Elongation and termination of transcription

Prokaryotic Elongation & Termination - The Speedy Scribe

• Elongation:

  • The RNA polymerase core enzyme synthesizes RNA in the 5' → 3' direction within a transcription bubble.
  • Topoisomerases relieve supercoiling ahead of the bubble.

• Termination Pathways:

  • Rho-Independent (Intrinsic):
    • The most common pathway in prokaryotes.
    • A GC-rich hairpin loop forms in the new RNA, causing RNA polymerase to stall.
    • Followed by a weak poly-U tail in the RNA, which promotes dissociation from the DNA template.
  • Rho-Dependent:
    • Requires Rho (ρ) factor, an ATP-dependent helicase.
    • Rho binds a C-rich "rut" (Rho utilization) site on the nascent RNA.
    • It moves along the RNA, catches the stalled polymerase, and unwinds the DNA-RNA hybrid.
    • 📌 Rho races up the rut site.

⭐ Actinomycin D inhibits elongation in both prokaryotes and eukaryotes by intercalating into the DNA template, preventing RNA polymerase movement.

Eukaryotic Elongation & Termination - Careful & Complex

• Elongation: RNA Polymerase II synthesizes mRNA in the 5'→3' direction, reading the template DNA strand.

  • Possesses some proofreading capability to correct errors.
  • Elongation factors assist in maintaining processivity.

• Termination: Unlike prokaryotes, termination is linked to mRNA processing.

  • RNA Pol II transcribes past the gene's end, including a key sequence.
  • Polyadenylation Signal Sequence (AAUAAA): This signal is recognized on the nascent mRNA transcript.

⭐ Mutations in the AAUAAA polyadenylation signal can lead to unstable mRNA that is rapidly degraded, causing a significant drop in protein production. This is a mechanism in some forms of β-thalassemia.

Transcriptional Inhibitors - Drugs vs. Bugs & Cells

• Eukaryotic Toxin: α-amanitin

  • Source: Amanita phalloides (death cap mushroom).
  • Mechanism: Potent inhibitor of RNA Polymerase II.
  • Result: Halts mRNA synthesis, leading to severe hepatotoxicity.

• Prokaryotic Drug: Rifampin (Rifampicin)

  • Mechanism: Inhibits the β-subunit of bacterial DNA-dependent RNA polymerase.
  • Use: Core agent in anti-tuberculosis treatment (RIPE regimen).
  • 📌 Rifampin's 4 R's: RNA polymerase inhibitor, Revs up P-450, Red/orange body fluids, Rapid resistance develops.

• General Inhibitor: Actinomycin D (Dactinomycin)

  • Mechanism: Intercalates in DNA, inhibiting RNA Polymerase in both prokaryotes and eukaryotes.
  • Use: Anticancer agent (e.g., Wilms tumor, Ewing sarcoma).

⭐ Rifampin is a powerful inducer of cytochrome P-450 enzymes, leading to numerous drug-drug interactions by increasing the metabolism of other drugs.

High‑Yield Points - ⚡ Biggest Takeaways

• RNA polymerase reads the DNA template 3'→5' to synthesize the mRNA transcript 5'→3'.
• Prokaryotic Rho-dependent termination uses the Rho factor helicase to dissociate the RNA-DNA complex.
• Rho-independent termination relies on a stable GC-rich hairpin followed by a weak poly-U tail.
• Eukaryotic RNA Pol II termination is coupled with cleavage after the polyadenylation signal (AAUAAA).
• Rifampin blocks the channel of prokaryotic RNA polymerase, preventing elongation.
• Actinomycin D intercalates into DNA, inhibiting elongation in both prokaryotes and eukaryotes.