Science News - February 12, 2011

Today, every protein found in the
cells of every organism has to originate
in a DNA or RNA blueprint, as far as
biologists can tell. But making DNA and
RNA — and proteins — requires proteins.
This chicken-and-egg conundrum has
flummoxed scientists for decades. In the
1980s, researchers discovered a particular
type of RNA called a ribozyme that may be
capable of making itself by catalyzing its
own synthesis. Many believe the ribozyme
could be the chicken and the egg — boost-
ing the popularity of what has been known
as the “RNA world hypothesis.”
Working in this context, biochem-
ist Michael Yarus of the University of
Colorado at Boulder imagines different
amino acids being chemically attracted
to different strands of RNA.

To test the idea, Yarus and colleagues mounted eight amino acids into test tubes and washed the molecules with a solution containing many RNA snippets. Though the interactions in general are weak, Yarus found that many amino acids have natural docking bays for the sequences of three nucleotides that encode them today. He and colleagues estimated in 2009 in the Journal of Molecular Evolution that there is a one in 1044 chance that the triplets occur at binding sites by pure chance. He suspects that about three-fourths of amino acids currently in the code entered via chemical attraction.

“If you think the triplets were not involved in binding amino acids, then you have to argue that this is all some mistake, some joke nature is playing,” Yarus says.

In his chemical theory, it would be inevitable that certain letters end up coding certain amino acids, like how the word for a cow’s vocalization is moo because that is what the cow sounds like. Any life evolving under similar conditions — say on an extrasolar planet — would thus have a similar code.

“My prediction is if life’s out there, it
has a similar core,” Yarus says. “That will
be a great day when we find out.”
In November, Wentao Ma of Wuhan
University in China proposed a model
in Biology Direct for how to get from
Yarus’ simple bonding scheme to today’s
sophisticated reality. But the proposal

now needs evidence to back it up, and some researchers point out that no one has been able to make the ribozyme, a key player in the RNA world, grab the specific amino acids that match up with its nucleotides. Instead, the ribozyme makes up random definitions for genetic words, like in the game Balderdash.

Freeland thinks, because of these major roadblocks, the RNA world may have already passed its prime. “The concept is simply we don’t know anything that can make RNA and use it as a living system,” Freeland says.

He says it’s just as believable that some earlier organism, not directly related to current life on Earth, invented RNA. In that case, scientists would have to go back even farther in time to make sense of the code.

Paying attention to proteins

Going back in time is exactly what researchers at the Georgia Institute of Technology in Atlanta are trying to do in two new approaches.

Biochemist Loren Williams has turned to the ribosome, that cellular factory where proteins are made. Scientists know that some RNA in the ribosome is very densely connected to other RNA through hydrogen bonds, suggesting those RNAs are among the oldest —the way people who have been on Facebook awhile have more friends than those who just joined. By looking in regions with dense connections, Williams has found what he argues is the oldest protein inside the ribosome. The protein’s tail is made of glycine and alanine, Williams and his colleagues recently found, leading them to think that these amino acids may have been the first to join the code.

A second approach, which involves resurrecting ancient proteins, may offer a good test for theories about the code’s origins. Astrobiologist Eric Gaucher, also of Georgia Tech, and his colleagues are comparing individual proteins in different living organisms to try to estimate a most likely protein ancestor, going back billions of years.

By studying how amino acids (lysine in
green) bond with RNA snippets (gray),
scientists may uncover chemistry’s role
in shaping the early genetic code.

Such ancient molecules can provide clues about which amino acids early life used, and the team’s findings agree with those from lab experiments and meteorite evidence.

Such ancestor proteins can also provide a valuable check on theories for the early genetic code, says Freeland. If the earliest proteins are made of five amino acids with codons that start with the letter G, for example, then any proposed earliest code had better be able to make those proteins. If it can’t, then that code should be scrapped.

Though not the inkblot it was four decades ago, the code still holds many mysteries. Until they are resolved, some scientists believe, the frozen accident is still a plausible possibility and life on other planets may turn out to be completely different from life on Earth. If texting teenagers could offer any consolation to those in search of answers, it would be “gud luk.” s