Talk:Capping enzyme

Suggestions for improving the article

Lead section: build upon the current description to provide an overview of the capping enzyme – structure, common names, its function/activity and impact of its activity while not being too technical. Find reliable and published sources to support the overview; include images of the enzyme and mechanism depictions. Content: Structure, Function (including location and other factors it interacts with), Impact of its activity, See also section (link it to other information sites such as transcription). Images to illustrate its function and interaction with other factors. SabFernMB (talk) 00:09, 11 March 2014 (UTC) Klbarnhill (talk) 01:00, 12 March 2014 (UTC)

As a step towards improving the article, we may want to delete the current information and replace it with a detailed overview that is properly cited.SabFernMB (talk) 22:33, 23 March 2014 (UTC)

Review by Graeme Bartlett

As this stands it looks very draft-like with many comments about the construction visible. In fact there is as much commenting about what to write as the new writing. So I think this is still a long way from being a B class page. Its probably still start class. I am looking forward to having a bit more material to review. The original lead definition is a better first sentence than the new proposed lead, so I suggest that you merge the content. Some of the new writing is a bit too technical, eg "cotranscriptionally", does this mean "during transcription"?

In Structure is there more to the human capping enzyme than the human guanylyltransferease domain? What kinds of cells produce this, is it all living organisms or just eucaryotes? I there more than one kind? Do mitochondria have them? Who discovered it? What is the effect of malfunction or mutations?

Images have limited types and .fcgi is not one of them. .svg format could be the preference. Before you use an image from a government web site, make sure that it was created by the US government, otherwise it is probably not free to use. Some images would be good here. The image at File:3D cystral structure of human mRNA guanylyltransferase.png is quite replaceable by an image that you have drawn yourself, so use is not fair. So you are going to have to do some more work and locate a free image, or draw one. A protein infobox would be good. Graeme Bartlett (talk) 10:00, 30 March 2014 (UTC)

Hey, thanks for the input, we are really struggling with the images, but we received some assistance so we hope to get some up, soon. I've added some information in the lead section, function, and see also sections. I'm continuing to look for more information to include in the structure section. Thanks, again Klbarnhill (talk) 00:52, 2 April 2014 (UTC)

Thank you Graeme for the great feedback! This will definitely help us polish the article.SabFernMB (talk) 23:21, 2 April 2014 (UTC)

Hi Graeme the enzyme is found in eukaryotic cells. We will include this information as it is relevant. We have created a section on "Impact of enzyme's activities to address effect of mutations. We will also address the different domains of the human CE. I may have found a free image from one of the protein databases, but will need to figure out how to add it to the article. We have included an enzyme infobox SabFernMB (talk) 02:02, 9 April 2014 (UTC)

Review by Cindy Atwell

A good start!

1.) The structure is a bit confusing in its current state, but I assume that you will merge the reference sections and the lead/ original introduction section?

2.) The lead or introduction section should not contain any citations as this is a summary of the rest of the article.

3.) Try to translate the technical terms into language for the lay person. As you probably have heard, we're trying to write for someone with a 12th grade education. For technical terms that you just can't leave out, make sure that you link those technical terms to the wiki article (e.g. beta sheets).

4.) For images/ pictures, you could try to draw your own in Inkscape.

Hope that this helps --Catwell99 (talk) 03:13, 2 April 2014 (UTC)

Thank you Cindy for your helpful feedback. We have quite a bit to do, and your suggestions will help us improve the article.SabFernMB (talk) 23:26, 2 April 2014 (UTC)

Cindy, thanks for the images suggestion, I've been trying it out! Additionally, I agree with the lead/intro section, we plan to alter it as we include more information in the article that we can summarize. I've found it rather difficult to use general terms for very technical subjects! Klbarnhill (talk) 19:23, 8 April 2014 (UTC)

Review by Deacon C

Hello, I am your fellow classmate Christopher Gerth and was assigned this article for initial review. I think you have a good start on the article. I know all the little things you forget about when trying to get an article started; plus the current article never looks like the final draft of the article you have in your head (unfortunately people can't read minds...Why not ?!). So if you have already noticed these things...my apologies.

