Talk:TRNA-intron endonuclease

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 31 August 2021 and 9 December 2021. Further details are available on the course page. Student editor(s): Ypasinos, Aldewald, Sheblin. Peer reviewers: Hstuhlma, Ikilde.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 04:01, 18 January 2022 (UTC)

Peer review and responses during the educational assignment in Fall 2021

Topic Peer Review 1 Lead The importance of the topic is not represented in the lead. What makes tRNA-intron-lyase interesting? The lead does not provide a good summary of the other sections of the article. There need to be 1-2 sentence summaries of structure, function, and regulation in the lead to provide more direction for the article. The lead focuses too much on the names of the enzyme and not enough on structure, function, and regulation.

Article structure I do believe that the article is organized in a sensible way that adds to the information. Maybe adding a few images to the article or a history of the enzyme would add meaning to the topic.

Article coverage and neutrality The length of each section is well balanced and given a good amount of importance. The article does reflect the perspectives of the research. However, I feel like the article does not apply to a broader audience. One must be into biochemistry to understand much of the article. The authors should try to make the article more accessible to the general public. The article is presented in a neutral perspective that summarizes the data rather than draws conclusions on the data.

Reliable sources Overall, the authors use a range of reliable sources to support their summaries of the research. The structure section of this article seems to rely too much on one source. Adding a few other citations in this section would help the neutrality of this article. The function section of this article has a few united statements that could use a source to back up the summary.

Hstuhlma (talk) 00:54, 14 October 2021 (UTC)Hstuhlma

TRNA-intron endonuclease Peer Review 1 Lead: Same from previous article. I think it would be helpful to also include the original database table from the original article as well as it’s an easy way for readers to find specific things. You should also add more to this section as it’s a very brief overview. I think it would be helpful to briefly mention the properties from each section of the article here too so readers can get a basic idea of what TRNA-intron endonuclease is.

Structure: You definitely need to add a picture here of the structure. This will make it much easier for readers to visualize what the TRNA-intron endonuclease looks like. If there is one of each of the 4 structures, include all of them so readers can easily see the difference. You did a good job describing the structure and what each part is for. However, you only used 1 source for the entire section. Make sure you’re using multiple sources so it is apparent that it is more well known than only having one source. You also want to make sure you’re not just copying from one source only.

Function: I think this would be another beneficial spot to have a picture because it is hard to visualize what is happening based on words alone. I also think you should add a paragraph in the beginning that explains the function very simply, and then you get more in depth in later paragraphs.

Regulation: I think you should add onto this section by going into more detail on the gene location in the chromosome. You could also go into transcription and translation, and if there are any factors that can encourage or discourage these.

Sources/References: All of the references are from the original article. There are new sources listed separately from the references. These need to be together in a comprehensive list. Also, make sure to link them in the article instead of saying “sources:” at the end of each section. Additionally, I think you should have more than 4 sources to include all the data about your topic.

Overall: The most important thing to me is that you need more sources. You only have 4, and that is not enough to go into the full details of TRNA-intron endonuclease in my opinion. You could easily have at least 10, especially once you add images and include the sources there. Having more sources also shows readers that you checked multiple sources to make sure that more data than just 1 source matches with what you have written. You also need to add the sources to the actual reference area like I mentioned before. Additionally, you need to link them in the article where you used them instead of putting “(1)”. I think it would also be helpful to link difficult terms to the other wikipedia articles like you see in major articles. This way readers can click the word they don’t know and learn more about it. I also think adding pictures would be great so readers can actually see what TRNA-intron endonuclease looks like. I am definitely more of a visual learner so seeing the pictures makes way more sense than just words. The last thing I would change would be to get rid of the “Article Body” and “Lead’ headings because I think they separate the sections in a weird way.

