Archaeal clusters of orthologous genes (arCOGs): An update and application for analysis of shared features between thermococcales, methanococcales, and methanobacteriales

Life

Volumn 5, Issue 1, 2015, Pages 818-840

  Makarova, Kira S ^a   Wolf, Yuri I ^a   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

ArCOGs; Genome annotation; Methanogens; Phylogenomics; Thermococci

Indexed keywords

ARCHAEA; EURYARCHAEOTA; METHANOBACTERIA; METHANOBACTERIALES; METHANOCOCCALES; METHANOCOCCI; THERMOCOCCALES; THERMOCOCCI;

EID: 84924356749     PISSN: None     EISSN: 20751729     Source Type: Journal    
DOI: 10.3390/life5010818     Document Type: Article

References (98)

1. Halachev, M.R.; Loman, N.J.; Pallen, M.J. Calculating orthologs in bacteria and Archaea: A divide and conquer approach. PLoS One 2011, 6, doi:10.1371/journal.pone.0028388.
2. Kristensen, D.M.; Wolf, Y.I.; Mushegian, A.R.; Koonin, E.V. Computational methods for Gene Orthology inference. Brief. Bioinform. 2011, 12, 379–391.
3. Altenhoff, A.M.; Dessimoz, C. Inferring orthology and paralogy. Methods Mol. Biol. 2012, 855, 259–279.
4. Trachana, K.; Larsson, T.A.; Powell, S.; Chen, W.H.; Doerks, T.; Muller, J.; Bork, P. Orthology prediction methods: A quality assessment using curated protein families. Bioessays 2011, 33, 769–780.
5. Poux, S.; Magrane, M.; Arighi, C.N.; Bridge, A.; O’Donovan, C.; Laiho, K. Expert curation in UniProtKB: A case study on dealing with conflicting and erroneous data. Database 2014, doi:10.1093/database/bau016.
6. Matsuya, A.; Sakate, R.; Kawahara, Y.; Koyanagi, K.O.; Sato, Y.; Fujii, Y.; Yamasaki, C.; Habara, T.; Nakaoka, H.; Todokoro, F, et al. Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. Nucleic Acids Res. 2008, 36, D787–D792.
7. Mazandu, G.K.; Mulder, N.J. The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines. Front. Genet. 2014, 5, doi:10.3389/fgene.2014.00264.
8. Trachana, K.; Forslund, K.; Larsson, T.; Powell, S.; Doerks, T.; von Mering, C.; Bork, P. A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PLoS One 2014, 9, doi:10.1371/journal.pone.0111122.
9. Bocs, S.; Danchin, A.; Medigue, C. Re-annotation of genome microbial coding-sequences: Finding new genes and inaccurately annotated genes. BMC Bioinform. 2002, 3, doi:10.1186/ 1471-2105-3-5.
10. Makarova, K.S.; Sorokin, A.V.; Novichkov, P.S.; Wolf, Y.I.; Koonin, E.V. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol. Direct 2007, 2, doi:10.1186/1745-6150-2-33.
11. Wolf, Y.I.; Makarova, K.S.; Yutin, N.; Koonin, E.V. Updated clusters of orthologous genes for Archaea: A complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol. Direct 2012, 7, doi:10.1186/1745-6150-7-46.
12. Yutin, N.; Puigbo, P.; Koonin, E.V, Wolf, Y.I. Phylogenomics of prokaryotic ribosomal proteins. PLoS One 2012, 7, doi:10.1371/journal.pone.0036972.
13. Marinsek, N.; Barry, E.R.; Makarova, K.S.; Dionne, I.; Koonin, E.V.; Bell, S.D. GINS, a central nexus in the archaeal DNA replication fork. EMBO Rep. 2006, 7, 539–545.
14. Makarova, K.; Kelman, Z.; Koonin, E.V. The archaeal CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes. Biol. Direct 2012, 13, doi:10.1186/1745-6150-7.
15. Makarova, K.S.; Anantharaman, V.; Grishin, N.V.; Koonin, E.V.; Aravind, L. CARF and WYL domains: Ligand-binding regulators of prokaryotic defense systems. Front. Genet. 2014, 5, doi:10.3389/fgene.2014.00102.
16. Makarova, K.S.; Aravind, L.; Wolf, Y.I.; Koonin, E.V. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol. Direct 2011, 6, doi:10.1186/1745-6150-6-38.
17. Makarova, K.S.; Koonin, E.V. Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea. Biol. Direct 2010, 5, doi:10.1186/ 1745-6150-5-33.
