A novel evolutionary strategy revealed in the Phaeoviruses

Phaeoviruses infect the brown algae, which are major contributors to primary production of coastal waters and estuaries. They exploit a Persistent evolutionary strategy akin to a K- selected life strategy via genome integration and are the only known representatives to do so within the giant algal viruses that are typified by r- selected Acute lytic viruses. In screening the genomes of five species within the filamentous brown algal lineage, here we show an unprecedented diversity of viral gene sequence variants especially amongst the smaller phaeoviral genomes. Moreover, one variant shares features from both the two major sub-groups within the phaeoviruses. These phaeoviruses have exploited the reduction of their giant dsDNA genomes and accompanying loss of DNA proofreading capability, typical of an Acute life strategist, but uniquely retain a Persistent life strategy

Phycodnavirus Potassium Ion Channel Proteins Question the Virus Molecular Piracy Hypothesis

Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K+ channels. To determine if these viral K+ channels are the product of molecular piracy from their hosts, we compared the sequences of the K+ channel pore modules from seven phycodnaviruses to the K+ channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K+ channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K+ channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K+ channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K+ channels in algae and perhaps even all cellular organisms

Life-Cycle and Genome of OtV5, a Large DNA Virus of the Pelagic Marine Unicellular Green Alga Ostreococcus tauri

Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon

The <i>Ectocarpus</i> genome and the independent evolution of multicellularity in brown algae

Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related1. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1).We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic2 approaches to explore these and other aspects of brown algal biology further

Comparisons of two large phaeoviral genomes and evolutionary implications

The evolution of viral genomes has recently attracted considerable attention. We compare the sequences of two large viral genomes, EsV-1 and FirrV-1, belonging to the family of phaeoviruses which infect different species of marine brown algae. Althoug

A DNA virus infecting the marine brown alga Pilayella littoralis (Ectocarpales, Phaeophyceae) in culture

A new large DNA virus (PlitV-1) infects the marine filamentous brown alga Pilayella littoralis. It was collected in Alaska and infects other P. littoralis isolates of different geographic origin. The virus has an icosahedral capsid of c. 161 nm in diam

Phycodnaviridae - large DNA algal viruses

Members and prospective members of the family Phycodnaviridae are large icosahedral, dsDNA (180 to 560 kb) viruses that infect eukaryotic algae. The genomes of two phycodnaviruses have been sequenced: the 331 kb genome of Paramecium bursaria chlorella

The complete DNA sequence of the Ectocarpus siliculosus virus EsV-1 genome

The Ectocarpus siliculosus Virus-1, EsV-1, is the type-species of a genus of Phycodnaviridae, the phaeoviruses, infecting marine filamentous brown algae. The EsV-1 genome of 335,593 by contains tandem and dispersed repetitive elements in addition to a

PERSONALIZED IMMUNE DIAGNOSTICS: EPITOPE MAPPING OF THE IMMUNOME

Statistical phage display is a highly complex, but rapid and efficient way to identify “binding peptides” from a unique and specially designed library. It avoids repeated selection rounds and can therefore provide much more complex data than just a few sequences usually obtained with repeated peptide library selection. The complexity of the data analyzed is sufficient to cover hundreds of potential binder/target combinations in parallel.Applying this novel way to generate and analyze data from peptide phage display with antibodies allows to predict potential epitopes at amino acid resolution. Fingerprinting of monoclonal antibodies reveals the large variety of peptides binding to any given antibody. Independent of such laborious and failure prone methods like peptide arrays or phage display with antigen gene fragments. Surprisingly easy this can explain the specificity of antibodies and it is a valuable tool for antibody quality control.Beyond the application to individual antibodies we are able to analyze the immunome of patient sera. Theoretically, there are hundreds of antibody molecules for each recently encountered antigen epitope in a few µl. This is enough to define individual antibody epitopes. Since a single patient sample allows to record the entire immunome data, there is a tremendous amount of information hidden in the data sets we obtain. Nevertheless, all patients show different epitope patterns and for the generation of diagnostic tools we must compare many different sera. Results from examples will be given for allergic disease, viral infection diagnostics and the vaccine imprint on the immunome of one individual patient history.In infectious disease diagnostics (e.g. EBV, COVID-19, influenza) epitope-based kits can provide a robust analysis of existing and past disease as well as effective monitoring of vaccine efficacy. The aspect that the immune system carries the memories of antigens at least for many months allows a complex analysis even identifying different viral strains in a single experiment.In allergic disease we carried out epitope mapping with hundreds of sera from patients with sensibilization to allergenic food ingredients. Predicted epitopes were validated by binding IgE and IgG from many more patient sera for the main food allergy agents. Since peptide epitope diagnostics do not suffer from the undefined cross reactivities of present methods, we are gathering now a rather different understanding of what food allergies really are. In particular, we can also use IgG measurement based on immunoassays with epitopes, which has been regarded as impossible.Presently we are extending our work also in auto-immune diseases connected to long-COVID and psychiatric diseases