-
1
-
-
69249126551
-
Bacterial cell division: Assembly, maintenance and disassembly of the Z ring.
-
Adams DW, Errington J. 2009. Bacterial cell division: Assembly, maintenance and disassembly of the Z ring. Nat Rev Microbiol 7: 642–653.
-
(2009)
Nat Rev Microbiol
, vol.7
, pp. 642-653
-
-
Adams, D.W.1
Errington, J.2
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs.
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
3
-
-
80855156621
-
New insights into the mechanisms of cytomotive actin and tubulin filaments.
-
Aylett CH, Lowe J, Amos LA. 2011. New insights into the mechanisms of cytomotive actin and tubulin filaments. Int Rev Cell Mol Biol 292: 1–71.
-
(2011)
Int Rev Cell Mol Biol
, vol.292
, pp. 1-71
-
-
Aylett, C.H.1
Lowe, J.2
Amos, L.A.3
-
4
-
-
84868624185
-
An archaeal origin for the actin cytoskeleton: Implications for eukaryogen-esis.
-
Bernander R, Lind AE, Ettema TJ. 2011. An archaeal origin for the actin cytoskeleton: Implications for eukaryogen-esis. Commun Integr Biol 4: 664–667.
-
(2011)
Commun Integr Biol
, vol.4
, pp. 664-667
-
-
Bernander, R.1
Lind, A.E.2
Ettema, T.J.3
-
5
-
-
70450240802
-
Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Cre-narchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea.
-
Blombach F, Makarova KS, Marrero J, Siebers B, Koonin EV, van der Oost J. 2009. Identification of an ortholog of the eukaryotic RNA polymerase III subunit RPC34 in Cre-narchaeota and Thaumarchaeota suggests specialization of RNA polymerases for coding and non-coding RNAs in Archaea. Biol Direct 4: 39.
-
(2009)
Biol Direct
, vol.4
, pp. 39
-
-
Blombach, F.1
Makarova, K.S.2
Marrero, J.3
Siebers, B.4
Koonin, E.V.5
vanderOost, J.6
-
6
-
-
57749185463
-
Parallel adaptations to high temperatures in the Archaean eon.
-
Boussau B, Blanquart S, Necsulea A, Lartillot N, Gouy M. 2008. Parallel adaptations to high temperatures in the Archaean eon. Nature 456: 942–945.
-
(2008)
Nature
, vol.456
, pp. 942-945
-
-
Boussau, B.1
Blanquart, S.2
Necsulea, A.3
Lartillot, N.4
Gouy, M.5
-
7
-
-
39149118031
-
Mesophilic Crenarchaeota: Proposal for a third ar-chaeal phylum, the Thaumarchaeota.
-
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. 2008. Mesophilic Crenarchaeota: Proposal for a third ar-chaeal 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
-
8
-
-
79959307333
-
Phylog-eny and evolution of the Archaea: One hundred genomes later.
-
Brochier-Armanet C, Forterre P, Gribaldo S. 2011. Phylog-eny and evolution of the Archaea: One hundred genomes later. Curr Opin Microbiol 14: 274–281.
-
(2011)
Curr Opin Microbiol
, vol.14
, pp. 274-281
-
-
Brochier-Armanet, C.1
Forterre, P.2
Gribaldo, S.3
-
10
-
-
84859229690
-
The natural history of ubiquitin and ubiquitin-related domains.
-
Burroughs AM, Iyer LM, Aravind L. 2012a. The natural history of ubiquitin and ubiquitin-related domains. Front Biosci 17: 1433–1460.
-
(2012)
Front Biosci
, vol.17
, pp. 1433-1460
-
-
Burroughs, A.M.1
Iyer, L.M.2
Aravind, L.3
-
11
-
-
84858259538
-
Structure and evolution of ubiquitin and ubiquitin-related domains.
-
Burroughs AM, Iyer LM, Aravind L. 2012b. Structure and evolution of ubiquitin and ubiquitin-related domains. Methods Mol Biol 832: 15–63.
-
(2012)
Methods Mol Biol
, vol.832
, pp. 15-63
-
-
Burroughs, A.M.1
Iyer, L.M.2
Aravind, L.3
-
13
-
-
60149088848
-
Origins and mechanisms of miRNAs and siRNAs.
-
Carthew RW, Sontheimer EJ. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell 136: 642–655.
-
(2009)
Cell
, vol.136
, pp. 642-655
-
-
Carthew, R.W.1
Sontheimer, E.J.2
-
14
-
-
0025875099
-
Archamoebae: The ancestral eu-karyotes?
-
Cavalier-Smith T. 1991. Archamoebae: The ancestral eu-karyotes? Biosystems 25: 25–38.
-
(1991)
Biosystems
, vol.25
, pp. 25-38
-
-
Cavalier-Smith, T.1
-
15
-
-
56949102616
-
Predation and eukaryote cell origins: A coevolutionary perspective.
-
Cavalier-Smith T. 2009. Predation and eukaryote cell origins: A coevolutionary perspective. Int J Biochem Cell Biol 41: 307–322.
-
(2009)
Int J Biochem Cell Biol
, vol.41
, pp. 307-322
-
-
Cavalier-Smith, T.1
-
17
-
-
33745951984
-
On the origin and functions of RNA-mediated silencing: From protists to man.