18. Makarova, K.S.; Koonin, E.V. Archaeology of eukaryotic DNA replication. Cold Spring Harb. Perspect. Biol. 2013, 5, doi:10.1101/cshperspect.a012963.
19. Makarova, K.S.; Wolf, Y.I.; Forterre, P.; Prangishvili, D.; Krupovic, M.; Koonin, E.V. Dark matter in archaeal genomes: A rich source of novel mobile elements, defense systems and secretory complexes. Extremophiles 2014, 18, 877–893.
20. Makarova, K.S.; Wolf, Y.I.; Snir, S.; Koonin, E.V. Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J. Bacteriol. 2011, 193, 6039–6056.
21. Makarova, K.S.; Yutin, N.; Bell, S.D.; Koonin, E.V. Evolution of diverse cell division and vesicle formation systems in Archaea. Nat. Rev. Microbiol. 2010, 8, 731–741.
22. Makarova, K.S.; Krupovic, M.; Koonin, E.V. Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery. Front. Microbiol. 2014, 5, doi:10.3389/fmicb.2014.00354.
23. Esser, D.; Pham, T.K.; Reimann, J.; Albers, S.V.; Siebers, B.; Wright, P.C. Change of carbon source causes dramatic effects in the phospho-proteome of the archaeon Sulfolobus solfataricus. J. Proteome Res. 2012, 11, 4823–4833.
24. Podar, M.; Makarova, K.S.; Graham, D.E.; Wolf, Y.I.; Koonin, E.V.; Reysenbach, A.L. Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park. Biol. Direct 2013, 8, doi:10.1186/1745-6150-8.
25. Podar, M.; Anderson, I.; Makarova, K.S.; Elkins, J.G.; Ivanova, N.; Wall, M.A.; Lykidis, A.; Mavromatis, K.; Sun, H.; Hudson, M.E, et al. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol. 2008, 9, doi:10.1186/gb-2008-9-11-r158.
26. Elkins, J.G.; Podar, M.; Graham, D.E.; Makarova, K.S.; Wolf, Y.; Randau, L.; Hedlund, B.P.; Brochier-Armanet, C.; Kunin, V.; Anderson, I, et al. A korarchaeal genome reveals insights into the evolution of the Archaea. Proc. Natl. Acad. Sci. USA 2008, 105, 8102–8107.
27. Borrel, G.; Parisot, N.; Harris, H.M.; Peyretaillade, E.; Gaci, N.; Tottey, W.; Bardot, O.; Raymann, K.; Gribaldo, S.; Peyret, P, et al. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 2014, 15, doi:10.1186/1471-2164-15-679.
28. Reimann, J.; Esser, D.; Orell, A.; Amman, F.; Pham, T.K.; Noirel, J.; Lindas, A.C.; Bernander, R.; Wright, P.C.; Siebers, B, et al. Archaeal signal transduction: Impact of protein phosphatase deletions on cell size, motility, and energy metabolism in Sulfolobus acidocaldarius. Mol. Cell. Proteomics 2013, 12, 3908–3923.
29. Goncearenco, A.; Berezovsky, I.N. Exploring the evolution of protein function in Archaea. BMC Evol. Biol. 2012, 12, doi:10.1186/1471-2148-12-75.
30. Leahy, S.C.; Kelly, W.J.; Altermann, E.; Ronimus, R.S.; Yeoman, C.J.; Pacheco, D.M.; Li, D.; Kong, Z.; McTavish, S.; Sang, C, et al. The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One 2010, 5, doi:10.1371/journal.pone.0008926.
31. Csuros, M.; Miklos, I. Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Mol. Biol. Evol. 2009, 26, 2087–2095.
32. Hooper, S.D.; Anderson, I.J.; Pati, A.; Dalevi, D.; Mavromatis, K.; Kyrpides, N.C. Integration of phenotypic metadata and protein similarity in Archaea using a spectral bipartitioning approach. Nucleic Acids Res. 2009, 37, 2096–2104.
33. Lindas, A.C.; Karlsson, E.A.; Lindgren, M.T.; Ettema, T.J.; Bernander, R. A unique cell division machinery in the Archaea. Proc. Natl. Acad. Sci. USA 2008, 105, 18942–18946.
34. Chan, P.P.; Holmes, A.D.; Smith, A.M.; Tran, D.; Lowe, T.M. The UCSC Archaeal Genome Browser: 2012 update. Nucleic Acids Res. 2012, 40, D646–D652.
35. Anderson, I.; Ulrich, L.E.; Lupa, B.; Susanti, D.; Porat, I.; Hooper, S.D.; Lykidis, A.; Sieprawska-Lupa, M.; Dharmarajan, L.; Goltsman, E, et al. Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS One 2009, 4, doi:10.1371/ journal.pone.0005797.
