Viruses infecting marine brown algae

Giant viruses in the environment: their origins and evolution

The recent identification of giant viruses has raised important questions, not only regarding their origin and evolution, but also regarding the differentiation between viruses and living organisms. These viruses possess large genomes encoding genes potentially involved in various metabolic processes and even protein synthesis, indicating their putative autonomy. Giant viruses of the Phycodnaviridae and Mimiviridae families appear to share a common evolutionary ancestor with members of the nucleo-cytoplasmic large DNA viruses. Many giant viruses are associated with protists in aquatic environments and might have evolved in protist cells. They may therefore play important roles in material cycling in natural ecosystems. With the advent of environmental metagenomic projects, there will be more chances to encounter novel giant viruses in the future.

Acquisition and maintenance of resistance to viruses in eukaryotic phytoplankton populations

Viruses are known to play a key role in the regulation of eukaryotic phytoplankton population densities; however, little is known about the mechanisms of how they interact with their hosts and how phytoplankton populations mediate their regulations. Viruses are obligate parasites that depend on host cell machinery for their dissemination in the environment (most of the time through host cell lysis that liberates many new particles). But viruses also depend on a reliable host population to carry on their replication before losing their viability. How do hosts cells survive when they coexist with their viruses? We show that clonal lines of three picoeukaryotic green algae (i.e. Bathycoccus sp., Micromonas sp., Ostreococcus tauri) reproducibly acquire resistance to their specific viruses following a round of infection. Our observations show that two mechanisms of resistance may operate in O. tauri. In the first resistant type, viruses can attach to their host cells but no new particles develop. In the second one, O. tauri acquires tolerance to its virus and releases these viruses consistently. These lines maintained their resistance over a 3-year period, irrespective of whether or not they were re-challenged with new viral inoculations. Co-culturing resistant and susceptible lines revealed resistance to be associated with reduced host fitness in terms of growth rate.

DNA viruses: the really big ones (giruses)

Viruses with genomes greater than 300 kb and up to 1200 kb are being discovered with increasing frequency. These large viruses (often called giruses) can encode up to 900 proteins and also many tRNAs. Consequently, these viruses have more protein-encoding genes than many bacteria, and the concept of small particle/small genome that once defined viruses is no longer valid. Giruses infect bacteria and animals although most of the recently discovered ones infect protists. Thus, genome gigantism is not restricted to a specific host or phylogenetic clade. To date, most of the giruses are associated with aqueous environments. Many of these large viruses (phycodnaviruses and Mimiviruses) probably have a common evolutionary ancestor with the poxviruses, iridoviruses, asfarviruses, ascoviruses, and a recently discovered Marseillevirus. One issue that is perhaps not appreciated by the microbiology community is that large viruses, even ones classified in the same family, can differ significantly in morphology, lifestyle, and genome structure. This review focuses on some of these differences than on extensive details about individual viruses.

Phycodnaviruses: a peek at genetic diversity

The family Phycodnaviridae encompasses a diverse collection of large icosahedral, dsDNA viruses infecting algae. These viruses have genomes ranging from 160 to 560kb. The family consists of six genera based initially on host range and supported by sequence comparisons. The family is monophyletic with branches for each genus, but the phycodnaviruses have evolutionary roots that connect with several other families of large DNA viruses, referred to as the nucleocytoplasmic large DNA viruses (NCLDV). The genomes of members in three genera in the Phycodnaviridae have recently been sequenced and the purpose of this manuscript is to summarize these data. The viruses have diverse genome structures, some with large regions of non-coding sequence and others with regions of single-stranded DNA. Typically, phycodnaviruses have the coding capacity for hundreds of genes. The genome analyses have revealed in excess of 1000 unique genes, with only 14 homologous genes held in common among the three genera of the phycodnavirses sequenced to date. Thus, the gene diversity far exceeds the number of so-called "core" genes. Little is known about the replication of these viruses, but the consequences of these infections of the phytoplankton have global affects, including altered geochemical cycling and weather patterns.

A hypothesis for DNA viruses as the origin of eukaryotic replication proteins

The eukaryotic replicative DNA polymerases are similar to those of large DNA viruses of eukaryotic and bacterial T4 phages but not to those of eubacteria. We develop and examine the hypothesis that DNA virus replication proteins gave rise to those of eukaryotes during evolution. We chose the DNA polymerase from phycodnavirus (which infects microalgae) as the basis of this analysis, as it represents a virus of a primitive eukaryote. We show that it has significant similarity with replicative DNA polymerases of eukaryotes and certain of their large DNA viruses. Sequence alignment confirms this similarity and establishes the presence of highly conserved domains in the polymerase amino terminus. Subsequent reconstruction of a phylogenetic tree indicates that these algal viral DNA polymerases are near the root of the clade containing all eukaryotic DNA polymerase delta members but that this clade does not contain the polymerases of other DNA viruses. We consider arguments for the polarity of this relationship and present the hypothesis that the replication genes of DNA viruses gave rise to those of eukaryotes and not the reverse direction.