Genetics of Bacteria and Archaea: Mutation, Selection, and Genomic Integrity

Genetics of Bacteria and Archaea

Introduction

This study guide summarizes key concepts from Chapter 9 of Brock Biology of Microorganisms, focusing on the genetics of bacteria and archaea. Topics include mutation types, selection methods, auxotrophs, mechanisms of DNA transfer, transposable elements, and systems for maintaining genomic integrity.

Mutation and Mutants

Definition and Types

A mutation is an inheritable change in the DNA sequence that can alter the phenotype of an organism. A mutant is a cell or virus derived from the wild type that carries a nucleotide sequence change and may exhibit a different phenotype.

• Wild type: The standard or reference strain of an organism.

• Mutant: An organism with a genetic change from the wild type.

• Phenotype: Observable characteristics resulting from genotype and environment.

Strain vs Mutant

• Strain: A genetic variant or subtype of a microorganism.

• Mutant: A strain with a specific genetic mutation.

Selection and Screening

Methods for Identifying Mutants

• Selection: Growth conditions that favor the propagation of specific genotypes (e.g., antibiotic resistance).

• Screening: Growth conditions where both mutant and wild type can grow, but mutants are identified phenotypically (e.g., color change, nutritional requirements).

Auxotrophs

Auxotrophs are microorganisms unable to synthesize an essential nutrient due to a gene mutation. They require supplementation of the missing nutrient for growth.

• Prototroph: Wild-type organism that can synthesize all required nutrients.

• Auxotroph: Mutant organism that cannot synthesize a specific nutrient.

Example: Screening for nutritional auxotrophs involves replica plating on complete and selective media to identify colonies unable to grow without supplementation.

Molecular Basis of Mutation

Types of Mutations

Mutations can be classified based on their molecular effects:

• Point mutations: Single nucleotide changes (e.g., transitions, transversions).

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

• Nonsense mutation: Changes a codon to a stop codon, producing an incomplete protein.

• Silent mutation: Alters a codon but does not change the amino acid sequence; protein remains normal.

• Frameshift mutation: Insertions or deletions that shift the reading frame, often resulting in nonfunctional proteins.

Example: A DNA sequence change from AAC to ATC can result in a missense mutation (asparagine to isoleucine).

DNA Transfer in Bacteria and Archaea

Mechanisms of Gene Transfer

Bacteria and archaea can exchange genetic material through several mechanisms:

• Transformation: Uptake of free DNA from the environment.

• Conjugation: Direct transfer of DNA between cells via cell-to-cell contact.

• Transduction: Transfer of DNA by bacteriophages (viruses).

Transferred DNA may be replicated and recombined into the recipient genome.

Transposable Elements

Definition and Types

Transposable elements are discrete DNA segments that can move within and between DNA molecules. They are found in all domains of life and are important for genetic diversity and evolution.

• Insertion sequences (IS): Simplest transposable elements, containing only genes for transposition (e.g., transposase) and inverted repeats.

• Transposons: Larger elements that may carry additional genes, such as antibiotic resistance.

Type	Size	Genes	Features
IS Element	~1000 bp	Transposase	Inverted repeats, found in chromosomes/plasmids
Transposon (e.g., Tn5)	Several kb	Transposase, antibiotic resistance	Inverted repeats, additional genes

Mechanisms of Transposition

• Conservative transposition: Element excised and inserted at a new site; original copy is lost.

• Replicative transposition: New copy produced and inserted at a second location; original remains.

Transposon mutagenesis is used to disrupt genes and study their function by screening for loss of function.

Genomic Integrity and Innate Immunity

Restriction Endonucleases

Restriction endonucleases protect cells from viral attack and foreign DNA by cleaving specific sequences. Host DNA is protected by methylation or other modifications.

• Phage exclusion: Modified restriction systems that recognize and destroy foreign DNA.

• Abortive infection: Host suicide triggered by toxin-antitoxin systems to prevent viral spread.

CRISPR-Cas Systems

Adaptive Immunity in Bacteria and Archaea

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a major antiviral defense system. It maintains genome stability by destroying foreign nucleic acids from horizontal gene transfer.

• CRISPR regions contain short repeats and variable spacers from previous invaders, acting as a "memory bank".

• Cas proteins: Endonucleases that cleave foreign DNA and incorporate new spacers.

• CRISPR is analogous to adaptive immunity due to its sequence specificity.

Distribution and Anti-CRISPR Mechanisms

• CRISPR systems are found in ~90% of archaea and 70% of bacteria.

• Viruses can evade CRISPR by mutating PAM regions, producing Cas inhibitors, or encoding their own CRISPR systems.

Example: Phage-encoded CRISPR in Vibrio cholerae bacteriophage targets the host defense system.

Additional info: The notes have been expanded with definitions, examples, and context for clarity and completeness.