Operon

In genetics, an operon is a functioning unit of DNA containing a cluster of genes under the control of a single promoter.^[1] The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, i.e. several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all. Several genes must be co-transcribed to define an operon.^[2]

Originally, operons were thought to exist solely in prokaryotes (which includes organelles like plastids that are derived from bacteria), but their discovery in eukaryotes was shown in the early 1990s, and are considered to be rare.^[3][4][5][6] In general, expression of prokaryotic operons leads to the generation of polycistronic mRNAs, while eukaryotic operons lead to monocistronic mRNAs.

Operons are also found in viruses such as bacteriophages.^[7][8] For example, T7 phages have two operons. The first operon codes for various products, including a special T7 RNA polymerase which can bind to and transcribe the second operon. The second operon includes a lysis gene meant to cause the host cell to burst.^[9]

History

The term "operon" was first proposed in a short paper in the Proceedings of the

for their discoveries concerning the operon and virus synthesis.

Overview

Polycistronic operon Regulatory sequence Regulatory sequence Enhancer Enhancer /silencer /silencer Operator Promoter 5'UTR ORF ORF UTR 3'UTR Start Start Stop Stop Terminator Transcription DNA RBS RBS Protein coding region Protein coding region mRNA Translation Protein The structure of a transcription of the gene into an mRNA. The mRNA untranslated regions (blue) regulate translation into the final protein products.[11]

Operons occur primarily in

All the structural genes of an operon are turned ON or OFF together, due to a single promoter and operator upstream to them, but sometimes more control over the gene expression is needed. To achieve this aspect, some bacterial genes are located near together, but there is a specific promoter for each of them; this is called gene clustering. Usually these genes encode proteins which will work together in the same pathway, such as a metabolic pathway. Gene clustering helps a prokaryotic cell to produce metabolic enzymes in a correct order.^[14] In one study, it has been posited that in the Asgard (archaea), ribosomal protein coding genes occur in clusters that are less conserved in their organization than in other Archaea; the closer an Asgard (archaea) is to the eukaryotes, the more dispersed is the arrangement of the ribosomal protein coding genes.^[15]

General structure

An operon is made up of 3 basic DNA components:

• transcribed. The promoter is recognized by RNA polymerase
  , which then initiates transcription. In RNA synthesis, promoters indicate which genes should be used for messenger RNA creation – and, by extension, control which proteins the cell produces.
• Operator – a segment of DNA to which a repressor binds. It is classically defined in the lac operon as a segment between the promoter and the genes of the operon.^[16] The main operator (O1) in the lac operon is located slightly downstream of the promoter; two additional operators, O2 and O3 are located at -82 and +412, respectively. In the case of a repressor, the repressor protein physically obstructs the RNA polymerase from transcribing the genes.
• Structural genes – the genes that are co-regulated by the operon.

Not always included within the operon, but important in its function is a

An inducer (small molecule) can displace a repressor (protein) from the operator site (DNA), resulting in an uninhibited operon.

Alternatively, a corepressor can bind to the repressor to allow its binding to the operator site. A good example of this type of regulation is seen for the trp operon.

Regulation

Control of an operon is a type of

Negative control involves the binding of a repressor to the operator to prevent transcription.

• In negative inducible operons, a regulatory repressor protein is normally bound to the operator, which prevents the transcription of the genes on the operon. If an inducer molecule is present, it binds to the repressor and changes its conformation so that it is unable to bind to the operator. This allows for expression of the operon. The lac operon is a negatively controlled inducible operon, where the inducer molecule is allolactose.
• In negative repressible operons, transcription of the operon normally takes place. Repressor proteins are produced by a regulator gene, but they are unable to bind to the operator in their normal conformation. However, certain molecules called corepressors are bound by the repressor protein, causing a conformational change to the active site. The activated repressor protein binds to the operator and prevents transcription. The trp operon, involved in the synthesis of tryptophan (which itself acts as the corepressor), is a negatively controlled repressible operon.

Operons can also be positively controlled. With positive control, an activator protein stimulates transcription by binding to DNA (usually at a site other than the operator).

• In positive inducible operons, activator proteins are normally unable to bind to the pertinent DNA. When an inducer is bound by the activator protein, it undergoes a change in conformation so that it can bind to the DNA and activate transcription. Examples of positive inducible operons include the MerR family of transcriptional activators.
• In positive repressible operons, the activator proteins are normally bound to the pertinent DNA segment. However, when an inhibitor is bound by the activator, it is prevented from binding the DNA. This stops activation and transcription of the system.

The lac operon

The lac operon of the

Discovered in 1953 by

Predicting the number and organization of operons

The number and organization of operons has been studied most critically in E. coli. As a result, predictions can be made based on an organism's genomic sequence.

One prediction method uses the intergenic distance between reading frames as a primary predictor of the number of operons in the genome. The separation merely changes the frame and guarantees that the read through is efficient. Longer stretches exist where operons start and stop, often up to 40–50 bases.^[19]

An alternative method to predict operons is based on finding gene clusters where gene order and orientation is conserved in two or more genomes.^[20]

Operon prediction is even more accurate if the functional class of the molecules is considered. Bacteria have clustered their reading frames into units, sequestered by co-involvement in protein complexes, common pathways, or shared substrates and transporters. Thus, accurate prediction would involve all of these data, a difficult task indeed.

Pascale Cossart's laboratory was the first to experimentally identify all operons of a microorganism, Listeria monocytogenes. The 517 polycistronic operons are listed in a 2009 study describing the global changes in transcription that occur in L. monocytogenes under different conditions.^[21]

See also

• Evolutionary developmental biology
• Genetic code
• Gene regulatory network
• L-arabinose operon
• Protein biosynthesis
• TATA box
• Umu Chromotest

References