Talk:WikiJournal of Medicine/Eukaryotic and prokaryotic gene structure

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WikiJournal of Medicine
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<meta name='citation_doi' value='10.15347/wjm/2017.002'>

Article information

Authors: Thomas Shafee Orcid icon.png , Rohan Lowe Orcid icon.png 

Plagiarism check[edit]

Artículo bueno.svg Approved - Plagiarism check by searchenginereports.net returned text matches with this same article only. Mikael Häggström (discusscontribs) 17:05, 30 November 2016 (UTC)

Initial Editorial comments[edit]

Dear Dr. Shafee,

on behalf of Wiki J Med, I would like to thank you, as the corresponding author, for this submission.

Comments by Michaël R. Laurent
These comments refer to this previous version of the article

Overall I think this Figure and accompanying article is an excellent illustration of gene structure in eukaryotic and prokaryotic organisms which provides a nice, understandable overview of the most important elements. The clickable hyperlinks which link to appropriate Wikipedia entries as well as the availability of raw material for translations are a real advantage. As such it provides a significant advancement making it eligible for publication provided that the comments from peer review are sufficiently addressed. Please find some of my initial editorial comments below and feel free to answer these and/or make appropriate editions to your submission as you see fit, while we await further peer reviewer comments.

1. As general comments, I find the current article quite technical, as opposed to being written for a general audience. After looking at the Gene article, this also appears to be difficult to understand for the average learner (per WP:TECHNICAL. I don't think this requires much more edits now but this may be something to consider for future publications. Explaining something difficult in such a way that it is easily understood is often much more helpful as a learning resource. Perhaps at the start of the Introduction it would be good to repeat some basic elements such as the central dogma of how DNA is transcribed to various RNA species or to mRNAs and then ultimately processed into proteins.

Response
Readability can definitely be improved. The technical jargon is largely necessary. However, I have gone through and simplified sentence structure where possible. In particular, I have split up some of the longest sentences (>40 syllables). I've also added a couple of background sentences at the start of the introduction. I'll do another round of simplification once the external reviewer comments are in so that I can go through all at once.

2. The explanation of the difference in promoter 'ground state' between pro- and eukaryotes appears to contain an error. As I understand it, prokaryotic genes are 'default on' and eukaryotic genes are 'default off', which is opposite to the first part of your sentence but in line with the second part of that specific sentence. Please correct.

Response
You're right that these were the wrong way round. I've corrected the error.

3. One of the limitations that could be added to the Limitations section, which was present in one of the previous diagrams, is the quaternary structure of DNA e.g. how it is organized in histones, the importance of looping etc. Also the importance of epigenetic control of gene expression and methylation/demethylation is omitted, this could perhaps also be added in addition to other the elements already mentioned such as alternative splicing etc. I agree that these are "extraneous flourishes" which can be omitted here, but nevertheless seem important enough to mention in that section.

Response
I've added quaternary structure and epigenetic control together in this section, since they're linked concepts.

4. Minor comment: Perhaps for enhancers and silencer regions, use of plural would be more appropriate since I believe there is usually more than one of these regulatory regions.

Response
I've clarified the text to state that there can be many of these regions. In the diagrams I have left the terms singular since they each refer to one instance of such a region (in the same way as each intron is labelled singularly)

--Michaël R. Laurent, MD PhD (Reply) 15:35, 5 December 2016 (UTC)

External reviewer comments[edit]

Review by prof. Robert Root-Bernstein, Professor of Physiology, Michigan State University, East Lansing, MI 48825 USA
This review refers to this previous version of the article

The images presented in this article are definite improvements over other publically available illustrations of the differences between eukaryotic and prokaryotic translation. I believe, however, that three minor improvements are still possible.

One is to make each of the exons a different shade of red (or orange…) so that that is more readily apparent that the eukaryote exons are ligated and the prokaryotic ones are not.

Response
We have edited the text and image caption of the eukaryote section to emphasise this element. Since exon boundaries are undetectable once they have been spliced into the mature mRNA, we think that it is clearer to keep them the same colour to avoid the impression that they have different functions.

Second, it would be nice to COLOR the introns (say, green) and show them discarded in the third step rather than representing them with carrot-shaped lines. It is easy to overlook the introns and not really see the difference between them and the non-coding regions in the prokaryote sequence.

Response
Good point - the introns have been replaced with rectangles to match the format of the other sequence regions. We have chosen to colour them light grey to match the dark grey of the sequence elements that are added or removed during post-translational modification. We have also centre-aligned the processed mRNA rather than left-align to make the removal of the introns more immediately clear. Finally, we have left in the carets mostly because it is such a common way of depicting splicing that it is useful for readers.

Third, in the prokaryote image, there are (in step three) regions listed as “RBS”, a term that is not defined anywhere in the article. This oversight should be fixed.

Response
Well spotted. This oversight also made us catch through the document and realise that the abbreviation ORF has similarly not been defined. We have now added the full names and abbreviations to the main text.

Otherwise, excellent!


Review by Alexandre P. Y. Lopes, PhD, Centro de Biotecnologia, Instituto Butantan, São Paulo, Brasil
This review refers to this previous version of the article

General comments: The figures presented in this submission are in perfect agreement with the purpose of the article. They allow a clear and objective understanding of the main features of the eukaryotic and prokaryotic genetic structures, evidencing their similarities and differences. Although I understand that some elements are omitted for clarity by the authors, I would suggest including information in the text regarding the organization of the operons in order to make it more complete:

  • Although some polycistronic prokaryotic mRNAs have a ribosome binding site for each open reading frame (ORF), others do not. In bacteria the so-called "translation coupling" phenomenon occurs providing a genetically encoded mechanism to control expression level ratios within polycistronic operons. In these operons, the termination codon of one ORF coincides with the initiation codon of another ORF so that when a ribosome has finished translating one reading frame it is in position to start translating the next one, without the need for another RBS.

Response
Good point, omitting translation coupling was an oversight on our part. We have added information to the prokaryote section that explains it. It is our understanding that there are a couple of mechanisms, and we have attempted to summarise both mechanisms where ribosome continues from one ORF to the next (where being in-frame is important) and where translation of ORF1 affects the accessibility of the RBS of ORF2 (where frame is less important than secondary structure).

In general, the article is very good.

Additional submission info[edit]

Could conceivably be added as its own page in Wikipedia: Gene structure

For formatting into a pdf, word document versions are available at this link