Bacterial Genetics

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Bacterial Genetics

• Xiao-Kui GUO PhD

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Bacterial Genomics
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Microbial Genomics
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Microbial Genome Features
GC content
68 Deinococcus radiodurans
29 Borrelia burgdorferi
single circular chromosome
Genome organization
two circular chromosomes
circular chromosome plus one or
more extrachromosomal elements
large linear chromosome plus 21 extrachromosomal
elements
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PLASMIDS Plasmids are extrachromosomal genetic
elements capable of autonomous replication. An
episome is a plasmid that can integrate into the
bacterial chromosome

• Classification of Plasmids
• Transfer properties
• Conjugative plasmids
• Nonconjugative plasmids
• Phenotypic effects
• Fertility plasmid (F factor)
• Bacteriocinogenic plasmids.
• Resistance plasmids 7 factors) .

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Insertion sequences (IS)- Insertion sequences are
transposable genetic elements that carry no known
genes except those that are required for
transposition.

• a. Nomenclature - Insertion sequences are given
  the designation IS followed by a number.  e.g.
  IS1
• b. Structure Insertion sequences are small
  stretches of DNA that have at their ends repeated
  sequences, which are involved in transposition.
  In between the terminal repeated sequences there
  are genes involved in transposition and sequences
  that can control the expression of the genes but
  no other nonessential genes are present.
• c. Importance
• i) Mutation - The introduction of an insertion
  sequence into a bacterial gene will result in the
  inactivation of the gene.
• ii) Plasmid insertion into chromosomes - The
  sites at which plasmids insert into the bacterial
  chromosome are at or near insertion sequence in
  the chromosome.
• iii) Phase Variation - The flagellar antigens are
  one of the main antigens to which the immune
  response is directed in our attempt to fight off
  a bacterial infection. In Salmonella there are
  two genes which code for two antigenically
  different flagellar antigens. The expression of
  these genes is regulated by an insertion
  sequences. In one orientation one of the genes is
  active while in the other orientation the other
  flagellar gene is active. Thus, Salmonella can
  change their flagella in response to the immune
  systems' attack. Phase variation is not unique to
  Salmonella flagellar antigens. It is also seen
  with other bacterial surface antigens. Also the
  mechanism of phase variation may differ in
  different species of bacteria (e.g. Neisseria
  transformation).

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Transposons (Tn) - Transposons are transposable
genetic elements that carry one or more other
genes in addition to those which are essential
for transposition.

• Nomenclature - Transposons are given the
  designation Tn followed by a number.
• Structure - The structure of a transposon is
  similar to that of an insertion sequence. The
  extra genes are located between the terminal
  repeated sequences. In some instances (composite
  transposons) the terminal repeated sequences are
  actually insertion sequences.
• Importance - Many antibiotic resistance genes are
  located on transposons. Since transposons can
  jump from one DNA molecule to another, these
  antibiotic resistance transposons are a major
  factor in the development of plasmids which can
  confer multiple drug resistance on a bacterium
  harboring such a plasmid. These multiple drug
  resistance plasmids have become a major medical
  problem because the indiscriminate use of
  antibiotics have provided a selective advantage
  for bacteria harboring these plasmids.

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Mechanism of bacterial variation

• Gene mutation
• Gene transfer and recombination
• Transformation
• Conjugation
• Transduction
• Lysogenic conversion
• Protoplast fusion

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Types of mutation

• Base substitution
• Frame shefit
• Insertion sequences

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What can cause mutation?

• Chemicals
• nitrous acid alkylating agents
• 5-bromouracil
• benzpyrene
• Radiation X-rays and Ultraviolet light
• Viruses

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Bacterial mutation

• Mutation rate
• Mutation and selectivity
• Backward mutation

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Transformation

• Transformation is gene transfer resulting from
  the uptake by a recipient cell of naked DNA from
  a donor cell. Certain bacteria (e.g. Bacillus,
  Haemophilus, Neisseria, Pneumococcus) can take up
  DNA from the environment and the DNA that is
  taken up can be incorporated into the recipient's
  chromosome.

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Conjugation

• Transfer of DNA from a donor to a recipient by
  direct physical contact between the cells. In
  bacteria there are two mating types a donor
  (male) and a recipient (female) and the direction
  of transfer of genetic material is one way DNA
  is transferred from a donor to a recipient.

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Physiological States of F Factor

• Autonomous (F)
• Characteristics of F x F- crosses
• F- becomes F while F remains F
• Low transfer of donor chromosomal genes

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Physiological States of F Factor

• Integrated (Hfr)
• Characteristics of Hfr x F- crosses
• F- rarely becomes Hfr while Hfr remains Hfr
• High transfer of certain donor chromosomal genes

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Physiological States of F Factor

• Autonomous with donor genes (F)
• Characteristics of F x F- crosses
• F- becomes F while F remains F
• High transfer of donor genes on F and low
  transfer of other donor chromosomal genes

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Mechanism of F x F- Crosses

• Pair formation
• Conjugation bridge

• DNA transfer
• Origin of transfer
• Rolling circle replication

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Mechanism of Hfr x F- Crosses

• Pair formation
• Conjugation bridge

• DNA transfer
• Origin of transfer
• Rolling circle replication
• Homologous recombination

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Mechanism of F x F- Crosses

• Pair formation
• Conjugation bridge

• DNA transfer
• Origin of transfer
• Rolling circle replication

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R Plasmid
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Transduction

• Transduction is defined as the transfer of
  genetic information between cells through the
  mediation of a virus (phage) particle. It
  therefore does not require cell to cell contact
  and is DNase resistant.

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Generalized Transduction

• Generalized transduction is transduction in which
  potentially any bacterial gene from the donor can
  be transferred to the recipient.

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The mechanism of generalizedtransduction
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Generalized transduction

• It is relatively easy.
• It is rather efficient (10-3 per recipient with
  P22HT, 10-6 with P22 or P1), using the correct
  phage.
• It moves only a small part of the chromosome
  which allows you to change part of a strain's
  genotype without affecting the rest of the
  chromosome.
• The high frequency of transfer and the small
  region transferred allows fine-structure mapping

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Specialized transduction

• Specialized transduction is transduction in which
  only certain donor genes can be transferred to
  the recipient.
• Different phages may transfer different genes but
  an individual phage can only transfer certain
  genes
• Specialized transduction is mediated by lysogenic
  or temperate phage and the genes that get
  transferred will depend on where the prophage has
  inserted in the chromosome.

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The mechanism of specialized transduction
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Specialized transduction

• Very efficient transfer of a small region--can be
  useful for fine-structure mapping
• Excellent source of DNA for the chromosomal
  region carried by the phage, since every phage
  carries the same DNA.
• Can often be used to select for deletions of some
  of the chromosomal genes carried on the phage.
• Merodiploids generated using specialized phage
  can be quite useful in complementation analyses.

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Lysogenic conversion

• The prophage DNA as a gene recombined with
  chromosome of host cell.

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Protoplast Fusion

• Fusion of two protoplasts treated with lysozyme
  and penicillin.

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Application of Bacterial Variation

• Use in medical clinic Diagnosis, Treatment,
  Prophylaxis.
• Use in Genetic Engineering