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

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.

Quantitative Assessment of Nucleocytoplasmic Large DNA Virus and Host Interactions Predicted by Co-occurrence Analyses

“…Conversely, our results suggested that retaining structural zeros did not negatively influence the result, which indicates that the “presence-absence” pattern is as informative as the “more-less” pattern when identifying NCLDV-host relationships. This result is consistent with a previous “K-r-strategist” hypothesis: some NCLDVs, like mimiviruses, are K-strategists that decay slowly and can form stable associations with their hosts ( 52 , 53 ). A recent report supported these non-“boom and bust” dynamics of prasinoviruses and their hosts with an experiment-based mathematical model ( 54 ).…”

Discovery of Viral Myosin Genes With Complex Evolutionary History Within Plankton

“…These genes, often called auxiliary metabolic genes, are considered to function in reprogramming host metabolism and molecular machinery during viral infection toward enhancing viral replication and subsequent transmission to another host. For example, the recently characterized Prymnesium kappa virus RF01 encodes genes for all four succinate dehydrogenase subunits, as well as genes for modulating β-oxidation pathway ( Blanc-Mathieu et al, 2021 ). These viral genes are suggested to boost energy production during viral replication, which can deteriorate host metabolism, or to enhance the supply of building blocks for viral replication.…”

Adaptive evolution of viruses infecting marine microalgae (haptophytes), from acute infections to stable coexistence

“…These genes make the viruses more independent from their hosts by allowing the virus to manipulate the host during infection. The functions of AMGs have been linked to central roles in photosynthesis in cyanobacteria (Lindell et al ., 2004), sphingolipid biosynthesis of E. huxleyi (Moniruzzaman et al ., 2020; Schulz et al ., 2020), nitrogen uptake in Ostreococcus (Monier et al ., 2017) and even central roles in the tricarboxylic acid (TCA) cycle/oxidative phosphorylation chain, potentially controlling energy production in the host cells during infections (Blanc‐Mathieu et al ., 2021).…”