Bacterial Genetics

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The science of genetics describes and analyze heredity of
physiologic functions that form the properties of organism.

These properties are determined by the total of all the

genetic information named genome.

The basic unit of genetics is gene, a segment of DNA that

carries in its nucleotide sequence information for a specific
biochemical or physiologic property.

A gene is relatively stable but occasionally may undergo a

nucleotide change, such a change is called as mutation.

Mutations may occur spontaneously or can be induced by a

number of physical or chemical agents.
Bacteria may have changes including:

 Morphological and/or structural changes

 Variations of cultural characteristics and biochemical
reactions

 Changes in virulence
 Variation of antigenicity
 Changes in drug resistance
These variations of bacteria can be divided

into two types:

a) Phenotypic variation: non-heritable

b) Genotypic variations: heritable (mutation)

 Phenotypic variations

Phenotypic variations are normal physiologic

responses of bacteria due to the change of bacteria
growth environment. The changes are limited, non-
hereditary, and revert back to their original state
when the conditions are changed back.
eg. Flagella of Salmonella spp. are absent due to the presence

of 0.1 % phenol in culture medium.

 Genotypic variations (Mutation)

Genotypic variations are stable, heritable

changes of bacteria. The changes are due to the
mutations in bacterial genomic nucleotide
sequences.
In this lecture, emphases are given to the
content about genotypic variations containing
bacterial genome, mutation types and mechanisms.
Bacterial genome
 Bacterial Genome
DNA/Genome:
the genetic materials relative to bacterial mutation.

A. chromosome
B. out of chromosome: a) plasmid
b) bacteriophage/phage
c) transposable genetic elements
 Bacterial Genome

DNA/Genome:
chromosome
out of chromosome:
plasmid
bacteriophage/phage
transposable genetic elements
 Chromosomal DNA

Bacterial chromosome consists of a single,

circle of double-stranded DNA.

in average 2 mm long

< 5 Mb (1 Mb = 1024 Kb)

The chromosome carry many genes.

 Bacterial Genome

DNA/Genome:
chromosome
out of chromosome:
plasmid
bacteriophage/phage
transposable genetic elements
 a). Plasmids
• Are small ， circular/line,

extra-chromosomal

double-stranded DNA that

are capable of autonomous

replication.

•Carry genes associated

with specialized functions

 Classification of plasmids
Transfer properties
Conjugative plasmids (mediate conjugation through sex pilus)
Non-conjugative plasmids (can not mediate conjugation
because of no gene for encoding sex pilus)
Phenotypic effects
Fertility (F factor: carrying a gene that encoding sex pilus
protein)
Bacteriocinogenic plasmid (carrying genes that encoding
bacteriocins that kill other bacteria)
Resistance plasmid (R factors: carrying genes that encoding
enzymes to destroy antibiotics and mediate conjugation )
 Structure of R Factors

RTF (Resistance Transfer Factor) RTF

Conjugative plasmid
Transfer genes
Tn 9
0

Tn 21
R determinant 1
Tn
Tn 8

Resistance genes
Are often parts of
transposons (Tn)
R determinant
 Mode of action of resistance genes

a) Modification (detoxification) of antibiotics - e.g. β-lactamase

b) Alteration of the target sites by antibiotics - e.g.

Streptomycin resistance

c) Alteration of the uptake ability of antibiotics - e.g.

Tetracycline resistance

d) Replacement of sensitive pathway - e.g. resistance to sulfa

drugs
 Bacterial Genome
DNA/Genome:
chromosome
out of chromosome:
plasmid
bacteriophage/phage
transposable genetic elements
 b). Bacteriophages/phages
Phages are obligate intracellular
parasites that multiply inside
bacteria by making use of some
or all of the host biosynthetic
machinery.
They are viruses that specially
infect bacteria (“bacterial virus”).
Composition of Bacteriophage

nucleic acid: either DNA or RNA but not both

ds DNA, ss RNA, ss DNA
Contain unusual or modified bases
Encode 3-5 gene products ~ approximate
100 gene products
protein: function in infection and protect the
nucleic acid
 Structure of Bacteriophage
different sizes and shapes

The first shape, like

a tadpole, is the
common
 Structure of T4 phage
Capsid
DNA Head

Contractile
Sheath
Tail

Tail Fibers

Base Plate

Head consists of DNA surrounded by a protein coat (capsid)

Tail is composed of a hollow core surrounded by a contractile
sheath with base plate at the end through which are tail
fibers.
Interaction between phages and bacteria
• Phages are wide spread throughout nature and can be found
infecting many different genera of bacteria.

• However, the host range of any specific phage is limit. A given

phage can usually infect only a single species of bacteria or
closely related species.

