Extensive domain shuffling in transcription regulators of DNA viruses and implications for the origin of fungal APSES transcription factors View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2002-02-13

AUTHORS

Lakshminarayan M Iyer, Eugene V Koonin, L Aravind

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 endonuclease. The amino-terminal module of the Bro proteins is another, distinct DNA-binding domain (the Bro-N domain) that is present in proteins whose domain architectures parallel those of the KilA-N domain-containing proteins. A detailed analysis of the KilA-N and Bro-N domains and the associated domains points to extensive domain shuffling and lineage-specific gene family expansion within DNA virus genomes. CONCLUSIONS: We define a large class of novel viral DNA-binding proteins and their cellular homologs and identify their domain architectures. On the basis of phyletic pattern analysis we present evidence for a probable viral origin of the fungus-specific cell-cycle regulatory transcription factors containing the APSES DNA-binding domain. We also demonstrate the extensive role of lineage-specific gene expansion and domain shuffling, within a limited set of approximately 24 domains, in the generation of the diversity of virus-specific regulatory proteins. More... »

PAGES

research0012.1-research0012.11

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/gb-2002-3-3-research0012

DOI

http://dx.doi.org/10.1186/gb-2002-3-3-research0012

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1011560169

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/11897024


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