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Phylogenomic analysis of the GIY-YIG nuclease superfamily
Open accessAbstract
BACKGROUND: The GIY-YIG domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-LTR retrotransposons) and in enzymes involved in DNA repair and recombination. However, to date no systematic search for novel members of the GIY-YIG superfamily or comparative analysis of these enzymes has been reported. RESULTS: We carried out database searches to identify all members of known GIY-YIG nuclease families. Multiple sequence alignments together with predicted secondary structures of identified families were represented as Hidden Markov Models (HMM) and compared by the HHsearch method to the uncharacterized protein families gathered in the COG, KOG, and PFAM databases. This analysis allowed for extending the GIY-YIG superfamily to include members of COG3680 and a number of proteins not classified in COGs and to predict that these proteins may function as nucleases, potentially involved in DNA recombination and/or repair. Finally, all old and new members of the GIY-YIG superfamily were compared and analyzed to infer the phylogenetic tree. CONCLUSION: An evolutionary classification of the GIY-YIG superfamily is presented for the very first time, along with the structural annotation of all (sub)families. It provides a comprehensive picture of sequence-structure-function relationships in this superfamily of nucleases, which will help to design experiments to study the mechanism of action of known members (especially the uncharacterized ones) and will facilitate the prediction of function for the newly discovered ones.
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“Organellar translation and splicing are mechanistically connected by the intron-encoded maturase proteins (Pel and Grivell 1993), but the ORF encoded in COB intron I contains the GIY–YIG motif (Kolondra et al. 2015) that is typical of homing endonucleases rather than maturases (Dunin-Horkawicz et al. 2006), suggesting that the effect of CaPpr7p on splicing cannot be explained by a maturase”
From Candida albicans PPR proteins are required for the expression of respiratory Complex I subunits (2024) · cites this paper as Dunin-Horkawicz et al. 2006
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Metadata
- Authors
- Dunin-Horkawicz, S., Feder, M., & Bujnicki, J. M.
- Affiliations
- International Institute of Molecular and Cell Biology (PL)
- Corresponding author
- Bujnicki, Janusz M
- Venue
- BMC Genomics
- Published
- 2006-04-28
- Volume
- 7
- Issue
- 1
- Pages
- 98-98
- ISSN
- 1471-2164 (ISSN-L)
- OpenAlex
- W1601234927
- Cited by
- 133
- References
- 84
- Citations by year
- 2026: 10 · 2025: 9 · 2024: 6 · 2023: 7 · 2022: 5 · 2021: 9 · 2020: 4 · 2019: 4 · 2018: 5 · 2017: 11 · 2016: 6 · 2015: 7 · 2014: 5 · 2013: 7 · 2012: 7
- FWCI
- 2.86
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Howard Hughes Medical Institute
- Warszawski Uniwersytet Medyczny
- Uniwersytet Warszawski
- National Institutes of Health (5r03tw007163-02)
- National Cancer Institute (1R21CA97899-01A, R21CA097899)
- Fogarty International Center (R03 TW007163, R03 TW007163-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Keywords
- homing endonucleases, restriction enzymes, non-LTR retrotransposons, DNA repair, DNA recombination, protein family classification, phylogenetic tree, sequence-structure-function relationships, hypothetical protein
- MeSH terms
- Bacterial Proteins, Deoxyribonucleases, DNA Repair, Models, Molecular, Phylogeny, Recombination, Genetic, Viral Proteins, Sequence Alignment, Protein Structure, Secondary, Archaeal Proteins, Genomics, Databases, Nucleic Acid
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