Prokaryotic Gene Regulation

Prokaryotic Gene Regulation

• In prokaryotes, the DNA coding segment is continuous.
• Transcripts are translated directly into protein without modification.
• Proteins needed for a specific function are encoded together in blocks called operons.
• Genes to use lactose as an energy source are coded next to each other in the lac operon.
• Repressors are regulatory molecules that suppress transcription in response to an external stimulus.
• Activators are regulatory proteins that increase transcription in response to an external stimulus.
• Inducers are small molecules that activate or repress transcription based on cell needs and substrate availability.
• The regulatory region has a promoter and surrounding region where transcription factors can bind.
• Transcription factors influence RNA polymerase binding to the promoter, which transcribes structural genes.
• Attenuation prevents transcription completion, unlike repression, which blocks initiation.
• The leader sequence encodes a short polypeptide with an attenuator sequence, forming hairpin structures when transcribed into mRNA.
• Once RNA polymerase starts transcription, a ribosome attaches and translates the leader region.
• The leader polypeptide is short, has 14 amino acids, and contains two tryptophan residues.
• When tryptophan is plentiful, the ribosome quickly finishes the leader polypeptide.
• With little tryptophan, the ribosome stalls at Trp codons, slowing leader translation.
• Catabolite Activator Protein (CAP) is an activator regulator.
• The lac operon is an inducible operon encoding genes to use lactose.
• Lac Operon activation needs very low or non-existent glucose levels and the presence of lactose.
• The lac operon is transcribed only when glucose is absent and lactose is present.

Eukaryotic Gene Regulation

• Activators recruit the transcriptional machinery to the gene.
• Polymerase is recruited indirectly by eukaryotic activators, which interact with transcription machinery, nucleosome modifiers, and initiation and elongation factors.
• Ex) TFIID and Mediator.
• Histone modifications (deacetylase, methyltransferase, and silencing) are the most common form of repression.
• DNA methylation is a stable, heritable epigenetic marker in eukaryotic organisms.
• Methylation involves adding a methyl group (CH3) to a specific nucleotide sequence.
• Acetylation involves adding an acetyl group (CH3CO) to a specific nucleotide sequence.
• These modifications can activate or repress genes.

CpG Islands and Gene Silencing

• CpG island methylation is associated with gene silencing.
• Methyl-CpG-binding domain (MBD) proteins are recruited by methylated DNA.
• MBD proteins induce histone methylations.

Azacytidine

• Azacytidine decitabine (5-aza-2'deoxycytidine) are cytidine analogs with a nitrogen atom replacing the carbon atom at position 5 in the pyrimidine ring.
• In low doses, these drugs can cause DNA demethylation by inactivating DNA methyltransferase-1 (DNMT-1).
• Low doses can induce re-expression of previously silenced genes.
• Reactivation of cell cycle-regulating genes silenced by hypermethylation may induce cell differentiation, reduce proliferation, or increase daughter cell apoptosis.

Human Gene Regulation

• There are four types of histones: H2A, H2B, H3, and H4, each nucleosome has 2 of each.
• Euchromatin is open for transcription, while heterochromatin is a compact DNA-protein structure that cannot be transcribed.
• If a gene is tightly bound with histone, the gene is "off".
• Histone methylation, adding a methyl group to a lysine, is generally repressive, supporting the heterochromatin state.
• Histone acetylation adds an acetyl group to a lysine, activating and supporting the euchromatin state.
• Histone acetyltransferases (HAT) transfer acetyl groups from acetyl coenzyme A to lysine molecules.
• This Transfer eliminates the natural positive charge of histone proteins.
• HAT reduces interaction with negatively charged DNA phosphates, leading to a euchromatin state and turning on gene expression.
• Histone deacetylases (HDACs) remove acetyl groups from lysine, leading to heterochromatin and turning off gene expression.