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  1. Classification of Bacteriophages
    1. The most important criteria used for classification are phage morphology and nucleic acid properties
    2. Most bacteriophages have double-stranded DNA (dsDNA), although single-stranded DNA (ssDNA) and RNA viruses are known
    3. Most can be placed in one of a few morphological groups: tailless icosahedral, viruses with contractile tails, viruses with noncontractile tails, and filamentous viruses
  2. Reproduction of Double-Stranded DNA Phages
    1. Lytic cycle-culminates with the host cell bursting and releasing virions
    2. The one-step growth experiment
      1. Reproduction is synchronized so that events during replication can be observed
        1. Bacteria are infected and then diluted so that the released phages will not immediately find new cells to infect
        2. The released phages are then enumerated
      2. Several distinct phases are observed in the viral replication cycle
        1. Latent period-no release of virions detected; represents the shortest time required for virus reproduction and release; the early part of this period is called the eclipse period, and during this period no infective virions can be found even inside infected cells
        2. Rise period (burst)-rapid lysis of host cells and release of infective phages; burst size is the number of infective virions released per infected cellc. Plateau period-no further release of infective virions
    3. Adsorption to the host cell and penetration
      1. Viruses attach to specific receptor sites (proteins, lipopolysaccharides, teichoic acids, etc.) on the host cell
      2. Many viruses inject DNA into the host cell, leaving an empty capsid outside
    4. Synthesis of phage nucleic acids and proteins
      1. mRNA molecules transcribed early in the infection (early mRNA) are synthesized using host RNA polymerase; early proteins, made at the direction of these mRNA molecules, direct the synthesis of protein factors and enzymes required to take over the host cell
      2. Transcription of viral genes then follows an orderly sequence due to the modification of the host RNA polymerase and changes in sigma factors
      3. Later in the infection viral DNA is replicated
        1. Synthesis of viral DNA sometimes requires the initial synthesis of alternate bases; these are sometimes used to protect the phage DNA from host enzymes (restriction endonucleases) that would otherwise degrade the viral DNA and thereby protect the host
        2. For some bacteriophages, concatemers of the DNA genome are formed; these are later cleaved during assembly
    5. The assembly of phage particles
      1. Late mRNA molecules (those made after viral nucleic acid replication) direct the synthesis of capsid proteins and other proteins involved in assembly (e.g., scaffolding proteins) and release of the virus
      2. Assembly proceeds sequentially by subassembly lines, which assemble different structural units (e.g., baseplate, tail tube); these are then put together to make the complete virion 3. DNA packaging is still not well understood
    6. Release of phage particles
      1. Many phages lyse their host by damaging the cell wall or the cytoplasmic membrane
      2. A few phages (e.g., filamentous fd phages) are released without lysing the host cell; instead the phages are released through a secretory process
  3. Reproduction of Single-Stranded DNA phages
    1. fX174 (+stand DNA virus-virus DNA that has the same sequence as the viral mRNA)
      1. ssDNA is converted to double-stranded replicative form (RF) by host DNA polymerase
      2. RF directs synthesis of more RF, RNA and +strand DNA genome
    2. Filamentous phages (e.g., fd)
      1. DNA enters via sex pilus
      2. Replicative form is synthesized
      3. Replicative form directs mRNA synthesis
      4. Protein encoded by mRNA then directs phage DNA replication via rolling circle method
  4. Reproduction of RNA Phages
    1. Single-stranded RNA phages
      1. RNA replicase-the virus must provide an enzyme for replicating the RNA genome because the host does not produce an enzyme with this capability
        1. The RNA genome is usually plus stranded (+) and can act as mRNA to direct the synthesis of the replicase during an initial step after penetration
        2. +strand RNA is then converted to dsRNA, the replicative form
        3. Replicative form is then used as a template for production of multiple copies of the genomic (and messenger) +strand RNA
      2. Capsid proteins are made, and +strand RNA is packaged into new virions
      3. One or more lysis proteins then function to release the phage
    2. Only one dsRNA phage has so far been discovered (f6); it infects Pseudomonas phaseolicola and possesses a membranous envelope
  5. Temperate Bacteriophages and Lysogeny
    1. Temperate phages are capable of lysogeny, a nonlytic relationship with their hosts (virulent phages lyse their hosts)
      1. In lysogeny, the viral genome (called a prophage) remains in the host (usually integrated into the host chromosome) but does not kill (lyse) the host cell; the cells are said to be lysogenic (or are called lysogens)
      2. It may switch to the lytic cycle at some later time; this process is called induction
    2. Most bacteriophages are temperate; it is thought that being able to lysogenize bacteria is advantageous; supporting this is the observation that certain conditions favor the establishment of lysogeny
    3. Lysogenic conversion is a change that is induced in the host phenotype by the presence of a prophage and that is not directly related to the completion of the viral life cycle; examples include:
      1. Modification of lipopolysaccharide structure in infected Salmonella
      2. Production of diphtheria toxin only by lysogenized strains of Corynebacterium diphtheriae
    4. Establishment of lysogeny (bacteriophage lambda)
      1. Two sets of promoters are available to host RNA polymerase
      2. A repressor protein may be made from genes adjacent to one of these promoters
      3. If this repressor binds to its target operator before the other promoter is used, then that promoter is blocked and lysogeny is established
      4. If genes associated with that second promoter are expressed before the repressor can bind to the operator, then the lytic cycle is established
      5. Induction (the termination of lysogeny and entry into the lytic cycle) will occur if the level of the repressor protein decreases; this is usually in response to environmental damage to the host DNA
    5. For lambda and most temperate phages, if lysogeny is established, the viral genome integrates into the host chromosome; however, some temperate phages can establish lysogeny without integration

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