Monday, August 13, 2018

BacterioFiles 351 - Tupanvirus Transports Translation Tools

Tupanvirus pictures
From: Abrahão et al,
2018, Nat Commun 9:749
This episode: A new giant virus has genes for a surprisingly complete system of protein synthesis!

Download Episode (10.1 MB, 11.1 minutes)

Show notes:
Microbe of the episode: Phocid alphaherpesvirus 1

Video of tupanvirus intracellular factory

Journal Paper:
Abrahão J, Silva L, Silva LS, Khalil JYB, Rodrigues R, Arantes T, Assis F, Boratto P, Andrade M, Kroon EG, Ribeiro B, Bergier I, Seligmann H, Ghigo E, Colson P, Levasseur A, Kroemer G, Raoult D, La Scola B. 2018. Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere. Nat Commun 9:749.

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Episode outline:
  • Background: Giant viruses mysterious in many ways
    • Lots of genes of unknown function
    • Also lots of genes unexpected in virus (like ep 348, have DNA-packing genes)
      • Genes for translation often present in intracellular parasites but not viruses
    • But many giant viruses have some
  • tRNAs, and now even aminoacyl tRNA synthetases
    • Mimi and others make several kinds each, up to 7
  • What’s new: Now, scientists publishing in Nature Communications have discovered that a giant virus called Tupanvirus has a surprisingly complete translation system!
  • Methods: Discovered new giant viruses with these large tails
    • In soda lake from Brazil – high pH and salt, harsh conditions
    • And also in deep ocean
  • Named after Tupa, Guaraní supreme/thunder god
    • Not the biggest; similar to other Mimis
    • But have large tail
    • Infect amoebas and such
  • Particles attach to host, get phagocytosed
    • Then merge virus membrane with phagosome, releasing genome
    • Make virus factory inside – see movies
    • Cell gets filled with particles and then bursts
  • Genomes are ~1.5 Mb, ~1300-1400 predicted genes, ~30% no known matches
  • Looked at genes and proteins predicted from the genomes
    • Not surprising – not much for energy metabolism, depends on host
    • But had a lot of translation related genes
      • 20 for attaching tRNAs to aminos – basically complete
      • And tRNAs for 46-47 codons (out of 64 possible)
      • Deep ocean version even has rare pyrrolysine tRNA
      • But no selenocysteine, sometimes lacking in cells anyway
      • Also a bunch more genes
      • Bigger set of such than some bacteria, archaea, even eukaryotes
  • Soda lake virus could infect multiple different protists
    • Not all allowed virus replication though
    • But some showed disease even without replication – not known before
    • Found that Tupanvirus can knock down host ribosome numbers, inhibit translation
    • New mechanism: captures and imprisons ribosomes in membrane compartment
    • And degrades structure of nucleus
    • Seems to be done by proteins in particle, not produced from genome by new host
  • Speculation that could prevent predators from reducing viral populations
  • Summary: Newly discovered giant viruses have most complete protein producing machinery of virus so far, and can disrupt protein production in hosts even when not able to replicate in them
  • Applications and implications: Helpful to have even more examples of variety
    • Compare and contrast
    • Understand history and what is possible
  • Clarifications if necessary: Haven't shown genes are being made into protein-producing enzymes, just know genes are present
  • What do I think: Two main hypotheses for origins of giant viruses
    • Came from even bigger things, lost genome content as parasite
    • Came from smaller things and acquired content
    • Could be some of both
  • Not sure what a lot of genome content is doing
    • Presumably something, otherwise smaller genomes would take over population
    • Much smaller viruses can be quite effective in infecting
    • But with more, can have a lot more control over host
  • Quite possible that "viruses" doesn't describe group that all came about the same way
    • Maybe some had one origin, others had another
    • And some new ones might've come from parts of already existing
      • Like ep 330 – plasmid in a particle
    • All just ways of genetic material moving around
  • But called "virus" cos replicates in host using host machinery/resources and then transfers externally
  • May not be alive, but can reveal a lot about life

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