-
1
-
-
33845898858
-
Lineages of acidophilic archaea revealed by community genomic analysis
-
Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF (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
-
2
-
-
77952691194
-
Enigmatic, ultrasmall, uncultivated Archaea
-
Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL, Banfield JF (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
-
3
-
-
0029832927
-
Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences
-
Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA 93:9188-9193
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 9188-9193
-
-
Barns, S.M.1
Delwiche, C.F.2
Palmer, J.D.3
Pace, N.R.4
-
4
-
-
0031587825
-
Another bridge between kingdoms: TRNA splicing in archaea and eukaryotes
-
Belfort M, Weiner A (1997) Another bridge between kingdoms: tRNA splicing in archaea and eukaryotes. Cell 89:1003-1006
-
(1997)
Cell
, vol.89
, pp. 1003-1006
-
-
Belfort, M.1
Weiner, A.2
-
5
-
-
39149118031
-
Mesophilic Crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota
-
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6:245-252
-
(2008)
Nat Rev Microbiol
, vol.6
, pp. 245-252
-
-
Brochier-Armanet, C.1
Boussau, B.2
Gribaldo, S.3
Forterre, P.4
-
6
-
-
79953861250
-
Discovery of permuted and recently split transfer RNAs in Archaea
-
Chan PP, Cozen AE, Lowe TM (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
-
7
-
-
72449195699
-
Formal proof that the split genes of tRNAs of Nanoarchaeum equitans are an ancestral character
-
Di Giulio M (2009) Formal proof that the split genes of tRNAs of Nanoarchaeum equitans are an ancestral character. J Mol Evol 69:505-511
-
(2009)
J Mol Evol
, vol.69
, pp. 505-511
-
-
Di Giulio, M.1
-
8
-
-
84861648979
-
The origin of the tRNA molecule: Independent data favor a specific model of its evolution
-
Di Giulio M (2012) The origin of the tRNA molecule: Independent data favor a specific model of its evolution. Biochimie 94:1464-1466
-
(2012)
Biochimie
, vol.94
, pp. 1464-1466
-
-
Di Giulio, M.1
-
9
-
-
45449093194
-
Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 50 and 30 tRNA halves
-
Fujishima K, Sugahara J, Tomita M, Kanai A (2008) Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 50 and 30 tRNA halves. PLoS One 3:e1622
-
(2008)
PLoS One
, vol.3
-
-
Fujishima, K.1
Sugahara, J.2
Tomita, M.3
Kanai, A.4
-
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, 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
-
-
77957232919
-
Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain
-
Fujishima K, Sugahara J, Tomita M, 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
-
12
-
-
83755220048
-
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity
-
Fujishima K, Sugahara J, Miller CS, Baker BJ, Di Giulio M, Takesue K, Sato A, Tomita M, Banfield JF, 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
-
13
-
-
82255185634
-
Cleavage of intron from the standard or non-standard position of the precursor tRNA by the splicing endonuclease of Aeropyrum pernix, a hyperthermophilic Crenarchaeon, involves a novel RNA recognition site in the Crenarchaea specific loop
-
Hirata A, Kitajima T, 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 hyperthermophilic 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
-
14
-
-
84869057710
-
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
-
Hirata A, Fujishima K, Yamagami R, Kawamura T, Banfield JF, Kanai A, Hori H (2012) 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 40:10554-10566
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 10554-10566
-
-
Hirata, A.1
Fujishima, K.2
Yamagami, R.3
Kawamura, T.4
Banfield, J.F.5
Kanai, A.6
Hori, H.7
-
15
-
-
0037007636
-
A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont
-
Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63-67
-
(2002)
Nature
, vol.417
, pp. 63-67
-
-
Huber, H.1
Hohn, M.J.2
Rachel, R.3
Fuchs, T.4
Wimmer, V.C.5
Stetter, K.O.6
-
16
-
-
0030854739
-
Trnascan-SE: A program for improved detection of transfer RNA genes in genomic sequence
-
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955-964
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 955-964
-
-
Lowe, T.M.1
Eddy, S.R.2
-
17
-
-
0034141968
-
Selection of functional tRNA primers and primer binding site sequences from a retroviral combinatorial library: Identification of new functional tRNA primers in murine leukemia virus replication
-
Lund AH, Duch M, Pedersen FS (2000) Selection of functional tRNA primers and primer binding site sequences from a retroviral combinatorial library: identification of new functional tRNA primers in murine leukemia virus replication. Nucleic Acids Res 28:791-799
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 791-799
-
-
Lund, A.H.1
Duch, M.2
Pedersen, F.S.3
-
18
-
-
0030812830
-
Primer tRNAs for reverse transcription
-
Mak J, Kleiman L (1997) Primer tRNAs for reverse transcription. J Virol 71:8087-8095
-
(1997)
J Virol
, vol.71
, pp. 8087-8095
-
-
Mak, J.1
Kleiman, L.2
-
19
-
-
0344874260
-
Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: Evolutionary implications
-
Marck C, 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
