Protein Conservation in Virus Evolution

Abstract

Evolution of viruses is considerably more rapid than that of the cellular organisms that they infect. The reach of sequence‐based evolutionary studies on viruses is therefore rather limited. The tertiary protein structure is generally conserved over longer time periods than the primary one. Indeed, structural studies proved to be more informative for reconstructing deep evolutionary connections between distantly related viruses. It has become apparent that certain viruses infecting hosts from different domains of life are remarkably similar in their virion assembly and architecture, suggesting a common ancestry for these structurally related viruses. Furthermore, the presence of several distinct architectural principles employed by viruses suggested that the origin of the current virosphere has multiple evolutionary origins. Insights obtained from numerous structural studies may not only be successfully used to refine the existing virus classification scheme, but may also lead to a major shift in our understanding on the origin, evolution and organisation of the viral domain. Key Concepts: Tertiary protein structure is conserved over longer periods of time than the primary one and thus allows recognising deep evolutionary connections between viruses that have diverged in a distant past. The ability to build virions (i.e., presence of capsid proteins) is a hallmark feature of viruses that distinguishes them from other mobile genetic elements, such as plasmids and transposons. Structural studies suggest that certain viruses infecting bacteria, archaea and eukaryotes are evolutionarily related. Viral lineage hypothesis predicts a common origin for structurally related viruses, infecting hosts from different domains of life. There are several different viral lineages of structurally distinct viruses, suggesting that the contemporary virosphere has multiple evolutionary origins. The molecular virion complexity shared by viruses in different domains of life suggests that at the time of the last universal cellular ancestor (LUCA) viruses were already very sophisticated.

Structure Unveils Relationships between RNA Virus Polymerases

“…Evolutionarily related proteins typically retain a common structure and similar function, even when their sequences have diverged beyond the limits of current sequence similarity detection [ 18 , 19 , 20 , 21 ]. Consequently, accumulating information on protein structures can be used to reconstruct deep evolutionary relations for functionally and structurally related (viral) proteins [ 22 , 23 ]. Previous structure-based comparisons have revealed substantial structural conservation among the RdRps of (+)RNA and dsRNA viruses [ 10 , 24 , 25 ].…”

Sequence and Structure Analysis of Distantly-Related Viruses Reveals Extensive Gene Transfer between Viruses and Hosts and among Viruses

“…All of them share the presence of the jelly-roll fold ( Figure 3 A). This structural motif has been previously reported to be found in a wide variety of viruses, including ssRNA, ssDNA, dsDNA and dsRNA viruses [ 8 , 59 ]. There are no structural homologs of the jelly-roll capsids among the proteins from cellular organisms, and jelly-roll capsids also belong to the viral hallmark proteins [ 7 ].…”

“…Generally, the similarity of sequences and virion structures is evident only up to the family level. In isolated cases, sequence homology can be detected between proteins of viruses with unrelated architecture, but it is unclear whether this can be attributed to horizontal gene transfer between ancestors of viral families or if this is a sign of a genuine evolutionary link, as discussed in great detail in [ 7 , 8 ] and other related work. It is hypothesized that in certain cases, the conserved viral genes are witnesses of evolutionary processes as ancient as the origin of life itself [ 7 ].…”

“…Another approach to the inference of viral phylogenies, capable of reaching into the distant past, is based on the comparison of the three-dimensional structures of viral capsid proteins [ 9 ]. It is well known that the three-dimensional structure of proteins is conserved over larger evolutionary distances than their sequences, and thus, several viral families can share a common fold of the capsid, although the sequences have diverged beyond similarity detection [ 8 ]. In certain cases, such viruses can be proven to have a common origin, particularly when the Baltimore class is also the same [ 10 ], but the relatedness to viruses of a different Baltimore class is more difficult to establish [ 11 ].…”