Cassette tape portrait of Jimi Hendrix by Erika Simmons
A cassette tape portrait of musician Jimi Hendrix from the “Ghost in the Machine” series by Erika Simmons. DNA, much like a tape, contains the identity of an organism (or musician). In this post, I talk about what happens when the “DNA tape” jams the cellular “tape deck”.

Deoxyribonucleic acid, more broadly known as DNA, is the blueprint of life. In humans, animals, and bacteria alike, it is used throughout the whole existence to run the shop. Making blood cells, producing nerve cells, regulating where to put an arm, where not to put a leg etc. Hopefully, before the end of its term, a life form would manage to pass on the DNA to an offspring, and the whole cycle starts over in the next generation. In short, DNA is pretty crucial to life, small or tall, complex or simple. Things get, let’s say, “interesting” once DNA is put at jeopardy. If you still know audio and video tapes, you will remember the hassle a knot, twist, or crack could cause. In this post I talk about how bacteria coordinate the clearing of “DNA tape” jamming their cellular “tape deck” – the topic of an article that David Albrecht, Michael C. Mackey and me recently published.

Kid: “Damn cassette player. Jammed by the bunched-up tape, nothing moves anymore.”

Well, that’s a little bit of a situation there. But, much worse, the same can happen to DNA. Physical damage to DNA molecules is frequent, and mostly it can be repaired on time to prevent any jamming of the “DNA tape deck”. If there are too many “knots” in the DNA, the production of molecules important for the cell stalls, and copying the “DNA tape” for cell doubling becomes impossible – the copy machinery simply stops at damaged positions.

Kid: “I will never get this fixed. Daddy, HELP!!! The tape deck, again.”
Father: “Okay sonny, I’ll get scissors and scotch tape.”

In 2005, Friedman and colleagues investigated this scenario closer in E. coli bacteria. Exposing the poor cells to increased doses of UV light, they could watch the cells’ response in a lot of detail. It was already known what roughly would happen: When too much physical damage (think “knots”, “twists”, or “cracks” in the tape) are caused by the UV light, the so called SOS response kicks in. Instead of carefully repairing the usually low number of damaged positions, the cells refute to more desperate measures: As in the case of the “helping” daddy called in by the desperate kid, the “DNA tape” gets patched together, filled in, and glued together with little regard to preserving the original content. This clumsy repair mostly makes the DNA practically useless,sometimes causes grotesquely mutated life forms, and very, very rarely gives something similar to the original life form. But, hey, the other option is no kids and slow death, so who wouldn’t understand?

Friedman and colleagues’ breaking news was a puzzling pattern in this “SOS response”. Instead of being activated when the damage is inflicted, and then shut off once the damage is cleared, the response is activated in pulses, or waves, recurring about every 30 minutes. For a panic, last resort response of an organism pushed to the edge, that seems quite well-refined. So, what was happening there?

Three SOS response waves after an UV irradiation dose of 50J/m². Friedman et al. experimental results.
Three SOS response waves after an UV irradiation with a 50J/m². Friedman et al. experimental results.

Friedman and colleagues already proposed that there should be a precise regulation mechanism at work. Intuitively, that makes a lot of sense – under normal conditions the rather crude patching and gluing together of DNA is not really helpful, and even under bad conditions, it should not be activated any longer than at all necessary. it did not take much longer, and the first explanations of the underlying control system came up. Krishna and colleagues gave a first theoretical account of what could be causing “those waves”. While the explanation was quite detailed, it went as far as explaining two consecutive waves – while the experiment clearly showed three waves.

So, sticking with the cassette player, let’s fast-forward to 2010. I am in Montreal, sitting in a Mathematical Biology course taught by Michael Mackey: “Now, when we increase the delay time τ in our model, the stable negative feedback loop becomes unstable, giving rise to persistent, periodic oscillations.” This was the answer – delayed negative feedback! What? Okay, let’s break this down a little…

Father: “So, should I fix the tape? I have the scissors and scotch tape here.”
Kid: “Eerrrmmhh, let me try a little more. Maybe you don’t have to cut it.”
Father: “Okay, but if it’s not working in five minutes I’ll do it.”
Kid: “I guess. It’s better than losing all the tape. Let me try first, but get the scissors ready in case.”

The SOS response gets the DNA tape back to working condition, yes. But, the price to pay is that it will likely sound really, really bad after. Still, unleashing the SOS response might be the necessary path of action to save the cell, or even its whole colony, from extinction. Here is a solution to this dilemma: a massive damage to DNA occurs and triggers the SOS response. Once triggered, the SOS “beast” gets worked up behind the scenes, while the more tame, regular DNA repair is working at the damage. With damage still persisting after 30 minutes, it is safe to say that the cell is headed for death without fast repair – the SOS repair gets unleashed onto the DNA. On the DNA, it either finds damage, which than gets repaired in the crudest ways possible, or all damage is gone, and it does – nothing. In either way, the alarming “heavy damage” signal is suppressed for some time, signaling that also the SOS response can be shut down for now. If there is more damage down the road, the cycle starts over and the next wave comes in.
This is the negative feedback loop – much damage signal, much SOS response; no damage signal, no SOS response. Delayed? Well, from signal to response, there is the grace period of a couple of minutes.

Father: “Good, now that it’s playing all smooth, I’ll get back to watching the match.”
Kid: “Thank you daddy, if it happens again later, can I call you again?”
Father: “Of course, it’s just going to take a moment till I’m ready.”

Sounds good so far? That’s what I thought. What came next: 1) Days of mad coding, 2) humiliating/insightful discussions of the biological background with with my dear Biochemist friend David Albrecht of the ETH Zürich, 3) a couple of meetings with Michael Mackey. And, there they were: Persistent, periodic waves of SOS repair activity, exactly as observed from experiment. A few more weeks of writing, a remarkably fast review and publication process over at Molecular Biosystems, and it saw the light of day: Small delay, big waves: a minimal delayed negative feedback model captures Escherichia coli single cell SOS kinetics.

Model results published in Molecular Biosystems, DOI: 10.1039/c1mb05122a.
Model results published in Molecular Biosystems, DOI: 10.1039/c1mb05122a, click image for original article.

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