Cited by 133CRISPR and Genetic EngineeringGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

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Phylogenomic analysis of the GIY-YIG nuclease superfamily

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Dunin-Horkawicz, Stanislaw, Feder, Marcin, Bujnicki, Janusz M·2006·BMC Genomics

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Abstract

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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Authors: Dunin-Horkawicz, S., Feder, M., & Bujnicki, J. M.
Affiliations: International Institute of Molecular and Cell Biology (PL)
Corresponding author: Bujnicki, Janusz M
ORCID: Feder, Marcin
Bujnicki, Janusz M
Venue: BMC Genomics
Publisher: Springer Science and Business Media LLC
Published: 2006-04-28
Volume: 7
Issue: 1
Pages: 98-98
ISSN: 1471-2164 (ISSN-L)
DOI: 10.1186/1471-2164-7-98
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: cc-by
creativecommons.org/licenses/by/2.0 (tdm)
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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Phylogenomic analysis of the GIY-YIG nuclease superfamily

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