The Experts below are selected from a list of 5082 Experts worldwide ranked by ideXlab platform

Bernard La Scola - One of the best experts on this subject based on the ideXlab platform.

  • clandestinoVirus a Giant Virus with chromatin proteins and a potential to manipulate the cell cycle of its host vermamoeba vermiformis
    Frontiers in Microbiology, 2021
    Co-Authors: Clara Rolland, Julien Andreani, Bernard La Scola, Anthony Levasseur, Dehia Sahmibounsiar, Mart Krupovic
    Abstract:

    For several decades, the vast world of DNA Viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA Viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a Giant Virus named "clandestinoVirus," grown on the amoebal host Vermamoeba vermiformis. This Virus was discovered in a mixed co-culture associated with another Giant Virus, FaustoVirus ST1. ClandestinoVirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinoVirus is most closely related to Acanthamoeba castellanii medusaVirus and was considered a member of the proposed Medusaviridae family. However, clandestinoVirus genome is 65% larger than that of medusaVirus, emphasizing the considerable genome size variation within this Virus family. Functional annotation of the clandestinoVirus genes suggests that the Virus encodes four core histones. Furthermore, clandestinoVirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinoVirus to optimize the intracellular environment for efficient Virus propagation.

  • diverse trajectories drive the expression of a Giant Virus in the oomycete plant pathogen phytophthora parasitica
    Frontiers in Microbiology, 2021
    Co-Authors: Sihem Hannat, Pierre Pontarotti, Bernard La Scola, Sarah Aherfi, Philippe Colson, Marieline Kuhn, Eric Galiana, Franck Panabieres
    Abstract:

    Giant Viruses of amoebas, recently classified in the class Megaviricetes, are a group of Viruses that can infect major eukaryotic lineages. We previously identified a set of Giant Virus sequences in the genome of Phytophthora parasitica, an oomycete and a devastating major plant pathogen. How viral insertions shape the structure and evolution of the invaded genomes is unclear, but it is known that the unprecedented functional potential of Giant Viruses is the result of an intense genetic interplay with their hosts. We previously identified a set of Giant Virus sequences in the genome of P. parasitica, an oomycete and a devastating major plant pathogen. Here, we show that viral pieces are found in a 550-kb locus and are organized in three main clusters. Viral sequences, namely RNA polymerases I and II and a major capsid protein, were identified, along with orphan sequences, as a hallmark of Giant Viruses insertions. Mining of public databases and phylogenetic reconstructions suggest an ancient association of oomycetes and Giant Viruses of amoeba, including faustoViruses, African swine fever Virus (ASFV) and pandoraViruses, and that a single viral insertion occurred early in the evolutionary history of oomycetes prior to the Phytophthora-Pythium radiation, estimated at ∼80 million years ago. Functional annotation reveals that the viral insertions are located in a gene sparse region of the Phytophthora genome, characterized by a plethora of transposable elements (TEs), effectors and other genes potentially involved in virulence. Transcription of viral genes was investigated through analysis of RNA-Seq data and qPCR experiments. We show that most viral genes are not expressed, and that a variety of mechanisms, including deletions, TEs insertions and RNA interference may contribute to transcriptional repression. However, a gene coding a truncated copy of RNA polymerase II along a set of neighboring sequences have been shown to be expressed in a wide range of physiological conditions, including responses to stress. These results, which describe for the first time the endogenization of a Giant Virus in an oomycete, contribute to challenge our view of Phytophthora evolution.

  • Giant Virus-related sequences in the 5300-year-old Ötzi mummy metagenome
    Virus Genes, 2021
    Co-Authors: Gabriel Augusto Pires De Souza, Bernard La Scola, Clara Rolland, Bariaa Nafeh, Philippe Colson
    Abstract:

    Giant Viruses have brought new perspectives on the virosphere. They have been increasingly described in humans, including in several metagenomic studies. Here, we searched into the metagenome of the 5300-year-old Ötzi mummy for the presence of Giant Virus-related sequences using MG-Digger pipeline. We found 19 reads (0.00006% of the total read number) that best matched (mean ± standard deviation (range) for e -values of 5.0E-6 ± 1.4E-6 (6.0E-5–4.0E-10) and for amino acid identity of 69.9 ± 8.7% (46.4–84.9%) and most significantly with sequences from various Giant Viruses, including mostly mimiViruses. This expands current knowledge on the ubiquity and relationship with humans of Giant Viruses.

