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Talk:WikiJournal of Science/Lysenin

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Latest comment: 5 years ago by Marshallsumter in topic Final before publication non-specialist editorial suggestions
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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/2019.006'>

Article information

Submitting author: Ignacio L. B. Munguira[a][i]   
Additional contributors: Wikipedia community

See author information ▼
  1. ↑ Faculty of Science and Engineering, University of Groningen, Neatherlands
  1. ↑ i.lopez.de.blas@rug.nl

 

Plagiarism check

Latest comment: 5 years ago1 comment1 person in discussion

  Pass. WMF copyvio tool using TurnItIn. Fully unique content. T.Shafee(Evo﹠Evo)talk 09:05, 6 February 2019 (UTC)Reply

Initial editorial comments

Latest comment: 5 years ago1 comment1 person in discussion


Comments by Thomas Shafee ,
These editorial comments were submitted on , and refer to this previous version of the article

The article is almost ready for peer review, however the abstract is very short. Ideally it should summarise the key points of the subsequent sections of the article. I would suggest it to 100-200 words long for a short review article such as this. Could you therefore expand the abstract to cover the main topics.


Comments by Ian Alexander ,
These editorial comments were submitted on , and refer to this previous version of the article

The article needs copy-editing for use of English, and I'd suggest also for readability by non-specialists. I will make a brief pass on this but I would suggest a thorough checking-over.


Comments by Marshallsumter ,
These editorial comments were submitted on , and refer to this previous version of the article

I made some minor copy-edits for use of English in the abstract as a non-specialist. Have a read to see if I've kept your meaning intact. --Marshallsumter (discuss • contribs) 02:38, 12 February 2019 (UTC)Reply

 
editor-annotated pdf

Comments by Jack Nunn ,
These editorial comments were submitted on , and refer to this previous version of the article

Copyedits for language and readability and comments in attached PDF. See also edits in this diff.

Response

I will like to thank all the Editors for their comments. After them the article has improve a lot. I have accepted most of the changes, except those in which the meaning was different from the original one.

For Peer review

Latest comment: 5 years ago2 comments2 people in discussion

I wish to peer review the article Lysenin and dedicate myself for this journal's welfare. Also to gain an opportunity to develop myself further and brush my knowledge and research skills time by time. I completed my Post graduation and M.Phil in Biotechnology. I published 2 research papers in journals and 2 in conference proceedings. Now I am helping and motivating students to pursue in their research.--Sreenandhini (discuss • contribs) 16:26, 6 February 2019 (UTC)Reply

@Sreenandhini: Thank you for your offer to help reviewer this article. Whilst we contact specific experts to provide peer reviews, we are always happy to have anyone give feedback on an article in review. I have sent you an email where you can confirm your identity and credentials to contact WikiJSci.org. T.Shafee(Evo﹠Evo)talk 03:08, 7 February 2019 (UTC)Reply

First peer review


Review by Daniel Fologea , Boise State University, USA
These assessment comments were submitted on , and refer to this previous version of the article

The review entitled “Lysenin” and intended for the WikiJournal of Science addresses recent advancements in relation to lysenin interaction with membranes, channel oligomerization and pore formation. The major focus of the review is on lysenin binding to sphingomyelin, oligomerization, and channel insertion. The intricate mechanism by which lysenin transition from a water soluble form to a fully-formed pore is supported by X-ray and Cryo-EM data, as well as AFM measurements.

The title of the review is too general to properly reflect what the author(s) chose to present. This review is chiefly limited to descriptions of the steps that lead to channel formation and structural data. In my opinion, this is far from sufficient. Lysenin is one of the most intriguing pore-forming toxins with respect to its biological activity and functionality yet the author(s) overlooked such features.

Lysenin is considered a pore-forming toxin owing to its cytolytic activity. However, lysenin shares multiple salient features specific to ion channels, and such important biophysical properties are not mentioned in this review.

