Transcription in Prokaryotes

Transcription in Prokaryotes

• Prokaryotic transcription uses a single RNA polymerase.
• In E. coli, RNA polymerase is a 465 kDa complex.
• It has several subunits: 2 α, 1 β, 1 β', 1 ω, and 1 σ.
• The σ subunit is crucial for binding to the promoter region of DNA
• Subunits work together to bind DNA, NTPs, recognize promoters and initiate transcription.
• RNA polymerase is quite accurate; only one error for every 10,000 bases.
• Many transcripts are made from each gene, mitigating the effect of errors.
• Prokaryotes have only one type of RNA polymerase to make all types of RNA

Stages of Transcription

• RNA polymerase holoenzyme binds to promoter sites (initiation).
• Polymerisation begins (initiation).
• Chain elongation follows (elongation).
• Termination is the final stage (termination).
• During elongation, RNA polymerase travels along the DNA template.
• Negative supercoils are relieved by topoisomerases.
• Elongation rate varies, slower in G/C-rich regions.

Properties of Promoters

• Promoters are typically 40 bp long, located upstream of the transcription start site.
• Two consensus sequence elements are crucial: -35 region (consensus TTGACA) and Pribnow box near -10 (consensus TATAAT).
• The -35 region is where the sigma subunit binds.
• The Pribnow box facilitates unwinding of DNA.
• Prokaryotic promoters contain specific sequences that RNA polymerase recognizes.

Eukaryotic Gene Promoter Sequences

• Eukaryotic genes have more complex promoter sequences.
• These sequences include the CAAT box (-70 to -80) and the TATA box (-30).
• RNA polymerase II recognizes these sequences, initiating transcription.
• These sequences provide binding sites for transcription factors necessary for the accurate initiation of transcription.

1- Initiation of Polymerization

• RNA polymerase has two distinct binding sites for NTPs.
• Initiation sites preferentially bind ATP and GTP.
• Elongation sites bind subsequent NTPs.
• The 3'-OH of the growing RNA chain attacks the α-P of the incoming NTP to form a phosphodiester bond.
• Sigma subunit dissociates after 6-10 nucleotides are incorporated, completing initiation.

2- Chain Elongation

• Core polymerase (without the σ subunit) carries out elongation.
• Elongation rate is 20-50 bases per second.
• The rate is influenced by the DNA sequence (faster in A/T-rich regions and slower in G/C rich regions)
• Supercoiling is corrected by topoisomerases.

3- Chain Termination

• Prokaryotic transcription termination has two key mechanisms.
• Rho-dependent termination involves a protein called Rho that disrupts the transcription complex.
• Rho-independent termination involves inverted repeats in the DNA that produce a hairpin structure in the nascent mRNA, causing the polymerase to detach.

Termination Strategies in Bacteria

• Rho-dependent termination requires a Rho protein that unwinds the RNA-DNA hybrid.
• Rho-independent termination is triggered by a specific sequence in the DNA that leads to hairpin formation in the mRNA, causing the polymerase to detach.

Rho - Protein

• Rho is an ATP-requiring helicase involved in Rho-dependent termination.
• It moves along the nascent mRNA transcript.
• The Rho protein interacts with the RNA polymerase complex to terminate transcription.

Comparison of Transcription in Prokaryotes and Eukaryotes

• Prokaryotes: transcription and translation occur simultaneously.
• Eukaryotes: transcription and translation occur in different cellular compartments.
• Prokaryotes use single RNA polymerase.
• Eukaryotes use multiple RNA polymerases (RNA Pol I, II, and III).
• Prokaryotic mRNA does not need processing.
• Eukaryotic mRNA undergoes extensive processing.
• Prokaryotic promoters are relatively simple.
• Eukaryotic promoters are more complex and have specific sequences.
• Prokaryotic termination is well understood.
• Eukaryotic termination is less clear.
• Prokaryotic DNA is found in the cytoplasm in a circular form.
• Eukaryotic DNA is found in the nucleus in a linear form, associated with histones.

This quiz covers the essential aspects of transcription in prokaryotes, with a focus on the function and structure of RNA polymerase. It includes the stages of transcription: initiation, elongation, and termination, emphasizing the role of different subunits and topoisomerases. Test your understanding of how prokaryotic cells carry out this vital process.