36. NCBI FTP site. Available online: ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ (accessed on 6 March 2015).
37. Galperin, M.Y.; Makarova, K.S.; Wolf, Y.I.; Koonin, E.V. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2014, 43, D261–D269.
38. Altschul, S.F.; Madden, T.L.; Schaffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 1997, 25, 3389–3402.
39. Marchler-Bauer, A.; Anderson, J.B.; Chitsaz, F.; Derbyshire, M.K.; DeWeese-Scott, C.; Fong, J.H.; Geer, L.Y.; Geer, R.C.; Gonzales, N.R.; Gwadz, M, et al. CDD: Specific functional annotation with the Conserved Domain Database. Nucleic Acids Res. 2009, 37, D205–D210.
40. Finn, R.D.; Bateman, A.; Clements, J.; Coggill, P.; Eberhardt, R.Y.; Eddy, S.R.; Heger, A.; Hetherington, K.; Holm, L.; Mistry, J, et al. Pfam: The protein families database. Nucleic Acids Res. 2014, 42, D222–D230.
41. Haft, D.H.; Loftus, B.J.; Richardson, D.L.; Yang, F.; Eisen, J.A.; Paulsen, I.T.; White, O. TIGRFAMs: A protein family resource for the functional identification of proteins. Nucleic Acids Res. 2001, 29, 41–43.
42. Soding, J.; Biegert, A.; Lupas, A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005, 33, W244–W248.
43. Krogh, A.; Larsson, B.; von Heijne, G.; Sonnhammer, E.L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 2001, 305, 567–580.
44. Petersen, T.N.; Brunak, S.; von Heijne, G.; Nielsen, H. SignalP 4.0: Discriminating signal peptides from transmembrane regions. Nat. Methods 2011, 8, 785–786.
45. Edgar, R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792–1797.
46. Katoh, K.; Standley, D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013, 30, 772–780.
47. Yutin, N.; Makarova, K.S.; Mekhedov, S.L.; Wolf, Y.I.; Koonin, E.V. The deep archaeal roots of eukaryotes. Mol. Biol. Evol. 2008, 25, 1619–1630.
48. Price, M.N.; Dehal, P.S.; Arkin, A.P. FastTree 2—Approximately maximum-likelihood trees for large alignments. PLoS One 2010, 5, doi:10.1371/journal.pone.0009490.
49. Petitjean, C.; Deschamps, P.; Lopez-Garcia, P.; Moreira, D. Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom proteoarchaeota. Genome Biol. Evol. 2014, 7, 191–204.
50. Wolf, Y.I.; Aravind, L.; Grishin, N.V.; Koonin, E.V. Evolution of aminoacyl-tRNA synthetases—Analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999, 9, 689–710.
51. Williams, C.H.; Stillman, T.J.; Barynin, V.V.; Sedelnikova, S.E.; Tang, Y.; Green, J.; Guest, J.R.; Artymiuk, P.J. E. coli aconitase B structure reveals a HEAT-like domain with implications for protein-protein recognition. Nat. Struct. Biol. 2002, 9, 447–452.
52. NCBI arCOG database. Available online: ftp://ftp.ncbi.nih.gov/pub/wolf/COGs/arCOG/(accessed on 6 March 2015).
53. Koonin, E.V.; Wolf, Y.I. Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world. Nucleic Acids Res. 2008, 36, 6688–6719.
54. Makarova, K.S.; Galperin, M.Y.; Koonin, E.V. Comparative genomic analysis of evolutionarily conserved but functionally uncharacterized membrane proteins in archaea: Prediction of novel components of secretion, membrane remodeling and glycosylation systems. Biochimie 2015, doi:10.1016/j.biochi.2015.01.004.
55. Koonin, E.V.; Makarova, K.S. CRISPR-Cas: Evolution of an RNA-based adaptive immunity system in prokaryotes. RNA Biol. 2013, 10, 679–686.
56. Makarova, K.S.; Wolf, Y.I.; Koonin, E.V. The basic building blocks and evolution of CRISPR-Cas systems. Biochem. Soc. Trans. 2013, 41, 1392–1400.
