Baltimore Classification

Replication & Expression

- Genome replication & gene expression very closely linked
- Characteristics depends on nature of genome

Replication Strategy of dsDNA Viruses

Steps in Replication
1. Primary transcription by host enzymes
2. Translation of early (=regulatory) proteins
3. Viral genomic DNA replication (usually by host enzymes)
4. Late transcription (usually mediated by viral proteins)
5. Synthesis of late (=structural) proteins
6. Assembly of structural protein and DNA into virions.

Type I: dsDNA
dsDNA viruses include:
- viruses infecting Eubacteria and Archaea, or phages (eg. the Podoviridae, phages of E coli);
- viruses of higher animals (Pox-, Herpes-, Adeno-, Papovaviridae);
- viruses of insects (Baculo- and Irido- and Polydnaviridae);
- and viruses of eukaryotic algae (Phycodnaviridae);
- viruses of fungi

These range in size from:
- 5-8 kb (Papovaviridae)
- through 30-40 kb (lambda phage and Adenoviridae)
- to about 200 kb (Baculoviridae)
- to over 300 kb (Herpes- and Pox- and Irido- and Phycodnaviridae)
- through ~400 kb (Phycodnaviridae)
- up to over 1 million bases (Mimivirus).

Marvellous mimivirus « MicrobiologyBytes via kwout

By contrast, the smallest prokaryote genome size is about 500 kb (E coli = 4000 kb)
They may have:
- circular genomes (Papova- and Baculo- and Polydnaviridae);
- linear genomes (Adeno- and Herpesviridae, some phages);
- have circularly permuted linear genomes (phage T4, some Iridoviridae);
- or linear genomes with covalently closed ends (Pox- and Phycodnaviridae).
All viruses except Polydnaviridae have single-component genomes; the latter have multiple components ranging in size from 2 - 20 kb, and the number which constitute an individual genome is not known.

Replication of the viruses is in all cases by the semi-conservative method favoured by cellular genomes; however, smaller circular genomes (eg. Papovaviridae) replicate by means of bidirectional replication forks from a single origin, like some plasmids. Among the viruses of Eukarya, replication mainly occurs in the nucleus, using cellular enzymes such as polymerases, methylases, etc. However,the replication of Poxviruses, some Baculoviruses (granulosis group), and some of the replication of iridoviruses, takes place in virus-specified "inclusion bodies" in the cytoplasm, using viral-coded enzymes, most important of which are DNA-dependent DNA polymerases.

DNA Viruses « MicrobiologyBytes via kwout

Type II: ssDNA

Replication Strategy of ssDNA Viruses

Steps in Replication
1. Conversion into dsDNA (=host repair process?)
2. Early transcription (by host enzymes)
3. Translation of (regulatory) protein and "rolling circle" ssDNA replication
4. Late transcription (usually mediated by viral proteins)
5. Synthesis of late (=structural) proteins
6. "Sequestering" of viral genomic ssDNA
7. Assembly into virions

ssDNA viruses include organisms infecting:
bacteria ("bacteriophages", eg. Inoviridae, Microviridae),
mammals (Circoviridae, Parvoviridae click for image),
birds (circovirus-like organisms),
and plants (Geminiviridae, banana bunchy top-like viruses or Nanoviruses).

They can have:
linear single-component genomes (Parvoviridae),
circular single-component genomes (Microviridae, Inoviridae, Circoviridae, some Geminiviridae),
circular two-component genomes (some Geminiviridae),
or circular multicomponent (>3) genomes (Nanoviruses).

The genomes are all relatively small:
the Circoviridae have genomes of about 3 kb;
Parvoviridae have genomes of 4-5 kb;
the Geminiviridae about 2.7 - 5.4 kb (depending on whether are mono- or bi-component);
the Microviridae (including the famous phiX 174) about 4.5 kb;
the Inoviridae and the Nanoviruses about 5-6 kb.

Replication of all of the viruses requires formation of a "replicative form" (RF) double- stranded DNA intermediate: this is formed soon after infection, almost certainly by the host cell DNA polymerases engaging in "repair" of the ssDNA.

The replication machinery of geminiviruses and nanoviruses from plants, circoviruses, anelloviruses and even parvoviruses from animals, and the aforementioned phages and even plasmids, all has a common origin - which may extend to the mobilisation mechanism used by bacteria like Agrobacterium tumefaciens. A general scheme for ssDNA virus replication can be seen here.
Geminiviruses, like other ssDNA entities, have a rep gene, producing a Rep protein: in plants, this is expressed from a double-stranded replicative intermediate form of the genome (RF), and cleaves the genome (+) strand at a specific ori sequence, binds to the free 5′ end, and then mediates ligation of the newly-displaced (+) strand. The accumulation of ssDNA seems to depend on the production of coat protein, which probably sequesters nascent ss(+)DNA, as CP- mutants produce no ssDNA.
There is a fair degree of specificity in all this, with viruses having a specified host range, and Reps having specificity for a narrow range of virus genomes.