Talk:WikiJournal Preprints/Arabinogalactan-proteins

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Article information

Authors: Yingxuan Ma[a], Kim Johnson[a][i]ORCID iD.svg 

Yingxuan Ma; Kim Johnson, Arabinogalactan-proteins, Wikidata Q99557488





Peer review 1[edit source]

Review by Milan Dragićević , Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Bul. despota Stefana 142, 11000 Belgrade, Serbia | In the last several years I have been investigating Arabinogalactan proteins from a data science perspective. Relevant publications are: [1] and [2]. I am lead developer and maintainer of ragp R package for HRGP filtering and analysis [3]. My other publications can be seen on my orcid page: [4]
This review was submitted on , and refers to this previous version of the article


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:

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:

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:

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.

References

Johnson KL, Cassin AM, Lonsdale A, Bacic A, Doblin MS, Schultz CJ (2017) Pipeline to Identify Hydroxyproline-Rich Glycoproteins. Plant Physiology 174: 886-903

Hwang Y, Lee H, Lee Y-S, Cho H-T (2016) Cell wall-associated ROOT HAIR SPECIFIC 10, a proline-rich receptor-like kinase, is a negative modulator of Arabidopsis root hair growth. Journal of Experimental Botany 67(6): 2007–2022.

Ma Y, Yan C, Li H, Wu W, Liu Y, Wang Y, Chen Q, Ma H. (2017) Bioinformatics prediction and evolution analysis of arabinogalactan proteins in the plant kingdom. Frontiers in Plant Science 8:66.

Dragićević M, Paunović D, Bogdanović M, Todorović S, Simonović A (2020) ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. Glycobiology 30(1):19–35

Oxley D, Bacic A (1999) Structure of the glycosylphosphatidylinositol anchor of an arabinogalactan protein from Pyrus communis suspension-cultured cells. PNAS 96(25):14246-14251

Kinoshita1 T, and Morihisa Fujita M (2016) Biosynthesis of GPI-anchored proteins: special emphasis on GPI lipid remodeling. The Journal of Lipid Research 57:6-24.

Response

We apologise for the disordered reference list. This has now been corrected.

Peer review 2[edit source]

Review by Elisabeth Jamet , CNRS
This review was submitted on , and refers to this previous version of the article


This is a clear review collecting the present knowledge about the description of arabinogalactan proteins (AGPs) and their functions.

I suggest adding their possible roles in calcium signaling as proposed by Lamport and Varnai (2013, New Phytol 197: 58), Lamport et al. (2018, Int J Mol Sci 19 : 2674) and Lamport et al (2020, Int J Mol 21: 1145). In the same way, the review article by Seifert (2018, Int J Mol Sci 19: 1628) could be quoted. It proposes roles in cell-to-cell or cell-to extracellular matrix adhesion for the fasciclin AGPs (FLAs).

Response

The following addition has been made in the AGP function section:

The functional mechanisms of AGPs in cell signalling is not well understood. One proposed model suggests AGPs can interact and control the release of calcium from AG glycan (via GlcA residues) to trigger downstream signalling pathways mediated by calcium. Another possible mechanism, largely based on the study of FLAs, suggest the combination of fascicilin domain and AG glycans can mediate cell-cell adhesion.

In addition, the description of Cys-rich domains could be more precise. They have also been called PAC domains by Baldwin et al. (2000, The C‐terminal PAC domain of a secreted arabinogalactan protein from carrot defines a family of basic proline‐rich proteins. In Cell and Developmental Biology ofArabinogalactan Proteins, New York: Kluwer Academic Publishers, pp 43‐50). They have been more precisely described in a recent review by Nguyen-Kim et al. (2020, Int J Mol Sci 21, 2488).

Response

The term PAC domain and references have been added.

Some minor points : (i) dry mass instead of dry weight, (ii) protein assembly instead of protein assemble, (iii) ref Fincher and Stone (1983) should be numbered, (iv) Tyr motifs are only mentioned in legend to figure 2, (v) organize the references quoted in the text in ascending order. Please carefully check the references: (i) some of them are mentioned twice, (ii) the title of ref 16 is missing and its doi is indicated twice, (iii) ref 78 is incomplete.

Response

These have been corrected.


Review by Elisabeth Jamet ,
This review was submitted on , and refers to this previous version of the article


My questions have been answered and I wish to thank the authors for the modifications already done.

However, I think that there is an incomplete sentence starting after Figure 1: "...component of AGPs is rich in the amino acids Proline (P), Alanine (A), Serine (S) and Threonine (T), or ‘PAST’.

Response

The sentence now reads: component of AGPs is rich in the amino acids Proline (P), Alanine (A), Serine (S) and Threonine (T), also known as ‘PAST’, and this amino acid bias is one of the features used to identify them.

A few minor modifications:

1- "Other ‘non-classical’ AGPs exist such as histidine(H)-rich and cysteine(C)-rich, also called PAC domains"

Rather: "Other non-classical AGPs exist such as those containing a histidine(H)-rich doamin and/or a cysteine(C)-rich domain, also called PAC domain."

Indeed, only the PAC domain is Cys-rich.

