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For: Marck C, Grosjean H. Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA 2003;9:1516-31. [PMID: 14624007 PMCID: PMC1370505 DOI: 10.1261/rna.5132503] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Accepted: 09/08/2003] [Indexed: 05/19/2023]
Number Cited by Other Article(s)
1
Hayashi S. Variation of tRNA modifications with and without intron dependency. Front Genet 2024;15:1460902. [PMID: 39296543 PMCID: PMC11408192 DOI: 10.3389/fgene.2024.1460902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Accepted: 08/26/2024] [Indexed: 09/21/2024]  Open
2
Valentin-Alvarado LE, Appler KE, De Anda V, Schoelmerich MC, West-Roberts J, Kivenson V, Crits-Christoph A, Ly L, Sachdeva R, Greening C, Savage DF, Baker BJ, Banfield JF. Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nat Commun 2024;15:6384. [PMID: 39085194 PMCID: PMC11291895 DOI: 10.1038/s41467-024-49872-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/20/2024] [Indexed: 08/02/2024]  Open
3
Yuan L, Han Y, Zhao J, Zhang Y, Sun Y. Recognition and cleavage mechanism of intron-containing pre-tRNA by human TSEN endonuclease complex. Nat Commun 2023;14:6071. [PMID: 37770519 PMCID: PMC10539383 DOI: 10.1038/s41467-023-41845-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023]  Open
4
Hayne CK, Sekulovski S, Hurtig JE, Stanley RE, Trowitzsch S, van Hoof A. New insights into RNA processing by the eukaryotic tRNA splicing endonuclease. J Biol Chem 2023;299:105138. [PMID: 37544645 PMCID: PMC10485636 DOI: 10.1016/j.jbc.2023.105138] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 07/27/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023]  Open
5
Nagato Y, Tomikawa C, Yamaji H, Soma A, Takai K. Intron-Dependent or Independent Pseudouridylation of Precursor tRNA Containing Atypical Introns in Cyanidioschyzon merolae. Int J Mol Sci 2022;23:ijms232012058. [PMID: 36292915 PMCID: PMC9602550 DOI: 10.3390/ijms232012058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022]  Open
6
Sekulovski S, Trowitzsch S. Transfer RNA processing - from a structural and disease perspective. Biol Chem 2022;403:749-763. [PMID: 35728022 DOI: 10.1515/hsz-2021-0406] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/24/2022] [Indexed: 01/05/2023]
7
Gerber JL, Köhler S, Peschek J. Eukaryotic tRNA splicing - one goal, two strategies, many players. Biol Chem 2022;403:765-778. [PMID: 35621519 DOI: 10.1515/hsz-2021-0402] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 05/10/2022] [Indexed: 12/28/2022]
8
Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova K, Koonin E, Shen Y, Söll D, Fu X. The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism. Nucleic Acids Res 2022;50:4601-4615. [PMID: 35466371 PMCID: PMC9071458 DOI: 10.1093/nar/gkac271] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 12/24/2022]  Open
9
Tocchini-Valentini GD, Tocchini-Valentini GP. Archaeal tRNA-Splicing Endonuclease as an Effector for RNA Recombination and Novel Trans-Splicing Pathways in Eukaryotes. J Fungi (Basel) 2021;7:jof7121069. [PMID: 34947051 PMCID: PMC8707768 DOI: 10.3390/jof7121069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022]  Open
10
Chan PP, Lin BY, Mak AJ, Lowe TM. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res 2021;49:9077-9096. [PMID: 34417604 PMCID: PMC8450103 DOI: 10.1093/nar/gkab688] [Citation(s) in RCA: 787] [Impact Index Per Article: 196.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022]  Open
11
Schwarz TS, Berkemer SJ, Bernhart SH, Weiß M, Ferreira-Cerca S, Stadler PF, Marchfelder A. Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea. Front Microbiol 2020;11:594838. [PMID: 33329479 PMCID: PMC7714728 DOI: 10.3389/fmicb.2020.594838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022]  Open
