-
1
-
-
0036792830
-
TRNomics: Analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features
-
Marck,C. and Grosjean,H. (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA, 8, 1189-1232.
-
(2002)
RNA
, vol.8
, pp. 1189-1232
-
-
Marck, C.1
Grosjean, H.2
-
2
-
-
56449099760
-
Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales
-
Sugahara,J., Kikuta,K., Fujishima,K., Yachie,N., Tomita,M. and Kanai,A. (2008) Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol. Biol. Evol., 25, 2709-2716.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 2709-2716
-
-
Sugahara, J.1
Kikuta, K.2
Fujishima, K.3
Yachie, N.4
Tomita, M.5
Kanai, A.6
-
3
-
-
42449113800
-
RNA-splicing endonuclease structure and function
-
Calvin,K. and Li,H. (2008) RNA-splicing endonuclease structure and function. Cell Mol. Life Sci., 65, 1176-1185.
-
(2008)
Cell Mol. Life Sci.
, vol.65
, pp. 1176-1185
-
-
Calvin, K.1
Li, H.2
-
4
-
-
0032502894
-
Crystal structure and evolution of a transfer RNA splicing enzyme
-
DOI 10.1126/science.280.5361.279
-
Li,H., Trotta,C.R. and Abelson,J. (1998) Crystal structure and evolution of a transfer RNA splicing enzyme. Science, 280, 279-284. (Pubitemid 28178070)
-
(1998)
Science
, vol.280
, Issue.5361
, pp. 279-284
-
-
Li, H.1
Trotta, C.R.2
Abelson, J.3
-
5
-
-
21144453167
-
Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization
-
DOI 10.1073/pnas.0502350102
-
Tocchini-Valentini,G.D., Fruscoloni,P. and Tocchini- Valentini,G.P. (2005) Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization. Proc. Natl Acad. Sci. USA, 102, 8933-8938. (Pubitemid 40881056)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.25
, pp. 8933-8938
-
-
Tocchini-Valentini, G.D.1
Fruscoloni, P.2
Tocchini-Valentini, G.P.3
-
6
-
-
0030670627
-
RNA-protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary history
-
DOI 10.1093/emboj/16.20.6290
-
Lykke-Andersen,J. and Garrett,R.A. (1997) RNA-protein interactions of an archaeal homotetrameric splicing endoribonuclease with an exceptional evolutionary history. EMBO J., 16, 6290-6300. (Pubitemid 27458349)
-
(1997)
EMBO Journal
, vol.16
, Issue.20
, pp. 6290-6300
-
-
Lykke-Andersen, J.1
Garrett, R.A.2
-
7
-
-
0024291338
-
Substrate recognition and splice site determination in yeast tRNA splicing
-
Reyes,V.M. and Abelson,J. (1988) Substrate recognition and splice site determination in yeast tRNA splicing. Cell, 55, 719-730.
-
(1988)
Cell
, vol.55
, pp. 719-730
-
-
Reyes, V.M.1
Abelson, J.2
-
8
-
-
0030730242
-
Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems
-
Kleman-Leyer,K., Armbruster,D.W. and Daniels,C.J. (1997) Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems. Cell, 89, 839-847. (Pubitemid 27513510)
-
(1997)
Cell
, vol.89
, Issue.6
, pp. 839-847
-
-
Kleman-Leyer, K.1
Armbruster, D.W.2
Daniels, C.J.3
-
9
-
-
0344874260
-
Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: Evolutionary implications
-
DOI 10.1261/rna.5132503
-
Marck,C. and Grosjean,H. (2003) Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA, 9, 1516-1531. (Pubitemid 37463477)
-
(2003)
RNA
, vol.9
, Issue.12
, pp. 1516-1531
-
-
Marck, C.1
Grosjean, H.2
-
10
-
-
62449123460
-
Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea
-
Fujishima,K., Sugahara,J., Kikuta,K., Hirano,R., Sato,A., Tomita,M. and Kanai,A. (2009) 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. USA, 106, 2683-2687.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 2683-2687
-
-
Fujishima, K.1
Sugahara, J.2
Kikuta, K.3
Hirano, R.4
Sato, A.5
Tomita, M.6
Kanai, A.7
-
11
-
-
13444251251
-
Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves
-
DOI 10.1038/nature03233
-
Randau,L., Munch,R., Hohn,M.J., Jahn,D. and Soll,D. (2005) Nanoarchaeum equitans creates functional tRNAs from separate genes for their 50- and 30-halves. Nature, 433, 537-541. (Pubitemid 40204312)
-
(2005)
Nature
, vol.433
, Issue.7025
, pp. 537-541
-
-
Randau, L.1
Munch, R.2
Hohn, M.J.3
Jahn, D.4
Soll, D.5
-
12
-
-
79953861250
-
Discovery of permuted and recently split transfer RNAs in Archaea
-
Chan,P.P., Cozen,A.E. and Lowe,T.M. (2011) Discovery of permuted and recently split transfer RNAs in Archaea. Genome Biol, 12, R38.
