Non‐Enzymic Cell Wall (glyco)Proteins

Johnson, Kim L.; Schultz, Carolyn J.; Bacic, Antony

doi:10.1002/9781119312994.apr0070

Cited by 13 publications

(18 citation statements)

References 225 publications

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“…Chimeric HRGPs have a recognized PFAM domain (black vertical lined box; B, E, and H) in addition to a HRGP region. (Johnson et al, 2003b), containing a PFAM domain like those identified in Populus trichocarpa using the revised BIO OHIO 2.0 program . Thus, Showalter et al (2010Showalter et al ( , 2016) used a combination of both bias and motifs to search for PRPs [45% or greater PVKCYT or 2 or more KKPCPP motifs or 2 or more PPVX(K/T) motifs] in Arabidopsis and P. trichocarpa.…”

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confidence: 99%

“…The protein backbone of AGPs is rich in the amino acids Pro/Hyp, Ala, Ser, and Thr of PAST (Schultz et al, 2002;Ma and Zhao, 2010;Showalter et al, 2010). A biased amino acid approach (50% or greater PAST) was developed to detect Arabidopsis (Arabidopsis thaliana) AGPs (Schultz et al, 2002), which also identified some EXTs and PRPs (Johnson et al, 2003b). Showalter et al (2010) modified this approach, developing BIO OHIO to include a mix of different strategies: a biased amino acid approach was used for AGPs (50% or greater PAST), a motif-based search for EXTs (two or more SP 4 [or SP 3 ]) motifs, and a combination of both methods for PRPs.…”

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confidence: 99%

“…Many EXTs also include Y-based CL motifs, and searching for SP 3-5 motifs identifies both EXTs with Y motifs (CL-EXTs) or without (non-CL-EXTs). PRPs are the most difficult class of HRGPs to define (Johnson et al, 2003b;Showalter et al, 2010). Arabidopsis has two distinct sub-classes of PRPs, one rich in PTYK (e.g.…”

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confidence: 99%

“…HRGPs are commonly divided into three major multigene families, the arabinogalactan proteins (AGPs), extensins (EXTs), and Pro-rich proteins (PRPs), but in reality, a continuum of HRGPs exists, including hybrids with features from multiple HRGP families, chimeric HRGPs that contain additional non-HRGP protein domains, and very small proteins, such as the arabinogalactan (AG)-peptides ( Fig. 1; Johnson et al, 2003b). The common thread that defines this diverse family is the hydroxylation of Pro to Hyp (O) and the subsequent attachment of O-linked glycans on Hyp residues.…”

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confidence: 99%

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Pipeline to Identify Hydroxyproline-Rich Glycoproteins

et al. 2017

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Intrinsically disordered proteins (IDPs) are functional proteins that lack a well-defined three-dimensional structure. The study of IDPs is a rapidly growing area as the crucial biological functions of more of these proteins are uncovered. In plants, IDPs are implicated in plant stress responses, signaling, and regulatory processes. A superfamily of cell wall proteins, the hydroxyprolinerich glycoproteins (HRGPs), have characteristic features of IDPs. Their protein backbones are rich in the disordering amino acid proline, they contain repeated sequence motifs and extensive posttranslational modifications (glycosylation), and they have been implicated in many biological functions. HRGPs are evolutionarily ancient, having been isolated from the protein-rich walls of chlorophyte algae to the cellulose-rich walls of embryophytes. Examination of HRGPs in a range of plant species should provide valuable insights into how they have evolved. Commonly divided into the arabinogalactan proteins, extensins, and proline-rich proteins, in reality, a continuum of structures exists within this diverse and heterogenous superfamily. An inability to accurately classify HRGPs leads to inconsistent gene ontologies limiting the identification of HRGP classes in existing and emerging omics data sets. We present a novel and robust motif and amino acid bias (MAAB) bioinformatics pipeline to classify HRGPs into 23 descriptive subclasses. Validation of MAAB was achieved using available genomic resources and then applied to the 1000 Plants transcriptome project (www.onekp.com) data set. Significant improvement in the detection of HRGPs using multiple-kmer transcriptome assembly methodology was observed. The MAAB pipeline is readily adaptable and can be modified to optimize the recovery of IDPs from other organisms.

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Pipeline to Identify Hydroxyproline-Rich Glycoproteins

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“…In the current study, protein and transcript levels of shikimate/quinate HCT were lower in MS than in FS, consistent with lower lignin accumulation in MS. Moreover, four lipid-transfer proteins, eight serine proteases, and six fasciclin domain proteins (including 3 fasciclin-like arabinogalactan protein, FLA) were also enriched in stems, and these proteins have been reported to participate in cell wall maturation and secondary growth [31,32].…”

Section: Involvement Of Lignin Biosynthesis In the Regulation Of Stemmentioning

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iTRAQ-based comparative proteomic analysis of differences in the protein profiles of stems and leaves from two alfalfa genotypes

Sun

Zhang

et al. 2020

BMC Plant Biol

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Background To explore the molecular regulatory mechanisms of early stem and leaf development, proteomic analysis was performed on leaves and stems of F genotype alfalfa, with thin stems and small leaves, and M genotype alfalfa, with thick stems and large leaves. Results Based on fold-change thresholds of > 1.20 or < 0.83 (p < 0.05), a large number of proteins were identified as being differentially enriched between the M and F genotypes: 249 downregulated and 139 upregulated in stems and 164 downregulated and 134 upregulated in leaves. The differentially enriched proteins in stems were mainly involved in amino acid biosynthesis, phenylpropanoid biosynthesis, carbon fixation, and phenylalanine metabolism. The differentially enriched proteins in leaves were mainly involved in porphyrin and chlorophyll metabolism, phenylpropanoid biosynthesis, starch and sucrose metabolism, and carbon fixation in photosynthetic organisms. Six differentially enriched proteins were mapped onto the porphyrin and chlorophyll metabolism pathway in leaves of the M genotype, including five upregulated proteins involved in chlorophyll biosynthesis and one downregulated protein involved in chlorophyll degradation. Eleven differentially enriched proteins were mapped onto the phenylpropanoid pathway in stems of the M genotype, including two upregulated proteins and nine downregulated proteins. Conclusion Enhanced chlorophyll synthesis and decreased lignin synthesis provided a reasonable explanation for the larger leaves and lower levels of stem lignification in M genotype alfalfa. This proteomic study aimed to classify the functions of differentially enriched proteins and to provide information on the molecular regulatory networks involved in stem and leaf development.

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