12
Qi L, Li J, Jia J, Yue L, Dong X. Comprehensive analysis of the pre-ribosomal RNA maturation pathway in a methanoarchaeon exposes the conserved circularization and linearization mode in archaea. RNA Biol 2020;17:1427-1441. [PMID: 32449429 DOI: 10.1080/15476286.2020.1771946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
13
Yang S, Qu G, Fu B, Yang F, Zeng W, Cai Y, Ye T, Yang Y, Deng X, Xiang W, Peng D, Zhou B. The function of KptA/Tpt1 gene - a minor review. FUNCTIONAL PLANT BIOLOGY : FPB 2020;47:577-591. [PMID: 32438974 DOI: 10.1071/fp19159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 02/06/2020] [Indexed: 06/11/2023]
14
Schmidt CA, Giusto JD, Bao A, Hopper AK, Matera AG. Molecular determinants of metazoan tricRNA biogenesis. Nucleic Acids Res 2020;47:6452-6465. [PMID: 31032518 PMCID: PMC6614914 DOI: 10.1093/nar/gkz311] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/18/2019] [Indexed: 12/22/2022]  Open
15
Payea MJ, Hauke AC, De Zoysa T, Phizicky EM. Mutations in the anticodon stem of tRNA cause accumulation and Met22-dependent decay of pre-tRNA in yeast. RNA (NEW YORK, N.Y.) 2020;26:29-43. [PMID: 31619505 PMCID: PMC6913130 DOI: 10.1261/rna.073155.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/11/2019] [Indexed: 05/20/2023]
16
Schmidt CA, Matera AG. tRNA introns: Presence, processing, and purpose. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019;11:e1583. [DOI: 10.1002/wrna.1583] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 12/18/2022]
17
Wang Y, Zeng Z, Liu TL, Sun L, Yao Q, Chen KP. TA, GT and AC are significantly under-represented in open reading frames of prokaryotic and eukaryotic protein-coding genes. Mol Genet Genomics 2019;294:637-647. [PMID: 30758669 DOI: 10.1007/s00438-019-01535-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/31/2019] [Indexed: 01/01/2023]
18
Hirata A. Recent Insights Into the Structure, Function, and Evolution of the RNA-Splicing Endonucleases. Front Genet 2019;10:103. [PMID: 30809252 PMCID: PMC6379350 DOI: 10.3389/fgene.2019.00103] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022]  Open
19
Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiol Rev 2018;42:579-613. [PMID: 29684129 DOI: 10.1093/femsre/fuy016] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022]  Open
20
Wu Y, Wu P, Wang B, Shao ZQ. Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea. Front Microbiol 2018;9:1245. [PMID: 29930548 PMCID: PMC6000648 DOI: 10.3389/fmicb.2018.01245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 05/23/2018] [Indexed: 12/02/2022]  Open
21
Kaneta A, Fujishima K, Morikazu W, Hori H, Hirata A. The RNA-splicing endonuclease from the euryarchaeaon Methanopyrus kandleri is a heterotetramer with constrained substrate specificity. Nucleic Acids Res 2018;46:1958-1972. [PMID: 29346615 PMCID: PMC5829648 DOI: 10.1093/nar/gky003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/25/2017] [Accepted: 01/03/2018] [Indexed: 11/14/2022]  Open
22
An Overview of Ribonuclease Repertoire and RNA Processing Pathways in Archaea. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-65795-0_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
23
Wang Y, Tao XF, Su ZX, Liu AK, Liu TL, Sun L, Yao Q, Chen KP, Gu X. Current Bacterial Gene Encoding Capsule Biosynthesis Protein CapI Contains Nucleotides Derived from Exonization. Evol Bioinform Online 2016;12:303-312. [PMID: 27980385 PMCID: PMC5154736 DOI: 10.4137/ebo.s40703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/18/2016] [Accepted: 09/22/2016] [Indexed: 12/04/2022]  Open
24
Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life. Life (Basel) 2016;6:life6010012. [PMID: 26999216 PMCID: PMC4810243 DOI: 10.3390/life6010012] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 11/17/2022]  Open
