Swiss Researchers are looking several billion years back in time,
when life on Earth was just beginning to examine how a primitive protein
was able to evolve. The journey into the past also afforded the
scientists a glimpse into the future of synthetic biology.
The first primitive life forms that developed on Earth around four
billion years ago had little in common with today's organisms. They
probably managed without proteins. And the first proteins that formed in
the following few hundred million years to become essential elements of
the living world also differed from those of today: scientists assume
that the first proteins were composed of a reduced repertoire of only
seven or eight different amino acids.
Apart from the twenty universal amino acids, a more complex
incorporation mechanism allows the use of a twenty-first amino acid
called selenocysteine. It is found in many living organisms, including
humans. In certain microorganisms, the archaea, there is even a
twenty-second amino acid: pyrrolysine. This leads scientists to conclude
that the genetic code has continued to evolve over the last billion
years.
"Evolution obviously isn't over. It could well be that additional
amino acids will be incorporated into the code in due course," says
Donald Hilvert, a professor at the Laboratory of Organic Chemistry at ETH-Zurich.
The repertoire of today's proteins, however, typically contains
twenty amino acids. A team of researchers headed by Hilvert, a professor
has simulated how the minimal starting amino acid repertoire might have
expanded in the course of evolution. Not only do the researchers draw
conclusions regarding the past from their work, they also gain important
insights into future directions for synthetic biology.
The ETH-Zurich researchers conducted evolution experiments with a
synthetic protein they developed some years ago in their lab. It is
based on an enzyme that actually exists, a so-called chorismate mutase.
While the real enzyme is composed of all twenty amino acids, however,
the synthetic protein contains a reduced repertoire of only nine.
"Our synthetic chorismate mutase has the same function as its natural
counterpart, but is less stable and less active," says Hilvert. The
scientists have now examined how far the simplified protein can be
optimised and how exactly it behaves if it is allowed to expand the
amino-acid repertoire – just as it may have occurred during millennia of
evolution. To this end, they introduced the corresponding gene for the
protein into bacteria that do not contain a natural chorismate mutase
and allowed the bacteria to grow in a bioreactor for one and a half
months.
In the course of this experiment, mutations naturally arose in the
genetic material. The researchers then studied the extent to which the
synthetic protein and its gene had changed. Both the gene and the
protein were altered in the experiment – only marginally but with major
effects: the enzymatic activity of the protein and its stability
increased. The fact that the changes in the sequence of amino acids were
comparatively minor surprised the scientists. While the protein
consists of roughly 100 individual amino acids, only two of them
changed.
At one site, the amino acid isoleucine was replaced with the amino
acid threonine, and at another site leucine with valine. "Structurally
speaking, these are only very minor changes. The new amino acids aren't
all that different from the ones they replace," says Hilvert.
The scientists would have expected a greater number of more
significant changes. "Even if the two mutations are very conservative,
we were able to show that they give the protein a clear selective
advantage," explains Hilvert.
The work of the ETH-Zurich scientists not only affords a glimpse into
the history of evolution as it might have occurred almost four billion
years ago; the researchers were also able to draw conclusions from it of
relevance to synthetic biology. Part of this research field involves
expanding the functionality of proteins and organisms through molecules
that do not exist naturally.
Today, synthetically produced enzymes are already used in medicine
and industry. In the future, not only might these contain the typical
twenty natural amino acids, but also additional synthetic ones. The hope
is that a larger repertoire will provide more possibilities in the
design of artificial enzymes, such as with regard to their catalytic
functionality. Moreover, enzymes made of synthetic amino acids are
expected to be broken down more slowly in the body or a manufacturing
process, which could be very beneficial for certain medical or
industrial applications.
"One lesson from this project is that you shouldn't consider only
spectacular synthetic amino acids in developing the amino-acid
repertoire further in synthetic biology," says Peter Kast, a professor
at the Laboratory of Organic Chemistry, who was also involved in the
project. "Amino acids with minor differences from natural ones also
proved to be very useful."
In fact, the genetic code upon which all present life on Earth is
based would permit more than the twenty universal amino acids it
contains. After all, the individual amino acids of proteins are encoded
at the genetic level by a sequence of three so-called nucleotide bases
(a base triplet) each. The alphabet of the genetic substance DNA
contains four different bases and the number of possible triplets from
these is sixty-four (four to the power of three). With the genetic code,
up to sixty-four different amino acids could therefore be described.
Instead, nature "only" programs a limited set of twenty amino acids and a
redundant code: typically, individual amino acids are each described by
several triplets.
But why? One reason is probably that this redundancy cushions the
impact of mutations in the DNA, which was evidently an advantage during
evolution. "With the repertoire of twenty universal amino acids,
evolution achieved a momentary optimum," says ETH-Zurich Professor
Donald Hilvert.
For more information: Muller, M. et al. Directed Evolution of a Model Primordial Enzyme Provides Insights into the Development of the Genetic Code. PLOS Genetics, 2013, 9: e1003187, doi: 10.1371/journal.pgen.1003187 Journal reference: PLoS Genetics
Image credit: With thanks to our friends at Gizmodo: http://gizmodo.com/a-giant-leap/
Source: The Daily Galaxy via ETH Zurich
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