1. I think you should move the lead section into the first paragraph of the article and then pear it down. My understanding is that the lead section should let a reader know if there is something in the article they might be interested in. 2. Obviously the references should all be in one section, I am assuming that you know this.

3. The structure for the 3-D enzyme doesn't appear. My guess is that you linked to a file that needs a viewer installed. Try to take a screen shot of the picture on your computer, save as a JPEG (or some suitable file) and then upload that. This will ensure that Wikipedia doesn't have to have the corresponding software installed to view the image (I guess you could review file guidelines).

4. An outlined chemical reaction as equations or pictorially would help the reader to understand the enzyme function more easily.

5. I think there is a template for "enzyme infoboxes" which you can add to your page and would make the page look very academic. In fact, I think this is recommended for enzyme and protein articles.

6. The "see also" section needs to be a bulleted list of articles in Wikipedia with links.

7. I would move the "function" section before the "structure" section, but this is my preference and just a stylistic point.

8. You may want to mention the highly conserved sub-units of the protein as from an evolutionary point this is very interesting.

Otherwise, great start ! Keep up the good work.

♠ Deacon C (talk) 21:51, 2 April 2014 (UTC)

Thank you Christopher for the very helpful feedback, especially your pointers on images, which is a weak point for us.SabFernMB (talk) 23:24, 2 April 2014 (UTC)

I just found some information about the highly conserved subunits and plan to include that immediately, great catch! We plan to include a picture of the overall reaction (as soon as we can figure out how to include pictures!) Thanks Klbarnhill (talk) 19:25, 8 April 2014 (UTC)

Thank for your tip on an enzyme infobox template. We have now include one in the article. We have come across equations for the reaction (suggestion 4) in our research. The infobox has a link to the equation. But we may end up including within the article. SabFernMB (talk) 01:54, 9 April 2014 (UTC)

Moved the function section ahead of the structure function as it flows better. We are still looking researching for articles on the conserved sub-units of the protein.SabFernMB (talk) 15:24, 21 April 2014 (UTC)

Hi Deacon C we addressed most of your comments. A paragraph on conserved regions under the structure section was added. Thank you for the suggestion. Let us know if the section is helpful. We are still working on an image of the chemical reaction that is copywright freeSabFernMB (talk) 03:19, 23 April 2014 (UTC)

Hi Deacon as you suggested in note 4 we added the chemical reaction. Thanks for the feedback.00:44, 29 April 2014 (UTC)SabFernMB (talk) 00:45, 29 April 2014 (UTC)

Review by Neelix

I like what you've done with this article so far. Here are some suggestions for further development:

1. Each section should contain more than one paragraph.
2. There should be no unsourced information in the article; the sentence "The function of the 5' cap is essential to the ultimate expression of the DNA" currently has no corresponding citation.
3. There is no need to include the same citation after every consecutive sentence; a citation at the end of a paragraph is sufficient to cover the entire paragraph if all of the information in that paragraph does indeed come from that source.
4. The "See also" section should only include a list of links; the paragraphical information currently in that section should be given its own section or appended to another existing section of the body.
5. Consider adding the article to more categories; surely there is more than one category that applies to this article.
6. Make the text as accessible as possible to a general audience; "use" is a simpler term than "utilize" and conveys the same meaning, and less reliance on technical terms in the lead would allow the average reader to at least have a basic idea of what the article is about.
7. This article could use more wikilinks, such as to Saccharomyces cerevisiae, Triphosphatase, etc.

You have done some great work with this article. Let me know if you have any questions about the above. Neelix (talk) 03:08, 14 April 2014 (UTC)

Thanks Neelix for the great feedback! There is still much to do on the article and we will incorporate your suggestions.SabFernMB (talk) 01:04, 16 April 2014 (UTC)

Hi Neelix, I forgot to log in before making changes to the article so the changes came up under my IP address. Is it possible to replace my IP address with my login name?SabFernMB (talk) 15:17, 21 April 2014 (UTC)

Hi Neelix, most of your comments have been addressed. We are still working on #1. For #5 do you mean to add more categories to the "see also" section? ThanksSabFernMB (talk) 03:32, 23 April 2014 (UTC)

Thanks for the suggestions, we definitely included more wikilinks and fixed some grammar mistakes. We did condense the see also section, but, as SabFernMB asked, what specifically are you referring to in #5?Klbarnhill (talk) 09:40, 23 April 2014 (UTC)

Comments from Jocelyn Munson

In the lead section, you wrote: “Pre-mRNA undergoes a series of modifications before becoming mature mRNA that exits the nucleus to be translated into functional proteins and capping of the 5' end is the first of these modifications.” You might want to list the other modifications.

