Recombination, Bacteriophages, and Horizontal Gene Transfer

1
Recombination, Bacteriophages, and Horizontal
Gene Transfer

• 2005

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Bacterial Conjugation

• transfer of DNA by direct cell to cell contact
• discovered 1946 by Lederberg and Tatum

3
F x F Mating

• F donor
• contains F factor
• F recipient
• does not contain F factor
• F factor replicated by rolling-circle mechanism
  and duplicate is transferred
• recipients usually become F
• donor remains F

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F factor

• The F factor can exist in three different states
  
• F refers to a factor in an autonomous,
  extrachromosomal state containing only the
  genetic information described above.
• The "Hfr" (which refers to "high frequency
  recombination") state describes the situation
  when the factor has integrated itself into the
  chromosome presumably due to its various
  insertion sequences.
• The F' or (F prime) state refers to the factor
  when it exists as an extrachromosomal element,
  but with the additional requirement that it
  contain some section of chromosomal DNA
  covalently attached to it. A strain containing no
  F factor is said to be "F-".

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Gene transfer and recombination

• Genes are transferred in a linear manner
• The F factor integrates into chromosomes at
  different points and its position determines the
  O site

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F? x F mating
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Hfr Conjugation

• Hfr strain
• donor having F factor integrated into its
  chromosome
• both plasmid genes and chromosomal genes are
  transferred

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Hfr

• Special class of F strains
• This was discovered because this strain underwent
  recombination 1000x more frequently than F
  strains
• In certain Hfr strains certain stains are more
  likely to recombine than others.
• The nonrandom pattern of gene transfer was shown
  to vary from Hfr strain to Hfr strain

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Interrupted mating

• Wollman explained the cells that are different
  between F and Hfr. To facilitate the recovery,
  the Hfr was sensitive to antibiotics and the F
  wasnt.
• The cells were separated at intervals of 5
  minutes is the F factor

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Mating
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Hfr x F mating
Figure 13.14b
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Recombination

• Exogenote
• Exogenote

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Mating

• The two strains were mixed
• There were incubated.
• At intervals of 5 minutes, samples were taken of
  the F- cells
• The cells were centrifuged so that they would
  know which genes were transferred.
• The distance between genes was measured by the
  time that it took for the genes to be
  transferred.
• During the first five minutes, the strains were
  mixed there was no recombination

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F x F mating

• In its extrachromosomal state the factor has a
  molecular weight of approximately 62 kb and
  encodes at least 20 tra genes. It also contains
  three copies of IS3, one copy of IS2, and one
  copy of a À sequence as well as genes for
  incompatibility and replication.

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F

• In 1959 during his experiments with the Hfr
  strains of E. coli Adelberg discovered that the F
  factor could lose its integrated status and
  revert to its F status.
• When this occurred, the F factor carries along
  several adjacent bacterial genes.
• When you have the F factor bacterial genes
  the condition is known as the F

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F? Conjugation
integrated F factor

• F? plasmid
• formed by incorrect excision from chromosome
• contains ? 1 genes from chromosome
• F? cell can transfer F? plasmid to recipient

chromosomal gene
Figure 13.15a
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Merozygotes

• When the F is then transferred to another
  bacterium
• The bacterium may contain genomic copies of a
  gene as well as an additional copy of the gene in
  the F.
• As a result the situation is a partial diploid
• Merozygotes have been extremely beneficial in the
  study of gene regulation

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Interrupted mating
Figure 13.22a
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Figure 13.22b
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Hfr mapping

• used to map relative location of bacterial genes
• based on observation that chromosome transfer
  occurs at constant rate
• interrupted mating experiment
• Hfr x F- mating interrupted at various intervals
• order and timing of gene transfer determined

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Gene mapping
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Recombinants

• Map distance can be determined by replating the
  resulting colonies on agar
• For example
• leu exconjugants by plating them on medium
  containing no leucine but containing methionine
  and arginine

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Mapping results
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Map distance

• The map distance is equal to the recombination

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Tra Y

• Characterization of the Escherichia coli F factor
  traY gene product and its binding sites
• WC Nelson, BS Morton, EE Lahue and SW Matson
  Department of Biology, University of North
  Carolina, Chapel Hill 27599.

