A new group of plant-specific ATP-dependent DNA ligases identified by protein phylogeny, hydrophobic cluster analysis and 3-dimensional modelling

Functional Plant Biology : FPB
Diego BonattoJoão Antonio Pêgas Henriques

Abstract

The eukaryotic ATP-dependent DNA ligases comprise a group of orthologous proteins that have distinct roles in DNA metabolism. In contrast with the well-known DNA ligases of animal cells, the DNA ligases of plant cells are poorly described. Until now, only two DNA ligases (I and IV) genes of Arabidopsis thaliana (L.) Heynh were isolated and characterised. Use of the complete genomic sequences of Oryza sativa L. and A. thaliana, as well as the partially assembled genomic data of Medicago truncatula L. and Brassica spp., allowed us to identify a new family of ATP-dependent DNA ligases that are found only in the Viridiplantae kingdom. An in-depth phylogenetic analysis of protein sequences showed that this family composes a distinct clade, which shares a last universal common ancestor with DNA ligases I. In silico sequence studies indicate that these proteins have distinct physico-chemical properties when compared with those of animal and fungal DNA ligases. Moreover, hydrophobic cluster analysis and 3-dimensional modelling allowed us to map two conserved domains within these DNA ligases I-like proteins. Additional data of microsynteny analysis indicate that these DNA ligases I-like genes are linked to the S and SLL2 loci of Brassic...Continue Reading

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Citations

Jul 26, 2011·The Plant Journal : for Cell and Molecular Biology·Dolores Córdoba-CañeroRafael R Ariza
Sep 25, 2019·International Journal of Molecular Sciences·Jara Teresa Parrilla-DoblasDolores Córdoba-Cañero
Sep 24, 2019·Frontiers in Plant Science·Teresa Roldán-ArjonaDolores Córdoba-Cañero
Nov 18, 2005·Computational Biology and Chemistry·Diego BonattoJoão Antonio Pêgas Henriques

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Software Mentioned

BLOSUM
TBLASTX
DRAWHCA
PdbViewer
PSI
ClustalX
GeneWise623
BioEdit
MEGA
NJ

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