Mechanochemical Reactivity of Ribonucleosides Mediated by Inorganic Species: Implications for Extraterrestrial Organic Matter Interpretation
, Catarina Gonçalves 1, Ana J. Carvalho 1, Vânia André 1,2, Adelino Galvão 1, Ana P. C. Ribeiro 1, Pedro F. Pinheiro 1 and José Armando Luísa da Silva 1,*
Round 1
Reviewer 1 Report
Comments and Suggestions for Authors
The authors report on the mechanochemical degradation of ribonucleosides such as guanosine, adenosine, cytidine, and uridine. While it is no surprise that the ribonucleosides can be chemically degraded by mechanochemical treatment, these studies reveal that there is some specificity to the degradation process. The efficacy depends on the chemical nature of added metal ions. While it would be nice if further chemical analysis (perhaps mass spectrometry) could be used to better characterize the degradation products, the results support the conclusions that mechanochemical degradation was achieved and that such chemical transformations may be important pathways for changing the chemical composition of extraterrestrial samples. The authors should change “it’s” to “it is” and add the word tube (I assume) after Eppendorf on page 3. Also, were the balls used during milling also stainless steel as was the jar? This along with the grade of stainless steel (or other composition) should be specified. After these few minor revisions, the manuscript will be acceptable for publication.
Author Response
Dear Revisor 1,
The authors would like to express their enlightenment for the time spent and the proposed alterations. Your comments, the changes (if applicable), corrections, and the author's comments have been inserted into Table 1 (below). When applied, the changes appear on the main text with a yellow background color.
Best regards,
Gustavo P. Maia, Catarina Gonçalves, Ana J. Carvalho1, Vânia André, Adelino M. Galvão, Ana P.C. Ribeiro, Pedro F. Pinheiro and José Armando Luísa da Silva
Table 1 - Revisors comments, document changes (if applicable) and authors comments. The changes are demarked on the main text in yellow
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Statement/Question |
Changes (if applied) |
Author Comments |
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Are the methods adequately described? Can be improved |
Some corrections were done |
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“While it is no surprise that the ribonucleosides can be chemically degraded by mechanochemical treatment” |
Not applied |
Indeed, nucleoside mechanochemistry has been explored [1], but in a very different scope. Ribonucleoside degradation via mechanical energy has also been poorly addressed, and this is a novel proposal in astrobiological studies. |
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“The authors should change “it’s” to “it is” (…)” |
Line 60 and 318 Before: it’s After: it is Line 330 Before: It’s After: It is |
The authors agree and change has been made |
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“The authors should (…) add the word tube (I assume) after Eppendorf on page 3” |
Line 199 Before: Eppendorf After: Eppendorf tube |
The authors agree and change has been made |
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“(…) were the balls used during milling also stainless steel as was the jar?” |
Line 104 Before: Two 7 mm balls After: Two stainless steel 7 mm balls |
Yes, the balls are also stainless steel. The authors agree and “stainless steel” has been added. The grade and composition are standard and are specified in Retsch® manual “Materials and Material Analyses” |
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[1] Eguaogie, O. et al., J. Org. Chem., 2018, 14, 955–970. DOI:10.3762/bjoc.14.81 |
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Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThe authors have tried to fill the gap of the pre-biological synthesis of RNA, based on the results obtained by mechanochemical-induced degradation of canonical purine and pyrimidine ribonucleosides. However, I consider that some large problems are contained in the manuscript as described in my comments below. Therefore, the authors should answer to the comments.
Major comments
The studies were carried out by the authors in an attempt to fill the gap of the pre-biological RNA synthesis with mechanochemical-induced degradation of ribonucleosides. However, only nucleobase except for a small number of unknown peaks is observed as degradation products of each ribonucleoside in Figures 1 and 2. The gap of the pre-biological synthesis of RNA could not be filled with the experimental results, because nucleobase is an already known component of ribonucleoside. Therefore, it seems to me that new knowledge for solving the synthetic pathway of RNA cannot be obtained.
1. Therefore, it should be more important to investigate on chemical structures of unknown peaks, which appeared in Figures 1 and 2 (the results of HPLC-UV).
2. Otherwise, it should be explicitly described in the manuscript, what was newly discovered from the studies carried out and/or how the gap of the pre-biological synthesis of RNA could be filled with the experimental results.
3. It is also described in the manuscript that the harsh conditions of exogenous delivery would induce its degradation (through ribose moiety decomposition), into their corresponding nucleobases. This means that life must emerge on the primitive Earth using nucleotides, which was re-synthesized with degradation products of extraterrestrial samples. This means that life emerged with nucleotides, which were synthesized on the primitive Earth but not with extraterrestrial samples. The authors should also answer to the problem.
