Analyses of the Kroon Virus Major Capsid Gene and Its Transcript Highlight a Distinct Pattern of Gene Evolution and Splicing among Mimiviruses

Abstract

The inclusion of members in the putative monophyletic nucleocytoplasmic large DNA virus (NCLDV) group is based on genomic and phylogenomic patterns. This shows that, along with other viral families, they share a set of genes known as core or "hallmark genes," including the gene for the major capsid protein (MCP). Although previous studies have suggested that the maturation of mimivirus MCP transcripts is dependent on splicing, there is little information about the processing of this transcript in other mimivirus isolates. Here we report the characterization of a new mimivirus isolate, called Kroon virus (KV) mimivirus. Analysis of the structure, synteny, and phylogenetic relationships of the MCP genes in many mimivirus isolates revealed a remarkable variation at position and types of intronic and exonic regions, even for mimiviruses belonging to the same lineage. In addition, sequencing of KV and Acanthamoeba polyphaga mimivirus (APMV) MCP transcripts has shown that inside the family, even related giant viruses may present different ways to process the MCP mRNA. These results contribute to the understanding of the genetic organization and evolution of the MCP gene in mimiviruses. Mimivirus isolates have been obtained by prospecting studies since 2003. Based on genomic and phylogenomic studies of conserved genes, these viruses have been clustered together with members of six other viral families. Although the major capsid protein (MCP) gene is an important member of the so-called "hallmark genes," there is little information about the processing and structure of this gene in many mimivirus isolates. In this work, we have analyzed the structure, synteny, and phylogenetic relationships of the MCP genes in many mimivirus isolates; these genes showed remarkable variation at position and types of intronic and exonic regions, even for mimiviruses belonging to the same lineage. These results contribute to the understanding of the genetic organization and evolution of the MCP gene in mimiviruses.

Fifteen Marseilleviruses Newly Isolated From Three Water Samples in Japan Reveal Local Diversity of Marseilleviridae

“…In this study, we successfully isolated at least 12 new viruses with different MCP genes in the family Marseilleviridae from three sampling locations in Japan. MCP is one of the core genes of NCLDVs and thus has been used for molecular phylogenetic analysis of giant viruses as a part of concatenated genes (Thomas et al, 2011; Dornas et al, 2016; Dos Santos et al, 2016; Chatterjee and Kondabagil, 2017; Boratto et al, 2018). Using the MCP gene alone, we reconstructed a molecular phylogenetic tree.…”

Faustovirus E12 Transcriptome Analysis Reveals Complex Splicing in Capsid Gene

“…This gene was depicted as composed of three exons separated by two introns. A recent study compared MCP gene splicing profiles in Mimiviridae members from lineages A, B, and C and showed a lineage-independent variation in the structure and synteny of exons and intronic regions of this gene ( Boratto et al, 2018 ). Introns were also detected in other conserved gene from giant viruses of amoebae, including those encoding DNA-dependent RNA polymerases and DNA polymerases ( Yoosuf et al, 2012 ; Philippe et al, 2013 ; Deeg et al, 2018 ).…”

Structural and Proteomic Characterization of the Initiation of Giant Virus Infection

“…A hallmark of newly discovered giant viruses (GVs) is their incredibly complex biology, including gargantuan capsids and large genomes. The sheer size and complexity of these viruses, especially the inclusion of ''junk'' DNA in the form of introns (Azza et al, 2009;Boratto et al, 2018), challenges the canonical view of viruses as small, streamlined, and efficient killing machines. For example, most GVs are larger than 300 nm and many have genomes exceeding 1 MB, containing an estimated 1,000+ open reading frames (Colson et al, 2017).…”