  • Image_2_ClandestinoVirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis.tiff
    'Frontiers Media SA', 2021
    Co-Authors: Clara Rolland, Julien Andreani, Bernard La Scola, Dehia Sahmi-bounsiar, Mart Krupovic, Anthony Levasseur
    Abstract:

    For several decades, the vast world of DNA Viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA Viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a Giant Virus named “clandestinoVirus,” grown on the amoebal host Vermamoeba vermiformis. This Virus was discovered in a mixed co-culture associated with another Giant Virus, FaustoVirus ST1. ClandestinoVirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinoVirus is most closely related to Acanthamoeba castellanii medusaVirus and was considered a member of the proposed Medusaviridae family. However, clandestinoVirus genome is 65% larger than that of medusaVirus, emphasizing the considerable genome size variation within this Virus family. Functional annotation of the clandestinoVirus genes suggests that the Virus encodes four core histones. Furthermore, clandestinoVirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinoVirus to optimize the intracellular environment for efficient Virus propagation.

  • Table_2_ClandestinoVirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis.xlsx
    'Frontiers Media SA', 2021
    Co-Authors: Clara Rolland, Julien Andreani, Bernard La Scola, Dehia Sahmi-bounsiar, Mart Krupovic, Anthony Levasseur
    Abstract:

    For several decades, the vast world of DNA Viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA Viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a Giant Virus named “clandestinoVirus,” grown on the amoebal host Vermamoeba vermiformis. This Virus was discovered in a mixed co-culture associated with another Giant Virus, FaustoVirus ST1. ClandestinoVirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinoVirus is most closely related to Acanthamoeba castellanii medusaVirus and was considered a member of the proposed Medusaviridae family. However, clandestinoVirus genome is 65% larger than that of medusaVirus, emphasizing the considerable genome size variation within this Virus family. Functional annotation of the clandestinoVirus genes suggests that the Virus encodes four core histones. Furthermore, clandestinoVirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinoVirus to optimize the intracellular environment for efficient Virus propagation.

Steven W. Wilhelm - One of the best experts on this subject based on the ideXlab platform.

  • structural and proteomic studies of the aureococcus anophagefferens Virus demonstrate a global distribution of Virus encoded carbohydrate processing
    Frontiers in Microbiology, 2020
    Co-Authors: Eric R Gann, Yuejiao Xian, Chuan Xiao, Todd B Reynolds, Paul E Abraham, Robert L Hettich, Steven W. Wilhelm
    Abstract:

    Viruses modulate the function(s) of environmentally relevant microbial populations, yet considerations of the metabolic capabilities of individual Virus particles themselves are rare. We used shotgun proteomics to quantitatively identify 43 Virus-encoded proteins packaged within purified Aureococcus anophagefferens Virus (AaV) particles, normalizing data to the per-virion level using a 9.5-A-resolution molecular reconstruction of the 1900-A (AaV) particle that we generated with cryogenic electron microscopy. This packaged proteome was used to determine similarities and differences between members of different Giant Virus families. We noted that proteins involved in sugar degradation and binding (e.g., carbohydrate lyases) were unique to AaV among characterized Giant Viruses. To determine the extent to which this virally encoded metabolic capability was ecologically relevant, we examined the TARA Oceans dataset and identified genes and transcripts of viral origin. Our analyses demonstrated that putative Giant Virus carbohydrate lyases represented up to 17% of the marine pool for this function. In total, our observations suggest that the AaV particle has potential prepackaged metabolic capabilities and that these may be found in other Giant Viruses that are widespread and abundant in global oceans.

  • internal nitrogen pools shape the infection of aureococcus anophagefferens ccmp 1984 by a Giant Virus
    Frontiers in Microbiology, 2020
    Co-Authors: Eric R Gann, Todd B Reynolds, Brennan J Hughes, Steven W. Wilhelm
    Abstract:

    The pelagophyte Aureococcus anophagefferens blooms annually in shallow bays around the world, where it is hypothesized to outcompete other phytoplankton in part by using alternative nitrogen sources. The high proportion of natural populations that are infected during the late stages of the bloom suggest Viruses cause bloom collapse. We hypothesized that the Aureococcus anophagefferens Virus (AaV) infection cycle would be negatively influenced in cultures acclimated to decreasing external nitrogen conditions, but that the real-time external nitrogen concentration would not influence the infection cycle. Cultures acclimated in NO 3 - concentrations (0.0147 mM; N:P = 0.1225) that showed reduced end point cell abundances, forward scatter (a proxy for size) and red fluorescence (a proxy for chlorophyll a), also produced fewer Viruses per cell at a slower rate. Decreasing the external concentration of nitrogen post infection did not alter burst size or time to lysis. These data suggest that the nitrogen used for new viral progeny is present within host cells at the time of infection. Flow cytometric data of an infection cycle showed a reduction in red fluorescence around twelve hours post infection, consistent with degradation of nitrogen-rich chloroplasts during the infection cycle. Using cell and Virus quota estimates, we determined that A. anophagefferens cells had sufficient nitrogen and carbon for the lower ranges of burst sizes determined but did not contain enough phosphorous. Consistent with this observation, expression of nitrate and sugar transporters did not increase in the publicly available transcriptome data of the infection cycle, while several phosphorus transporters were. Our data demonstrate that dynamics of Viruses infecting Aureococcus over the course of a bloom is dictated by the host cell state upon infection, which is set a priori by external nutrient supplies.

  • influence of light on the infection of aureococcus anophagefferens ccmp 1984 by a Giant Virus
    PLOS ONE, 2020
    Co-Authors: Eric R Gann, Jackson P Gainer, Todd B Reynolds, Steven W. Wilhelm
    Abstract:

    The pelagophyte Aureococcus anophagefferens has caused recurrent brown tide blooms along the northeast coast of the United States since the mid-1980’s, and more recently spread to other regions of the globe. These blooms, due to the high cell densities, are associated with severe light attenuation that destroys the sea grass beds which provide the basis for many fisheries. Data collected by transmission electron microscopy, PCR, and metatranscriptomic studies of the blooms, support the hypothesis that large dsDNA Viruses play a role in bloom dynamics. While a large (~140 nm) icosahedral Virus, with a 371 kbp genome, was first isolated more than a decade ago, the constraints imposed by environmental parameters on bloom infection dynamics by Aureococcus anophagefferens Virus, (AaV) remain unknown. To investigate the role light plays in infection by this Virus, we acclimated A. anophagefferens to light intensities of 30 (low), 60 (medium) or 90 μmol photons m-2 s-1 (high) and infected cultures at these irradiance levels. Moreover, we completed light shift experiments where acclimated cultures were exposed to even lower light intensities (0, 5, and 15 μmol photons m-2 s-1) consistent with irradiance found during the peak of the bloom when cell concentrations are highest. The abundance of Viruses produced per lytic event (burst size) was lower in the low irradiance acclimated cultures compared to the medium and high acclimated cultures. Transferring infected cultures to more-limiting light availabilities further decreased burst size and increased the length of time it took for cultures to lyse, regardless of acclimation irradiance level. A hypothetical mechanism for the reduced efficiency of the infection cycle in low light due to ribosome biogenesis was predicted from pre-existing transcriptomes. Overall, these studies provide a framework for understanding light effects on infection dynamics over the course of the summer months when A. anophagefferens blooms occur.

  • infection by a Giant Virus aav induces widespread physiological reprogramming in aureococcus anophagefferens ccmp1984 a harmful bloom algae
    Frontiers in Microbiology, 2018
    Co-Authors: Mohammad Moniruzzaman, Eric R Gann, Steven W. Wilhelm
    Abstract:

    While Viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, "Giant" dsDNA Viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of Giant Virus-host interactions remain largely unknown. Aureococcus anophagefferens Virus (AaV), a Giant Virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens. To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host-Virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional response of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid, and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription, and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal-expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides insights into the Aureococcus cells infected by a Giant Virus and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.

  • infection by a Giant Virus induces widespread physiological reprogramming in aureococcus anophagefferens a harmful bloom algae
    bioRxiv, 2018
    Co-Authors: Mohammad Moniruzzaman, Eric R Gann, Steven W. Wilhelm
    Abstract:

    While Viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, "Giant" dsDNA Viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of Giant Virus - host interactions remain largely unknown. AaV, a Giant Virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens . To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host-Virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional reprogramming of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal-expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides the insight into the Aureococcus "virocell", and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.

Philippe Colson - One of the best experts on this subject based on the ideXlab platform.

