Understanding Transcription in Prokaryotes

Aug 4, 2024

Transcription in Prokaryotes

Overview

  • Transcription: Process of converting genetic information from DNA to mRNA.
  • Coding region: Contains information about proteins or functional RNAs (e.g., ribosomal RNA).
  • Transcription Start Site (TSS): Marks the beginning of the coding region.

Key Terms

  • Plus one position: First base of the coding region.
  • Downstream: Refers to the direction towards the end of the coding region (after TSS).
  • Upstream: Refers to the direction before the plus one site (before TSS).
  • Promoter region: Located upstream of the TSS, initiates transcription.

Steps of Transcription

  1. Initiation
  2. Elongation
  3. Termination

Organization of Promoter DNA

  • TSS Reference:
    • Downstream: +1, +2, +3...
    • Upstream: -1, -2, ... (no site 0).
  • Promoter Elements:
    • Upstream Promoter Element (UPE): -58 to -37 position.
    • -35 Element: -35 to -30 position.
    • -10 Element: -12 to -7 position, also known as the Pribnow box (TATA box in eukaryotes).

Spacing Between Elements

  • Optimal spacing between -35 and -10 elements: ~17 bases.
  • Extended -10 Element: Found at positions -17 to -14.
  • Discriminator Element: Usually 3 bases long.

Functionality of Promoter Elements

  • UPE: Frequently contacted by RNA polymerase, stabilizing it.
  • -35, Extended -10, and -10: Contacted by sigma factors during transcription initiation.
  • Discriminator Element: Stabilizes RNA polymerase binding.

Consensus Sequences

  • UPE: Long consensus sequence (uses IUPAC symbols).
  • -35 Element: Consensus sequence is TTGACA.
  • Extended -10 Element: Consensus is TRTG.
  • -10 Element: Consensus is TATAAT.
  • Discriminator Element: Consensus is usually a G triplet.

Important Notes on Consensus

  • Consensus sequences are averages and may vary across different genes.
  • Example: -10 element's consensus (TATAAT) is biased toward Sigma Factor D (Sigma 70).
  • Different sigma factors can bind different consensus sequences in different genes.

Promoter Strength

  • Strong promoters: Closely match consensus sequences, produce more transcripts.
  • Weak promoters: Deviate from consensus sequences, produce fewer transcripts.

DNA Structure and Promoters

  • Sequence composition can cause DNA to bend or curve, impacting protein binding and function.

Conclusion

  • Understanding bacterial promoters is crucial for comprehending transcription processes.