Gene Expression: Transcription, Regulation, and RNA Maturation
Transcription Regulation
The activation or inhibition of transcription varies depending on the cell’s needs for different gene products. Transcription of each gene is carefully regulated to produce gene products in the necessary proportions. Any stage of transcription can be regulated, but the binding of polymerase and initiation stages are preferentially regulated. Proteins bound near and far from promoter sequences can affect gene expression levels. Protein binding can both activate and repress transcription.
In E. coli, a protein that activates transcription is the cAMP protein. Repressors are proteins that block RNA synthesis in specific genes. The antibiotic actinomycin D inhibits the elongation of RNA chains by RNA polymerase in bacteria and eukaryotes. These molecules intercalate between base pairs in the DNA double helix, deforming the DNA.
Termination of RNA Synthesis
Transcription is a process that must be carefully terminated. Premature release of an RNA transcript prevents the resumption of RNA synthesis, requiring a restart. RNA synthesis terminates when RNA polymerase encounters specific sequences. In E. coli, there are two termination signals: Rho-dependent and Rho-independent. Rho-independent termination has two features:
- A region of the RNA transcript is self-complementary, allowing the formation of a hairpin structure 15-20 nucleotides before the end of the RNA strand.
- A series of three residues in the DNA strand that transcribe into uracil residues near the 3′ end.
When the polymerase reaches this structure, it stalls. Rho-dependent termination lacks this sequence.
RNA Maturation (mRNA, tRNA)
Many RNA molecules in bacteria and eukaryotes are modified after synthesis. Some enzymes that carry out RNA maturation reactions are themselves proteins. A newly synthesized RNA molecule is called the primary transcript. Eukaryotic mRNA and tRNA undergo more extensive modification than their bacterial counterparts.
mRNA Maturation
A primary eukaryotic mRNA transcript contains sequences from a gene, but the sequences encoding the polypeptide may not be contiguous. These non-coding fragments are called introns, while the coding regions are called exons. During splicing, introns are removed from the primary transcript, and the exons are joined to form a continuous sequence that encodes a functional polypeptide.
tRNA Maturation
Primary transcripts of eukaryotic and prokaryotic tRNA are modified by removing sequences from each end and, in some cases, by removing introns.
The degradation of RNA is regulated and complete. The turnover rate of RNA is fundamental to determining its steady-state level and the rate at which expression of a gene ceases when its product is no longer needed. During the development of multicellular organisms, it is important that certain proteins are expressed only at one stage and that the mRNAs encoding them are synthesized and destroyed in a timely manner.
Most eukaryotic mRNAs have a cap at the 5′ end, which protects the mRNA from ribonucleases. They also have a tail of 80-250 adenosine residues at the 3′ end, forming a poly(A) tail, which also protects the mRNA from enzymatic degradation. The poly(A) tail is added in a multi-step process. tRNA precursors also undergo RNA processing.