25
Jay ZJ, Inskeep WP. The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales. Biol Direct 2015;10:35. [PMID: 26156036 PMCID: PMC4496867 DOI: 10.1186/s13062-015-0065-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]  Open
26
Lopes RRS, Kessler AC, Polycarpo C, Alfonzo JD. Cutting, dicing, healing and sealing: the molecular surgery of tRNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015;6:337-49. [PMID: 25755220 DOI: 10.1002/wrna.1279] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/13/2015] [Accepted: 01/15/2015] [Indexed: 11/09/2022]
27
Disrupted tRNA Genes and tRNA Fragments: A Perspective on tRNA Gene Evolution. Life (Basel) 2015;5:321-31. [PMID: 25629271 PMCID: PMC4390854 DOI: 10.3390/life5010321] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/14/2015] [Accepted: 01/21/2015] [Indexed: 01/17/2023]  Open
28
Experimental confirmation of a whole set of tRNA molecules in two archaeal species. Int J Mol Sci 2015;16:2187-203. [PMID: 25608653 PMCID: PMC4307357 DOI: 10.3390/ijms16012187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 01/14/2015] [Indexed: 11/17/2022]  Open
29
Mitra S, Das P, Samadder A, Das S, Betai R, Chakrabarti J. Eukaryotic tRNAs fingerprint invertebrates vis-à-vis vertebrates. J Biomol Struct Dyn 2015;33:2104-20. [PMID: 25581620 DOI: 10.1080/07391102.2014.990925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
30
Yoshihisa T. Handling tRNA introns, archaeal way and eukaryotic way. Front Genet 2014;5:213. [PMID: 25071838 PMCID: PMC4090602 DOI: 10.3389/fgene.2014.00213] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 06/20/2014] [Indexed: 11/25/2022]  Open
31
Irimia M, Roy SW. Origin of spliceosomal introns and alternative splicing. Cold Spring Harb Perspect Biol 2014;6:a016071. [PMID: 24890509 PMCID: PMC4031966 DOI: 10.1101/cshperspect.a016071] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
32
Fujishima K, Kanai A. tRNA gene diversity in the three domains of life. Front Genet 2014;5:142. [PMID: 24904642 PMCID: PMC4033280 DOI: 10.3389/fgene.2014.00142] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/28/2014] [Indexed: 11/29/2022]  Open
33
RNA Processing. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
34
Soma A. Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development. Front Genet 2014;5:63. [PMID: 24744771 PMCID: PMC3978253 DOI: 10.3389/fgene.2014.00063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/12/2014] [Indexed: 12/02/2022]  Open
35
Soma A, Sugahara J, Onodera A, Yachie N, Kanai A, Watanabe S, Yoshikawa H, Ohnuma M, Kuroiwa H, Kuroiwa T, Sekine Y. Identification of highly-disrupted tRNA genes in nuclear genome of the red alga, Cyanidioschyzon merolae 10D. Sci Rep 2014;3:2321. [PMID: 23900518 PMCID: PMC3728597 DOI: 10.1038/srep02321] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/10/2013] [Indexed: 12/03/2022]  Open
36
Su AAH, Tripp V, Randau L. 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 Res 2013;41:6250-8. [PMID: 23620296 PMCID: PMC3695527 DOI: 10.1093/nar/gkt317] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 04/03/2013] [Accepted: 04/05/2013] [Indexed: 11/29/2022]  Open
37
Zuo Z, Peng D, Yin X, Zhou X, Cheng H, Zhou R. Genome-wide analysis reveals origin of transfer RNA genes from tRNA halves. Mol Biol Evol 2013;30:2087-98. [PMID: 23744908 DOI: 10.1093/molbev/mst107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
38
Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machné R, Mörl M, Hoffmann S, Stadler PF. Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. RNA Biol 2013;10:1204-10. [PMID: 23702463 DOI: 10.4161/rna.24972] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
39
