9. 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 include transformation, transduction, and conjugation.

Horizontal Gene Transfer (HGT)

Overview of HGT

• Horizontal gene transfer refers to 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:

1. Undergo recombination with the host genome.

2. Be degraded by cellular nucleases.

3. Exist independently as a plasmid (if it has an origin of replication).

Homologous Recombination

Definition and Mechanism

• Homologous recombination is the physical exchange of DNA between genetic elements with similar sequences.

• Key steps include:

  1. Endonuclease nicks donor DNA.

  2. Binding of single-strand binding protein (SSB).

  3. Strand invasion mediated by RecA protein.

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

  5. Resolution into patches or splices, resulting in recombinant DNA molecules.

Detecting Genetic Recombination

• Recombination can be detected by introducing DNA from a donor strain into a recipient strain lacking a specific gene (e.g., trp gene for tryptophan synthesis).

• Recombinants are identified by their ability to grow on selective media lacking the nutrient (e.g., tryptophan).

Genetic Recombination: Key Terms

• 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 bacteriophage.

Transformation

Definition and Discovery

• Transformation is the genetic transfer process by which free DNA is taken up by a recipient cell, resulting in genetic change.

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

• Demonstrated that non-virulent bacteria could become virulent by acquiring DNA from heat-killed virulent cells.

Competence in Transformation

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

• Competence is genetically determined and often involves the formation of pili (e.g., in Vibrio cholerae).

• Natural competence is regulated by mechanisms such as quorum sensing (e.g., in Bacillus subtilis and Vibrio cholerae).

General Mechanism of Transformation

1. Binding of free DNA to the cell surface via competence-specific proteins.

2. Uptake of single-stranded DNA into the cell; nucleases degrade one strand.

3. RecA-mediated homologous recombination integrates the DNA into the host genome.

Transduction

Definition and Types

• Transduction is the transfer of DNA from one cell to another via 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 to another cell.

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

Mechanisms

• In generalized transduction, random fragments of host DNA are mistakenly packaged into phage particles during the lytic cycle.

• In specialized transduction, a temperate phage excises incorrectly, taking adjacent host genes with it, which are then transferred to the next host cell.

Phenotypic Changes: Phage Conversion

• Phage conversion is the alteration of a host cell's phenotype due to lysogenization by a temperate phage (prophage formation).

• Host cell becomes immune to further infection by the same phage.

• Other phenotypic changes may include altered surface polysaccharides or toxin production (e.g., pathogenicity).

Conjugation

Definition and Mechanism

• Bacterial conjugation is the transfer of genetic material between cells via direct cell-to-cell contact, typically mediated by a plasmid.

• Donor cell contains a conjugative plasmid (e.g., F plasmid); recipient cell does not.

• Transfer occurs through a pilus structure.

F (Fertility) Plasmid

• The F plasmid is a circular DNA molecule (~99 kbp) that contains:

  • Genes for DNA replication regulation

  • Several transposable elements

  • tra genes encoding transfer functions

  • oriT (origin of transfer) and oriV (origin of replication)

Transfer of Plasmid DNA by Conjugation

• DNA is transferred from donor (F+) to recipient (F-) via rolling circle replication.

• Both cells become F+ after transfer.

Formation of Hfr Strains and Chromosome Mobilization

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

• Cells with non-integrated F plasmid are F+; those with integrated F plasmid are Hfr.

• Integration is facilitated by insertion sequences present in both the F plasmid and the chromosome.

Transfer of Chromosomal DNA by Conjugation

• During Hfr x F- mating, only a portion of the integrated F plasmid and adjacent chromosomal genes are transferred.

• The recipient cell does not become Hfr because the entire F plasmid is rarely transferred.

F' Plasmids and Merodiploids

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

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

Barriers to Horizontal Gene Transfer

• Several mechanisms limit HGT in bacteria:

  • Restriction-modification systems degrade foreign DNA.

  • CRISPR-Cas systems provide adaptive immunity against foreign genetic elements.

  • Surface exclusion and abortive infection systems prevent successful transfer or establishment of foreign DNA.

Summary Table: Mechanisms of Horizontal Gene Transfer

Mechanism	Agent	DNA Source	Requirement	Example
Transformation	Free DNA	Environment	Competent cells	Streptococcus pneumoniae
Transduction	Bacteriophage	Donor cell (via phage)	Phage infection	Escherichia coli phages
Conjugation	Plasmid (F factor)	Donor cell	Cell-to-cell contact	E. coli F plasmid

Review Questions

• What is the purpose of oriT and oriV in the F plasmid? oriT is the origin of transfer (site where DNA transfer initiates); oriV is the origin of replication (site where plasmid replication begins).

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

• Why does an Hfr x F- mating not yield two Hfr cells? Only a portion of the integrated F plasmid is transferred, so the recipient does not receive the entire F factor and remains F-.

Additional info: This guide covers material relevant to Chapter 9 (Genetics of Bacteria and Archaea) and provides foundational knowledge for understanding microbial evolution, antibiotic resistance, and biotechnology applications.