Bacterial Gene Expression

Gene Expression Overview - Genes to Proteins

• Central Dogma (Bacteria): DNA $\xrightarrow{\text{Transcription}}$ RNA $\xrightarrow{\text{Translation}}$ Protein.
  • Pathway: genetic info to functional proteins.
• Key Molecules & Structures:
  • DNA: Double-stranded; stores genetic code.
  • RNA: Single-stranded; key types:
    • mRNA (messenger): Carries genetic code from DNA to ribosomes.
    • tRNA (transfer): Delivers specific amino acids to ribosomes.
    • rRNA (ribosomal): Major component of ribosomes; catalytic activity.
  • Proteins: Functional molecules (e.g., enzymes, structural elements).
  • Ribosomes: Cellular machinery for protein synthesis (translation).
  • RNA Polymerase: Enzyme catalyzing transcription (DNA $\rightarrow$ RNA).
• Prokaryotic Hallmark: Transcription and translation are coupled (occur simultaneously in cytoplasm).

⭐ Bacterial mRNA: often polycistronic (one mRNA codes multiple proteins), short half-life; facilitates rapid environmental response.

Bacterial Transcription - Making the Message

Bacterial Transcription: DNA template → mRNA synthesis (5'→3').

• Enzyme: DNA-dependent RNA Polymerase (RNAP).
  • • Holoenzyme: Core enzyme (α₂ββ'ω) + Sigma (σ) factor.
  • • Sigma (σ) factor: Recognizes promoter, initiates transcription. Different σ factors for different gene sets (e.g., σ⁷⁰ for housekeeping).
• Promoter Elements (E. coli):
  • • Pribnow box (-10): TATAAT
  • • -35 sequence: TTGACA
    • 📌 Mnemonic: "TTGACA" for -35, "TATAAT" for -10.
• Termination:
  • • Rho-dependent: Requires Rho protein (ATPase with helicase activity).
  • • Rho-independent (Intrinsic): GC-rich hairpin loop followed by a U-rich sequence in RNA transcript.

⭐ Rifampicin inhibits bacterial transcription by binding to the β-subunit of RNA polymerase, preventing initiation.

Bacterial Translation - Building the Blocks

• Ribosomes: 70S (30S + 50S). Site of protein synthesis.
  • 30S subunit: Binds mRNA (via Shine-Dalgarno sequence upstream of AUG). Decodes mRNA.
  • 50S subunit: Contains peptidyltransferase center (23S rRNA - a ribozyme); catalyzes peptide bond formation.
• Genetic Code: Triplet codons, non-overlapping, degenerate. Start: AUG (codes for N-formylmethionine - fMet in bacteria). Stop: UAA, UAG, UGA.
• tRNA: Adaptor molecule. Anticodon pairs with mRNA codon. Aminoacyl-tRNA synthetase ensures correct amino acid loading (charging).
• Process:
  • 📌 Mnemonic for tRNA sites: A (Aminoacyl - Arrives) → P (Peptidyl - Peptide bond) → E (Exit).

⭐ Many antibiotics target bacterial translation: e.g., Aminoglycosides (Streptomycin) bind 30S causing misreading; Macrolides (Erythromycin) bind 50S blocking translocation.

Gene Regulation - Smart Switching

• Bacteria use operons to regulate gene expression for adaptation.

• Operon: Promoter, Operator, Structural genes. Regulator gene → repressor.

• Lac Operon (Inducible - default OFF):

  • Lactose metabolism. Inducer: Allolactose.
  • No lactose: Repressor active, binds operator → transcription OFF.
  • Lactose: Allolactose inactivates repressor → transcription ON.
  • 📌 LACtose Is Needed (for INduction).

• Trp Operon (Repressible - default ON):

  • Tryptophan synthesis. Corepressor: Tryptophan.
  • Trp low: Repressor inactive → transcription ON.
  • Trp high: Trp activates repressor, binds operator → transcription OFF.

• Catabolite Repression (Lac operon):

  • Glucose preferred.
  • ↑Glucose → ↓cAMP → CAP inactive → ↓Lac transcription.
  • ↓Glucose → ↑cAMP → CAP active → ↑Lac transcription.

⭐ Glucose inhibits adenylate cyclase, ↓cAMP. cAMP is vital for CAP binding to enhance Lac operon transcription.

High‑Yield Points - ⚡ Biggest Takeaways

• Operons (e.g., lac, trp) are key for coordinated gene regulation in bacteria.
• Sigma factors direct RNA polymerase to specific promoters, initiating transcription.
• Coupled transcription-translation in the cytoplasm enables rapid cellular responses.
• Polycistronic mRNA encodes multiple proteins from one transcript, ensuring efficient pathway synthesis.
• Regulation primarily occurs at transcription initiation via inducers (e.g., allolactose) and repressors.
• Catabolite repression (glucose effect) prioritizes efficient energy sources, a global control mechanism.