It’s an RNA world

Last Thursday, Jack Szostak, a Nobel laureate in Physiology or Medicine 2009, delivered a lecture titled The Origin of Cellular Life here in Karolinska Institutet, in the same hall where the Nobel prize in Physiology or Medicine is announced every year (fun fact for non-KI people: Nobels forum is situated at… you guess it, Nobels väg 1).

The lecture announcement did not go into the details, but I was pleasantly surprised that Szostak mainly discussed about RNA biochemistry, which is right up my alley. Several of my projects involves RNA systems, and I have a colleague in the group who closely looks at RNA structural models. RNA is really a fascinating biomolecule to study. Why, you ask? I will list for you some fun facts about RNA, along with several things that Szostak mentioned in his lecture:

  1. RNA has much more diverse structures compared to DNA. That extra 2′ hydroxyl is an extra electron pair donor (or two) and more hydrogen bonding and metal ion bonding is possible. DNA secondary structure is usually just the double helix, but RNA can be found as a single strand, hairpin, junction, bulge, loop; and forms complicated tertiary structures like tRNAs and the ribosomal RNA.
  2. RNA is less stable than DNA. The extra hydroxyl makes it more prone to hydrolysis. Also, RNases are produced by human skin as defense mechanism against RNA viruses, making it a pain in the ___ for scientists who do experiments with RNA.
  3. RNA world hypothesis. RNA has been hypothesised to be the ancient information storage, self-replicating and catalytic molecules before DNA and protein came along. Consider the ribosome, an ancient machinery which is a complex of proteins and RNAs: it is thought that the proto-ribosome was all RNA and parts were gradually replaced by proteins.
  4. The nucleic acid building block ribonucleoside triphosphate as we know it today seems to be modern. When no protein enzymes were available, replication has to done non-enzymatically with high-energy monomers. Szostak’s group has shown that ribonucleoside phosphoromethylimidazolides can undergo template-directed polymerisation without polymerase (PDF of paper here).
  5. Phosphodiester linkage problem. Since RNA has 2′ and 3′ hydroxyls, phosphodiester linkage is possible for either. The polymerase will direct 5′ to 3′ linkage, but what about before polymerase evolved? Szostak’s group synthesised a ribozyme with random 5′-2′ or 5′-3′ linkages and found that it is still biologically functional. This surprising finding challenges the deep-seated assumption that homogeneity of 5′ to 3′ phosphodiester linkages are structurally needed to perform the ribozyme’s function. Random linkages actually introduce flexibility to the structure and this might even be beneficial for the molecular evolution of RNA.
  6. Why 4 base letters? Szostak mentioned that with 4 letters it is easy to generate structures with single energy minimum; while with 2 or 3 letters, there are more structures that are energetically degenerate. The RNA also has a diverse set of base modifications, especially in tRNA and ribosomal RNA, while for DNA, methylation seems to be the most common modification.
  7. Distinguishing base pairs. The two base-pairs A:U and G:U are energetically close and this might be problematic in prebiotic life (higher incorporation error rate). One solution might be base modification from U to 2-thioU; the basepairs now have larger energy difference. Szostak also compared the geometries of A:U and A:2-thioU and they are nearly identical.
  8. Special ions. Due to the negatively-charged phosphate backbones, RNA often needs divalent ions (usually Mg2+) to stabilise the tertiary structures. Ask a crystallographer who works with ribosome and they will tell you that ribosome will not crystallise if the Mg2+ concentration is too low. But again Szostak points out a problem in the context of prebiotic chemistry: too high Mg2+ concentration will disrupt the membrane. Szostak’s group screens many small molecules to find something that will keep the divalent cations in check while preserving RNA and membrane structures. The result? Citrate was found to be a good chelator to Mg and protects the vesicles. It’s at least a proof of concept.
  9. The RNA society. No, no this not an Illuminati-type secret society that uses eugenics for world domination (hopefully?). They are researchers who devote their life (and grant money) to the study of RNA. Their upcoming meeting is this summer in Kyoto! Locally here in Stockholm, there is also Stockholm RNA club, which was founded by a KI student in 2012.

I left out a couple of things from the lecture but #4-8 is pretty much the bulk of the lecture. There was a lot of biochemistry in the lecture, and I find it interesting that it is applied to try to trace molecular evolution of RNA from prebiotic times. All in all, it was a privilege to attend this lecture.

If you want to know more about nucleic acid at structural level, KI offers a doctoral course Principles of nucleic acid structure, which I took last term. I can attest that it is an excellent course!

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