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

Motohiro Akashi,Masaharu Takemura

doi:10.3390/v11030267

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.

Highlights

Understanding the mechanism of genomic replication for all organisms, including the “giant viruses”, is an important scientific endeavor
The most frequently observed type of KOPS sequence was from L. lactis, whereas those of B. subtilis and E. coli were hardly encountered (L. lactis, 50 -GAGAAG-30 : 225; B. subtilis, 50 -GAGAAGGG-30 : 5; E. coli, 50 -GGGNAGGG-30 : 9; Figure 10a). This KOPS distribution pattern was different between the positive and negative strand, and the density graphs showed that these two patterns crossed at the estimated ori position (Figure 10b). These KOPS distribution patterns were analyzed in each bacterial genome, and the results suggested that the density of KOPS on the positive/negative strand switched on the exact points of the ori/ter region (Figure 10c)
The estimated ori region exists at the 382 kb position in the genome, which contains the chi-like sequence recognized by B. subtilis AddA, which is homologous to the UvrD/Rep-like helicase of Acanthamoeba polyphaga mimivirus (APMV)

Summary

Introduction

Understanding the mechanism of genomic replication for all organisms, including the “giant viruses”, is an important scientific endeavor. The first model suggested that the replication of the lagging strand of APMV’s linear genome is mediated by homologous recombination of approximately 617 bp located on both ends of the viral chromosome, similar to T4 phage replication, and is processed with Mimivirus R555 recombinase (Mre11/Rad fusion protein) [3,4]. The second model of replication termination and segregation of APMV was proposed [5]. In this model, the FtsK-like protein ( called packaging ATPase), binds FtsK orienting polar sequences (KOPS) and is localized to both ends of the nucleosome, resulting in chromosome segregation by the recombination of dif sequences [5].

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Discussion

Conclusion