Response

The fact that the reviewer treat pore-forming toxins as channels for biotechnological purposes do not change its very nature as unspecific pores. Being unspecific pores its properties as channels are of none importance for the natural function of lysenin. However I included some studies about its biophysical properties as channels in a new section entitled “Applications” at the end of the review.

Lysenin forms a voltage gated channel when reconstituted in bilayers lipid membranes (1-4); interestingly, this feature is abrogated when the target membrane is composed of neutral lipids. In the presence of multivalent ions, lysenin channels present an intriguing ligand-induced gating (5, 6). While trivalent metals induce rapid and complete channel closing, divalent metal and multivalent organic ions elicit only partial closing of the channel (sub-conducting states), suggesting that charge density rather than net charge plays an important role in the gating mechanism. Notably, large polymeric cations induce irreversible blockage of the channels most probably through a trapping mechanism (7). Lysenin channels show a strong hysteresis in conductance (2), which may be linked to a gating mechanism that implies movement of the voltage sensor domain from the eater environment into the hydrophobic core of the membrane (8). Lysenin is a molecular tool useful for investigating the effects of surface crowding on the functionality of transmembrane transporters (9).

Response

Its true that lysenin was used to study the effects of crowding and I include the following paragraph about that at the end of the section "Lysenin binding, oligomerization and insertion"

"The prepore to pore transition can be blocked in crowded conditions, a mechanism that could be general to all β-PFTs.. The first hint of crowding effect on prepore to pore transition was given by congestion effects in electrophysiology experiments.[1] High-Speed AFM studies incubating Lysenin on sphingomyelin/cholesterol membranes has shown that under crowded conditions the prepore to pore transition gets blocked by steric interactions.[2][3]"

  1. ↑ Eric Krueger et al., “Intramembrane Congestion Effects on Lysenin Channel Voltage-Induced Gating,” European Biophysics Journal 45, no. 2 (2016): 187–94.
  2. ↑ Ignacio L.B. Munguira, “Effect of Crowdedness in the Life Cycle of Lysenin Studied by High-Speed Atomic Force Microscopy” (Aix-Marseille Universite, 2017), http://www.theses.fr/2017AIXM0124.
  3. ↑ Ignacio L.B. Munguira, Alfonso Barbas, and ignacio Casuso, “Mechanism of Blocking and Unblocking of the Pore Formation of the Toxin Lysenin Regulated by Local Crowding,” Under Submision.

Similar to other pore-forming proteins, lysenin may be used for single molecule detection and characterization by the resistive pulse technique (10) or to investigate interactions between protein channels and nanomaterials (11).

Response

The reviewer rise and important point that I overlock. I have added a section about the biotechnological applications of lysenin after the section entitled "Biological role".

"Lysenin conductive properties have been studied for years.[1] As most pore-forming toxins lysenin forms an unspecific channel also permeable to small peptides.[2] 2 Behind all those studies along more than three decades underlie the interest of finding a sequencing system biocompatible and with tunable conductive properties by point mutation.[3] Owing its binding affinity for sphingomyelin, lysenin or lysenin receptor binding domain has been used as a fluorescence marker to detect sphingomyelin domain in membranes.[4]"

  1. ↑ Bryant, S. et al. Insights into the Voltage Regulation Mechanism of the Pore-Forming Toxin Lysenin. Toxins 10, 334 (2018).
  2. ↑ Shrestha, N. et al. Stochastic sensing of angiotensin II with lysenin channels. Scientific reports 7, 2448 (2017).
  3. ↑ Deamer, D., Akeson, M. & Branton, D. Three decades of nanopore sequencing. Nature biotechnology 34, 518 (2016).
  4. ↑ Reiko Ishitsuka and Toshihide Kobayashi, “Lysenin: A New Tool for Investigating Membrane Lipid Organization,” Anatomical Science International 79, no. 4 (2004): 184.

