Difference between revisions of "Team:Bielefeld-CeBiTec/Project/translational system/library and selection"
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Synthetases form a family of enzymes which attach amino acids to the tRNA in a two-step reaction. Therefore, each tRNA synthetase (aaRS) aminoacylates all the tRNAs in an isoaccepting group, representing a particular amino acid. ‘Isoaccepting’ implies that each amino acid can be transported to the ribosome by more than one tRNA. | Synthetases form a family of enzymes which attach amino acids to the tRNA in a two-step reaction. Therefore, each tRNA synthetase (aaRS) aminoacylates all the tRNAs in an isoaccepting group, representing a particular amino acid. ‘Isoaccepting’ implies that each amino acid can be transported to the ribosome by more than one tRNA. | ||
− | The tRNA recognition is based on particular nucleotides, labelled as identity set. This identity set is often concentrated in the acceptor stem and anticodon loop region of the tRNA. However, the anticodon sequence of the tRNA is not necessary for a specific tRNA synthetase recognition due identity determinants which vary in their importance. | + | The tRNA recognition is based on particular nucleotides, labelled as identity set. This identity set is often concentrated in the acceptor stem and anticodon loop region of the tRNA. However, the anticodon sequence of the tRNA is not necessary for a specific tRNA synthetase recognition due identity determinants which vary in their importance. <br> |
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The first step of the two-step reaction is the formation of an aminoacylated intermediate by the reaction of the amino acid and ATP. This is possible through the Rossmann fold. This domain describes a six-stranded parallel β-sheet with connecting helices. The Rossmann fold acts homologous to the active site domains of hydrogenases and is responsible for binding ATP, the amino acid and the 3’-terminus of the tRNA. | The first step of the two-step reaction is the formation of an aminoacylated intermediate by the reaction of the amino acid and ATP. This is possible through the Rossmann fold. This domain describes a six-stranded parallel β-sheet with connecting helices. The Rossmann fold acts homologous to the active site domains of hydrogenases and is responsible for binding ATP, the amino acid and the 3’-terminus of the tRNA. | ||
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The incorporation of a non-canonical amino acid (ncAA) requires a tRNA/synthetase (tRNA/aaRS) pair which can accept and bind the ncAA. The tRNA/aaRS pair should be very specific in the incorporation of the ncAA and most importantly does not cross-react with endogenous amino acids (Ryu<i> et al.</i></i>, 2006). | The incorporation of a non-canonical amino acid (ncAA) requires a tRNA/synthetase (tRNA/aaRS) pair which can accept and bind the ncAA. The tRNA/aaRS pair should be very specific in the incorporation of the ncAA and most importantly does not cross-react with endogenous amino acids (Ryu<i> et al.</i></i>, 2006). | ||
This is achieved by the use of an orthogonal tRNA/aaRS pair, which does not cross-react with the endogenous components of the translational system. The cognate tRNA is not recognized by the endogenous synthetase and the cognate synthetase does not incorporate the endogenous amino acids due to differences in tRNA identity elements, especially in the acceptor stem (Kwok<i> et al.</i></i>, 1980). At the same time, the orthogonal tRNA/synthetase pair has a good translational function (Wang<i> et al.</i></i>, 2001, Chang<i> et al.</i></i>, 2010). | This is achieved by the use of an orthogonal tRNA/aaRS pair, which does not cross-react with the endogenous components of the translational system. The cognate tRNA is not recognized by the endogenous synthetase and the cognate synthetase does not incorporate the endogenous amino acids due to differences in tRNA identity elements, especially in the acceptor stem (Kwok<i> et al.</i></i>, 1980). At the same time, the orthogonal tRNA/synthetase pair has a good translational function (Wang<i> et al.</i></i>, 2001, Chang<i> et al.</i></i>, 2010). | ||
+ | <br> | ||
Since the tRNA recognition by the aaRS can be domain or species specific (Kwok<i> et al.</i></i>, 1980) a heterologous aaRS/tRNA pair from a different organism is used. A possible source for an orthogonal tRNA/synthetase pair to be applied in bacterial cells can be eukaryotic. However, the adaption of these tRNA/aaRS pair which aminoacylates in <i>Escherichia coli</i> is very difficult (Liu<i> et al.</i></i>, 1999). In contrast, evolved synthetases from archaea can be expressed efficiently in <i>E. coli</i> (Wang<i> et al.</i></i>, 2001, Wang<i> et al.</i></i>, 2000) and at the same time are more similar to eukaryotic organisms than to the prokaryotic (Kwok<i> et al.</i></i>, 1980, Zhang<i> et al.</i></i>, 2005). The reason are significant differences in the acceptor stem and anticodon binding recognition domain between prokaryotic and archaea tRNA/aaRS (Wang<i> et al.