synthetic gene design

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ggkk
ggkk's picture
synthetic gene design

Hi all,
 I am trying to design a syntheic gene which has to be codon optimised for tomato plant.
please tell me is there any software or program to design  the gene. steps need to be taken care in designing .
thank u in advance

Rolando
Rolando's picture
Hi,

Hi,

Check out this publication, it deals with a similar problem of fow expression of a exogenous gene in tomato.

"

High-level accumulation of recombinant miraculin protein in transgenic tomatoes expressing a synthetic miraculin gene with optimized codon usage terminated by the native miraculin terminator
Kyoko Hiwasa-Tanase, Mpanja Nyarubona, Tadayoshi Hirai, Kazuhisa Kato, Takanari Ichikawa and Hiroshi Ezura

Abstract

In our previous study, a transgenic tomato line that expressed the MIR gene under control of the cauliflower mosaic virus 35S promoter and the nopaline synthase terminator (tNOS) produced the taste-modifying protein miraculin (MIR). However, the concentration of MIR in the tomatoes was lower than that in the MIR gene’s native miracle fruit. To increase MIR production, the native MIR terminator (tMIR) was used and a synthetic gene encoding MIR protein (sMIR) was designed to optimize its codon usage for tomato. Four different combinations of these genes and terminators (MIR-tNOS, MIR-tMIR, sMIR-tNOS and sMIR-tMIR) were constructed and used for transformation. The average MIR concentrations in MIR-tNOS, MIR-tMIR, sMIR-tNOS and sMIR-tMIR fruits were 131, 197, 128 and 287 μg/g fresh weight, respectively. The MIR concentrations using tMIR were higher than those using tNOS. The highest MIR accumulation was detected in sMIR-tMIR fruits. On the other hand, the MIR concentration was largely unaffected by sMIR-tNOS. The expression levels of both MIR and sMIR mRNAs terminated by tMIR tended to be higher than those terminated by tNOS. Read-through mRNA transcripts terminated by tNOS were much longer than those terminated by tMIR. These results suggest that tMIR enhances mRNA expression and permits the multiplier effect of optimized codon usage.
"
there are software suites out there, that can help to optimize the codon usage for the different hosts expressed in.

Hope this helps a little.

cheers

ggkk
ggkk's picture
Thank you Rolando.

Thank you Rolando.