The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea

Deeg, Christoph; Chow, Cheryl-Emiliane T.; Suttle, Curtis A.

doi:10.1101/214536

Cited by 12 publications

(19 citation statements)

References 58 publications

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“…and V. vermiformis 37 . However, most commonly, the permissivity of known eukaryotic hosts to giant viruses differs considerably according to the host strain or to the viral family or lineage, as previously described for mimiviruses, pandoraviruses, and Bodo saltans virus 32,48 . The analysis of giant virus homologs in the V. vermiformis genome showed here that the most represented sequences were those of giant viruses that grew in V. vermiformis, including faustovirus isolates and Orpheovirus IHUMI-LCC2, whereas a small proportion included genes from giant viruses isolated from Acanthamoeba spp.. Ankyrin repeats, which are associated with protein-protein interactions, were highly represented among V. vermiformis genes best matching with giant viruses 49,50 in addition to DUF4114 domains which are conserved domains that help to adapt to nutrient-depleted conditions by down-regulating protein biosynthesis 51 .…”

Section: Discussionmentioning

confidence: 97%

“…This suggests a considerable gene trafficking between this amoeba and Klosneuvirinae members. Among this group, only the Bodo saltans virus was isolated (only the genomes assembled from metagenomic data being available for the other described members) and this was on the kinetoplastid Bodo saltans, a microzooplankton 48 . Other recently described mimiviruses named tupanviruses can grow on both Acanthamoeba spp.…”

Section: Discussionmentioning

confidence: 99%

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Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses

Chelkha

Hasni

Louazani

et al. 2020

Sci Rep

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Vermamoeba vermiformis is a predominant free-living amoeba in human environments and amongst the most common amoebae that can cause severe infections in humans. it is a niche for numerous amoeba-resisting microorganisms such as bacteria and giant viruses. Differences in the susceptibility to these giant viruses have been observed. V. vermiformis and amoeba-resisting microorganisms share a sympatric lifestyle that can promote exchanges of genetic material. This work analyzed the first draft genome sequence of a V. vermiformis strain (CDC-19) through comparative genomic, transcriptomic and phylogenetic analyses. the genome of V. vermiformis is 59.5 megabase pairs in size, and 22,483 genes were predicted. A high proportion (10% (n = 2,295)) of putative genes encoded proteins showed the highest sequence homology with a bacterial sequence. the expression of these genes was demonstrated for some bacterial homologous genes. In addition, for 30 genes, we detected best BLAST hits with members of the Candidate Phyla Radiation. Moreover, 185 genes (0.8%) best matched with giant viruses, mostly those related to the subfamily Klosneuvirinae (101 genes), in particular Bodo saltans virus (69 genes). Lateral sequence transfers between V. vermiformis and amoeba-resisting microorganisms were strengthened by Sanger sequencing, transcriptomic and phylogenetic analyses. This work provides important insights and genetic data for further studies about this amoeba and its interactions with microorganisms. Amoebozoa species are widely distributed in different environments from terrestrial to aquatic ecosystems, where they can play important ecological roles 1,2. Members of the family Hartmannellidae are frequently detected along with a few other amoebae belonging to different genera of the taxon Amoebozoa 3. Vermamoeba vermiformis, a free-living amoeba of the family Hartmannellidae, formerly named Hartmannella vermiformis, was first isolated in freshwater from the Pigeon Lake, Wisconsin, and the Kankakee River, Indiana (United States) 4. V. vermiformis was thereafter commonly found in fresh surface water 5 , and also in tap water, bottled mineral water, thermal water, and recreational water environments such as fountains and swimming pools 6-8. Its density in drinking water sources and biofilms is higher than that of Acanthamoeba castellanii 9. V. vermiformis has two-stage life, switching between trophozoite and cystic form 3. Free-living amoebae (FLA) are commonly in contact with animals including humans. V. vermiformis was found to be the predominant amoeba in human environments 10,11 , and has been isolated more frequently from different hospital water systems than Acanthamoeba spp. 12. This amoeba is of special interest for human health as it is able, along with other Amoebozoa members including Acanthamoeba spp., to cause severe infections such as human keratitis 13-15. Despite its prevalence in human environments and its pathogenicity in humans, the genome of V. vermiformis had not been sequenced.

