Bacterial Genetics
Xiao-Kui GUO PhD
Bacterial Genomics
Microbial Genomics
68%
Deinococcus
radiodurans
Microbial Genome Features
G+C content
29%
Borrelia
burgdorferi
Genome organization
single circular chromosome
large linear chromosome plus
21 extrachromosomal elements
circular chromosome
plus one or more
extrachromosomal
elements
two circular
chromosomes
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),
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),
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,
Mechanism of bacterial variation
? Gene mutation
? Gene transfer and recombination
? Transformation
? Conjugation
? Transduction
? Lysogenic conversion
? Protoplast fusion
Types of mutation
? Base substitution
? Frame shefit
? Insertion sequences
What can cause mutation?
? Chemicals,
nitrous acid; alkylating agents
5-bromouracil
benzpyrene
? Radiation,X-rays and Ultraviolet
light
? Viruses
Bacterial mutation
? Mutation rate
? Mutation and selectivity
? Backward mutation
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,
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,
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
F+
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
F+ Hfr
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
Hfr F’
Mechanism of F+ x F- Crosses
? DNA transfer
– Origin of
transfer
– Rolling circle
replication
? Pair formation
– Conjugation
bridge
F+ F- F+ F-
F+ F+ F+ F+
Mechanism of Hfr x F- Crosses
? DNA transfer
– Origin of transfer
– Rolling circle
replication
? Homologous
recombination
? Pair formation
– Conjugation
bridge
Hfr F- Hfr F-
Hfr F- Hfr F-
Mechanism of F’ x F- Crosses
? DNA transfer
– Origin of
transfer
– Rolling circle
replication
? Pair formation
– Conjugation
bridge
F’ F’ F’ F’
F’ F- F’ F-
R Plasmid
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,
Generalized Transduction
? Generalized transduction is transduction in
which potentially any bacterial gene from
the donor can be transferred to the
recipient,
The mechanism of generalized
transduction
Generalized transduction
1,It is relatively easy,
2,It is rather efficient (10-3 per recipient with
P22HT,10-6 with P22 or P1),using the
correct phage,
3,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,
4,The high frequency of transfer and the
small region transferred allows fine-
structure mapping
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,
The mechanism of specialized
transduction
Specialized transduction
1,Very efficient transfer of a small region--can be
useful for fine-structure mapping
2,Excellent source of DNA for the chromosomal
region carried by the phage,since every phage
carries the same DNA,
3,Can often be used to select for deletions of
some of the chromosomal genes carried on the
phage,
4,Merodiploids generated using specialized
phage can be quite useful in complementation
analyses,
Lysogenic conversion
? The prophage DNA as a gene
recombined with chromosome
of host cell,
Protoplast Fusion
? Fusion of two protoplasts treated with
lysozyme and penicillin,
Application of Bacterial Variation
? Use in medical clinic,Diagnosis,
Treatment,Prophylaxis,
? Use in Genetic Engineering
Xiao-Kui GUO PhD
Bacterial Genomics
Microbial Genomics
68%
Deinococcus
radiodurans
Microbial Genome Features
G+C content
29%
Borrelia
burgdorferi
Genome organization
single circular chromosome
large linear chromosome plus
21 extrachromosomal elements
circular chromosome
plus one or more
extrachromosomal
elements
two circular
chromosomes
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),
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),
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,
Mechanism of bacterial variation
? Gene mutation
? Gene transfer and recombination
? Transformation
? Conjugation
? Transduction
? Lysogenic conversion
? Protoplast fusion
Types of mutation
? Base substitution
? Frame shefit
? Insertion sequences
What can cause mutation?
? Chemicals,
nitrous acid; alkylating agents
5-bromouracil
benzpyrene
? Radiation,X-rays and Ultraviolet
light
? Viruses
Bacterial mutation
? Mutation rate
? Mutation and selectivity
? Backward mutation
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,
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,
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
F+
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
F+ Hfr
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
Hfr F’
Mechanism of F+ x F- Crosses
? DNA transfer
– Origin of
transfer
– Rolling circle
replication
? Pair formation
– Conjugation
bridge
F+ F- F+ F-
F+ F+ F+ F+
Mechanism of Hfr x F- Crosses
? DNA transfer
– Origin of transfer
– Rolling circle
replication
? Homologous
recombination
? Pair formation
– Conjugation
bridge
Hfr F- Hfr F-
Hfr F- Hfr F-
Mechanism of F’ x F- Crosses
? DNA transfer
– Origin of
transfer
– Rolling circle
replication
? Pair formation
– Conjugation
bridge
F’ F’ F’ F’
F’ F- F’ F-
R Plasmid
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,
Generalized Transduction
? Generalized transduction is transduction in
which potentially any bacterial gene from
the donor can be transferred to the
recipient,
The mechanism of generalized
transduction
Generalized transduction
1,It is relatively easy,
2,It is rather efficient (10-3 per recipient with
P22HT,10-6 with P22 or P1),using the
correct phage,
3,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,
4,The high frequency of transfer and the
small region transferred allows fine-
structure mapping
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,
The mechanism of specialized
transduction
Specialized transduction
1,Very efficient transfer of a small region--can be
useful for fine-structure mapping
2,Excellent source of DNA for the chromosomal
region carried by the phage,since every phage
carries the same DNA,
3,Can often be used to select for deletions of
some of the chromosomal genes carried on the
phage,
4,Merodiploids generated using specialized
phage can be quite useful in complementation
analyses,
Lysogenic conversion
? The prophage DNA as a gene
recombined with chromosome
of host cell,
Protoplast Fusion
? Fusion of two protoplasts treated with
lysozyme and penicillin,
Application of Bacterial Variation
? Use in medical clinic,Diagnosis,
Treatment,Prophylaxis,
? Use in Genetic Engineering
