MICROBIOLOGY PPT LECTURE NOTES | Karya Tulis Ilmiah
Bacterial Genetics
Xiao-Kui GUO PhD
Bacterial Genomics
Microbial Genomics
Microbial Genome Features
29%
Borrelia
burgdorferi
G+C content
68%
Deinococcus
radiodurans
single circular chromosome
two circular
chromosomes
circular chromosome
plus one or more
extrachromosomal
elements
Genome organization
large linear chromosome plus
21 extrachromosomal elements
PLASMIDS
Plasmids are extrachromosomal genetic elements capable of autono
mous replication. An episome is a plasmid that can integrate into the bacterial chromo
some
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 i
n transposition and sequences that can control the expression of the genes but no other nonessential gene
s are present.
c. Importance
i) Mutation - The introduction of an insertion sequence into a bacterial gene will result in the inactivation of t
he gene.
ii) Plasmid insertion into chromosomes - The sites at which plasmids insert into the bacterial chromosome a
re 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 di
rected 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 sequen
ces. In one orientation one of the genes is active while in the other orientation the other flagellar gene is acti
ve. Thus, Salmonella can change their flagella in response to the immune systems' attack. Phase variation i
s 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 th
at carry one or more other genes in addition to those which are essential for tran
sposition.
• Nomenclature - Transposons are given the designation Tn followed by a n
•
•
umber.
Structure - The structure of a transposon is similar to that of an insertion s
equence. The extra genes are located between the terminal repeated sequen
ces. In some instances (composite transposons) the terminal repeated seque
nces are actually insertion sequences.
Importance - Many antibiotic resistance genes are located on transposons.
Since transposons can jump from one DNA molecule to another, these anti
biotic resistance transposons are a major factor in the development of plas
mids which can confer multiple drug resistance on a bacterium harboring s
uch a plasmid. These multiple drug resistance plasmids have become a maj
or medical problem because the indiscriminate use of antibiotics have prov
.
ided a selective advantage for bacteria harboring these plasmids
Mechanism of bacterial
variation
• Gene mutation
• Gene transfer and recombinati
on
• 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 f
rom the uptake by a recipient cell of nake
d DNA from a donor cell. Certain bacteria
(e.g. Bacillus, Haemophilus, Neisseria, Pn
eumococcus) can take up DNA from the e
nvironment and the DNA that is taken up
can be incorporated into the recipient's c
hromosome.
Conjugation
• Transfer of DNA from a donor to a recipie
nt by direct physical contact between th
e cells. In bacteria there are two mating t
ypes a donor (male) and a recipient (fem
ale) and the direction of transfer of gene
tic material is one way; DNA is transferre
d from a donor to a recipient.
Physiological States of F
Factor
• Autonomous (F+)
– Characteristics of F+ x Fcrosses
• 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 rem
ains Hfr
• High transfer of c
ertain donor chro
mosomal 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
• Pair formation
– Conjugation
bridge
• DNA transfer
F+
F-
F+
F-
F+
F+
F+
F+
– Origin of
transfer
– Rolling circle
replication
Mechanism of Hfr x F- Crosses
• Pair formation
– Conjugation
bridge
• DNA transfer
Hfr
F-
Hfr
F-
– Origin of transfer
– Rolling circle
replication
• Homologous
recombination
Hfr
F-
Hfr
F-
Mechanism of F’ x F- Crosses
• Pair formation
– Conjugation
bridge
• DNA transfer
F’
F-
F’
F-
F’
F’
F’
F’
– Origin of
transfer
– Rolling circle
replication
R Plasmid
Transduction:
• Transduction is defined as the transfer o
f genetic information between cells thro
ugh the mediation of a virus (phage) par
ticle. 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 fr
om the donor can be transferred to the r
ecipient.
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 finestructure mapping
Specialized transduction
• Specialized transduction is transduction in which
only certain donor genes can be transferred to th
e recipient.
• Different phages may transfer different genes but a
n individual phage can only transfer certain genes
• Specialized transduction is mediated by lysogenic
or temperate phage and the genes that get transfer
red will depend on where the prophage has insert
ed in the chromosome.
The mechanism of specialized
transduction
Specialized transduction
1. Very efficient transfer of a small region--can be us
2.
3.
4.
eful for fine-structure mapping
Excellent source of DNA for the chromosomal regi
on carried by the phage, since every phage carrie
s 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
.
Lysogenic conversion
• The prophage DNA as a gene r
ecombined with chromosome
of host cell.
