Fishy Clue Helps Establish How Proteins Evolve
- From: VoiceOfReason <papa_fox57@xxxxxxxxxxx>
- Date: Sat, 7 Feb 2009 04:22:18 -0800 (PST)
Fishy Clue Helps Establish How Proteins Evolve
Three billion years ago, a "new" amino acid was added to the alphabet
of 20 that commonly make up proteins in organisms today. Now
researchers at Yale and the University of Tokyo have demonstrated how
this rare amino acid - and, by example, other amino acids - made its
way into the menu for protein synthesis. The study appeared in the
December 31 advance online publication of the journal Nature.
The rare amino acid the Yale researchers studied, pyrrolysine (Pyl),
gave the researchers a molecular handle by being an extreme example of
an amino acid that evolved to serve a highly specific need.
The amino acid alphabet shapes the language of proteins. When the
genetic code was deciphered four decades ago, scientists believed that
there were no more than 20 amino acid "letters" that universally
meshed with the nucleic acid part of the protein code. But, like many
alphabets, the language of proteins has letters with modifications -
like accent marks - that modify their use.
When cells make proteins, a tightly coordinated pair of molecules - a
tRNA and a tRNA synthetase - ensure that the correct amino acid is
added in a growing protein chain. These molecules are highly specific
for the amino acid they "manage" and are coded directly in the genome.
All of the 20 common amino acids are incorporated into proteins in
this way. However, only two uncommon amino acids, including Pyl, have
been discovered that follow this pattern.
In most cases, an uncommon amino acid in proteins - like letters with
accent marks - results from modification of one of the standard 20
amino acids after it has become part of the protein. Many human
proteins are modified in this way, and deficiencies in these
modifications are linked to myriad human diseases including cancer,
neurodegeneration, and metabolic disorders.
"Pyl turns out to be special because it represents an uncommon amino
acid that is incorporated during normal protein synthesis," said Yale
postdoctoral fellow and lead co-author Patrick O'Donoghue. "This is
the key difference that makes Pyl so interesting and valuable to
molecular biologists. It opens the door to engineering the genetic
code."
Pyl is so rare that it has been found in only seven organisms. Each of
these microbes evolved in an unusual environmental niche and all use
methylamines - the compounds that make fish smell "fishy" - as a
source of energy. Soll's research team characterized and crystallized
the molecules that "manage" Pyl and created images that show how these
molecules have evolved to work together.
"This is the handle we needed to effectively produce an 'expanded'
genetic code," said O'Donoghue. "Now we have the ability to directly
genetically encode other uncommon amino acids. By doing that, we will
be able to isolate the role of particular modifications and to begin
to understand their functions and their role in human disease."
"We have found why it is probably not accidental that out of more than
300 amino acids found in natural proteins, only two have been added
beyond the standard 20-member amino acid alphabet," said principal
investigator Dieter Soll, Sterling Professor of Molecular Biophysics
and Biochemistry and professor of chemistry at Yale.
"This work provides a tantalizing glimpse into how proteins have
evolved in living cells," said Laurie Tompkins, who oversees protein
synthesis grants at the National Institutes of Health's National
Institute of General Medical Sciences, which partially supported the
work. "The unique way in which the synthetase binds its tRNA substrate
is a testament to the ancient roots of this remarkable enzyme."
http://www.terradaily.com/reports/Fishy_Clue_Helps_Establish_How_Proteins_Evolve_999.html
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