I was studying this article about Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome in order to try to extrapolate some features that could explain, at least in part, the survival strategy of Pyrococcus Furiosus exposed to gamma irradiation.

In this article, they compare the Pyrococcus Furiosus reference genome with the genome of a variant designated COM1, which is a genetically tractable strain.

In the Introduction they say:

The COM1 strain was obtained by targeted gene disruption of the pyrF locus (PF1114) using a plasmid designed for double-crossover recombination (37).

I would like to see if, after this targeted gene disruption, there is some amplification of some genes that I suspect they are involved in the servival strategy of these extremophiles to gamma irradiation, because then in the article they say that a number of genes involved in DNA repair could potentially be inactive in COM1 (as they fall into the minor protein-level differences category) but nevertheless it shows no significant changes in its ability to recover from exposure to UV or gamma irradiation.

For this reason, I would like to see if maybe some other genes involved in genetic material protection are amplified in response to this targeted gene disruption (in the sense that there are more copies of a gene being present in the genome). In fact, since I saw from NIH that:

cancer cells sometimes make multiple copies of genes in response to erroneous signals from other cells or because of signals they're getting from the environment.

Could this be valid also for my situation? In the sense that now I am not considering cancer cells but Pyrococcus Furiosus cells and as signal from the environment I consider the targeted gene disruption ?

Thus, my question leads to: what are the causes of gene amplification in archaea ? In few words, I need to understand this last question in order to see if it makes sense to try to detect gene amplification with the DNA sequencing data that I have. Anyway, I gave you all the background I am working with because I hope that, in this way, you can understand better what I want to know.

Thank you in advance.

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    $\begingroup$ Re: "what are the causes of gene amplification in archaea ? " I suspect trying to answer that would make for a good research career! :) I'm not familiar with archaea, but I think the NIH "signals" statement above only means that pre-existing signal-based gene amplification systems are induced in those cases. However, perhaps Pyr. does have mechanisms to detect loss-of-function in a gene and respond as you suggest. Sounds like an interesting research project! $\endgroup$
    – Armand
    Jun 9 at 12:45
  • $\begingroup$ Thank you very much for your opinion :) ok I do not really understand the meaning of pre-existing signal-based gene amplification systems but knowing that it is not a completely nonsense reasoning is already something very important! I think that there are few people studying archaea and I do not know why... They are so interesting, as you say . $\endgroup$
    – Manuela
    Jun 9 at 13:15
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    $\begingroup$ The best science often comes from reasoning that gets close to "nonsense", but not quite. You've got an interesting idea to pursue -- good luck! $\endgroup$
    – Armand
    Jun 9 at 13:29
  • $\begingroup$ Just to clarify, are you interested in gene amplification (more copies of a gene being present in the genome), or increased gene expression (more copies of a gene being transcribed into mRNA and/or translated into protein)? In a pure culture system (clonal lineage), I think it makes more sense to look into transcriptional regulation before looking for gene amplification, though gene amplification can be favored at times (some forms of acquired antibiotic resistance in bacteria, for example). $\endgroup$
    – MikeyC
    Jun 9 at 16:02
  • $\begingroup$ @MikeyC I am interested in the first one: gene amplification (more copies of a gene being present in the genome). I have already studied gene expression... not really in this exact context. I made statistical data analysis of quantity of mRNA produced from some particular genes when P. Furiosus cell coltures were exposed to gamma irradiation. Now the idea is just to check if the genes, that in that study increased the mRNA production after the irradiation, are amplified if you do targeted gene disruption . $\endgroup$
    – Manuela
    Jun 9 at 16:22

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