•Based on the pattern of interaction between a given phage and

it’s host, phages are divided into two major groups: virulent
phages and temperate phages.
Interaction between phages and bacteria
Infection with a virulent phage results in phage replication with

the production of new phage particles and their subsequent

release that causing death and lysis of the host bacteria.

Infection with a temperate phage does not necessarily lead to

bacterial lysis and death, and the phage may integrate into the

bacterial genome without new phase production.

 Virulent Phages
Virulent phages can multiply in bacteria and kill the bacterial cell
by lysis at the end of their life cycle.

The life cycle of a virulent phage can be divided into four phases:

I. adsorption / attachment

II. penetration

III. biosynthesis / intracellular development

IV. maturation and release

 I. Adsorption

Recognition of host bacterial surface receptors by the tail fibers

 II. Penetration

The tail sheath contracts, pushing the rigid tail core through the
bacterial cell envelope and the phage’s nucleic acid is injected
through the hollow core into the bacterial cytoplasm.
 III. Biosynthesis

Protein synthesis and production of many new copies of new

phage DNA or RNA.
 IV. Maturation and Release

Irreversible combination of phage nucleic acid with it’s protein

coat. Induce cell lysis and release of the newly formed phages.
 Temperate Phages
Temperate phages are capable to invade host bacteria and
inducing lysogenic state without necessarily producing a lethal
lytic infection.
A temperate phage can either go through the lytic cycle or
induce lysogeny by integrating the host DNA in the form of a
prophage.
Prophage is only a genome of the phage that integrated in
genomic DNA of its host bacterium.
The bacterial cell harboring a prophage is termed as lysogenic
bacterium and this state is called as lysogenization.
 Prophage formation

II. peneration
I. adsorption

III. integrate of phage IV. prophage replicates along

DNA into host genome with host chromosome
Prophages in
lysogenic bacteria
will spontaneously
proceed through
the lytic cycle.
 Bacterial Genome
DNA/Genome:
chromosome
out of chromosome:
plasmid
bacteriophage/phage
transposable genetic elements
 C). Transposable Genetic Elements

Definition:
segments of DNA that have the capacity to
move from one bacterial DNA molecule (bacterial
chromosome or plasmid) to another or from one
location to another in one DNA molecule.
(jumping gene / movable gene)
Properties of transposable genetic elements
“Random” movement: move with no any regularity.

Transposase: mediates transposition and coded by the transposable

genetic elements.
Not capable of self replication: usually replicated as a part of some
other replicon (plasmid or chromosome).
Site-specific recombination: dependent on the inserted sites, but
does not require homology between the recombining molecules.
Transposition may be accompanied by replication: In some
cases, one copy remains of the element at the original site and the other is
moves to a new site.
Types of Transposable Genetic Elements

I. Insertion sequences (IS)

II. Transposons (Tn)

 Insertion sequences (IS)
Definition: a type of transposable Genetic Elements that
carry no other genes except the genes involving in
transposition (transposase coding genes).
Structure: a small DNA that has repeated sequences at its
ends, which are involved in transposition. In the middle
between the terminal repeated sequences there is a
transposase coding gene (usually one and occasionally
more).
Function: introduction of an insertion sequence into a
bacterial gene will result in the inactivation of the gene.

ABCDEFG Transposase GFEDCBA

 Transposons (Tn)
Definition: a type of transposable Genetic Elements that carry other
genes and insertion sequences (IS).

Structure: the extra genes are located between the terminal repeated
sequences.

Function: Since transposons can jump from one DNA molecule to

another and frequently carry antibiotic resistance genes, these
transposons participate the development of drug resistance in
bacteria.

IS Resistance Gene(s) IS

IS Resistance Gene(s) IS
Mutation types
 Mutation types
Self Mutations: low frequency
Spontaneous mutation: Mutations for a given gene
spontaneously occur with a certain frequency (from 10-8-10-6) in a
population derived from a single bacterium.
Induced mutation: Some chemical agents and radiation can
induce bacterial mutation.

Gene transfer and recombination: high frequency

one bacterium uptake exogenous DNA segment from another

bacterium or phage (Gene transfer) and then the DNA segment is
incorporated into DNA of itself (recombination).
 Terms about Bacteria Gene Transfer

Donor: a bacterium to offer DNA (but not entire

chromosome) to other bacteria.

Recipient: a bacterium to receive DNA offered by

other bacteria. 　

*Bacterial genes are usually transferred among members of

the same species but occasionally transferred to other species.
 Major mechanisms and modes
of Bacterial Gene Transfer

Transformation

Transduction (Lysogenic conversion)

Conjugation
 Transformation
Definition: a bacterial recipient uptake naked
chromosomal DNA segment offered by bacterial
donor in environment and then the DNA segment
recombinate with the recipient’s chromosomal
DNA .
 Factors affecting transformation

DNA size: Double stranded DNA of at least 500, 000 daltons

works best.