Minor comments
1. Line 178: “Ribonucleosides” in legend of Figure 1 should be “ribonucleoside”.
2. Line 194: “purine” in legend of Figure 2 should be “pyrimidine”.
Author Response
Dear Revisor 2,
The authors would like to express their enlightenment for the time spent and the proposed alterations. Your comments, the changes (if applicable), corrections, and the author's comments have been inserted into Table 1 (below). When applied, the changes appear on the main text with a yellow background color.
Best regards,
Gustavo P. Maia, Catarina Gonçalves, Ana J. Carvalho1, Vânia André, Adelino M. Galvão, Ana P.C. Ribeiro, Pedro F. Pinheiro and José Armando Luísa da Silva
Table 1 - Revisors comments, document changes (if applicable) and authors comments. The changes are demarked on the main text in yellow
|
Statement/Question |
Changes (if applied) |
Author Comments |
|
Is the research design appropriate? Are the conclusions supported by the results? Must be improved |
Some corrections are carried out (end of Introductions, Material and Methods and Conclusions) |
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“(…)The gap of the pre-biological synthesis of RNA could not be filled with the experimental results, because nucleobase is an already known component of ribonucleoside. (…) ” |
Not applicable |
The synthesis of ribonucleosides in early-Earth conditions (meaning, prebiotic conditions) has been a major challenge in prebiotic chemistry. Studies point out that the direct condensation reaction between ribose moiety and nucleobases is not favorable (high steric hindrance, lack of regioselectivity, yield, etc). The most suitable pathway so far has been through intermediate species, when linked together to ribose, can cyclize, giving rise to purine and pyrimidine ribonucleosides. It is also known that extraterrestrial bodies, asteroids, and meteorites have many organic molecules, and has been found that the same building blocks that make up ribonucleosides (i.e. ribose and nucleobases) are present in meteorite samples. Since ribonucleosides were never found, and the direct condensation of these molecules is not plausible, hence, we propose that ribonucleosides could have existed somewhere in extraterrestrial environments and in it is “journey” to Earth (or any other place) were degraded into its stable entities. |
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“1. Therefore, it should be more important to investigate on chemical structures of unknown peaks, which appeared in Figures 1 and 2 (the results of HPLC-UV).” |
Not applicable |
The main objective of this study was to demonstrate that the main components of ribonucleosides (mainly nucleobase) could be obtained by the degradation of ribonucleosides. Some studies on the resulting degradation products are being made, however, the authors don’t find suitable (yet) to include in this manuscript. On the other hand, the identification of canonical nucleobases is important since they are not starting material for the synthesis of ribonucleosides (compare with last comment) supports the hypothesis that more complex prebiological molecules could be formed out of Earth. |
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“2. Otherwise, it should be explicitly described in the manuscript, what was newly discovered from the studies carried out and/or how the gap of the pre-biological synthesis of RNA could be filled with the experimental results.” |
Not applicable |
As mentioned before, the main result is the detection of nucleobase through ribonucleoside degradation. Based on these, from an astrobiological point of view, “reverse engineering” can be made to understand the suitable conditions of ribonucleoside formation in extraterrestrial environments. |
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3. It is also described in the manuscript that the harsh conditions of exogenous delivery would induce its degradation (through ribose moiety decomposition), into their corresponding nucleobases. This means that life must emerge on the primitive Earth using nucleotides, which was re-synthesized with degradation products of extraterrestrial samples. This means that life emerged with nucleotides, which were synthesized on the primitive Earth but not with extraterrestrial samples. The authors should also answer to the problem. |
Not applicable |
Similar to what was mentioned, the prebiological pathway for ribonucleoside formation does not involve nucleobase, but rather, intermediate species (e.g. 3-aminoisoxazole for pyrimidines). Nucleobase is detected in chondrite carbonaceous meteorites, but cannot be involved on the prebiological evolution, hence, its formation must come from another molecule, perhaps more complex. Our proposal refers to ribonucleosides as those molecules. |
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Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Comments and Suggestions for AuthorsTo the authors,
I have read the Author response. So, I have understood now significance of the results described in the manuscript. However, I have some questions about the results and authors idea as described below still now.
1. The authors describe in the Author Response that “Since ribonucleosides were never found, and the direct condensation of these molecules is not plausible, hence, we propose that ribonucleosides could have existed somewhere in extraterrestrial environments and in it is “journey” to Earth (or any other place) were degraded into its stable entities”.
It seems to me that the facts, that “ribonucleosides were never found, and the direct condensation of these molecules is not plausible”, may mean that ribonucleoside did not exist in any region of outer space, which human beings investigated thus far. In other words, the reason, why the authors have such ideas, would be because the authors firmly believe the RNA world hypothesis and space-origin theory on the origin of life. Therefore, the authors’ ideas might become not practical, if either one or both ideas are wrong.