-
(2011)
Genome Biol
, vol.12
-
-
Chan, P.P.1
Cozen, A.E.2
Lowe, T.M.3
-
13
-
-
72449205918
-
Disrupted tRNA gene diversity and possible evolutionary scenarios
-
Sugahara,J., Fujishima,K., Morita,K., Tomita,M. and Kanai,A. (2009) Disrupted tRNA gene diversity and possible evolutionary scenarios. J. Mol. Evol., 69, 497-504.
-
(2009)
J. Mol. Evol.
, vol.69
, pp. 497-504
-
-
Sugahara, J.1
Fujishima, K.2
Morita, K.3
Tomita, M.4
Kanai, A.5
-
14
-
-
27344434409
-
Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea
-
DOI 10.1073/pnas.0506750102
-
Tocchini-Valentini,G.D., Fruscoloni,P. and Tocchini- Valentini,G.P. (2005) Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea. Proc. Natl Acad. Sci. USA, 102, 15418-15422. (Pubitemid 41528072)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.43
, pp. 15418-15422
-
-
Tocchini-Valentini, G.D.1
Fruscoloni, P.2
Tocchini-Valentini, G.P.3
-
15
-
-
33845898858
-
Lineages of acidophilic archaea revealed by community genomic analysis
-
DOI 10.1126/science.1132690
-
Baker,B.J., Tyson,G.W., Webb,R.I., Flanagan,J., Hugenholtz,P., Allen,E.E. and Banfield,J.F. (2006) Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314, 1933-1935. (Pubitemid 46026116)
-
(2006)
Science
, vol.314
, Issue.5807
, pp. 1933-1935
-
-
Baker, B.J.1
Tyson, G.W.2
Webb, R.I.3
Flanagan, J.4
Hugenholtz, P.5
Allen, E.E.6
Banfield, J.F.7
-
16
-
-
77952691194
-
Enigmatic, ultrasmall, uncultivated Archaea
-
Baker,B.J., Comolli,L.R., Dick,G.J., Hauser,L.J., Hyatt,D., Dill,B.D., Land,M.L., Verberkmoes,N.C., Hettich,R.L. and Banfield,J.F. (2010) Enigmatic, ultrasmall, uncultivated Archaea. Proc. Natl Acad. Sci. USA, 107, 8806-8811.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 8806-8811
-
-
Baker, B.J.1
Comolli, L.R.2
Dick, G.J.3
Hauser, L.J.4
Hyatt, D.5
Dill, B.D.6
Land, M.L.7
Verberkmoes, N.C.8
Hettich, R.L.9
Banfield, J.F.10
-
17
-
-
0030854739
-
TRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
DOI 10.1093/nar/25.5.955
-
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. (Pubitemid 27298263)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.5
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
18
-
-
1242297827
-
ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences
-
DOI 10.1093/nar/gkh152
-
Laslett,D. and Canback,B. (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res., 32, 11-16. (Pubitemid 38228599)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.1
, pp. 11-16
-
-
Laslett, D.1
Canback, B.2
-
19
-
-
33845244847
-
SPLITS: A new program for predicting split and intron-containing tRNA genes at the genome level
-
Sugahara,J., Yachie,N., Sekine,Y., Soma,A., Matsui,M., Tomita,M. and Kanai,A. (2006) SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biol., 6, 411-418. (Pubitemid 44857638)
-
(2006)
In Silico Biology
, vol.6
, Issue.5
, pp. 411-418
-
-
Sugahara, J.1
Yachie, N.2
Sekine, Y.3
Soma, A.4
Matsui, M.5
Tomita, M.6
Kanai, A.7
-
20
-
-
75549090603
-
The Pfam protein families database
-
Finn,R.D., Mistry,J., Tate,J., Coggill,P., Heger,A., Pollington,J.E., Gavin,O.L., Gunasekaran,P., Ceric,G., Forslund,K. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
Coggill, P.4
Heger, A.5
Pollington, J.E.6
Gavin, O.L.7
Gunasekaran, P.8
Ceric, G.9
Forslund, K.10
-
21
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
DOI 10.1093/bioinformatics/btg180
-
Ronquist,F. and Huelsenbeck,J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574. (Pubitemid 37038874)
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
22
-
-
33845873289
-
Interactive Tree Of Life (iTOL): An online tool for phylogenetic tree display and annotation
-
DOI 10.1093/bioinformatics/btl529
-
Letunic,I. and Bork,P. (2007) Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics, 23, 127-128. (Pubitemid 46017867)
-
(2007)
Bioinformatics
, vol.23
, Issue.1
, pp. 127-128
-
-
Letunic, I.1
Bork, P.2
-
23
-
-
77949820848
-
Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea
-
Ikeuchi,Y., Kimura,S., Numata,T., Nakamura,D., Yokogawa,T., Ogata,T., Wada,T. and Suzuki,T. (2010) Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Nat. Chem. Biol., 6, 277-282.