Competence of the recipient: Only the bacteria in a particular

time during their growth cycle called as competent stage can

take up DNA by transformation, while the non-competent

bacteria can not.

 Steps in transformation
Steps
Uptake of DNA

Recombination
 Significance for transformation
Transformation occurs in nature and it can lead to increased virulence ( e.g.
Streptococcus pneumoniae) and drug resistance.

In addition transformation is widely used in recombinant DNA technology.

 Transduction
Definition: a bacterial donor’s chromosomal DNA

segment transferred to a bacterial recipient by

way of a bacteriophage, and then the DNA

segment recombinate with the recipient’s

chromosomal DNA .
 Types of Transduction
Generalized Transduction: is the transduction in
which potentially any genes of the bacterial donor
can be transferred to the recipient.

Specialized transduction: is the transduction that

only certain bacterial genes can be transferred to the
recipient.
 Generalized Transduction
Virulent phages that mediate generalized transduction generally
breakdown host DNA into smaller pieces.
Occasionally, one of the host DNA pieces is randomly packaged
into the phage particle. Thus, any genes of bacteria can be
potentially transferred.
When the bacterial DNA contained phage infect a bacterial
recipient, donor DNA enters the recipient.
In the recipient, the event of a recombination of donor DNA and
recipient DNA can occur.
 Specialized Transduction
•As the introduction above, sometimes prophage, like virulent
phage, can spontaneously entry the lytic cycle.
•During the excision of prophage, occasionally some of the host
DNA segments at either sides of prophage gene sequence is
excised with the phage DNA.
•After a bacterial recipient is infected with this phage and then

forms its lysogenization, the recipient’s genomic DNA contains the

donor DNA.
 Lysogenic conversion
In some text books, lysogenic conversion is included in
tranduction.

Definition: a bacterial recipient is infected with

bacteriophage from a bacterial donor, and the genes of
phage itself, but not genes of the bacterial donor,
recombinate with the recipient’s chromosomal DNA.

As an example, Corynebacterium diphtheriae will produces

diphtheria toxin after it is infected by the β- phage, because
the gene encoding the toxin is carried by the phage.
Significance for Transduction

Transduction occurs in nature and it can

lead to increased virulence and drug
resistance of recipient bacteria.
 Conjugation
Definition: Gene transfer from a donor
to a recipient by direct physical contact
between two bacterial cells.
Donor: A bacterium presents a plasmid Donor
called as F factor. The F factor offers
the bacterium an ability to produce a
sex pilus.
Recipient: A bacterium that lack of F
factor.

Recipient
 Physiological States of F Factor (I)
According to the different patterns and characteristics of gene transfer,
conjugation can divided into three types.
I. Autonomous (F+):
the F factor is autonomous and carries only those genes
necessary for its replication and for DNA transfer (no
chromosomal genes of bacterial donor).
So in this type of conjugation, there is low transfer level of
bacterial donor’s genes.
In crosses of the F+ and F- bacteria, the F- bacterium becomes
F+ and the F+ bacterium remains F+.
 Model of Autonomous Conjugation by F+

F+ F- F+ F- F+ F-

F+ F+ F+ F+
The F+ bacterium transfers extra chain of F+ factor and then
the completed F+ factors in the two bacteria is synthesized
by rolling circle replication.
 Physiological States of F Factor (II)
II. Integrated (Hfr):

The F factor has integrated on bacterial chromosome, and only

bacterial DNA is transferred with a high frequency.

In crosses of the Hfr and F- bacteria, the F- bacterium rarely

becomes Hfr and the Hfr bacterium remains Hfr.

 Model of Integrated Conjugation

Hfr F - Hfr F- Hfr F-

Hfr F-
 Physiological States of F Factor (III)
III. Autonomous (F’):
In this pattern, the F factor is autonomous but it now carries
some of bacterial chromosomal genes (F’), because this F
factor is a excised integrated F with host’s chromosomal
sequences at its two sides.

In crosses of the F' and F- bacteria, the F- bacterium becomes

F' and the F' bacterium remains F'.
 Model of autonomous Conjugation by F’

F’ F’ F’
Hfr F’ F-
 Significance for conjugation
In most of Gram negative bacteria, conjugation is
the major way of bacterial gene transfer, which
frequently result in multiple antibiotic resistance.
In some of Gram positive bacteria, conjugation is
also an active way of bacterial gene transfer.
Multiple antibiotic resistance genes in a Gram
positive bacterium can be obtained by conjugation
or by transduction.
 Summary

The most important contents in this lecture are

displayed as the followings:
1) The Agents (plasmid, phage, bacterial chromosomal DNA)
associated with bacterial mutation.
2) Concepts of Transformation, Transduction, Conjugation
and Lysogenic conversion
3) The Significance of bacterial mutation (changes of
bacterial virulence, drug resistance, antigenicity and so
on).