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Tra Genes

• Tra Y gene codes for the protein binds to the Ori
  T
• Initiates the transfer of plasmid across the
  bridge between the two cells
• Tra I Gene is a helicase responsible for the
  conjugation
• strand-specific transesterification (relaxase)

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Conjugative Proteins

• Key players are the proteins that initiate the
  physical transfer of ssDNA, the conjugative
  initiator proteins
• They nick the DNA and open it to begin the
  transfer
• Working in conjunction with the helicases they
  facilitate the transfer of ss RNA to the F- cell

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DNA Transformation

• Uptake of naked DNA molecule from the environment
  and incorporation into recipient in a heritable
  form
• Competent cell
• capable of taking up DNA
• May be important route of genetic exchange in
  nature

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Streptococcus pneumoniae
nuclease nicks and degrades one strand
DNA binding protein
competence-specific protein
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Artificial transformation

• Transformation done in laboratory with species
  that are not normally competent (E. coli)
• Variety of techniques used to make cells
  temporarily competent
• calcium chloride treatment
• makes cells more permeable to DNA

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Cloning vectors
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pAmp
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Transformation mapping

• used to establish gene linkage
• expressed as frequency of cotransformation
• if two genes close together, greater likelihood
  will be transferred on single DNA fragment

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Microbial Genetics

• Bacteriophages

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Diversification of Escherichia coli genomes are
bacteriophages the major contributors? Makoto
Ohnishi Trends in Microbiology

• E. coli is a diverse species
• 4.5 5.5 MB
• E. coli strains are commensals of higher
  vertebrates, but some are pathogenic
• There are 5subtypes of the diarrheagneic strainsd
• The pathogenicity of the strains has been traced
  to a subtype that retains a large segment of
  virulence factors or pathogenicity islands

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E. Coli O 157

• Sixteen sections of this pathogenic strain differ
  from the lab strain
• These are subtype specific
• Within sections of the DNA and these large
  segments
• The G-C content varies from the lab strain
• The 4.1 kb common backbone sequence mainly
  represent the DNA that RE. coli possesses from a
  common ancestor.

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E. coli

• There are 98 copies of IS elements within this
  section as well as genes enxoding hemolysins,
  proteases, and other virulence factors.
• More interesting O 157 also contains 18 remnants
  of prophages

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Horizontal gene transfer

• Clearly this plays a central role in the
  diversity of E. coli
• Among the 18 prophage remnants on O157 12
  resemble lambda pahge
• They all contain a variety of deletions and or
  insertions
• Some of the phages are so similar that they
  contain a 20 kb segment tat is identical.

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Recombinant phages

• It is believed that the phages have undergone
  recombination and diversification
• Recombination could occur with in a single cell
• It could occur as the result of recombination

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Virulence and Strptococcus pyogenes

• Streptococcal pyrogenic exotoxins(SPE)
  contribute to the diverse symptoms of a
  streptococcal infection.
• These antigens compare to Staphylococcal
  antigens of the same type.
• The A C genes coding for these toxins were
  horizontally transferred from strain to strain by
  a lysogenic bacteriophage.
• In addition the genes contributed by the phages
  produce hyaluronidase, mitogenic factor, and
  leukocyte( WBC) toxins

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Streptococcus pyogenes

• There are 15 prophages that have been identified
  in E. coli
• These prophages belong to the group Siphoridae
• All but one of these produce a toxin
• In both strep and staph the prophage is found
  at the site of recombination

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Bacteriophages
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Bacteriophages

• Bacterial viruses
• Obligate intracellular parasites
• Inject themselves into a host bacterial cell
• Take over the host machinery and utilize it for
  protein synthesis and replication

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T- 4 Bacteriophage

• Ds DNA virus
• 168, 800 base pairs
• Phage life cycles studied by Luria and Delbruck

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Bacteriophage structure
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Bacteriophage structure(con)

• Most bacteriophages have tails
• The size of the tail varies.
• It is a tube through which the nucleic acid is
  injected as a result of attachment of the
  bacteriophage to the host bacterium
• In the more complex phages the tail is surrounded
  by a contractile sheath for injection of the
  nucleic acids

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Bacteriophage structure

• Many bacteriophages have a base plate and tail
  fibers
• Some have icosahedral capsids
• M13 has a helical capsid

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Bacteriophage structure(con)

• Most bacteriophages have tails
• The size of the tail varies.
• It is a tube through which the nucleic acid is
  injected as a result of attachment of the
  bacteriophage to the host bacterium
• In the more complex phages the tail is surrounded
  by a contractile sheath for injection of the
  nucleic acids

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Bacteriophage structure

• Many bacteriophages have a base plate and tail
  fibers
• Some have icosahedral capsids
• M13 has a helical capsid

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PhiX 174

• The spherical phage (PhiX174, G4, S13) are
  broadly similar to the filamentous phage.
• The capsid is icosahedral not helical and is not
  enveloped (these phage lyse the host cell).
• Their genome consists of a circular ssDNA
  molecule. A well-known examples is PhiX174, which
  was the first genome to be sequenced - by Fred
  Sanger's group in 1976.
• Its genome of 5386 bp coded for 11 genes,
  including several examples of overlapping genes.

