Hi all,
I am new to this subject and would be thankful if you share some rencent progress and experience on identification of new genes involved in degradation of not-well studied compounds (derivatives of carboxylic acid, in my case)?
Thank you for your comments/suggestions.
Best
The usual way would be doing differential expression analysis of transcriptomic or proteomic data based on a control vs culturing in presence of the compound. Ideally, you should have the genome of your organism too.
SIP can be used to track if specific atoms from the compound of interest are incorporated into the cell or not. But it won't give you information about implicated genes.
Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50 - mer oligonucleotide microarrays has been developed. Using the method the target genes of these probe are involved in degradation - transformation processes of a variety chemical compounds, such as a monoaromatic - compound oxidation ( 546 probes ), PAH oxidation ( 212 probes ), biphenyl oxidation ( 76 probes ), ring cleavage reaction ( 417 probes ), aliphatic - compound tranformation ( 131 probes ). For details consult https://www.ncbi.nlm.nih.gov.-------PMC444823
Could try native PAGE followed by activity assays on gel slices and then LCMSMS of active slices
Matthew Lee Would you be able to share some article titles adapting this strategy? Thanks
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