Gene regulation

Gene regulation

Organisms do not want all of their genes to be expressed all of the time. This would use up too many resources and energy. So, cells have evolved mechanisms for controlling gene expression. By turning off the expression of genes when their products are not needed, an organism can save energy and can utilize the conserved energy to synthesize products that maximize growth rate.

Definition: Any mechanism used by a cell to increase or decrease the production of specific gene products (protein or RNA). Cells can modify their gene expression patterns to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources.

There are three broad levels of regulating gene expression in bacteria:

  • Transcriptional control (whether and how much a gene is transcribed into mRNA)
  • Translational control (whether and how much an mRNA is translated into protein)
  • Post-translational control (whether the protein is in an active or inactive form and whether the protein is stable or degraded)

In case of eukaryotes gene expression can be regulated at post transcriptional level too.

Based on our shared evolutionary origin, there are many similarities in the ways that prokaryotes and eukaryotes regulate gene expression; however, there are also many differences.

All three domains of life use positive regulation (turning on gene expression), negative regulation (turning off gene expression) and co-regulation (turning multiple genes on or off together) to control gene expression, but there are some differences in the specifics of how these jobs are carried out between prokaryotes and eukaryotes.

The regulatory mechanisms with the largest effects on phenotype act at the level of transcription.

Figure 1: Gene expression in bacteria can be regulated at three levels

Regulation of Transcription

Regulating transcription enables a cell to determine when a gene is transcribed. It also allows a cell to increase or decrease the amount of mRNA generated from each gene.

There are five different ways that RNA polymerase (the enzyme that makes RNA from a DNA template) can be affected:

  1. A cell can change the specificity of RNA polymerase for promoters. It does this by using specificity factors. These regulatory proteins will make RNA polymerase more or less likely to bind to a promoter. An example is the sigma factors used in prokaryotic transcription.
  2. Repressor proteins can be used to bind an upstream coding sequence called an operator to inhibit the ability of RNA polymerase to transcribe the gene. This causes decreased expression of a gene.
  3. Activator proteins can bind to the operator region to increase the attraction of RNA polymerase for the promoter. This action increases the expression of the gene.
  4. There are also regulatory regions that lie far upstream to their target gene. These are called enhancer regions. Binding of an activator to enhancer causes the DNA t form loop, which brings the enhancer next to its target gene. This causes increased expression of the target gene.
  5. When a cell wants to completely turn off the expression of a gene, it uses silencer regions. When a silencer is bound by transcription factors, the gene is silenced. This means there is no expression of genes.

The various regulatory mechanisms used to control transcription seem to fit into two general categories:

  1. Mechanisms that involve the rapid turn-on and turn-off of gene expression in response to environmental changes.
  • Regulatory mechanisms of this type are important in microorganisms because of the frequent exposure of these organisms to sudden changes in environment.
  • They provide microorganisms with considerable “plasticity,” an ability to adjust their metabolic processes rapidly in order to achieve maximal growth and reproduction under a wide range of environmental conditions.
  1. Mechanisms referred to as preprogrammed circuits or cascades of gene expression.
  • In these cases, some event triggers the expression of one set of genes. The product(s) of one or more of these genes functions by turning off the transcription of the first set of genes or turning on the transcription of a second set of genes. Then, one or more of the products of the second set acts by turning on a third set, and so on.
  • In these cases, the sequential expression of genes is genetically preprogrammed, and the genes cannot usually be turned on out of sequence.
  • Such preprogrammed sequences of gene expression are well documented in prokaryotes and the viruses that attack them.

Example: When a lytic bacteriophage infects a bacterium, the viral genes are expressed in a predetermined sequence, and this sequence is directly correlated with the temporal sequence of gene-product involvement in the reproduction and morphogenesis of the virus.

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