  • diverse trajectories drive the expression of a Giant Virus in the oomycete plant pathogen phytophthora parasitica
    Frontiers in Microbiology, 2021
    Co-Authors: Sihem Hannat, Pierre Pontarotti, Bernard La Scola, Sarah Aherfi, Philippe Colson, Marieline Kuhn, Eric Galiana, Franck Panabieres
    Abstract:

    Giant Viruses of amoebas, recently classified in the class Megaviricetes, are a group of Viruses that can infect major eukaryotic lineages. We previously identified a set of Giant Virus sequences in the genome of Phytophthora parasitica, an oomycete and a devastating major plant pathogen. How viral insertions shape the structure and evolution of the invaded genomes is unclear, but it is known that the unprecedented functional potential of Giant Viruses is the result of an intense genetic interplay with their hosts. We previously identified a set of Giant Virus sequences in the genome of P. parasitica, an oomycete and a devastating major plant pathogen. Here, we show that viral pieces are found in a 550-kb locus and are organized in three main clusters. Viral sequences, namely RNA polymerases I and II and a major capsid protein, were identified, along with orphan sequences, as a hallmark of Giant Viruses insertions. Mining of public databases and phylogenetic reconstructions suggest an ancient association of oomycetes and Giant Viruses of amoeba, including faustoViruses, African swine fever Virus (ASFV) and pandoraViruses, and that a single viral insertion occurred early in the evolutionary history of oomycetes prior to the Phytophthora-Pythium radiation, estimated at ∼80 million years ago. Functional annotation reveals that the viral insertions are located in a gene sparse region of the Phytophthora genome, characterized by a plethora of transposable elements (TEs), effectors and other genes potentially involved in virulence. Transcription of viral genes was investigated through analysis of RNA-Seq data and qPCR experiments. We show that most viral genes are not expressed, and that a variety of mechanisms, including deletions, TEs insertions and RNA interference may contribute to transcriptional repression. However, a gene coding a truncated copy of RNA polymerase II along a set of neighboring sequences have been shown to be expressed in a wide range of physiological conditions, including responses to stress. These results, which describe for the first time the endogenization of a Giant Virus in an oomycete, contribute to challenge our view of Phytophthora evolution.

  • Giant Virus-related sequences in the 5300-year-old Ötzi mummy metagenome
    Virus Genes, 2021
    Co-Authors: Gabriel Augusto Pires De Souza, Bernard La Scola, Clara Rolland, Bariaa Nafeh, Philippe Colson
    Abstract:

    Giant Viruses have brought new perspectives on the virosphere. They have been increasingly described in humans, including in several metagenomic studies. Here, we searched into the metagenome of the 5300-year-old Ötzi mummy for the presence of Giant Virus-related sequences using MG-Digger pipeline. We found 19 reads (0.00006% of the total read number) that best matched (mean ± standard deviation (range) for e -values of 5.0E-6 ± 1.4E-6 (6.0E-5–4.0E-10) and for amino acid identity of 69.9 ± 8.7% (46.4–84.9%) and most significantly with sequences from various Giant Viruses, including mostly mimiViruses. This expands current knowledge on the ubiquity and relationship with humans of Giant Viruses.

  • Tricarboxylic acid cycle and proton gradient in PandoraVirus massiliensis: Is it still a Virus?
    2020
    Co-Authors: Sarah Aherfi, Jonatas Abrahao, Anthony Levasseur, Philippe Colson, D. Brahim Belhaouari, L. Pinault, Jean-pierre Baudoin, Philippe Decloquement, D. C. Lamb, Eric Chabriere
    Abstract:

    ABSTRACTSince the discovery of Acanthamoeba polyphaga MimiVirus, the first Giant Virus of amoeba, the historical hallmarks defining a Virus have been challenged. Giant virion sizes can reach up to 2.3 µm, making them visible by optical microscopy. They have large genomes of up to 2.5 Mb that encode proteins involved in the translation apparatus. Herein, we investigated possible energy production in PandoraVirus massiliensis, the largest of our Giant Virus collection. MitoTracker and TMRM mitochondrial membrane markers allowed for the detection of a membrane potential in virions that could be abolished by the use of the depolarizing agent CCCP. An attempt to identify enzymes involved in energy metabolism revealed that 8 predicted proteins of P. massiliensis exhibited low sequence identities with defined proteins involved in the universal tricarboxylic acid cycle (acetyl Co-A synthase; citrate synthase; aconitase; isocitrate dehydrogenase; α-ketoglutarate decarboxylase; succinate dehydrogenase; fumarase). All 8 viral predicted ORFs were transcribed together during viral replication, mainly at the end of the replication cycle. Two of these proteins were detected in mature viral particles by proteomics. The product of the ORF132, a predicted protein of P. massiliensis, cloned and expressed in Escherichia coli, provided a functional isocitrate dehydrogenase, a key enzyme of the tricarboxylic acid cycle, which converts isocitrate to α-ketoglutarate. We observed that membrane potential was enhanced by low concentrations of Acetyl-CoA, a regulator of the tricarboxylic acid cycle. Our findings show for the first time that energy production can occur in Viruses, namely, pandoraViruses, and the involved enzymes are related to tricarboxylic acid cycle enzymes. The presence of a proton gradient in P. massiliensis coupled with the observation of genes of the tricarboxylic acid cycle make this Virus a form a life for which it is legitimate to question ‘what is a Virus?’.

