Regulation of Gene Expression

The mechanism which stimulates the expression of certain genes and inhibits that of others is called regulation of gene expression.

1.0What is Gene? 

A gene is a specific sequence of nucleotides in DNA that serves as the unit of hereditary information. It encodes the instructions for synthesising RNA and proteins, which are essential for the biological functions and development of an organism. 

2.0Gene Expression

Gene expression is the process by which information from a gene is used to produce a functional product, typically a protein. It occurs in two main steps:

• Transcription: The DNA sequence of a gene is copied into messenger RNA (mRNA), which carries the genetic information out of the nucleus (in eukaryotes) and into the cytoplasm.
• Translation: The mRNA sequence is read by a ribosome to assemble amino acids into a polypeptide chain, which then folds into a functional protein.

This process is tightly regulated to ensure that proteins are produced at the right time, place, and in appropriate quantities. Gene expression enables cells to respond to their environment, perform specific functions, and maintain homeostasis.

3.0Regulation of Gene Expression

Gene regulation refers to the complex system of mechanisms that cells use to increase or decrease the production of specific gene products (protein or RNA). It is a critical process that allows cells to respond adaptively to their environments, control growth and development, and maintain homeostasis. Gene regulation can occur at various stages of gene expression, including:

• Transcriptional Regulation: This is the most common form of gene regulation. It involves controlling the initiation of transcription of specific genes. Factors such as transcription factors (proteins that bind to specific DNA sequences to activate or repress transcription), enhancers, silencers, and the accessibility of DNA (e.g., whether the DNA is tightly wound around histones or loosely packed) play significant roles in this process.
• Post-transcriptional Regulation: After an mRNA molecule is produced, its stability, localization, and efficiency of translation can be regulated. This includes processes such as RNA splicing, RNA interference (RNAi), and the regulation of mRNA by microRNAs (miRNAs) which can degrade mRNA or inhibit its translation into protein.
• Translational Regulation: This involves controlling the rate at which proteins are synthesised from mRNA. Factors that influence this stage include the availability of ribosomes and the interaction of initiation factors with the 5' cap structure of mRNA.
• Post-translational Regulation: After a protein has been synthesised, its activity can be regulated by modifications (such as phosphorylation, methylation, acetylation), its location within the cell, or the degradation of the protein.

4.0Gene Regulation In Prokaryotes

In 1961, Francis Jacob and Jacques Monod at the Pasteur Institute in Paris introduced the operon model to explain gene regulation in Escherichia coli. The operon concept outlines how a set of genes can be regulated together as a unit, which includes structural genes, an operator, a promoter, and a regulator gene. Operons are classified into two types: inducible and repressible.

5.0The Lac Operon of E. coli - Inducible System

An inducible operon, such as the lac operon, typically remains inactive until the presence of a specific substrate necessitates its activation, commonly seen in catabolic pathways. The lac operon of E. coli exemplifies this system, which activates to metabolise lactose only when lactose is present in the environment.

6.0Structure of the Lac Operon

• Structural Genes (Z, Y, A): These genes encode enzymes essential for lactose metabolism. Gene Z produces β-galactosidase, which breaks lactose into glucose and galactose. Gene Y codes for lactose permease, facilitating lactose's entry into the cell, and Gene A encodes transacetylase, which transfers an acetyl group from acetyl-CoA to β-galactosidase. Together, these genes produce a polycistronic mRNA, reflecting their linked and coordinated expression.
• Operator Gene: Positioned next to the structural genes, it regulates mRNA synthesis. A repressor protein can bind to the operator to inhibit transcription, which can be reversed by an inducer molecule, effectively 'switching on' the gene.
• Promoter Gene: It serves as the binding site for RNA polymerase, initiating transcription. The promoter becomes accessible when the operator is activated, allowing RNA polymerase to transcribe the structural genes.
• Regulator Gene: This gene codes for the repressor protein. The repressor can attach to the operator, preventing transcription of the structural genes.

7.0Mechanism of Action

The lac operon's regulatory mechanism involves the interaction between the repressor, produced by the regulator gene, and an inducer molecule. Lactose, or specifically its isomer allolactose, acts as the inducer. When lactose is present, it is partially converted into allolactose, which then binds to the repressor. This binding alters the repressor's shape, preventing it from attaching to the operator. With the operator gene activated, RNA polymerase can transcribe the structural genes, leading to the production of enzymes necessary for lactose metabolism.

This elegant mechanism allows E. coli to efficiently adapt to changes in its nutritional environment, illustrating a fundamental principle of genetic regulation in prokaryotes.

Tryptophan operon of E. coli - Repressible System: 

The tryptophan operon also known as trp operon of Escherichia coli serves as a prime example of a repressible operon system. Unlike inducible operons that activate in the presence of a substrate, repressible operons are typically active and only shut down when their end product is in excess or externally supplied. This mechanism is commonly seen in anabolic pathways where the synthesis of essential molecules, like amino acids, is tightly controlled.

8.0Structure of the Tryptophan Operon

• Structural Genes (E, D, C, B, A): These genes code for enzymes involved in the biosynthesis of tryptophan. Lined up consecutively, they produce the enzymes necessary for the sequential steps required to synthesize tryptophan from a precursor molecule.
• Operator Gene (trp O): Positioned next to the structural genes, it regulates their activity. Under normal conditions, it is active, allowing transcription. However, it becomes inactivated when a co-repressor binds to the repressor protein, preventing transcription.
• Promoter Gene (trp P): This is the site where RNA polymerase attaches to begin transcription. The promoter facilitates the transcription of the structural genes as long as the operator is active.
• Regulator Gene (trp R): It generates an apo-repressor (inactive repressor). By itself, the apo-repressor cannot inhibit the operator gene. It requires binding with a co-repressor to form an active repressor complex capable of shutting down the operator gene.

9.0Mechanism of Regulation

In the repressible operon model, tryptophan itself acts as the co-repressor. When tryptophan levels within the cell rise, it binds to the apo-repressor, forming an active repressor complex. This complex then attaches to the operator gene, effectively halting transcription of the structural genes by preventing RNA polymerase from progressing past the operator. This feedback mechanism ensures that the cell does not waste energy producing tryptophan when it is already abundant.

The tryptophan operon exemplifies negative control in genetic regulation, where the binding of a repressor to the DNA inhibits gene expression. This regulatory strategy enables E. coli to efficiently manage its resources by synthesizing tryptophan only when needed, demonstrating the elegance and economy of bacterial gene regulation systems as initially outlined by Jacob and Monod.