KAP
Biology Dept
Kenyon College
Bacterial Gene Exchange
and Mobile Genes
Fall Section Spring Section 1 Spring Section 2

Bacterial Gene Transfer

Bacterial gene exchange differs from eukaryotes:

  • Bacteria do not exchange genes by meiosis.  (Why not?)  They rarely exchange two entire genomes.
  • Bacteria commonly exchange small pieces of genome, a few genes at a time, through transformation, transduction, or conjugation.
  • Transfer between species, even kingdoms, is common; less common  in eukaryotes, though it does occur.
Transformation.
Transformation is the uptake of DNA from outside the cell.  Only a single strand is taken up, through a special protein  complex in the cell membrane.  The process requires calcium ion (Ca2+).  Transformation occurs at extremely low frequency, but with large populations of bacteria, it offers a significant route for genetic transfer.

Phage Transduction
There are two types:

  • Generalized transduction (depicted below).  A piece of host DNA gets packaged by mistake, instead of the phage DNA.  This rare event results in a phage delivering only bacterial DNA to the next host.  The DNA then recombines homologously, replacing the host allele.
  • Specialized transduction, in which a lysogenic prophage recombines itself out of the genome (by site-specific recombination) and mistakenly includes a piece of bacterial DNA.  The resulting phage progeny can infect cells to produce lysogens with a second copy of the allele they had packaged, attached to the phage DNA.
Diagram of generalized transduction:

Plasmids

Plasmids are small circles of DNA that contain an origin of replication (ori) and a small number of genes, some of which may confer a survival advantage on a host.  Some plasmids can transfer between different species; even between different kingdoms.  A shuttle vector is a plasmid engineered in the test tube to contain an ori site for bacteria, and an ori site for animal or plant cells.  Shuttle vectors are enormously useful to clone a gene conveniently in bacteria, then express it in tissue culture.

Conjugation

Conjugation is the process by which a plasmid is transferred from an F+ cell into an F- cell.  The F factor in the F+ cell contains genes which express pili for attachment, and special membrane proteins for the transfer complex.  Some conjugative plasmids carry drug resistant strains--a big problem for hospitals.

If an F plasmid is integrated into a host genome (an Hfr, for high frequency recombination) the F factor can transfer part or all of the genome into the recipient F- cell.

I
Electronic Companion to Genetics, Cogito Learning MediaI
Episomes and Hfr
The F plasmid can recombine itself into the host chromosome by site-specific recombination.  It can then (a) transfer part or all of the chromosome into a recipient F- cell, as an Hfr; or (b) recombine itself out again, and mistakenly pick up a piece of the host chromosome to carry into the next F- host.

Problem (5)  Explain two different genetic processes in bacteria that can create a "partial diploid" for a small part of the genome.  Explain why these processes are useful for bacterial genetic analysis.

Mobile genes.
Some genes, such those encoding resistance to antibiotics, can move from one genome to another, at a new place in the genetic map.  Some of these mobile genes can even transfer between two distantly related species of organism.

Transposable elements
The first transposable elements to be characterized genetically were controling elements for seed coat color in maize (corn.)  Barbara McClintock won the Nobel Prize for showing that DNA is not all "fixed" in the genome, but that some sequences can insert and excise by intramolecular recombination.

There are  many classes of transposons.  In bacteria, a common structure of a transposon contains:

  • An insertion sequence (IS) at the right and left ends.  The IS contains the gene encoding the transposase enzyme.
  • A gene encoding antibiotic resistance.  This gene confers a selective advantage to bacteria containing the transposon, in  the presence of the antibiotic.


Transposons

Some bacterial transposons can be exchanged among many different species, usually carried by plasmids.
Other transposed pieces of DNA can be inverted at one place in one species, to turn on or off the regulation of a gene.  An example of such a site-specific transposition event is the flagellar gene regulation catalyzed by hin recombinase.


Genomic Islands

Bacterial genomes often contain "islands" of DNA transferred relatively recently from another species. The "genomic island" may confer special properties to a pathogen, or two a strain inhabiting a special niche in an ecosystem.

 


Herbert Schmidt and Michael Hensel, Clinical Microbiology Reviews, January 2004, Vol. 17, p. 14-56.

A pathogenicity island is a genomic island that converts a "harmless" bacterium to a pathogen.

The pathogenicity island is a distinct region of DNA present in the genome of pathogenic bacteria but absent in nonpathogenic strains of the same species. Transfer may be mediated by an integrase enzyme (int).

The island is typically inserted at a tRNA gene in the core genome.

The pathogenicity island typically contains virulence genes (V1 to V4) interspersed with other mobility elements, such as insertion sequences (IS).

How do we recognize a recently inserted pathogenicity island? One clue typically is a difference in percent GC content, compared to the core genome.

Examples of Pathogenicity Islands

 

A. The cag island of H. pylori (cause of stomach ulcers) harbors genes for a type IV secretion system that can translocate the toxin CagA into human cells, causing an inflammatory response.

B. The SP-1 island of Salmonella typhimurium (typhus and food poisoning) encodes a type III secretion system (grey), secreted proteins (dark grey), and regulatory proteins. The same island includes metabolic proteins unrelated to virulence.

C. The HPI island of Yersinia enterocolitica has genes that encode a high-affinity iron uptake system (dark grey) needed for extracellular growth of the pathogen during colonization of the host.

D. The vSAL island of multiple drug-resistant Staphylococcus aureus (MRSA) encodes a remarkably high number of enterotoxins.

Genomic islands in two strains of a marine phototroph, Prochlorococcus

The two strains of Prochlorococcus marinus are cyanobacteria, major oxygenic producers in the oceans, consuming a large part of atmospheric CO2. The strains MED4 and MIT96512 differ by only 0.8% of their genome, yet their distributions throughout the ocean are very different, for unknown reasons. The reason for the difference in distribution may have to do with genes encoded within five genomic islands specific to MED4 (ISL1, ISL4, ISL5) or to MIT9312 (ISL2, ISL3).
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