I agree with replacing codons if it is one or 2.  More becomes a big project. 

Try an expression system that is more tolerant to these codons like insect cell line.

Hi Himanshu,

You don't provide a lot of information about what you've already tried. When you say that you didn't get expression do you mean that you had very low yield or no expression at all? If there is no expression at all then maybe your protein is toxic to the cells. Have you tried Rosetta pLysS?  Also don't forget to add chloramphenicol in addition to your selection antibiotic.

Does your protein have a fusion tag (MBP, GB1, SUMO etc)? That could also help expression.

Your best bet, if you want to express in bacteria, is to mutate the rare codons by using something like QuickChange Multi Site-directed mutagenesis kit where you can mutate up to 5 different sites simultaneously in one reaction.

Also you can try to induce at lower temperature (18-22oC) and with lower IPTG concentrations.

Hope this helps.

thanks Nikolaos, for ur suggestion ill try expression in plysS,

the protein I'm trying to express is toxic to cell and having rare codon on its seq, that protein also having anti bacterial property, may be truncated peptides of my desire protein is expressing, that I have concluded from gel filtration profile..