A giant virus in amoebae

Broad spectrum of mimiviridae virophage allows its isolation using a mimivirus reporter

The giant virus Mimiviridae family includes 3 groups of viruses: group A (includes Acanthamoeba polyphaga Mimivirus), group B (includes Moumouvirus) and group C (includes Megavirus chilensis). Virophages have been isolated with both group A Mimiviridae (the Mamavirus strain) and the related Cafeteria roenbergensis virus, and they have also been described by bioinformatic analysis of the Phycodnavirus. Here, we found that the first two strains of virophages isolated with group A Mimiviridae can multiply easily in groups B and C and play a role in gene transfer among these virus subgroups. To isolate new virophages and their Mimiviridae host in the environment, we used PCR to identify a sample with a virophage and a group C Mimiviridae that failed to grow on amoeba. Moreover, we showed that virophages reduce the pathogenic effect of Mimivirus (plaque formation), establishing its parasitic role on Mimivirus. We therefore developed a co-culture procedure using Acanthamoeba polyphaga and Mimivirus to recover the detected virophage and then sequenced the virophage's genome. We present this technique as a novel approach to isolating virophages. We demonstrated that the newly identified virophages replicate in the viral factories of all three groups of Mimiviridae, suggesting that the spectrum of virophages is not limited to their initial host.

A new species of nucleo-cytoplasmic large DNA virus (NCLDV) associated with mortalities in Manitoba lake sturgeon Acipenser fulvescens

A newly discovered virus, Namao virus, associated with morbidity and mortality, was detected among juvenile lake sturgeon Acipenser fulvescens being propagated by a conservation stocking program for this endangered species in Manitoba, Canada. The outbreaks resulted in cumulative mortalities of 62 to 99.6% among progeny of wild Winnipeg River or Nelson River lake sturgeon and occurred at 2 geographically separate facilities. Namao virus was detected in almost 94% of the moribund or dead lake sturgeon according to a conventional polymerase chain reaction (cPCR) test that is based upon amplification of a 219 bp fragment of the virus major capsid protein (MCP). The virus itself was large (242 to 282 nm) and icosahedral-shaped with 2 capsids and a condensed bar-shaped core. It was found in virus factories within the host cell cytoplasm and displayed a tropism for the integument. Namao virus caused cellular changes characterized by enlarged eosinophilic epithelial cells in the gills and skin. Samples suspected of containing Namao virus did not have cytopathic effects on primary lake sturgeon or established white sturgeon cell lines. However, viral nucleic acid was detected in the former after prolonged incubation periods. Using primers designed from conserved regions of the MCP from NCLDVs, an estimated 95 to 96% of the Namao virus MCP open reading frame was captured. Phylogenetic analysis using the MCP of Namao virus and 27 other NCLDVs suggested that Namao virus and white sturgeon iridovirus share a common evolutionary past and might be members of the family Mimiviridae or a new, as yet unrecognized, virus family.

Amoebae as battlefields for bacteria, giant viruses, and virophages

When amoebae are simultaneously infected with Acanthamoeba polyphaga Mimivirus (APM) and the strictly intracellular BABL1 bacterium, the latter is always lost after serial subculturing. We showed that the virophage Sputnik 1, by reducing APM fitness, preserved BABL1 growth in acute and chronic models. This capability of a virophage to modulate the virulence of mimiviruses highlights the competition that occurs between them during natural host infection.

Acanthamoeba polyphaga mimivirus virophage seroconversion in travelers returning from Laos

During January 2010, a husband and wife returned from Laos to France with probable parasitic disease. Increased antibodies against an Acanthamoeba polyphaga mimivirus virophage indicated seroconversion. While in Laos, they had eaten raw fish, a potential source of the virophage. This virophage, associated with giant viruses suspected to cause pneumonia, could be an emerging pathogen.

High-throughput isolation of giant viruses of the Mimiviridae and Marseilleviridae families in the Tunisian environment

Giant viruses of the Megavirales order have been recently isolated from aquatic environments and have long been neglected because they are removed from samples during viral purification for viral metagenomic studies. Due to bacterial overgrowth and susceptibility to high concentrations of antibiotics, isolation by amoeba co-culture has a low efficiency and is highly time-consuming. Thus, few environments have been exhaustively investigated to date, although the ubiquitous distribution of the Acanthamoeba sp. suggests that these viruses could also be ubiquitous. In this work, we have implemented a high-throughput method to detect amoebae lysis on agar plates that allows the testing of hundreds of samples in a few days. Using this procedure, a total of 11 new Marseilleviridae strains and four new Mimiviridae strains, including a virus infected with a virophage, were isolated from 1000 environmental samples from Tunisia. Of these, four corresponded to new genotypic variants. These isolates are the first African environmental isolates identified from these two families, and several samples were obtained from a hypersaline aquatic environment. These results demonstrate that this technique can be used for the evaluation and characterization of large collections of giant viruses to provide insight into understanding their ecology.

