Talk:Toxin-antitoxin system

GA Review

This review is transcluded from Talk:Toxin-antitoxin system/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Sasata (talk) 21:42, 7 October 2010 (UTC)

Greetings, I have signed up for this review. Should have comments up in a few days. Sasata (talk) 21:42, 7 October 2010 (UTC)

Reviewer: Graham Colm (talk) 21:55, 9 October 2010 (UTC)

I commented at the peer review and was impressed with this contribution. I'm interested to see what Sasata has to say. I will leave the GA decision to Sasata, but might leave some comments either here or on the article's discussion page. At the moment I think this is the best article on plasmid addiction on the Internet. It is very well written, but we might have to work on some of the technical terms such as "direct repeats of a ...nucleotide motif". Graham Colm (talk) 21:55, 9 October 2010 (UTC)

Your suggestions are very welcome Graham, the more heads the better. Here's some comments I had on a first readthrough:

• A special effort typically has to be made in hardcore science articles to ensure that the lead is inviting and friendly to those who might not know the jargon, so I will pay special attention to that
• "A toxin-antitoxin system is a set of two or more closely linked genes which together encode both a protein 'poison' and a corresponding regulatory 'antidote'." I'm not completely comfortable with the word regulatory here; to those who don't know the implications of the word "regulation" as it is meant in biochemistry/cell biology, it might seem like a confusing adjective.

• I agree. I'm not sure 'regulatory' is entirely correct either. --Paul (talk) 22:02, 11 October 2010 (UTC)

• "plasmids – transferable genetic elements" I associate "genetic element" with transposon (and that's the article to which this phrase will link),

• I disagree here, a transposon is a genetic element, sure, but I don't think the average reader would make the same association. I would argue genetic element would better redirect to Mobile genetic elements, which lists plasmids as an example Jebus989^✰ 12:17, 19 October 2010 (UTC)

• "they ensure that the plasmid is inherited by daughter cells during cell division." Isn't it more accurate to say that only the daughter cells that inherit the plasmid will survive after cell division?
• I think the second paragraph needs to start out with an introductory sentence like "Toxin-antitoxin systems are typically classified according to how they blah blah… "or something similar, to give the reader a gentler lead-in to the nitty-gritty that follows.
• "In a type I toxin-antitoxin system, the translation of messenger RNA which encodes the toxin is inhibited by the binding of a small non-coding RNA." Leaves me hanging… what does it bind to?
• "Type III toxin-antitoxin systems have recently been described…" What's recently? This is a phrase that's best avoided as it's easily dated, and subjective (I made the same mistake in a FAC very recently!)
• "Adaptive theories also exist," to explain what?
• what's a positive selection vector?

• Hopefully a bit better explained in the section now. I'm guessing it's the introductory mention which is unclear but hopefully the reader will connect it to the titled heading if they are unsure of this application? Jebus989^✰ 19:30, 1 November 2010 (UTC)

• in the 1st image, part (A and B), left side: why is the first gray cell dividing to form progeny? Doesn't the toxin kill it?
• "It has also been proposed that chromosomal copies of plasmid toxin-antitoxin systems may serve as anti-addiction modules." Perhaps a few words to explain what these are so the reader doesn't have to read another article to figure it out.
• I don't think one can assume readers to intuitively understand what the nine listed function of TA systems are supposed to be based on those descriptors. What's a "genomic parasite"? How would an antiphage system work? etc.
• how exactly do the hydrophobic proteins of type I toxins damage cell membranes?

• This is a good question, it would be really useful and I would really like to write a section on it. However, at the moment I think the toxin mechanisms are generally poorly understood. Hayes' Science review noted "Surprisingly few intracellular targets of plasmid-encoded toxin proteins have been elucidated definitively" (Hayes, 2003). I've added a sentence echoing this, hopefully that is enough until more information becomes available Jebus989^✰ 20:08, 30 October 2010 (UTC)

• SOS response should be linked on 1st mention in the 1st (not 2nd) table
• link upstream, downregulating
• "Only one example has been discovered to date:" what date? Maybe just leave out "to date"
• "The biotechnological applications … has begun" needs fixin
• "In an experiment testing the effect of temperature on the hok/sok locus" effect of temperature on the what of the hok/sok? expression? effectiveness? inheritability? various parameters?
• "…it was found that segregational stability of an inserted plasmid expressing beta-galactosidase was increased by between 8 and 22 times…" an inserted plasmid expressing the hok/sok I'm assuming?

• The entire sentence is 'In an experiment testing the effect of temperature on the effectiveness of the hok/sok locus, it was found that segregational stability of an inserted plasmid expressing beta-galactosidase was increased by between 8 and 22 times compared to a control culture lacking a toxin-antitoxin system' which admittedly does seem confusing because although the study was temperature focused the data I quoted is not. I'm therefore going to remove the temperature mention as unimportant

• "The antibiotic works by either inhibiting the transcription of translation of the MazE antitoxin." …or?
• "This technique was applied to the paralysis toxin of Ixodes holocyclus." … and?

