Chloroviruses

Etten, James L. Van; Agarkova, Irina V.; Dunigan, David D.

doi:10.3390/v12010020

Cited by 53 publications

(54 citation statements)

References 264 publications

(359 reference statements)

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“…With a plausible hypothesis about the function of the prasinophyte ACRs in hand, we turned to the analysis of the origin of their putative viral homologues that motivated our study in the first place. None of the available NCLDV genomes demonstrated close similarity to the metagenomic fragments in terms of synteny and sequence identity, including those viruses that are known to infect green algae 47 and specifically prasinophytes 48 . First we noticed that the v Py ACRs originated from a particular clade of prasinophyte ACRs from Pyramimonas as suggested by phylogenetic analysis (see Fig.…”

Section: Vpyacrs Indeed Come From Giant Virusesmentioning

confidence: 99%

Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses

Rozenberg

Oppermann

Wietek

et al. 2020

Preprint

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Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2 . Four ChR families are currently known. Green algal 3-5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7 , and the MerMAID ChRs 8 . Here, we report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. These previously unknown viral and green algal ChRs act as ACRs when expressed in cultured neuroblastoma-derived cells and are likely involved in behavioral responses to light. MAINChannelrhodopsins (ChRs) are microbial rhodopsins that directly translate absorbed light into ion fluxes along electrochemical gradients across cellular membranes controlling behavioural light responses in motile algae 9 . They are widely used in optogenetics to manipulate cellular activity using light 10 , and therefore a constant demand for new types of ChRs with different functions, be it different absorption spectra 11 , ion selectivity 12 , or kinetics 11 . So far, ChRs have only been reported from cultured representatives of two groups of algae: cryptophytes and green algae 2,13 . Recently, metagenomics proved to be a useful tool to identify novel ChRs, as a new family of anion-conducting ChRs (ACRs) with intensely desensitizing photocurrents were detected in uncultured and yet to be identified marine microorganisms 8 . Channelrhodopsins in metagenomic contigs of putative viral origin.To extend the search for uncharacterized distinct ChRs with potentially new functions, we further screened various metagenomic datasets from Tara Oceans 14-16 . In total, four unique ChR sequences were found in five metagenomic contigs from tropical and temperate waters of the Atlantic and Pacific Oceans. Two of the contigs were long enough (SAMEA2620979_21821, 11 kb and SAMEA2623079_2164382, 20 kb) to provide sufficient genomic context (Fig. 1a). We attempted to search for similar sequences in several metagenomic datasets, and located multiple contigs with synteny to the two longer ChR-containing contigs (Fig. 1a, Suppl. File 1). These two longer contigs recruited two clusters of related fragments (v21821 and v2164382 contig clusters) mostly from marine samples of Tara Oceans. Interestingly, the v21821-cluster contigs came from the same South Atlantic station as SAMEA2620979_21821 itself, except for one contig with lower identity and synteny length from a soda lake metagenome 17 (LFCJ01000229.1, see Fig.

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Section: Vpyacrs Indeed Come From Giant Virusesmentioning

confidence: 99%

Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses

Rozenberg

Oppermann

Wietek

et al. 2020

Preprint

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“…While we assume that the chloroviruses require Kcv activity to replicate, we do have to mention that out of the more than 150 chloroviruses that have been examined for a kcv gene, two NC64A viruses either lack a kcv gene or have a truncated form [ 1 ]. We would like to disrupt the kcv gene in some of the chloroviruses to see what effect this has on virus replication, however, currently the technology to do this experiment is not available.…”

Section: Discussionmentioning

confidence: 99%

“…Chloroviruses (family Phycodnaviridae ) are large, plaque-forming, dsDNA viruses that infect certain chlorella-like green algae that live in a symbiotic relationship with protists [ 1 ]. Chloroviruses have an internal membrane and they are icosahedral in shape with a spike structure at one of their vertices [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Potassium Ion Channel Proteins Encoded by Chloroviruses That Infect Chlorella heliozoae

Murry

Agarkova

Ghosh

et al. 2020

Viruses

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Chloroviruses are large, plaque-forming, dsDNA viruses that infect chlorella-like green algae that live in a symbiotic relationship with protists. Chloroviruses have genomes from 290 to 370 kb, and they encode as many as 400 proteins. One interesting feature of chloroviruses is that they encode a potassium ion (K+) channel protein named Kcv. The Kcv protein encoded by SAG chlorovirus ATCV-1 is one of the smallest known functional K+ channel proteins consisting of 82 amino acids. The KcvATCV-1 protein has similarities to the family of two transmembrane domain K+ channel proteins; it consists of two transmembrane α-helixes with a pore region in the middle, making it an ideal model for studying K+ channels. To assess their genetic diversity, kcv genes were sequenced from 103 geographically distinct SAG chlorovirus isolates. Of the 103 kcv genes, there were 42 unique DNA sequences that translated into 26 new Kcv channels. The new predicted Kcv proteins differed from KcvATCV-1 by 1 to 55 amino acids. The most conserved region of the Kcv protein was the filter, the turret and the pore helix were fairly well conserved, and the outer and the inner transmembrane domains of the protein were the most variable. Two of the new predicted channels were shown to be functional K+ channels.

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“…If the loss of viral genes duplicating cytoplasmic functions (amino acids and nucleotide synthesis, energy metabolism, protein translation) probably can happen quickly, in an almost random manner (the virus benefiting from a free lunch within the cell), the loss of the functional virus-encoded DNA replication or transcription machineries must be concomitantly compensated by an access to the cellular ones, in the host nucleus. The viruses must thus evolve a strategy to either transport their genomes to the intact nucleus [ 42 , 65 ], or make it functionally “leaky” [ 23 , 66 ], or even dissolve it altogether [ 67 ]. The passage from a purely cytoplasmic replication cycle to a nuclear one is thus a major step in the continuous retrogressive evolution of viruses.…”

Section: The Random Walk Of Gene Losses: Another Main Hurdle In Thmentioning

confidence: 99%

Fundamental Difficulties Prevent the Reconstruction of the Deep Phylogeny of Viruses

Claverie

2020

Viruses

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The extension of virology beyond its traditional medical, veterinary, or agricultural applications, now called environmental virology, has shown that viruses are both the most numerous and diverse biological entities on Earth. In particular, virus isolations from unicellular eukaryotic hosts (heterotrophic and photosynthetic protozoans) revealed numerous viral types previously unexpected in terms of virion structure, gene content, or mode of replication. Complemented by large-scale metagenomic analyses, these discoveries have rekindled interest in the enigma of the origin of viruses, for which a description encompassing all their diversity remains not available. Several laboratories have repeatedly tackled the deep reconstruction of the evolutionary history of viruses, using various methods of molecular phylogeny applied to the few shared “core” genes detected in certain virus groups (e.g., the Nucleocytoviricota). Beyond the practical difficulties of establishing reliable homology relationships from extremely divergent sequences, I present here conceptual arguments highlighting several fundamental limitations plaguing the reconstruction of the deep evolutionary history of viruses, and even more the identification of their unique or multiple origin(s). These arguments also underline the risk of establishing premature high level viral taxonomic classifications. Those limitations are direct consequences of the random mechanisms governing the reductive/retrogressive evolution of all obligate intracellular parasites.

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Chloroviruses

Cited by 53 publications

References 264 publications

Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses

Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses

Genetic Diversity of Potassium Ion Channel Proteins Encoded by Chloroviruses That Infect Chlorella heliozoae

Fundamental Difficulties Prevent the Reconstruction of the Deep Phylogeny of Viruses

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