-
1
-
-
0344874260
-
Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: Evolutionary implications
-
Marck, C. and Grosjean, H. (2003) Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications. RNA, 9, 1516-1531.
-
(2003)
RNA
, vol.9
, pp. 1516-1531
-
-
Marck, C.1
Grosjean, H.2
-
2
-
-
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
-
3
-
-
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
-
4
-
-
0032557557
-
TRNA splicing
-
Abelson, J., Trotta, C. and Li, H. (1998) tRNA splicing. J. Biol. Chem., 273, 12685-12688.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 12685-12688
-
-
Abelson, J.1
Trotta, C.2
Li, H.3
-
5
-
-
0032502990
-
Conservation of substrate recognition mechanisms by tRNA splicing endonucleases
-
Fabbri, S., Fruscoloni, P., Bufardeci, E., Di Nicola Negri, E., Baldi, M., Attardi, D., Mattoccia, E. and Tocchini-Valentini, G. (1998) Conservation of substrate recognition mechanisms by tRNA splicing endonucleases. Science, 280, 284-286.
-
(1998)
Science
, vol.280
, pp. 284-286
-
-
Fabbri, S.1
Fruscoloni, P.2
Bufardeci, E.3
Di Nicola Negri, E.4
Baldi, M.5
Attardi, D.6
Mattoccia, E.7
Tocchini-Valentini, G.8
-
6
-
-
33646538487
-
RNA recognition and cleavage by a splicing endonuclease
-
Xue, S., Calvin, K. and Li, H. (2006) RNA recognition and cleavage by a splicing endonuclease. Science, 312, 906-910.
-
(2006)
Science
, vol.312
, pp. 906-910
-
-
Xue, S.1
Calvin, K.2
Li, H.3
-
7
-
-
0030730820
-
The yeast tRNA splicing endonuclease: A tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases
-
Trotta, C., Miao, F., Arn, E., Stevens, S., Ho, C., Rauhut, R. and Abelson, J. (1997) The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell, 89, 849-858.
-
(1997)
Cell
, vol.89
, pp. 849-858
-
-
Trotta, C.1
Miao, F.2
Arn, E.3
Stevens, S.4
Ho, C.5
Rauhut, R.6
Abelson, J.7
-
8
-
-
0242395997
-
The eucaryal tRNA splicing endonuclease recognizes a tripartite set of RNA elements
-
Di Nicola Negri, E., Fabbri, S., Bufardeci, E., Baldi, M., Gandini Attardi, D., Mattoccia, E. and Tocchini-Valentini, G. (1997) The eucaryal tRNA splicing endonuclease recognizes a tripartite set of RNA elements. Cell, 89, 859-866.
-
(1997)
Cell
, vol.89
, pp. 859-866
-
-
Di Nicola Negri, E.1
Fabbri, S.2
Bufardeci, E.3
Baldi, M.4
Gandini Attardi, D.5
Mattoccia, E.6
Tocchini-Valentini, G.7
-
9
-
-
21144453167
-
Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization
-
Tocchini-Valentini, G., Fruscoloni, P. and Tocchini-Valentini, G. (2005) Structure, function, and evolution of the tRNA endonucleases of Archaea: an example of subfunctionalization. Proc. Natl Acad. Sci. USA, 102, 8933-8938.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 8933-8938
-
-
Tocchini-Valentini, G.1
Fruscoloni, P.2
Tocchini-Valentini, G.3
-
10
-
-
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. and Daniels, C. (1997) Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems. Cell, 89, 839-847.
-
(1997)
Cell
, vol.89
, pp. 839-847
-
-
Kleman-Leyer, K.1
Armbruster, D.2
Daniels, C.3
-
11
-
-
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
-
12
-
-
0024291338
-
Substrate recognition and splice site determination in yeast tRNA splicing
-
Reyes, V. 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.1
Abelson, J.2
-
13
-
-
27144449031
-
Structural characterization of the catalytic subunit of a novel RNA splicing endonuclease
-
Calvin, K., Hall, M., Xu, F., Xue, S. and Li, H. (2005) Structural characterization of the catalytic subunit of a novel RNA splicing endonuclease. J. Mol. Biol., 353, 952-960.