As per Wikipedia’s Style Guidelines, you might want to mention mRNA guanylyltransferase in the lead section. It is an alternative name for capping enzyme.

Regarding the Structure section:

• “Capping enzymes are found in the nucleus of eukaryotic cells.” I couldn’t really find anything in the two cited sources to support this sentence.

• “Depending on the organism, the capping enzyme is either a monofunctional or polyfunctional polypeptide”. Your source mentions monofunctional and bifunctional, but it doesn't mention polyfunctional.

• This section would be easier to understand if it had images. Link to Inkscape and Wikipedia’s tutorials on pictures and uploading images.

Regarding the Function section:

• “After successful capping, an additional phosphorylation event initiates the recruitment of machinery necessary for RNA splicing, a process by which introns are removed to produce a mature mRNA”. Be more specific. What does this have to do with the cap?

• “The addition of the cap onto mRNA confers protection to the transcript from exonucleases that degrade unprotected DNA and assist in the nuclear export transport process so that the mRNA can be translated to form proteins.” Don’t you mean unprotected mRNA?

Regarding the Formation of the cap section:

• It needs images.

• “Collectively, these enzymes that are involved in the addition of the 5' cap to the mRNA are called ‘capping enzymes.’” In my opinion, this sentence belongs in the lead section. It could be the last sentence of the lead section.

Regarding the Impact of the enzyme's activity section:

• Elaborate a little more on the defect in RNA splicing. What is the the role of the capping enzyme in RNA splicing?

• “Mutations in S. cerevisiae methyltransferase inhibited the recruitment of RNA Pol II to the promoter” Why is that?

• “Furthermore, mutations in guanylyltransferase can also result in defects in transcription elongation” Again, elaborate.

The header of the See also section is in the wrong place.

The paragraph about transcription needs its own header. To be honest, I don’t think this paragraph is needed because it seems extraneous. Wikipedia already has an article about transcription.

Remove references that are not cited anywhere in the article (i.e.: the “bulleted” references)

I agree with Deacon C; the Function section should go before the Structure section

Reference 2 should have a doi and/or PMID for easier access

You refer to the capping enzyme as “guanylyltransferase” throughout the article. You might want to refer to it only as “capping enzyme”, so as not to confuse your readers.

S. cerevisiae, CEG1 gene, and CET1 gene should be italicized.

More Wikilinks are needed

Some questions arose in my mind while reading the article:

• What is the structure of the cap itself?

• How does the cap specifically recruit the mRNA to the ribosomes? (hint: eIF4E)

• Do capping enzymes have more functions aside from those already mentioned?

• Have mutations in capping enzymes been implicated in any diseases?

Overall, the article is progressing nicely. It isn’t written in an overly technical way, which is good. The references you chose were informative, and easily accessible. As far as I can tell, everything is written in your own words. Great job, so far! --Jocelyn Munson (talk) 04:12, 14 April 2014 (UTC)

I see that you added an image of the capping enzyme. It looks good, but I would make it sightly larger. --Jocelyn Munson (talk) 21:03, 15 April 2014 (UTC)

Thank you Jocelyn for the great feedback. Your suggestions for improving the article are very helpful, and we will incorporate them in our next update.SabFernMB (talk) 01:06, 16 April 2014 (UTC)

Jocelyn Wikicommons provides two options for the image, thumb and the actual image size. The actual image size is too large. Do you know of a way to reduce the size without using the thumb option?SabFernMB (talk) 15:28, 21 April 2014 (UTC)

