chapter 9 gene transfer mutations and genome evolution
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Chapter 9: Gene Transfer, Mutations, and Genome Evolution. 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

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chapter overview
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
  • 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.

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.

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.
gene transfer by transformation
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


Gene Transfer by Transformation

  • Not all bacteria can take up free or naked DNA (<1%).
  • Some microbes become competent sometime during their growth cycle

Gene Transfer by Transformation

Natural Transformation occus Bacillus sp., Haemophilussp., Neisseriasp., Acinetobactersp., Streptococcus sp., Pseudomonas sp.

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 sequence-specific.

Thus limiting gene exchange between genera


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 malesand without it are females
gene transfer by conjugation
Gene Transfer by Conjugation

Conjugation is the transfer of DNA from one bacterium to another, following cell-to-cell contact by pilus on the donor cell.

- The pilus attaches to the receptor on the recipient cell

- Two cell fuse and single-stranded DNA passes from donor to recipient cell.

Conjugationrequires 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.



Female cells become male cells and be able to transfer the plasmid



The F-factor plasmid can integrate into the chromosome.

- The cell is now designated Hfr, or high-frequency recombination strain.



Hfr + F-  Hfr + F-

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-,

since not all Hfr

genes are transferes.

The entire chromosome take about 100 min to transfer as opposed only 5 min for free plasmid

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

Some bacteria can actually transfer genes across biological domains.

Transfer of Genes into Eukaryotes

- 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

gene transfer by transduction
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


Generalized Transduction

Salmonella enterica

Any gene from a donor chromosome is packaged into a bacteriophage and transferred to a new cell upon infection.


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.


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
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

DNA Restriction and Modification


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



Homologus DNA





RecA proteins or Synaptases play critical role in recombination

-double stranded DNA becomes single-stranded DNA by creating a nick

-DNA unwinds

-single-stranded binding proteins bind to the ssDNA

-RecA finds homology and mediated strand invasion

A mutation is a heritable change in the DNA.

Mutations can come in several different forms:

Types of Mutations

- 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

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


Amino acid  Phenylalanine  Phenylalanine

Though DNA strand has changed, the protein sequence is the same


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 base-pairing properties [ GT or A  C]

2) Oxidative deamination of bases

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

Mutations Arise in Diverse Ways