Characterization of Mimivirus DNA Topoisomerase IB Suggests Horizontal Gene Transfer between Eukaryal Viruses and Bacteria

Abstract

Mimivirus, a parasite of Acanthamoeba polyphaga, is the largest DNA virus known; it encodes dozens of proteins with imputed functions in nucleic acid transactions. Here we produced, purified, and characterized mimivirus DNA topoisomerase IB (TopIB), which we find to be a structural and functional homolog of poxvirus TopIB and the poxvirus-like topoisomerases discovered recently in bacteria. Arginine, histidine, and tyrosine side chains responsible for TopIB transesterification are conserved and essential in mimivirus TopIB. Moreover, mimivirus TopIB is capable of incising duplex DNA at the 5-CCCTT cleavage site recognized by all poxvirus topoisomerases. Based on the available data, mimivirus TopIB appears functionally more akin to poxvirus TopIB than bacterial TopIB, despite its greater primary structure similarity to the bacterial TopIB group. We speculate that the ancestral bacterial/viral TopIB was disseminated by horizontal gene transfer within amoebae, which are permissive hosts for either intracellular growth or persistence of many present-day bacterial species that have a type IB topoisomerase.DNA topoisomerases are found in all free-living organisms; they modify DNA topology by introducing reversible enzymelinked breaks in the DNA phosphodiester backbone (reviewed in reference 6). Topoisomerases accomplish this either by cleaving one strand of the DNA duplex and passing the intact complementary strand through the nick (type I topoisomerase) or by cleaving both strands and passing an intact duplex segment through the double-strand break (type II topoisomerase). Type II topoisomerases are oligomeric proteins that form covalent tyrosyl-5Ј-phosphodiester linkages at the two sites of strand scission. Type I enzymes are monomeric and are classified as having either type IA or type IB mechanisms. Type IA enzymes form a tyrosyl-5Ј-phosphodiester linkage at the break site, whereas type IB topoisomerases generate a tyrosyl-

Giant virus with a remarkable complement of genes infects marine zooplankton

“…CroV TopoIB is the first viral homolog of the eukaryotic subfamily, whereas the TopoIB encoded by Mimivirus falls within the bacterial group (SI Appendix, Fig. S7) and is functionally more similar to the poxvirus enzymes (23). Despite apparently different evolutionary trajectories, the presence of three Topo genes in CroV and Mimivirus suggests a crucial role for these enzymes in transcription, replication, or packaging of giant virus genomes.…”

Gene Exchange and the Origin of Giant Viruses

“…Additionally, a topoisomerase might be involved in promoting recombination, Vaccinia virus topoisomerase IB possesses several biochemical properties that support this view [34] . Moreover, a topoisomerase IB gene from Mimivirus produces a biochemically similar enzyme [35] .…”

Mimivirus Giant Particles Incorporate a Large Fraction of Anonymous and Unique Gene Products

“…Based on its highly specific characteristics, this double-stranded-DNA icosahedral virus (47) is the first member of the new Mimiviridae family (33,43). Computational annotation of its 1.2-Mb genome (33) revealed many atypical features, including the presence of key translation enzymes, a full complement of DNA repair pathway components, and the unique presence of three different topoisomerases (of types IA, IB, and II) (2,33). Another unique characteristic of mimivirus is the presence of nearly identical promoter sequence motifs upstream of half of its 911 proteinencoding genes (42), which are presumably associated with proteins expressed during the early or late-early phase.…”