Can ribosomes read ssDNA?

Question

My question is whether translation can be done, either naturally or artificially, through a ribosome reading (single-stranded) DNA directly. If not, I would like to know what allows ssRNA to be translated but not ssDNA.

Answer 1

Summary

Messenger RNAs that are recruited to the ribosome for protein synthesis in vivo, need to satisfy particular structural requirements and must interact with the protein initiation factors that deliver them to the ribosome. Generic single-stranded DNA (ssDNA) does not have these structural characteristics and so cannot be translated on ribosomes under natural conditions.

A single reported attempt to translate deoxyribose-based analogues of these mRNAs under conditions equivalent to those within the cell was unsuccessful. Thus, although experiments suggest that ssDNA may be able to bind transfer-RNA and allow some polypeptide synthesis under non-physiological conditions, this reflects only those aspects of protein biosynthesis that involve base-pairing interactions between the message and other RNAs involved in translation. In contrast, the stages involved in the selection of the first initiation codon and the recognition of termination codons involve interactions between protein factors and the message, where recognition of a hydroxyl group in the 2ʹ-position (and discrimination between thymine and uracil) may well occur and would prevent translation of a synthetic ssDNA message.

If, in fact, no discrimination against DNA has evolved for the ribosomal- and transfer-RNA components of the translation apparatus, this may be because the system arose in an ‘RNA World’ before DNA evolved, and because free ssDNA in the cell has never been a competitor with mRNA for ribosomes, especially after sophisticated protein-based systems arose for the selection of the appropriate initiation codon.

Contemporary physiological interactions of mRNA with ribosomes

Translation of mRNA by ribosomes (protein biosynthesis) is a complex process which can be divided into a number of stages, each generally involving a variety of RNA and protein molecules — initiation factors (IF), elongation factors (EF) and termination or release factors (RF). The reader who is not familiar with this is advised to read a text-book account such as that in Chapter 29 of Berg et al.. However, to summarize briefly, they are: selection of the correct AUG (usually) on the mRNA for initiation, IF-dependent binding of the initiator-tRNA to the P site, EF-dependent and codon-directed binding of an elongator-tRNA, peptide bond formation catalysed by the large ribosomal subunit, EF-dependent translocation, and eventually stop-codon directed and RF-dependent release of the completed polypeptide chain.

The first step, is crucial for the binding of natural mRNAs — the subject of this question. Under natural cellular conditions prokaryotes and eukaryotes have different methods of ensuring that the ribosome interacts with the correct mRNA codon to start translation. In prokaryotes a specific ribosome-binding signal (Shine and Dalgarno sequence) must interact with the 16S rRNA and a particular initiation factor protein is involved in this step. In eukaryotes the main method is recognition of a modified 5ʹ structure on the mRNA and unwinding of secondary structure, also modulated by protein initiation factors.

I am aware of one report of an attempt to translate a DNA-based analogue of such natural mRNA structures under any conditions. This was by Damian et al. (Biochim. Biophys. Res. Commun 385, 296-301 (2009)), and was unsuccessful, even though physical methods indicated binding to the ribosome. I imagine that recognition by the protein initiation factors did not occur but I cannot be sure that base-pairing to the 16S rRNA was also hindered.

Regardless, one can answer the question posed:

The fact that ‘random’ single-stranded DNA would lack the structural features for selection of the correct initiation codon explains why it would not be translated under natural conditions — it could not bind to the ribosome.

Artificial systems of protein synthesis

The full details of the reactions on the ribosome only emerged gradually. Nevertheless the lack of understanding of the features of natural mRNA required for binding to the ribosome did not prevent either the dissection of subsequent steps of protein biosynthesis, nor the use of ribosomal systems to decipher the genetic code. This is because it was possible to bypass the initial steps by using suitable unphysiological conditions, that allowed polynucleotides or oligonucleotide triplets to bind to the ribosome, where further reactions were possible, albeit generally less efficiently than in the cell. Such conditions included high concentrations of magnesium ions and certain antibiotics that affect the accuracy of protein synthesis. It has been suggested that the neutralization of the charge on the backbone phosphates of the RNA by Mg²⁺ enhances (non-specific hydrophobic interactions at the mRNA-binding channel, and that the antibiotics stabilize a state of the ribosome in which amino-acyl tRNA can bind more easily (and hence promote the binding of polynucleotides by base pairing). Once bound with the codons hydrogen-bonded to the cognate anticodons of tRNA, subsequent elongation reactions depended on components of the ribosome other than the artificial messenger.

