Does the cell have a mechanism to determine DNA sequence from protein?

Question

Something like a reverse genetic code.

Answer 1

"Reverse translation"

Translation is the process by which an mRNA is "translated" into a protein.

It is impossible to get the exact DNA sequence from the protein sequence because a large number different DNA strands could code for the exact same proteins. In other words, there is a loss of information in the translation process. See codon redundancy and I am not even talking about introns and UTR.

Now, it is theoretically possible to get one of the large number of possible DNA sequence from the protein sequence. I am not aware of any natural process that does this job.

"Reverse transcription"

Transcription is the process by which DNA is "transcribed" into a mRNA.

It is possible to get the DNA sequence from an mRNA. And it just so happen that such process does exist! A "reverse transcription" if you want. The enzyme that does this job is called reverse transcriptase. Reverse transcriptase is mainly found in retro-viruses but there are a number of non-retro viruses that have a reverse transcriptase.

Answer 2

A Reverse Translatase, if it was discovered, would be the biggest discovery in biology (maybe in science generally?) in the last 30 years. We would LOVE to be able to treat proteins as strings of information in the same way as we do nucleotides.

But there are good theoretical reasons why it's unlikely. As already mentioned above - the RNA->protein map isn't unique, so the enzyme would only give you one possible mRNA for the protein. But there are bigger issues. DNA, and to a lesser extent RNAs, all have pretty similar physical properties regardless of sequence. proteins really, really don't. Any enzyme going from protein to RNA would have to be ridiculously complex and versatile (much more so than the already bewildering ribosome), to disassemble the almost infinite varieties of protein. Moreover proteins almost always get further modifications that aren't clearly encoded by their RNA sequence - they get chopped up, bonded to themselves, and have extra chemical groups, sometimes big ones, stuck on.The map from RNA->protein is really, really complicated. And this is kind of the point of proteins.

Going from DNA to RNA or backwards is like converting between the master copy of a blueprint, and the working copy used on a building site. It can be done almost perfectly. Going from protein to RNA is more like going from the building itself to the blueprint. The difficulty of the problem is of a completely different level.

Answer 3

What is involved in making a specific antibody to a specific antigen? The immune system recognizes an unfamiliar epitope on a molecule and a dance of enzymatic activity begins where V and J gene segments are cleaved and spliced, d-nucleotidyl transferases may insert nucleotides in V and D segments, with as many possible choreography as there are possible antibody specificity. The master choreographer for all these possible scenarios must by necessity reside ultimately in our germ cell line. Ultimately, even if some predisposed somatic mutations take place, we must assume that this ability to respond to any antigen, even the myriad of synthetic antigens created in modern laboratories, is inherited. And therein lies the problem.

Back in 1976, I wrote the following to Dr. Marvin Fishman, one of the pioneers in Immune RNA research at St Jude Children Research Hospital:

It is hard to conceive how genes for antigens that had yet to come into existence would have been preserved through eons of evolution since there would be absolutely no natural selective pressure to insure their continuation in the germ line. One possible mechanism for the generation of antibody diversity is the formation of informational RNA in certain specialized cells in response to a given antigen and the distribution of this RNA to other cells involved in the immune response. Your work has shown the existence of I-RNA and its informational role. Its mechanism of formation is not yet known. It seems unlikely to me, for reasons stated above, that the macrophages responsible for making I-RNA carry this information in their genome. It would have been evolutionarily simpler to develop an enzyme system capable of making the appropriate I-RNA when it comes in contact with the Ag in question. This system would only have to provide information for the combining site of an immunoglobulin. Once this piece of RNA is made, it can be incorporated into the macrophage’s genome by the reverse transcriptase at the appropriate site and then the information for a whole specific immunoglobulin could be released through transcription. This hypothesis can be checked by adding an inhibitor of the reverse transcriptase along with the antigen. This should prevent release of I-RNA capable of coding for a whole Ab in a cell free system. Actinomycin-D would also inhibit the release by the macrophages of I-RNA...