-
Cerutti H, Casas-Mollano JA. 2006. On the origin and functions of RNA-mediated silencing: From protists to man. Curr Genet 50: 81–99.
-
(2006)
Curr Genet
, vol.50
, pp. 81-99
-
-
Cerutti, H.1
Casas-Mollano, J.A.2
-
18
-
-
33644700003
-
Toward automatic reconstruction of ahigh-ly resolved tree of life.
-
Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P. 2006. Toward automatic reconstruction of ahigh-ly resolved tree of life. Science 311: 1283–1287.
-
(2006)
Science
, vol.311
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
19
-
-
58149512792
-
The archaebacterial origin of eukaryotes.
-
Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM. 2008. The archaebacterial origin of eukaryotes. Proc Natl Acad Sci 105: 20356–20361.
-
(2008)
Proc Natl Acad Sci
, vol.105
, pp. 20356-20361
-
-
Cox, C.J.1
Foster, P.G.2
Hirt, R.P.3
Harris, S.R.4
Embley, T.M.5
-
20
-
-
77955038643
-
Count: Evolutionary analysis of phyloge-netic profiles with parsimony and likelihood.
-
Csurö s M. 2010. Count: Evolutionary analysis of phyloge-netic profiles with parsimony and likelihood. Bioinfor-matics 26: 1910–1912.
-
(2010)
Bioinfor-matics
, vol.26
, pp. 1910-1912
-
-
Csurös, M.1
-
21
-
-
68949207909
-
Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model.
-
Csurö s M, Miklos I. 2009. Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Mol Biol Evol 26: 2087–2095.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 2087-2095
-
-
Csurös, M.1
Miklos, I.2
-
22
-
-
69549084648
-
Identification of a crenarchaeal orthologue of Elf1: Implications for chromatin and transcription in Archaea.
-
Daniels JP, Kelly S, Wickstead B, Gull K. 2009. Identification of a crenarchaeal orthologue of Elf1: Implications for chromatin and transcription in Archaea. Biol Direct 4: 24.
-
(2009)
Biol Direct
, vol.4
, pp. 24
-
-
Daniels, J.P.1
Kelly, S.2
Wickstead, B.3
Gull, K.4
-
23
-
-
0035988323
-
The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea.
-
Deppenmeier U, JohannA,HartschT, MerklR, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baumer S, Jacobi C, et al. 2002. The genome of Methanosarcina mazei: Evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4: 453–461.
-
(2002)
J Mol Microbiol Biotechnol
, vol.4
, pp. 453-461
-
-
Deppenmeier, U.1
Johann, A.2
Hartsch, T.3
Merkl, R.4
Schmitz, R.A.5
Martinez-Arias, R.6
Henne, A.7
Wiezer, A.8
Baumer, S.9
Jacobi, C.10
-
24
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput.
-
Edgar RC. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792–1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
25
-
-
45849112155
-
A korarchaeal genome reveals insights into the evolution of the Archaea.
-
Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, et al. 2008. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc Natl Acad Sci 105: 8102–8107.
-
(2008)
Proc Natl Acad Sci
, vol.105
, pp. 8102-8107
-
-
Elkins, J.G.1
Podar, M.2
Graham, D.E.3
Makarova, K.S.4
Wolf, Y.5
Randau, L.6
Hedlund, B.P.7
Brochier-Armanet, C.8
Kunin, V.9
Anderson, I.10
-
26
-
-
33645456207
-
Eukaryotic evolution, changes and challenges.
-
Embley TM, Martin W. 2006. Eukaryotic evolution, changes and challenges. Nature 440: 623–630.
-
(2006)
Nature
, vol.440
, pp. 623-630
-
-
Embley, T.M.1
Martin, W.2
-
27
-
-
4143093598
-
A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.
-
Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, Gelius-Dietrich G, Henze K, Kretschmann, Richly E, Leister D, et al. 2004. A genome phylogeny for mitochondria among α-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 21: 1643–1660.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1643-1660
-
-
Esser, C.1
Ahmadinejad, N.2
Wiegand, C.3
Rotte, C.4
Sebastiani, F.5
Gelius-Dietrich, G.6
Henze, K.7
Richly, E.8
Leister, D.9
-
28
-
-
34547793558
-
The origin of mitochondria in light of a fluid prokaryotic chromosome model.
-
Esser C, Martin W, Dagan T. 2007. The origin of mitochondria in light of a fluid prokaryotic chromosome model. Biol Lett 3: 180–184.
-
(2007)
Biol Lett
, vol.3
, pp. 180-184
-
-
Esser, C.1
Martin, W.2
Dagan, T.3
-
29
-
-
67650641167
-
Cell division and the ESCRT complex: A surprise from the Archaea.
-
Ettema TJ, Bernander R. 2009. Cell division and the ESCRT complex: A surprise from the Archaea. Commun Integr Biol 2: 86–88.
-
(2009)
Commun Integr Biol
, vol.2
, pp. 86-88
-
-
Ettema, T.J.1
Bernander, R.2
-
31
-
-
0028989816
-
Thermoreduction, a hypothesis for the origin of prokaryotes.
-
Forterre P. 1995. Thermoreduction, a hypothesis for the origin of prokaryotes. CR Acad Sci III 318: 415–422.