Thus, it was that the genetic code was deciphered using bacterial cell-free systems to which were added simple synthetic polynucleotides, lacking Shine and Dalgarno sequences or start (or stop) codons; and by experiments in which amino acyl-tRNAs were bound to triplet codons in the absence of both IFs and EFs. Other partial reactions of protein synthesis were similarly dissected artificially — the peptidyl transferase reaction was studied on isolated 50S subunits using just a fragment of tRNA and puromycin by conducting the reaction in 50% ethanol!

Experiments with single-stranded DNA

Understanding that ribosomes can be induced to bind and translate ‘non-mRNA’ oligo-ribonucleotides under certain artificial conditions, we are in a position to consider the significance of reports of translation of oligo-deoxyribonucleotides — ssDNA.

The original experiments in this area by McCarthy and Holland in 1965 showed that denatured DNA from various sources (including animal cells) could stimulate the incorporation of radioactive amino acids in a bacterial cell-free system, but this depended on the presence of antibiotics. Furthermore, it was shown in Khorana’s lab that only certain synthetic poly-deoxynucleotides (analogous to the poly-ribonucleotides he used to decipher the genetic code) were active. Thus, it would appear that under the non-physiological conditions that favour promiscuous binding of poly- and oligo-ribonucleotides, there is some binding of ssDNA, and subsequent translation.

A paper by Ricker and Kaji mentioned by @Mesentery — reports that oligodeoxynucleotides could function in some partial reactions (fmet-tRNA binding) although not in others. In particular it was not possible to perform RF-dependent termination reaction with oligonucleotides containing termination codons, but — in the presence of antibiotics — termination independent of release factors did occur.

It is, thus, obvious that these experiments in which ssDNA is translated on ribosomes have no physiological significance. However it is still pertinent to ask the complement to the question of the poster, why does the system work at all?

Why are deoxyribose (and thymine) not discriminated against under artificial conditions?

Enzymes of synthesis and degradation of nucleic acids — RNA and DNA polymerases; ribonucleases and deoxyribonucleases — are specific for either RNA or DNA (or in some cases DNA/RNA hybrids). This is both important to ensure they fulfil their specific functions, and perhaps an inevitable consequence of the nature of their reactions — the making or breaking of sugar–phosphate bonds. Here we are dealing with catalysis by a protein enzyme that binds these structures at its active site.

In contrast, those reactions of protein synthesis for which certain requirements may be relaxed under non-physiological conditions involve base-pairing interactions. In modern ribosomes they may be optimized by associated proteins, but it is thought that the latter only evolved later. Artificial conditions, such as high concentrations of magnesium ions or antibiotics, may be thought of as allowing the essential interactions that existed in ‘ur-ribosomes’. And, of course as DNA/RNA hybrids readily form, the participation of DNA in such interactions is not so surprising. (In the RNA world of ‘ur-ribosomes’ — or even an RNA/protein world — there would be no need to discriminate against DNA, because it had not yet arisen. And chemically, the substitution of a hydrogen for a hydroxyl group could not hinder an interaction — at the worst it would only weaken it.)

It is pertinent that the contemporary AUG-selection and termination reactions depends on RNA–protein interaction. These might well involve recognition of ribose as well as base sequence, explaining the observations by Ricker and Kaji, and by Damian et al., mentioned above.

Answer 2

My question is whether translation can be done, either naturally or artificially, through a ribosome reading (single-stranded) DNA directly.

Ribosomes participate into the translation of mRNA into proteins. See the wikipedia article for more information

If not, I would like to know what allows ssRNA to be translated and ssDNA not.

The "if not" makes no sense because answering yes or no to the first question does not really have much to do with the second question.

ssRNA and ssDNA refers to the genetic material of some viruses. Most of the time, I do not think we use the terms ssDNA and ssRNA to refer to a virus that reverse transcribe the RNA into DNA, so your question is unclear and confusing.

Some viruses do reverse transcribe RNA to DNA. They do so with a reverse transcriptase.

What I want to know with the second question is what structural or chemical characteristic allows the reading of RNA but not DNA.

Oh I think I understand your question...

Double stranded DNA cannot be translated by a ribosome for sure. I suppose ssDNA could eventually fit in a ribosome (or a slightly modified one), however, the tRNA should be adapted to using T and not U. I am not a molecular biologist and I can't say more than that.

I want to know how DNA lacking a 2-hydroxy group and using thymine instead of uracyl makes it unreadable to a ribosome

I don't know if it does and, if it does, then I don't know why! Sorry, I am not able to help more!