Phylogenomic analysis of the GIY-YIG nuclease superfamily.

BMC Genomics
Stanislaw Dunin-HorkawiczJanusz M Bujnicki

Abstract

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. 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. An evolutionary classification of the GIY-YIG superfamily is presented for the very first time, along with the structural annotation...Continue Reading

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Citations

May 9, 2012·Proceedings of the National Academy of Sciences of the United States of America·Benjamin P KleinstiverDavid R Edgell
Aug 28, 2009·The Journal of Biological Chemistry·Marlene Belfort
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Oct 5, 2019·Nucleic Acids Research·Vineet GaurMarcin Nowotny

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Datasets Mentioned

BETA
MCA0838

Methods Mentioned

BETA
X-ray
glucosylation
CLANS
Nuclear Magnetic Resonance
sequence-based prediction

Software Mentioned

PROF
BLAST
PSIPRED
JUFO
HHSEARCH
CLANS
T02
JPRED
mGenThreader
HHmake

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