Clandestinovirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis.

Clara Rolland,Bernard La Scola,Dehia Sahmi-Bounsiar,Julien Andreani,Anthony Levasseur,Mart Krupovic

doi:10.3389/fmicb.2021.715608

Abstract

For several decades, the vast world of DNA viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a giant virus named “clandestinovirus,” grown on the amoebal host Vermamoeba vermiformis. This virus was discovered in a mixed co-culture associated with another giant virus, Faustovirus ST1. Clandestinovirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinovirus is most closely related to Acanthamoeba castellanii medusavirus and was considered a member of the proposed Medusaviridae family. However, clandestinovirus genome is 65% larger than that of medusavirus, emphasizing the considerable genome size variation within this virus family. Functional annotation of the clandestinovirus genes suggests that the virus encodes four core histones. Furthermore, clandestinovirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinovirus to optimize the intracellular environment for efficient virus propagation.

Highlights

Exploration of the giant viruses in amoeba began in 2003 with the discovery of Acanthamoeba polyphaga mimivirus (La Scola et al, 2003)
Genomic DNA of clandestinovirus was extracted in two steps: a mechanical treatment was first performed by glass beads acid washed (G4649-500g Sigma) using a FastPrepTM24 5G Grinder at maximum speed (6.5) for 90 s
We considered a gene to belong to a cluster of orthologous genes (COG) if at least one reciprocal best hit was obtained between clandestinovirus and one virus included in the family tested

Summary

Introduction

Exploration of the giant viruses in amoeba began in 2003 with the discovery of Acanthamoeba polyphaga mimivirus (La Scola et al, 2003). The giant viruses are classified into the phylum Nucleocytoviricota, previously designated as Nucleo-cytoplasmic large DNA viruses (NCLDV) (Iyer et al, 2001; Walker et al, 2019; Koonin et al, 2020). Recent progress in metagenomics and sequence assembly made it possible to detect and reconstruct in silico complete genomes of giant viruses from diverse environments (Moniruzzaman et al, 2020a; Schulz et al, 2020b). This contribution enabled the discovery of unexpected metabolic pathways and functions, which were once thought not to be encoded by viruses. This phenomenon appears to be widespread and highlights the need to further characterize those viruses in order to fully understand their global contributions to the evolution and ecology of eukaryotes

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Results

Conclusion