  • a virophage cross species infection through mutant selection represses Giant Virus propagation promoting host cell survival
    Communications Biology, 2020
    Co-Authors: Said Mougari, Fabrizio Di Pinto, Jonatas Abrahao, Philippe Colson, Nisrine Chelkha, Dehia Sahmibounsiar, Bernard La Scola
    Abstract:

    Virus adaptation to new hosts is a major cause of infectious disease emergence. This mechanism has been intensively studied in the context of zoonotic Virus spillover, due to its impact on global health. However, it remains unclear for virophages, parasites of Giant Viruses and potential regulators of microbial communities. Here, we present, for the first time to our knowledge, evidence of cross-species infection of a virophage. We demonstrated that challenging the native population of Guarani virophage with two previously unidentified Giant Viruses, previously nonpermissive to this virophage, allows the selection of a mutant genotype able to infect these Giant Viruses. We were able to characterize the potential genetic determinant (deletion) carried by the virophage with the expanded-host range. Our study also highlights the relevant biological impact of this host adaptation by demonstrating that coinfection with the mixture containing the mutant virophage abolishes Giant Virus production and rescues the host cell population from lysis.

  • A virophage cross-species infection through mutant selection represses Giant Virus propagation, promoting host cell survival
    Communications Biology, 2020
    Co-Authors: Said Mougari, Fabrizio Di Pinto, Philippe Colson, Jonatas Abrahao, Nisrine Chelkha, Dehia Sahmi-bounsiar, Bernard La Scola
    Abstract:

    Virus adaptation to new hosts is a major cause of infectious disease emergence. This mechanism has been intensively studied in the context of zoonotic Virus spillover, due to its impact on global health. However, it remains unclear for virophages, parasites of Giant Viruses and potential regulators of microbial communities. Here, we present, for the first time to our knowledge, evidence of cross-species infection of a virophage. We demonstrated that challenging the native population of Guarani virophage with two previously unidentified Giant Viruses, previously nonpermissive to this virophage, allows the selection of a mutant genotype able to infect these Giant Viruses. We were able to characterize the potential genetic determinant (deletion) carried by the virophage with the expanded-host range. Our study also highlights the relevant biological impact of this host adaptation by demonstrating that coinfection with the mixture containing the mutant virophage abolishes Giant Virus production and rescues the host cell population from lysis. Mougari et al. show that coinfection with a mixture containing mutant virophages abolishes the production of their host Giant Viruses, protecting the cells infected with these Giant Viruses. This study provides insights into multi-level parasitic interactions among virophages, Giant Viruses, and protists.

Eric R Gann - One of the best experts on this subject based on the ideXlab platform.

  • structural and proteomic studies of the aureococcus anophagefferens Virus demonstrate a global distribution of Virus encoded carbohydrate processing
    Frontiers in Microbiology, 2020
    Co-Authors: Eric R Gann, Yuejiao Xian, Chuan Xiao, Todd B Reynolds, Paul E Abraham, Robert L Hettich, Steven W. Wilhelm
    Abstract:

    Viruses modulate the function(s) of environmentally relevant microbial populations, yet considerations of the metabolic capabilities of individual Virus particles themselves are rare. We used shotgun proteomics to quantitatively identify 43 Virus-encoded proteins packaged within purified Aureococcus anophagefferens Virus (AaV) particles, normalizing data to the per-virion level using a 9.5-A-resolution molecular reconstruction of the 1900-A (AaV) particle that we generated with cryogenic electron microscopy. This packaged proteome was used to determine similarities and differences between members of different Giant Virus families. We noted that proteins involved in sugar degradation and binding (e.g., carbohydrate lyases) were unique to AaV among characterized Giant Viruses. To determine the extent to which this virally encoded metabolic capability was ecologically relevant, we examined the TARA Oceans dataset and identified genes and transcripts of viral origin. Our analyses demonstrated that putative Giant Virus carbohydrate lyases represented up to 17% of the marine pool for this function. In total, our observations suggest that the AaV particle has potential prepackaged metabolic capabilities and that these may be found in other Giant Viruses that are widespread and abundant in global oceans.

