Bacterial Genome Organization

Bacterial Chromosome - The Main Blueprint

• Primary genetic element: typically single, circular, double-stranded DNA (dsDNA).
• Location: Cytoplasmic region called nucleoid; not membrane-bound.
• Ploidy: Usually haploid (one chromosome copy).
• Compaction:
  • Supercoiling: Maintained by DNA gyrase (introduces negative supercoils) & topoisomerase IV (decatenation).
  • Nucleoid-Associated Proteins (NAPs): e.g., HU, H-NS, IHF; histone-like proteins that help organize DNA.
• Size: Variable; E. coli genome is ~4.6 million base pairs (Mbp).
• Replication: Single origin of replication (oriC); proceeds bidirectionally.
• Genetic Content:
  • High gene density; minimal non-coding DNA.
  • No introns in protein-coding genes.
  • Genes for related functions often grouped into operons.

⭐ The enzyme DNA gyrase (a type II topoisomerase) is unique to bacteria and is a key target for quinolone antibiotics (e.g., ciprofloxacin).

Plasmids - Accessory Genetic Gear

• Extrachromosomal, circular, dsDNA; self-replicating.

• Smaller than chromosome; variable copy number (e.g., 1-100+).

• Non-essential for viability; confer selective advantages (e.g., survival).

• Key Types & Functions:

  • R (Resistance) plasmids: Antibiotic resistance (e.g., β-lactamases, tetracycline resistance).

    ⭐ R-plasmids are key drivers of multidrug resistance (MDR) spread via horizontal gene transfer.

  • F (Fertility) plasmids: Mediate conjugation (gene transfer via sex pili).
  • Col plasmids: Produce bacteriocins (e.g., colicins), kill competing bacteria.
  • Virulence plasmids: Encode toxins or adhesion factors (e.g., ETEC toxins, Bacillus anthracis pXO1/pXO2).
  • Degradative plasmids: Metabolize unusual compounds (e.g., toluene).

• Transfer: Horizontal (conjugation, transduction, transformation) & Vertical.

• Curing: Spontaneous or induced plasmid loss. Incompatibility: Some plasmids cannot coexist in the same cell line without selection pressure (e.g. if they belong to the same incompatibility group Inc.).

Mobile Genetic Elements - Genome Shufflers

• DNA segments ("jumping genes") that move within or between genomes, mediating genetic variation.
• Types:
  • Insertion Sequences (IS): Simplest; code only for transposase enzyme, flanked by inverted repeats (IRs).
  • Transposons (Tn): Larger; carry additional genes (e.g., antibiotic resistance) besides transposition genes.
    • Composite transposons: Central resistance genes flanked by IS elements.
    • Non-composite transposons: Lack IS elements; have their own transposition genes.
• Mechanisms:
  • Replicative ("Copy & Paste"): Element is duplicated, one copy moves.
  • Non-replicative ("Cut & Paste"): Element moves directly without duplication.
• Significance:
  • Major cause of mutations and genome rearrangements.
  • Dissemination of antibiotic resistance (e.g., via R-plasmids carrying transposons).
  • Facilitate bacterial evolution and diversity.

⭐ Transposons are a primary mechanism for the horizontal transfer of antibiotic resistance genes in bacteria.

Operons & Gene Regulation - Smart Gene Switches

• Operon: Prokaryotic gene cluster, co-regulated by single promoter/operator.
  • Components: Regulator gene, Promoter (P), Operator (O), Structural Genes (SGs).
• Regulation Types:
  • Inducible (e.g., Lac Operon): Default OFF. Inducer (Allolactose) activates.
    • Genes: lacZ, lacY, lacA.
    • No lactose: Repressor binds Operator → OFF.
    • Lactose: Allolactose binds repressor → inactive → ON.

    ⭐ Catabolite Repression: ↓Glucose → ↑cAMP. cAMP-CAP complex boosts lac operon if lactose present.

  • Repressible (e.g., Trp Operon): Default ON. Co-repressor (Tryptophan) + Repressor deactivates.
    • Genes: trpE,D,C,B,A (Trp synthesis).
    • Low Trp: Repressor inactive → ON.
    • High Trp: Trp (co-repressor) + Repressor → binds Operator → OFF.
• 📌 Mnemonic (Lac Operon): Lactose Absent, Genes Off (LAGO).

High-Yield Points - ⚡ Biggest Takeaways

• Single, circular chromosome is typical, located in the nucleoid (lacks nuclear membrane).
• Genomes are haploid, meaning one copy of each gene per cell.
• Plasmids: extrachromosomal circular DNA; often carry antibiotic resistance or virulence factors.
• Genes often organized into operons for coordinated expression (e.g., lac operon).
• Bacterial DNA: high gene density, minimal non-coding DNA, no introns.
• Mobile genetic elements (transposons, IS) contribute to genetic diversity and adaptation.
• Replication: bidirectional from a single origin of replication (oriC).