Superimposition of Viral Protein Structures: A Means to Decipher the Phylogenies of Viruses

Abstract

Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is lost. Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and thoughts that have led to the current established structure-based phylogeny of viruses: starting from the original observation that the major capsid proteins of plant and animal viruses possess similar folds, to the idea that each virus has an innate “self”. This latter idea fueled the conceptualization of the PRD1-adenovirus lineage whose members possess a major capsid protein (innate “self”) with a double jelly roll fold. Based on this approach, long-range viral evolutionary relationships can be detected allowing the virosphere to be classified in four structure-based lineages. However, this process is not without its challenges or limitations. As an example of these hurdles, we finally touch on the difficulty of establishing structural “self” traits for enveloped viruses showcasing the coronaviruses but also the power of structure-based analysis in the understanding of emerging viruses

Phylogeny of the Varidnaviria Morphogenesis Module: Congruence and Incongruence With the Tree of Life and Viral Taxonomy

“…The Asfarviridae branch between Polintoviruses and Nucleocytoviricota in our Bamfordvirae tree without Poxviridae (Figure 4), whereas they emerged within Megaviricetes in our previous concatenation of the MCP and pATPase, which was limited to Nucleocytoviricota (except Poxviridae) and Polintoviruses (Guglielmini et al, 2019). The grouping of Asfarviridae with Megaviricetes was also observed in the MCP structural tree of Ravantti et al (2020). We did not recover this grouping here and this is possibly due to long-branch attraction of Asfarviridae by the out-group sequences.…”

“…Adenoviridae , which have rather small genomes, have been tentatively included by the ICTV in the phylum Preplasmiviricota and the class Tectiliviricetes ( Koonin et al, 2020 ) ( Table 1 ). However, Adenoviridae exhibit more connection with Nucleocytoviricota than with Tectiliviricetes in a sequence similarity network ( Sinclair et al, 2017 ) and branch far from Tectiliviricetes in a recent MCP structural tree ( Ravantti et al, 2020 ), suggesting that classification of Adenoviridae within Tectiliviricetes could be premature.…”

“…To evaluate the validity of the above scenario and eventually propose new ones, as well as to test the validity of the newly proposed ICTV classification, it is essential to determine the evolutionary history of Varidnaviria based on robust phylogenetic analyses. Several trees based on the structural comparison of MCPs from a set of Bamfordvirae representatives have been published ( Ravantti et al, 2013 , 2020 ). The evolutionary relationships among Bamfordvirae were also investigated using pairwise amino-acid sequence similarities networks ( Sinclair et al, 2017 ; Yutin et al, 2018 ).…”

Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes

“…The results are supported by the analyses of 58 nucleotide sequences of isolates of the three known species whose P15 amino acid sequences cover a spectrum of identity ranging from 14 to 100%. The main predictions have been obtained by integrating the results of different computational methods because of the premise that each of these elements taken in isolation does not allow to draw solid conclusions about the activity and function of a given protein (Omer et al, 2017;Ponting, 2017;Ravantti et al, 2020). Taken them together, we posit a theory that partially describes the evolution of the cilevirus genomes that involves elements denoting the likely close interplay during the coevolutionary history of Brevipalpus-transmitted viruses.…”

Basics for Improved Use of Phages for Therapy

“…For example, double-stranded DNA phages are homologs of herpesviruses [ 32 , 33 ]. Phages in other categories also have eukaryotic virus homologs [ 34 , 35 ]. However, to our knowledge, no coronavirus-like phage has ever been described in a publication.…”