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses

Chelkha

Hasni

Louazani

et al. 2020

Sci Rep

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“…Nevertheless, CroV replication suppression and enhanced survival of the host population were thereafter observed, suggesting the acquisition of a protection conferred by mavirus reactivation. Other putative defence mechanisms of mimiviruses against sympatric organisms were recently suggested for Bodo saltans virus [23]. Competitive interference between different Bodo saltans virus strains or related viruses co-infecting the same host cell may occur through the site-specific homing endonucleases encoded by introns and inteins that have invaded the essential genes of this mimivirus, including DNA-dependent RNA polymerase subunits.…”

Section: Mimivirus and Virophage Defence Mechanismsmentioning

confidence: 97%

“…Recently, the 0.9-to 1.6-Mbp genomes of four putative giant viruses, named klosneuviruses and related to amoeba mimiviruses, have been assembled from environmental metagenomes [22]. Subsequently, a new giant virus (Bodo saltans virus) infecting Bodo saltans, an aquatic protozoan, was isolated and classified as a klosneuvirus [23]. Two mimivirus-like strains were also isolated within or using Saccamoeba lacustris strains, from the bark of plane trees [24].…”

Section: Mimivirusesmentioning

confidence: 99%

“…It was later shown that RNA silencing of the gene encoding a putative translation initiation factor (R458) was associated with a prolonged eclipse phase and a delay in the appearance of the mimivirus factory, along with modulation of expression of 32 mimivirus genes [75]. Recently, the mimivirus translation component set showed a dramatic expansion with the assembly of genomes of putative non-isolated mimivirus relatives, named klosneuviruses [22], followed by the discovery of the Bodo saltans virus [23]. Nevertheless, the current record holders are tupanviruses, whose genomes harbor the most complete set of translation-related genes of the virosphere, with all 20 aminoacyl-tRNA synthetases, and 67e70 tRNAs associated with 46e47 codons [5].…”

Section: The Growing Mismatch Between Giant Viruses and The Criteria mentioning

confidence: 99%

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Giant mimiviruses escape many canonical criteria of the virus definition

Colson

Ominami

Hisada

et al. 2019

Clinical Microbiology and Infection

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Background: The discovery of mimivirus in 2003 prompted the quest for other giant viruses of amoebae. Mimiviruses and their relatives were found to differ considerably from other viruses. Their study led to major advances in virology and evolutionary biology. Aims: We summarized the widening gap between mimiviruses and other viruses. Sources: We collected data from articles retrieved from PubMed using as keywords 'giant virus', 'mimivirus' and 'virophage', as well as quoted references from these articles. Content: Data accumulated during the last 15 years on mimiviruses and other giant viruses highlight that there is a quantum leap between these infectious agents, the complexity of which is similar to that of intracellular microorganisms, and classical viruses. Notably, in addition to their giant structures and genomes, giant viruses have abundant gene repertoires with genes unique in the virosphere, including a tremendous set of translation components. The viruses contain hundreds of proteins and many transcripts. They share a core of central and ancient proteins but their genome sequences display a substantial level of mosaicism. Finally, mimiviruses have a specific mobilome, including virophages that can integrate into their genomes, and against which they can defend themselves through integration of short fragments of the DNA of these invaders. Implications: Mimiviruses and subsequently discovered giant viruses have changed the virus paradigm and contradict many virus definition criteria delineated for classical viruses. The major cellular hallmark that is still lacking in giant viruses is the ribosome, including both ribosomal protein and RNA encoding genes, which makes them bona fide microbes without ribosomes.

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The Astounding World of Glycans from Giant Viruses

Speciale¹,

Notaro

Abergel

et al. 2022

Chem. Rev.

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Viruses are a heterogeneous ensemble of entities, all sharing the need for a suitable host to replicate. They are extremely diverse, varying in morphology, size, nature, and complexity of their genomic content. Typically, viruses use host-encoded glycosyltransferases and glycosidases to add and remove sugar residues from their glycoproteins. Thus, the structure of the glycans on the viral proteins have, to date, typically been considered to mimick those of the host. However, the more recently discovered large and giant viruses differ from this paradigm. At least some of these viruses code for an (almost) autonomous glycosylation pathway. These viral genes include those that encode the production of activated sugars, glycosyltransferases, and other enzymes able to manipulate sugars at various levels. This review focuses on large and giant viruses that produce carbohydrate-processing enzymes. A brief description of those harboring these features at the genomic level will be discussed, followed by the achievements reached with regard to the elucidation of the glycan structures, the activity of the proteins able to manipulate sugars, and the organic synthesis of some of these virus-encoded glycans. During this progression, we will also comment on many of the challenging questions on this subject that remain to be addressed. CONTENTS AJ 4.2. Chlorovirus N-Glycans AJ 5. Conclusions and Future Perspectives AN Author Information

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The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea

Cited by 12 publications

References 58 publications

Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses

Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses

Giant mimiviruses escape many canonical criteria of the virus definition

The Astounding World of Glycans from Giant Viruses

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