-
20
-
-
77951529990
-
Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes
-
Maruyama S, Sugahara J, Kanai A, Nozaki H (2010) Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes. Mol Biol Evol 27:1070-1076
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1070-1076
-
-
Maruyama, S.1
Sugahara, J.2
Kanai, A.3
Nozaki, H.4
-
21
-
-
79955598535
-
Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
-
Nunoura T, Takaki Y, Kakuta J, Nishi S, Sugahara J, Kazama H, Chee GJ, Hattori M, Kanai A, Atomi H et al (2011) Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Res 39:3204-3223
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 3204-3223
-
-
Nunoura, T.1
Takaki, Y.2
Kakuta, J.3
Nishi, S.4
Sugahara, J.5
Kazama, H.6
Chee, G.J.7
Hattori, M.8
Kanai, A.9
Atomi, H.10
-
22
-
-
78650417167
-
A conserved lysine residue in the crenarchaea-specific loop is important for the crenarchaeal splicing endonuclease activity
-
Okuda M, Shiba T, Inaoka DK, Kita K, Kurisu G, Mineki S, Harada S, Watanabe Y, 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
-
23
-
-
84864815932
-
RNA processing in the minimal organism Nanoarchaeum equitans
-
Randau L (2012) RNA processing in the minimal organism Nanoarchaeum equitans. Genome Biol 13:R63
-
(2012)
Genome Biol
, vol.13
-
-
Randau, L.1
-
24
-
-
46449136416
-
Transfer RNA genes in pieces
-
Randau L, Soll D (2008) Transfer RNA genes in pieces. EMBO Rep 9:623-628
-
(2008)
EMBO Rep
, vol.9
, pp. 623-628
-
-
Randau, L.1
Soll, D.2
-
25
-
-
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, Soll D (2005a) 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
Soll, D.7
-
26
-
-
13444251251
-
Nanoarchaeum equitans creates functional tRNAs from separate genes for their 50-and 30-halves
-
Randau L, Munch R, Hohn MJ, Jahn D, Soll D (2005b) Nanoarchaeum equitans creates functional tRNAs from separate genes for their 50-and 30-halves. Nature 433:537-541
-
(2005)
Nature
, vol.433
, pp. 537-541
-
-
Randau, L.1
Munch, R.2
Hohn, M.J.3
Jahn, D.4
Soll, D.5
-
27
-
-
0027391685
-
Group I and group II introns
-
(official publication of the Federation of American Societies for Experimental Biology)
-
Saldanha R, Mohr G, Belfort M, Lambowitz AM (1993) Group I and group II introns. FASEB J 7:15-24 (official publication of the Federation of American Societies for Experimental Biology)
-
(1993)
FASEB J
, vol.7
, pp. 15-24
-
-
Saldanha, R.1
Mohr, G.2
Belfort, M.3
Lambowitz, A.M.4
-
28
-
-
35348946378
-
Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae
-
Soma A, Onodera A, Sugahara J, Kanai A, Yachie N, Tomita M, Kawamura F, Sekine Y (2007) Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science 318:450-453
-
(2007)
Science
, vol.318
, pp. 450-453
-
-
Soma, A.1
Onodera, A.2
Sugahara, J.3
Kanai, A.4
Yachie, N.5
Tomita, M.6
Kawamura, F.7
Sekine, Y.8
-
29
-
-
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, 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
-
(2006)
In Silico Biol
, vol.6
, pp. 411-418
-
-
Sugahara, J.1
Yachie, N.2
Sekine, Y.3
Soma, A.4
Matsui, M.5
Tomita, M.6
Kanai, A.7
-
30
-
-
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, 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
-
31
-
-
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, 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
-
32
-
-
0029805902
-
Activity and thermostability of the small self-splicing group I intron in the pre-tRNA(lle) of the purple bacterium Azoarcus
-
Tanner M, Cech T (1996) Activity and thermostability of the small self-splicing group I intron in the pre-tRNA(lle) of the purple bacterium Azoarcus. RNA 2:74-83
-
(1996)
RNA
, vol.2
, pp. 74-83
-
-
Tanner, M.1
Cech, T.2
-
34
-
-
21144453167
-
Structure, function, and evolution of the tRNA endonucleases of Archaea: An example of subfunctionalization
-
Tocchini-Valentini GD, Fruscoloni P, Tocchini-Valentini GP (2005b) 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.D.1
Fruscoloni, P.2
Tocchini-Valentini, G.P.3
-
35
-
-
0030730820
-
The yeast tRNA splicing endonuclease: A tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases
-
Trotta CR, Miao F, Arn EA, Stevens SW, Ho CK, Rauhut R, Abelson JN (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.R.1
Miao, F.2
Arn, E.A.3
Stevens, S.W.4
Ho, C.K.5
Rauhut, R.6
Abelson, J.N.7
-
36
-
-
0242300069
-
The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism
-
Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, Beeson KY, Bibbs L, Bolanos R, Keller M et al (2003) The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism. Proc Natl Acad Sci USA 100:12984-12988
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 12984-12988
-
-
Waters, E.1
Hohn, M.J.2
Ahel, I.3
Graham, D.E.4
Adams, M.D.5
Barnstead, M.6
Beeson, K.Y.7
Bibbs, L.8
Bolanos, R.9
Keller, M.10
-
37
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
-
Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 74:5088-5090
-
(1977)
Proc Natl Acad Sci USA
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
38
-
-
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 DK, Itoh T, Kurisu G, Harada S, Kita K, 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
|