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Genetic Diversity and Evolution | Spotlight

A Persistent Giant Algal Virus, with a Unique Morphology, Encodes an Unprecedented Number of Genes Involved in Energy Metabolism

Romain Blanc-Mathieu, Håkon Dahle, Antje Hofgaard, David Brandt, Hiroki Ban, Jörn Kalinowski, Hiroyuki Ogata, Ruth-Anne Sandaa
Joanna L. Shisler, Editor
Romain Blanc-Mathieu
aInstitute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
bLaboratoire de Physiologie Cellulaire & Végétale, CEA, Université Grenoble Alpes, CNRS, INRA, IRIG, Grenoble, France
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  • ORCID record for Romain Blanc-Mathieu
Håkon Dahle
cDepartment of Biological Sciences, University of Bergen, Bergen, Norway
dK.G. Jebsen Center for Deep Sea Research, University of Bergen, Bergen, Norway
gComputational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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Antje Hofgaard
eDepartment of Biosciences, University of Oslo, Oslo, Norway
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David Brandt
fCenter for Biotechnology, Bielefeld University, Bielefeld, Germany
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Hiroki Ban
aInstitute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
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Jörn Kalinowski
fCenter for Biotechnology, Bielefeld University, Bielefeld, Germany
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Hiroyuki Ogata
aInstitute for Chemical Research, Kyoto University, Gokasho, Uji, Japan
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Ruth-Anne Sandaa
cDepartment of Biological Sciences, University of Bergen, Bergen, Norway
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Joanna L. Shisler
University of Illinois at Urbana Champaign
Roles: Editor
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DOI: 10.1128/JVI.02446-20
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ABSTRACT

Viruses have long been viewed as entities possessing extremely limited metabolic capacities. Over the last decade, however, this view has been challenged, as metabolic genes have been identified in viruses possessing large genomes and virions—the synthesis of which is energetically demanding. Here, we unveil peculiar phenotypic and genomic features of Prymnesium kappa virus RF01 (PkV RF01), a giant virus of the Mimiviridae family. We found that this virus encodes an unprecedented number of proteins involved in energy metabolism, including all four succinate dehydrogenase (SDH) subunits (A to D), as well as key enzymes in the β-oxidation pathway. The SDHA gene was transcribed upon infection, indicating that the viral SDH is actively used by the virus, potentially to modulate its host’s energy metabolism. We detected orthologous SDHA and SDHB genes in numerous genome fragments from uncultivated marine Mimiviridae viruses, which suggests that the viral SDH is widespread in oceans. PkV RF01 was less virulent than other cultured prymnesioviruses, a phenomenon that may be linked to the metabolic capacity of this virus and is suggestive of relatively long coevolution with its hosts. It also has a unique morphology compared to those of other characterized viruses in the Mimiviridae family. Finally, we found that PkV RF01 is the only alga-infecting Mimiviridae virus encoding two aminoacyl-tRNA synthetases and enzymes corresponding to an entire base excision repair (BER) pathway, as seen in heterotroph-infecting Mimiviridae viruses. These Mimiviridae encoded-enzymes were found to be monophyletic and branching at the root of the eukaryotic tree of life. This placement suggests that the last common ancestor of Mimiviridae was endowed with a large, complex genome prior to the divergence of known extant eukaryotes.

IMPORTANCE Viruses on Earth are tremendously diverse in terms of morphology, functionality, and genomic composition. Over the last decade, the conceptual gap separating viruses and cellular life has tightened because of the detection of metabolic genes in viral genomes that express complex virus phenotypes upon infection. Here, we describe Prymnesium kappa virus RF01, an alga-infecting large virus with a unique morphology, an atypical infection profile, and an unprecedented number of genes involved in energy metabolism (such as the tricarboxylic acid [TCA] cycle and the β-oxidation pathway). Moreover, we show that the gene corresponding to one of these enzymes (the succinate dehydrogenase subunit A) is transcribed during infection and is widespread among marine viruses. This discovery provides evidence that a virus has the potential to actively regulate energy metabolism with its own genes.

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A Persistent Giant Algal Virus, with a Unique Morphology, Encodes an Unprecedented Number of Genes Involved in Energy Metabolism
Romain Blanc-Mathieu, Håkon Dahle, Antje Hofgaard, David Brandt, Hiroki Ban, Jörn Kalinowski, Hiroyuki Ogata, Ruth-Anne Sandaa
Journal of Virology Mar 2021, 95 (8) e02446-20; DOI: 10.1128/JVI.02446-20

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A Persistent Giant Algal Virus, with a Unique Morphology, Encodes an Unprecedented Number of Genes Involved in Energy Metabolism
Romain Blanc-Mathieu, Håkon Dahle, Antje Hofgaard, David Brandt, Hiroki Ban, Jörn Kalinowski, Hiroyuki Ogata, Ruth-Anne Sandaa
Journal of Virology Mar 2021, 95 (8) e02446-20; DOI: 10.1128/JVI.02446-20
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KEYWORDS

β-oxidation
Mimiviridae
algal virus
aminoacyl-tRNA synthetases
coevolution
energy production
metabolism
persistent
succinate dehydrogenase

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