Genetics of Bacteria

Introduction

The genetics of bacteria encompasses the study of their DNA structure, mutation processes, and mechanisms of gene transfer. These processes are fundamental to understanding bacterial evolution, adaptation, and the development of traits such as antibiotic resistance.

Vibrio cholerae: An Example of Bacterial Genetics

Characteristics and Habitat

• Gram-negative, comma-shaped bacterium; facultative anaerobe with a flagellum at one cell pole and pili.

• Natural habitat: brackish or saltwater; can flourish in nutrient-rich human intestine.

Pathogenicity and Gene Transfer

• Causes cholera by releasing a toxin that triggers diarrheal purges.

• Employs proteins to kill neighboring cells in marine environments.

• Uses Type VI secretion system (T6SS) and DNA uptake system (natural competence) for horizontal gene transfer.

Type VI Secretion System (T6SS)

• Facilitates horizontal gene transfer by assembling on chitin surfaces (e.g., exoskeletons of zooplankton).

• Induced by environmental cues, such as the presence of chitin.

I. Mutation

Mutations and Mutants

• Mutation: Heritable change in DNA sequence that can alter phenotype.

• Wild-type strain: Strain isolated from nature; can refer to a gene or organism.

• Mutant: Derived from wild-type, carries a genotype change; phenotype may also be altered.

Genetic Nomenclature

• Genotype: Italicized (three lowercase letters + capital letter), e.g., hisC.

• Mutation: Number indicates order of isolation, e.g., hisC2.

• Phenotype: Capital letter + two lowercase letters and +/- for presence/absence, e.g., His+ or His-.

• Multiple loci: Use capital letters after locus symbol, e.g., araA, araB, araC.

• Promoter/operator sites: e.g., lacZp, lacAt, lacZo.

• Mutation in protein: e.g., H14Q (histidine to glutamate at position 14).

Isolation of Mutants

• Selectable mutations: Confer advantage (e.g., antibiotic resistance).

• Nonselectable mutations: No advantage; detected by screening (e.g., pigment loss).

Isolation of Nutritional Auxotrophs

• Replica plating: Screens for mutants unable to grow without a specific nutrient.

• Auxotroph: Requires additional nutrient (e.g., His- needs histidine).

• Prototroph: Parental strain, does not require additional nutrients (e.g., His+).

Mutant Isolation: Replica Plating Technique

• Used to identify mutants by negative selection (e.g., loss of ability to synthesize histidine).

• Process: Inoculate master plate, transfer cells to velvet, then to selective media, compare growth.

Auxotrophic and Catabolic Mutants

• Catabolic mutants: Cannot use specific nitrogen or phosphate sources.

• Both types result from mutations in genes encoding metabolic enzymes.

Common Classes of Mutants and Detection

Molecular Basis of Mutation

Types of Mutations

• Spontaneous mutations: Occur without external intervention; often due to DNA polymerase errors.

• Induced mutations: Result from environmental factors (radiation, chemicals).

• Point mutations: Change a single base pair; can cause amino acid changes, incomplete proteins, or no effect.

Conditional Lethal Mutations

• Used to identify essential genes in haploid organisms.

• Detected by growth under permissive but not restrictive conditions.

• Examples: Temperature-sensitive, cold-sensitive, and nonsense mutations (UAA, UAG, UGA codons).

Base-Pair Substitutions: Missense, Nonsense, and Silent Mutations

• Silent mutations: No effect on polypeptide or phenotype (often third base of codon).

• Missense mutations: Change amino acid sequence; effect depends on location and properties of substituted amino acid.

• Nonsense mutations: Introduce stop codon, resulting in truncated protein.

Example:

• If the substituted amino acid has similar properties to the original, the protein may retain function.

Transitions and Transversions

• Transitions: Purine (A/G) substituted for another purine.

• Transversions: Purine substituted for pyrimidine (C/T) or vice versa.

Frameshifts and Other Insertions/Deletions

• Frameshift mutations: Insertions/deletions that shift the reading frame; can scramble polypeptide sequence.

• Insertion/deletion of three base pairs adds/deletes an amino acid (less severe).

• Large insertions may be due to transposable elements.

Reversion and Mutation Rates

Reversions and Suppressors

• Reversion: Point mutations are often reversible.

• Revertant: Strain in which original phenotype is restored.

• Same-site revertant: Mutation at the same site restores original sequence.

• Second-site revertant: Mutation at a different site compensates for the original effect (e.g., suppressor tRNA).

Mutation Rates

• Errors in DNA replication: to per kb.

• Typical gene (~1 kb): similar mutation frequency.

• Eukaryotes: 10-fold lower error rates.

• DNA viruses: 100–1000× higher error rates.

• RNA viruses: Even higher due to lack of proofreading and repair.

Additional info:

• Single base errors more likely to cause missense than nonsense mutations.

• Silent mutations are the next most frequent.

• Mutation pool can be increased by mutagenic agents or stress.

Mutagenesis

Mutagens

• Mutagens: Chemical, physical, or biological agents that increase mutation rates.

• Chemical mutagens: Include nucleotide base analogs, alkylating agents, and intercalating agents.

• Radiation: Nonionizing (UV) and ionizing (X-rays, gamma rays) can cause DNA damage.

Table: Chemical and Physical Mutagens and Their Modes of Action

DNA Repair and the SOS System

• In Bacteria, stalled replication or major DNA damage activates the SOS repair system.

• Initiates many DNA repair processes, some error-free, some error-prone (translesion synthesis).

• Master regulators: LexA (repressor) and RecA (recombination protein).

• DNA polymerase V (umuCD genes) and DNA polymerase IV (dinB gene) are error-prone polymerases involved.

II. Gene Transfer in Bacteria

Overview

• Genetic recombination

• Transformation

• Transduction

• Conjugation

• Formation of Hfr strains and chromosome mobilization