Yes, there is. More info can be found here. I resized the image for you. Overall, the improvements to the article have been excellent! --Jocelyn Munson (talk) 00:51, 23 April 2014 (UTC)

Thanks Jocelyn! We are still working on some of the suggestions you provided.SabFernMB (talk) 03:22, 23 April 2014 (UTC)01:14, 23 April 2014 (UTC) — Preceding unsigned comment added by SabFernMB (talk • contribs)

Wow, thanks so much for your thorough review, we will be sure to incorporate your suggestions!Klbarnhill (talk) 09:32, 23 April 2014 (UTC)

The new figures you added to the article are great! I'm just not sure the figure in the lead section is in the correct place. It should probably be moved to the "Formation of the cap" section. --Jocelyn Munson (talk) 20:43, 28 April 2014 (UTC)

I originally had it under the formation of the cap, then decided to put it in the lead section. I will move it to the cap section. Thanks for all your feedback.00:43, 29 April 2014 (UTC) SabFernMB (talk) 00:46, 29 April 2014 (UTC) — Preceding unsigned comment added by SabFernMB (talk • contribs)

You're welcome! :) I have one more suggestion: in the caption for the first figure, it would be a good idea to briefly explain the roles of TFIIH, RNMT, and RNGTT. --Jocelyn Munson (talk) 03:16, 6 May 2014 (UTC)

Review by Lisawisa

Formation of the cap: It sounds a bit redundant to say that it's a three step process in back to back sentences. I'd rewrite the second sentence to remove that. The images are good, but could use short captions briefly explaining what they're showing. The first image also needs the abbreviations explained; I was able to figure out what they are, but it'd be better to just explicitly state it in a caption. The image of the reactions looks useful, but with no explanation I'm not entirely sure what I'm looking at.

Structure: If possible, any explanation about why a particular structure element is important for a function would be good to add. I italicized CEG1 and CET1; I think that's how you wanted it, but had the wiki formatting wrong.

Impact: Can you explain a little more in-depth about how mutations effect splicing and transcription elongation?

It's good that you're referencing, but I think you're overdoing the inline citations, you don't need to have a citation after every sentence. When you have several sentences that use the same sources, just put the citations at the end of the last sentence. For example, in the impact section, everything is from one source, so just put that citation at the end of the paragraph; it's assumed all the information precluding that citation are from that source. It'll look cleaner and be easier to read without so many in-line citations. The references themselves look good and support the information you're referencing. The reference to our textbook isn't the best choice though; we may have access to it but the general public won't. It looks like you're using to reference somewhat basic knowledge that you could probably find a more easily accessible source for. A few more wikilinks would be good too: splicing in the lead, DNA/RNA ligases, Saccharomyces cerevisiae. The function section looks particularly bare on links. Overall it looks pretty good, keep it up! Lisawisa (talk) 02:43, 29 April 2014 (UTC)

Lisa thank you for your great feedback! I agree the figures do need captions. We are looking of additional resources for the impact section, and hope to expand on the information. We will incorporate your other suggestions as we finalize the article.SabFernMB (talk) 23:28, 4 May 2014 (UTC)

Lisa, thanks for the imput, it's far too easy to be redundant and thank you for the fresh pair of eyes! Additionally, we will clean up the references (a problem that has been mentioned quite a few times!) Klbarnhill (talk) 00:12, 7 May 2014 (UTC)

Comments from Lxu27

Overall, the article follows the Style Guidelines. Structure looks good and each section is well developed with neutral tone. Content of this article is detailed and cited correctly.