-
(2010)
Nat. Chem. Biol.
, vol.6
, pp. 277-282
-
-
Ikeuchi, Y.1
Kimura, S.2
Numata, T.3
Nakamura, D.4
Yokogawa, T.5
Ogata, T.6
Wada, T.7
Suzuki, T.8
-
24
-
-
77649263055
-
Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine
-
Mandal,D., Kohrer,C., Su,D., Russell,S.P., Krivos,K., Castleberry,C.M., Blum,P., Limbach,P.A., Soll,D. and RajBhandary,U.L. (2010) Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine. Proc. Natl Acad. Sci. USA, 107, 2872-2877.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 2872-2877
-
-
Mandal, D.1
Kohrer, C.2
Su, D.3
Russell, S.P.4
Krivos, K.5
Castleberry, C.M.6
Blum, P.7
Limbach, P.A.8
Soll, D.9
Rajbhandary, U.L.10
-
25
-
-
69049083528
-
Functional importance of crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease
-
Yoshinari,S., Shiba,T., Inaoka,D.K., Itoh,T., Kurisu,G., Harada,S., Kita,K. and Watanabe,Y. (2009) Functional importance of crenarchaea-specific extra-loop revealed by an X-ray structure of a heterotetrameric crenarchaeal splicing endonuclease. Nucleic Acids Res., 37, 4787-4798.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4787-4798
-
-
Yoshinari, S.1
Shiba, T.2
Inaoka, D.K.3
Itoh, T.4
Kurisu, G.5
Harada, S.6
Kita, K.7
Watanabe, Y.8
-
26
-
-
34547630914
-
The dawn of dominance by the mature domain in tRNA splicing
-
DOI 10.1073/pnas.0705537104
-
Tocchini-Valentini,G.D., Fruscoloni,P. and Tocchini- Valentini,G.P. (2007) The dawn of dominance by the mature domain in tRNA splicing. Proc. Natl Acad. Sci. USA, 104, 12300-12305. (Pubitemid 47206132)
-
(2007)
Proceedings of the National Academy of Sciences of the United States of America
, vol.104
, Issue.30
, pp. 12300-12305
-
-
Tocchini-Valentini, G.D.1
Fruscoloni, P.2
Tocchini-Valentini, G.P.3
-
27
-
-
78650417167
-
A conserved lysine residue in the crenarchaea-specific loop is important for the crenarchaeal splicing endonuclease activity
-
Okuda,M., Shiba,T., Inaoka,D.K., Kita,K., Kurisu,G., Mineki,S., Harada,S., Watanabe,Y. and Yoshinari,S. (2011) A conserved lysine residue in the crenarchaea-specific loop is important for the crenarchaeal splicing endonuclease activity. J. Mol. Biol., 405, 92-104.
-
(2011)
J. Mol. Biol.
, vol.405
, pp. 92-104
-
-
Okuda, M.1
Shiba, T.2
Inaoka, D.K.3
Kita, K.4
Kurisu, G.5
Mineki, S.6
Harada, S.7
Watanabe, Y.8
Yoshinari, S.9
-
28
-
-
33646248891
-
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)
-
Di Giulio,M. (2006) 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., 240, 343-352.
-
(2006)
J. Theor. Biol.
, vol.240
, pp. 343-352
-
-
Di Giulio, M.1
-
29
-
-
77957232919
-
Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain
-
Fujishima,K., Sugahara,J., Tomita,M. and Kanai,A. (2010) Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain. Mol. Biol. Evol., 27, 2233-2243.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 2233-2243
-
-
Fujishima, K.1
Sugahara, J.2
Tomita, M.3
Kanai, A.4
-
30
-
-
46449136416
-
Transfer RNA genes in pieces
-
DOI 10.1038/embor.2008.101, PII EMBOR2008101
-
Randau,L. and Soll,D. (2008) Transfer RNA genes in pieces. EMBO Rep., 9, 623-628. (Pubitemid 351927682)
-
(2008)
EMBO Reports
, vol.9
, Issue.7
, pp. 623-628
-
-
Randau, L.1
Soll, D.2
-
31
-
-
73649130281
-
The CRISPR system: Small RNA-guided defense in bacteria and Archaea
-
Karginov,F.V. and Hannon,G.J. (2010) The CRISPR system: small RNA-guided defense in bacteria and Archaea. Mol. Cell, 37, 7-19.
-
(2010)
Mol. Cell
, vol.37
, pp. 7-19
-
-
Karginov, F.V.1
Hannon, G.J.2
|