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Research: Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
- Marco Mariotti,
- Didac Santesmasses,
- Salvador Capella-Gutierrez,
- Andrea Mateo,
- Carme Arnan,
- Rory Johnson,
- Salvatore D'Aniello,
- Sun Hee Yim,
- Vadim N. Gladyshev,
- Florenci Serras,
- Montserrat Corominas,
- Toni Gabaldón,
- and Roderic Guigó
Genome Res. September 2015 25: 1256-1267; Published in Advance July 20, 2015, doi:10.1101/gr.190538.115
...traits (Sec and SeU) in prokaryotic s.Within eukaryotes, specifically within metazoans, we detected a number of SPS homologs with amino acids other than Sec or Cys at the homologous UGA position. We found that Cys- or Sec-containing SPS genes (SPS2) are found in all s encoding selenoproteins, whereas s...
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LETTER: Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic Approach
- Eugene V. Koonin,
- Yuri I. Wolf,
- and L. Aravind
Genome Res. February 1, 2001 11: 240-252; doi:10.1101/gr.162001
....V. ( 1999 ) DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res. 27 : 4658 – 4670 . ↵ ( 2000 ) Eukaryote-specific domains in translation initiation factors: Implications for translation regulation and evolution of the translation system. Genome Res. 10 : 1172...
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LETTER: The Role of Lineage-Specific Gene Family Expansion in the Evolution of Eukaryotes
- Olivier Lespinet,
- Yuri I. Wolf,
- Eugene V. Koonin,
- and L. Aravind
Genome Res. July 1, 2002 12: 1048-1059; doi:10.1101/gr.174302
...with the potassium channel tetramerization domain. J. Mol. Biol. 285 : 1353 – 1361 . ↵ ( 2000 ) Eukaryote-specific domains in translation initiation factors: Implications for translation regulation and evolution of the translation system. Genome Res. 10 : 1172 – 1184 , ibid . ↵ ( 2001 ) The DNA-repair protein Alk...
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Research: Overlapping codes within protein-coding sequences
- Shalev Itzkovitz,
- Eran Hodis,
- and Eran Segal
Genome Res. November 2010 20: 1582-1589; Published in Advance September 14, 2010, doi:10.1101/gr.105072.110
...of transcription and translation initiation signals, and eukaryote-specific enrichment of microRNA target sites. Our results suggest that genomes may have evolved to encode extensive overlapping information within protein-coding regions. Footnotes ↵ 4 Corresponding author. E-mail eran...
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LETTER: Comparative Analysis of Apicomplexa and Genomic Diversity in Eukaryotes
- Thomas J. Templeton,
- Lakshminarayan M. Iyer,
- Vivek Anantharaman,
- Shinichiro Enomoto,
- Juan E. Abrahante,
- G.M. Subramanian,
- Stephen L. Hoffman,
- Mitchell S. Abrahamsen,
- and L. Aravind
Genome Res. September 2004 14: 1686-1695; doi:10.1101/gr.2615304
.... 2A-D ). Most notably, the apicomplexan proteomes have a large component devoted to pathogenesis, immune evasion, and adhesion rather than transcription, posttranscriptional regulation, or metabolism. The apicomplexans confirm large-scale trends in the evolution of the eukaryotes, specifically...
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REPORT: Sequence and Analysis of Chromosome I of the Amitochondriate Intracellular Parasite Encephalitozoon cuniculi (Microspora)
- Pierre Peyret,
- Michael D. Katinka,
- Simone Duprat,
- Francis Duffieux,
- Valérie Barbe,
- Martin Barbazanges,
- Jean Weissenbach,
- William Saurin,
- and Christian P. Vivarès
Genome Res. February 1, 2001 11: 198-207; doi:10.1101/gr.164301
...or are clearly eukaryote-specific. [The sequence data described in this paper have been submitted to the EMBL data library under accession no. AL 391737.] Footnotes ↵ 4 Present address: Laboratoire de Résonance Magnétique Nucléaire, Département de Chimie Structurale et Organique, Ecole...
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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
...that the absence of these two residues is unlikely to disrupt the extended region characteristic of this fold (Fig. 4 B). Thus, it appears likely that SAP domain is a derived, eukaryote-specific version of the HEH fold, which interacts with DNA via the charged surfaces of the helices. Notably, the SAP domain...
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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
...as a result of convergent evolution and therefore are not homologous. The above considerations have led us to focus our analysis on the following three objectives: (i) to estimate the extent to which the known proteomes can be annotated in terms of structure and function and how reliable we consider...

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