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RESEARCH: Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell
- Kira S. Makarova,
- L. Aravind,
- Michael Y. Galperin,
- Nick V. Grishin,
- Roman L. Tatusov,
- Yuri I. Wolf,
- and Eugene V. Koonin
Genome Res. July 1, 1999 9: 608-628; doi:10.1101/gr.9.7.608
...A superfamily proteins and domains are nucleotide-binding signal transducers that play a central regulatory role in both archaeal and bacterial cells. View larger version: In this window In a new window Figure 6. Previously undetected protein family conservation in archaea, bacteria, and eukaryotes—the Usp...
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ARTICLE: Biosynthesis of Isoprenoids via Mevalonate in Archaea: The Lost Pathway
- Arian Smit and
- Arcady Mushegian
Genome Res. October 1, 2000 10: 1468-1484; doi:10.1101/gr.145600
...of this pathway in various eukaryotes and in archaea, and its apparent substitution in bacteria by an alternative route involving biosynthesis and reductive isomerization of deoxy-D-xylulose phosphate (DXP) ( Eisenreich et al. 1998 ; Fig. 1 ). We used comparative sequence analysis to show that most of the species...
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Research: Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)
- Sünje J. Pamp,
- Eoghan D. Harrington,
- Stephen R. Quake,
- David A. Relman,
- and Paul C. Blainey
Genome Res. June 2012 22: 1107-1119; Published in Advance March 20, 2012, doi:10.1101/gr.131482.111
...), but on average, 8.6% of the predicted proteins showed no significant sequence similarity. Comparative genomics In Bacteria and Archaea, size and number of genes are directly proportional to each other (Konstantinidis and Tiedje 2004). The ratio of gene number to assembly size for SFB-co and for SFB...
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LETTER: Data-Mining Approaches Reveal Hidden Families of Proteases in the Genome of Malaria Parasite
- Yimin Wu,
- Xiangyun Wang,
- Xia Liu,
- and Yufeng Wang
Genome Res. April 1, 2003 13: 601-616; doi:10.1101/gr.913403
...proteins. This serine protease family consists of two subtypes, SP1 and signalase, based on their distinct structural, functional, and evolutionary features. To date, SPs have been found in bacteria, archaea, fungi, plants, and animals; however, SP has never been reported previously in protists, despite...
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LETTER: Prokaryotic Homologs of the Eukaryotic DNA-End-Binding Protein Ku, Novel Domains in the Ku Protein and Prediction of a Prokaryotic Double-Strand Break Repair System
- L. Aravind and
- Eugene V. Koonin
Genome Res. August 1, 2001 11: 1365-1374; doi:10.1101/gr.181001
...signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J. Mol. Biol. 289 : 729 – 745 . ↵ Raaijmakers H. , Vix O. , Toro I. , Golz S. , Kemper B. , Suck D. ( 1999 ) X-ray structure of T4 endonuclease VII: A DNA junction resolvase with a novel fold and unusual...
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LETTER: Eukaryote-specific Domains in Translation Initiation Factors: Implications for Translation Regulation and Evolution of the Translation System
- L. Aravind and
- Eugene V. Koonin
Genome Res. August 1, 2000 10: 1172-1184; doi:10.1101/gr.10.8.1172
...a number of specific domains that are not represented in bacteria or archaea. Most of these eukaryote-specific domains are known or predicted to possess an α-helical structure, which suggests that such domains are easier to invent in the course of evolution than are domains of other structural classes...
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RESEARCH: A Prokaryotic Gene Cluster Involved in Synthesis of Lysine through the Amino Adipate Pathway: A Key to the Evolution of Amino Acid Biosynthesis
- Hiromi Nishida,
- Makoto Nishiyama,
- Nobuyuki Kobashi,
- Takehide Kosuge,
- Takayuki Hoshino,
- and Hisakazu Yamane
Genome Res. December 1, 1999 9: 1175-1183; doi:10.1101/gr.9.12.1175
...and the corresponding region in P. horikoshii . The percentages show amino acid sequence identity between the homologous genes. However, the trees also indicate that the branching point is deep, probably close to the early divergence of bacteria and archaea. Considering that the earliest organisms had lived under hot...
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ARTICLE: Structural Characterization of the Human Proteome
- Arne Müller,
- Robert M. MacCallum,
- and Michael J.E. Sternberg
Genome Res. November 1, 2002 12: 1625-1641; doi:10.1101/gr.221202
...superfamilies in human, fly, worm, yeast, and average values for archaea and bacteria. Complete tables can be downloaded from our web site, http://www.sbg.bio.ic.ac.uk . View this table: In this window In a new window Table 1. Commonly Occurring SCOP Superfamilies in the Proteomes First, we consider...
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LETTER: Functional insights from the distribution and role of homopeptide repeat-containing proteins
- Noel G. Faux,
- Stephen P. Bottomley,
- Arthur M. Lesk,
- James A. Irving,
- John R. Morrison,
- Maria Garcia de la Banda,
- and James C. Whisstock
Genome Res. April 2005 15: 537-551; doi:10.1101/gr.3096505
...of this region arose after the archaea/bacteria split, but prior to the emergence of eukaryotes. A major question in repeat-related research fields is the role of RCPs and, in particular, the role of the repeat region itself. Evolutionary pressure on repeat regions is likely to include functional requirement...
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LETTER: Comparison of the Small Molecule Metabolic Enzymes of Escherichia coli and Saccharomyces cerevisiae
- Oliver Jardine,
- Julian Gough,
- Cyrus Chothia,
- and Sarah A. Teichmann
Genome Res. June 1, 2002 12: 916-929; doi:10.1101/gr.228002
...between bacteria and eukaryotes. Gene Fusions and Protein–Protein Interactions In the previous sections, we have seen that there is extensive conservation of domain architecture in the set of shared enzymes in small molecule metabolism of E. coli and yeast. In common enzymes that have identical domain...

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