Editing Bacerial Expression Strategy (section)

= Vector Components<br>  =

'''Selectable marker.''' In the absence of selective pressure plasmids are lost from the host. Especially in the case of very high copy number plasmids and when plasmid-borne genes are toxic to the host or otherwise significantly reduce its growth rate. The simplest way to address this problem is to express from the same plasmid an antibiotic-resistance marker and supplement the medium with the appropriate antibiotic to kill plasmid-free cells. The most used antibiotics and their effective concentrations are listed in table 1. 

<br> The use of ampicillin requires special care. The selectable marker, b-lactamase, is secreted into the medium where it hydrolysis all of the ampicillin. This point is already reached when the culture is barely turbid. From here on, cells that lack the plasmid will not be killed and could overgrow the culture. Some possible solution are: 

<br> 

*grow overnight cultures at 30°C or less. 
*spin overnight cultures and resuspend the pellet in fresh medium to remove the produced b-lactamase. 
*use the more stable carbenicillin instead of ampicillin.

'''Regulatory gene (repressor).''' Many promoters show leakiness in their expression ''i.e.'' gene products are expressed at low level before the addition of the inducer. This becomes a problem when the gene product is toxic for the host. This can be prevented by the constitutive expression of a repressor protein. 

<br> The '''lac'''-derived promoters are especially leaky. These promoters can be controlled by the insertion of a '''lac'''-operator sequence downstream the promoter and the expression of the '''lac'''-repressor by host strains carrying the '''lacI<sup>q</sup>''' allele (for medium copy number plasmids) or from the same or a helper plasmid (for higher copy number plasmids). Alternatively, repression can be achieved by the addition of 1% glucose to the culture medium. 

<br> '''Origin of replication.''' The origin of replication controls the plasmid copy number. 

<br> '''Promoter.''' The promotor initiates transcription and is positioned 10-100 nucleotides upstream of the ribosome binding site. The ideal promoter exhibits several desirable features: 

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*It is strong enough to allow product accumulation up to 50% of the total cellular protein. 
*It has a low basal expression level (''i.e.'' it is tightly regulated to prevent product toxicity). 
*It is easy to induce.

An extensive list of possible promoters is given in table 2. The most used promoters are indicated in red. 

<br> '''Transcription terminator.''' The transcription terminator reduces unwanted transcription and increases plasmid and mRNA stability. 

<br> '''Shine-Delgarno sequence.''' The Shine-Dalgarno (SD) sequence is required for translation initiation and is complementary to the 3'-end of the 16S ribosomal RNA. The efficiency of translation initiation at the start codon depends on the actual sequence. The concensus sequence is: 5'-'''TAAGGAGG'''-3'. It is positioned 4-14 nucleotides upstream the start codon with the optimal spacing being 8 nucleotides. To avoid formation of secondary structures (which reduces expression levels) this region should be rich in A residues. 

<br> '''Start codon.''' Initiation point of translation. In ''E.'' coli''the most used start codon is '''ATG'''. '''GTG''''' is used in 8% of the cases. '''TTG''' and '''TAA''' are hardly used. 

<br> '''Tags and fusion proteins.''' N- or C-terminal fusions of heterologous proteins to short peptides (tags) or to other proteins (fusion partners) offer several potential advantages: 

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*'''Improved expression.''' Fusion of the N-terminus of a heterologous protein to the C-terminus of a highly-expressed fusion partner often results in high level expression of the fusion protein. 
*'''Improved solubility.''' Fusion of the N-terminus of a heterologous protein to the C-terminus of a soluble fusion partner often improves the solubility of the fusion protein. 
*'''Improved detection.''' Fusion of a protein to either terminus of a short peptide (epitope tag) or protein which is recognized by an antibody or a binding protein (Western blot analysis) or by biophysical methods (''e.g.'' GFP by fluorescence) allows for detection of a protein during expression and purification. 
*'''Improved purification.''' Simple purification schemes have been developed for proteins fused at either end to tags or proteins which bind specifically to affinity resins (see table 3 and references therein).

'''Protease cleavage site.''' Protease cleavage sites are often added to be able to remove a tag or fusion partner from the fusion protein after expression. Most commonly used proteases are listed in table 4. However, cleavage is rarely complete and often additional purification steps are required. 

<br> '''Multiple cloning site.''' A series of unique restriction sites that enables you to clone your gene of interest into the vector. 

<br> '''Stop codon.''' Termination of translation. There are 3 possible stop codons but '''TAA''' is preferred because it is less prone to read-through than '''TAG''' and '''TGA'''. The efficiency of termination is increased by using 2 or 3 stop codons in series. 

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