Genetics of Bacteria and Archaea

Introduction

The genetics of bacteria and archaea encompasses the study of mutations, mechanisms of genetic variation, and horizontal gene transfer. These processes are fundamental to microbial evolution, adaptation, and the spread of traits such as antibiotic resistance.

Mutations and Mutants

Definition and Types of Mutations

A mutation is a heritable change in the nucleotide sequence of an organism's genome. Mutations can result in altered phenotypes and are a primary source of genetic diversity.

• Wild-type: The standard or reference genotype/phenotype found in nature.

• Mutant: An organism with a heritable change in its DNA sequence, resulting in a different phenotype from the wild-type.

Classes of Mutants

Mutants are classified based on their phenotypic changes and how they are detected:

Selectable and Nonselectable Mutants

Selectable mutants confer a growth advantage under certain conditions (e.g., antibiotic resistance), while nonselectable mutants do not provide an obvious advantage and require screening to identify.

Screening for Nutritional Auxotrophs

Auxotrophs are mutants that have lost the ability to synthesize a particular nutrient. They are detected by replica plating onto selective media lacking the nutrient.

Types of Mutations

Point Mutations

Point mutations involve a single base pair change in DNA. They can be classified as:

• Missense mutation: Changes a codon, resulting in a different amino acid and a faulty protein.

• Nonsense mutation: Converts a codon to a stop codon, producing a truncated, incomplete protein.

• Silent mutation: Alters a codon but does not change the amino acid due to redundancy in the genetic code.

Frameshift Mutations

Frameshift mutations result from insertions or deletions of base pairs, altering the reading frame of the gene and usually producing nonfunctional proteins.

Suppression of Nonsense Mutations

Some nonsense mutations can be suppressed by mutations in tRNA genes, allowing the translation machinery to read through stop codons and produce full-length proteins.

Mutation Rates and Mutagenesis

Mutation Rates

• Spontaneous mutation rates in bacteria are typically to per kilobase per generation.

• DNA viruses have higher error rates; RNA viruses have the highest due to lack of proofreading.

• Most single base changes result in missense or silent mutations; nonsense mutations are less common.

Mutagenesis: Chemical and Physical Mutagens

Mutagenesis is the process of inducing mutations using physical or chemical agents called mutagens.

Horizontal Gene Transfer (HGT)

Overview of HGT Mechanisms

Horizontal gene transfer is the movement of genetic material between organisms other than by vertical transmission (parent to offspring). The three main mechanisms are transformation, transduction, and conjugation.

Transformation

Transformation is the uptake of free DNA from the environment by a competent bacterial cell, followed by integration into the genome.

• Competence is the physiological state allowing cells to take up DNA.

• DNA is incorporated by homologous recombination.

Transduction

Transduction is the transfer of bacterial genes by bacteriophages (viruses that infect bacteria).

• Generalized transduction: Any bacterial gene can be transferred by a lytic phage.

• Specialized transduction: Only specific genes near the prophage insertion site are transferred by a lysogenic phage.

Conjugation

Conjugation is the direct transfer of DNA from a donor to a recipient cell via cell-to-cell contact, typically mediated by a plasmid (e.g., F plasmid in Escherichia coli).

• Requires a conjugative pilus (sex pilus) for DNA transfer.

• Can transfer plasmids or chromosomal DNA (in Hfr strains).

Hfr Strains and Chromosome Mobilization

High-frequency recombination (Hfr) strains have the F plasmid integrated into the chromosome, allowing transfer of chromosomal genes during conjugation.

Mobile DNA: Transposable Elements

Types of Transposable Elements

Transposable elements are DNA sequences that can move within the genome. They include:

• Insertion sequences (IS): Simple elements with only the genes required for transposition.

• Transposons (Tn): Larger elements that carry additional genes, such as antibiotic resistance.

Preserving Genomic Integrity: CRISPR

CRISPR-Cas System

The CRISPR-Cas system is an adaptive immune mechanism in bacteria and archaea that provides resistance to foreign genetic elements such as phages and plasmids.

• CRISPR loci contain short repeats and spacers derived from foreign DNA.

• Cas proteins use crRNA to recognize and cleave matching foreign DNA.

Summary Table: Key Mechanisms of Genetic Variation in Bacteria and Archaea