Bacterial Genome Organization

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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. Bacterial Nucleoid Organization and Replication

⭐ 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.

Insertion Sequence and Transposon Structures

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).

Lac operon induction mechanism

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).

Practice Questions: Bacterial Genome Organization

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Flashcards: Bacterial Genome Organization

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