[The role of atypical microorganisms and viruses in severe acute community-acquired pneumonia]

Usually, intensivists do not focus on atypical bacteria and viruses in severe community-acquired pneumonia (CAP). Only Legionella pneumophila and influenza virus, following the recent H1N1 influenza pandemic, are routinely suggested as responsible agents. However, CAP due to atypical bacteria may represent up to 44% of all CAP. Viral CAP is considered less severe than the usual bacterial ones, although 25% of them warrant hospitalization and 15% result in severe sepsis. Even though L. pneumophila is the most frequently atypical pathogen involved in severe cases, Mycoplasma pneumoniae may be responsible for multiorgan failure. To date, tools including detection of Legionella antigen in urine and Mycoplasma using polymerase chain reaction (PCR) allow rapid and accurate diagnosis. The treatment is based on macrolides and fluoroquinolones that can be associated in severe Legionnaire diseases. The presence of virus in CAP, either alone or in association with bacteria, has been demonstrated using molecular biology tests. These techniques also allowed the identification of several new viruses in CAP. However, the exact role of these detected viruses in CAP as well as the efficiency of antiviral therapy still represent major unsolved concerns.

Translation in giant viruses: a unique mixture of bacterial and eukaryotic termination schemes

Mimivirus and Megavirus are the best characterized representatives of an expanding new family of giant viruses infecting Acanthamoeba. Their most distinctive features, megabase-sized genomes carried in particles of size comparable to that of small bacteria, fill the gap between the viral and cellular worlds. These giant viruses are also uniquely equipped with genes coding for central components of the translation apparatus. The presence of those genes, thought to be hallmarks of cellular organisms, revived fundamental interrogations on the evolutionary origin of these viruses and the link they might have with the emergence of eukaryotes. In this work, we focused on the Mimivirus-encoded translation termination factor gene, the detailed primary structure of which was elucidated using computational and experimental approaches. We demonstrated that the translation of this protein proceeds through two internal stop codons via two distinct recoding events: a frameshift and a readthrough, the combined occurrence of which is unique to these viruses. Unexpectedly, the viral gene carries an autoregulatory mechanism exclusively encountered in bacterial termination factors, though the viral sequence is related to the eukaryotic/archaeal class-I release factors. This finding is a hint that the virally-encoded translation functions may not be strictly redundant with the one provided by the host. Lastly, the perplexing occurrence of a bacterial-like regulatory mechanism in a eukaryotic/archaeal homologous gene is yet another oddity brought about by the study of giant viruses.

Giant viruses, such as Mimivirus and Megavirus, have huge near-micron-sized particles and possess more genes than several cellular organisms. Furthermore their genomes encode functions not supposed to be in a virus, such as components of the protein translation apparatus. Since Lwoff in 1957, viruses are defined as ultimate obligate intracellular parasites from their need to hijack the peptide synthesis machinery of their host to replicate. We looked at the Mimivirus and Megavirus proteins that recognize the stop codons, the translation termination factors. We found that these genes contain two internal stop codons, meaning that their translation bypasses two distinct stop codons to produce a functional translation termination factor. These types of autoregulatory mechanisms are found in bacterial termination factors, although it involves only a single internal stop codon and not two, and are absent from their eukaryotic and archaeal homologs. Despite these bacterial-like features, giant viruses' termination factors have sequences that do not resemble bacterial genes but are clearly related to the eukaryotic and archaeal termination factors. Thus, giant viruses' termination factors surprisingly combine elements from eukaryotes/archaea and bacteria.

An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales

BACKGROUND

Horizontal gene transfer (HGT) is considered to be a major force driving the evolutionary history of prokaryotes. HGT is widespread in prokaryotes, contributing to the genomic repertoire of prokaryotic organisms, and is particularly apparent in Rickettsiales genomes. Gene gains from both distantly and closely related organisms play crucial roles in the evolution of bacterial genomes. In this work, we focus on genes transferred from distantly related species into Rickettsiales species.

RESULTS

We developed an automated approach for the detection of HGT from other organisms (excluding alphaproteobacteria) into Rickettsiales genomes. Our systematic approach consisted of several specialized features including the application of a parsimony method for inferring phyletic patterns followed by blast filter, automated phylogenetic reconstruction and the application of patterns for HGT detection. We identified 42 instances of HGT in 31 complete Rickettsiales genomes, of which 38 were previously unidentified instances of HGT from Anaplasma, Wolbachia, Candidatus Pelagibacter ubique and Rickettsia genomes. Additionally, putative cases with no phylogenetic support were assigned gene ontology terms. Overall, these transfers could be characterized as "rhizome-like".

CONCLUSIONS

Our analysis provides a comprehensive, systematic approach for the automated detection of HGTs from several complete proteome sequences that can be applied to detect instances of HGT within other genomes of interest.