-
(1995)
CR Acad Sci III
, vol.318
, pp. 415-422
-
-
Forterre, P.1
-
33
-
-
77957134043
-
The origin of eukaryotes and their relationship with the Archaea: Are we at a phylogenomic impasse?
-
Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Ar-manet C. 2010. The origin of eukaryotes and their relationship with the Archaea: Are we at a phylogenomic impasse? Nat Rev Microbiol 8: 743–752.
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 743-752
-
-
Gribaldo, S.1
Poole, A.M.2
Daubin, V.3
Forterre, P.4
Brochier-Armanet, C.5
-
34
-
-
82355180998
-
The archaeal “TACK” superphylum and the origin of eukaryotes.
-
Guy L, Ettema TJ. 2011. The archaeal “TACK” superphylum and the origin of eukaryotes. Trends Microbiol 19: 580– 587.
-
(2011)
Trends Microbiol
, vol.19
, pp. 580-587
-
-
Guy, L.1
Ettema, T.J.2
-
35
-
-
1642534172
-
A genomic timescale for the origin of eukaryotes.
-
Hedges SB, Chen H, Kumar S, Wang DY, Thompson AS, Watanabe H. 2001. A genomic timescale for the origin of eukaryotes. BMC Evol Biol 1: 4.
-
(2001)
BMC Evol Biol
, vol.1
, pp. 4
-
-
Hedges, S.B.1
Chen, H.2
Kumar, S.3
Wang, D.Y.4
Thompson, A.S.5
Watanabe, H.6
-
36
-
-
0027234324
-
Cytoskeleton in the archae-bacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts.
-
Hixon WG, Searcy DG. 1993. Cytoskeleton in the archae-bacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts. Biosystems 29: 151–160.
-
(1993)
Biosystems
, vol.29
, pp. 151-160
-
-
Hixon, W.G.1
Searcy, D.G.2
-
37
-
-
0034253588
-
Evolution and function of ubiquitin-like protein-conjugation systems.
-
Hochstrasser M. 2000. Evolution and function of ubiquitin-like protein-conjugation systems. Nat Cell Biol 2: E15– E17.
-
(2000)
Nat Cell Biol
, vol.2
, pp. E15-E17
-
-
Hochstrasser, M.1
-
38
-
-
43549096196
-
The Argonaute protein family.
-
Hock J, Meister G. 2008. The Argonaute protein family. Genome Biol 9: 210.
-
(2008)
Genome Biol
, vol.9
, pp. 210
-
-
Hock, J.1
Meister, G.2
-
39
-
-
16444372420
-
The origin of eukaryotes is suggested as the symbiosis of py-rococcus into γ-proteobacteria by phylogenetic tree based on gene content.
-
Horiike T, Hamada K, Miyata D, Shinozawa T. 2004. The origin of eukaryotes is suggested as the symbiosis of py-rococcus into γ-proteobacteria by phylogenetic tree based on gene content. J Mol Evol 59: 606–619.
-
(2004)
J Mol Evol
, vol.59
, pp. 606-619
-
-
Horiike, T.1
Hamada, K.2
Miyata, D.3
Shinozawa, T.4
-
40
-
-
73849149089
-
Ubiq-uitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii.
-
Humbard MA, Miranda HV, Lim JM, Krause DJ, Pritz JR, ZhouG, Chen S,Wells L, Maupin-Furlow JA. 2010. Ubiq-uitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii. Nature 463: 54–60.
-
(2010)
Nature
, vol.463
, pp. 54-60
-
-
Humbard, M.A.1
Miranda, H.V.2
Lim, J.M.3
Krause, D.J.4
Pritz, J.R.5
Zhou, G.6
Chen, S.7
Wells, L.8
Maupin-Furlow, J.A.9
-
42
-
-
13444259388
-
TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics.
-
Jobb G, von Haeseler A, Strimmer K. 2004. TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4: 18.
-
(2004)
BMC Evol Biol
, vol.4
, pp. 18
-
-
Jobb, G.1
von Haeseler, A.2
Strimmer, K.3
-
43
-
-
84874964884
-
Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukary-otes.
-
Kelly S, Wickstead B, Gull K. 2011. Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukary-otes. Proc Biol Sci 278: 1009–1018.
-
(2011)
Proc Biol Sci
, vol.278
, pp. 1009-1018
-
-
Kelly, S.1
Wickstead, B.2
Gull, K.3
-
44
-
-
34047175831
-
The origin of introns and their role in eukaryogenesis: A compromise solution to the introns-early versus introns-late debate?
-
Koonin EV. 2006. The origin of introns and their role in eukaryogenesis: A compromise solution to the introns-early versus introns-late debate? Biol Direct 1: 22.
-
(2006)
Biol Direct
, vol.1
, pp. 22
-
-
Koonin, E.V.1
-
45
-
-
0034780910
-
Horizontal gene transfer in prokaryotes—Quantification and classification.
-
Koonin EV, Makarova KS, Aravind L. 2001. Horizontal gene transfer in prokaryotes—Quantification and classification. Annu Rev Microbiol 55: 709–742.
-
(2001)
Annu Rev Microbiol
, vol.55
, pp. 709-742
-
-
Koonin, E.V.1
Makarova, K.S.2
Aravind, L.3
-
46
-
-
39049143397
-
Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and “Korarchaeota.”
