Does DNA carry a signature that allows us to decipher its evolution?
Although this idea has been popular, a recent paper in PNAS by Stephen
Freeland and co-workers at Princeton University suggests that this
signature is illegible.
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Terres A. Ronneberg, Laura F. Landweber, and Stephen J. Freeland
Testing a biosynthetic theory of the genetic code: Fact or artifact?
"Proceedings of the National Academy of Sciences USA", 2000, 97,
13690-13695.
Abstract.
It has long been conjectured that the canonical genetic code evolved
from a simpler primordial form that encoded fewer amino acids [e.g.,
Crick, F. H. C. (1968) J. Mol. Biol. 38, 367-379]. The most
influential form of this idea, "code coevolution" [Wong, J. T.-F.
(1975) Proc. Natl. Acad. Sci. USA 72, 1909-1912], proposes that the
genetic code coevolved with the invention of biosynthetic pathways
for
new amino acids. It further proposes that a comparison of modern codon
assignments with the conserved metabolic pathways of amino acid
biosynthesis can inform us about this history of code expansion. Here
we re-examine the biochemical basis of this theory to test the
validity of its statistical support. We show that the theory's
definition of "precursor-product" amino acid pairs is unjustified
biochemically because it requires the energetically unfavorable
reversal of steps in extant metabolic pathways to achieve desired
relationships. In addition, the theory neglects important biochemical
constraints when calculating the probability that chance could assign
precursor-product amino acids to contiguous codons. A conservative
correction for these errors reveals a surprisingly high 23%
probability that apparent patterns within the code are caused purely
by chance. Finally, even this figure rests on post hoc assumptions
about primordial codon assignments, without which the probability
rises to 62% that chance alone could explain the precursor-product
pairings found within the code. Thus we conclude that coevolution
theory cannot adequately explain the structure of the genetic code.
Oryginal: http://www.pnas.org/cgi/content/abstract/97/25/13690
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Genes can't tell us everything
PHILIP BALL
"Nature Science Updates", 18 December 2000
New research casts doubt on the theory that genes contain 'signatures'
that can provide an insight into how the genetic code itself evolved.
According to the coevolution theory, first mooted over 25 years ago,
the DNA that makes up the genetic code in any organism contains a
signature of its own development. In other words, genes hold a
'historical' record of the origins of life.
Stephen Freeland and co-workers at Princeton University have revisited
the theory and say that this signature is illegible. There is more
than a 1 in 2 chance that any record of how the genetic code developed
has been scrambled beyond meaningful interpretation, the team reports
in the Proceedings of the National Academy of Sciences USA (1).
The genetic code translates one molecular language into another.
Proteins, the workhorse molecules of the cell, are chains of
interlinked small molecules - 'amino acids' - of which 20 types appear
in nature. The sequence of amino acids along the protein chain is
recorded in DNA by a string of different molecules, 'nucleotides',
along the double helix.
There are only four kinds of nucleotide, denoted A, C, G and T. They
are read in groups of three by the molecular machinery that makes
proteins. This gives enough different permutations to encode all 20
amino acids.
Each group of three nucleotides - AAC, say, or GCT - is called a
'codon'. In almost every organism on Earth, a particular codon encodes
the same amino acid, indicating that this universal genetic code
sprung from a single evolutionary source.
Coevolution theory suggests that the genetic code was once simpler,
because there would have been fewer types of amino acids on the early
Earth. The idea is that as the earliest organisms got more complex,
they made new amino acids from the ones that already existed.
Then, the theory says, a new amino acid would have usurped one of the
codons that previously represented the amino acid from which the new
one was made.
So by inspecting the present-day genetic code, we should be able to
figure out the sequence of steps by which the earliest code expanded
to encompass more amino acids. This amounts to a kind of evolutionary
history of genes, extending the 'tree of life' back even before the
earliest recognizable single-celled organisms.
But the theory would fall down if the relationships between codons and
amino acids could have occurred by chance. For example, the amino-acid
leucine (for which one of several codons is CTT) is said to have been
made from valine (codon GTT). The single nucleotide difference between
the two codons points to this evolutionary relationship, the theory
claims.
But this depends on whether it is reasonable to suppose that valine
was made from leucine rather than from some other amino acid. And
Freeland's team argues that some of the precursor/product pairs
assumed by coevolution theory don't make biochemical sense. The theory
also fails to take into account the shortcomings of the protein-making
machinery that translates the code, the researchers say.
After correcting these misconceptions, they find that there is a 62
percent probability that the codon relationships between precursors
and products claimed as support for the coevolution theory could arise
by pure chance.
1. Ronneberg, T. A., Landweber, L. F. & Freeland, S. J. Testing
a
biosynthetic theory of the genetic code: fact or artifact? Proceedings
of the National Academy of Sciences USA, 97, 13690-13695 (2000).
Oryginal: http://helix.nature.com/nsu/001221/001221-4.html
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