Viruses in the Oceans

Question 1

Viruses in the ocean

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

Answer 3

Is it a virus or an obliogate intracellular bacterium?
- 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

Viruses as nature ́s greatest genetic experiment?
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!

Question 4

A virus gets infected by a virus

Answer 4

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 5

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

Answer 5

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 6

Giant viruses with an expanded complement of translation system components

Answer 6

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.

Length: 2.3 µm

For protein synthesis only ribosomes are missing!!!

Question 7

New scheme to categorize organisms

Answer 7

Redefinition of „living organism“
Clusters of orthologous groups (COGs) of gene categories
- Translation
- Transcription
- RNA processing/mod. …
LUCA
Last Universal Common Anchestor
All living organisms
contain probably 34 ribosomal genes which are still shared by archaeal, bacterial and eucaryotic organisms
These most conserved elements of living organisms
Were inpart found in Klosneuviruses and could thus be compared

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