-
Koonin EV, Makarova KS, Elkins JG. 2007. Orthologs of the small RPB8 subunit of the eukaryotic RNA polymerases are conserved in hyperthermophilic Crenarchaeota and “Korarchaeota.” Biol Direct 2: 38.
-
(2007)
Biol Direct
, vol.2
, pp. 38
-
-
Koonin, E.V.1
Makarova, K.S.2
Elkins, J.G.3
-
47
-
-
33646726959
-
Genomics and the irreducible nature of eukaryote cells.
-
Kurland CG, Collins LJ, Penny. 2006. Genomics and the irreducible nature of eukaryote cells. Science 312: 1011– 1104.
-
(2006)
Science
, vol.312
, pp. 1011-1104
-
-
Kurland, C.G.1
Collins, L.J.2
-
48
-
-
0024285855
-
Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences.
-
Lake JA. 1988. Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences. Nature 331: 184–186.
-
(1988)
Nature
, vol.331
, pp. 184-186
-
-
Lake, J.A.1
-
49
-
-
0031828814
-
Optimally recovering rate variation information from genomes and sequences: Pattern filtering.
-
Lake JA. 1998. Optimally recovering rate variation information from genomes and sequences: Pattern filtering. Mol Biol Evol 15: 1224–1231.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 1224-1231
-
-
Lake, J.A.1
-
50
-
-
0039861672
-
Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes.
-
Lake JA, Henderson E, Oakes M, Clark MW. 1984. Eocytes: A new ribosome structure indicates a kingdom with a close relationship to eukaryotes. Proc Natl Acad Sci 81: 3786–3790.
-
(1984)
Proc Natl Acad Sci
, vol.81
, pp. 3786-3790
-
-
Lake, J.A.1
Henderson, E.2
Oakes, M.3
Clark, M.W.4
-
51
-
-
79959629502
-
Energetics and genetics across the prokary-ote–eukaryote divide.
-
Lane N. 2011. Energetics and genetics across the prokary-ote–eukaryote divide. Biol Direct 6: 35.
-
(2011)
Biol Direct
, vol.6
, pp. 35
-
-
Lane, N.1
-
52
-
-
84988044805
-
The energetics of genome complexity.
-
Lane N, Martin W. 2010. The energetics of genome complexity. Nature 467: 929–934.
-
(2010)
Nature
, vol.467
, pp. 929-934
-
-
Lane, N.1
Martin, W.2
-
53
-
-
84880261576
-
The effects of model choice and mitigating bias on the ribosomal tree of life.
-
Lasek-Nesselquist E,Gogarten JP. 2013. The effects of model choice and mitigating bias on the ribosomal tree of life. Mol Phylogenet Evol 69: 17–38.
-
(2013)
Mol Phylogenet Evol
, vol.69
, pp. 17-38
-
-
Lasek-Nesselquist, E.1
Gogarten, J.P.2
-
55
-
-
57749087001
-
A unique cell division machinery in the Archaea.
-
Lindas AC, Karlsson EA, Lindgren MT, Ettema TJ, Bernander R. 2008. A unique cell division machinery in the Archaea. Proc Natl Acad Sci 105: 18942–18946.
-
(2008)
Proc Natl Acad Sci
, vol.105
, pp. 18942-18946
-
-
Lindas, A.C.1
Karlsson, E.A.2
Lindgren, M.T.3
Ettema, T.J.4
Bernander, R.5
-
56
-
-
84876291747
-
Predominant archaea in marine sediments degrade detrital proteins.
-
Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, Stepanauskas R, Richter M, Kleindienst S, Lenk S, et al. 2013. Predominant archaea in marine sediments degrade detrital proteins. Nature 496: 215– 218.
-
(2013)
Nature
, vol.496
, pp. 215-218
-
-
Lloyd, K.G.1
Schreiber, L.2
Petersen, D.G.3
Kjeldsen, K.U.4
Lever, M.A.5
Steen, A.D.6
Stepanauskas, R.7
Richter, M.8
Kleindienst, S.9
Lenk, S.10
-
57
-
-
33646360208
-
Selective forces for the origin of the eukaryotic nucleus.
-
Lopez-Garcia P, Moreira D. 2006. Selective forces for the origin of the eukaryotic nucleus. Bioessays 28: 525–533.
-
(2006)
Bioessays
, vol.28
, pp. 525-533
-
-
Lopez-Garcia, P.1
Moreira, D.2
-
58
-
-
56949093012
-
Evolution of cytomotive filaments: The cytoskeleton from prokaryotes to eukaryotes.
-
Lowe J, Amos LA. 2009. Evolution of cytomotive filaments: The cytoskeleton from prokaryotes to eukaryotes. Int J Biochem Cell Biol 41: 323–329.
-
(2009)
Int J Biochem Cell Biol
, vol.41
, pp. 323-329
-
-
Lowe, J.1
Amos, L.A.2
-
59
-
-
78249260025
-
Archaeal ubiquitin-like proteins: Functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis.
-
Makarova KS, Koonin EV. 2010. Archaeal ubiquitin-like proteins: Functional versatility and putative ancestral involvement in tRNA modification revealed by comparative genomic analysis. Archaea pii: 710303.