That being said, I have some comments and suggestions:

1. The lead section is a little bit difficult to follow for general readers without any background, maybe try to use a more straight forward kind of expression. And explain the technical terms. And rearrange the sentences to make it flow a little bit better. For example, “The enzyme can only catalyze its reaction when bound to the phosphorylated carboxyl-terminal domain of RNA polymerase II; therefore it is specific to RNAs synthesized by this polymerase rather than those synthesized by RNA polymerase I or RNA polymerase III.” can be express in a different way like “The enzymatic reaction is catalyzed specifically by the phosphorylated carboxyl-terminal domain of RNA polymerase II.”
2. The article also needs more citations. More citations need to be added to the lead section and function section.
3. I recommend changing the order of different sections to make it better to understand. First you can introduce the structure properties then formation steps, enzymes involved, and lastly function of cap and its implications.
4. The last part where the article talks about impact of enzyme’s activity, it is confusing. Maybe you guys want to incorporate this into the function and enzymatic implication section. Perhaps look into the literature and find some relevant functional experiments have been done and make a summary out of them.
5. As the article is talking about capping enzymes, maybe it is best to list the family of enzymes all into a table and describe them as a family. Luyao Kevin Xu (talk) 20:33, 29 April 2014 (UTC)

Thank you for the great feedback Luyao! As we finalize the article this week, we will make every effort to incorporate your recommendations. For the impact section, we are still looking into additional papers for more information. Hopefully we can expand on this section. If not incorporate it with the function section.SabFernMB (talk) 23:32, 4 May 2014 (UTC)

Review from Keilana

Great job so far guys, here are a few suggestions for you as you finish out the semester. Let me know via email or my talk page if you have any questions.

• In several places, you're repeating citations unnecessarily. For example, you don't need to cite Cowling 4 times in the Impact section, you just need to have it at the end of the paragraph there.
• Your image could do with a caption; I don't think the average reader would be able to interpret the diagram successfully.
• You could do with a few more wikilinks throughout.
• Do a final read through and copyedit to make sure your language is as clear as possible. To be honest, I didn't find that much you need to work on here, you've done a great job!

All the best, Keilana|^{Parlez ici} 15:36, 3 May 2014 (UTC)

Thank you for the great feedback Keilana. We will incorporate your recommendations in our final review of the article.SabFernMB (talk) 23:33, 4 May 2014 (UTC)

Thanks for the final feedback, Keilana, I've included more wikilinks!! Klbarnhill (talk) 00:10, 7 May 2014 (UTC)

License of uploaded image files

Hi, @SabFernMB:, I want to get a check on the licenses of the image files you uploaded to Commons. For example, Bic035i001.jpg -- see c:File_talk:Bic035i001.jpg. That image shows license CC0, but it doesn't match the license of the article, which is CC-BY-NC. Media licensed under non-commercial (NC) licenses are not accepted on commons (might be okay on Wikipedia though -- I'd have to check). Did you contact the author or publisher directly, to get this released under CC0? Klortho (talk) 02:08, 7 May 2014 (UTC)

Hi Klortho, I looked up the copyright license on the image "Copyright © 2010 The Author(s) The author(s) has paid for this article to be freely available under the terms of the Creative Commons Attribution Non-Commercial Licence (http://creativecommons.org/licenses/by-nc/2.5/) which permits unrestricted non-commercial use, distribution and reproduction in any medium, provided the original work is properly cited." Based on this info I did not contact the author/publisher directly. If I have incorrectly uploaded the images, please let me know how to fix it, or if I have to remove the images. Thanks.SabFernMB (talk) 02:46, 7 May 2014 (UTC)

They're marked with the wrong license then. I'll mark them correctly, and I think they'll probably be taken down by somebody in Commons. I'll let Dr. Ogg know that it was a mistake, and you can contact her yourself. I can't say what, if any, impact this will have on your grade, or if there's time to remedy it. Klortho (talk) 03:12, 9 May 2014 (UTC)

Klortho thank you for catching the error and fixing the license. I have informed Dr. Ogg of the error. ThanksSabFernMB (talk) 16:19, 9 May 2014 (UTC)

Fair use candidate from Commons: File:Bic035i003.jpg

The file File:Bic035i003.jpg, used on this page, has been deleted from Wikimedia Commons and re-uploaded at File:Bic035i003.jpg. It should be reviewed to determine if it is compliant with this project's non-free content policy, or else should be deleted and removed from this page. If no action is taken, it will be deleted after 7 days. Commons fair use upload bot (talk) 06:50, 9 May 2014 (UTC)

Use is not fair in this case as it is easily replaceable by another redrawn image. Graeme Bartlett (talk) 08:59, 11 May 2014 (UTC)