Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors.docVIP

/2002/3/3/research/0012.1 Research Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors Lakshminarayan M Iyer, Eugene V Koonin and L Aravind Address: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. Correspondence: L Aravind. E-mail: aravind@ Published: 13 February 2002 Received: 16 November 2001 Revised: 9 January 2002 Accepted: 10 January 2002 GenomeBiology 2002, 3(3):research0012.1–0012.11 The electronic version of this article is the complete one and can be found online at /2002/3/3/research/0012 ? 2002 Iyer et al., licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: Viral DNA-binding proteins have served as good models to study the biochemistry of transcription regulation and chromatin dynamics. Computational analysis of viral DNA-binding regulatory proteins and identification of their previously undetected homologs encoded by cellular genomes might lead to a better understanding of their function and evolution in both viral and cellular systems. Results: The phyletic range and the conserved DNA-binding domains of the viral regulatory proteins of the poxvirus D6R/N1R and baculoviral Bro protein families have not been previously defined. Using computational analysis, we show that the amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain is suggested to be homologous to the fungal DNA-binding APSES domain. We provide evidence for the KilA-N and APSES domains sharing a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endon