"Marseilleviridae", a new family of giant viruses infecting amoebae

The family "Marseilleviridae" is a new proposed taxon for giant viruses that infect amoebae. Its first member, Acanthamoeba polyphaga marseillevirus (APMaV), was isolated in 2007 by culturing on amoebae a water sample collected from a cooling tower in Paris, France. APMaV has an icosahedral shape with a diameter of ≈250 nm. Its genome is a double-stranded circular DNA that is 368,454 base pairs (bp) in length. The genome has a GC content of 44.7 % and is predicted to encode 457 proteins. Phylogenetic reconstructions showed that APMaV belongs to a new viral family among nucleocytoplasmic large DNA viruses, a group of viruses that also includes Acanthamoeba polyphaga mimivirus (APMV) and the other members of the family Mimiviridae as well as the members of the families Poxviridae, Phycodnaviridae, Iridoviridae, Ascoviridae, and Asfarviridae. In 2011, Acanthamoeba castellanii lausannevirus (ACLaV), another close relative of APMaV, was isolated from river water in France. The ACLaV genome is 346,754 bp in size and encodes 450 genes, among which 320 have an APMaV protein as the closest homolog. Two other giant viruses closely related to APMaV and ACLaV have been recovered in our laboratory from a freshwater sample and a human stool sample using an amoebal co-culture method. The only currently identified hosts for "marseilleviruses" are Acanthamoeba spp. The prevalence of these viruses in the environment and in animals and humans remains to be determined.

Prevalence of Acanthamoeba and superbugs in a clinical setting: coincidence or hyperparasitism?

Antibacterial strategies to eradicate superbugs from hospitals/nursing homes have had limited success, suggesting the need for employing innovative preventative measures and better understanding of the prevalence of microbial pathogens in close proximity of susceptible populations. A total of 120 environmental samples were collected from the Aga Khan University hospital. Amoebae were identified using morphological characteristics as well as PCR using genus-specific primers, while bacteria were identified using standard biochemical testing. Out of 120 samples tested, 52 (43.3 %) samples were positive for Acanthamoeba, while all 120 (100 %) samples were positive for bacteria. Following bacterial identification, samples showed mixed bacterial populations. Out of 120 samples, 76 (63.3 %) samples were positive for Bacillus spp., 64 (53.3 %) samples were positive for Corynebacterium spp., 32 (26.6 %) samples were positive for Staphylococcus spp., and 9 (7.5 %) samples were positive for Micrococcus spp. The antibiotic susceptibility showed that all bacterial isolates recovered were multiple drug-resistant. The current findings suggest that Acanthamoeba and bacteria coexist in a clinical environment. Given that Acanthamoeba can harbor bacteria, anti-amoebic approaches may represent a strategy in eradicating "superbugs" from the clinical setting in addition to the current measures.

Acanthamoeba spp. as vehicle and reservoir of adenoviruses

Adenoviruses are important pathogens which are responsible for human enteritic, respiratory and eye infections. These viruses have been found to be prevalent in several natural and artificial water reservoirs worldwide. Free-living amoebae (FLA) have been recovered from similar water reservoirs, and it has been shown that FLA may act as reservoirs or vehicles of various microorganisms living in the same environment. To examine the ability of FLA to harbour adenoviruses, an in vitro study was conducted. Several Acanthamoeba strains were ‘co-cultivated’ with adenoviruses (adenoviruses 11 and 41), grown on A549 cells, using a proven test protocol. After phagocytosis and ingestion, the adenoviruses could be found within the cytoplasm of the Acanthamoeba trophozoites. The intake of the viruses into the cytoplasm of the trophozoites was demonstrated in an Acanthamoeba castellanii strain with the help of fluorescence microscopy and electron microscopy. An adenovirus DFA kit, which utilizes a direct immunofluorescent antibody technique for identifying adenovirus in infected tissue cultures, was used. In our study, it was demonstrated that adenoviruses were incorporated into the host amoebae (Acanthamoeba sp. Grp. II, three strains). So far, there were only a few publications concerning the relationship of free-living amoebae and viruses; only one of these described the detection of adenoviruses within acanthamoebae with molecular biological methods. We conducted this descriptive study to further examine the association between viable adenoviruses and FLA. To our knowledge, this is the first study to demonstrate directly the adenoviruses within FLA as vectors and vehicles. Therefore, we concluded that free-living amoebae appear able to act as carriers or vectors of the adenoviruses and thus may play a certain role in the dispersal of adenoviruses.

Genomics of Megavirus and the elusive fourth domain of Life

We recently described Megavirus chilensis, a giant virus isolated off the coast of Chile, also replicating in fresh water acanthamoeba. Its 1,259,197-bp genome encodes 1,120 proteins and is the largest known viral genome. Megavirus and its closest relative Mimivirus only share 594 orthologous genes, themselves sharing only 50% of identical residues in average. Despite this divergence, comparable to the maximal divergence exhibited by bacteria within the same division (e.g., gamma proteobacteria), Megavirus retained all of the genomic features unique to Mimivirus, in particular its genes encoding key-elements of the translation apparatus, a trademark of cellular organisms. Besides homologs to the four aminoacyl-tRNA synthetases (aaRS) encoded by Mimivirus, Megavirus added three additional ones, raising the total of known virus-encoded aaRS to seven: IleRS, TrpRS, AsnRS, ArgRS, CysRS, MetRS, TyrRS. This finding strongly suggests that large DNA viruses derived from an ancestral cellular genome by reductive evolution. The nature of this cellular ancestor remains hotly debated.

Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

Background

The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.

Results

Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a ‘fourth supergroup’ along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity.

Conclusions

Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet’s biosphere.

Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms

Based on Darwin's concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions, and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host's factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT) that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms (ARMs).

Structures of giant icosahedral eukaryotic dsDNA viruses

In the last twenty years, numerous giant, dsDNA, icosahedral viruses have been discovered and assigned to the nucleocytoplasmic large dsDNA virus (NCLDV) clade. The major capsid proteins of these viruses consist of two consecutive jelly-roll domains, assembled into trimers, with pseudo 6-fold symmetry. The capsomers are assembled into arrays that have either p6 (as in Paramecium bursaria Chlorella virus-1) or p3 symmetry (as in Mimivirus). Most of the NCLDV viruses have a membrane that separates the nucleocapsid from the external capsid.

The unusual cell biology of the hyperthermophilic Crenarchaeon Ignicoccus hospitalis

The Crenarchaeon Ignicoccus hospitalis is an anaerobic, obligate chemolithoautotrophic hyperthermophile, growing by reduction of elemental sulfur using molecular hydrogen as electron donor. Together with Nanoarchaeum equitans it forms a unique, archaeal biocoenosis, in which I. hospitalis serves as host for N. equitans. Both organisms can be cultivated in a stable coculture which is mandatory for N. equitans but not for I. hospitalis. This strong dependence is affirmed by the fact that N. equitans obtains its lipids and amino acids from the host. I. hospitalis cells exhibit several unique features: they can adhere to surfaces by extracellular appendages ('fibers') which are not used for motility; they use a novel CO(2) fixation pathway, the dicarboxylate/4-hydroxybutyrate pathway; and they exhibit a unique cell envelope for Archaea consisting of two membranes but lacking an S-layer. These membranes form two cell compartments, a tightly packed cytoplasm surrounded by a weakly staining intermembrane compartment (IMC) with a variable width from 20 to 1,000 nm. In this IMC, many round or elongated vesicles are found which may function as carriers of lipids or proteins out of the cytoplasm. Based on immuno-EM analyses and immuno-fluorescence experiments it was demonstrated recently that the A(1)A(O) ATP synthase, the H(2):sulfur oxidoreductase complex and the acetyl-CoA synthetase (ACS) of I. hospitalis are located in its outermost membrane. Therefore, this membrane is energized and is here renamed as "outer cellular membrane" (OCM). Among all prokaryotes possessing two membranes in their cell envelope, I. hospitalis is the first organism with an energized outermost membrane and ATP synthesis outside the cytoplasm. Since DNA and ribosomes are localized in the cytoplasm, energy conservation is separated from information processing and protein biosynthesis in I. hospitalis. This raises questions concerning the function and characterization of the two membranes, the two cell compartments and of a possible ATP transfer to N. equitans.

Legionella tunisiensis sp. nov. and Legionella massiliensis sp. nov., isolated from environmental water samples

Two isolates of intra-amoeba-growing bacteria, LegA(T) ( = DSM 24804(T) = CSUR P146(T)) and LegM(T) ( = DSM 24805(T) = CSUR P145(T)), were characterized on the basis of microscopic appearance, staining characteristics, axenic growth at different temperatures and the sequences of the mip, rpoB, 16S rRNA and rnpb genes, as well as the 23S-5S region. Phylogenetic analysis showed that these two isolates lay within the radius of the family Legionellaceae. Furthermore, the analysis of these genes yielded congruent data that indicated that, although strain LegM(T) clusters specifically with Legionella feeleii ATCC 35072(T) and LegA(T) clusters with Legionella nautarum ATCC 49596(T), the divergence observed between these species was greater than that observed between other members of the family. Taken together, these results support the proposal that these two isolates represent novel members of the genus Legionella, and we propose to name them Legionella tunisiensis sp. nov. for LegM(T) ( = DSM 24805(T) = CSUR P145(T)) and Legionella massiliensis sp. nov. for LegA(T) ( = DSM 24804(T) = CSUR P146(T)).

Crystalloid body, refractile body and virus-like particles in Apicomplexa: what is in there?

The phylum of Apicomplexa comprises parasitic protozoa that share distinctive features such as the apical complex, the apicoplast, specialized cytoskeletal components and secretory organelles. Other unique cytoplasmic inclusions sharing similar features have been described in some representatives of Apicomplexa, although under different denominations. These are the crystalloid body, present for example in Cryptosporidium, Plasmodium and Cystoisospora; the refractile body in Eimeria and Lankesterella; and virus-like particles, also present in Eimeria and Cryptosporidium. Yet, the specific role of these cytoplasmic inclusions in the cell cycle of these protozoa is still unknown. Here, we discuss their morphology, possible inter-relatedness and speculate upon their function to bring these organelles back to the attention of the scientific community and promote new interest towards original research on these elusive structures.

