Talk:WikiJournal of Science/Arabinogalactan-proteins

Peer review 1
{{review
 * reviewer = Milan Dragićević
 * affiliation = Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Bul. despota Stefana 142, 11000 Belgrade, Serbia
 * credentials = In the last several years I have been investigating Arabinogalactan proteins from a data science perspective. Relevant publications are: and . I am lead developer and maintainer of ragp R package for HRGP filtering and analysis . My other publications can be seen on my orcid page:
 * link = http://www.ibiss.bg.ac.rs/index.php/en/
 * version = https://en.wikiversity.org/w/index.php?title=WikiJournal_Preprints/Arabinogalactan-proteins&oldid=2189570
 * date = 18 August 2020
 * text = The WikiJournal article by Ma and Johnson about arabinogalactan-proteins (AGPs) is an excellent overview of the current knowledge about AGPs. The article is short but dense with information covering specificities in AGP protein backbones, classification, biosynthesis of the carbohydrate chains, addition of GPI, as well functional roles.

The article is clear and well written, and I found it quite easy to follow. I trust it will be accessible to a wide readership.

Some potential issues I noticed are:


 * In the introductory paragraph the authors mention APGs have industrial and health applications however this is not covered later in the text. A short subsection about the human uses of AGP-s could be beneficial for the readers.

{{response|The following has been added to the AGP functions section:
 * {{tq|Human uses of AGPs include the use of Gum arabic in the food and pharmaceutical industries because of natural properties in thickening and emulsification, AGPs in cereal grains have potential applications in biofortification, as sources of dietary fibre to support gut bacteria and protective agents against ethanol toxicity.}}

}}


 * I found it surprising that it was not mentioned in the article AGPs/AGP-regions are intrinsically disordered (Johnson et al., 2017). I trust one or two sentences about this would fit in the "AGP protein backbones and classification" subsection.

{{response|The following has been added to the AGP protein backbones and classification section:
 * {{tq|AGPs are intrinsically disordered proteins as they contain a high proportion of disordering amino acids such as Proline that disrupt the formation of stable folded structures. Characteristic of intrinsically disordered proteins, AGPs also contain repeat motifs and post-translational modifications.}}

}}
 * In my opinion addition of hyperlinks would enhance the article since it would allow the readers to quickly expand on some topic they find interesting. For instance PubMed (or other) links for cited articles and Uniprot links for sequences in table 1.

{{response|Hyperlinks to additional references have been added throughout.}}


 * When discussing chimeric AGPs it could be mentioned that based on sequence analysis other domains (for instance protein kinase domain, X8 and some others) can most likely be partnered with AGP-like sequences (Hwang et al., 2016, Ma et al., 2017, Dragićević et al., 2020).

{{response|We have added the following to the chimeric AGP section:
 * {{tq|Several other putative chimeric AGP classes have been identified that include AG glycomotifs associated with protein kinase, leucine-rich repeat, X8, FH2 and other protein family domains’}}

}}

I suggest rearranging "PFAM (protein family)" to "protein family (PFAM)".

{{response|corrected}}

"cysteine (C)-containing domains" should be rephrased if the authors meant to say cysteine-rich.

{{response|corrected}}

An additional figure (Figure 3) with the schematic structure of a typical AG glycan, with marked enzymes involved in specific steps, would make the section "AGP biosynthesis" easier to follow.

{{response|While we appreciate this would be a good addition, this exact figure is about to be published elsewhere and we would prefer to add the reference.}}

The sentence:

"These include the assembly of tri-mannose, galactose and ethanolamine phosphate to form the mature GPI moiety."

should be checked. Specifically galactose should most likely be replaced with non-N-acetylated glucosamin (Oxley and Bacic 1999, Kinoshita and Fujita, 2016) as mentioned latter in the paragraph:

"The core glycan structure of GPI anchors is Man-α-1,2-Man-α-1,6-Man-α-1,4-GlcN-inositol..."

Or if the authors intended to reference the partial substitution of the 6-linked Man with Gal (Oxley and Bacic 1999) then the mention of Gal should be left as is, while GlcN should just be added to the sentence.

