A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses

Resources to Discover and Use Short Linear Motifs in Viral Proteins

Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. Host cells cannot easily coordinate changes to conserved motif recognition and binding interfaces under selective pressure to maintain critical signaling pathways. SLiMs offer potential for use in synthetic biology, such as better immunogens and therapies, but may also present biosecurity challenges. We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. As the number of examples continues to grow, knowledge management tools are essential to help organize and compare new findings.

Virophages and Their Interactions with Giant Viruses and Host Cells

Virophages are small dsDNA viruses that were first isolated in association with some giant viruses (GVs), and then found in metagenomics samples. They encode about 20–34 proteins. Some virophages share protein similarity with Maverick/Polinton transposons or are considered as a provirophage, whereas about half of the protein’s repertoire remain of unknown function. In this review, we aim to highlight the current understanding of the biology of virophages, as well as their interactions with giant viruses and host cells. Additionally, the virophage proteomes were analyzed to find the functional domains that distinguish each virophage. This bioinformatics analysis will benefit further experimental investigations to understand the protein-protein interactions between virophages, giant viruses, and host cells.

A comparative review of viral entry and attachment during large and giant dsDNA virus infections

Viruses enter host cells via several mechanisms, including endocytosis, macropinocytosis, and phagocytosis. They can also fuse at the plasma membrane and can spread within the host via cell-to-cell fusion or syncytia. The mechanism used by a given viral strain depends on its external topology and proteome and the type of cell being entered. This comparative review discusses the cellular attachment receptors and entry pathways of dsDNA viruses belonging to the families Adenoviridae, Baculoviridae, Herpesviridae and nucleocytoplasmic large DNA viruses (NCLDVs) belonging to the families Ascoviridae, Asfarviridae, Iridoviridae, Phycodnaviridae, and Poxviridae, and giant viruses belonging to the families Mimiviridae and Marseilleviridae as well as the proposed families Pandoraviridae and Pithoviridae. Although these viruses have several common features (e.g., topology, replication and protein sequence similarities) they utilize different entry pathways to infect wide-range of hosts, including humans, other mammals, invertebrates, fish, protozoa and algae. Similarities and differences between the entry methods used by these virus families are highlighted, with particular emphasis on viral topology and proteins that mediate viral attachment and entry. Cell types that are frequently used to study viral entry are also reviewed, along with other factors that affect virus-host cell interactions.