Interaction of Escherichia coli K1 and K5 with Acanthamoeba castellanii trophozoites and cysts

The existence of symbiotic relationships between Acanthamoeba and a variety of bacteria is well-documented. However, the ability of Acanthamoeba interacting with host bacterial pathogens has gained particular attention. Here, to understand the interactions of Escherichia coli K1 and E. coli K5 strains with Acanthamoeba castellanii trophozoites and cysts, association assay, invasion assay, survival assay, and the measurement of bacterial numbers from cysts were performed, and nonpathogenic E. coli K12 was also applied. The association ratio of E. coli K1 with A. castellanii was 4.3 cfu per amoeba for 1 hr but E. coli K5 with A. castellanii was 1 cfu per amoeba for 1 hr. By invasion and survival assays, E. coli K5 was recovered less than E. coli K1 but still alive inside A. castellanii. E. coli K1 and K5 survived and multiplied intracellularly in A. castellanii. The survival assay was performed under a favourable condition for 22 hr and 43 hr with the encystment of A. castellanii. Under the favourable condition for the transformation of trophozoites into cysts, E. coli K5 multiplied significantly. Moreover, the pathogenic potential of E. coli K1 from A. castellanii cysts exhibited no changes as compared with E. coli K1 from A. castellanii trophozoites. E. coli K5 was multiplied in A. castellanii trophozoites and survived in A. castellanii cysts. Therefore, this study suggests that E. coli K5 can use A. castellanii as a reservoir host or a vector for the bacterial transmission.

Endosymbiotic bacteria associated with nematodes, ticks and amoebae

Endosymbiosis is a mutualistic, parasitic or commensal symbiosis in which one symbiont is living within the body of another organism. Such symbiotic relationship with free-living amoebae and arthropods has been reported with a large biodiversity of microorganisms, encompassing various bacterial clades and to a lesser extent some fungi and viruses. By contrast, current knowledge on symbionts of nematodes is still mainly restricted to Wolbachia and its interaction with filarial worms that lead to increased pathogenicity of the infected nematode. In this review article, we aim to highlight the main characteristics of symbionts in term of their ecology, host cell interactions, parasitism and co-evolution, in order to stimulate future research in a field that remains largely unexplored despite the availability of modern tools.

The cell biology of receptor-mediated virus entry

The cell imposes multiple barriers to virus entry. However, viruses exploit fundamental cellular processes to gain entry to cells and deliver their genetic cargo. Virus entry pathways are largely defined by the interactions between virus particles and their receptors at the cell surface. These interactions determine the mechanisms of virus attachment, uptake, intracellular trafficking, and, ultimately, penetration to the cytosol. Elucidating the complex interplay between viruses and their receptors is necessary for a full understanding of how these remarkable agents invade their cellular hosts.

The influence of rickettsiologists on post-modern microbiology

Many of the definitions in microbiology are currently false. We have reviewed the great denominations of microbiology and attempted to free microorganisms from the theories of the twentieth century. The presence of compartmentation and a nucleoid in Planctomycetes clearly calls into question the accuracy of the definitions of eukaryotes and prokaryotes. Archaea are viewed as prokaryotes resembling bacteria. However, the name archaea, suggesting an archaic origin of lifestyle, is inconsistent with the lifestyle of this family. Viruses are defined as small, filterable infectious agents, but giant viruses challenge the size criteria used for the definition of a virus. Pathogenicity does not require the acquisition of virulence factors (except for toxins), and in many cases, gene loss is significantly inked to the emergence of virulence. Species classification based on 16S rRNA is useless for taxonomic purposes of human pathogens, as a 2% divergence would classify all Rickettsiae within the same species and would not identify bacteria specialized for mammal infection. The use of metagenomics helps us to understand evolution and physiology by elucidating the structure, function, and interactions of the major microbial communities, but it neglects the minority populations. Finally, Darwin’s descent with modification theory, as represented by the tree of life, no longer matches our current genomic knowledge because genomics has revealed the occurrence of de novo-created genes and the mosaic structure of genomes, the Rhizome of life is therefore more appropriate.

A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses

Alphaherpesviruses are widespread in the human population, and include herpes simplex virus 1 (HSV-1) and 2, and varicella zoster virus (VZV). These viral pathogens cause epithelial lesions, and then infect the nervous system to cause lifelong latency, reactivation, and spread. A related veterinary herpesvirus, pseudorabies (PRV), causes similar disease in livestock that result in significant economic losses. Vaccines developed for VZV and PRV serve as useful models for the development of an HSV-1 vaccine. We present full genome sequence comparisons of the PRV vaccine strain Bartha, and two virulent PRV isolates, Kaplan and Becker. These genome sequences were determined by high-throughput sequencing and assembly, and present new insights into the attenuation of a mammalian alphaherpesvirus vaccine strain. We find many previously unknown coding differences between PRV Bartha and the virulent strains, including changes to the fusion proteins gH and gB, and over forty other viral proteins. Inter-strain variation in PRV protein sequences is much closer to levels previously observed for HSV-1 than for the highly stable VZV proteome. Almost 20% of the PRV genome contains tandem short sequence repeats (SSRs), a class of nucleic acids motifs whose length-variation has been associated with changes in DNA binding site efficiency, transcriptional regulation, and protein interactions. We find SSRs throughout the herpesvirus family, and provide the first global characterization of SSRs in viruses, both within and between strains. We find SSR length variation between different isolates of PRV and HSV-1, which may provide a new mechanism for phenotypic variation between strains. Finally, we detected a small number of polymorphic bases within each plaque-purified PRV strain, and we characterize the effect of passage and plaque-purification on these polymorphisms. These data add to growing evidence that even plaque-purified stocks of stable DNA viruses exhibit limited sequence heterogeneity, which likely seeds future strain evolution.

