A new group of plant-specific ATP-dependent DNA ligases identified by protein phylogeny, hydrophobic cluster analysis and 3-dimensional modelling
Diego Bonatto A , Martin Brendel A B and João Antonio Pêgas Henriques A C DA Departamento de Biofísica / Centro de Biotecnologia, UFRGS, Av. Bento Gonçalves 9500, 91507-970 Porto Alegre, RS, Brazil.
B Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, BA, Brazil.
C Curso de Farmácia, Universidade Luterana do Brasil (ULBRA), Canoas, RS, Brazil.
D Instituto de Biotecnologia, Universidade de Caxias do Sul (UCS), Caxias do Sul, RS, Brazil. Corresponding author. Email: pegas@cbiot.ufrgs.br
Functional Plant Biology 32(2) 161-174 https://doi.org/10.1071/FP04143
Submitted: 10 August 2004 Accepted: 6 January 2005 Published: 24 February 2005
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 Brassica spp. and A. thaliana, respectively. Combining the results of all analyses, we propose the creation of the DNA ligases VI (LIG6) family, which is composed by plant-specific DNA ligases.
Keywords: DNA ligase I, eukaryotic DNA ligases, hydrophobic cluster analysis, plant DNA ligases, protein phylogeny, Pso2p / Snm1p / Artemis.
Acknowledgments
We thank Drs Arthur G. Fett-Neto and Giancarlo Pasquali for critical reading of this manuscript. This work was supported by research grants from Fundação de Amparo a Pesquisa do Estado do Rio Grande do Sul (FAPERGS), CAPES and GENOTOX (Laboratório de Genotoxicidade, UFRGS).
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