1. Cavicchioli R. General Characteristics and Important Model Organisms. In: Cavicchioli R, editor. Archaea: Molecular and Cellular Biology. Washington, DC, USA: ASM Press; 2007.
3. Maizels N, Weiner AM. Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation.
Proc Natl Acad Sci U S A. 1994;
91(15):6729-6734.
doi: 10.1073/pnas.91.15.6729 pmid: 8041690
4. Weiner AM, Maizels N. The genomic tag hypothesis: modern viruses as molecular fossils of ancient strategies for genomic replication, and clues regarding the origin of protein synthesis.
Biol Bull. 1999;
196(3):327-328; discussion 329-330.
doi: 10.2307/1542962 pmid: 10390830
5. Di Giulio M. The non-monophyletic origin of the tRNA molecule and the origin of genes only after the evolutionary stage of the last universal common ancestor (LUCA).
J Theor Biol. 2006;
240(3):343-352.
doi: 10.1016/j.jtbi.2005.09.023 pmid: 16289209
8. Tanaka T, Kikuchi Y. Origin of the cloverleaf shape of transfer RNA-the double-hairpin model: implication for the role of tRNA intron and the long extra loop. Viva Origino. 2001;29(134):134-142.
9. Marck C, Grosjean H. tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features.
RNA. 2002;
8(10):1189-1232.
doi: 10.1017/s1355838202022021 pmid: 12403461
10. Sugahara J, Yachie N, Sekine Y, Soma A, Matsui M, Tomita M, et al. SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.
In Silico Biol. 2006;
6(5):411-418.
pmid: 17274770
11. Sugahara J, Yachie N, Arakawa K, Tomita M. In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs.
RNA. 2007;
13(5):671-681.
doi: 10.1261/rna.309507 pmid: 17369313
12. Randau L, Munch R, Hohn MJ, Jahn D, Soll D. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves.
Nature. 2005;
433(7025):537-541.
doi: 10.1038/nature03233 pmid: 15690044
13. Fujishima K, Sugahara J, Kikuta K, Hirano R, Sato A, Tomita M, et al. Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea.
Proc Natl Acad Sci U S A. 2009;
106(8):2683-2687.
doi: 10.1073/pnas.0808246106 pmid: 19190180
14. Randau L, Calvin K, Hall M, Yuan J, Podar M, Li H, et al. The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves.
Proc Natl Acad Sci U S A. 2005;
102(50):17934-17939.
doi: 10.1073/pnas.0509197102 pmid: 16330750
15. Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP. Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea.
Proc Natl Acad Sci U S A. 2005;
102(43):15418-15422.
doi: 10.1073/pnas.0506750102 pmid: 16221764
16. Fujishima K, Sugahara J, Miller CS, Baker BJ, Di Giulio M, Takesue K, et al. A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity.
Nucleic Acids Res. 2011;
39(22):9695-9704.
doi: 10.1093/nar/gkr692 pmid: 21880595
19. Sakonju S, Bogenhagen DF, Brown DD. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region.
Cell. 1980;
19(1):13-25.
doi: 10.1016/0092-8674(80)90384-0 pmid: 7357599
20. Bogenhagen DF, Sakonju S, Brown DD. A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3' border of the region.
Cell. 1980;
19(1):27-35.
doi: 10.1016/0092-8674(80)90385-2 pmid: 7357604
24. Ciliberto G, Castagnoli L, Melton DA, Cortese R. Promoter of a eukaryotic tRNAPro gene is composed of three noncontiguous regions.
Proc Natl Acad Sci U S A. 1982;
79(4):1195-1199.
doi: 10.1073/pnas.79.4.1195 pmid: 6951168
26. Murray J. Mathematical Biology: An Introduction. Berlin: Springer 2002.
28. el-Mabrouk N, Lisacek F. Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome.
J Mol Biol. 1996;
264(1):46-55.
doi: 10.1006/jmbi.1996.0622 pmid: 8950266
36. Minagawa A, Ishii R, Takaku H, Yokoyama S, Nashimoto M. The flexible arm of tRNase Z is not essential for pre-tRNA binding but affects cleavage site selection.
J Mol Biol. 2008;
381(2):289-299.
doi: 10.1016/j.jmb.2008.05.016 pmid: 18602113
37. Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing.
Nucleic Acids Res. 2006;
34(8):e63.
doi: 10.1093/nar/gkl151 pmid: 16682442