Alphaherpesviruses such as herpes simplex virus (HSV) are ubiquitous in the human population. HSV causes oral and genital lesions, and has co-morbidities in acquisition and spread of human immunodeficiency virus (HIV). The lack of a vaccine for HSV hinders medical progress for both of these infections. A related veterinary alphaherpesvirus, pseudorabies virus (PRV), has long served as a model for HSV vaccine development, because of their similar pathogenesis, neuronal spread, and infectious cycle. We present here the first full genome characterization of a live PRV vaccine strain, Bartha, and reveal a spectrum of unique mutations that are absent from two divergent wild-type PRV strains. These mutations can now be examined individually for their contribution to vaccine strain attenuation and for potential use in HSV vaccine development. These inter-strain comparisons also revealed an abundance of short repetitive elements in the PRV genome, a pattern which is repeated in other herpesvirus genomes and even the unrelated Mimivirus. We provide the first global characterization of repeats in viruses, comparing both their presence and their variation among different viral strains and species. Repetitive elements such as these have been shown to serve as hotspots of variation between individuals or strains of other organisms, generating adaptations or even disease states through changes in length of DNA-binding sites, protein folding motifs, and other structural elements. These data suggest for the first time that similar mechanisms could be widely distributed in viral biology as well.

Distant Mimivirus relative with a larger genome highlights the fundamental features of Megaviridae

Mimivirus, a DNA virus infecting acanthamoeba, was for a long time the largest known virus both in terms of particle size and gene content. Its genome encodes 979 proteins, including the first four aminoacyl tRNA synthetases (ArgRS, CysRS, MetRS, and TyrRS) ever found outside of cellular organisms. The discovery that Mimivirus encoded trademark cellular functions prompted a wealth of theoretical studies revisiting the concept of virus and associated large DNA viruses with the emergence of early eukaryotes. However, the evolutionary significance of these unique features remained impossible to assess in absence of a Mimivirus relative exhibiting a suitable evolutionary divergence. Here, we present Megavirus chilensis, a giant virus isolated off the coast of Chile, but capable of replicating in fresh water acanthamoeba. Its 1,259,197-bp genome is the largest viral genome fully sequenced so far. It encodes 1,120 putative proteins, of which 258 (23%) have no Mimivirus homologs. The 594 Megavirus/Mimivirus orthologs share an average of 50% of identical residues. Despite this divergence, Megavirus retained all of the genomic features characteristic of Mimivirus, including its cellular-like genes. Moreover, Megavirus exhibits three additional aminoacyl-tRNA synthetase genes (IleRS, TrpRS, and AsnRS) adding strong support to the previous suggestion that the Mimivirus/Megavirus lineage evolved from an ancestral cellular genome by reductive evolution. The main differences in gene content between Mimivirus and Megavirus genomes are due to (i) lineages specific gains or losses of genes, (ii) lineage specific gene family expansion or deletion, and (iii) the insertion/migration of mobile elements (intron, intein).

Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids

BACKGROUND

The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes.

RESULTS

Our bioinformatics analysis revealed that R555 protein sequence is constituted from the fusion of an N-terminal Mre11-like domain with a C-terminal Rad50-like domain. A systematic database search revealed twelve additional cases of Mre11/Rad50 (or SbcD/SbcC) fusions in a wide variety of unrelated organisms including unicellular and multicellular eukaryotes, the megaplasmid of a bacterium associated to deep-sea hydrothermal vents (Deferribacter desulfuricans) and the plasmid of Clostridium kluyveri. We also showed that R555 homologs are abundant in the metagenomes from different aquatic environments and that they most likely belong to aquatic viruses. The observed phyletic distribution of these fusion proteins suggests their recurrent creation and lateral gene transfers across organisms.

CONCLUSIONS

The existence of the fused version of protein sequences is consistent with known functional interactions between Mre11 and Rad50, and the gene fusion probably enhanced the opportunity for lateral transfer. The abundance of the Mre11/Rad50 fusion genes in viral metagenomes and their sporadic phyletic distribution in cellular organisms suggest that viruses, plasmids and transposons played a crucial role in the formation of the fusion proteins and their propagation into cellular genomes.

Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses

Mimivirus is a nucleocytoplasmic large DNA virus (NCLDV) with a genome size (1.2 Mb) and coding capacity ( 1000 genes) comparable to that of some cellular organisms. Unlike other viruses, Mimivirus and its NCLDV relatives encode homologs of broadly conserved informational genes found in Bacteria, Archaea, and Eukaryotes, raising the possibility that they could be placed on the tree of life. A recent phylogenetic analysis of these genes showed the NCLDVs emerging as a monophyletic group branching between Eukaryotes and Archaea. These trees were interpreted as evidence for an independent "fourth domain" of life that may have contributed DNA processing genes to the ancestral eukaryote. However, the analysis of ancient evolutionary events is challenging, and tree reconstruction is susceptible to bias resulting from non-phylogenetic signals in the data. These include compositional heterogeneity and homoplasy, which can lead to the spurious grouping of compositionally-similar or fast-evolving sequences. Here, we show that these informational gene alignments contain both significant compositional heterogeneity and homoplasy, which were not adequately modelled in the original analysis. When we use more realistic evolutionary models that better fit the data, the resulting trees are unable to reject a simple null hypothesis in which these informational genes, like many other NCLDV genes, were acquired by horizontal transfer from eukaryotic hosts. Our results suggest that a fourth domain is not required to explain the available sequence data.

Mimivirus shows dramatic genome reduction after intraamoebal culture

Most phagocytic protist viruses have large particles and genomes as well as many laterally acquired genes that may be associated with a sympatric intracellular life (a community-associated lifestyle with viruses, bacteria, and eukaryotes) and the presence of virophages. By subculturing Mimivirus 150 times in a germ-free amoebal host, we observed the emergence of a bald form of the virus that lacked surface fibers and replicated in a morphologically different type of viral factory. When studying a 0.40-μm filtered cloned particle, we found that its genome size shifted from 1.2 (M1) to 0.993 Mb (M4), mainly due to large deletions occurring at both ends of the genome. Some of the lost genes are encoding enzymes required for posttranslational modification of the structural viral proteins, such as glycosyltransferases and ankyrin repeat proteins. Proteomic analysis allowed identification of three proteins, probably required for the assembly of virus fibers. The genes for two of these were found to be deleted from the M4 virus genome. The proteins associated with fibers are highly antigenic and can be recognized by mouse and human antimimivirus antibodies. In addition, the bald strain (M4) was not able to propagate the sputnik virophage. Overall, the Mimivirus transition from a sympatric to an allopatric lifestyle was associated with a stepwise genome reduction and the production of a predominantly bald virophage resistant strain. The new axenic ecosystem allowed the allopatric Mimivirus to lose unnecessary genes that might be involved in the control of competitors.

What does virus evolution tell us about virus origins?

Despite recent advances in our understanding of diverse aspects of virus evolution, particularly on the epidemiological scale, revealing the ultimate origins of viruses has proven to be a more intractable problem. Herein, I review some current ideas on the evolutionary origins of viruses and assess how well these theories accord with what we know about the evolution of contemporary viruses. I note the growing evidence for the theory that viruses arose before the last universal cellular ancestor (LUCA). This ancient origin theory is supported by the presence of capsid architectures that are conserved among diverse RNA and DNA viruses and by the strongly inverse relationship between genome size and mutation rate across all replication systems, such that pre-LUCA genomes were probably both small and highly error prone and hence RNA virus-like. I also highlight the advances that are needed to come to a better understanding of virus origins, most notably the ability to accurately infer deep evolutionary history from the phylogenetic analysis of conserved protein structures.

The giant Cafeteria roenbergensis virus that infects a widespread marine phagocytic protist is a new member of the fourth domain of Life

Background

A recent work has provided strong arguments in favor of a fourth domain of Life composed of nucleo-cytoplasmic large DNA viruses (NCLDVs). This hypothesis was supported by phylogenetic and phyletic analyses based on a common set of proteins conserved in Eukarya, Archaea, Bacteria, and viruses, and implicated in the functions of information storage and processing. Recently, the genome of a new NCLDV, Cafeteria roenbergensis virus (CroV), was released. The present work aimed to determine if CroV supports the fourth domain of Life hypothesis.

Methods

A consensus phylogenetic tree of NCLDVs including CroV was generated from a concatenated alignment of four universal proteins of NCLDVs. Some features of the gene complement of CroV and its distribution along the genome were further analyzed. Phylogenetic and phyletic analyses were performed using the previously identified common set of informational genes present in Eukarya, Archaea, Bacteria, and NCLDVs, including CroV.

Findings

Phylogenetic reconstructions indicated that CroV is clearly related to the Mimiviridae family. The comparison between the gene repertoires of CroV and Mimivirus showed similarities regarding the gene contents and genome organization. In addition, the phyletic clustering based on the comparison of informational gene repertoire between Eukarya, Archaea, Bacteria, and NCLDVs unambiguously classified CroV with other NCLDVs and clearly included it in a fourth domain of Life. Taken together, these data suggest that Mimiviridae, including CroV, may have inherited a common gene content probably acquired from a common Mimiviridae ancestor.

Conclusions

This further analysis of the gene repertoire of CroV consolidated the fourth domain of Life hypothesis and contributed to outline a functional pan-genome for giant viruses infecting phagocytic protistan grazers.

Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees

Background

Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species.

Methodology/Principal Findings

We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences.

Conclusions/Significance

Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.

Single mimivirus particles intercepted and imaged with an X-ray laser

X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions. Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma. The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval. Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a non-crystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source. Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.