-
(2010)
Archaea Pii
-
-
Makarova, K.S.1
Koonin, E.V.2
-
60
-
-
38949147846
-
Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.
-
Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV. 2007. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct 2: 33.
-
(2007)
Biol Direct
, vol.2
, pp. 33
-
-
Makarova, K.S.1
Sorokin, A.V.2
Novichkov, P.S.3
Wolf, Y.I.4
Koonin, E.V.5
-
61
-
-
70849123800
-
Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.
-
Makarova KS, Wolf YI, van der Oost J, Koonin EV. 2009. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements. Biol Direct4: 29.
-
(2009)
Biol Direct
, vol.4
, pp. 29
-
-
Makarova, K.S.1
Wolf, Y.I.2
van der Oost, J.3
Koonin, E.V.4
-
62
-
-
77957130448
-
Evolution of diverse cell division and vesicle formation systems in Archaea.
-
Makarova KS, Yutin N, Bell SD, Koonin EV. 2010. Evolution of diverse cell division and vesicle formation systems in Archaea. Nat Rev Microbiol 8: 731–741.
-
(2010)
Nat Rev Microbiol
, vol.8
, pp. 731-741
-
-
Makarova, K.S.1
Yutin, N.2
Bell, S.D.3
Koonin, E.V.4
-
63
-
-
69949158186
-
Sculpting the bacterial cell.
-
Margolin W. 2009. Sculpting the bacterial cell. Curr Biol 19: R812–R822.
-
(2009)
Curr Biol
, vol.19
, pp. R812-R822
-
-
Margolin, W.1
-
64
-
-
0030035039
-
Archaeal–eubacterial mergers in the origin of Eukarya: Phylogenetic classification of life.
-
Margulis L. 1996. Archaeal–eubacterial mergers in the origin of Eukarya: Phylogenetic classification of life. Proc Natl Acad Sci 93: 1071–1076.
-
(1996)
Proc Natl Acad Sci
, vol.93
, pp. 1071-1076
-
-
Margulis, L.1
-
65
-
-
0021753185
-
Cell symbiosis theory: Status and implications for the fossil record.
-
Margulis L, Stolz JF. 1984. Cell symbiosis theory: Status and implications for the fossil record. Adv Space Res 4: 195– 201.
-
(1984)
Adv Space Res
, vol.4
, pp. 195-201
-
-
Margulis, L.1
Stolz, J.F.2
-
66
-
-
0034691073
-
The chimeric eu-karyote: Origin of the nucleus from the karyomastigont in amitochondriate protists.
-
Margulis L, Dolan MF, Guerrero R. 2000. The chimeric eu-karyote: Origin of the nucleus from the karyomastigont in amitochondriate protists. Proc Natl Acad Sci97: 6954– 6959.
-
(2000)
Proc Natl Acad Sci
, vol.97
, pp. 6954-6959
-
-
Margulis, L.1
Dolan, M.F.2
Guerrero, R.3
-
67
-
-
84873164495
-
From archaeon to eukaryote: The evolutionary dark ages of the eukaryotic cell.
-
Martijn J, Ettema TJ. 2013. From archaeon to eukaryote: The evolutionary dark ages of the eukaryotic cell. Bio-chem Soc Trans 41: 451–457.
-
(2013)
Bio-chem Soc Trans
, vol.41
, pp. 451-457
-
-
Martijn, J.1
Ettema, T.J.2
-
68
-
-
33644783626
-
Introns and the origin of nu-cleus–cytosol compartmentation.
-
Martin W, Koonin EV. 2006. Introns and the origin of nu-cleus–cytosol compartmentation. Nature 440: 41–45.
-
(2006)
Nature
, vol.440
, pp. 41-45
-
-
Martin, W.1
Koonin, E.V.2
-
69
-
-
2642689666
-
The hydrogen hypothesis for the first eukaryote.
-
Martin W, Muller M. 1998. The hydrogen hypothesis for the first eukaryote. Nature 392: 37–41.
-
(1998)
Nature
, vol.392
, pp. 37-41
-
-
Martin, W.1
Muller, M.2
-
70
-
-
34247575639
-
The evolution of eukaryotes.
-
Martin W, Dagan T, Koonin EV, Dipippo JL, Gogarten JP, Lake JA. 2007. The evolution of eukaryotes. Science 316: 542–543.
-
(2007)
Science
, vol.316
, pp. 542-543
-
-
Martin, W.1
Dagan, T.2
Koonin, E.V.3
Dipippo, J.L.4
Gogarten, J.P.5
Lake, J.A.6
-
71
-
-
84871695877
-
Ubiquitin-like proteins and their roles in Archaea.
-
Maupin-Furlow JA. 2013. Ubiquitin-like proteins and their roles in Archaea. Trends Microbiol 21: 31–38.
-
(2013)
Trends Microbiol
, vol.21
, pp. 31-38
-
-
Maupin-Furlow, J.A.1
-
72
-
-
84860507088
-
Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning.
-
Miller-Coleman RL, Dodsworth JA, Ross CA, Shock EL, Williams AJ, Hartnett HE, McDonald AI, Havig JR, Hed-lund BP. 2012. Korarchaeota diversity, biogeography, and abundance in Yellowstone and Great Basin hot springs and ecological niche modeling based on machine learning. Plos ONE 7: e35964.