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PhiX174 economy and overlapping genes

• The coding frames for 7 proteins overlap A is a
  truncated form of A
• B is coded within A in a different reading frame
  
• K is encoded in a third reading frame at the end
  of A which extends into and overlaps with that of
  C E is coded within D in a different reading
  frame. These were the first examples of
  overlapping genes.
• Other relatives of PhiX174 are G4 and S13.

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PhiX174

• Gene A RF replication viral strand synthesis
• A Turning off host DNA synthesis
• B Formation of capsid
• E Lysis of bacterium
• F major coat protein
• G Major spike protein

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Genetics

• Conversion of a parental single stranded DNA
  molecule to the viral strand to a covalently
  closed double stranded molecule
• This is called the Replicative form( RFI)
• Synthesis of many copies of RFI. The strand is
  transcribed. Gene A product is made and the
  process continuew

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Synthesis of strands for encapsidation

• There is not switch It just occurs
• During the period that the phage capsids( heads )
  are being synthesized

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Ss RNA viruses

• ssRNA phages
• Tailess icosahedral
• Single stranded linear molecule, having a great
  deal of intramolecular hydrogen bonding
• Consists of 3600 nucleotides
• Genes for attachment, coat protein and an RNA
  polymerase

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Replication

• The RNA molecule serves a both a replication
  template and the mRNA

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Filamentous phages

• Fd
• Filamentous
• Circular ss DNA
• Lies in the middle of the filment
• Infects through the pilus
• Create a symbiotic relationship with the host

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M 13
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Sequential steps- M13Cloning vector Joachim
Messier

• phage particles bind to F pilus
• only infects F, Hfr, F' cells
• single-stranded DNA genome enters cell
• designated as strand
• strand repaired
• double-stranded replicative form (RF)
• RF contains and strands
• strand is template for mRNA synthesis
• for production of new strands
• by rolling circle replication
• strands are packaged in phage coat protein
• exit cell as phage particle
• Important points for cloning vectors

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M13 and cloning

• M13 occurs in both single and double stranded
  forms
• RF can be digested with restriction endonucleases
• inserts can be cloned in like plasmid
• strands from phage particles
• convenient source of single-stranded DNA
•  

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M13

• used for sequencing and site-directed
  mutagenesis
• different sized DNA molecules packaged as phage
  particle
• (within reason)
• phage with inserts gt 2 kb replicated slower
• different sized DNA molecules
• produce different size phage particles

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M13 Phage
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General Steps
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T even phagesLuria and Delbruck

• Four distinct periods in the release of phages
  from host cells
• Latent period- follows the addition of phage( no
  release of virions)
• Eclipse period virions were detectable before
  infection and are now hidden or eclipsed
• Rise or burst period Host cells rapidly burst
  and release viruses
• The total number of phages released can be
  determined by the burst size the number of
  viruses produced per
• infected cell

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Steps in the life cycle

• Adsorption of the virus to the host
• This is mediated by tail fibers or some analagous
  structure
• When the tail fibers make contact, the base plate
  settles to the surface
• This connection which is maintianed by
  electrostatic attraction and the ions Mg and
  Ca

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Attachment

• There is host specificity in the attachment and
  adsorption of the bacteriophage
• There are receptors for the attachment. They
  vary from bacteria to bacteria
• The receptors are on the bacteria for other
  purposes the bacteriophages evolved to utilize
  them for their invasion

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T even phages

• The phage sheath shortens from 24 rings to 12
  rings
• The sheath becomes shorter and wider
• This causes the central tube to push through the
  bacterial cell wall

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Gp5

• The baseplate contains the protein gp5 with
  lysozyme activity which made aid in the
  penetration of the host

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Penetration and other Phages

• Penetration by other phages may differ
• PRD1 phage attaches to a surface receptor by a
  spike on one of its capsid vertices

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Conformational Changes and PRD1

• As a result of the binding a tubular structure is
  formed that allows the virus to penetrate the
• Penetration of the membrane tube is made by the
  membrane enzyme P7
• These phages have a major effect on the
  bacteriaceae

