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The team reconstructed an ancestral enzyme by searching the database for the corresponding modern enzyme, calculated the original sequence using the obtained sequence, and introduced the corresponding gene sequence into the laboratory bacteria to produce the desired protein
.
This enzyme was then studied in detail and compared
with modern enzymes.
The research team, led by Prof.
Mario Mörl and Prof.
Sonja Prohaska, focused on an enzyme called tRNA nucleotide-based transferase, which attaches three nucleotide building blocks in the C-C-A sequence to small RNAs (tRNA) in cells
.
These tRNAs are then used to provide amino acids
for protein synthesis.
Through phylogenetic reconstruction, the team reconstructed a candidate enzyme for an ancestral enzyme that existed in bacteria about 2 billion years ago and compared
it to modern bacterial enzymes.
They found that the two enzymes worked with similar precision, but there were significant differences
in their responses.
Previously, scientists couldn't understand why modern enzymes often interrupt their activity, but this study shows that this tendency is actually an evolutionary advantage, a problem that has puzzled biochemists for decades
.
The enzyme of the ancestors is processed, that is, it works uninterrupted, but every now and then the nucleotide components
that have been correctly added are removed.
The results show that much can be learned about the evolution and properties of modern enzymes from the reconstruction of enzymes, and that many problems can only be solved through the interaction between bioinformatics and biochemistry – switching back and forth between computer calculations and laboratory experiments
.
Using genetic sequences, it is also possible to create an evolutionary phylogenetic tree
of bacteria.
Starting with the broad biodiversity in today's species tree, the evolutionary paths of individual genes can be reconstructed along relationships and branches, and painstakingly traced back to a common origin
.
Rebuilding is basically a three-step process
.
First, the corresponding modern enzyme is searched in the database to be able to examine the sequence
of amino acid building blocks.
The resulting sequence can be used to calculate what the original sequence should look like
.
The corresponding gene sequences encoding the old enzymes are then introduced into laboratory bacteria to form the desired proteins
.
The enzyme can then be studied in detail to determine its properties and compare them with
modern enzymes.
Prohaska recalls: "It was a breakthrough
when news came from the lab that the reconstituted enzyme could do C-C-A additions, and it could do so over a wider temperature range than the enzymes do now.
"
Like living organisms, enzymes are being optimized
in evolution.
The stronger the binding of the enzyme to the substrate, the faster and better
the catalytic action of the enzyme is usually achieved.
The reconstituted progenitor enzyme does exactly that, grabbing the substrate tRNA and ligating three C-C-A nucleotides one after the other without letting go
.
Modern tRNA nucleotidyl transferases, on the other hand, are dispersed, i.
e.
they work in stages, during which they repeatedly release substrates
.
However, they are more efficient and faster
than their ancestors.
This confused
the researchers.
Why do modern enzymes keep abandoning their substrates? The explanation lies in the phenomenon of reverse reactions, in which the merged nucleotides are again removed
by the enzyme.
While the strong binding of the ancestral enzyme to the substrate led to subsequent removal, the reverse reaction in modern enzymes is almost completely blocked
by the release of the substrate.
This makes them more productive than their predecessors
.
Mörl said: "We are now finally able to explain why modern tRNA nucleotide transferases work
so efficiently despite their distributed nature.
This discovery was completely unexpected for our team
.
We didn't expect this to happen
.
We had this question 20 years ago, and now we can finally answer it
with bioinformatics reconstruction.
This close cooperation between bioinformatics and biochemistry has been around in Leipzig for several years and is not the first time it has proven to be a huge advantage
for both parties.
”
References:
Substrate Affinity Versus Catalytic Efficiency: Ancestral Sequence Reconstruction of tRNA Nucleotidyltransferases Solves an Enzyme Puzzle.Molecular Biology and Evolution