{{response|Corrected to include non-N-acetylated glucosamine (GlcN).}}

The reference list should be cleaned. It contains duplicates with slightly different formatting. Some examples are:

Knoch E, Dilokpimol A, Tryfona T, Poulsen CP, Xiong G, Harholt J (2013) A β–glucuronosyltransferase from Arabidopsis thaliana involved in biosynthesis of type II arabinogalactan has a role in cell elongation during seedling growth. Plant J 76 Knoch E, Dilokpimol A, Tryfona T, Poulsen CP, Xiong G, Harholt J, Petersen BL, Ulvskov P, Hadi MZ, Kotake T, Tsumuraya Y, Pauly M, Dupree P, Geshi N (2013) A beta-glucuronosyltransferase from Arabidopsis thaliana involved in biosynthesis of type II arabinogalactan has a role in cell elongation during seedling growth. Plant J 76: 1016-1029

Oxley D, & Bacic, A (1999) Structure of the glycosylphosphatidylinositol anchor of an arabinogalactan protein from Pyrus communis suspension-cultured cells. Proc Natl Acad Sci U S A 96: 14246-14251 Oxley D, Bacic A (1999) Structure of the glycosylphosphatidylinositol anchor of an arabinogalactan protein from Pyrus communis suspension-cultured cells. Proc Natl Acad Sci U S A 96: 14246-14251

Showalter AM, Keppler B, Lichtenberg J, Gu D, Welch LR (2010) A bioinformatics approach to the identification, classification, and analysis of hydroxyproline-rich glycoproteins. Plant Physiol 153: 485-513 Showalter AM, Keppler B, Lichtenberg J, Gu D, Welch R (2010) A Bioinformatics approach to the identification, classification, and analysis of hydroxyproline-Rich glycoproteins. Plant Physiol 153: 485–513

Tang XC, He YQ, Wang Y, Sun MX (2006) The role of arabinogalactan proteins binding to Yariv reagents in the initiation, cell developmental fate, and maintenance of microspore embryogenesis in Brassica napus L. cv. Topas. J Exp Bot 57: 2639-2650 Tang XC, He YQ, Wang Y, Sun MX (2006) The role of arabinogalactan proteins binding to Yariv reagents in the initiation, cell developmental fate, and maintenance of microspore embryogenesis in Brassica napus L. cv. Topas. J Exp Bot. 57: 2639-2650

Van-Hengel AJ, Roberts K (2003) AtAGP30, an arabinogalactan-protein in the cell walls of the primary root, plays a role in root regeneration and seed germination. Plant J 36: 256–270 van Hengel AJ, Roberts K (2003) AtAGP30, an arabinogalactan-protein in the cell walls of the primary root, plays a role in root regeneration and seed germination. Plant Journal 36: 256-270

Johnson KL, Cassin AM, Lonsdale A, Wong GK-S, Soltis D, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ (2017b) Insights into the evolution of hydroxyproline rich glycoproteins from 1000 plant transcriptomes. Plant Physiology Johnson KL, Cassin AM, Lonsdale A, Wong GK, Soltis DE, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ (2017) Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes. Plant Physiol 174: 904-921

Johnson KL, Cassin AM, Lonsdale A, Bacic A, Doblin MS, Schultz CJ (2017) Pipeline to Identify Hydroxyproline-Rich Glycoproteins. Plant Physiol 174: 886-903 Johnson KL, Cassin AM, Lonsdale A, Bacic A, Doblin MS, Schultz CJ (2017a) A motif and amino acid bias bioinformatics pipeline to identify hydroxyproline-rich glycoproteins. Plant Physiology

Gaspar Y, Johnson KL, McKenna JA, Bacic A, Schultz CJ (2001) The complex structures of arabinogalactan-proteins and the journey towards understanding function. Plant Mol Biol. 47: 161-176 Gaspar Y, Johnson, K. L., McKenna, J. A., Bacic, A., & Schultz, C. J. (2001) The complex structures of arabinogalactan-proteins and the journey towards understanding function. Plant Mol Biol 47: 161-176

Gaspar YM, Nam J, Schultz CJ, Lee L-Y, Gilson PR, Gelvin SB, Bacic A (2004) Characterization of the Arabidopsis Lysine-Rich Arabinogalactan-Protein AtAGP17 Mutant (rat1) That Results in a Decreased Efficiency of Agrobacterium Transformation. Plant Physiology 135: 2162-2171 Gaspar YM, Nam J, Schultz CJ, Lee LY, Gilson PR, Gelvin SB, Bacic A (2004) Characterization of the Arabidopsis lysine-rich arabinogalactan-protein AtAGP17 mutant (rat1) that results in a decreased efficiency of agrobacterium transformation. Plant Physiol 135: 2162-2171

Ellis M, Egelund J, Schultz CJ, Bacic A (2010) Arabinogalactan-Proteins: Key Regulators at the Cell Surface? Plant Physiol 153: 403-419 Ellis M, Egelund J, Schultz CJ, Bacic A (2010) Arabinogalactan-proteins: key regulators at the cell surface? Plant Physiol 153: 403-419 Ellis M, Egelund J, Schultz CJ, Bacic A (2010) Arabinogalactan proteins: key regulators at the cell surface? Plant Physiol 153: 403-419

Overall the article is a good review of the current knowledge about AGPs.