Response

The sentence has been modified as follows to improve clarity: Other non-classical AGPs exist such as those containing a cysteine(C)-rich domain, also called PAC domains, and/or histidine(H)-rich domain,[1][2] as well as many hybrid HRGPs that have motifs characteristic of AGPs and other HRGP members, usually extensin and Tyr motifs

2- "a suite of glycosyl *transferases* (GTs)"

Response

Corrected.

3- "The GT31 family is the most likely family involved in AGP glycan backbone biosynthesis."

Rather: "The GT31 family is one of the families involved in AGP glycan backbone biosynthesis"

Indeed, as mentioned, several GT families are involved in the biosynthesis of AGP glycans.

Response

This has been corrected as suggested and we thank the reviewer for their suggestions that have greatly improved the article.

Peer review 3[edit source]

Review by Azeddine Driouich , University of Rouen, France
This review was submitted on , and refers to this previous version of the article


This is an interesting contribution. However, certain important information is lacking: to be completed (see comments below)

Line 10 ” …AGPs are particularly abundant in the stems of gymnosperms…”. This is not true. Please check and correct. And again the authors wrote: “AGPs are particularly abundant in floral organs” (see line 4, first paragraph of Functional Roles). This is quite confusing…AGPs are abundant in many other organs, tissues and secretions (root..etc.). The relative abundance of AGPs between organs, tissues, and species…is not known!

Response

The following has been deleted in the Line 10:

‘and are particularly abundant in the stems of gymnosperms and angiosperms’

The following change has been made in “AGPs functional roles” paragraph 2:

‘AGPs are found in a wide range of plant tissues, in secretions of cell culture medium of root, leaf, endosperm and embryo tissues, and some exudate producing cell types such as stylar canal cells.’

The last sentence of the second paragraph “The addition of the GPI occurs in most but not all AGPs”. This is not known! Clearly we do not know if most of them or half of them, or whatsoever % of them are GPI-anchored….it may also depend on the cell type, organs, species…etc.!

Response

The following change has been made in paragraph 3 of “AGP biosynthesis” section:

‘Bioinformatic analysis predicts the addition of a GPI-anchor on many AGPs’

In Fig. 2, I do not see where the Gal residues (green square) are on the structures presented. I would suggest to make that figure simpler!

Response

The Gal residues (green square) are presented in the middle and C-terminal end of “Hybrid AGP” structure. The size of Gal is in comparison to the (Ara)1-4 structure.

On AGP biosynthesis: are we sure that the O-glycosylation of AGP occurs in the ER (as the authors wrote)? It is well established that the N-glycosylation (of N-linked glycoproteins) does occur in the ER? But how about the O-glycosylation of AGPs? A number of papers do present O-glycosylation of AGPs as occurring in the Golgi not in the ER! To check please and correct!

Response

The text has been modified as follows to clarify this point:

Glycosylation of the AGP backbone is suggested to initiate in the ER with the addition of first Gal by O-galactosyltransferase, which is predominantly located in ER fractions (Oka et al., 2010). Chain extension then occurs primarily in the GA (Kato et al., 2003)

On Functional roles. This part is not complete. Nothing is said on the role of AGP in root-microbe interaction although a number of papers are published on that aspect (see the papers by Cannesan et al., 2012. Plant Physiology; NguemaOna et al., 2013 Trends in Plant science; Xie et al., 2012 Mol. Plant. Interact) : these are some of the papers to be considered in this review.

Response

We apologise for missing this information. The following changes have been made to paragraph 2 of “AGPs functional roles” section.

AGPs have been shown to regulate many aspects of plant growth and development including male-female recognition in reproduction organs, cell division and differentiation in embryo and post-embryo development, seed mucilage cell wall development, root salt tolerance and root-microbe interactions (see Table 1). ) (Ellis et al., 2010; NguemaOna et al., 2013).

Do add the rat1 mutant in the table (paper by Gaspar, et al. 2004. Plant Physiology.

Response

AtAGP17 has been added to Table 1

As for the role of AGP in development: it would be good to add the information found in the paper by Seifert et al., 2002. Current biology, on the reb1-1 mutant! Also the paper by NguemaOna et al., on the reb1-1 mutant (Plant Physiology, 2006).

Response

In Table 1 we list functions of AGPs or clusters of AGPs and do not include proteins involved in AGP synthesis (like reb1-1 mutant and many others). We believe this information is best covered in a separate article.

On the effect of beta-glucosyl Yariv in relation to development: the information on the effect of Yariv on the relationship between cortical microtubules and AGP (for the control of cell morphology and root development) is something to be considered here as well (see paper by NguemaOna et al., 2007. The Plant J and the paper by Driouich and Baskin, 2008. American J Bot).

Response

As these articles are largely hypothetical mechanisms for how beta-glucosyl Yariv might regulate plant development via regulating AGPs/microtubules we have not included this information.

AGPs do also occur in Algae (not only in higher plants): see the paper by Herve et al., 2016. New Phytologist. Should be included.

Response

Brown algal AGPs are listed in Table 1: “FsAGP” in “Embryogenesis” section. In addition we have added the following to the AGP protein backbones and classification section.

AGPs are evolutionarily ancient and have been identified in green algae as well as Chromista and Glaucophyta {Johnson, 2017b; Herve, 2016}. Found throughout the entire plant lineage, land plants are suggested to have inherited and diversified the existing AGP protein backbone genes present in algae to generate an enormous number of AGP glycoforms.