VIRAL GENETICS

Molecular Polarity of Viral Genomes

Both DNAP and RNAP enzymes work or orient themselves only in the 5' to 3' direction of the new molecule.

Positive Sense

• Positive (+) single strand of RNA ==> 5' to the 3' terminal
• A positive (+) single strand of RNA has the same sequence order as mRNA. Thus, it can proceed to translation.

Negative or Anti-Sense

• Negative (-) ssRNA ==> 3' to the 5' terminal. Serves as template for the production of (+) strands or mRNAs.
• A negative (-) ssRNA has a complementary sequence of N-bases to mRNA. It can not proceed to translation. It is not a "messenger".
• A negative (-) ssRNA serves as a TEMPLATE for the production of (+) ssRNA ( = mRNA).The reaction is catalyzed by an RNA-dependant RNA polymerase (RNADP).

Positive/Negative

• A positive-negative (+/-) dsRNA. It has one strand that can proceed to ribosomes.

The Genome of Viruses

• Viral nucleic acids display a remarkable array of structural and compositional varieties.
• Viruses are the only organisms to still have RNA as their sole genetic material. Also the only ones with ssDNA.
• All viruses have a common need for cellular machinery for the synthesis of virus-coded proteins
• Recognition of the central role of mRNA leads to a molecular biological classification of viruses based on the relationship between the viral genome and mRNA, and also on the genome's mode of replication.
• It is easy to understand the relationship between ds DNA virus genomes to the synthesis of mRNA, since this process is identical to that used by the host.

• There is a wide diversity in virus replication and expression strategies.

Peculiarities of Viral Genomes

• DNA from certain bacteriophages contains unusual bases. Cytosine is replaced by hydroxymethylcytosine (T2, T4, T6).
• In these T-even phages, hydroxymethylcytsine can be further substituted with glucose or gentiobiose.
• In animal viruses all nucleic acid segments are present within one particle.
• In plant viruses each particle usually contains only one segment. Plant viruses have up to 4 RNAs.

For example, the four RNAs of brome mosaic virus are contained in three particles, all of which are essential for infectivity.

• Frequently the smallest RNA of multicomponent plant viruses duplicates information contained in one of the other segments: Its significance is not known.

For example, in brome mosaic virus, segment 4 is an exact copy of part of segment 3.

The Baltimore Classification

• An organizing scheme that is particularly useful that emphasizes the interaction of viruses with their hosts. Proposed by David Baltimore (1971)
• All viruses, regardless of the nature of their genomes, must use mRNA as the template for the synthesis of proteins.
• mRNA is defined as a positive strand molecule by conventions of molecular biology.
• Nucleic acid molecules that have sequences that are the complement of mRNA are designated as negative strands.

• Most DNA viruses replicate in the nucleus where they can have access to the cell's RNA polymerase, as well as capping, splicing, and poly A-adding enzymes, to process their transcripts.
• The poxvirus is the only known DNA virus that replicate in the cytoplasm instead of the nucleus.
• ssDNA genomes also have a fairly conventional relationship to mRNA, since they quickly become dsDNA after infection and can follow the same fate as cellular genes.
• Some has RNA genomes that correspond to mRNA that can function as messages even in vitro (+ strand genomes).
• Many other RNA viruses have (-) strand genomes, meaning they are complementary to the sense or mRNA strand.

• Since animal cells lack enzymes to copy RNA, and since the negative strand can not be translated, (-) strand RNA is functionally dead.
• Viruses with (-) strand genomes must encode a transcriptase that can synthesize mRNA from a (-) strand RNA template.
• The enzyme must be packaged in the virion in association with the viral genome.
• Viruses with ds RNA genomes must also carry a transcriptase within their particles, since like the (-) strand RNA, ds RNA is not a normal template for replication or transcription in animal cells and cannot be translated.

The Baltimore Scheme Classifies Viruses According to Genome Type

dsDNA viruses (Class I or Type I)

• (Except types of Poxvirus) use cellular RNA polymerase for mRNA synthesis.
• All these viruses encode both capsid proteins and nonvirion proteins required for replication of their genomes.
  
• mRNA is synthesized in the normal fashion using (-) strand DNA as a template.
  
• Include viruses infecting Eubacteria and Archae, phages and higher animals (Pox, Herpes, Adeno and Polyomavirus); viruses of insects (Baculo, Iirido and Polydnavirus); and, viruses that infect eukaryotic algae (Phycodnavirus).
  

