Linking Virus Genomes with Host Taxonomy

Mihara, Tomoko; Nishimura, Yosuke; Shimizu, Yoshihisa; Nishiyama, Hiroki; Yoshikawa, Genki; Uehara, Hideya; Hingamp, Pascal; Goto, Susumu; Ogata, Hiroyuki

doi:10.3390/v8030066

Cited by 312 publications

(331 citation statements)

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“…Humans were reported to be infected by hundreds of viruses (Geoghegan et al, 2016;Mihara et al, 2016). Most of the human emerging infectious diseases are zoonotic, with viruses that originate in mammals of particular concern (Olival et al, 2017), such as the Human Immunodeficiency Virus (HIV) (Sharp and Hahn, 2011) and Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) (Ge et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors

Zhang

Zhu

Cai

et al. 2018

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Receptor mediated entry is the first step for viral infection. There are thousands of cell membrane proteins, yet only a few of them were identified as viral receptors. How the virus selects receptors is an unsolved important question. Here, by manually curating a high-quality database of 268 pairs of mammalian virus-host receptor interaction, which included 128 unique viral species or sub-species and 119 virus receptors, we found the viral receptors were structurally and functionally diverse, yet they had several common features when compared to other cell membrane proteins: more protein domains, higher level of N-glycosylation, higher ratio of self-interaction and more interaction partners, and higher expression in most tissues of the host.Additionally, the receptors used by the same virus tended to co-evolve. This work could deepen our understanding towards the viral receptor selection and help for identification of viral receptors.

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Section: Introductionmentioning

confidence: 99%

Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors

Zhang

Zhu

Cai

et al. 2018

Preprint

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“…foram utilizados como referência para a busca na plataforma do GenomeNet Virus-Host DB, que busca, com base na literatura, prever os fagos conforme já foram descritos anteriormente para determinados hospedeiros (MIHARA et al, 2016). BrMgv02 aconteceu há 30 anos e a comunidade microbiana teve tempo suficiente para se estabilizar frente as mudanças nas condições ambientais.…”

Section: Predição Das Linhagens De Bacteriófagos Com Base Nos Hospedeunclassified

Elementos genéticos móveis no microbioma dos sedimentos de manguezais

Nunes¹

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“…Therefore, a viral vector of HGTs from bacteria to animals is unlikely, since to my knowledge, no virus is currently known to infect both animals and bacteria (Glansdorff et al 2009;Bilewitch and Degnan 2011;Nilsson 2014;Mihara et al 2016). However, of significance to animal HGT is that these studies show that TEs can act as vectors too, and can also transfer hitchhiking non-LTR retrotransposons that are not transfer prone (Ivancevic et al 2013).…”

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confidence: 99%

“…bacterial viruses/phages typically can only infect one or limited numbers of bacterial strains -a phage that infects 20 strains is considered to have a broad host range (Mihara et al 2016). Therefore, a viral vector of HGTs from bacteria to animals is unlikely, since to my knowledge, no virus is currently known to infect both animals and bacteria (Glansdorff et al 2009;Bilewitch and Degnan 2011;Nilsson 2014;Mihara et al 2016).…”

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confidence: 99%

“…Although viruses have specific and restricted host ranges that to date are not known to span wide taxonomic distances (Glansdorff et al 2009;Bilewitch and Degnan 2011;Nilsson 2014;Mihara et al 2016), the same virus need not infect both donor and recipient to be a HGT vector since the process could involve a ME as an intermediary vector. Through environmental contact within the extracellular space of an animal, a mobilised donor ME could move or copy genetic material to a viral genome that then infects an animal cell via membrane fusion, penetration or endocytosis (Schönknecht et al 2014).…”

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confidence: 99%

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Horizontal gene transfer in the sponge Amphimedon queenslandica

Higgie¹

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Horizontal gene transfer (HGT) is the nonsexual transfer of genetic sequence across species boundaries.Historically, HGT has been assumed largely irrelevant to animal evolution, though widely recognised as an important evolutionary force in bacteria. From the recent boom in whole genome sequencing, many cases have emerged strongly supporting the occurrence of HGT in a wide range of animals.However, the extent, nature and mechanisms of HGT in animals remain poorly understood. Here, I explore these uncertainties using 576 HGTs previously reported in the genome of the demosponge Amphimedon queenslandica.The HGTs derive from bacterial, plant and fungal sources, contain a broad range of domain types, and many are differentially expressed throughout development. Some domains are highly enriched; phylogenetic analyses of the two largest groups, the Aspzincin_M35 and the PNP_UDP_1 domain groups, suggest that each results from one or few transfer events followed by post-transfer duplication.Their differential expression through development, and the conservation of domains and duplicates, together suggest that many of the HGT-derived genes are functioning in A. queenslandica. The largest group consists of aspzincins, a metallopeptidase found in bacteria and fungi, but not typically in animals.I detected aspzincins in representatives of all four of the sponge classes, suggesting that the original sponge aspzincin was transferred after sponges diverged from their last common ancestor with the Eumetazoa, but before the contemporary sponge classes emerged. In A. queenslandica, the aspzincins may have been co-opted for multiple functions, since 54 of the 90 fit into one of four ontogenetic expression profiles, each of which is putatively co-expressed with different suites of native genes.Based on secretion signals and the conservation of key catalytic residues, I propose that proteolytic activity is maintained in at least one of the aspzincin roles in A. queenslandica.Mobile elements are capable of genomic excision, movement and integration, they enable HGT in bacteria, and some animal HGTs are genomically close to eukaryotic transposable elements (TEs); as such, mobile elements are speculated as possible players in the mechanisms of interkingdom and interdomain HGT to animals. In A. queenslandica, the overall repeats densities around predicted Together, these results offer novel insight on HGT in A. queenslandica and demonstrate that HGT has a varied nature in this animal with an extensive impact, partially due to post-transfer duplications. Further, this work offers insights on possible mechanisms that led to the HGT derived genes of this sponge. iv Declaration by authorThis thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis.

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Linking Virus Genomes with Host Taxonomy

Cited by 312 publications

References 20 publications

Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors

Membrane proteins with high N-glycosylation, high expression, and multiple interaction partners were preferred by mammalian viruses as receptors

Elementos genéticos móveis no microbioma dos sedimentos de manguezais

Horizontal gene transfer in the sponge Amphimedon queenslandica

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