Transcription and RNA Processing in Prokaryotes and Eukaryotes

Transcription & RNA: Synthesis and Termination

Overview of Transcription

Transcription is the process by which RNA is synthesized from a DNA template. This process is fundamental to gene expression and is divided into three main stages: initiation, elongation, and termination. In both prokaryotes and eukaryotes, transcription is tightly regulated and involves multiple enzymes and regulatory factors.

• Initiation: RNA polymerase binds to the promoter region of DNA, unwinding the DNA to begin RNA synthesis.

• Elongation: RNA polymerase moves along the DNA, synthesizing RNA in the 5' to 3' direction.

• Termination: The process by which RNA synthesis ends and the RNA transcript is released.

Transcription Termination in Prokaryotes

Termination in prokaryotes can occur via two main mechanisms: intrinsic (Rho-independent) and Rho-dependent termination.

Intrinsic (Rho-independent) Termination

This mechanism relies on specific sequences in the DNA that, when transcribed, form a hairpin structure in the RNA followed by a string of uracils. The hairpin causes RNA polymerase to pause, and the weak A-U base pairing destabilizes the RNA-DNA hybrid, leading to transcript release.

• Key features: Inverted repeats in DNA, formation of a GC-rich hairpin in RNA, followed by a poly-U tract.

• Result: RNA polymerase dissociates from the DNA, releasing the RNA transcript.

Rho-dependent Termination

Rho-dependent termination requires the Rho (ρ) protein, which binds to a specific site on the RNA (rut site) and moves toward the RNA polymerase. When RNA polymerase stalls at a hairpin, Rho catches up and uses its helicase activity to unwind the RNA-DNA hybrid, releasing the transcript.

• Key features: Rho utilization (rut) site on RNA, Rho protein, hairpin structure, no poly-U tract required.

• Result: Rho protein disrupts the RNA-DNA hybrid, terminating transcription.

Transcription in Eukaryotes

RNA Polymerases in Eukaryotes

Eukaryotes possess three main RNA polymerases, each responsible for transcribing different classes of genes:

Polymerase	Product	Location
I	rRNA	Nucleolus
II	mRNA, snRNA	Nucleoplasm
III	5S rRNA, tRNA	Nucleoplasm

Termination and Processing in Eukaryotes

Termination mechanisms in eukaryotes differ from those in prokaryotes, especially for RNA polymerase II, where the 3' end of the transcript is defined by RNA processing rather than a specific termination sequence. Eukaryotic transcripts undergo extensive processing before becoming mature mRNA.

• 5' Capping: Addition of a 7-methylguanosine cap to the 5' end, which protects the RNA and aids in export and translation initiation.

• 3' Polyadenylation: Addition of a poly(A) tail to the 3' end, enhancing stability and export.

• Splicing: Removal of non-coding introns and joining of exons to form the mature mRNA.

RNA Splicing and Processing

Splicing Mechanisms

Splicing is the process by which introns are removed from the pre-mRNA transcript. This can occur via self-splicing (Group I and II introns) or by the spliceosome (Group III introns).

• Self-splicing: Certain introns can catalyze their own removal without proteins (ribozymes).

• Spliceosome-dependent splicing: The spliceosome, a complex of snRNAs and proteins (snRNPs), recognizes conserved sequences at exon-intron boundaries and catalyzes intron removal.

In mammals, the 5' splice site is typically GU and the 3' splice site is AG. The average human gene contains about nine introns, which are much larger than exons.

Comparison: Prokaryotic vs. Eukaryotic Transcription

• Prokaryotes: Transcription and translation are coupled; mRNA is often polycistronic and not processed.

• Eukaryotes: Transcription and translation are separated by the nuclear envelope; mRNA is monocistronic and extensively processed.

Genetic Code

Codons and the Genetic Code

The genetic code is a set of rules by which information encoded in mRNA is translated into proteins. Each codon (a sequence of three nucleotides) specifies a particular amino acid or a stop signal for translation.

Summary Table: Key Differences in Transcription Termination

Feature	Prokaryotes	Eukaryotes
Termination Mechanism	Intrinsic (hairpin + U's), Rho-dependent	Polymerase-specific, often via processing
RNA Processing	Minimal	5' capping, splicing, 3' polyadenylation
Coupling of TC & TL	Yes	No

Key Terms

• RNA polymerase: Enzyme that synthesizes RNA from a DNA template.

• Terminator: DNA sequence signaling the end of transcription.

• Hairpin (stem-loop): Secondary structure in RNA important for termination.

• Rho factor: Protein involved in Rho-dependent termination in prokaryotes.

• Spliceosome: Complex responsible for removing introns from pre-mRNA in eukaryotes.

• Exon/Intron: Coding/non-coding regions of a gene, respectively.