Talk:WikiJournal of Science/Lysine: biosynthesis, catabolism and roles

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WikiJournal of Science is an open-access, free-to-publish, Wikipedia-integrated academic journal for science, mathematics, engineering and technology topics. WJS WikiJSci Wiki.J.Sci. WikiJSci WikiSci WikiScience Wikiscience Wikijournal of Science Wikiversity Journal of Science WikiJournal Science Wikipedia Science Wikipedia science journal STEM Science Mathematics Engineering Technology Free to publish Open access Open-access Non-profit online journal Public peer review

<meta name='citation_doi' value='10.15347/wjs/2018.004'>

Article information

Authors: Cody J. Hall, Tatiana P. Soares da Costa Orcid icon.png [i]

Plagiarism check[edit]

Artículo bueno.svg Pass. Report from WMF copyvio tool using TurnItIn, with no plagiarism detected. T.Shafee(Evo﹠Evo)talk 11:09, 9 January 2018 (UTC)

Reader Comments[edit]

Would it be possible for the authors to include a section on compliance with ethical standards to the end of this manuscript. A suitable section for this paper would be (if there are indeed no conflicts of interest and no studies with human or animal subjects):

Compliance with Ethical Standards
Conflicts of Interest
Cody J. Hall has not declared any potential conflits of interest
Tatiana P. Soares da Costa has not declared any potential conflicts of interest
Human and animal Subjects
This article does not contain any studes with human or animal subjects performed by any of the authors

Van Vlijmen (discusscontribs) 07:05, 15 February 2018 (UTC)

First peer review[edit]

Lysine Biosnythesis Catabolism Roles review TL.pdf

A


Reviewer-annotated pdf file.

Review by Tom Leustek  
This review was submitted on 2018-02-15, and refers to this previous version of the article

The reviewer submits suggested edits in the attached PDF

Second peer review[edit]

Review by Sander Houten  
This review was submitted on 2018-03-27, and refers to this previous version of the article

This is a nicely written article on lysine. It is difficult to tackle such a massive topic in a comprehensive article. With my main comments I try to make sure that despite its comprehensiveness, the article is accurate. I have mainly focused on my expertise, which is lysine degradation.


The role of lysine in carnitine biosynthesis: This is a complex topic that is almost impossible to cover. A few points are important though. Carnitine is not synthesized directly from free lysine. Carnitine is synthesized from trimethyllysine, which is derived from protein degradation. Thus lysine first needs to be incorporated in specific proteins and then trimethylated (dependent on methionine as every other methylation reaction). Upon turnover of this protein the trimethyllysine becomes available for carnitine biosynthesis. In most people, the majority of carnitine is not derived from biosynthesis but directly from food intake. For more info see PMID: 11802770.

I am not so sure how often humans have deficiencies of lysine. This may be more frequent in the context of general malnutrition. But with general malnutrition, carnitine intake will also be low. In any case, I thought it is problematic to list impaired fatty acid metabolism as a disease state associated with a lack of lysine.

Overabundance of lysine (hyperlysinemia) is caused by mutations in AASS. Although hyperlysinemia has been associated with neurological disease, the consensus in the field is that hyperlysinemia is a biochemical phenotype of questionable clinical significance. For more info see PMID: 6407303. This paper is important and needs to be referenced.

The description of the catabolic pathway could be improved. I note the following points:

The bifunctional enzyme harboring LKR and SDH activities has been named alpha-aminoadipic semialdehyde synthase encoded by AASS.

It would be nice if the official gene names are mentioned for each enzyme. For example, AASD is encoded by ALDH7A1, and PLP-AT is encoded by AADAT.

You are considering the decarboxylation of 2-ketoadipic as the final step (“Finally”). I would argue that you should at least include glutaryl-CoA dehydrogenase, because this enzyme step is generally considered as part of the lysine catabolic pathway. Glutaryl-CoA dehydrogenase is encoded by GCDH.

2-Ketoadipic acid is not decarboxylated by the oxoglutarate dehydrogenase complex (OGDHc). Although this step has not been fully elucidated yet, it is clear that there is a homolog of the E1 subunit of OGDHc encoded by DHTKD1 that is crucial for the decarboxylation of 2-ketoadipic acid. It is probably safe to call this enzyme the 2-oxoadipate dehydrogenase complex.

The following sentence: ”There is also a hereditary genetic disease that involves mutations in the enzymes responsible for lysine catabolism, namely the bifunctional LKR-SDH enzyme of the saccharopine pathway (Fig. 3)” is incomplete. It is probably better to highlight that in addition the hyperlysinemia (due to mutations in AASS), there are 3 other inborn errors of lysine catabolism. Pyridoxine-dependent epilepsia is caused by mutations in ALDH7A1, alpha-aminoadipic and alpha-ketoadipic aciduria is caused by mutations in DHTKD1 and finally Glutaric Aciduria Type 1 is caused by mutations in GCDH. Of these alpha-aminoadipic and alpha-ketoadipic aciduria is considered a biochemical phenotype of questionable clinical significance, just like hyperlysinemia. Pyridoxine-dependent epilepsia and Glutaric Aciduria Type 1 are clinically relevant disorders.

It is also interesting to note that all these catabolic enzymes are mitochondrial. Thus lysine catabolism is a mitochondrial process.

This text is available under the Creative Commons Attribution/Share-Alike 3.0 Unported License
The reviewer has not declared any potential conflits of interest

Author response[edit]

The authors responded to the above reviews on with these updates between 15 January and 11 April.

The use of the term "psychomotor retardation"[edit]

Comments by Andrew Leung
After consulting with WJM editorial board, we agreed to replace "psychomotor retardation" with "psychomotor impairment" due to the negative connotation associated with the use of the word "retardation". 23:11, 27 May 2018 (UTC)