In terms of "usefulness," I was actually thinking about cells learning how
to make new proteins from other cells, or perhaps an immune system could use
the info to make the right choice of starting materials. Also, codon bias
could be explained as resulting from the nature of the reverse translatase
machinery. Or an invader could copy the host's membrane proteins to evade
detection. Ah, so many possibilities! And as I said before, considering that
it would be so useful, and that the genius of macromolecular design observed
in nature is apparently so unlimited, shouldn't it be out there somewhere?
Nobel prize to the one who finds it...
Jacob
NB It should not cross our minds, I don't think, that if it were there, it
would have been found. Small RNA phenomena, for example, went undetected for
years, despite their commonness and high importance.
----- Original Message -----
From: "Artem Evdokimov" <[email protected]>
To: <[email protected]>
Sent: Tuesday, September 07, 2010 8:29 PM
Subject: Re: [ccp4bb] Reverse Translatase
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 <[email protected]> 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,
--
=======================================================================
All Things Serve the Beam
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
[email protected]
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: [email protected]
*******************************************
