(Viruses in the ocean)

Question 1

Viruses in the oceans

Answer 1

Abundancy
EM studies show
~108 virus particles ml–1
marine sediments 108–109 viruses cm–3
(concentration declines with distance to coast and with depth of water)

Genetic variability
Thousands of different viral genotypes found in 200 l sea water
1 million different viruses in 1 kg sediment

3x109 viruses in l–1 sea water = total amount x 1.3x1021 l

~4x1030 viruses
correlates with respect to carbon amount ~75 million Blue Whales

Question 2

A giant virus in Amoebae

Answer 2

• 1992 cooling tower in Bradford England: First isolation of ameba with inclusion bodies
• 2003 Acanthamoeba polyp>haga Mimivirus („mimicking microbe“)
• Mimivirus: 800 kbp
• Mamavirus: 1200 kbp (linear ds DNA)
  -> Smallest intracellular bacterium: Mycoplasma genitalium 580 kbp

Is this really a virus?
APMV: Size 400 nm
The giant virus particles contain mRNA and more than 100 proteins

Question 3

A giant virus in Amoebae
-> Is it a virus or an obliogate intracellular bacterium?

Answer 3

• capsid protein (double jelly-roll fold)
• ikosahedral structure
• eklipse phase („disappearance“) as part of life cycle
• absence of genes for ribosomes (but for aminoacyl tRNA synthetases), energy production and energy conversion
• phylogeny

Question 4

A giant virus in Amoebae
-> Viruses as nature’s greatest genetic experiment?

Answer 4

Acanthamoeba polyphaga Mimivirus
- 975 transcribed genes
Where do the genes come from?
- 30% from eukaryotic host
- 70% from the virosphere
= gene pool of viruses

A giant virus!
Largest Megaviridae family member: Megavirus chilensis (1.259 Mb encoding 1120 proteins)

Question 5

A virus gets infected by a virus

Answer 5

Sputnik, a virophage
- 50 nm
- 18.3 kb circular ds DNA
- depends in its replication on mamavirus (helper virus)
- its 21 genes are a mixture from viruses infecting Archaea, Bacteria and Eukarya
- tree genes derived from Acanthamoeba polyphaga Mamavirus
- archaeal integrase
- packaging ATPase related to bacteriophages/ DNA viruses

Attractive hypotesis based on presence of integrase protein: Gene transfer by virophages

Viruses as a genetic tool box between kingdoms of life?
A lot of recombinations found between host and virus or in between different viruses!

Question 6

Pandoraviruses: Amoeba Viruses with Genomes up to 2.5 Mb Reaching That of Parasitic Eukaryotes

Answer 6

Their micrometer-sized ovoid particles contain DNA genomes of at least 2.5 and 1.9 megabases!

Question 7

Giant viruses open Pandora’s box
-> Genome of largest viruses yet discovered hints at “fourth domain” of life

Answer 7

• Pandoravirus salinus found in a water sample collected off the coast of Chile
• P. dulcis, from a pond near Melbourne

Pandoraviruses are wide spread!

Do they represent remnants of another ancient domain of life?
“But these viruses…are more than mere record-breakers — they also hint at unknown parts of the tree of life. Just 7% of their genes match those in existing databases.”

Pandoraviruses
1 micrometre long and 0.5 micrometres across, and their respective genomes top out at 1.9 million and 2.5 million bases

Question 8

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandora virus morphology

Answer 8

This discovery, which suggests giant viruses are not uncommon and are very diverse, also proves that the capacity of viruses to survive in the permafrost for very long periods is not limited by a particular type of virus, but probably covers viral families with different replication strategies and therefore potentially pathogenic,” the official statement by France’s National Centre for Scientific Research (CNRS) said.

Question 9

Giant viruses with an expanded complement of translation system components

Answer 9

Klosneuviruses did not evolve from a cellular ancestor but rather are derived from a much smaller virus through extensive gain of host genes.

Our results rather imply piecemeal capture of eukaryotic translation machinery components and are most compatible with independent origins of giant viruses from much smaller viruses.

Question 10

Tupanvirus - the longest tailed Mimiviridae member isolated in amoebae

Answer 10

• 1.44-1.51 mb linear ds DNA
• 1276-1425 predicted proteins including 20 aminoacyl tRNA Synthetases and 11 other translation factors
• for protein synthesis only ribosomes are missing!

Question 11

New scheme to categorize organisms
-> redefinition of “living organism”

Answer 11

Clusters of orthologous groups (COGs) of gene categories
- Translation
- Transcription
- RNA processing/mod

LUCA: Cast Universal Common Anchestor

All living organisms contain probably 34 ribosomal genes which are still shared by Rachael, bacterial and eukaryotic organisms

These most conserved elements of livening organisms were impart found in Klosneuviruses and could thus be compared

Still the case: Viruses (including Klosneuviruses) do not encode ribosomal proteins or rRNAs