57. Marquez, V.; Frohlich, T.; Armache, J.P.; Sohmen, D.; Donhofer, A.; Mikolajka, A.; Berninghausen, O.; Thomm, M.; Beckmann, R.; Arnold, G.J, et al. Proteomic characterization of archaeal ribosomes reveals the presence of novel archaeal-specific ribosomal proteins. J. Mol. Biol. 2011, 405, 1215–1232.
58. Wu, P.; Brockenbrough, J.S.; Paddy, M.R.; Aris, J.P. NCL1, a novel gene for a non-essential nuclear protein in Saccharomyces cerevisiae. Gene 1998, 220, 109–117.
59. Makarova, K.S.; Wolf, Y.I.; Mekhedov, S.L.; Mirkin, B.G.; Koonin, E.V. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res. 2005, 33, 4626–4638.
60. Koonin, E.V. Carl Woese’s vision of cellular evolution and the domains of life. RNA Biol. 2014, 11, 197–204.
61. Puigbo, P.; Wolf, Y.I.; Koonin, E.V. Seeing the Tree of Life behind the phylogenetic forest. BMC Biol. 2013, 11, doi:10.1186/1741-7007-11-46.
62. Beauregard-Racine, J.; Bicep, C.; Schliep, K.; Lopez, P.; Lapointe, F.J.; Bapteste, E. Of woods and webs: Possible alternatives to the tree of life for studying genomic fluidity in E. Coli. Biol. Direct 2011, 6, doi:10.1186/1745-6150-6-3.
63. Bapteste, E.; O’Malley, M.A.; Beiko, R.G.; Ereshefsky, M.; Gogarten, J.P.; Franklin-Hall, L.; Lapointe, F.J.; Dupre, J.; Dagan, T.; Boucher, Y, et al. Prokaryotic evolution and the tree of life are two different things. Biol. Direct 2009, 4, doi:10.1186/1745-6150-4-34.
64. Koonin, E.V.; Wolf, Y.I. The fundamental units, processes and patterns of evolution, and the tree of life conundrum. Biol. Direct 2009, 4, doi:10.1186/1745-6150-4-33.
65. Bapteste, E.; Susko, E.; Leigh, J.; Ruiz-Trillo, I.; Bucknam, J.; Doolittle, W.F. Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol. Biol. Evol. 2008, 25, 83–91.
66. Doolittle, W.F.; Bapteste, E. Pattern pluralism and the Tree of Life hypothesis. Proc. Natl. Acad. Sci. USA 2007, 104, 2043–2049.
67. Dagan, T.; Martin, W. The tree of one percent. Genome Biol. 2006, 7, doi:10.1186/gb-2006-7-10-118.
68. Williams, T.A.; Embley, T.M. Archaeal “dark matter” and the origin of eukaryotes. Genome Biol. Evol. 2014, 6, 474–481.
69. Nelson-Sathi, S.; Sousa, F.L.; Roettger, M.; Lozada-Chavez, N.; Thiergart, T.; Janssen, A.; Bryant, D.; Landan, G.; Schonheit, P.; Siebers, B, et al. Origins of major archaeal clades correspond to gene acquisitions from bacteria. Nature 2014, 517, 77–80.
70. Matte-Tailliez, O.; Brochier, C.; Forterre, P.; Philippe, H. Archaeal phylogeny based on ribosomal proteins. Mol. Biol. Evol. 2002, 19, 631–639.
71. Raymann, K.; Forterre, P.; Brochier-Armanet, C.; Gribaldo, S. Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea. Genome Biol. Evol. 2014, 6, 192–212.
72. Brochier, C.; Forterre, P.; Gribaldo, S. An emerging phylogenetic core of Archaea: Phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol. Biol. 2005, 5, doi:10.1186/1471-2148-5-36.
73. Huber, H.; Hohn, M.J.; Rachel, R.; Fuchs, T.; Wimmer, V.C.; Stetter, K.O. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 2002, 417, 63–67.
74. Waters, E.; Hohn, M.J.; Ahel, I.; Graham, D.E.; Adams, M.D.; Barnstead, M.; Beeson, K.Y.; Bibbs, L.; Bolanos, R.; Keller, M, et al. The genome of Nanoarchaeum equitans: Insights into early archaeal evolution and derived parasitism. Proc. Natl. Acad. Sci. USA 2003, 100, 12984–12988.
75. Brochier, C.; Gribaldo, S.; Zivanovic, Y.; Confalonieri, F.; Forterre, P. Nanoarchaea: Representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biol. 2005, 6, doi:10.1186/gb-2005-6-5-r42.
76. Brochier, C.; Forterre, P.; Gribaldo, S. Archaeal phylogeny based on proteins of the transcription and translation machineries: Tackling the Methanopyrus kandleri paradox. Genome Biol. 2004, 5, R17.
77. Luo, H.; Sun, Z.; Arndt, W.; Shi, J.; Friedman, R.; Tang, J. Gene order phylogeny and the evolution of methanogens. PLoS One 2009, 4, doi:10.1371/journal.pone.0006069.
