 245-247.
10. Burggraf, S., Stetter, K.O., Rouviere, P. and Woese, C.R. (1991) Methanopyrus kandleri: an archaeal methanogen unrelated to all other known methanogens. Syst. Appl. Microbiol., 14, 346-351.
11. Brochier, C, Forterre, P. and Gribaldo, S. (2004) Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol., 5, R17.
12. Mat, W.K., Xue, H. and Wong, J.T. (2008) The genomics of LUCA. Front. Biosci., 13, 5605-5613.
13. Kehr, S., Bartschat, S., Stadler, P.F. and Tafer, H. (2011) PLEXY: efficient target prediction for box C/D snoRNAs. Bioinformatics, 27, 279-280.
14. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
15. Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
16. Chan, P.P. and Lowe, T.M. (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res., 37, D93-D97.
17. Lowe, T.M. and Eddy, S.R. (1999) A computational screen for methylation guide snoRNAs in yeast. Science, 283, 1168-1171.
18. Grissa, I., Vergnaud, G and Pourcel, C. (2007) The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics, 8, 172.
19. Larkin, MA., Blackshields, G, Brown, N.P., Chenna, R., McGettigan, PA., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
20. Darty, K., Denise, A. and Ponty, Y. (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974-1975.
21. Sauerwald, A., Sitaramaiah, D., McCloskey, JA., Soll, D. and Crain, P.F. (2005) N6-Acetyladenosine: a new modified nucleoside from Methanopyrus kandleri tRNA. FEBS Lett., 579, 2807-2810.
22. Findeiss, S., Langenberger, D., Stadler, P.F. and Hoffmann, S. (2011) Traces of post-transcriptional RNA modifications in deep sequencing data. Biol. Chem., 392, 305-313.
23. Fechter, P., Rudinger-Thirion, J., Theobald-Dietrich, A. and Giege, R. (2000) Identity of tRNA for yeast tyrosyl-tRNA synthetase: tyrosylation is more sensitive to identity nucleotides than to structural features. Biochemistry, 39, 1725-1733.
24. Marck, C. and Grosjean, H. (2003) Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA, 9, 1516-1531.
25. Omer, A.D., Lowe, T.M., Russell, A.G., Ebhardt, H., Eddy, S.R. and Dennis, P.P. (2000) Homologs of small nucleolar RNAs in Archaea. Science, 288, 517-522.
26. Makarova, K.S., Haft, D.H., Barrangou, R., Brouns, S.J., Charpentier, E., Horvath, P., Moineau, S., Mojica, F.J., Wolf, Y.I., Yakunin, A.F. et al. (2011) Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol., 9, 467-477.
27. Jore, M.M., Lundgren, M., van Duijn, E., Bultema, J.B., Westra, E.R., Waghmare, S.P., Wiedenheft, B., Pul, U., Wurm, R., Wagner, R. et al. (2011) Structural basis for CRISPR RNA-guided DNA recognition by Cascade. Nat. Struct. Mol. Biol., 18, 529-536.
28. Haas, E.S., Daniels, C.J. and Reeve, J.N. (1989) Genes encoding 5S rRNA and tRNAs in the extremely thermophilic archaebacterium Methanothermus fervidus. Gene, 77, 253-263.
29. Kowalak, J.A., Dalluge, J.J., McCloskey, J.A. and Stetter, K.O. (1994) The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochemistry, 33, 7869-7876.
30. Palmer, J.R., Baltrus, T., Reeve, J.N. and Daniels, C.J. (1992) Transfer RNA genes from the hyperthermophilic Archaeon, Methanopyrus kandleri. Biochim. Biophys. Acta., 1132, 315-318.
31. Klein, D.J., Schmeing, T.M., Moore, P.B. and Steitz, T.A. (2001) The kink-turn: a new RNA secondary structure motif. EMBO J., 20, 4214-4221.
32. Rozhdestvensky, T.S., Tang, T.H., Tchirkova, I.V., Brosius, J., Bachellerie, J.P. and Huttenhofer, A. (2003) Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res., 31, 869-877.
33. Kiss, T. (2001) Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J., 20, 3617-3622.
34. Danan, M., Schwartz, S., Edelheit, S. and Sorek, R. (2012) Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res., 40, 3131-3142.
35. Starostina, N.G., Marshburn, S., Johnson, L.S., Eddy, S.R., Terns, R.M. and Terns, M.P. (2004) Circular box C/D RNAs in Pyrococcus furiosus. Proc. Natl Acad. Sci. USA, 101, 14097-14101.
36. Randau, L. (2012) RNA processing in the minimal organism Nanoarchaeum equitans. Genome Biol., 13, R63.
37. Puttaraju, M. and Been, M.D. (1995) Generation of nuclease resistant circular RNA decoys for HIV-Tat and HIV-Rev by autocatalytic splicing. Nucleic Acids Symp. Ser., 49-51.
38. Salzman, J., Gawad, C., Wang, P.L., Lacayo, N. and Brown, P.O. (2012) Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One, 7, e30733.
39. Yoshihisa, T., Yunoki-Esaki, K., Ohshima, C., Tanaka, N. and Endo, T. (2003) Possibility of cytoplasmic pre-tRNA splicing: the yeast tRNA splicing endonuclease mainly localizes on the mitochondria. Mol. Biol. Cell, 14, 3266-3279.
40. Randau, L. and Soll, D. (2008) Transfer RNA genes in pieces. EMBO Rep., 9, 623-628.
41. Liu, Y., Zhu, X., Nakamura, A., Orlando, R., Soll, D. and Whitman, W.B. (2012) Biosynthesis of 4-thiouridine in tRNA in the methanogenic archaeon Methanococcus maripaludis. J. Biol. Chem., 287, 36683-36692.