Protoplast Fusion
• Fusion of two protoplasts treated with ly
sozyme 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
Microbial Genome Features
29%
Borrelia
burgdorferi
G+C content
68%
Deinococcus
radiodurans
single circular chromosome
two circular
chromosomes
circular chromosome
plus one or more
extrachromosomal
elements
Genome organization
large linear chromosome plus
21 extrachromosomal elements
PLASMIDS
Plasmids are extrachromosomal genetic elements capable of autono
mous replication. An episome is a plasmid that can integrate into the bacterial chromo
some
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 i
n transposition and sequences that can control the expression of the genes but no other nonessential gene
s are present.
c. Importance
i) Mutation - The introduction of an insertion sequence into a bacterial gene will result in the inactivation of t
he gene.
ii) Plasmid insertion into chromosomes - The sites at which plasmids insert into the bacterial chromosome a
re 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 di
rected 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 sequen
ces. In one orientation one of the genes is active while in the other orientation the other flagellar gene is acti
ve. Thus, Salmonella can change their flagella in response to the immune systems' attack. Phase variation i
s 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 th
at carry one or more other genes in addition to those which are essential for tran
sposition.
• Nomenclature - Transposons are given the designation Tn followed by a n
•
•
umber.
Structure - The structure of a transposon is similar to that of an insertion s
equence. The extra genes are located between the terminal repeated sequen
ces. In some instances (composite transposons) the terminal repeated seque
nces are actually insertion sequences.
Importance - Many antibiotic resistance genes are located on transposons.
Since transposons can jump from one DNA molecule to another, these anti
biotic resistance transposons are a major factor in the development of plas
mids which can confer multiple drug resistance on a bacterium harboring s
uch a plasmid. These multiple drug resistance plasmids have become a maj
or medical problem because the indiscriminate use of antibiotics have prov
.
ided a selective advantage for bacteria harboring these plasmids
Mechanism of bacterial
variation
• Gene mutation
• Gene transfer and recombinati
on
• 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 f
rom the uptake by a recipient cell of nake
d DNA from a donor cell. Certain bacteria
(e.g. Bacillus, Haemophilus, Neisseria, Pn
eumococcus) can take up DNA from the e
nvironment and the DNA that is taken up
can be incorporated into the recipient's c
hromosome.
Conjugation
• Transfer of DNA from a donor to a recipie
nt by direct physical contact between th
e cells. In bacteria there are two mating t
ypes a donor (male) and a recipient (fem
ale) and the direction of transfer of gene
tic material is one way; DNA is transferre
d from a donor to a recipient.
Physiological States of F
Factor
• Autonomous (F+)
– Characteristics of F+ x Fcrosses
• 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 rem
ains Hfr
• High transfer of c
ertain donor chro
mosomal 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
• Pair formation
– Conjugation
bridge
• DNA transfer
F+
F-
F+
F-
F+
F+
F+
F+
– Origin of
transfer
– Rolling circle
replication
Mechanism of Hfr x F- Crosses
• Pair formation
– Conjugation
bridge
• DNA transfer
Hfr
F-
Hfr
F-
– Origin of transfer
– Rolling circle
replication
• Homologous
recombination
Hfr
F-
Hfr
F-
Mechanism of F’ x F- Crosses
• Pair formation
– Conjugation
bridge
• DNA transfer
F’
F-
F’
F-
F’
F’
F’
F’
– Origin of
transfer
– Rolling circle
replication
R Plasmid
Transduction:
• Transduction is defined as the transfer o
f genetic information between cells thro
ugh the mediation of a virus (phage) par
ticle. 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 fr
om the donor can be transferred to the r
ecipient.
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 finestructure mapping
Specialized transduction
• Specialized transduction is transduction in which
only certain donor genes can be transferred to th
e recipient.
• Different phages may transfer different genes but a
n individual phage can only transfer certain genes
• Specialized transduction is mediated by lysogenic
or temperate phage and the genes that get transfer
red will depend on where the prophage has insert
ed in the chromosome.
The mechanism of specialized
transduction
Specialized transduction
1. Very efficient transfer of a small region--can be us
2.
3.
4.
eful for fine-structure mapping
Excellent source of DNA for the chromosomal regi
on carried by the phage, since every phage carrie
s 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
.
Lysogenic conversion
• The prophage DNA as a gene r
ecombined with chromosome
of host cell.
Protoplast Fusion
• Fusion of two protoplasts treated with ly
sozyme and penicillin.
Application of Bacterial
Variation
• Use in medical clinic: Diagnosis,
Treatment, Prophylaxis.
• Use in Genetic Engineering