78. Slesarev, A.I.; Mezhevaya, K.V.; Makarova, K.S.; Polushin, N.N.; Shcherbinina, O.V.; Shakhova, V.V.; Belova, G.I.; Aravind, L.; Natale, D.A.; Rogozin, I.B, et al. The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc. Natl. Acad. Sci. USA 2002, 99, 4644–4649.
79. Guy, L.; Ettema, T.J. The archaeal “TACK” superphylum and the origin of eukaryotes. Trends Microbiol. 2011, 19, 580–587.
80. Williams, T.A.; Foster, P.G.; Nye, T.M.; Cox, C.J.; Embley, T.M. A congruent phylogenomic signal places eukaryotes within the Archaea. Proc. Biol. Sci. 2012, 279, 4870–4879.
81. Rinke, C.; Schwientek, P.; Sczyrba, A.; Ivanova, N.N.; Anderson, I.J.; Cheng, J.F.; Darling, A.; Malfatti, S.; Swan, B.K.; Gies, E.A, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013, 499, 431–437.
82. 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.; Banfield, J.F, et al. Enigmatic, ultrasmall, uncultivated Archaea. Proc. Natl. Acad. Sci. USA 2010, 107, 8806–8811.
83. Gatesy, J.; Springer, M.S. Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol. Phylogenet. Evol. 2014, 80, 231–266.
84. Lanier, H.C.; Huang, H.; Knowles, L.L. How low can you go? The effects of mutation rate on the accuracy of species-tree estimation. Mol. Phylogenet. Evol. 2014, 70, 112–119.
85. Martin, W.; Roettger, M.; Lockhart, P.J. A reality check for alignments and trees. Trends Genet. 2007, 23, 478–480.
86. Brochier-Armanet, C.; Forterre, P.; Gribaldo, S. Phylogeny and evolution of the Archaea: One hundred genomes later. Curr. Opin. Microbiol. 2011, 14, 274–281.
87. NCBI FTP site. Available online: ftp://ftp.ncbi.nih.gov/pub/wolf/_suppl/arCOG2014/ (accessed on 6 March 2015).
88. Ciccarelli, F.D.; Doerks, T.; von Mering, C.; Creevey, C.J.; Snel, B.; Bork, P. Toward automatic reconstruction of a highly resolved tree of life. Science 2006, 311, 1283–1287.
89. Lehnik-Habrink, M.; Lewis, R.J.; Mader, U.; Stulke, J. RNA degradation in Bacillus subtilis: An interplay of essential endo- and exoribonucleases. Mol. Microbiol. 2012, 84, 1005–1017.
90. Kaberdin, V.R.; Lin-Chao, S. Unraveling new roles for minor components of the E. coli RNA degradosome. RNA Biol. 2009, 6, 402–405.
91. Rogozin, I.B.; Makarova, K.S.; Murvai, J.; Czabarka, E.; Wolf, Y.I.; Tatusov, R.L.; Szekely, L.A.; Koonin, E.V. Connected gene neighborhoods in prokaryotic genomes. Nucleic Acids Res. 2002, 30, 2212–2223.
92. Lynch, M.; Force, A. The probability of duplicate gene preservation by subfunctionalization. Genetics 2000, 154, 459–473.
93. Bork, P.; Koonin, E.V. A P-loop-like motif in a widespread ATP pyrophosphatase domain: Implications for the evolution of sequence motifs and enzyme activity. Proteins 1994, 20, 347–355.
94. Ikeuchi, Y.; Soma, A.; Ote, T.; Kato, J.; Sekine, Y.; Suzuki T. Molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol. Cell 2005, 19, 235–246.
95. Valverde, R.; Edwards, L.; Regan, L. Structure and function of KH domains. FEBS J. 2008, 275, 2712–2726.
96. Planet, P.J.; Kachlany, S.C.; DeSalle, R.; Figurski, D.H. Phylogeny of genes for secretion NTPases: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification. Proc. Natl. Acad. Sci. USA 2001, 98, 2503–2508.
97. Szabo, Z.; Stahl, A.O.; Albers, S.V.; Kissinger, J.C.; Driessen, A.J.; Pohlschroder, M. Identification of diverse archaeal proteins with class III signal peptides cleaved by distinct archaeal prepilin peptidases. J. Bacteriol. 2007, 189, 772–778.
98. Puigbo, P.; Wolf, Y.I.; Koonin, E.V. Search for a “Tree of Life” in the thicket of the phylogenetic forest. J. Biol. 2009, 8, doi:10.1186/jbiol159.