Chapter 9: Gene Transfer,
Mutations, and Genome
Evolution
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Chapter Overview
The mosaic nature of genomes
● Gene transfer: Transformation; conjugation;
and transduction
● Genetic recombination
● Mutations: Types and causes
● Mechanisms of DNA repair
● Mobile genetic elements
●
- Insertion sequences and transposons
●
How genomes evolve
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Introduction
DNA sequences change over generations
through various mutations, rearrangements,
and inter- and intraspecies gene transfer.
But what are the consequences of DNA
plasticity?
This chapter explores long-standing
evolutionary questions and shows how
microbial genomes continually change.
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The Mosaic Nature of Genomes
A surprise arising from bioinformatic studies is
the mosaic nature of all microbial genomes.
- For example, E. coli’s genome is rife with
genomic islands, inversions, deletions, and
paralogs and orthologs
- This is the result of heavy horizontal
gene transfer, recombinations, and a
variety of mutagenic and DNA repair
strategies.
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Recombination: Mechanisms of
Genetic Transfer
In bacteria recombination occurs in a number
of ways:
•
•
•
Transformation: Free DNA is transferred
Transduction: DNA transfer via a virus
Conjugation: Cell-to-cell contact and a
plasmid is involved.
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Gene Transfer by Transformation
Transformation is the process of importing
free DNA into bacterial cells.
- the cells need to be competent.
Many cells are capable of natural
transformation and naturally competent.
-others require artificial manipulations.
- Perturbing the membrane by chemical
(CaCl2) or electrical (electroporation)
methods
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Gene Transfer by Transformation
•
•
Not all bacteria can take up free or naked DNA
(<1%).
Some microbes become competent sometime
during their growth cycle
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Gene Transfer by Transformation
Natural Transformation occus  Bacillus sp.,
Haemophilus sp., Neisseria sp., Acinetobacter
sp., Streptococcus sp., Pseudomonas sp.
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Gram-positive bacteria transform DNA
using a transformasome complex.
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Gram-negative bacteria transform DNA without
the use of competence factors (CF).
• some Gram negative organisms are always
competent or they become competent when
starved.
• also, they do not use transformasomes.
• most Gram-negative species is sequencespecific.
Thus limiting gene exchange between genera
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Conjugation (mating)
Conjugation involves a cell-to-cell contact
mediated by a special plasmid, conjugative
plasmid
• Gram Negative: The plasmid carries genes
that code for a sex-pilus
• Gram Positive: Sticky molecules help bind
two cells together.
• Gram Negative Bacteria with conjugative
plasmids are males and without it are
females
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Gene Transfer by Conjugation
Conjugation is the transfer of DNA from
one bacterium to another, following cell-tocell contact by pilus on the donor cell.
- The pilus attaches to the
receptor on the recipient cell
- Two cell fuse and singlestranded DNA passes from
donor to recipient cell.
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Conjugation requires the
presence of special
transferable plasmids
(conjugative plasmids).
A well-studied example in E. coli is the fertility
factor (F factor). Also called fertility plasmid
Conjugation begins with contact between the
donor cell, called the F+ cell, and a recipient F–
cell.
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Conjugation
Conjugation
•
The cells with an unintegrated conjugative plasmid
are called F+ (males) and cells that act as recipient
for F+ are F- (Females)
•
When a donor with F+ plasmid transfers a copy of
the plasmid to a recipient (F-), the recipient
becomes F+
Figure 8.27a
F+ + F-  F+ + F+
Female cells become male cells and be
able to transfer the plasmid
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Relaxosome: many genes necessary for DNA transfer (halicase,
endonuclease, etc.
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The F-factor plasmid can integrate into the
chromosome.
- The cell is now designated Hfr, or highfrequency recombination strain.
Conjugation
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Conjugation between
an Hfr and F-, the
recipient gets some
of the Hfr genes
plus some of the donor’s
genes. The recipient
becomes a
recombinant F-,
Hfr + F-  Hfr + FConjugation
since not all Hfr
genes are transferes.
The entire chromosome take about 100 min to
transfer as opposed only 5 min for free plasmid
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An integrated F-factor can excise from the
chromosome.
