How Thermophiles Survive, Part II: DNA

on 2nd of September, 2009 in PCR & Real-time PCR
About the Author:
I'm a writer, editor, and communications consultant, specializing in biotech, life sciences and healthcare. I've worked for the Salk Institute, Life Technologies, Amgen, academic institutions, startups, non-profits and consulting firms. I've got a BA from the University of Pennsylvania, and a MS in biotech management from the University of Maryland.

In part I, I answered the question, "How do proteins in thermophiles survive under high temperatures?"

In this part, I'll look look at how nucleic acids survive -thrive, even- in conditions that are too hot for most of us, but ideal for a number of organisms, including the one that gave us Taq polymerase and ultimately, PCR.

Proteins managed to adapt to high temperatures using a number of very small, simple chemical tweaks. Nucleic acids, it turns out, also survive using some small changes, but some novel molecular adaptations have occurred, too.

"Normal" DNA is denatured at high temperatures, whereupon the molecule loses its double helix structure and literally unzips into two separate strands.

Here's how thermophiles avoid that situation:

By not being a eukaryote

All thermophilic organisms are prokaryotes, or in the case of archaea, more prokaryotic than eukaryotic. No eukaryotic organism, with its accompanying internal membranes, nucleus, and organelles, has been found above 60°C. In fact, most thermophile genetic material resembles a plasmid.

By getting lots of K+

Salts like potassium and magnesium are found at higher levels in thermophilic archaea. These salts protect double-stranded DNA from phosphodiester bond degradation.

By generating novel polyamines

Working similarly to potassium and other salts, polyamines also protect against degradation. Studies on T. thermophilus revealed several novel polyamines, found only in thermophiles.

By making more reverse DNA gyrase

This enzyme catalyzes positive supercoiling of closed circular DNA. Positively supercoiled DNA appears to resist degradation more than negatively supercoiled DNA.

By using a primitive histone?

An interesting finding among thermophiles was the existence of histone-like proteins. They look a lot like eukaryotic histones; they wind DNA into tight structures that look like nucleosomes, and appear to keep DNA double-stranded at high temperatures. Tiny DNA-binding proteins, such as Sac7d found in archaea, bend DNA and increase its degradation temperatures. Molecules like Sac7d may represent the earliest stages of histone evolution.

How hot is enough?

How hot does it have to get to eliminate life? Obviously, life can exist above the earlier assumptions of 80°C. Some suggest 140-150°C, but undersea hydrothermal vent studies show evidence of prokaryotic existence in vents that have been recorded at 350°C! No evidence of oven mitts, though.

References:

Madigan, M.T. & Oren, A. (1999). Thermophilic and halophilic extremophiles. Current Opinion in Microbiology, 2, 265-269.

Terui, Y., et al. (2005). Stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, Thermus thermophilus. Biochem. J. 388, 427-433.

Grosjean, H. & Oshima, T. (2007). How nucleic acids cope with high temperatures. In Gerday, C. & Glansdorff, N., eds. Physiology and Biochemistry of Extremophiles. Washington, D.C.: ASM Press. 39-56.

3 thoughts on “How Thermophiles Survive, Part II: DNA”

  1. qetzal says:

    Interesting stuff! One question though: did you really mean to say that things like salts, polyamines, and Sac7d protect DNA from degradation (i.e. chemical breakdown), or should that really be denaturation (strand separation)?

  2. Andrew says:

    Hey, thanks. I think I need to (using poker terms) call a degradation and raise you a denaturation! For salts and polyamines, they're keeping the phosphodiester and other bonds along each strand together (protecting against degradation in those cases). But for histone-like structures and supercoiling, it's preventing denaturation. I'll go in and change that.

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