In my opinion, the current version of the review on lysenin does not address many of the channel’s salient features; such additions will make the review more palatable to a broader audience and enhance the scientific impact.

Response

I add some references about the channel properties in a new section about the applications.

The current version also needs serious editing with regards to language, grammar, and English composition. A careful check of the references is needed; identical references appear multiple times and with different numbers in the list.

Response

I have revised the references in order to remove those references that appear multiple times with different names. The article was checked by some native speakers, however, any additional specific comment is welcome.

I would not recommend including work referenced as “under submission” in a review article since the interested readers may not have immediate access to those references.

  1. Fologea, D.; Krueger, E.; Lee, R.; Naglak, M.; Mazur, Y.; Henry, R.; Salamo, G. Controlled Gating of Lysenin Pores. Biophysical Chemistry 2010, 146, (1), 25-29.
  2. Fologea, D.; Krueger, E.; Mazur, Y. I.; Stith, C.; Okuyama, Y.; Henry, R.; Salamo, G. J. Bi-stability, hysteresis, and memory of voltage-gated lysenin channels. Biochimica et Biophysica Acta, Biomembranes 2011, 1808, (12), 2933-2939.
  3. Ide, T.; Aoki, T.; Takeuchi, Y.; Yanagida, T. Lysenin forms a voltage-dependent channel in artificial lipid bilayer membranes. Biochemical and Biophysical Research Communications 2006, 346, (1), 288-292.
  4. Kwiatkowska, K.; Hordejuk, R.; Szymczyk, P.; Kulma, M.; Abdel-Shakor, A.-B.; Plucienniczak, A.; Dolowy, K.; Szewczyk, A.; Sobota, A. Lysenin-His, a sphingomyelin-recognizing toxin, requires tryptophan 20 for cation-selective channel assembly but not for membrane binding. Molecular Membrane Biology 2007, 24, (2), 121-134.
  5. Fologea, D.; Al Faori, R.; Krueger, E.; Mazur, Y. I.; Kern, M.; Williams, M.; Mortazavi, A.; Henry, R.; Salamo, G. J. Potential analytical applications of lysenin channels for detection of multivalent ions. Analytical and Bioanalytical Chemistry 2011, 401, 1871-1879.
  6. Fologea, D.; Krueger, E.; Al Faori, R.; Lee, R.; Mazur, Y. I.; Henry, R.; Arnold, M.; Salamo, G. J. Multivalent ions control the transport through lysenin channels. Biophysical Chemistry 2010, 152, (1-3), 40-45.
  7. Fologea, D.; Krueger, E.; Rossland, S.; Bryant, S.; Foss, W.; Clark, T. Cationic polymers inhibit the conductance of lysenin channels. TheScientificWorldJournal 2013, 2013, 316758-316758.
  8. Bryant, S. L.; Clark, T.; Thomas, C. A.; Ware, K. S.; Bogard, A.; Calzacorta, C.; Prather, D.; Fologea, D. Insights into the Voltage Regulation Mechanism of the Pore-Forming Toxin Lysenin. Toxins 2018, 10, (8), 334.
  9. Krueger, E.; Bryant, S.; Shrestha, N.; Clark, T.; Hanna, C.; Pink, D.; Fologea, D. Intramembrane congestion effects on lysenin channel voltage-induced gating. European biophysics journal : EBJ 2016, 45, (2), 187-194.
  10. Shrestha, N.; Bryant, S. L.; Thomas, C.; Richtsmeier, D.; Pu, X.; Tinker, J.; Fologea, D. Stochastic sensing of Angiotensin II with lysenin channels. Scientific Reports 2017, 7, (1), 2448.
  11. Bryant, S. L.; Eixenberger, J. E.; Rossland, S.; Apsley, H.; Hoffmann, C.; Shrestha, N.; McHugh, M.; Punnoose, A.; Fologea, D. ZnO nanoparticles modulate the ionic transport and voltage regulation of lysenin nanochannels. Journal of Nanobiotechnology 2017, 15, (1), 90.