- Aberrant excision results in an F′ factor or F′
plasmid, which carries chromosomal genes.
Figure 9.5
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Transfer of Genes into Eukaryotes
Some bacteria can actually transfer genes
across biological domains.
- Agrobacterium tumefaciens,
which causes crown gall
disease
- Contains a tumor-inducing
plasmid (Ti) that can be
transferred via conjugation to
plant cells
Figure 9.6
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Gene Transfer by Transduction
Transduction is the process in which
bacteriophages carry host DNA from one
cell to another.
There are two basic types:
- Generalized transduction: Can transfer
any gene from a donor to a recipient cell
- Specialized transduction: Can transfer
only a few closely linked genes between
cells
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Generalized Transduction
Salmonella enterica
Any gene from a donor chromosome is packaged into a bacteriophage
and transferred to a new cell upon infection.
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Steps of generalized transduction
• Bacteriophases with a foreign DNA are called
transducing particles.
•The transducing particles transfer any part of the
host DNA to a new host (recipient) cells.
•Recombination occurs at low frequency
P1 phage of E.Coli. and P22 phage of Samonella
are examples of generalized transduction.
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Specialized Transduction
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Specialized Transduction
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Specialized Transduction
• The Phage genome is integrated into the host DNA
at a specific site.
• On induction (UV light), the viral DNA separates
from the host genome.
• Under rare events, the phage DNA maybe excised
incorrectly.
• Some of the adjacent bacterial genes are excised
along with the viral genome.
• When the phage infects new crop of cells, it allows
transduction to occur at high frequency
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DNA Restriction and Modification
Bacteria have developed a kind of “safe sex”
approach to gene exchange.
This protection system, called restriction and
modification, involves:
- Enzymatic cleavage (restriction) of alien
DNA, by restriction endonucleases
- Protective methylation (modification) of
host DNA
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Figure 9.9
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Recombination
Two different DNA molecules in a cell can
recombine by one of several mechanisms:
- Generalized recombination requires that the
two recombining molecules have a considerable
stretch of homologous DNA sequences (>50
bp).
- Site-specific recombination requires very
little sequence homology between the
recombining DNA molecules.
- But it does require a short sequence
recognized by the recombination enzyme
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Recombination
Homologus
DNA
Crossing
over
Recombinants
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RecA proteins or Synaptases play
critical role in recombination
-double stranded DNA becomes singlestranded DNA by creating a nick
-DNA unwinds
-single-stranded binding proteins bind to
the ssDNA
-RecA finds homology and mediated
strand invasion
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Types of Mutations
A mutation is a heritable change in the DNA.
Mutations can come in several different forms:
- Point mutation: Change in a single base
- Insertion (addition) and deletion (subtraction) of
one or more bases
- Inversion: DNA is flipped in orientation
- Reversion: DNA mutates back to original sequence
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Mutations
Mutations can be categorized into several
information classes:
- Silent mutation: Does not change the
amino acid sequence
DNA template  TTT point mutation  T TC
DNA coding  AAA
 AAG
m-RNA
 UUU
 UUC
Amino acid  Phenylalanine
 Phenylalanine
Though DNA strand has changed, the protein
sequence is the same
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Missense mutation: Changes the
amino acid sequence to another
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Nonsense mutation: Changes the
amino acid sequence to a stop codon
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Frame-shift mutation: Changes the openreading frame of the gene
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Mutation due to inversion in DNA strands
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Mutations Arise in Diverse Ways
Spontaneous mutations are rare because of the
efficiency of DNA proofreading and repair
pathways.
However, they can arise for many reasons:
1)Tautomeric shifts in DNA bases that alter basepairing properties [ GT or A  C]
2) Oxidative deamination of bases
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3) Formation of apurinic sites [loss of
purine]
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Mutations Arise in Diverse Ways
Mutations can be caused by mutagens:
Chemical agents
- Base analogs
- Base modifiers
- Intercalators
Electromagnetic radiation
- X-rays and gamma rays: Break the DNA
- Ultraviolet rays: Form pyrimidine dimers
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Mutagenic agents and their effects.
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UV radiation can
induce dimerization
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