4- Viral Genomes

Question 1

What are viruses?

Answer 1

Viruses are entities whose genomes are elements of nucleic acid that replicate inside living cells using the cellular synthetic machinery and cause the synthesis of specialized elements (virions) that can transfer the genome to other cells

Question 2

What is the Baltimore classification?

Answer 2

The way viruses are classified, by the nature of their genome (eg. dsDNA, ssDNA, dsRNA, ssRNA(+), ssRNA(-), ssRNA-RT, dsRNA-RT)

RNA-RT is a DNA intermediate

Question 3

What are four ways of classifying viruses?

Answer 3

• Nature of genome (Baltimore classification)
• Shape and capsid structure
• Presence/absence of envelope
• Type of host organism (eg. bacteriophage)

Question 4

How many viral particles are there per drop of seawater?

Answer 4

10 million

They are the major abundant type of life, but account for a small amount of biomass.

Question 5

List six typical features of viral genomes

Answer 5

• There is no typical structure! Linear, circular or alternate between the two.
• Gene expression patterns are also diverse
• High gene density (about 1 per kbp, often with overlap)
• Fast evolving, divergent gene sequence, RNA viruses especially
• Extremely diverse coding capacity

Question 6

Why are RNA viruses especially fast evolving and divergent?

Answer 6

• Viral RNA polymerase lacks proofreading

- Reverse transcription is error prone in retroviruses

Question 7

What are the 5 types of viral genes?

Answer 7

Genes with readily detectable homologs in cellular life forms:

• Genes with homologs in cellular organisms (typically host)
• Genes conserved among a group of viruses or groups of viruses, also distant homologs in cell life

Virus-specific genes:

• ORFans (genes without homologs)
• Conserved (among viruses only) genes

Viral ‘hallmark’ genes
- Genes shared by many (but not necessarily all) groups of viruses, with only very distant homologs in cell life (eg. capsid proteins, reverse transcriptases, RNA-dependent RNA polymerase). Very few of these, none that all viruses share.

Question 8

What are the relative frequencies of ORFans in viruses?

Answer 8

It depends on the virus, the bigger the genome the more ORFans there are.

Question 9

Which family of viruses do giant viruses belong to?

Answer 9

Nucleo-cytoplasmic large DNA virus (NCLDV) family

Question 10

What type of eukaryotes do giant viruses (specifically pandoravirus) have a little bit of overlap with, in terms of genome size?

Answer 10

Parasitic eukaryotes

also parasitic bacteria and both parasitic AND free living archaea

Question 11

GIve some peculiar qualities of Mimiviruses genome

Answer 11

• Double stranded DNA
• 10% of ORFs similar to proteins of known function
• Presence of numerous genes encoding central protein translation components, including amino-acyl transfer RNA synthetases, peptide release factor 1, translation elongation factor EF-TU, and translation initiation factor 1. tRNA
• May reveal information about early evolution of eukaryotes

Question 12

Give the life cycle of mimivirus

Answer 12

• Phagocytosis into host
• Microbe in vacuole
• Stargate capsid opening
• Early virion factory
• Mature virion factory with budding capsids
• viron factory after 12 h

Virion factory: AN intracellular compartment (nuclear or cytoplasmic) that serves as the site of viral replication and assembly using the host cell’s metabolites and protein machinery.

Question 13

Mimivirus kind of appears to represent a fourth domain of life with its translation/transcription expressed proteins. Is this true? Why?

Answer 13

Likely not. A better thought would be viruses as pickpockets, mimivirus appears to have acquired genes from its host (amoeba), rather than generating them itself.

The origin of giant viruses is from smaller DNA viruses.

Very few genes in giant viruses are most similar to those in other viruses, they are more similar to eukaryotes.

Question 14

True or false? A large percent of pandoravirus’s genome is ORFans. How is pandoravirus similar to Mimivirus in uniqueness as a virus?

Answer 14

True! Up to 93%

16 genes were found to have spliceosomal (eukaryotic) introns!

Some but not all of the translation-associated genes found in mimivirus were found in pandoraviruses and vice versa.

Question 15

True or false, pandoravirus is closely related to other giant viruses.

Answer 15

False. It is not closely related to any other known group of viruses, including mimivirus!

This is based on polymerase phylogeny.

Question 16

Give three lines of evidence for giant viruses not being a new form of life

Answer 16

• Translation associated genes in giant viruses exhibit a patchy distribution
• Universal genes (those with homologs in at least two of the three domains of life) have been independently acquired by different giant viruses from their eukaryotic hosts (often Acanthamoeba, the host of mimivirus and pandoravirus)
• Each group of giant viruses appears to have evolved from viruses with substantially smaller gene repertoires

Question 17

Describe virophages

Answer 17

Eg. sputnik, grows rapidly in virion factory of mimivirus, but can’t multiply in the amoeba alone. Sputnik contains dsDNA that contains genes linked to viruses infecting each of the three domains of life, eukarya, archaea and bacteria.

• Virophages could by mediating lateral gene transfer between giant viruses! (similar to bacteriophages)

Question 18

True or false, viruses are part of the tree of life

Answer 18

Currently being debated!

What is clear is that viruses are very much ‘plugged in’ to the tree of life.

They reproduce and evolve.

Question 19

What is a new definition for a virus after mimivirus discovery?

Answer 19

A capsid containing organism that is composed of proteins and nucleic acids. Self assembles in a nucleocapsid and uses a ribosome encoding organism for the completion of its life cycle

The virion factory is kind of like a transient microorganism

A virus breaks up and then becomes reconstituted after replication from newly synthesized parts.