Racngiles (talk) 20:57, 14 October 2021 (UTC)Racngiles

Topic Peer Review 3 1. Lead I think the lead needs to include additional context and general details about tRNA-intron lyase. It is very brief and does not necessarily provide me with a great overview about what the rest of the page will discuss. It also gives some nitty gritty details right out of the gate with a very specific chemical reaction. While that can still be included in the lead, it might be more beneficial to begin with a broader explanation as to what that reaction is (i.e. it catalyzes the last stage of tRNA maturation). And even maybe go further to explain what that is or why it might be important.

2. Clear Structure I like the way you have the page set up, starting with the enzyme's structure, then leading into its function, and finally its regulation. That seems like a logical path/order that can be easily followed. One thing to think about is maybe keeping your wording consistent. For example, the title of the Wikipedia page is tRNA-intron endonuclease, then it is specifically referred to as tRNA-intro lyase in the lead, then as tRNA splicing endonuclease (EndA) in the structure section. While I realize this enzyme goes by many names, it might be helpful to stay consistent so as to not confuse the readers. (But still definitely keep the list of alternative names that are listed in the lead!)

Another note, I am not sure if this is possible, but if you are able to add an image of tRNA-intron lyase, I think it would enhance the structure section. Also, try adding more sub-links to other Wikipedia articles- such as "protein subunit", "active site", "Alpha helix", etc.

3. Balancing Act Each of the sections seem to be an appropriate length and only encompass relevant material. Ad discussed a bit more in the next section, "Neutral Content", it does seem like the one study presented in the regulation section is heavily emphasized. Perhaps you could present the information in a way that puts less emphasis on the information coming from that specific study?

4. Neutral Content The information presented seems pretty neutral overall, presenting what is currently available. Possibly be careful of mentioning a specific study, as that may come off as biased. It did seem like that part at the end was trying to convince me why I should think this negative regulator, CLP1, is important just from the way it was worded. Also try to refrain from using phrases like "it is believed".

5. Reliable Sources Your sources seem reliable and credible, however I would say that certain sections, particularly "structure" rely too heavily on a single source. Are there possibly any other sources that also provide information about the structure of tRNA-intron lyase?

6. Wording These are just suggestions for areas where I felt like the wording was awkward or where I found grammatical mistakes.

under structure: "The homotetrameric EndA, α4, only found in Methanocaldococcus jannaschii, takes on a rectangular parallelepiped conformation consisting of four α subunits of 179 amino acids each" --> possibly change to "α4, the homotetrameric EndA that is only found in Methanocaldococcus jannaschii, takes on a rectangular parallelepiped conformation consisting of four α subunits that contain 179 amino acids each"

under structure: "with similar function as both previously described structures" --> possibly change to "with similar function as both of the previously described structures"

under structure: "Eukaryotic tRNA splicing endonuclease structure is less known" --> possibly change to: "Less is known about the structure of Eukaryotic tRNA splicing endonuclease"

under structure: "Both yeast (Saccharomyces cerevisiae) and human (Homo sapience) EndA have four subunits: α (Sen2/TSen2), β (Sen34/TSen34), γ (Sen15/TSen15), σ (Sen54/TSen54)" --> add an "and" between γ and σ

under function: I would probably remove the phrase "In simple terms" altogether. under function: "canonical position’s" should not have an apostrophe because it is not possessive. under function: " ...tRNA endonucleases have shown to have conserved base pairing to some introns in the anticodon site" --> possibly change to "it has been shown that tRNA endonucleases have conserved base pairing to some introns in the anticodon site"

Abbykelly99 (talk)Abbykelly99 — Preceding undated comment added 03:29, 15 October 2021 (UTC)

Topic Peer Review 4 Lead The lead should contain sentences which connect to the other main sections of the article. Maybe include the systematic name at the head of the lead, and then go a little bit about what each part of the name means, such as brief descriptions of tRNA, introns, what lyase enzymes in general do. The reaction scheme should be given in a figure Expand on the first sentence, ex. “tRNA-intron lyase is an enzyme that…” Ikilde (talk) 17:47, 15 October 2021 (UTC)

Clear structure Overall, very good structure and well organized sections. Again, I would connect body paragraphs in the lead I would also recommend putting the function section before the structure section, because I think more people would be interested in that aspect of the enzyme. Ikilde (talk) 17:46, 15 October 2021 (UTC)

