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Viruses 2019, 11(3), 267; https://doi.org/10.3390/v11030267

Gram-Positive Bacteria-Like DNA Binding Machineries Involved in Replication Initiation and Termination Mechanisms of Mimivirus

Laboratory of Biology, Department of Liberal Arts, Faculty of Science, Tokyo University of Science, Shinjuku, Tokyo 162-8601, Japan
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Received: 29 January 2019 / Revised: 14 March 2019 / Accepted: 14 March 2019 / Published: 17 March 2019
(This article belongs to the Special Issue Virus Bioinformatics)
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Abstract

The detailed mechanisms of replication initiation, termination and segregation events were not yet known in Acanthamoeba polyphaga mimivirus (APMV). Here, we show detailed bioinformatics-based analyses of chromosomal replication in APMV from initiation to termination mediated by proteins bound to specific DNA sequences. Using GC/AT skew and coding sequence skew analysis, we estimated that the replication origin is located at 382 kb in the APMV genome. We performed homology-modeling analysis of the gamma domain of APMV-FtsK (DNA translocase coordinating chromosome segregation) related to FtsK-orienting polar sequences (KOPS) binding, suggesting that there was an insertion in the gamma domain which maintains the structure of the DNA binding motif. Furthermore, UvrD/Rep-like helicase in APMV was homologous to Bacillus subtilis AddA, while the chi-like quartet sequence 5′-CCGC-3′ was frequently found in the estimated ori region, suggesting that chromosomal replication of APMV is initiated via chi-like sequence recognition by UvrD/Rep-like helicase. Therefore, the replication initiation, termination and segregation of APMV are presumably mediated by DNA repair machineries derived from gram-positive bacteria. Moreover, the other frequently observed quartet sequence 5′-CGGC-3′ in the ori region was homologous to the mitochondrial signal sequence of replication initiation, while the comparison of quartet sequence composition in APMV/Rickettsia-genome showed significantly similar values, suggesting that APMV also conserves the mitochondrial replication system acquired from an ancestral genome of mitochondria during eukaryogenesis. View Full-Text
Keywords: DNA replication; ori; mitochondria; Rickettsia; gram-positive bacteria; APMV; Mimivirus; giant virus; eukaryogenesis DNA replication; ori; mitochondria; Rickettsia; gram-positive bacteria; APMV; Mimivirus; giant virus; eukaryogenesis
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Akashi, M.; Takemura, M. Gram-Positive Bacteria-Like DNA Binding Machineries Involved in Replication Initiation and Termination Mechanisms of Mimivirus. Viruses 2019, 11, 267.

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