Friday, May 09, 2008

DNA Replication in E. coli: The Problem

 
I've started reading microcosm by my favorite science writer, Carl Zimmer [Buy This Book!]. Watch for a review, coming soon.

I was mildly disappointed to see Carl repeat a common myth about DNA replication in E. coli on page 29. Since we often use this myth to teach critical thinking in our undergraduate classes, I thought it would be worthwhile to discuss it here.

Today I'm going to present the problem and let everyone think about a possible solution. On Sunday, I'll publish the answer. (If you know the solution, you are not allowed to post it in the comments—I'll delete those comments. You can ask for clarification or speculate.)

Here's what Carl says at the top of page 29.
E. coli faces a far bigger challenge to its order when it reproduces. To reproduce, it must create a copy of its DNA, pull those chromosomes to either end of its interior, and slice itself in half. Yet E. coli can do all of that with almost perfect accuracy in as little as twenty minutes.
Today, we're not concerned about the 20 minute generation time but I note, for the record, that the average generation time of E. coli, in vivo, 1s about one day. I also want to mention that the 20 minute generation time is an extreme example that's achieved only under the most extraordinary circumstances. Typical generation times in the lab are about 30 minutes.

However, that's not the problem. Let's assume a generation time of 20 minutes.

In the next paragraph Carl says ...
The first step in building a new E. coli—copying more than a million base pairs of DNA—begins when two dozen different kinds of enzymes swoop down on a single spot along E. coli's chromosome. Some of them pull the two strands of DNA apart while others grip the strands to prevent them from twisting away or collapsing back on each other. Two squadrons of enzymes begin marching down each strand, grabbing loose molecules to build it a partner. The squadrons can add a thousand new bases to a strand every second.
What Carl is referring to the the assembly of replication complexes (replisomes) at the origin of replication. Once those complexes are assembled, replication fires off and proceeds in opposite directions (bidirectionally) until the two fork meet at the opposite side of the chromosome.



Carl is correct when he says that the forks move at 1000 nucleotides per second. Later on in his book he mentions that the size of the E. coli chromosome is 4,600,000 base pairs or 4,600 kb (p. 116). At 1000 nucs per second it would take 4600 second to replicate this DNA if there was only one replication fork. Since there are two, it will take 2,300 seconds.

You can do the math. This is 38 minutes. It is a correct number—it takes at least 38 minutes to replicate the E. coli chromosome, not 20 minutes as stated earlier. It is true that the generation time of E. coli can be as short as 20 minutes under extraordinary circumstances.

Here's the problem. How can E. coli divide faster than it can replicate it's chromosome?


19 comments:

  1. There can be only one answer, surely. If a bacterium has multiple copies of genome, it can divide without having to first replicate its genome.

    Just out of interest, though, what is the fastest normal replication time known among bacteria?

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  2. Larry: Nice one. Michael: close, but no cigar. You'll need to be more specific to get credit in my course or, I suspect, Larry's... ;-)

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  3. Today, we're not concerned about the 20 minute generation time but I note, for the record, that the average generation time of E. coli, in vivo, 1s about one day

    Another good question: Guess why the average generation time is about one day.

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  4. Can the new copies begin to replicate before they have finished replicating themselves? Can the daughter cells form with DNA that is already in the process of replicating?
    I guess generation time is highly dependent on the environment, resources, temperature, pH, etc

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  6. Perhaps these unusual examples of fast replication in lab have a mutation that gives them 2 or more origins of replication, enabling them to go faster.

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  7. From way out in left field... (past the bleachers and the parking lot)

    light-dark cycle as a factor in replication timing, ability to speed up dependent on if light-dark cycle is speeded up?

    (it would indeed be awesome if that were the trigger to the biochemical change inducing replication)

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  10. Nice! I used the same question when I taught Intro to Microbiology. It was one of those question I left them with to think about until next class.

    I am not a bacteriologist, but I always wanted to know (based on the answer to this question), if the genes required for rapid growth were located closer to the ORI. Using a gene dosage -> protein concentration argument.

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  11. (cough cough) Helmstetter (cough) Cooper (cough cough)

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  12. Another good question: Guess why the average generation time is about one day.

    How was the average generation time determined? What's the "average" environment for E. coli? How would you even measure that?

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  13. don cates for the win.

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  14. How was the average generation time determined? What's the "average" environment for E. coli? How would you even measure that?

    Another good question...

    Your digestive tract is a chemostat (w/ heterogeneous zones). In a chemostat, generation times are set by dilution rates, which in this case would be a function of the transit time for one's digestive system. How to measure transit time? Try a meal or whole corn kernels or beets.

    The "average generation time of 24hrs" figure was literally pulled out of someone's ass. YGMMV*.

    http://en.wikipedia.org/wiki/Chemostat

    *Your Gastrointestinal Motility May Vary.

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  15. Unsympathetic Reader, that was sheer greatness.

    I need to get a t-shirt with "chemostat" written on it and an arrow pointing at my gut.

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  16. Okay, I don't see how Michael's argument leads to sustainable division rates. But the idea does, as multiple genomes can be parallel replicated.

    Options along that line: multiple copies of genome (but presumably only one chromosome from the post) or equivalently multiple paired replication forks in parallel, or multiple paired replication forks in series. Or possibly both, to mess up the division thoroughly. :-)

    Hmm. I wish I could eliminate other options as "impossible" to follow Sherlock Holmes lead.

    Oh, and UR comment waz LOLasinine.

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  17. Well , the genome replication starts before cell division . So its possible

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  18. Yeh..explanation of "future origin" is talks it well..

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  19. I cultured unknown strains of E. coli and S. aureus in nutrient broth medium at 35 Degrees Celsius and the generation times were found to be 29 and 32 minutes respectively.

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