Examples

dsDNA Genomes

Myoviridae: bacteria; complex, T4

Siphoviridae: bacteria; complex, lambda

Podoviridae: bacteria; complex, T7

Papoviridae: animal; naked, icosahedral, Polyomavirus, SV40

Adenoviridae: animal; naked, icosahedral, Adenovirus

Herpesviridae: animal; enveloped, icosahedral, herpes, varicella

Poxiviridae: animal; complex, smallpox, vaccinia

Hepadnaviridae: animal; enveloped, icosahedral, hepatitis B

Caulimoviridae: plant; naked, icosahedral, caulifolower mosaic

ssDNA Viruses (Class II or Type II)

• At the time the Baltimore scheme was proposed, only (+) strand viruses were known. But (-) strand viruses have since been found and are designated as Class II a and Class II b.
• Synthesis of mRNA by these viruses involves a dsDNA intermediate.
• Unlike dsDNA viruses, ss DNA viruses encode capsid proteins only.
• They rely on cellular systems for both their transcription and their replication.
• Includes bacteriophages (Inoviridae, Microviridae), mammal viruses (Circovirus, Parvoviridae); birds (Circovirus), and plants (Geminiviridae).

Examples of Class II Viruses

ssDNA Genomes

Microviridae, bacteria; naked, icosahedral, X174.

Parvoviridae, animal; naked, icosahedral, Parvovirus.

Geminiviridae, plant; fused-pair, icosahedral, maize streak.

dsRNA (Class III or Type III)

• One strand equivalent to mRNA.
• ds RNA viruses carry virus-coded enzymes within the virion that can synthesize mRNA from this type of template.

Examples:

Enveloped phages (Cystoviridae).

The animal- plant- and insect- infecting Reoviridae virus.

The vertebrate and invertebrate virus infecting Birnaviridae.

The Totiviridae which appears limited to primitive Eukarya (fungi and protozoa).

The Partitiviridae which only infect fungi.

The Cryptovirus which occur in plants but are apparently only transmissible via seed or pollen.

ssRNA (Class IV)

• ssRNA viruses can serve as mRNA directly, so these are (+) strand viruses.
• There are two subclases (IV a and IV b) based on differences in mechanisms of expression and replication of the genome in these viruses.

Examples:

Leviviridae: bacteria; naked, icosahedral, MS2, Q.

Picornaviridae: animal; naked, icosahedral, polio, Rhinovirus

Togaviridae: animal; enveloped, icosahedral, Sindbis

Coronaviridae: animal; enveloped, helical, murine hepatitis

Potyvirus: plant; naked, helical, potato Y.

Tymovirus: plant; naked, icosahedral, turnip yellow mosaic.

Tobamovirus: plant; naked, helical, TMV.

Comovirus: plant; naked, icosahedral, cowpea mosaic.

(-) Strand RNA (Class V)

• Can not serve directly as mRNA, but instead the template for the synthesis of viral mRNA by virion transcriptase soon after infection.
• These genomes lack the terminal modifications that characterize eucaryotic mRNAs.
• Class Va and Vb viruses are also distinguished by differences in the mechanisms of expression and replication of their genomes.

Examples:

(-)ssRNA genomes

Rhabdoviridae: animal, enveloped, helical, rabies, vesicular stomatitis

Paramyxoviridae: animal, enveloped, helical, mumps, measles

Orthomyxoviridae: animal, enveloped, helical, influenza

Bunyaviridae: animal, enveloped, helical, Phlebovirus

Arenaviridae: animal, enveloped, helical, Lassa virus

Retroviruses (Class VI)

• Have (+) ssRNA genomes that can serve as mRNA.
• Their expression and replication require synthesis of a dsDNA molecule.
• This dsDNA integrates into host chromosomal DNA, from which it serves as a template for transcription of viral mRNA and progeny genomes.
• Reverse transcriptase, a virus-encoded enzyme carried inside the virion, makes viral DNA from the genomic RNA template.

Example:

Retroviridae: animal, enveloped, icosahedral, HIV.

Notes on the Hepatitis B Virus Genome

(Hepadnavirus -- Class I Genome)

• Have genomes with a full length (-) DNA strand and a short (+) strand.
• Virions contain a DNA polymerase that completes the (+) strand soon after infection, resulting in a ds DNA molecule that can be transcribed by the cell to yield viral mRNAs.
• The replication of the viruses is quite different from most dsDNA viruses and resembles the replication of retroviruses.