My bacterium was degrading a specific antibiotic. I am looking to identify a gene which is involved in this process. But, I dont have much idea about this work. Could someone help me to solve this problem.
Hello,
There might be different pathways - and hence different genes not sharing sequence identities - for degrading the same molecules. So I am afraid you will have to make the bibliography to find out what might be the genes involved in this process in other bacteria (or other organisms too) and see if you have related genes in your favorite bacterium.
No. For example, aromatic compounds with single rings can undergo meta- or ortho- cleavage depending on the enzymes that the organism owns. I recommend you this database, which includes a predictor based on degradation rules based on research data.
http://eawag-bbd.ethz.ch/
Dear Dr. Frederique Van Gijsegem,
Thank you very much for your suggestions. However, there is no information about the genes involved in this antibiotic degradative pathway. Is there any other way to find these genes.
Dear Xabier Vazquez Campos,
Thank you very much for your suggestions...........
Hi, I was dealing with the same problem and finally I conducted a metagenome analysis to identify genes that were expressed in higher levels than others. For a first idea what genes might be involved you could also try these to biodegradation pathway prediction tool:
http://www.genome.jp/tools/pathpred/
and the one already stated above.
Dear Dr. BAstian Herzog,
Thank you very much for your kind help.
Dear Dr. Rene Kaden,
Thank you very much for for your kind help.........
Unless the antibiotic you have discovered is a totally novel compound there are likely known resistance mechanisms for the class of antibiotics, which would give you an idea of likely modifications of your specific compound. If this information is not available, you could examine the chemical modification of your antibiotic by LCMS. In this way you might be able to determine what the modification is (e.g. acetylation) and this would allow you to narrow your search for the modifying enzyme.
Dear Brad Haltli,
Thank you very much for your suggestions..........
I will look antibiotic chemical modification in LC-MS
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