Spontaneous review

Latest comment: 5 years ago1 comment1 person in discussion

In my view the article entitled “lysenin” is good. But need some modifications and corrections. In my opinion,

a) Abstract: An ideal abstract should be the brief summary of the article (usually not exceeding 200 words) which helps to understand the key points of the article. I think it would be nice to have or expand the abstract with biological role of lysenin also.

b) The lysenin article only focused on the general idea of lysenin interaction, channel oligomerization and pore formation. And the biological information provided is not enough for a good scientific review. Due to these, the article is very far from adequate data. Could you please add more general and applied biological information about lysenin with suitable reference?

Response

If the reviewer find more biological information about the biological role of lysenin I will be really interested in read and include it.

c) I think these links will be useful for the lysenin article (biological information).

Response

There is no new biological information in those references.

d) Reference : Kindly provide links to the journals in the reference (that can be made more convenient by taking readers to a specific page and also helps to locate the source).

Response

I have no idea of how to do it, feel welcome to do it if you consider that is important. However, be aware that not all journals are open access.

e) I have made some minor changes directly to the article (Corrected the identical reference appeared in multiple times and also provided the links). Kindly go through it. And one thing also, the article needs serious editing with regards to English composition.

I hope the comments will be helpful for the authors.--Sreenandhini (discuss • contribs) 09:08, 15 May 2019 (UTC)Reply

Second peer review


Review by Milda Plečkaitytė , Institute of Biotechnology Vilnius University
These assessment comments were submitted on , and refer to this previous version of the article

The article Lysenin needs more condensed, structured information on the object presented in a clearer way. Below, please, find my suggestions to improve the article.

Abstract: the second sentence should be modified, as follows ‘Pore-forming toxins (PFTs) are proteinaceous virulence factors produced by many pathogenic bacteria. PFTs are produced also by archea, fungi, plants and animals’.

Response

I have modified the sentence following reviewer advice, to include all kingdoms of nature in which PFTs can be found.

The sentences “After the membrane attachment, the oligomerization results in a nonamer on top of the membrane. This oligomer is known as a prepore” need revision. I propose ‘After the membrane attachment, oligomerization of lysenin takes place and results in a nonamer on the lipid bilayer forming prepore before membrane insertion’.

Abstract also needs information on biological significance of lysenin.

Response

I have modified the sentence following reviewer advice and add two sentences at the end of the abstract in order to give some biological information.

I propose to rename the subchapter ‘Monomer’ to ‘Protein’ and present more structured information of lysenin as a protein in the following way

(starting from the 3rd sentence): ‘The topology of the lysenin structural fold specifies it to the aerolysin family of small β-pore-forming toxins (β- PFT) (Bokori-Brown et al., 2016). Structurally lysenin contains a receptor binding domain and a Pore Forming Module (PFM), which contributes

to β-barrel pore. Lysenin like other PFT’s is secreted as inactive, water-soluble monomer (33 kDa). Lysenin binds to sphingomyelin (SM) that is a

major lipid of the plasma membrane located mainly in its outer leaflet. Upon binding to SM, lysenin executes common assembly pathway for β- PFT: it forms oligomers, undergo structural rearrangements, inserts into membrane bilyer and form a pore.’

Response

There were two important data that I forgot to include. First, that monomer are water soluble. Second, sphingomyelin is mostly found in the outer membrane leaflet. Both are now included. I keep the section almost in its aroginal form since I want to keep all the information contained in it.

Subchapter ‘Membrane receptors’ should be modified as information like “In lysenin, the detergent belt is 32 Å in height” is not clear for the readers. I propose to combine this subchapter with the next one under the name like ‘Mechanism of oligomeric assembly and pore formation’. This subchapter needs revision presenting the described events of lysenin pore formation in a coherent and sequential way, e.g. nine monomers that compose oligomeric lysenin is repeated twice.