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Early Genes

• E. coli RNA polymerase starts transcribing
  genes( phage genes) within minutes of entering
  the bacterial cell
• The early m RNA direct the synthesis of proteins
  and enzymes that are needed for hostile tack over
• Some early virus specific enzymes degrade host
  DNA to nucleotides wo that virus DNA synthesis
  can commence

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Hydroxymethylcytosine

• HMC is needed for synthesis instead of cytosine
• HMC must be glucosylated by the addition of
  glucose to protect from restriction enzymes

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T4 and terminal redundancy

• The end has terminal redundancy
• When multiple coies have been made enzymes join
  the copies by therse ends
• When several untis are linked together this forms
  concatamers

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Late mRNA

• Phage structural structural proteins
• Proteins that help with pahge assembly
• Proteins involved in cell lysis and release

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Capsid

• The base plate requires 12 protein products
• The head or capsid requires 10 genes
• The capside requires scaffolding proteins for
  assembly
• DNA packaging a mysterious process
• Many phages lyse their host cells at the end of
  the intracellular phase

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Release

• Interference with the synthesis of the bacterial
  cell wall
• PhiX 174 produces a lytic enzyme that interfers
  with the urein precursos

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Irreversible attachment

• The attachment of the tail ribers to the
  bacterium is a weak attachment
• The attachment of the bacterophage is also
  accompanied by a stronger interaction usually by
  the base plate

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Sheath contraction

• The irreversible binding results in the sheath
  contraction

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Injection

• When the irreversible attachment has been made
  and the sheath contracts, the nucleic acid passes
  through the tail and enters the cytoplasm

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Phage Multiplication Cycle Lytic phages

• Lytic phages or virulent phages enter the
  bacterial cell, complete protein synthesis,
  nucleic acid replication, and then cause lysis of
  the bacterial cell when the assembly of the
  particles has been completed.

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Eclipse Period

• The bacteriophages may be seen inside or outside
  of the bacterial cells
• The phages take over the cells machinery and
  phage specific mRNAs are made
• Early mRNAs are generally needed for DNA
  replication
• Later mRNAs are required for the synthesis of
  phage proteins

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Intracellular accumulation phase

• The bacteriophage sub units accumulate in the
  cytoplasm of the bacterial cell and are assembled

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Lysis or Release Phase

• A lysis protein is released
• The bacterial cell breaks open
• The viruses escape to invade other bacterial cells

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Plaque assay

• Phage infection and lysis can easily be detected
  in bacterial cultures grown on agar plates
• Typically bacterial cells are cultured in high
  concentrations on the surface of an agar plate
• This produces a bacterial lawn
• Phage infection and lysis can be seen as a clear
  area on the plate. As phage are released they
  invade neighboring cells and produce a clear area

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Plaque assay
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Lambda and Plaques

• The plaque produced by Lambda had a different
  appearance on the Petri Dish.
• It is considered to be turbid rather than clear
• The turbidiy is the result of the growth of phage
  immune lysogens in the plaque
• The agar surface contains a ratio of about a
  phage /107 bacteria

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MOI

• Average number of phages /bacterium
• After several lytic cycles the MOI gets higher
  due to the release of phage particles

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Transduction

• Transfer of bacterial genes by viruses
• Virulent bacteriophages
• reproduce using lytic life cycle
• Temperate bacteriophages
• reproduce using lysogenic life cycle

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Generalized transduction

• http//www.cat.cc.md.us/courses/bio141/lecguide/un
  it4/genetics/recombination/transduction/gentran.ht
  ml
• http//www.cat.cc.md.us/courses/bio141/lecguide/un
  it1/control/genrec/u4fg21a.html

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Generalized transduction

• E. coli phage P21 or P22.
• As a part of the lytic cycle, the phage cuts the
  bacterial DNA into fragments
• This fragmentation prevents the expression of
  bacterial genes
• Nucleotides can be used to make phage DNA
• Occasionally these DNA fragments are about the
  same size as phage DNA
• They become mistakenly packaged into phage
  capsids in place of phage DNA

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Types of Lysogenic Cycle

• The most common type is the classic model of the
  Lambda phage
• The DNA molecule is injected into a bacterium
• In a short period of time, after a brief period
  of transcription, an integration factor and a
  repressor are synthesized
• A phage DNA molecule typically a replica of the
  injected molecules is inserted into the DNA
• As the bacterium continue to grow and multiply
  and the phage genes replicate as part of the
  bacterial chromosome

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The P1 temperate phage

• There is not integration into the host
• The phage becomes a plasmid
• It exists as an independently replicating entity
  in the bacterial cell in the same way a plasmid
  exists.

