Mechanisms of Genetic Variation in Prokaryotes: Horizontal Gene Transfer and Recombination

Mechanisms of Genetic Variation in Prokaryotes

Introduction

Genetic variation in prokaryotes is primarily driven by horizontal gene transfer (HGT) and recombination. These processes enable bacteria and archaea to acquire new genetic traits, adapt to changing environments, and evolve rapidly. The main mechanisms of HGT are transformation, transduction, and conjugation.

Horizontal Gene Transfer (HGT)

Overview of HGT

• Horizontal gene transfer is the movement of genetic material between organisms other than by vertical transmission (from parent to offspring).

• HGT is a major source of genetic diversity in prokaryotes.

• Three main mechanisms: Transformation, Transduction, and Conjugation.

Fates of Incoming DNA

When foreign DNA enters a bacterial cell, it can have three possible fates:

• Recombination with the host genome: The incoming DNA integrates into the host chromosome via homologous recombination.

• Degradation: The foreign DNA is recognized as non-self and degraded by nucleases.

• Stable existence as an autonomous element: The DNA persists as a plasmid or other replicon without integrating into the chromosome.

Homologous Recombination

Definition and Mechanism

• Homologous recombination is the physical exchange of DNA between similar or identical genetic elements.

• Key steps include:

  1. Endonuclease nicks donor DNA.

  2. Binding of single-strand binding protein.

  3. Strand invasion mediated by RecA protein.

  4. Development of cross-strand exchange (Holliday junction).

  5. Resolution into patches or splices.

Example: Homologous recombination is essential for integrating foreign DNA during transformation, transduction, or conjugation.

Detecting Genetic Recombination

• Recombination can be detected by mixing two bacterial strains with different nutritional requirements and selecting for recombinants that can grow on minimal media.

• Example: Mixing Trp- and Trp+ cells and plating on tryptophan-deficient media; only recombinants form colonies.

Merodiploids and Complementation

• Merodiploid: A bacterial strain carrying two copies of a particular chromosomal segment (one on the chromosome, one on a plasmid or phage).

• Complementation: Restoration of wild-type phenotype when a functional gene copy is supplied on a plasmid or phage.

Transformation

Definition and Discovery

• Transformation is the genetic transfer process by which free DNA is incorporated into a recipient cell, causing genetic change.

• Discovered by Frederick Griffith in the 1920s using Streptococcus pneumoniae.

• Example: Griffith's experiment showed that heat-killed virulent cells could "transform" non-virulent cells into virulent ones.

Competence in Transformation

• Competent cells are capable of taking up DNA and being transformed.

• Competence is genetically determined and often involves pili for DNA uptake.

• Vibrio cholerae is a model for natural competence in Gram-negative bacteria.

Mechanism of Transformation

1. Binding of free DNA to the cell surface.

2. Uptake of single-stranded DNA into the cell.

3. RecA-mediated homologous recombination integrates the DNA into the chromosome.

Regulation of Competence

• Natural competence is regulated by various mechanisms, including quorum sensing.

• Bacillus subtilis and Vibrio cholerae use quorum sensing to regulate competence development.

Transduction

Definition and Types

• Transduction is the transfer of DNA from one cell to another by a bacteriophage (virus that infects bacteria).

• Two main types:

  • Generalized transduction: Any portion of the host genome can be packaged into a phage and transferred.

  • Specialized transduction: Only specific regions of the host chromosome adjacent to the prophage are transferred.

Generalized Transduction

• Occurs during the lytic cycle of a bacteriophage.

• Random fragments of host DNA are mistakenly packaged into phage particles.

• These defective phages can inject host DNA into new recipient cells, where it may recombine with the recipient genome.

Specialized Transduction

• Occurs with temperate phages during the lysogenic cycle.

• When the prophage excises incorrectly, it takes adjacent host genes with it.

• Only specific genes near the integration site are transferred.

Phenotypic Changes: Phage Conversion

• Phage conversion: Alteration of the phenotype of a host cell by lysogenization with a temperate phage.

• The host cell becomes immune to further infection by the same phage and may acquire new traits (e.g., toxin production).

• Examples:

  • Change in cell surface polysaccharide structure.

  • Production of toxins (e.g., Shiga toxin in Escherichia coli).

Conjugation

Definition and Mechanism

• Bacterial conjugation is a mechanism of genetic transfer that involves direct cell-to-cell contact.

• It is a plasmid-encoded process, typically involving the F (fertility) plasmid in E. coli.

• Donor cell contains the conjugative plasmid; recipient cell does not.

F (Fertility) Plasmid

• Circular DNA molecule (~99 kbp) containing genes for DNA replication, transfer (tra genes), and transposable elements.

• Key regions:

  • oriV: Origin of replication for the plasmid.

  • oriT: Origin of transfer during conjugation.

Transfer of Plasmid DNA

• During conjugation, a single strand of the F plasmid is transferred from donor (F+) to recipient (F-), and both cells synthesize the complementary strand.

• Both cells become F+ after conjugation.

Formation of Hfr Strains and Chromosome Mobilization

• The F plasmid can integrate into the host chromosome, forming an Hfr (high frequency of recombination) cell.

• Hfr cells can transfer chromosomal genes to recipient cells during conjugation.

• Only part of the F plasmid and adjacent chromosomal DNA are usually transferred, so the recipient does not become Hfr.

Integration and Mobilization

• Integration is facilitated by insertion sequences (IS elements) present in both the F plasmid and the host chromosome.

• Homologous recombination between IS elements allows the F plasmid to integrate or excise from the chromosome.

F' Plasmids and Merodiploids

• F' plasmids are F plasmids that have excised from the chromosome, carrying some chromosomal genes with them.

• Transfer of F' plasmids can create merodiploid cells (partial diploids for certain genes).

Barriers to Horizontal Gene Transfer

• Bacteria have evolved mechanisms to limit HGT, including:

  • Restriction-modification systems: Enzymes that degrade foreign DNA.

  • CRISPR-Cas systems: Adaptive immunity that targets and destroys invading genetic elements.

  • Surface exclusion and entry exclusion systems.

Review Questions

• What is the purpose of oriT and oriV in the F plasmid? oriV is the origin of replication for the plasmid; oriT is the origin of transfer during conjugation.

• Why is phage conversion considered beneficial to host cells? It can provide immunity to further infection by the same phage and may confer new phenotypic traits, such as toxin production or altered surface structures.

• Why does an Hfr x F- mating not yield two Hfr cells? Only part of the F plasmid is transferred during conjugation, so the recipient does not receive the entire F factor and does not become Hfr.

Summary Table: Mechanisms of Horizontal Gene Transfer

Mechanism	Definition	Key Features	Example
Transformation	Uptake of free DNA from the environment	Requires competence; DNA may integrate by recombination	Streptococcus pneumoniae transformation
Transduction	Transfer of DNA via bacteriophage	Generalized (any gene) or specialized (specific genes)	Shiga toxin genes in E. coli
Conjugation	Direct transfer of DNA via cell-to-cell contact	Plasmid-encoded; involves F plasmid in E. coli	F plasmid transfer in E. coli