First discovered by the clearing of spots in a bacterial lawn.

• Bacterial viruses infect bacteria, and are called bacteriophages.
  • The thought was that they might be able to fight bacterial infections. Therefore, researchers found adequate funding to study them.
  • These viruses are made of protein and nucleic acids. See Figure 15.1.
• They are classified by the nature of their genetic material and protein coat.
  • Some have single-stranded, others have double-stranded DNA molecules.
  • Some use RNA, some DNA as their genetic transfer molecule.
  • Some have a membranous envelope derived from the infected cell.
• T4 phage of E. coli is an example of a bacteriophage. See Figure 15.1.
• T4 life cycle is as follows:

• At 37^oC the full life cycle takes just 22 minutes.
• Phage absorbs onto the cell wall.
• Phage DNA is expressed.
• Early phage proteins are translated from phage RNA.
• Early phage proteins stop transcription and translation of bacterial genes.
• Next, host DNA gets degraded.
• Phage DNA gets replicated by early phage proteins.
• The late proteins appear next.
• These make up the head and tail structures.
• Phage DNA gets packaged.
• Lysozyme is produced using a phage gene.
• This causes bacteria to lyse releasing around 200 phage particles. See Figure 15.2.
• T4 is a double-stranded DNA virus.
  • It has a distinguishing modification to its cytosine residues, 5-hydroxymethylcytosine, which protects its DNA from the nucleases it uses to fragment the host's DNA. See Figure 15.3.
  • It also protects the phage from the endonucleases bacteria used to protect themselves from foreign DNA or viruses.

   

Mapping the Bacteriophage

• How do you map a virus?
• You need some observable traits. See Figure 15.5.
• Plaque morphology can be used,
• smooth or rough edges for the plaques.
• Also host range can be used. Some mutants fail to infect certain strains of E. coli, for example.

• If one bacterial cell gets infected by 2 phages at the same time;
• if the phage are of different genotypes;
• recombinants can be recovered. See Figure 15.6.
• The number of recombinants can be used to estimate the distance between two or more genes.
• This is a little different than what we did in eukaryotes; however, the basic concept is the same.
  • Genes that are close tend to stay together; genes that are further apart tend to separate.
  • Few recombinants will be observed if the genes are close together, more will if further apart. See Figure 15.7.
• Complementation crosses are used to determine if mutation was for the same genes or for different genes. If for different genes, then wild-types could be frequently recovered. If for the same gene, the frequency was very rare.
• Finer mapping was by using defined deletion mutants to study mutants with point mutations. If the point mutation were in a deletion zone, recombinants would never be recovered. See Figure 15.11.
• It was found that some regions of the genome of viruses are more prone to mutation. These were called hot spots. See Figure 15.14.

T-4 phage: How do you get a round genome map from a linear DNA molecule?

• It was determined that the DNA molecule of T-4 was linear.
• But the gene mapping was consistent with it being circular. See Figure 15.15.
• It was then discovered that the ends of the linear DNA molecules were repeated. They can form concatamers that join together. These get packaged into the viral heads, as much as will fit. The rest gets whacked off. Therefore, each head has a bit more than one copy in it. See Figure 15.16 and Figure 15.17.

Phi Chi 174 is a virus with sequences that are read out in different directions from the same sequences to code for different mRNAs.

• These are overlapping genes. See Figure 15.20.
• It would seem that there would be little room for mistakes in these regions.

How can one phage yield two kinds of phage?

• This was discovered. It gives clues to how recombination between different DNA molecules takes place.
• Single stranded regions hybridize from the two recombining molecules and might resolve by changing in one or the other direction. See Figure 15.22.

HIV See Figure 15.23.

• HIV is a retrovirus.
• It infects helper T-cells and others.
• After infection, it generates a DNA from its RNA, and the DNA integrates into the cell's genome.
• It generates copies of itself for release.
• The infected cells are killed off over time but the infection continues ahead and cell lines get depleted. See Figure 15.24.

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