Tryptophan Operon

Trp operon is an operon in bacteria which promotes the production of tryptophan when tryptophan isn't present in the environment. Discovered in 1953 by Jacques Monod and colleagues, the trp operon in E. coli was the first repressible operon to be discovered. While the lac operon can be activated by a chemical (allolactose), the tryptophan (Trp) operon is inhibited by a chemical (tryptophan). This operon contains five structural genes: trp E, trp D, trp C, trp B, and trp A, which encodes tryptophan synthetase. It also contains a promoter which binds to RNA polymerase and an operator which blocks transcription when bound to the protein synthesized by the repressor gene (trp R) that binds to the operator. In the lac operon, lactose binds to the repressor protein and prevents it from repressing gene transcription, while in the trp operon, tryptophan binds to the repressor protein and enables it to repress gene transcription. Also unlike the lac operon, the trp operon contains a leader peptide and an attenuator sequence which allows for graded regulation.

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It is an example of negative regulation of gene expression. Within the operon's regulatory sequence, the operator is blocked by the repressor protein in the presence of tryptophan (thereby preventing transcription) and is liberated in tryptophan's absence (thereby allowing transcription). The process of attenuation complements this regulatory action. Repression The repressor for the trp operon is produced upstream by the trpR gene, which is continually expressed. It creates monomers, which associate into tetramers. When tryptophan is present, it binds to the tryptophan repressor tetramers, and causes a change in conformation, which allows the repressor to bind the operator, which prevents RNA polymerase from binding or transcribing the operon, so tryptophan is not produced. When tryptophan is not present, the repressor cannot bind the operator, so transcription can occur. This is therefore a negative feedback mechanism.

Attenuation Because repression of this operon is still "leaky," another system of controlling expression is also needed: Attenuation. At the beginning of the transcribed genes of the trp operon is a leader sequence, which codes for a very short polypeptide. Near the end of this sequence, two tryptophans are coded for next to each other. Because tryptophan is a fairly uncommon amino acid, this is highly unusual. Since in prokaryotes the ribosomes begin translating the mRNA as soon as the RNA polymerase has moved farther down the DNA sequence, upstream translation occurs simultaneously with transcription of downstream genes. So, as soon as the polymerase has created the mRNA for the leader sequence, it is being translated. When the ribosome reaches the double-trp codons, if enough trp is present, the ribosome will not be delayed, and will continue translating until it reaches the stop codon and falls off the leader transcript. A hairpin will then form in the mRNA transcript (remember, still attached to RNA polymerase on other end) between regions 1-2, and 3-4, which destabilizes the RNA polymerase and halts transcription of the rest of the operon, thus preventing production of trp. On the other hand, if there is little or no trp available, the ribosome will be delayed or stopped on the double-trp, and a hairpin will form between regions 2-3 of the mRNA instead. This does not destabilize the polymerase, so transcription and translation occur. Similar mechanism regulates the synthesis of histidine, phenylalanine and threonine.

Lac Operon Animation

The lac operon is an operon required for the transport and metabolism of lactose in Escherichia coli and some other enteric bacteria. It consists of three adjacent structural genes, a promoter, a terminator, and an operator. The lac operon is regulated by several factors including the availability of glucose and of lactose. Gene regulation of the lac operon was the first genetic regulatory mechanism to be elucidated and is often used as the canonical example of prokaryotic gene regulation.

The lac operon consists of three structural genes, a promoter, a terminator,(author forgot regulator, please edit this) and an operator. The three structural genes are:: lacZ, lacY, and lacA.

* lacZ encodes β-galactosidase (LacZ), an intracellular enzyme that cleaves the disaccharide lactose into glucose and galactose.
* lacY encodes β-galactoside permease (LacY), a membrane bound transport protein that pumps lactose into the cell.
* lacA encodes β-galactoside transacetylase (LacA), an enzyme that transfers an acetyl group from acetyl-CoA to β-galactosides.

Only lacZ and lacY appear to be necessary for lactose catabolism.

Specific control of the lac genes depends on the availability of the substrate lactose to the bacterium. The proteins are not produced by the bacterium when lactose is unavailable as a carbon source. The lac genes are organized into an operon; that is, they are oriented in the same direction immediately adjacent on the chromosome and are co-transcribed into a single polycistronic mRNA molecule. Transcription of all genes starts with the binding of the enzyme RNA polymerase (RNAP), a DNA-binding protein, to a specific DNA binding site immediately upstream of the genes, the promoter. From this position RNAP proceeds to transcribe all three genes (lacZYA) into mRNA. The DNA sequence of the E. coli lac operon, the lacZYA mRNA, and the lacI genes are available from GenBank (view).

The regulatory response to lactose requires an intracellular regulatory protein called the lactose repressor. The lacI gene encoding repressor lies nearby the lac operon and is always expressed (constitutive). If lactose is missing from the growth medium, the repressor binds very tightly to a short DNA sequence just downstream of the promoter near the beginning of lacZ called the lac operator. Repressor bound to the operator interferes with binding of RNAP to the promoter, and therefore mRNA encoding LacZ and LacY is only made at very low levels. When cells are grown in the presence of lactose, a lactose metabolite called allolactose binds to the repressor, causing a change in its shape. Thus altered, the repressor is unable to bind to the operator, allowing RNAP to transcribe the lac genes and thereby leading to high levels of the encoded proteins.

Genetic nomenclature

Three-letter mnemonics are used to describe phenotypes in bacteria including E. coli.

Examples include:

* Lac (the ability to use lactose),
* His (the ability to synthesize the amino acid histidine)
* Mot (swimming motility)
* Str (response to the antibiotic streptomycin)

In the case of Lac, wild type cells are Lac+ and are able to use lactose as a carbon and energy source, while Lac- mutant derivatives cannot use lactose. The same three letters are typically used (lower-case, italicized) to label the genes involved in a particular phenotype, where each different gene is additionally distinguished by an extra letter. The lac genes encoding enzymes are lacZ, lacY, and lacA. The fourth lac gene is lacI, encoding the lactose repressor---I stands for inducibility.

One may distinguish between structural genes encoding enzymes, and regulatory genes encoding proteins that affect gene expression. Current usage expands the phenotypic nomenclature to apply to proteins: thus, LacZ is the protein product of the lacZ gene, β-galactosidase. Various short sequences that are not genes also affect gene expression, including the lac promoter, lac p, and the lac operator, lac o. Although it is not strictly standard usage, mutations affecting lac o are referred to as lac oc, for historical reasons.

Use in molecular biology

The lac gene and its derivatives are amenable to use as a reporter gene in a number of bacterial-based selection techniques such as two hybrid analysis, in which the successful binding of a transcriptional activator to a specific promoter sequence must be determined. In LB plates containing X-gal, the colour change from white colonies to a shade of blue, corresponds to about 20-100 β-galactosidase units, while tetrazolium lactose and MacConkey lactose media have a range of 100-1000 units, being most sensitive in the high and low parts of this range respectively. Since MacConkey lactose and tetrazolium lactose media both rely on the products of lactose breakdown, they require the presence of both lacZ and lacY genes. The many lac fusion techniques which include only the lacZ gene are thus suited to the X-gal plates or ONPG liquid broths