We have sequenced a bacteria and found multiple copies of antibiotic resistance genes. The sequences of the copies are not identical. I was wondering if this diversity of copies is to increase the chances of being resistant to many forms of the same antibiotic ?
That is indeed a very interesting question! Which antibiotic is it? And did you test (at list in the computer) that all CDSs are actually enable of coding a protein (i.e. no stop codons, frame shifts etc.)?
Yoram
The paper is very near the publication stage so i will limit my discussion, however it's not such a major part of the work but an interesting observation. The predicted genes I was looking at were tetracycline repressor protein class B (x2) and tetracycline repressor protein class E (x4). I compared the translated AA sequences and they were not that similar. I have tested (in vitro) the organism against tetracycline and tigecycline. The organism was resistant to tetracycline and tigecycline resistance took a few more days. I was interested because tigecycline is a chemical modification of tetracycline . Then i thought would there be enough redundancy in the tetracycline resistance proteins for the bacteria to adapt ? however there are many other resistance genes in the sequence and 1/4 ---> 1/3 of the genome is not annotated. At this point I haven't checked for stop codons as I was primarily interested in looking at the annotated amino acid files but perhaps I should also look at the fna files I have . thanks
Surely evolution does not have a purpose? Various functions can appear, and because they are found to be useful, improving fitness, they persist. Are there not examples of biological properties that have evolved for various reasons but are not in themselves advantageous, though associated with other properties that are?
Many thanks for the detailed description. I will urge you to differentiate TetR ( tetracycline repressor ) as the transcriptional regulators and tetR as a name for the gene encoding Tetracyclin resistance (namely TetA). Which one are you talking about?
Ah, ok , this is good to know since I was writing the paper. These genes control of tetracyline production rather than resist it. The mechanism for the resistance to tetracyline must then be controlled by another gene probably not annotated. I cannot find the TetA gene in our sequence. Maybe it wasn't such a good example. However we did find macrolide resistance element MacB in variations to which our organism had intermediate resistance ie scattered colonies grew up to the edge of the disc after 6 days incubation
Multi copies gene of AMR are common, in case of there were continously challenged with antibiotic, nd also would be longer gene; The different antibioticis alos make some mutation, and thus make different sequences;
A few colonies growing within the hallow after a few days is something I have seed before, although I did not try macrolides specifically. As for the TetR - it could simply be different transcription regulators, not necessarily has to do with tetracycline. Try to look for tet promoter like sequences in your genome and for what CDSs are after them - especialy try to look near the tetR like sequences as many times related genes are organized in operons although this is not a must.
Also, google "operon prediction", as there are many tools online. If you find tetR-like sequence near Ptet-like (Ptet = tet promoter) sequence and in an operon that will make the idea more likely.
Yoram
Hi Dear Gerry
how can you know that there are multiple copies of ARG in single pure bacterial isolate?
BR
good point, the DNA was taken from one colony which was subcultured onto several plates and the DNA extracted . DNA sequencing was by Illumina hiSeq . Annotation of genes was by RAST. From the annotated genome I noted quite a few antimicrobial genes with multiple copies . I compared the sequences of a few of these but they were not that similar. amongst other genes we had YokD(x2), Metallo b lactamse L1 (x3) , MacB (x3), multidrug resistance protein 3 (x8), multidrug resistance protein Stp (x11), MdtH (x4) and tunicamycin resistance protein (x2).
Great discovery Indeed. Was there any pathogenicity island or islet associated? If so, should we not investigate whether this is an insertional event or not? Often bacteria use tetracycline resistance genes for their metabolism purpose. Could it be linked to that aspect?
Its possible for the bacterial to demonstrate resistance to both tetracyclicine and tigecycline because they share the same mechanism of action in what is called co-resistance. Different types of Tet genes (I would prefer types to copies) may render the entire tetracycline class of antimicrobial resistant. However some types have higher affinity for some tetracycline substrate.
its not purpose, its functions. this mean that there are many gens for different functions .
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