</i></i>, 2000). | Since the tRNA recognition by the aaRS can be domain or species specific (Kwok<i> et al.</i></i>, 1980) a heterologous aaRS/tRNA pair from a different organism is used. A possible source for an orthogonal tRNA/synthetase pair to be applied in bacterial cells can be eukaryotic. However, the adaption of these tRNA/aaRS pair which aminoacylates in <i>Escherichia coli</i> is very difficult (Liu<i> et al.</i></i>, 1999). In contrast, evolved synthetases from archaea can be expressed efficiently in <i>E. coli</i> (Wang<i> et al.</i></i>, 2001, Wang<i> et al.</i></i>, 2000) and at the same time are more similar to eukaryotic organisms than to the prokaryotic (Kwok<i> et al.</i></i>, 1980, Zhang<i> et al.</i></i>, 2005). The reason are significant differences in the acceptor stem and anticodon binding recognition domain between prokaryotic and archaea tRNA/aaRS (Wang<i> et al.</i></i>, 2000). | ||
+ | <br> | ||
One possible orthogonal tRNA/aaRS pair is the tyrosine tRNA/aaRS pair of <i>Methanococcus jannaschii</i>, where the first base pair of the acceptor stem CG as a tRNA<sup>Tyr</sup>identity element differs from those of <i>E. coli</i> tRNA<sup>Tyr</sup> containing a GC (Wang<i> et al.</i></i>, 2001). | One possible orthogonal tRNA/aaRS pair is the tyrosine tRNA/aaRS pair of <i>Methanococcus jannaschii</i>, where the first base pair of the acceptor stem CG as a tRNA<sup>Tyr</sup>identity element differs from those of <i>E. coli</i> tRNA<sup>Tyr</sup> containing a GC (Wang<i> et al.</i></i>, 2001). | ||
The orthogonal tRNA/aaRS pair is incorporated as a response of the amber stop-codon, which does not incorporate any of the 20 canonical amino acids. We use the amber stop-codon (UAG), because this codon is rare in <i>E.coli</i> and incorporation of random amino acids has been shown before. | The orthogonal tRNA/aaRS pair is incorporated as a response of the amber stop-codon, which does not incorporate any of the 20 canonical amino acids. We use the amber stop-codon (UAG), because this codon is rare in <i>E.coli</i> and incorporation of random amino acids has been shown before. |
Revision as of 11:56, 28 August 2017
Translational System
Transational Mechanism
Amber-codon
tRNA/aminoacyl-synthetase
The first step of the two-step reaction is the formation of an aminoacylated intermediate by the reaction of the amino acid and ATP. This is possible through the Rossmann fold. This domain describes a six-stranded parallel β-sheet with connecting helices. The Rossmann fold acts homologous to the active site domains of hydrogenases and is responsible for binding ATP, the amino acid and the 3’-terminus of the tRNA.
The class I synthetases are monomeric synthetases and feature all structurally similar active site Rossmann fold domains in the region of the N-terminal. Beside this region, there are no significant structural or sequence similarities among the class I enzymes.
There is an acceptor binding site inserted into the Rossmann-fold domain at a common location which binds the single stranded terminal end of the tRNA, while its C-terminal domain binds in the minor groove of the L-shaped tRNA and the anticodon arm. That is the point for the discrimination among the different tRNAs. The binding requires the formation of a hairpin structure of the single stranded 3’-terminus with the amino acid and the ATP in the active site (Chang et al., 2010, Krebs et al., 2014).
Figure 1: Crystal structure of a class I tRNA/aminoacyl synthetase.
The tRNA is shown in red and the protein i n blue (Krebs et al., 2014).
An orthogonal tRNA/aminoacyl-synthetase pair
Since the tRNA recognition by the aaRS can be domain or species specific (Kwok et al., 1980) a heterologous aaRS/tRNA pair from a different organism is used. A possible source for an orthogonal tRNA/synthetase pair to be applied in bacterial cells can be eukaryotic. However, the adaption of these tRNA/aaRS pair which aminoacylates in Escherichia coli is very difficult (Liu et al., 1999). In contrast, evolved synthetases from archaea can be expressed efficiently in E. coli (Wang et al., 2001, Wang et al., 2000) and at the same time are more similar to eukaryotic organisms than to the prokaryotic (Kwok et al., 1980, Zhang et al., 2005). The reason are significant differences in the acceptor stem and anticodon binding recognition domain between prokaryotic and archaea tRNA/aaRS (Wang et al., 2000).
One possible orthogonal tRNA/aaRS pair is the tyrosine tRNA/aaRS pair of Methanococcus jannaschii, where the first base pair of the acceptor stem CG as a tRNATyridentity element differs from those of E. coli tRNATyr containing a GC (Wang et al., 2001). The orthogonal tRNA/aaRS pair is incorporated as a response of the amber stop-codon, which does not incorporate any of the 20 canonical amino acids. We use the amber stop-codon (UAG), because this codon is rare in E.coli and incorporation of random amino acids has been shown before.