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Temperate

• A bacteriophage that can exist as a lytic or
  lysogenic phage is referred to as a temperate
  phage
• A bacterium containing a full set of phage genes
  is a lysogen
• The process of infecting a bacterial culture with
  a temperate phage is called lysogenization

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Immunization

• A bacterial cell or lysogen cannot be reinfected
  by a phage of the same type
• This is resistance to superinfection is called
  immunity
• More than 90 of the bacteriophages are temperate
• These are unable to produce bursts such as T4 and
  T7

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Lysogenic Phage
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Lambda Phage

• Temperate phage
• Alternate life cycle
• Ds DNA linear then circularizes when it enters
  the host
• 48,502 base pairs
• Molecular biology workhorse because of its life
  cycle

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Genes

• Lambda genes
• 46 genes have been identified
• 14 are non esswential to the lytic cycle
• Only 7 are nonessential to both the lytic and
  lysogenic cycles

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Lambda Gene Map

• Genes are clustered according to function
• There are four clusters
• Head
• Tail
• Replication
• Recombination genes
• Regulatory genes act at specific site on the DNA

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Restriction sites
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Life cycle of ? Phage
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Latency

• Lysogenic conversion can lead to virulence
• Botulism, cholera,and diptheria toxins are
  encoded by prophages that convert their host into
  a pathogenic bacterium

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Control of lysogeny and lytic cycle

• Genes needed to establish lysogeny
• cI yes
• cII yes
• cIII yes

• Genes needed for maintenance of lysogeny
• cI yes
• cII no
• cIII no

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Lambda

• In order for the lambda prophage to exist in a
  host E. coli cell, it must integrate into the
  host chromosome which it does by means of a
  site-specific recombination reaction.

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Preferred site of integration

• It is inserted into the E. coli chromosome
  between the gal operon and the biotin operon.
• The site of attachment is specific just for the
  Lambda phage ( att)

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Lambda Phage Genes

• repression of all lytic functions
• cI the lambda repressor, when present and
  active, will repress lytic functions. The
  counterpart of cI is cro, a repressor of cI. The
  initial "decision" that lambda makes is based on
  the outcome of a battle over cI synthesis
• lambda DNA is injected and circularized
• initially, cII is made
• cII is a positive regulator of cI synthesis. If
  cII is around long enough, then cI will be made,
  and cI will repress cro and other lytic functions
  
• if cII is degraded quickly, cro will build up,
  and cI will not be synthesized

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Lambda Phage Genes

• whether cII is degraded or not depends on the
  health of the host. A healthy cell will degrade
  cII quickly, and in effect signal to lambda that
  a lytic cycle would be good. An unhealthy cell
  will not degrade cII, which is like telling
  lambda that the cell is too sick to make viral
  progeny, so lysogeny is the better idea

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Terminology

• LEGEND
• att an E.coli seqence for the "attachment" or
  integration of lambda's circular chromosome.
• oriC E.coli's origin of Chromosome replication
  (given here for orientation only)
• gal E.coli's gene for galactose utilization
• peprophage ends (site of integration)
• cos joined sticky ends of vegetative DNA
  sometimes called ve ("vegetative ends")
• int gene for the enzyme integrase
• c gene for lambda repressor to maintain
  lysogeny
• Q another gene concerned with lysogeny
• h the last of the many capsomer genes.

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Bacteriophages
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Specialized transduction
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Attachment site

• The E. coli chromosome contains one site at which
  lambda integrates. The site, located between the
  gal and bio operons, is called the attachment
  site and is designated attB since it is the
  attachment site on the bacterial chromosome.
• The site is only 30 bp in size and contains a
  conserved central 15 bp region where the
  recombination reaction will take place.
• The structure of the recombination site was
  determined originally by genetic analyses and is
  usually represented as BOB', where B and B'
  represent the bacterial DNA on either side of the
  conserved central element

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Recombination site

• The bacteriophage recombination site - attP - is
  more complex. It contains the identical central
  15 bp region as attB.
• The overall structure can be represented as POP'.
  However, the flanking sequences on either side of
  attP are very important since they contain the
  binding sites for a number of other proteins
  which are required for the recombination
  reaction. The P arm is 150 bp in length and the
  P' arm is 90 bp in length.