  • internal nitrogen pools shape the infection of aureococcus anophagefferens ccmp 1984 by a Giant Virus
    Frontiers in Microbiology, 2020
    Co-Authors: Eric R Gann, Todd B Reynolds, Brennan J Hughes, Steven W. Wilhelm
    Abstract:

    The pelagophyte Aureococcus anophagefferens blooms annually in shallow bays around the world, where it is hypothesized to outcompete other phytoplankton in part by using alternative nitrogen sources. The high proportion of natural populations that are infected during the late stages of the bloom suggest Viruses cause bloom collapse. We hypothesized that the Aureococcus anophagefferens Virus (AaV) infection cycle would be negatively influenced in cultures acclimated to decreasing external nitrogen conditions, but that the real-time external nitrogen concentration would not influence the infection cycle. Cultures acclimated in NO 3 - concentrations (0.0147 mM; N:P = 0.1225) that showed reduced end point cell abundances, forward scatter (a proxy for size) and red fluorescence (a proxy for chlorophyll a), also produced fewer Viruses per cell at a slower rate. Decreasing the external concentration of nitrogen post infection did not alter burst size or time to lysis. These data suggest that the nitrogen used for new viral progeny is present within host cells at the time of infection. Flow cytometric data of an infection cycle showed a reduction in red fluorescence around twelve hours post infection, consistent with degradation of nitrogen-rich chloroplasts during the infection cycle. Using cell and Virus quota estimates, we determined that A. anophagefferens cells had sufficient nitrogen and carbon for the lower ranges of burst sizes determined but did not contain enough phosphorous. Consistent with this observation, expression of nitrate and sugar transporters did not increase in the publicly available transcriptome data of the infection cycle, while several phosphorus transporters were. Our data demonstrate that dynamics of Viruses infecting Aureococcus over the course of a bloom is dictated by the host cell state upon infection, which is set a priori by external nutrient supplies.

  • influence of light on the infection of aureococcus anophagefferens ccmp 1984 by a Giant Virus
    PLOS ONE, 2020
    Co-Authors: Eric R Gann, Jackson P Gainer, Todd B Reynolds, Steven W. Wilhelm
    Abstract:

    The pelagophyte Aureococcus anophagefferens has caused recurrent brown tide blooms along the northeast coast of the United States since the mid-1980’s, and more recently spread to other regions of the globe. These blooms, due to the high cell densities, are associated with severe light attenuation that destroys the sea grass beds which provide the basis for many fisheries. Data collected by transmission electron microscopy, PCR, and metatranscriptomic studies of the blooms, support the hypothesis that large dsDNA Viruses play a role in bloom dynamics. While a large (~140 nm) icosahedral Virus, with a 371 kbp genome, was first isolated more than a decade ago, the constraints imposed by environmental parameters on bloom infection dynamics by Aureococcus anophagefferens Virus, (AaV) remain unknown. To investigate the role light plays in infection by this Virus, we acclimated A. anophagefferens to light intensities of 30 (low), 60 (medium) or 90 μmol photons m-2 s-1 (high) and infected cultures at these irradiance levels. Moreover, we completed light shift experiments where acclimated cultures were exposed to even lower light intensities (0, 5, and 15 μmol photons m-2 s-1) consistent with irradiance found during the peak of the bloom when cell concentrations are highest. The abundance of Viruses produced per lytic event (burst size) was lower in the low irradiance acclimated cultures compared to the medium and high acclimated cultures. Transferring infected cultures to more-limiting light availabilities further decreased burst size and increased the length of time it took for cultures to lyse, regardless of acclimation irradiance level. A hypothetical mechanism for the reduced efficiency of the infection cycle in low light due to ribosome biogenesis was predicted from pre-existing transcriptomes. Overall, these studies provide a framework for understanding light effects on infection dynamics over the course of the summer months when A. anophagefferens blooms occur.

  • infection by a Giant Virus aav induces widespread physiological reprogramming in aureococcus anophagefferens ccmp1984 a harmful bloom algae
    Frontiers in Microbiology, 2018
    Co-Authors: Mohammad Moniruzzaman, Eric R Gann, Steven W. Wilhelm
    Abstract:

    While Viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, "Giant" dsDNA Viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of Giant Virus-host interactions remain largely unknown. Aureococcus anophagefferens Virus (AaV), a Giant Virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens. To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host-Virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional response of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid, and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription, and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal-expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides insights into the Aureococcus cells infected by a Giant Virus and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.

