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Chapter 8: Bacterial Genetics

A Glimpse of History

Barbara McClintock (1902-1992)

• Research Focus: Studied maize (corn) and observed unpredictability in kernel colors, leading to groundbreaking discoveries in genetics.

• Key Findings: Concluded that segments of DNA, later named transposons or “jumping genes,” could move in and out of genes linked to color. This mobility could disrupt gene functions and contribute to genetic diversity.

• Publication: Published her findings in 1950, which faced initial skepticism because at the time, the prevailing belief was that DNA was stable and unchanging.

• Recognition: Her revolutionary work gained acceptance by the 1970s, culminating in her receiving the Nobel Prize in Physiology or Medicine in 1983.

Introduction

Adaptation through Natural Selection

• Mechanisms: Organisms adapt to their environments through two primary mechanisms: regulation of gene expression (how genes are activated or suppressed) and genetic change (actual alterations in DNA).

• Model Organism: Escherichia coli (E. coli) serves as a prime model organism for studying genetic change due to its rapid growth rates, ease of manipulation, and well-mapped genetics.

Genetic Change in Bacteria

Mechanisms of Genetic Change

1. Mutation: Changes in the nucleotide sequences of the genome.

2. Horizontal Gene Transfer (HGT): The transfer of DNA between organisms, which can be passed to progeny through vertical gene transfer, contributing to genetic diversity.

   • Impact: Changes in DNA not only affect the genotype (nucleotide sequence) but also lead to changes in phenotype (observable traits), which can also be influenced by environmental conditions.

Types of Mutations

• Spontaneous Mutations: Random genetic changes that occur during normal cellular processes, rather than due to external agents.

  • Mutation Rates: Generally low, but can be consistent within specific organisms.

• Base-Pair Substitutions: The most common type of mutations, which can be classified as:

  • Synonymous Mutation: No change in amino acid and therefore typically has no immediate effect on protein function.

  • Missense Mutation: Alters the amino acid sequence, which can potentially disrupt protein function or lead to new functions.

  • Nonsense Mutation: Introduces a premature stop codon, leading to truncated, nonfunctional proteins.

• Nucleotide Insertions/Deletions: Changes in DNA sequences where nucleotides are added or removed.

  • Impact Variability: Alterations can range from causing a single codon change (if three bases are added or deleted) to causing frameshift mutations if one or two bases are affected, often resulting in nonfunctional proteins due to altered downstream coding sequences.

Transposons (Jumping Genes)

• Definition: Segments of DNA that can move within the genome, potentially inactivating other genes through a process known as insertional inactivation.

• Significance: Critical in understanding genetic variance and can play roles in antibiotic resistance by transferring resistance genes between bacteria.

Induced Mutations

• Chemical Mutagens: Substances that increase mutation rates by directly modifying nucleobases, including:

  • Alkylating Agents: Add alkyl groups to bases, altering their pairing properties.

  • Base Analogs: Incorporate into DNA during replication instead of normal bases, leading to errors.

  • Intercalating Agents: Insert themselves between DNA bases, causing frameshifts during replication and transcription.

• Radiation Effects: Different forms of radiation cause specific types of DNA damage:

  • Ultraviolet Light: Causes thymine dimers, leading to mispairing during DNA replication.

  • X-rays: Can induce strand breaks in DNA, often resulting in lethal mutations.

DNA Repair Mechanisms

• Importance of Repair: DNA damage poses a significant risk of cell death if not repaired properly.

• Key Repair Mechanisms:

  • Proofreading: Carried out by DNA polymerases during replication to correct errors.

  • Mismatch Repair: Identifies and repairs mismatches that escape proofreading immediately after DNA synthesis.

  • Base Excision Repair: Involves removal of damaged bases and filling in the resulting gaps with correct nucleotides.

  • SOS Repair: An emergency repair mechanism for extensive damage that can lead to increased mutation rates due to error-prone repair processes.

Mutant Selection Techniques

• Methods: Techniques to isolate and identify mutants include:

  • Direct Selection: Promotes the growth of mutants under specific conditions (e.g., selective medium).

  • Indirect Selection: Requires techniques like replica plating to identify auxotrophs, organisms that require additional nutrients due to mutations affecting biosynthetic pathways.

Overview of Horizontal Gene Transfer (HGT)

Mechanisms of HGT

1. Bacterial Transformation: The uptake of naked DNA from the environment by a competent cell, which can then integrate this genetic material into its genome.

2. Transduction: The process by which bacteriophages (viruses that infect bacteria) mediate the transfer of DNA between bacterial cells.

3. Conjugation: Direct transfer of DNA between bacterial cells through physical contact, typically mediated by plasmids.

Detailed Processes of HGT

• Transformation: Requires cells to be in a state of competence; involves homologous recombination following DNA uptake to integrate exogenous DNA into the chromosomal genome.

• Transduction: Bacteriophages can engage in generalized transduction, wherein randomized bacterial DNA is packaged into phage particles and subsequently transferred to other bacteria during infection.

• Conjugation: Often facilitated by plasmids such as the F plasmid which allows transfer of genetic material, including antibiotic resistance genes, through a physical connection between cells.

Genome Variability

• Genetic Diversity: Strains of the same bacterial species (like E. coli) show significant genetic heterogeneity, featuring core genes essential for basic functions, accessory genes that confer various advantages, and unique genes that may provide specialization in different environments.

Mobile Genetic Elements (MGEs)

• Plasmids: Circular pieces of DNA that can harbor genes for advantageous traits such as antibiotic resistance, capable of transferring between bacteria.

• Transposons and Genomic Islands: Unique mechanisms that facilitate the movement and acquisition of DNA, contributing to genetic diversity and adaptability of bacterial populations.

Bacterial Defense Mechanisms

• Defense Systems: Bacteria possess elaborate systems like Restriction-Modification and CRISPR that recognize and destroy foreign genetic material, thus conferring protection against phages and plasmids.

Key Takeaway

• Understanding bacterial genetics is crucial for advancing microbiology' efforts to combat infectious diseases and manage antibiotic resistance, highlighting the importance of genetic studies in developing effective medical treatments and interventions.