What I was proposing to Dr. Fishman and all of my professors at the time was the existence of “Reverse Translatase”, an enzyme that could read the epitope site of a foreign protein and encode the proper nucleic acid sequence that would then become the template on which the amino acid chain that would constitute an anti-epitope could be assembled. At this point, let me provide a little background on Immune RNA.

It was found that a percentage of macrophages from peritoneal exudates, induced by injection of mineral oil into the peritoneal cavity of mice, incubated in vitro with antigens the donor animals never came in contact with, could process these antigens and elaborate specialized RNA that could transfer immunity. The first hints that macrophages played a crucial role in antibody production came in the late 50s when Fishman et al. showed that antibody production to a specific antigen could be initiated in vitro in lymph node fragments after their stimulation with cell free extract from macrophages that had been incubated with the antigen in question. It was shown that adding the antigen itself to these fragments initiated no response. Only the extract from the macrophage-antigen soup elicited a response. Furthermore, treating this extract with RNase before adding it to the lymph node fragments totally destroyed its capacity to stimulate antibody production in those fragments. Immune RNA was born. Later the standard experiments were conducted with spleen cell cultures mainly instead of lymph node fragments. It seems to me that the most economical system that could have evolved is the capability to process antigens with a Reverse Translatase system of enzymes that would then transmit information that would be incorporated in the hypervariable or combining site of a specific antibody. This new RNA could then be inserted in the appropriate gene segment of B cells via Reverse Transcriptase that would henceforth become memory cells capable of a secondary immune response. It would be a much more efficient and more easily attainable way for nature to achieve specificity rather than the cleavage, splicing and recombination of gene segments in a predetermined choreography with a billion variations. A few experimental facts that were known in the 70s on the elaboration of I-RNA seem, if not confirm, to at least suggest such a hypothesis.

1. The addition of Actinomycin D, rifampicin or dimethylrifampicin inhibit the formation of I-RNA by these specialized macrophages indicating the need for RNA polymerase and Reverse Transcriptase activity for its formation. This is what one would expect if a new nucleic acid chain was formed by reverse translation and then had to be incorporated into the macrophage’s genome before a completed I-RNA could be transcribed.

2. And this is a most important point: the formation of RNA-antigen complexes that is found in those peritoneal exudates macrophages as a precursor to the completed I-RNA strands was not inhibited by either Actinomycin D or rifampin suggesting that the RNA formed in those complexes during the antigen processing phase was not transcribed but formed in another manner, perhaps by Reverse Translatase.

3. The ability of I-RNA to stimulate antibody production in spleen cell cultures is not inhibited by Actinomycin D nor rifampicin indicating clearly that there is no need for transcription of any gene for the antibody produced. The information for the whole antibody must be completely contained in the I-RNA.

So the evidence suggests that some antigens are first sequestered by a specialized sub-population of macrophages that process them by first forming RNA-antigen complexes. That RNA does not need to be transcribed from any gene region since its formation is not blocked by inhibitors of RNA polymerase, but is perhaps elaborated by a Reverse Translatase that probably makes up the major protein component of those complexes. The next step seems to be incorporation of that RNA into a gene region by reverse transcriptase and then transcription of the complete strand of I-RNA. This I-RNA is released and picked up by B lymphocytes that can then initiate an antibody response. Once this I-RNA is incorporated in the appropriate gene region of the B cells by reverse transcription, they become committed memory cells capable of a more rapid secondary immune response if stimulated again by the antigen.

Proof of the existence of such an enzyme would be in RNA-DNA hybridization studies. If one could extract the RNA from the RNA-protein complexes that seem crucial as a precursor to the formation of I-RNA in those specialized cells and show that it would only hybridize with DNA from V or D gene segments of committed memory B cells but not unsensitized B cells from the same donor, it would be a powerful argument for the existence of reverse translation. An assay for such an enzyme or enzyme system by demonstrating uptake of an appropriate tritiated nucleic acid could also be attempted. Its most likely source, if it exists, would be those RNA-protein complexes found in peritoneal exudates cells exposed to antigen.