Keeping Track of Viruses

This chapter reviews methods of isolating, identifying, and tracking viruses with potential applications to microbial forensic investigations. Viruses are the most abundant biological entities on earth. These obligate parasites infect every form of life, from archaea and eubacteria to fungi, plants, and animals. Viruses play key roles in global ecology—they form a vast reservoir of genetic diversity, influence the composition and evolution of host populations, and affect the cycling of chemical compounds through the environment. Research has focused on the tiny fraction that causes disease in humans, domestic animals, and crops; sequencing surveys have suggested that the majority of viruses are completely unknown. The ability of viruses to jump species barriers, move between habitats, and circle the globe rapidly underscores the importance of continued vigilance for naturally emerging or deliberately engineered outbreaks. Viruses are extremely simple “life” forms without metabolic capacity, organelles, translational machinery, or autonomous replicative potential. Virus particles constitute a minimal set of components, primarily those required to deliver the genome to the target cell and initiate replication. Consequently, virus particles (or virions) are extremely small, most in the range of 20 to 200 nm in diameter. Virions are diverse not only in size but also in composition, morphology, and genome characteristics. Virus particles may be irregular in shape or possess a distinct symmetry, such as helical or icosahedral. Particles may be surrounded by a host-derived membrane, termed “enveloped,” or a tight protein shell, termed “nonenveloped.”

Evidence of transfer by conjugation of type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba

Background

Bartonella species cospeciate with mammals and live within erythrocytes. Even in these specific niches, it has been recently suggested by bioinformatic analysis of full genome sequences that Lateral Gene Transfer (LGT) may occur but this has never been demonstrated biologically. Here we describe the sequence of the B. rattaustraliani (AUST/NH4^T) circular plasmid (pNH4) that encodes the tra cluster of the Type IV secretion system (T4SS) and we eventually provide evidence that Bartonella species may conjugate and exchange this plasmid inside amoeba.

Principal Findings

The T4SS of pNH4 is critical for intracellular viability of bacterial pathogens, exhibits bioinformatic evidence of LGT among bacteria living in phagocytic protists. For instance, 3 out of 4 T4SS encoding genes from pNH4 appear to be closely related to Rhizobiales, suggesting that gene exchange occurs between intracellular bacteria from mammals (bartonellae) and plants (Rhizobiales). We show that B. rattaustraliani and Rhizobium radiobacter both survived within the amoeba Acanthamoeba polyphaga and can conjugate together. Our findings further support the hypothesis that tra genes might also move into and out of bacterial communities by conjugation, which might be the primary means of genomic evolution for intracellular adaptation by cross-talk of interchangeable genes between Bartonella species and plant pathogens.

Conclusions

Based on this, we speculate that amoeba favor the transfer of genes as phagocytic protists, which allows for intraphagocytic survival and, as a consequence, promotes the creation of potential pathogenic organisms.

Mimivirus: the emerging paradox of quasi-autonomous viruses

What is a virus? Are viruses alive? Should they be classified among microorganisms? One would expect these simple questions to have been settled a century after the discovery of the first viral disease. For years, modern virology successfully unravelled the huge diversity of viruses in terms of genetic material, replication mechanism, pathogenicity, host infection, and more recently particle structure, planet-wide distribution and ecological significance. Yet, little progress was made in understanding their evolutionary origin(s), as well as the fundamental nature of their relationship with the cellular world. Thanks to the recent studies on Mimivirus and other large DNA viruses, we are now entering a new era where the most basic concepts about viruses are revisited, including their true nature, how fundamentally different they are from cellular microorganisms, and how essential they might have been in the major innovations that punctuated the evolution of life.

The three-dimensional structure of Mimivirus

Mimivirus, the prototypic member of the new family of Mimiviridae, is the largest virus known to date. Progress has been made recently in determining the three-dimensional structure of the 0.75-microm diameter virion using cryo-electron microscopy and atomic force microscopy. These showed that the virus is composed of an outer layer of dense fibers surrounding an icosahedrally shaped capsid and an internal membrane sac enveloping the genomic material of the virus. Additionally, a unique starfish-like structure at one of the fivefold vertices, required by the virus for infecting its host, has been defined in more detail.

Defining life: the virus viewpoint

Are viruses alive? Until very recently, answering this question was often negative and viruses were not considered in discussions on the origin and definition of life. This situation is rapidly changing, following several discoveries that have modified our vision of viruses. It has been recognized that viruses have played (and still play) a major innovative role in the evolution of cellular organisms. New definitions of viruses have been proposed and their position in the universal tree of life is actively discussed. Viruses are no more confused with their virions, but can be viewed as complex living entities that transform the infected cell into a novel organism—the virus—producing virions. I suggest here to define life (an historical process) as the mode of existence of ribosome encoding organisms (cells) and capsid encoding organisms (viruses) and their ancestors. I propose to define an organism as an ensemble of integrated organs (molecular or cellular) producing individuals evolving through natural selection. The origin of life on our planet would correspond to the establishment of the first organism corresponding to this definition.