-
(2012)
Plos ONE
, vol.7
-
-
Miller-Coleman, R.L.1
Dodsworth, J.A.2
Ross, C.A.3
Shock, E.L.4
Williams, A.J.5
Hartnett, H.E.6
McDonald, A.I.7
Havig, J.R.8
Hedlund, B.P.9
-
73
-
-
79952729890
-
E1-and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in Archaea.
-
Miranda HV, Nembhard N, Su D, Hepowit N, Krause DJ, Pritz JR, Phillips C, Soll D, Maupin-Furlow JA. 2011. E1-and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in Archaea. Proc Natl Acad Sci 108: 4417–4422.
-
(2011)
Proc Natl Acad Sci
, vol.108
, pp. 4417-4422
-
-
Miranda, H.V.1
Nembhard, N.2
Su, D.3
Hepowit, N.4
Krause, D.J.5
Pritz, J.R.6
Phillips, C.7
Soll, D.8
Maupin-Furlow, J.A.9
-
74
-
-
0031735879
-
Symbiosis between meth-anogenic archaea and δ-proteobacteria as the origin of eukaryotes: The syntrophic hypothesis.
-
Moreira D, Lopez-Garcia P. 1998. Symbiosis between meth-anogenic archaea and δ-proteobacteria as the origin of eukaryotes: The syntrophic hypothesis. J Mol Evol 47: 517–530.
-
(1998)
J Mol Evol
, vol.47
, pp. 517-530
-
-
Moreira, D.1
Lopez-Garcia, P.2
-
75
-
-
77955245722
-
First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat.
-
Muller F, Brissac T, Le Bris N, Felbeck H, Gros O. 2010. First description of giant Archaea (Thaumarchaeota) associated with putative bacterial ectosymbionts in a sulfidic marine habitat. Environ Microbiol 12: 2371–2383.
-
(2010)
Environ Microbiol
, vol.12
, pp. 2371-2383
-
-
Muller, F.1
Brissac, T.2
Le Bris, N.3
Felbeck, H.4
Gros, O.5
-
76
-
-
84874400864
-
Acquisition of 1000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea.
-
Nelson-Sathi S, Dagan T, Landan G, Janssen A, Steel M, McInerney JO, Deppenmeier U, Martin WF. 2012. Acquisition of 1000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea. Proc Natl Acad Sci 109: 20537–20542.
-
(2012)
Proc Natl Acad Sci
, vol.109
, pp. 20537-20542
-
-
Nelson-Sathi, S.1
Dagan, T.2
Landan, G.3
Janssen, A.4
Steel, M.5
McInerney, J.O.6
Deppenmeier, U.7
Martin, W.F.8
-
77
-
-
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
-
78
-
-
0030982247
-
A molecular view of microbial diversity and the biosphere.
-
Pace NR. 1997. A molecular view of microbial diversity and the biosphere. Science 276: 734–740.
-
(1997)
Science
, vol.276
, pp. 734-740
-
-
Pace, N.R.1
-
79
-
-
33744982063
-
Time for a change.
-
Pace NR. 2006. Time for a change. Nature 441: 289.
-
(2006)
Nature
, vol.441
, pp. 289
-
-
Pace, N.R.1
-
80
-
-
71449100076
-
Mapping the tree of life: Progress and prospects.
-
Pace NR. 2009. Mapping the tree of life: Progress and prospects. Microbiol Mol Biol Rev 73: 565–576.
-
(2009)
Microbiol Mol Biol Rev
, vol.73
, pp. 565-576
-
-
Pace, N.R.1
-
81
-
-
80054845081
-
Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopu-milus maritimus.
-
Pelve EA, Lindas AC, Martens-Habbena W, de la Torre JR, Stahl DA, Bernander R.2011. Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopu-milus maritimus. Mol Microbiol 82: 555–566.
-
(2011)
Mol Microbiol
, vol.82
, pp. 555-566
-
-
Pelve, E.A.1
Lindas, A.C.2
Martens-Habbena, W.3
delaTorre, J.R.4
Stahl, D.A.5
Bernander, R.6
-
82
-
-
4344618574
-
Ancestral lipid biosynthesis and early membrane evolution.
-
Pereto J, Lopez-Garcia P, Moreira D. 2004. Ancestral lipid biosynthesis and early membrane evolution. Trends Bio-chem Sci 29: 469–477.
-
(2004)
Trends Bio-chem Sci
, vol.29
, pp. 469-477
-
-
Pereto, J.1
Lopez-Garcia, P.2
Moreira, D.3
-
83
-
-
79959289950
-
The Thaumarch-aeota: An emerging view of their phylogeny and ecophys-iology.
-
Pester M, Schleper C, Wagner M. 2011. The Thaumarch-aeota: An emerging view of their phylogeny and ecophys-iology. Curr Opin Microbiol 14: 300–306.
-
(2011)
Curr Opin Microbiol
, vol.14
, pp. 300-306
-
-
Pester, M.1
Schleper, C.2
Wagner, M.3
-
84
-
-
34547751897
-
Supertrees disentangle the chimerical origin of eukaryotic genomes.
