Ligase ribozyme

Ligase Ribozymes

RNA Ligase ribozymes are the first of several types of synthetic ribozymes produced by in vitro evolution and selection techniques. They are an important class of ribozymes because they catalyze the assembly of RNA fragments into phosphodiester RNA polymers, a reaction required of all extant nucleic acid polymerases and thought to be required for any self-replicating molecule in a pre-biotic RNA World.

Context

The "Central Dogma" of molecular biology (an idea formulated by Francis Crick) is that DNA makes RNA which then is used to make proteins.

DNA ---> RNA ---> Protein

Information flows from left to right. DNA is what genes are made of. Proteins do a lot of stuff, like make structures (muscle fibers, for example), are receptors on the surfaces of cells, and are enzymes, that catalyze chemical reactions of biological importance (eg: metabolic enzymes digest sugars and liberate energy, releasing CO2 in the process).

Irreducible Complexity?

If you are worried about how life originated, this creates a bit of a problem:

# You need proteins to copy the DNA.
# You need DNA to code for (and ultimately to make) proteins.

So which came first?

This is an example of what Creationists have termed "irreducible complexity"; there seems no way out of this conundrum except to invoke divine intervention (or creation).

A Seminal Discovery

Then, in the early 1980s, Sidney Altman, Thomas Cech and Norman Pace discovered that some RNAs could also be enzymes. This provides a potential way out of the difficulty.

RNA is much like DNA, except a bit less stable. (DNA is a better long-term information storage devise, and RNA, though less stable, is easier to get information out of, so DNA is first "transcribed" into RNA, which shares a similar four-letter alphabet, and is then "translated" into proteins.)

So if RNA can be both an information-storage molecule, and an enzyme (or "ribozyme"), it is a good candidate for the first self-replicating molecule, and it gets us out of the above-mentioned Catch-22.

Theories of the origin of life that start out with an assumption that the first self-replicating molecules were ribozymes are called RNA World hypotheses. This isn't the only idea for how life originated, but it is probably the most favored one currently.

Another Major Problem

But there's a catch.

In order to copy RNA, fragments or monomers (individual building blocks) that have 5'-triphosphates must be ligated together. This is true for modern (protein-based) polymerases, and is also the most likely mechanism by which a ribozyme self-replicase in an RNA World might function. Yet no one has found a modern natural ribozyme that can do this reaction.

In vitro Evolution and Selection

RNA in vitro evolution or SELEX enables the artificial evolution and selection of RNA molecules that possess a desired property, such as binding affinity for a particular ligand or an activity such as that of an enzyme or catalyst. The first such selections involved isolation of various aptamers that bind to small molecules. The first catalytic RNAs produced by in vitro evolution were RNA ligases, catalytic RNAs that join two RNA fragments to produce a single adduct.

RNA test tube (in vitro) evolution and selection has thus enabled several research groups to discover RNA sequences that can in fact catalyze the required chemical reaction for 5'-triphosphate RNA fragment ligation, and one group has even produced a functional RNA polymerase ribozyme. This provides a Proof of Principle that RNA is capable of such feats, and absent time travel, this is likely the best we will be able to do.

The ligase ribozyme family

Type 1 ligases

Type 2 ligases

From Ligase to Polymerase

The L1 Ligase: A simple Type 1 ligase

Michael Robertson and Andrew Elington evolved a ligase ribozyme that performs the desired 5'-3' RNA assembly reaction, and called this the L1 ligase. To better understand the details of how this ribozyme folds into a structure that permits it to catalyze this fundamental reaction, the X-ray crystal structure has been solved.

The L1 Ligase Ribozyme Crystal Structure

A Three-Dimensional Glimpse of The First Enzyme

So what we have here is basically [http://xanana.ucsc.edu/L1/jmol/ a three-dimensional photograph of the molecule] that shows where all the atoms are located. Seeing where the atoms are positioned in space helps us figure out how the ribozyme works.

More Information

Links:

* [http://www.sciencemag.org/cgi/content/full/315/5818/1549 The primary reference for the L1 Ligase structure]
* [http://www.sciencemag.org/cgi/content/full/315/5818/1507 An accompanying general audience Perspective] , authored by Gerald Joyce
* [http://xanana.ucsc.edu/L1/l1x6c.html More details on the Ligase Ribozyme] .