Origins of Life: General RNA Polymerases

ResearchBlogging.org

Yesterday, I discovered a new set of studies that I had not previously known about.  I may write about all of them, but I definitely want to talk about this particular study for two reasons.

 The first reason is that it shows some additional evidence that the RNA World hypothesis is feasible.  By that, I mean that there is no physical and chemical reason why things that need to occur during the transition from inorganic molecules to life cannot occur.  Also, this paper shows that a needed step, ribozymes (RNA strands that also catalyze reactions) that can build other long chain ribozymes can exist.

 I will say that this is not a paper of the ‘we dumped a bunch of stuff together to see what happens’ variety.  The authors had a specific goal and used a variety of techniques to establish that goal.

 This brings up the second reason that I want to talk about this paper.  In it, the authors describe the reason for what they want to accomplish.  Then they talk about the problems surrounding the goal and the end result.  Then, they develop a whole new technique to solve those problems.  Only after that, do they actually start looking at the problem in detail.

 And that, ladies and gentlemen, is what science is all about.  It’s not just answering these kinds of questions.  It’s also about figuring out how to even begin to answer these questions.  How to deal with the problems in answering questions.  How to prevent issues from impacting data and analysis.  This is a process that few people, even some graduate students in science fields, just don’t get.

 You can’t just sit down, do some experiments and get an answer.  You have to figure out what you’re going to observe and measure, how to observe and measure it, and only then can you actually start an experiment.

With all that, I give you “Ribozyme-Catalyzed Transcription of an Active Riboyzme”

 An important point in the RNA World hypothesis is that an RNA must be found that can synthesize a long chain RNA molecule, preferably one exactly like itself.  (I’ve talked about such a system before.) However, a general replicator would be useful too.  An RNA that could assemble many other ribozymes.

 The authors started with the general RNA polymerase R18.  While R18 is a general polymerase, it can only make 14 nucleotide polymers and it is limited in terms of the template.  So, starting with that, the authors applied evolutionary principles to encourage changes that would increase the function of R18.

 They took the resulting strands and combined some of the best features into a completely new strand, tC19Z.  The Z and C19 were evolutionary offshoots of the original R18, each with improved function over R18.  Some specific changes were engineered by the authors to C19, resulting in tC19, which, when combined with some of the evolved aspects of Z resulted in a very powerful RNA polymerase.*

This is the length of nucleotide change that each version produces:

  •  R18 – around 14 nucleotides (from a specific template)
  •  C19 – roughly 18-19 nucleotides
  •  tC19 – up to around 95 nucleotides

The Z strain of RNAs resulted in high fidelity and greater template generality (meaning it could copy just about anything).  In all cases, tC19Z performed more effectively on longer template sequences than any of the previous versions (R18, Z, tC19).

But could tC19Z synthesize a modern, functioning, catalytic ribozyme?  The authors attempted this with a hammerhead nuclease ribozyme.  It worked.  tC19z could manufacture the hammerhead ribozyme.  Further the resulting ribozymes all showed catalytic activity.

So, there is an RNA that can construct long chain, catalytic RNAs. 

 Again though, what I find interesting (and tellingly not found in some other works) is that the authors first listed the problems that they had to solve before even beginning this work.

They listed 3 issues

  1. evolution of RNA polymerase ribozymes is difficult because of poor extension ability (it’s hard for the polymerase to make longer chain RNAs)
  2. The evolutionary selection is further complicated by the usual need for a powerful polymerase, which is so much more efficient than the ones that are trying to evolve that it masks everything else.
  3. The difficulty in distinguishing between real template based polymerase activity and other similar processes that might have similar results (in other words, how can we tell this is doing what we think it’s doing?)

The authors examine these problems and have developed a strategy that mitigates each of them.  I won’t get into the details of the strategy (because honestly, it’s a few organic chem courses beyond me), but the main point is that the authors identify and acknowledge potential problems and develop methods to deal with those problems. 

 This is an important, yet often overlooked area of science and many people would do well to follow this path.  Identify the problems (before someone else publically and loudly identifies them for you).  Then figure out how to mitigate those problems.  Then and only then can the results be considered useful and accurate.

 Finally, I’d like to thank Dr. Phillipp Holliger of the Medical Research Laboratory for his assistance in my project.

 * Please remember that this was not an experiment to see if this system could evolve naturally.  The point is whether such and RNA polymerase could exist at all.

___________________________________

Wochner A, Attwater J, Coulson A, & Holliger P (2011). Ribozyme-catalyzed transcription of an active ribozyme. Science (New York, N.Y.), 332 (6026), 209-12 PMID: 21474753

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