2. The authors also describe in the Author Responce that “Nucleobase is detected in chondrite carbonaceous meteorites, but cannot be involved on the prebiological evolution, hence, its formation must come from another molecule, perhaps more, complex. Our proposal refers to ribonucleosides as those molecules”.
Here again, it seems to me that the reason, why nucleobase is detected in chondrite carbonaceous meteorites, although nucleoside cannot be detected, might be because simply structured nucleobase could be synthesized prebiotically, but more complex nucleoside could not be synthesized. Furthermore, I also consider that the fact, that nucleobase could be found in degradation products of ribonucleoside, does not always mean that ribonucleoside had been produced prebiotically.
Although I have some questions described above, I admit the authors’ idea, if the results described in the manuscript are sufficiently meaningful from viewpoints of RNA world hypothesis and astrobiology.
Author Response
Dear Revisor 2,
Once again, the authors would like to express their enlightenment for the time spent and the proposed alterations. Your comments, the changes (if applicable), corrections, and the author's comments have been inserted into Table 1 (below). When applied, the changes appear on the main text with a blue background color.
The main objective of this work is to present a hypothesis for the degradation of extraterrestrial organic matter, via mechanochemical reactions, using ribonucleosides as an example. The authors can agree that the conclusions might be slightly out of scope for the manuscript objective and therefore agreed to perform some modifications. The degradation model is not restricted to ribonucleosides but can be applied (or tested) to other types of extraterrestrial organic matter.
Best regards,
Gustavo P. Maia, Catarina Gonçalves, Ana J. Carvalho1, Vânia André, Adelino M. Galvão, Ana P.C. Ribeiro, Pedro F. Pinheiro and José Armando Luísa da Silva
Table 1 - Revisors comments, document changes (if applicable) and authors comments. The changes are demarked on the main text in blue
|
Statement/Question |
Changes (if applied) |
Author Comments |
|
|
1. (…) It seems to me that the facts, that “ribonucleosides were never found, and the direct condensation of these molecules is not plausible”, may mean that ribonucleoside did not exist in any region of outer space, which human beings investigated thus far. In other words, the reason, why the authors have such ideas, would be because the authors firmly believe the RNA world hypothesis and space-origin theory on the origin of life. Therefore, the authors’ ideas might become not practical, if either one or both ideas are wrong |
Not applicable |
Indeed, the detection of ribonucleosides in extraterrestrial environments is poorly understood. In addition to that, ribonucleosides are a “complex” molecule to be synthesized in extraterrestrial environments. Nevertheless, although the choice of words might not be the most adequate, we propose a hypothesis based on ribonucleoside reactivity and organic input of extraterrestrial samples (i.e. meteorites and asteroids). With the advancement in extraction and detection methodologies, we have been able to detect molecules that were considered not plausible for extraterrestrial environments (e.g. ribose, hexamethylenetetramine, N-heterocycles, including all canonical RNA and DNA nucleobases, among others). The same could happen to ribonucleosides, but the fact that harsh conditions can be met on the asteroid journey could explain the lack of ribonucleosides in these samples. |
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2. (…) Here again, it seems to me that the reason, why nucleobase is detected in chondrite carbonaceous meteorites, although nucleoside cannot be detected, might be because simply structured nucleobase could be synthesized prebiotically, but more complex nucleoside could not be synthesized. Furthermore, I also consider that the fact, that nucleobase could be found in degradation products of ribonucleoside, does not always mean that ribonucleoside had been produced prebiotically. |
Not applicable |
Although nucleobase prebiotic synthesis can be accomplished in extraterrestrial environments, does not imply that ribonucleosides could not. Meteorites comprise a wide range of organic molecules, apparently without any type of relationship with each other. This “degradation model” proposes a novel point of view, where chemical transformation might have occurred in the past, and the detected molecules are the “remnants” of this transformation. Ribonucleosides is just one plausible proposal, based on the current detected limits and molecules. Although this work is restricted to ribonucleosides and nucleobases, this model can include all other molecules, and further studies are being conducted. Indeed, the degradation of ribonucleosides into nucleobase does not state that degradation is mandatory. However, does not exclude it. In addition to tht, further efforts are being made to understand other degradation products that are ut of the scope of this work. |
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Line 327 - 328 |
Before: However, several events, between the formation of the first planetesimals until today, could lead to several chemical transformations After: However, mechanochemical events could lead to several chemical transformations |
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Line 328 – 329 |
Before: Minerals and other inorganic species are used as fingerprints on processes of extraterrestrial samples After: Minerals and other inorganic species are used as fingerprints on formation processes of extraterrestrial bodies |
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Line 335 |
Before: amino acid glycine After: glycine |
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Line 336 |
Before: for the synthesis and interconversion After: for the interconversion |
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Line 342 |
Before: could be synthetized out of Earth. After: could be synthetized outside of Earth. |
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Author Response File: 
Author Response.docx
