I need to identify the gene responsible for production of bacteriocin, and cloned it into another organism but I don't know how to identify the gene from 16S rRNA sequence.
Dear Marimuthu,
i think you want to amplify the bacteriocin from your own isolated bacteria. you have identified it using 16S rDNA sequencing, now search the similarity of 16s Sequence of this organism with others using the clustalW analysis of your sequence and avilabkle sequences in NCBI. Once you will identify the most common organism from your bacterium then download the Bacteriocin gene cds sequences of these from NCBI, (if not available in NCBI DATA then try the reverse genetics tools; go to Expacy download the bacteriocin protein and convert it into DNA sequence...). now design the specific primers for bacteriocin gene by adding the restriction sites at the 5' and 3' terminals of ORF (at 5' ends of forward and reverse primers). also search the restriction sites for these enzymes within the gene sequence (if you will not do this then your gene may cut from the mid after digestion with enzymes) thus you have to select and add only those restriction enzymes for whoom the restriction sites are absent in the gene.(0 cutters); do it using NEB cutter tool, send the designed primer (by OLIGOS OR DNAMAN OR BIOEDIT) for synethsis. after getting synthesised primers ude the template DNA of your bacteria in PCR reaction mixture and surely you will get complete ORF. but before designing primers first read about the optimal primer conditions , TA CLONING and restriction cloning.
16S gene give match for species similarity, not for any other character directly. But matching in databases can explore the possibility of other genes/proteins by same species. You can get idea if the species have been reported for bacteriocin production or not. then work on gene amplification by searching primers from literature or design new.
Best option is to 1st check the microorganisms against some indicator strains if those strains get inhibited or not (I think you might have already finished this task).
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