Prokaryotic and Eukaryotic Gene Regulation Mechanisms
Gene Regulation: Operons and DNA-Binding Motifs
Repressors are usually near the promoter. Regulation by a repressor that blocks protein transcription is called negative regulation. Activators, contrary to repressors, potentiate the activity of RNA polymerase at the promoter; this is upregulation. Adjacent promoters are common.
An operon is defined as the group of genes and the promoter that act together in regulation. The lactose operon (Lac) is subject to negative regulation. In the absence of lactose, the Lac operon genes are inhibited. Mutations in the operator or in another gene cause synthesis of gene products.
The arabinose operon is another example of an inducible operon, like the lac operon, but in the arabinose operon (ara), a regulatory protein exerts both positive and negative control.
The tryptophan operon encodes for 5 enzymes involved in tryptophan synthesis. If this amino acid (AA) is present in sufficient quantities, the synthesis enzymes are repressed; tryptophan acts as a co-repressor.
DNA-Binding Motifs
Regulatory proteins generally bind specific DNA sequences. Most of them have independent DNA-binding substructures (domains) containing an interaction; the rate is exact.
- Helix-turn-helix: This DNA-binding motif, crucial for the interaction of many prokaryotic regulatory proteins with DNA, has approximately 20 amino acids in two short alpha-helix segments. This structure is not stable on its own.
- Zinc finger: This is another type of DNA binding domain found in some proteins that act as regulators of transcription, especially during the development of eukaryotes. This domain, called a homeodomain, presents around 60 amino acids.
Attenuation of Transcription
The attenuation of the operon mechanism uses signals encoded in sequences within a leader region. This region forms a hairpin structure called an attenuator; this sequence acts as a transcription terminator. When AA concentrations are high, translation can be quickly performed, forming the transcription attenuator structure and interrupting transcription. When, by contrast, we found low concentrations, it allows transcription of the whole operon. The proportion of transcripts that fade decreases as the concentration of AA decreases.
Termination of Replication in Eukaryotes
The termination of replication of linear chromosomes requires special structures called telomeres. These usually consist of multiple copies of a short oligonucleotide sequence, in which one of the two strands is longer than the complementary strand; therefore, a single-stranded region remains at the 3′ end. The ends of a linear chromosome cannot be replicated by cellular DNA polymerase. Replication requires a template and a primer, but beyond the end of a linear DNA molecule, a template is not available for primer pairing. Without a special mechanism, telomeres would shorten with each replication cycle. The problem is solved by an enzyme called telomerase, which incorporates telomeres at the ends of a chromosome. Telomerase contains both proteins and RNA, and the RNA acts as a template for the synthesis of the telomere TxGy strand. After the synthesis of the telomere, it folds, forming a specialized structure called a T-loop, protecting the 3′ ends of the chromosomes, making them inaccessible to nucleases.