-
Pisani D, Cotton JA, McInerney JO. 2007. Supertrees disentangle the chimerical origin of eukaryotic genomes. Mol Biol Evol 24: 1752–1760.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1752-1760
-
-
Pisani, D.1
Cotton, J.A.2
McInerney, J.O.3
-
85
-
-
34250838604
-
Eukaryote evolution: Engulfed by speculation.
-
Poole A, Penny D. 2007a. Eukaryote evolution: Engulfed by speculation. Nature 447: 913.
-
(2007)
Nature
, vol.447
, pp. 913
-
-
Poole, A.1
Penny, D.2
-
86
-
-
33846632221
-
Evaluating hypotheses for the origin of eukaryotes.
-
Poole AM, Penny D. 2007b. Evaluating hypotheses for the origin of eukaryotes. Bioessays 29: 74–84.
-
(2007)
Bioessays
, vol.29
, pp. 74-84
-
-
Poole, A.M.1
Penny, D.2
-
87
-
-
68149093715
-
Search for a tree of life in the thicket of the phylogenetic forest.
-
Puigbo P, Wolf YI, Koonin EV. 2009. Search for a tree of life in the thicket of the phylogenetic forest. J Biol 8: 59.
-
(2009)
J Biol
, vol.8
, pp. 59
-
-
Puigbo, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
88
-
-
78651414310
-
Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond.
-
Rajendhran J, Gunasekaran P. 2011. Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond. Microbiol Res 166: 99–110.
-
(2011)
Microbiol Res
, vol.166
, pp. 99-110
-
-
Rajendhran, J.1
Gunasekaran, P.2
-
89
-
-
77149156633
-
Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka.
-
Reigstad LJ, Jorgensen SL, Schleper C. 2010. Diversity and abundance of Korarchaeota in terrestrial hot springs of Iceland and Kamchatka. ISME J 4: 346–356.
-
(2010)
ISME J
, vol.4
, pp. 346-356
-
-
Reigstad, L.J.1
Jorgensen, S.L.2
Schleper, C.3
-
90
-
-
0026684272
-
Evidence that eukaryotes and eocyte prokaryotes are immediate relatives.
-
Rivera MC, Lake JA. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science 257: 74–76.
-
(1992)
Science
, vol.257
, pp. 74-76
-
-
Rivera, M.C.1
Lake, J.A.2
-
91
-
-
4544313053
-
The ring of life provides evidence for a genome fusion origin of eukaryotes.
-
Rivera MC, Lake JA. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431: 152–155.
-
(2004)
Nature
, vol.431
, pp. 152-155
-
-
Rivera, M.C.1
Lake, J.A.2
-
94
-
-
70350326378
-
Ancient ESCRTs and the evolution of binary fission.
-
Samson RY, Bell SD. 2009. Ancient ESCRTs and the evolution of binary fission. Trends Microbiol 17: 507–513.
-
(2009)
Trends Microbiol
, vol.17
, pp. 507-513
-
-
Samson, R.Y.1
Bell, S.D.2
-
95
-
-
58149230938
-
A role for the ESCRT system in cell division in Archaea.
-
Samson RY, ObitaT,Freund SM, Williams RL, Bell SD. 2008. A role for the ESCRT system in cell division in Archaea. Science 322: 1710–1713.
-
(2008)
Science
, vol.322
, pp. 1710-1713
-
-
Samson, R.Y.1
Obita, T.2
Freund, S.M.3
Williams, R.L.4
Bell, S.D.5
-
96
-
-
0017957162
-
Phylogenetic affinities between eukaryotic cells and a thermophilic myco-plasma.
-
Searcy DG, Stein DB, Green GR. 1978. Phylogenetic affinities between eukaryotic cells and a thermophilic myco-plasma. Biosystems 10: 19–28.
-
(1978)
Biosystems
, vol.10
, pp. 19-28
-
-
Searcy, D.G.1
Stein, D.B.2
Green, G.R.3
-
97
-
-
51449085579
-
Origins and evolution of eukaryotic RNA interference.
-
Shabalina SA, Koonin EV. 2008. Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol 23: 578– 587.
-
(2008)
Trends Ecol Evol
, vol.23
, pp. 578-587
-
-
Shabalina, S.A.1
Koonin, E.V.2
-
98
-
-
77957955710
-
Mitochondrion-related or-ganelles in eukaryotic protists.
-
Shiflett AM, Johnson PJ. 2010. Mitochondrion-related or-ganelles in eukaryotic protists. Annu Rev Microbiol 64: 409–429.
-
(2010)
Annu Rev Microbiol
, vol.64
, pp. 409-429
-
-
Shiflett, A.M.1
Johnson, P.J.2
-
99
-
-
55449085523
-
Genome trees from conservation profiles.
-
TekaiaF, Yeramian E. 2005. Genome trees from conservation profiles. PLoS Comput Biol 1: e75.
-
(2005)
PLoS Comput Biol
, vol.1
, pp. e75
-
-
Tekaia, F.1
Yeramian, E.2
-
100
-
-
41149093627
-
Uncultured archaea in deep marine subsurface sediments: Have we caught them all?
-
Teske A, Sorensen KB. 2008. Uncultured archaea in deep marine subsurface sediments: Have we caught them all? ISME J 2: 3–18.
-
(2008)
ISME J
, vol.2
, pp. 3-18
-
-
Teske, A.1
Sorensen, K.B.2
-
101
-
-
84862562185
-
An evolutionary network of genes present in the eukaryote common ancestorpollsgenomesoneukaryotic and mitochondrial origin.