• This is just an example of the assay biotech application I was attempting to explain, the findings of the research cited aren't really important and it is cited if the reader is interested by it Jebus989^✰ 19:06, 19 October 2010 (UTC)

• "Ensuring a plasmid accepts an insert is a common problem" insert should be linked here rather than the next sentence
• Binomial species names should be italicized in the refs

Just a note to say I'm incredibly busy this week but will address these points as soon as I have time, thanks very much for the constructive feedback Jebus989^✰ 07:42, 11 October 2010 (UTC)

This is great feedback. Thanks Sasata. I'll do what I can.--Paul (talk) 20:20, 11 October 2010 (UTC)

• please check my copyedits to ensure I haven't unintentionally altered the meaning of something important

 Done Thanks for the in-depth ce, that must have taken some time

• can you add a sentence about fruiting body formation in Myxococcus xanthus, this is an unusual occurrence and a few words would help the reader (most drive-by readers will be unfamiliar with the idea of bacteria forming fruiting bodies). Perhaps also a brief explanation of the "stress pathway" which triggers this.

 Done Added sentence and ref regarding fruiting body formaiton, I made it clearer it was a nutrient-stress pathway without going into the nitty gritty metabolics

• the MOS says to avoid repeating the article title in section headers; currently "toxin-antitoxin" is repeated thrice. It might be worthwhile to consider combining the three types into one section and putting them into subsections (i.e. level three headers)

 Done I was aware of this but could not think of a way round it without making the titling awkward. I have take your advice and given an L2 Heading 'System types' which doesn't read that well but I'm stumped for something better.

• I'm not convinced the Biological applications section needs to be divided into subheaders, especially since some of the subsections are only two or three sentences long. Consider removing subheadings and just using paragraphs.

 Done Added a conjunctive to try and make them sit better as paragraphs

Sasata (talk) 22:38, 2 November 2010 (UTC)

I think my work is done here. As a service to the readers, you may want to finish the job of adding (subscription required) to external links to journal articles that are paywalled, as the tool only seems to catch those that don't have redirects. Otherwise, nice work, the article meets the GA criteria below, and I think is an excellent addition to the encyclopedia. Sasata (talk) 15:46, 6 November 2010 (UTC)

GA review (see here for criteria)

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The article Toxin-antitoxin system passes this review, and has been promoted to good article status. The article is found by the reviewing editor to be deserving of good article status based on the following criteria:

1. It is reasonably well written.

   a (prose): b (MoS):

2. It is factually accurate and verifiable.

   a (references): b (citations to reliable sources): c (OR):

3. It is broad in its coverage.

   a (major aspects): b (focused):

4. It follows the neutral point of view policy.

   Fair representation without bias:

5. It is stable.

   No edit wars, etc.:

6. It is illustrated by images, where possible and appropriate.

   a (images are tagged and non-free images have fair use rationales): b (appropriate use with suitable captions):

7. Overall:

   Pass/Fail: Pass

Additional infoboxes

The 6 new Pfam infoboxes stack awkwardly and have a negative effect on the page's layout, but to avoid acting own-y I don't think I should revert the additions at this point. They do of course have some useful links but may be better suited either in a gallery of sorts or just cut down to 2 or 3. I'd be interested if to hear if anyone else has an opinion on this. Thanks Jebus989^✰ 23:36, 11 January 2013 (UTC)

I wouldn't consider deleting these being "own-y". They don't contribute much to the page, other than the Pfam links. Perhaps an additional 'Pfam/X-links' column in the tables will suffice. Pfam should really be creating individual pages for the TA systems. --Paul (talk) 00:45, 14 January 2013 (UTC)

Hi

I will put the infoboxes into a table, as this will tidy the whole article. There are several more that need adding, as in E coli there are at least 19 protein-protein pairs, as well as 12 RNA-protein pairs of type I systems and several hop/sok systems.

thanks 2001:630:206:FFFF:0:0:3128:B (talk) —Preceding undated comment added 09:35, 14 January 2013 (UTC)

Ok thanks for input; for now I've commented out 5 of the infoboxes, they can still be found in the article source if anyone wants to work in a tidier solution. Maybe just a single collapsed infobox for all the type II? I'm not sure, if they're still commented out at some time in the future I'll try to find a solution or else remove the comments Jebus989^✰ 22:48, 16 January 2013 (UTC)

Expansion

There was a special issue of RNA Biology published recently with several reviews relating to TA systems. Could be some great sources for expanding this article Jebus989^✰ 14:55, 11 May 2013 (UTC)

There is also toxin/antitoxin system Type IV

References