-
(2005)
J. Mol. Biol.
, vol.353
, pp. 952-960
-
-
Calvin, K.1
Hall, M.2
Xu, F.3
Xue, S.4
Li, H.5
-
14
-
-
19444384556
-
The complete set of tRNA species in Nanoarchaeum equitans
-
Randau, L., Pearson, M. and Söll, D. (2005) The complete set of tRNA species in Nanoarchaeum equitans. FEBS Lett., 579, 2945-2947.
-
(2005)
FEBS Lett.
, vol.579
, pp. 2945-2947
-
-
Randau, L.1
Pearson, M.2
Söll, D.3
-
15
-
-
29144466626
-
The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves
-
Randau, L., Calvin, K., Hall, M., Yuan, J., Podar, M., Li, H. and Söll, D. (2005) The heteromeric Nanoarchaeum equitans splicing endonuclease cleaves noncanonical bulge-helix-bulge motifs of joined tRNA halves. Proc. Natl Acad. Sci. USA, 102, 17934-17939.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 17934-17939
-
-
Randau, L.1
Calvin, K.2
Hall, M.3
Yuan, J.4
Podar, M.5
Li, H.6
Söll, D.7
-
16
-
-
27344434409
-
Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea
-
Tocchini-Valentini, G., Fruscoloni, P. and Tocchini-Valentini, G. (2005) Coevolution of tRNA intron motifs and tRNA endonuclease architecture in Archaea. Proc. Natl Acad. Sci. USA, 102, 15418-15422.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15418-15422
-
-
Tocchini-Valentini, G.1
Fruscoloni, P.2
Tocchini-Valentini, G.3
-
17
-
-
33745206275
-
Archaeal pre-mRNA splicing: A connection to hetero-oligomeric splicing endonuclease
-
Yoshinari, S., Itoh, T., Hallam, S., DeLong, E., Yokobori, S., Yamagishi, A., Oshima, T., Kita, K. and Watanabe, Y. (2006) Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease. Biochem. Biophys. Res. Commun., 346, 1024-1032.
-
(2006)
Biochem. Biophys. Res. Commun.
, vol.346
, pp. 1024-1032
-
-
Yoshinari, S.1
Itoh, T.2
Hallam, S.3
Delong, E.4
Yokobori, S.5
Yamagishi, A.6
Oshima, T.7
Kita, K.8
Watanabe, Y.9
-
18
-
-
34547630914
-
The dawn of dominance by the mature domain in tRNA splicing
-
Tocchini-Valentini, G., Fruscoloni, P. and Tocchini-Valentini, G. (2007) The dawn of dominance by the mature domain in tRNA splicing. Proc. Natl Acad. Sci. USA, 104, 12300-12305.
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 12300-12305
-
-
Tocchini-Valentini, G.1
Fruscoloni, P.2
Tocchini-Valentini, G.3
-
19
-
-
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., 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.3
Itoh, T.4
Kurisu, G.5
Harada, S.6
Kita, K.7
Watanabe, Y.8
-
20
-
-
13444251251
-
Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves
-
Randau, L., Münch, R., Hohn, M., Jahn, D. and Söll, D. (2005) Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5'- and 3'-halves. Nature, 433, 537-541.
-
(2005)
Nature
, vol.433
, pp. 537-541
-
-
Randau, L.1
Münch, R.2
Hohn, M.3
Jahn, D.4
Söll, D.5
-
21
-
-
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
-
22
-
-
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
-
23
-
-
82255185634
-
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
-
Hirata, A., Kitajima, T. and Hori, H. (2011) 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., 39, 9376-9389.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 9376-9389
-
-
Hirata, A.1
Kitajima, T.2
Hori, H.3
-
24
-
-
83755220048
-
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity
-
Fujishima, K., Sugahara, J., Miller, C.S., Baker, B.J., Di Giulio, M., Takesue, K., Sato, A., Tomita, M., Banfield, J.F. and Kanai, A. (2011) A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res., 39, 9695-9704.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 9695-9704
-
-
Fujishima, K.1
Sugahara, J.2
Miller, C.S.3
Baker, B.J.4
Di Giulio, M.5
Takesue, K.6
Sato, A.7
Tomita, M.8
Banfield, J.F.9
Kanai, A.10
-
25
-
-
33845898858
-
Lineages of acidophilic archaea revealed by community genomic analysis
-
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.
