Abstract
Putative promoter motifs have been described in viruses belonging to the nucleocytoplasmic large DNA viruses (NCLDVs) group; however, few studies have been conducted to search for promoter sequences in newly discovered amoebal giant viruses. Faustovirus and kaumoebavirus are two Asfarviridae-related giant viruses belonging to the NCLDVs group. The phylogenetic relationships among these viruses led us to investigate if the promoter regions previously identified in the asfarvirus genome could be shared by its amoebal virus relatives. Previous studies demonstrated the role of A/T-rich motifs as promoters of asfarvirus. In this study, we reinforce the importance of A/T rich motifs in asfarvirus and show that the TATTT and TATATA motifs are also shared in abundance by faustovirus and kaumoebavirus. Here, we demonstrate that TATTT and TATATA are mostly present in faustovirus and kaumoebavirus genomic intergenic regions (IRs) and that they are widely distributed at 0 to -100 bp upstream to the start codons. We observed that putative promoter motifs are present as one to dozens of repetitions in IRs of faustovirus, kaumoebavirus, and asfarvirus, which is similar to that described previously for marseilleviruses. Furthermore, the motifs were found in most of the upstream regions of the core genes of faustovirus, kaumoebavirus, and asfarvirus, which suggests that the motifs could already be present in the ancestor of these viruses before the irradiation of this group. Our work provides an in-depth analysis of the putative promoter motifs present in asfarvirus, kaumoebavirus, and faustovirus, which reinforces the relationship among these viruses.
Highlights
The nucleocytoplasmic large DNA viruses (NCLDVs) group has been expanding in number and diversity since the discovery of the Acanthamoeba polyphaga mimivirus (APMV) in 2003 (La Scola et al, 2003; Boyer et al, 2009; Pagnier et al, 2013; Philippe et al, 2013; Legendre et al, 2014, 2015)
The search for repeated motifs in the intergenic regions (IRs) of faustovirus and kaumoebavirus revealed the wide distribution of the TATTT and TATATA motifs that play a promoter role in asfarvirus (Rodríguez et al, 1996; GarcíaEscudero and Viñuela, 2000; Rodríguez and Salas, 2013)
Given the phylogenetic proximity demonstrated between faustovirus, kaumoebavirus, and asfarvirus and associated with the wide distribution of the same motifs in the IR of these viruses, we suggest that the regions containing the motifs TATTT and TATATA can play an important role in the gene expression of faustovirus and kaumoebavirus
Summary
The nucleocytoplasmic large DNA viruses (NCLDVs) group has been expanding in number and diversity since the discovery of the Acanthamoeba polyphaga mimivirus (APMV) in 2003 (La Scola et al, 2003; Boyer et al, 2009; Pagnier et al, 2013; Philippe et al, 2013; Legendre et al, 2014, 2015). Faustovirus has a double-stranded DNA with a circular shape genome (except for the Faustovirus Liban strain for which a linear genome was suggested) with approximately 466 kbp encoding 451 predicted proteins. These viruses form 200 nm particles (icosahedral symmetry) with a unique structure and two protein shells (Reteno et al, 2015; Benamar et al, 2016; Klose et al, 2016; Louazani et al, 2017). A phylogenetic analysis revealed a relationship between faustoviruses and asfarvirus, which suggests a shared origin (Reteno et al, 2015; Benamar et al, 2016)
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