  • infection by a Giant Virus induces widespread physiological reprogramming in aureococcus anophagefferens a harmful bloom algae
    bioRxiv, 2018
    Co-Authors: Mohammad Moniruzzaman, Eric R Gann, Steven W. Wilhelm
    Abstract:

    While Viruses with distinct phylogenetic origins and different nucleic acid types can infect and lyse eukaryotic phytoplankton, "Giant" dsDNA Viruses have been found to be associated with important ecological processes, including the collapse of algal blooms. However, the molecular aspects of Giant Virus - host interactions remain largely unknown. AaV, a Giant Virus in the Mimiviridae clade, is known to play a critical role in regulating the fate of brown tide blooms caused by the pelagophyte Aureococcus anophagefferens . To understand the physiological response of A. anophagefferens CCMP1984 upon AaV infection, we studied the transcriptomic landscape of this host-Virus pair over an entire infection cycle using a RNA-sequencing approach. A massive transcriptional reprogramming of the host was evident as early as 5 min post-infection, with modulation of specific processes likely related to both host defense mechanism(s) and viral takeover of the cell. Infected Aureococcus showed a relative suppression of host-cell transcripts associated with photosynthesis, cytoskeleton formation, fatty acid and carbohydrate biosynthesis. In contrast, host cell processes related to protein synthesis, polyamine biosynthesis, cellular respiration, transcription and RNA processing were overrepresented compared to the healthy cultures at different stages of the infection cycle. A large number of redox active host-selenoproteins were overexpressed, which suggested that viral replication and assembly progresses in a highly oxidative environment. The majority (99.2%) of annotated AaV genes were expressed at some point during the infection cycle and demonstrated a clear temporal-expression pattern and an increasing relative expression for the majority of the genes through the time course. We detected a putative early promoter motif for AaV, which was highly similar to the early promoter elements of two other Mimiviridae members, indicating some degree of evolutionary conservation of gene regulation within this clade. This large-scale transcriptome study provides the insight into the Aureococcus "virocell", and establishes a foundation to test hypotheses regarding metabolic and regulatory processes critical for AaV and other Mimiviridae members.

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  • clandestinoVirus a Giant Virus with chromatin proteins and a potential to manipulate the cell cycle of its host vermamoeba vermiformis
    Frontiers in Microbiology, 2021
    Co-Authors: Clara Rolland, Julien Andreani, Bernard La Scola, Anthony Levasseur, Dehia Sahmibounsiar, Mart Krupovic
    Abstract:

    For several decades, the vast world of DNA Viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA Viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a Giant Virus named "clandestinoVirus," grown on the amoebal host Vermamoeba vermiformis. This Virus was discovered in a mixed co-culture associated with another Giant Virus, FaustoVirus ST1. ClandestinoVirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinoVirus is most closely related to Acanthamoeba castellanii medusaVirus and was considered a member of the proposed Medusaviridae family. However, clandestinoVirus genome is 65% larger than that of medusaVirus, emphasizing the considerable genome size variation within this Virus family. Functional annotation of the clandestinoVirus genes suggests that the Virus encodes four core histones. Furthermore, clandestinoVirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinoVirus to optimize the intracellular environment for efficient Virus propagation.

  • Table_2_ClandestinoVirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis.xlsx
    'Frontiers Media SA', 2021
    Co-Authors: Clara Rolland, Julien Andreani, Bernard La Scola, Dehia Sahmi-bounsiar, Mart Krupovic, Anthony Levasseur
    Abstract:

    For several decades, the vast world of DNA Viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA Viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a Giant Virus named “clandestinoVirus,” grown on the amoebal host Vermamoeba vermiformis. This Virus was discovered in a mixed co-culture associated with another Giant Virus, FaustoVirus ST1. ClandestinoVirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinoVirus is most closely related to Acanthamoeba castellanii medusaVirus and was considered a member of the proposed Medusaviridae family. However, clandestinoVirus genome is 65% larger than that of medusaVirus, emphasizing the considerable genome size variation within this Virus family. Functional annotation of the clandestinoVirus genes suggests that the Virus encodes four core histones. Furthermore, clandestinoVirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinoVirus to optimize the intracellular environment for efficient Virus propagation.