-
(2006)
Science
, vol.314
, 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
-
26
-
-
0031059866
-
Processing of X-ray diffraction data collected in oscillation mode
-
Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
27
-
-
14244272868
-
PHENIX: Building new software for automated crystallographic structure determination
-
Adams, P., Grosse-Kunstleve, R., Hung, L., Ioerger, T., McCoy, A., Moriarty, N., Read, R., Sacchettini, J., Sauter, N. and Terwilliger, T. (2002) PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr., 58, 1948-1954.
-
(2002)
Acta Crystallogr. D Biol. Crystallogr.
, vol.58
, pp. 1948-1954
-
-
Adams, P.1
Grosse-Kunstleve, R.2
Hung, L.3
Ioerger, T.4
McCoy, A.5
Moriarty, N.6
Read, R.7
Sacchettini, J.8
Sauter, N.9
Terwilliger, T.10
-
28
-
-
0037242985
-
Automated side-chain model building and sequence assignment by template matching
-
Terwilliger, T.C. (2003) Automated side-chain model building and sequence assignment by template matching. Acta Crystallogr. D Biol. Crystallogr., 59, 45-49.
-
(2003)
Acta Crystallogr. D Biol. Crystallogr.
, vol.59
, pp. 45-49
-
-
Terwilliger, T.C.1
-
30
-
-
34447508216
-
Phaser crystallographic software
-
McCoy, A., Grosse-Kunstleve, R., Adams, P., Winn, M., Storoni, L. and Read, R. (2007) Phaser crystallographic software. J. Appl. Crystallogr., 40, 658-674.
-
(2007)
J. Appl. Crystallogr.
, vol.40
, pp. 658-674
-
-
McCoy, A.1
Grosse-Kunstleve, R.2
Adams, P.3
Winn, M.4
Storoni, L.5
Read, R.6
-
31
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski, R., MacArthur, M., Moss, D. and Thoronton, J. (1992) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst, 26, 283-291.
-
(1992)
J. Appl. Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.1
MacArthur, M.2
Moss, D.3
Thoronton, J.4
-
32
-
-
71849117870
-
Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease
-
Mitchell, M., Xue, S., Erdman, R., Randau, L., Söll, D. and Li, H. (2009) Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease. Nucleic Acids Res., 37, 5793-5802.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 5793-5802
-
-
Mitchell, M.1
Xue, S.2
Erdman, R.3
Randau, L.4
Söll, D.5
Li, H.6
-
33
-
-
77954288774
-
Dali server: Conservation mapping in 3D
-
Holm, L. and Rosenström, P. (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res., 38, W545-W549.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Holm, L.1
Rosenström, P.2
-
34
-
-
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
-
35
-
-
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
-
36
-
-
9144256178
-
Sequential 2'-O-methylation of archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA
-
Singh, S.K., Gurha, P., Tran, E.J., Maxwell, E.S. and Gupta, R. (2004) Sequential 2'-O-methylation of archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J. Biol. Chem., 279, 47661-47671.
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 47661-47671
-
-
Singh, S.K.1
Gurha, P.2
Tran, E.J.3
Maxwell, E.S.4
Gupta, R.5
-
37
-
-
46449136416
-
TRNA genes in pieces
-
Randau, L. and Söll, D. (2008) TRNA genes in pieces. EMBO Rep., 9, 623-628.
-
(2008)
EMBO Rep.
, vol.9
, pp. 623-628
-
-
Randau, L.1
Söll, D.2
-
38
-
-
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
-
39
-
-
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
-
40
-
-
84857703908
-
Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption
-
Sugahara, J., Fujishima, K., Nunoura, T., Takaki, Y., Takami, H., Takai, K., Tomita, M. and Kanai, A. (2012) Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PLoS One, 7, e32504.
-
(2012)
PLoS One
, vol.7
-
-
Sugahara, J.1
Fujishima, K.2
Nunoura, T.3
Takaki, Y.4
Takami, H.5
Takai, K.6
Tomita, M.7
Kanai, A.8
-
41
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T., Higgins, D. and Thompson, J. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.5
Higgins, D.6
Thompson, J.7
-
42
-
-
0032961270
-
ESPript: Analysis of multiple sequence alignments in PostScript
-
Gouet, P., Courcelle, E., Stuart, D. and Métoz, F. (1999) ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics, 15, 305-308.
-
(1999)
Bioinformatics
, vol.15
, pp. 305-308
-
-
Gouet, P.1
Courcelle, E.2
Stuart, D.3
Métoz, F.4
|