Differences Between Prokaryotic and Eukaryotic Transcription

Differences Between Prokaryotic and Eukaryotic Transcription

• Transcription mechanisms differ significantly between prokaryotic and eukaryotic systems.

  • Eukaryotic transcription involves DNA in the form of chromatin, requiring interaction with histone proteins.

  • Eukaryotic DNA is sequestered within a nucleus, separating transcription and translation processes.

    • In eukaryotes, transcription and translation do not occur concurrently, unlike in prokaryotes.

      • In prokaryotic cells, ribosomes attach to mRNA as it is synthesized, allowing immediate translation.

      • Eukaryotic mRNA undergoes splicing and processing before leaving the nucleus.

Key Components of Eukaryotic Transcription

• mRNA Processing

  • Eukaryotic mRNA undergoes several modifications post-transcription:

    • Splicing: Removal of introns and joining of exons.

    • Capping: Addition of a 5’ cap for protection and recognition.

    • Polyadenylation: Addition of a poly(A) tail at the 3’ end for stability and export from the nucleus.

      • These modifications facilitate protection and transport as mRNA transitions from nucleus to cytoplasm.

• RNA Polymerases in Eukaryotes

  • Eukaryotes utilize three main RNA polymerases:

    • RNA Polymerase I: Synthesizes pre-ribosomal RNA (rRNA), specifically for ribosomal RNA precursor.

      • Operates with a single promoter.

    • RNA Polymerase II: Responsible for the synthesis of mRNA.

      • Recognizes various promoter sequences with the aid of transcription factors.

      • Works at a rate of 500 to 1000 nucleotides per second.

    • RNA Polymerase III: Synthesizes tRNAs and small RNA products.

      • Requires transcription factor TFIII.

    • Plant-specific: Some plants have RNA Polymerase IV for producing small interfering RNAs.

    • Mitochondria: Have their own distinct RNA polymerases.

Transcription Factors in Eukaryotic Cells

• Transcription factors play critical roles in regulating transcription:

  • TFIII: For RNA Polymerase III and specifically for 5S rRNA synthesis.

    • TFIII A is a zinc finger protein regulating transcription via binding with ribosomal RNA precursors.

      • Zinc finger: Characterized by zinc coordination that stabilizes protein folds.

      • Each zinc finger consists of an alpha helix and an antiparallel beta sheet.

      • Existence of 9 tandem zinc fingers for TFIII A, involved in recognizing DNA major grooves.

RNA Polymerase II and Its Mechanism

• The assembly of RNA Polymerase II and transcription factors forms the Pre-Initiation Complex (PIC):

  • Components of PIC include:

    • TFIID: Contains the TATA-binding protein (TBP), which bends DNA to facilitate binding.

    • TFIIA and TFIIB: Stabilize the complex.

    • TFIIF: Recruits RNA Polymerase II.

    • TFIIE and TFIIH: Assist in helicase activity (DNA unwinding) and polymerase activation.

      • TFIIH phosphorylates the CTD (carboxy-terminal domain) for initiating elongation.

  • Transcription initiation begins once the DNA strands are unwound to create the Open Complex.
    - This region, known as the transcription bubble, exposes the template strand for mRNA synthesis.

• Transcription:

  • RNA polymerase synthesizes RNA from the template strand.

  • The transcription initiation phase can experience setbacks, termed abortive initiation, where initial RNA synthesis may abort multiple times before stabilizing.

    • Once stabilization occurs, promoter clearance allows for productive elongation.

  • Elongation Stage:

    • Occurs similarly to prokaryotic polymerases.

      • Elongation can experience pauses and requires elongation factors to enhance processivity and manage transcription complexities.

Termination of Transcription

• Termination involves desphosphorylation of the carboxy terminus of RNA Polymerase II and cleavage of the RNA transcript by endonucleases recognizing polyadenylation signals (like AAUAAA).

  • The addition of a poly(A) tail stabilizes the mRNA for export from the nucleus.

Summary Mechanism of RNA Production

• Transcription yields a functional RNA molecule, with a focus on the coding strand and template strand during synthesis.

  • Initiation involves forming a Transcription Initiation Complex that recognizes core promoter elements and assembles numerous transcription factors and polymerases.

    • Significant steps include:

      • Binding of TFIID (TBP) to TATA box, followed by stabilization through additional transcription factors.

      • Formation of an open complex via ATP-dependent unwinding by TFIIH and further transcription machinery assembly.

      • Successful synthesis of the RNA occurring in a specified 5’ to 3’ direction, culminating with processing including capping, polyadenylation, and final mRNA release.