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Let's say we have two DNA molecules of equal length, one belonging to a prokaryote and the other to an eukaryote. It's known that replication of the eukaryotic DNA is faster in this case. One clear reason for this is that linear DNA has multiple origins of replication whereas circular DNA only has one.

Now back to the real question: Does it matter for rate of replication whether the DNA is circular or linear? Does it contribute to eukaryotic DNA replication being faster in our specific case?

One thing I found in an old revision of this Wikipedia article is as such:

One reason that many organisms have evolved to having linear chromosomes is due to the size of their genome. Linear chromosomes make it easier for transcription and replication of large genomes. If an organism had a very large genome arranged in a circular chromosome, it would have the potential problems when unwinding due to torsional strain.

What I make out from this is that the rate of replication isn't directly affected. It's more closely related to avoiding other issues that arise from eukaryotic DNA molecules being typically longer than prokaryotic ones. But in our case where we declare both DNA to be of equal length, I'm assuming circular vs linear has no bearing on the rate of DNA replication.

So am I correct on my assumptions?

Edit in response to the answer below:

It's known that replication of the eukaryotic DNA is faster in this case (where DNA molecules are of equal length) because eukaryotes have linear chromosomes whereas prokaryotes have circular ones

If it makes sense to form a sentence like this, presenting linearity as the cause, then it's enough to satisfy my definition of directly affected in this case. For example, it's easy to make this claim if you present the number of origins of replication as the cause. I looked at the textbook you mentioned and the quantity of origins of replication is in fact mentioned this way.

Conclusion:

I went ahead and did a bit more reading in that textbook. What I've understood is: An eukaryotic linear chromosome has multiple replication origins rather than a single one in order to compensate for its much larger size. So while the shape might be a factor (possibly, not certainly), the primary and "direct" reason is the difference in size, not the shape.

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    $\begingroup$ The current Wikipedia entry has modified this to "In an organism with a very large genome, circular chromosomes could potentially cause problems relating to torsional strain.[citation needed]". The much more cautious language presumably reflects the lack of citation in support of the postulated effect of torsional strain. Naively I would imagine less torsional strain in a larger circular chromosome, but in any case, there is no evidence presented that torsional strain is actually relevant. $\endgroup$
    – David
    Jul 6, 2020 at 10:13
  • $\begingroup$ @David Yeah, I agree that it's definitely not a highly credible claim the way it currently stands. But still it doesn't directly matter for the real question since it was only a (somewhat baseless) idea for why circularity/linearity might not have a direct impact on the speed of replication. $\endgroup$
    – Ved
    Jul 6, 2020 at 15:52
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    $\begingroup$ I'll see if I can find anything about this when I have a moment. As you may be aware, many closed circular DNA genomes are replicated by the rolling circle method — which in itself may have different characteristics to the standard replication method. $\endgroup$
    – David
    Jul 6, 2020 at 16:01
  • $\begingroup$ @David Thanks. I guess if we consider the method of replication as well that might further complicate reaching an answer. It looks like this question does require generalizing and neglecting a bit to reach any answer at all. $\endgroup$
    – Ved
    Jul 6, 2020 at 17:06

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I am not sure if I well understand what you mean by directly affected.

I will list some possibilities below (For reference you can see any genetics textbook, I use, Genetics: A conceptual approach by Pierce, but I guess any textbook would do).

  1. Porkaryotic polymerases (usually processing circular DNA) have a higher nucleotdie per second speed than eukaryotic polymerases (processing linear DNA). Does this mean that shape directly affects speed? In this case I would say no. It's just a difference between prokaryotic and eukariotic polymerases. Some prokaryotes have linear chromosomes and their polymerase will still be faster than eukaryotic polymerases.

  2. One prokaryotic chromosome has only one origin of replication, while one eukaryotic chromosome has several of them, so that eukaryotes parallelize even in a single chromosome. Does this mean that shape directly affects speed? In this case, I would say yes. Due to steric effects, the shape of the chromosome has to do with the ability of having several origins of replications, even if the lengths are the same. Edit: After Ved's comment, I realized that this is also not necessarily true. Not all circular chromosomes have one single origin of replication; archaea have circular chromosomes with more than one origin of replication

  3. Linear chromosomes are easier to unwind. Does this mean that shape directly affects speed? I would say, yes for large chromosome and no for small chromosomes. Edit: After David's comment, I realized that I am not really sure that linear chromosomes are easier to unwind. A Wikipedia entry states this, but I gave a look at the paper they referenced and found no real statement about this.

Importantly, if the DNA molecules you compare are one prokaryotic and one eukaryotic and they are very short, I would bet my 5 bucks on prokaryotic (circular) being faster, because in absence of all the parallelization the eukaryotic DNA polymerases are slower than prokaryotic ones.

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    $\begingroup$ Could you provide a reference or detailed mechanical argument in support of your assertion that linear chromosomes are easier to unwind. This would seem to be the crux of the matter. What you say and what you would bet is not the point. The Wikipedia entry acknowledges lack of support for this sort of assertion. Please provide it if you want your answer to be considered seriously. $\endgroup$
    – David
    Jul 6, 2020 at 20:23
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    $\begingroup$ Well in that case, could you provide a reference for steric effects affecting the quantity of replication origins? I looked at two textbooks but couldn't locate anything relevant. $\endgroup$
    – Ved
    Jul 7, 2020 at 9:34
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    $\begingroup$ While I was looking for a reference to support the steric effects affecting quantity of replication origins, I actually found out that archaea have circular chromosomes and more than one origin of replication. I edited my answer to incorporate this. $\endgroup$
    – Fabio Marroni
    Jul 7, 2020 at 10:09
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    $\begingroup$ While the question may not have gotten a definite answer (might be impossible anyway), I think the findings here are indication enough to reach some conclusion at least: It's not possible to generalize and say that the shape of DNA will certainly have an effect on the rate of replication. Number of replication origins on the other hand seems to almost certainly always have a direct effect on the rate. I will mark this as the answer, thanks. $\endgroup$
    – Ved
    Jul 7, 2020 at 10:18
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    $\begingroup$ I agree that it may be impossible to generalize. But I want to point you to this paper I just found: ncbi.nlm.nih.gov/pmc/articles/PMC6056714 . Give a look at the "separation mtDNA" section. It deals with the structural problems with the circular mtDNA, and also references some work on prokaryotes. Maybe it will not answer your question, but it may be useful for information. $\endgroup$
    – Fabio Marroni
    Jul 7, 2020 at 10:26

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