2
$\begingroup$

I am going to analyze DNA sequencing data in order to try to extrapolate some information about the survival strategy of Pyrococcus Furiosus to gamma irradiation, as maybe you already know from all the previous questions that I published .

In particular, among my previous posts there was the one titled as What does genetically tractable strain mean? in which I asked the meaning of genetically tractable strain because I was reading the article about Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome in which they compare the Pyrococcus Furiosus reference genome sequence (the one that was firstly sequenced in the year 2000) with the sequence of a variant in a lab strain population, designated COM1 and that is the genetically tractable strain which has undergone targeted gene disruption of the pyrF gene (I have clarified the meaning of this process here What is targeted gene disruption?).

Now, what I still can't really understand is why do they compare the "modified" genome sequence of the variant with the reference genome sequence ? I would have aligned the "modified" genome sequence of the variant with its sequence before the targeted gene disruption. Then, of course, I would have all the properties of the variant and not of the "main" strain ( the reference Pyrococcus Furiosus genome).

Instead, in the article they compare first the reference genome sequence with the one of its manipulated variant and then they also compare the sequences of some particular genes, obtaining some properties as if they were discussing of the same genome. For example:

the protein products of 102 of the total 2,134 genes in the NCBI reference sequence are disrupted in COM1 at the translational level through nonsynonymous mutations. These result in amino acid changes, insertions and deletions introducing premature stop codons, and frameshifts producing longer or shorter products with alternate coding sequences. These were subdivided into 36 major changes (Table 4) and 66 minor changes (see Table S1 in the supplemental material) based on the Needleman-Wunsch global alignment identity compared with the protein sequences in the NCBI reference sequence.

This and many other extracts show that they compare the reference and the variant as if they were, respectively, the "control" and the sample that has been treated, ignoring the fact that they were actually distinct genomes.

In the post What does genetically tractable strain mean?, the answer to the question "why do they do this comparison?" was essentially that results obtained by manipulation of the tractable strain can inform your understanding of the reference form. But why are we allowed to treat them as if they were the same genome? And so, can we consider the properties refered to the COM1 valid also for the reference Pyrococcus Furiosus and for all its existing variants ? For instance, here they say:

a number of genes involved in DNA repair, including an uncharacterized RadA domain protein (PF0872), DNA repair helicase Rad3 (PF0933), 5'-to-3' exonuclease NurA (PF1168 [23]), and DNA repair helicase (PF1902), could potentially be inactive in COM1 as they fall into the minor protein-level differences category (see Table S1 in the supplemental material). However, COM1, Parent, and DSMZ showed no significant differences in their ability to recover from exposure to UV or gamma irradiation under conditions previously reported for P. furiosus (14).

Can I say that this could be valid also for the reference Pyrococcus Furiosus, in the sense that if the mentioned set of DNA repair genes are inactive, it will show no significant differences in its ability to recover from exposure to UV or gamma irradiation ?

My conclusion, months ago, was that a variant can be considered as if it was the main strain since the definition that I read in Wikipedia is:

In microbiology and virology, the term variant or "genetic variant" is used to describe a subtype of a microorganism that is genetically distinct from a main strain, but not sufficiently different to be termed a distinct strain.

Now this conclusion does not satisfy me anymore and I would like to really understand the reason of this comparison and how to interpret the relationships between genomes. Can we consider the main strain and its variant simply the same since the last one is not "sufficiently different to be termed a distinct strain"? Are all the phenotypic properties observed for the variant COM1 (like for example the fact that although a set of DNA repair genes are inactive, the ability to recover from exposure to UV or gamma irradiation, under certain conditions, is still the same) valid also for the "main" strain (that is the NCBI reference genome) ?

Thank you in advance.

$\endgroup$
4
$\begingroup$

... I was reading the article about Genome Sequencing of a Genetically Tractable Pyrococcus furiosus Strain Reveals a Highly Dynamic Genome in which they compare the Pyrococcus Furiosus reference genome sequence ... with the sequence of a variant in a lab strain population, designated COM1 and that is the genetically tractable strain which has undergone targeted gene disruption.

Instead, in the article they compare first the reference genome sequence with the one of its manipulated variant and then they also compare the sequences of some particular genes, obtaining some properties as if they were discussing of the same genome.

I think this is from where your confusion originates. From my reading, the paper you link is a comparative genomics paper, and the authors do not perform any genetic manipulations of the tractable COM1 strain. All mentions of "disrupted" genes are referring to the effects of naturally occurring insertion sequences or nonsynonymous mutations. "Natural", here, meaning not purposefully disrupted. Based on the comparison with the Parent and DSMZ strains, it seems like COM1 accumulated its various disruptions and rearrangements while it was propagated as a wild-type lab strain.

For more on how the COM1 strain was "discovered", I suggest reading the original paper in which it was described.

$\endgroup$
7
  • $\begingroup$ Thank you for your answer @acvill but I do not understand many things: 1. Where is the term "natural" that you mention ? 2. So coming to the main question: why do they do this comparison ? Is it just to describe the difference between the two genomes ? $\endgroup$
    – Manuela
    Jun 10 at 17:08
  • $\begingroup$ @Manuela (1) "natural" is in reference to my use of "naturally" in the previous sentence. I wanted to avoid confusion concerning the origin of the COM1 mutations. I'll italicize for emphasis. (2) Yes, they are describing the differences between the COM1 genome and the reference genome, as well as structural variants in the Parent and DSMZ genomes. $\endgroup$
    – acvill
    Jun 10 at 17:13
  • $\begingroup$ Ok @acvill in fact it makes sense, thank you. But I am still confused because in the part of the article that I posted, when they align the COM1 with the reference they say something like "these proteins in COM1 could be inactive because the protein sequences are different with respect to the protein sequences of the reference". Why do they expected to be the same ? $\endgroup$
    – Manuela
    Jun 10 at 17:33
  • $\begingroup$ Let's continue this discussion in chat. $\endgroup$
    – acvill
    Jun 10 at 17:39
  • 1
    $\begingroup$ Then I found this definition in Springer about targeted gene disruption that tells that it is Experimental replacement of an endogenous gene by a mutated (non‐functional) version within the otherwise unchanged genome is called targeted gene disruption. So I said that they did genetic manipulations . But honestly now I do not understand if this was done by the authors of the original paper that you linked or it occured naturally. The original paper is too much complificated for me :/ $\endgroup$
    – Manuela
    Jun 11 at 11:14

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.