-
Thiergart T, Landan G, Schenk M, Dagan T, Martin WF. 2012. An evolutionary network of genes present in the eukaryote common ancestorpollsgenomesoneukaryotic and mitochondrial origin. Genome Biol Evol 4: 466–485.
-
(2012)
Genome Biol Evol
, vol.4
, pp. 466-485
-
-
Thiergart, T.1
Landan, G.2
Schenk, M.3
Dagan, T.4
Martin, W.F.5
-
103
-
-
65849420352
-
Hydrogenosomes and mitosomes: Conservation and evolution of functions.
-
van der Giezen M. 2009. Hydrogenosomes and mitosomes: Conservation and evolution of functions. J Eukaryot Microbiol 56: 221–231.
-
(2009)
J Eukaryot Microbiol
, vol.56
, pp. 221-231
-
-
van der Giezen, M.1
-
105
-
-
79952142375
-
Role of the ubiquitin-like protein Urm1 as a noncanonical ly-sine-directed protein modifier.
-
Van der Veen AG, Schorpp K, Schlieker C, Buti L, Damon JR, Spooner E, Ploegh HL, Jentsch S. 2011. Role of the ubiquitin-like protein Urm1 as a noncanonical ly-sine-directed protein modifier. Proc Natl Acad Sci 108: 1763–1770.
-
(2011)
Proc Natl Acad Sci
, vol.108
, pp. 1763-1770
-
-
Van der Veen, A.G.1
Schorpp, K.2
Schlieker, C.3
Buti, L.4
Damon, J.R.5
Spooner, E.6
Ploegh, H.L.7
Jentsch, S.8
-
106
-
-
0031949255
-
A new aspect to the origin and evolution of eukaryotes.
-
Vellai T, Takacs K, Vida G. 1998. A new aspect to the origin and evolution of eukaryotes. J Mol Evol 46: 499–507.
-
(1998)
J Mol Evol
, vol.46
, pp. 499-507
-
-
Vellai, T.1
Takacs, K.2
Vida, G.3
-
107
-
-
7444250756
-
Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes.
-
Vishwanath P, Favaretto P, Hartman H, Mohr SC, Smith TF. 2004. Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes. Mol Phylogenet Evol 33: 615–625.
-
(2004)
Mol Phylogenet Evol
, vol.33
, pp. 615-625
-
-
Vishwanath, P.1
Favaretto, P.2
Hartman, H.3
Mohr, S.C.4
Smith, T.F.5
-
108
-
-
80053067622
-
The dual role of ubiquitin-like protein Urm1 as a protein modifier and sulfurcarrier.
-
Wang F, LiuM, Qiu R, Ji C. 2011. The dual role of ubiquitin-like protein Urm1 as a protein modifier and sulfurcarrier. Protein Cell 2: 612–619.
-
(2011)
Protein Cell
, vol.2
, pp. 612-619
-
-
Wang, F.1
Liu, M.2
Qiu, R.3
Ji, C.4
-
109
-
-
84869133972
-
A congruent phylogenomic signal places eukaryotes within the Archaea.
-
Williams TA, Foster PG, Nye TM, Cox CJ, Embley TM. 2012. A congruent phylogenomic signal places eukaryotes within the Archaea. Proc Biol Sci 279: 4870–4879.
-
(2012)
Proc Biol Sci
, vol.279
, pp. 4870-4879
-
-
Williams, T.A.1
Foster, P.G.2
Nye, T.M.3
Cox, C.J.4
Embley, T.M.5
-
110
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya.
-
Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci 87: 4576–4579.
-
(1990)
Proc Natl Acad Sci
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
111
-
-
84881612486
-
Genome reduction as the dominant mode of evolution.
-
Wolf YI, Koonin EV. 2013. Genome reduction as the dominant mode of evolution. BioEssays 35: 829–837.
-
(2013)
BioEssays
, vol.35
, pp. 829-837
-
-
Wolf, Y.I.1
Koonin, E.V.2
-
112
-
-
84870950237
-
Updated clusters of orthologous genes for Archaea: A complex ancestor of the Archaea and the byways of horizontal gene transfer.
-
Wolf YI, Makarova KS, Yutin N, Koonin EV. 2012. Updated clusters of orthologous genes for Archaea: A complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol Direct 7: 46.
-
(2012)
Biol Direct
, vol.7
, pp. 46
-
-
Wolf, Y.I.1
Makarova, K.S.2
Yutin, N.3
Koonin, E.V.4
-
113
-
-
84858968457
-
Archaeal origin of tubulin.
-
Yutin N, Koonin EV. 2012. Archaeal origin of tubulin. Biol Direct 7: 10.
-
(2012)
Biol Direct
, vol.7
, pp. 10
-
-
Yutin, N.1
Koonin, E.V.2
-
114
-
-
47649125916
-
The deep archaeal rootsof eukaryotes.
-
Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV. 2008. The deep archaeal rootsof eukaryotes. Mol Biol Evol 25: 1619–1630.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1619-1630
-
-
Yutin, N.1
Makarova, K.S.2
Mekhedov, S.L.3
Wolf, Y.I.4
Koonin, E.V.5
|