  • Image_2_ClandestinoVirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis.tiff
    'Frontiers Media SA', 2021
    Co-Authors: Clara Rolland, Julien Andreani, Bernard La Scola, Dehia Sahmi-bounsiar, Mart Krupovic, Anthony Levasseur
    Abstract:

    For several decades, the vast world of DNA Viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA Viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a Giant Virus named “clandestinoVirus,” grown on the amoebal host Vermamoeba vermiformis. This Virus was discovered in a mixed co-culture associated with another Giant Virus, FaustoVirus ST1. ClandestinoVirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinoVirus is most closely related to Acanthamoeba castellanii medusaVirus and was considered a member of the proposed Medusaviridae family. However, clandestinoVirus genome is 65% larger than that of medusaVirus, emphasizing the considerable genome size variation within this Virus family. Functional annotation of the clandestinoVirus genes suggests that the Virus encodes four core histones. Furthermore, clandestinoVirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinoVirus to optimize the intracellular environment for efficient Virus propagation.

  • Tricarboxylic acid cycle and proton gradient in PandoraVirus massiliensis: Is it still a Virus?
    2020
    Co-Authors: Sarah Aherfi, Jonatas Abrahao, Anthony Levasseur, Philippe Colson, D. Brahim Belhaouari, L. Pinault, Jean-pierre Baudoin, Philippe Decloquement, D. C. Lamb, Eric Chabriere
    Abstract:

    ABSTRACTSince the discovery of Acanthamoeba polyphaga MimiVirus, the first Giant Virus of amoeba, the historical hallmarks defining a Virus have been challenged. Giant virion sizes can reach up to 2.3 µm, making them visible by optical microscopy. They have large genomes of up to 2.5 Mb that encode proteins involved in the translation apparatus. Herein, we investigated possible energy production in PandoraVirus massiliensis, the largest of our Giant Virus collection. MitoTracker and TMRM mitochondrial membrane markers allowed for the detection of a membrane potential in virions that could be abolished by the use of the depolarizing agent CCCP. An attempt to identify enzymes involved in energy metabolism revealed that 8 predicted proteins of P. massiliensis exhibited low sequence identities with defined proteins involved in the universal tricarboxylic acid cycle (acetyl Co-A synthase; citrate synthase; aconitase; isocitrate dehydrogenase; α-ketoglutarate decarboxylase; succinate dehydrogenase; fumarase). All 8 viral predicted ORFs were transcribed together during viral replication, mainly at the end of the replication cycle. Two of these proteins were detected in mature viral particles by proteomics. The product of the ORF132, a predicted protein of P. massiliensis, cloned and expressed in Escherichia coli, provided a functional isocitrate dehydrogenase, a key enzyme of the tricarboxylic acid cycle, which converts isocitrate to α-ketoglutarate. We observed that membrane potential was enhanced by low concentrations of Acetyl-CoA, a regulator of the tricarboxylic acid cycle. Our findings show for the first time that energy production can occur in Viruses, namely, pandoraViruses, and the involved enzymes are related to tricarboxylic acid cycle enzymes. The presence of a proton gradient in P. massiliensis coupled with the observation of genes of the tricarboxylic acid cycle make this Virus a form a life for which it is legitimate to question ‘what is a Virus?’.

  • Isolation and genomic characterization of a new mimiVirus of lineage B from a Brazilian river
    Archives of Virology, 2020
    Co-Authors: Ludmila Karen Dos Santos Silva, Julien Andreani, Bernard La Scola, Anthony Levasseur, Ana Claudia Santos Pereira Andrade, Rodrigo Araujo Lima Rodrigues, Hiroyuki Hikida, Jonatas Abrahao
    Abstract:

    Since its discovery, the first identified Giant Virus associated with amoebae, Acanthamoeba polyphaga mimiVirus (APMV), has been rigorously studied to understand the structural and genomic complexity of this Virus. In this work, we report the isolation and genomic characterization of a new mimiVirus of lineage B, named “Borely moumouVirus”. This new Virus exhibits a structure and replicative cycle similar to those of other members of the family Mimiviridae . The genome of the new isolate is a linear double-strand DNA molecule of ~1.0 Mb, containing over 900 open reading frames. Genome annotation highlighted different translation system components encoded in the DNA of Borely moumouVirus, including aminoacyl-tRNA synthetases, translation factors, and tRNA molecules, in a distribution similar to that in other lineage B mimiViruses. Pan-genome analysis indicated an increase in the genetic arsenal of this group of Viruses, showing that the family Mimiviridae is still expanding. Furthermore, phylogenetic analysis has shown that Borely moumouVirus is closely related to moumouVirus australiensis. This is the first mimiVirus lineage B isolated from Brazilian territory to be characterized. Further prospecting studies are necessary for us to better understand the diversity of these Viruses so a better classification system can be established.