Avatar pre-tRNAs help elucidate the properties of tRNA-splicing endonucleases that produce tRNA from permuted genes. Proc Natl Acad Sci U S A 2012;109:21325-9. [PMID: 23236183 DOI: 10.1073/pnas.1219336110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
40
Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, Hori H. X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Nucleic Acids Res 2012;40:10554-66. [PMID: 22941657 PMCID: PMC3488258 DOI: 10.1093/nar/gks826] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
41
Popow J, Schleiffer A, Martinez J. Diversity and roles of (t)RNA ligases. Cell Mol Life Sci 2012;69:2657-70. [PMID: 22426497 PMCID: PMC3400036 DOI: 10.1007/s00018-012-0944-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/01/2012] [Accepted: 02/13/2012] [Indexed: 12/29/2022]
42
Sugahara J, Fujishima K, Nunoura T, Takaki Y, Takami H, Takai K, Tomita M, Kanai A. Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PLoS One 2012;7:e32504. [PMID: 22403667 PMCID: PMC3293823 DOI: 10.1371/journal.pone.0032504] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 01/31/2012] [Indexed: 11/27/2022]  Open
43
Chen WY, Singh D, Lai LB, Stiffler MA, Lai HD, Foster MP, Gopalan V. Fidelity of tRNA 5'-maturation: a possible basis for the functional dependence of archaeal and eukaryal RNase P on multiple protein cofactors. Nucleic Acids Res 2012;40:4666-80. [PMID: 22298511 PMCID: PMC3378863 DOI: 10.1093/nar/gks013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
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Moreira S, Breton S, Burger G. Unscrambling genetic information at the RNA level. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012;3:213-28. [PMID: 22275292 DOI: 10.1002/wrna.1106] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Chan PP, Holmes AD, Smith AM, Tran D, Lowe TM. The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res 2011;40:D646-52. [PMID: 22080555 PMCID: PMC3245099 DOI: 10.1093/nar/gkr990] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
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Fujishima K, Sugahara J, Miller CS, Baker BJ, Di Giulio M, Takesue K, Sato A, Tomita M, Banfield JF, Kanai A. A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res 2011;39:9695-704. [PMID: 21880595 PMCID: PMC3239211 DOI: 10.1093/nar/gkr692] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
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Yamazaki S, Yoshinari S, Kita K, Watanabe YI, Kawarabayasi Y. Identification of an entire set of tRNA molecules and characterization of cleavage sites of the intron-containing tRNA precursors in acidothermophilic crenarchaeon Sulfolobus tokodaii strain7. Gene 2011;489:103-10. [PMID: 21872648 DOI: 10.1016/j.gene.2011.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/01/2011] [Accepted: 08/03/2011] [Indexed: 11/25/2022]
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Hirata A, Kitajima T, Hori H. Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyper-thermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop. Nucleic Acids Res 2011;39:9376-89. [PMID: 21846775 PMCID: PMC3241643 DOI: 10.1093/nar/gkr615] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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Chan PP, Cozen AE, Lowe TM. Discovery of permuted and recently split transfer RNAs in Archaea. Genome Biol 2011;12:R38. [PMID: 21489296 PMCID: PMC3218864 DOI: 10.1186/gb-2011-12-4-r38] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 03/30/2011] [Accepted: 04/13/2011] [Indexed: 01/19/2023]  Open
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Das S, Mitra S, Sahoo S, Chakrabarti J. Novel Hybrid Encodes both Continuous and Split tRNA Genes? J Biomol Struct Dyn 2011;28:827-31. [DOI: 10.1080/07391102.2011.10508610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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