Re: [ccp4bb] Reverse Translatase

[aaleshin]

I shell correct myself.
The Darwin evolution of species is not sufficient to perform all  
functions of the reverse translatase. The Nature also uses viruses in  
order to "translate" proteins from different species. The other forms  
of reverse translation were probably not needed before the  
introduction of the immune system.

Alex

On Sep 7, 2010, at 7:26 PM, aaleshin wrote:

Doesn't natural selection act like a Reverse Translatase? Which is
quite an elegant implementation of the idea...

On Sep 7, 2010, at 6:29 PM, Artem Evdokimov wrote:

Regardless of whether a system like this exists in Nature or not -
it's fun to imagine!

On a microscopic scale one could propose a hypothetical mechanism by
which a completely unfolded polypeptide chain could be fed into a
gated (or state-locked) peptidase that may break the chain down in a
co-ordinated stepwise fashion; releasing individual aa's into some
sort of a nanoscale channel. The released aa's would then be
sequentially coupled to something resembling tRNA - with pre-formed
trinucleotides attached on the other end. Coupling would then
presumably permit the triplets to ligate to one another  
sequentially -
the resulting ssDNA or ssRNA would then have to be converted into a
stable ds-form via the usual means, or otherwise protected in one of
the usual ways. Codon space could be expanded by pre-loading carrier
molecules with more than one type of triplet per carrier (biased
towards whatever codon frequencies are prominent in the organism of
choice) although this in no way resolves the random nature of the
actual codon use within the resulting nucleotide sequence.

The issue of amino acid coupling selectivity is pretty hairy - the
best I could think of on a short notice is to have the receptor sites
for individual aa's arranged in order of dropping selectivity --
however there is still the matter of shape/property similarities
throwing wrenches into the works. An alternative would be a series of
binary gates working on an exclusion principle.

As to practicality of this kind of stuff - I am not sure; I can
imagine an application similar to nano-scale multiparallel
pyrosequencing: an unknown protein would be broken down into peptides
via nonselective protease of some sort and then relatively short
individual peptides are 'sequenced' in parallel, producing short DNA
sequences that would later be complemented to dsDNA and allowed to
cross-anneal and self-assemble via overlaps, similar to gapped gene
assembly from short synthetic fragments (that first protease better  
be
*really* non-specific!). At the end one could sequence the resulting
long DNA to see what the original protein was like.

A.

On Tue, Sep 7, 2010 at 8:35 AM, David Schuller <dj...@cornell.edu>
wrote:
On 09/06/10 21:36, Jacob Keller wrote:

Dear Crystallographers,

does anyone know of any conceptual reason why a reverse
translatase enzyme
(protein-->nucleic acid) could not exist? I can think of so many
things
for
which such an enzyme would be helpful, both to cells and to
scientists...!
Unless there is something I am missing, it would seem to me
conceptually
almost impossible that it *not* exist.

See: "The RNA/Protein Symmetry Hypothesis: Experimental Support for
Reverse
Translation of Primitive Proteins"
Masayuki Nahimoto, J. Theor. Biol. (2001) 209, pp 181-187.

In which Nahimoto proposes such a system, and additionally proposes
that it
actually existed early in the development of life on this planet.

Reasons why it "could not exist" - No. Reasons why it would be very
difficult - yes. And plenty of reasons why Nahimoto is probably
wrong about
it having actually existed:

There is absolutely no evidence presented that such a system was
ever in
operation in the history of life on this planet.

Current theories such as the RNA World are much more likely
explanations for
how life as we currently know it may have developed from a pre-
biotic state.

DNA replication, DNA=>RNA transcription, and RNA=>Protein
translation all
depend on nucleic acid base pairing for part of their specificity.
It truly
is the secret of life. And it would not be especially helpful in
Protein=>RNA reverse translation.

Forward translation takes place in the ribosome, but extra
specificity is
"smuggled in" via a large set of tRNAs and tRNA charging enzymes, in
reactions which took place beforehand, which are then made use of
through
the base-pairing codon:anti-codon recognition.
Reverse translation would most definitely not be running forward
translation
in reverse;
the specificity cannot be handled ahead of time, it needs to be
available at
the site of reverse translation itself when each successive peptide
residue
is presented.

Progressivity: If different recognition sites are swapped in, this
has to be
done while keeping place in both the protein chain and in the  
growing
nucleotide chain. Possibly the protein chain might be cleaved
during the
process. The chemistry and geometry of peptide residues is far more
variable
than that of nucleotide residues.

The genetic code of reverse translation would be completely
independent of
that in forward translation. For the two to have matched up (in the
proposed
naturally occurring RT system) would have been extremely fortuitous,
imposing a strong barrier to the introduction of such a system.

Difficulty in dealing with post-translational modifications
disulfides,
cyclical peptides, acetylation, phosphorylation, etc.

A peptide sequencer coupled with a nucleotide synthesizer
accomplishes
somewhat the same thing, but on a macroscopic scale. This is an
impediment
to the motivation for constructing a reverse translatase enzymatic
system.

Cheers,

--
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All Things Serve the Beam
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                             David J. Schuller
                             modern man in a post-modern world
                             MacCHESS, Cornell University
                             schul...@cornell.edu