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Integration

• Integration of bacteriophage lambda requires one
  phage-encoded protein - Int, which is the
  integrase - and one bacterial protein - IHF,
  which is Integration Host Factor.
• Both of these proteins bind to sites on the P and
  P' arms of attP to form a complex in which the
  central conserved 15 bp elements of attP and attB
  are properly aligned.
• The integrase enzyme carries out all of the steps
  of the recombination reaction, which includes a
  short 7 bp branch migration.

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Enzymes and Recombination

• There are two major groups of enzymes that carry
  out site-specific recombination reactions one
  group - known as the tyrosine recombinase family
  - consists of over 140 proteins.
• These proteins are 300-400 amino acids in size,
  they contain two conserved structural domains,
  and they carry out recombination reactions using
  a common mechanism involving a the formation of a
  covalent bond with an active site tyrosine
  residue.

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Enzymes and Recombination

• The strand exchange reaction involves staggered
  cuts that are 6 to 8 bp apart within the
  recognition sequence.
• All of the strand cleavage and re-joining
  reactions proceed through a series of
  transesterification reactions like those mediated
  by type I topoisomerases.

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Excision of bacteriophages

• Excision of bacteriophage lambda requires two
  phage-encoded proteins
• Int (again!) and Xis, which is an excisionase. It
  also requires several bacterial proteins.
• In addition to IHF, a protein called Fis is
  required.
• All of these proteins bind to sites on the P and
  P' arms of attL and attR forming a complex in
  which the central conserved 15 bp elements of
  attL and attR are properly aligned to promote
  excision of the prophage.

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Normal Excision
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Excision and lysis

• The reverse of integration happens upon induction
  
• UV light is a good inducer
• induction actually involves RecA. RecA is
  activated by ssDNA. Activated RecA interacts with
  cI, and causes cI to proteolyze itself. Without
  cI, lytic functions are derepressed, and the
  lytic cycle begins.
• induction also results in the synthesis of both
  Int and Xis
• only int is required for integration, but both
  are required for excision
• normal excision (which usually occurs) produces
  the cicular viral genome, and lysis continues

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Generalized Transduction

• Any part of bacterial genome can be transferred
• Occurs during lytic cycle
• During viral assembly, fragments of host DNA
  mistakenly packaged into phage head
• generalized transducing particle

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Generalized transduction
126
Specialized Transduction

• also called restricted transduction
• carried out only by temperate phages that have
  established lysogeny
• only specific portion of bacterial genome is
  transferred
• occurs when prophage is incorrectly excised

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Specialized transduction
Figure 13.20
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Figure 13.20
129
Generalized Transduction Mapping

• used to establish gene linkage
• expressed as frequency of cotransduction
• if two genes close together, greater likelihood
  will be carried on single DNA fragment in
  transducing particle

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Recombination and Genome Mapping in Viruses

• viral genomes can also undergo recombination
  events
• viral genomes can be mapped by determining
  recombination frequencies
• physical maps of viral genomes can also be
  constructed using other techniques

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Specialized transduction mapping

• provides distance of genes from viral genome
  integration sites
• viral genome integration sites must first be
  mapped by conjugation mapping techniques

132
Recombination mapping

• recombination frequency determined when cells
  infected simultaneously with two different viruses

Figure 13.24
133
Physical maps

• heteroduplex maps
• genomes of two different viruses denatured, mixed
  and allowed to anneal
• regions that are not identical, do not reanneal
• allows for localization of mutant alleles

134
Physical maps

• restriction endonuclease mapping
• compare DNA fragments from two different viral
  strains in terms of electrophoretic mobility
• sequence mapping
• determine nucleotide sequence of viral genome
• identify coding regions, mutations, etc.

135
Lambda Phage Genes

• repression of all lytic functions
• cI the lambda repressor, when present and
  active, will repress lytic functions. The
  counterpart of cI is cro, a repressor of cI. The
  initial "decision" that lambda makes is based on
  the outcome of a battle over cI synthesis
• lambda DNA is injected and circularized
• initially, cII is made
• cII is a positive regulator of cI synthesis. If
  cII is around long enough, then cI will be made,
  and cI will repress cro and other lytic functions
  
• if cII is degraded quickly, cro will build up,
  and cI will not be synthesized

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Lamda Phage Genes

• whether cII is degraded or not depends on the
  health of the host. A healthy cell will degrade
  cII quickly, and in effect signal to lambda that
  a lytic cycle would be good. An unhealthy cell
  will not degrade cII, which is like telling
  lambda that the cell is too sick to make viral
  progeny, so lysogeny is the better idea