Balancing act I would also recommend having the beginning of each subsection include a shorter, easier to digest summary section so it is easier to navigate for people who aren’t trying to go as in-depth in their research. Ikilde (talk) 17:47, 15 October 2021 (UTC)

Neutral content This doesn’t seem to be a controversial topic, but there are sometimes discrepancies in the scientific literature that should be addressed if it’s something you come across. If there are any review articles about this subject, these often present some alternate perspectives which could be incorporated. Ikilde (talk) 17:47, 15 October 2021 (UTC)

Sources For the most part, you seem to be sourcing primary research which is ideal: However, only two sources listed were published within the last five years. If there are more sources you can work with that are more recent, that would be good to incorporate and prioritize. While older articles can offer foundational perspectives on function, newer articles may contradict older publications

Other I think that you should clarify a few things to make sure people who are unfamiliar with reading scientific articles a little more comfortable.

Is tRNA-intron lyase a class of enzyme or a specific protein? Homologs/orthologs? Could potentially subdivide structural section into eukaryotes, prokaryotes, archaea Ikilde (talk) 17:47, 15 October 2021 (UTC)

Catherine's feedback You have already received a lot of detailed feedback, so I will just add a few things.

Images would really strengthen a lot of your descriptions. You should be able to include a PDB structure of the enzyme if the structure has been solved. Your descriptions and differentiation of pre-tRNA and mature tRNA are incomplete. You should further define these and perhaps use images to support your descriptions of them. Based on your writing, it is unclear whether you understand the full maturation process of a pre-tRNA to mature tRNA. Intron cleavage is one of the first steps, but there are many additional steps prior to mature tRNA formation. There are helpful figures in these papers: https://doi-org/10.1007/978-3-319-34175-0_2 http://www.genesdev.org/cgi/doi/10.1101/gad.1956510

The introduction seems very incomplete. There is definitely more info that could be included here. Cawilhel (talk) 17:21, 17 October 2021 (UTC)

Nils Comments Good start! See whether you can find more recent (review) articles to include and aim to link to existing Wikipedia articles.

Ngwalter (talk) — Preceding undated comment added 21:37, 17 October 2021 (UTC)

MLibrarian Comments I agree with the aforementioned comments. Responding to them would really strengthen this article. MLibrarian (talk) 02:37, 20 October 2021 (UTC)

Digital Pedagogy Librarian Feedback I agree with some of the feedback, specifically that you should expand the lead section to give readers more context. Since most readers are not specialists, they'll need a couple of sentences explaining what tRNA-intron-lyase actually is, more than just an enzyme--what is its function? The lead section does not need to explain the structure of the article or summarize the other sections, however. DrLibraryCat (talk) 19:57, 22 October 2021 (UTC)

Responses/edits that will be incorporated: Lead- Adding sentences briefly reflecting the new sections Defining specific terms itself to break down the content for non-experts Breaking down name for enzyme name non-experts Provide background on what role the enzyme plays in tRNA Maturation

Structure- Will incorporate other sources Minor grammar/wording suggestions Will create similar image using Pymol Will create a useful table of types

Function- Major updates: Add images Improve neutral content Remove phrases such as “In simple terms..” Make more accessible to general public by breaking down difficult concepts Find more review articles Acknowledge that this is just one step in the maturation process

Minor updates: Grammar/punctuation/sentence structure Directly link sources

Regulation- MAJOR UPDATES: Focus on regulation in steps of both transcription and translation CURRENTLY ONLY ONE TRANSLATION REGULATION MECHANISM Use more sources instead of depending on a few strong ones FINDING NEWER AND MORE SPECIFIC RESEARCH ON THE TOPIC

MINOR UPDATES Switch up wording to be more objective READERS SHOULD NOT FEEL THAT WRITING IS PERSUASIVE Add imagery to better visualize regulation processes

Incorporating more review papers on endonucleases Expanding to include 2 more sections Link to other wiki pages