Response

I have tried to remove redundancies and clarify some concepts.

Final before publication non-specialist editorial suggestions

Latest comment: 5 years ago1 comment1 person in discussion
  1. Line 1: "Lysenin is a pore-forming toxin in the coelomic fluid of the earthworm Eisenia fetida." to "Lysenin is a pore-forming toxin (PFT) produced by the earthworm Eisenia fetida in its coelomic fluid."
  2. Line 2: "Pore-forming toxins (PFTs) are proteinaceous virulence factors produced by many pathogenic bacteria." to "PFTs are often proteinaceous virulence factors produced by many pathogenic bacteria."
  3. Line 11: "the most plausible theory is that it is part of an immune-avoiding mechanism. " to "the most plausible theory is that it is part of an immune-avoidance mechanism."
  4. Line 13: "There are many proposed technological applications proposed for lysenin, and understanding its molecular role in bacterial infection could help in developing different antibiotic strategies to solve the problem of multiple drug resistance in bacteria." to "The technological applications proposed for lysenin include its molecular role in bacterial infection to help develop different antibiotic strategies for the problem of multiple drug resistance in bacteria."
  5. Line 23: "Lysenin is a relatively small water-soluble molecule with a molecular weight of 33 kDa (Figure 1)." to "Lysenin is a relatively small water-soluble molecule (Figure 1) with a molecular weight of 33 kDa."
  6. Line 24: "Using X-ray crystallography, lysenin was classified as a member of the Aerolysin protein family by structure and function." to "Using X-ray crystallography, lysenin was classified as a member of the aerolysin protein family by structure and function."
  7. Line 37: "involving at least three of its phosphatidylcholines (PC) groups." to "involving at least three of its phosphatidylcholines groups." The abbreviation PC isn't used again.
  8. Line 44: "The region of the lysenin pore β-barrel expected to be inmersed in the hydrophobic region" to "The lysenin pore β-barrel expected to be immersed in the hydrophobic region".
  9. Line 45: "'detergent belt', the 3.2 nm high region occupied by detergent in" to "3.2 nm high 'detergent belt' in".
  10. Line 46: "sphingomyelin/Cholesterol" to "sphingomyelin/cholesterol".
  11. Line 54: "As with most PFTs, lysenin oligomerization occurs in a two-step process, as was recently imaged." to "As with most PFTs, lysenin oligomerization occurs in a two-step process recently imaged."
  12. Line 63: "Determining the prepore's structure by X-ray or Cryo-EM is a challenging process that so far has not produced any results." to "Determining the prepore's structure by X-ray or Cryo-EM has not produced results."
  13. Line 66: "and the width 118 Å" to "and the diameter 118 Å".
  14. Line 68: "A recent study in aerolysin suggests that the currently accepted model for the lysenin prepore should be revisited, according to the new available data on the aerolysin insertion." to "A recent study of aerolysin insertion suggests that the currently accepted model for the lysenin prepore should be revisited."
  15. Line 83: "and glutamic acids are found in aerolysin family members in its PFMs." to "and these are found in aerolysin family members."
  16. Line 91: "width 115 Å" to "diameter 115 Å".
  17. Line 94: "a mechanism that could be general to all β-PFTs. The first hint of crowding effect on" to "a mechanism that may occur in all β-PFTs. The first hint of crowding on".
  18. Line 95: "High-Speed AFM studies incubating lysenin on sphingomyelin/cholesterol membranes has shown" to "High-Speed AFM studies incubating lysenin on sphingomyelin/cholesterol membranes have shown".
  19. Line 99: "however, it is through to induce apoptosis via three possible hypotheses:" to "however, apoptosis can be induced via three possible hypotheses:". --Marshallsumter (discuss • contribs) 17:40, 9 August 2019 (UTC)Reply
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