Bacteria Gene Linkage

Gene Linkage in Bacteria

• Lecture 9: Genes to Genomes Version 1.25.S 2025

• Design: J. Fonta 2024, Revised by: M. J. Michelsohn 2025

Review of Previous Material

• Topics:

  • Gene Linkage

  • Linkage Mapping

  • Chromosome Mapping

Overview of New Material

• Topics:

  • Conjugation

  • Transformation

  • Transduction

Genetic Architecture in Bacteria

• Bacterial DNA

  • Contained in nucleoid (DNA, protein, RNA)

  • Typically haploid

  • Usually circular chromosome

  • Plasmids: Small extrachromosomal circular DNA that replicate independently

  • Bacterial chromosomes contain essential genetic material for life

  • Bacteria may have numerous plasmids

Horizontal Genetic Transfer in Bacteria

• Conjugation: Direct cell-to-cell contact to transfer genetic material

• Transformation: Uptake of external genetic material to incorporate into genome

• Transduction: Virus (bacteriophage) transfers genetic material between bacteria

Fertility Factor

• F factor: A plasmid with genes for conjugation

• F+ cells: Bacterial cells with F factor act as donors

• F- cells: Cells without F factor, can accept DNA

  • A pilus connects the cytoplasm of two bacterial cells

  • Endonuclease opens dsDNA of plasmid, initiating ssDNA transfer

  • DNA synthesis replaces the missing strand in both cells

Mapping through Conjugation

• Interrupted mating technique: Determines gene positions during conjugation

• Integrated F factor creates an origination point (O point) for endonuclease activity

• Chromosome transferred sequentially through pilus unless interrupted

Conjugant Strains

• F factor integration at various placements creates bacterial lineages with different O points

• Excision of F factor can include additional genes

• Conjugation leads to horizontal recombination of alleles that alter phenotype

Transformation

• Requires recognition and active uptake of exogenous DNA

• Nuclease digestion reduces dsDNA to ssDNA

• ssDNA aligns with bacterial chromosome complement and replaces the original strand

• Following binary fission, one offspring inherits the parent allele, the other the new allele

Mapping through Transformation

• Proximal genes on exogenous DNA are cotransformed

• Cotransformation allows mapping of proximity within the genome

• Unlinked genes need separate transformations for genome incorporation

Transduction

• Bacteriophages infect bacterial hosts and insert their genome

• They cleave the host genome; new phages can include both viral and bacterial DNA

• Infected cells lyse to release new phages

• Chimeric phages insert bacterial DNA into new hosts

Mapping through Transduction

• Proximal genes are cotransduced

• Identifying cotransduced genes helps map proximity in the bacterial genome

• Unlinked genes require separate transduction events

Bacterial Growth on Media

• Bacteria as model organisms due to fast reproduction and haploid genome

• Prototrophs: Can live on minimal medium

• Auxotrophs: Have alleles that cause loss-of-function, need supplemental nutrients

Conjugation Mapping Example

• Example involves genes: his, leu, mal, xyl

• Recipient cells are auxotrophic for all four genes

• After 25 minutes of mating, the occurrence rates in recipient cells are:

  • his: 15%

  • leu: 75%

  • mal: 40%

  • xyl: 0%

  • Diagram the relative positions of these genes and the O point of the F factor

Study Review 2.3

• Vocabulary:

  Nucleoid: The region in a bacterial cell where its DNA is located (since bacteria don’t have a nucleus).

  Circular chromosome: The main DNA structure in bacteria, shaped like a closed loop instead of linear chromosomes in eukaryotes.

  Plasmids: Small, extra pieces of DNA in bacteria that can carry helpful genes, like antibiotic resistance.

  Conjugation: A process where bacteria transfer genetic material to each other through direct contact.

  Transformation: When a bacterium takes in free DNA from its environment.

  Transduction: When a virus (bacteriophage) transfers DNA from one bacterium to another.

  Bacteriophage: A virus that infects bacteria.

  Fertility factor (F factor): A special piece of DNA that allows bacteria to transfer genes through conjugation.

  Pilus: A hair-like structure on bacteria used to connect to other bacteria during conjugation.

  Interrupted mating technique: A method used to map bacterial genes by stopping conjugation at different times.

  Origination point (origin of transfer): The place where DNA transfer begins during conjugation.

  Exogenous: DNA or substances that come from outside the cell.

  Binary fission: The way bacteria reproduce by splitting into two identical cells.

  Prototroph: A bacterium that can grow on minimal nutrients because it can make all the compounds it needs.

  Auxotroph: A bacterium that cannot grow without extra nutrients because it has a mutation preventing it from making a necessary compound.

• Questions:

  • Phenotypic implications of haploid bacteria vs diploid eukaryotes

  Haploid bacteria: Since bacteria have only one copy of their chromosome, any mutation immediately affects their phenotype. There is no second copy to mask harmful mutations.

  Diploid eukaryotes: They have two copies of each gene, so a mutation in one copy may not show if the other copy is functional (dominant vs. recessive traits).

  Impact on evolution: Bacteria can quickly adapt to their environment because beneficial mutations show up right away and spread fast.

  • Differences between eukaryotic chromosomes and bacterial chromosomes

  Structure:

  • Bacterial chromosomes are circular and found in the nucleoid (no nucleus).

  • Eukaryotic chromosomes are linear and located inside the nucleus.

  Number:

  • Bacteria typically have one chromosome.

  • Eukaryotes have multiple chromosomes.

  Packaging:

  • Bacterial DNA is supercoiled but lacks histones (except in some archaea).

  • Histones are proteins that help package and organize DNA inside the nucleus of a cell

  • Eukaryotic DNA wraps around histones to form chromatin.

  Replication Origin:

  • Bacteria have one origin of replication.

  • Eukaryotic chromosomes have multiple origins for faster replication.

  • How can transformation turn an auxotrophic bacterium into a prototroph?

  Transformation allows a bacterium to take up foreign DNA from its environment.

  If an auxotrophic bacterium (unable to synthesize a needed nutrient) takes in a functional gene from a prototroph, it can regain the ability to produce that nutrient.

  Example: A his⁻ (histidine auxotroph) bacterium can become his⁺ (prototroph) if it absorbs a working his gene from the environment.

  This process is useful in genetics for studying gene function and bacterial adaptation.

Study Review 2.4

• Describe conjugation, transformation, and transduction

Conjugation

• A direct transfer of DNA between bacteria through physical contact.

• A bacterium with an F factor (F⁺ cell) forms a pilus to connect to an F⁻ cell and transfers DNA.

• Can spread plasmids, including antibiotic resistance genes.

• Hfr conjugation involves the transfer of chromosomal DNA, helping in bacterial gene mapping.

Transformation

• A bacterium takes up free DNA from its environment.

• This DNA might come from dead bacteria that released their genetic material.

• If the DNA contains functional genes, it can change the recipient’s traits (e.g., turning an auxotroph into a prototroph).

• Used in genetic engineering to introduce new genes into bacteria.

Transduction

• Viruses (bacteriophages) accidentally transfer bacterial DNA from one cell to another.

• Generalized transduction: Any bacterial gene can be transferred.

• Specialized transduction: Only specific genes near the viral integration site are transferred.

• Helps bacteria acquire new traits, including toxin production or antibiotic resistance.

• Contrast horizontal gene transfer with vertical gene transfer