ArticlePlant physiology2010
A bioinformatics approach to the identification, classification, and analysis of hydroxyproline-rich glycoproteins.
Article in Plant physiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 176 papers.
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176 citing papers in PubMed, 319 citations in OpenAlex.
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- Cell walls: a comparative view of the composition of cell surfaces of plants, algae, and microorganisms.Journal of experimental botany · 2025Review
- Reactivation of the tRNASer/tRNATyr gene cluster in Arabidopsis thaliana root tips.The Plant cell · 2025Article
- Determining the Role of OsAGP6P in Anther Development Within the Arabinogalactan Peptide Family of Rice (International journal of molecular sciences · 2025Article
- Genome-wide identification unravels the role of the arabinogalactan peptide (AGP) gene family in cotton plant architecture.Plant cell reports · 2025Article
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- A review on the function of arabinogalactan-proteins during pollen grain development.Plant reproduction · 2025Review
- Transcriptomic insights into arabinogalactan protein mechanism of action in galactosyltransferase octuple mutants.Frontiers in plant science · 2025Article
- Differential prolyl hydroxylation by six Physcomitrella prolyl-4 hydroxylases.Computational and structural biotechnology journal · 2024Article
- Genetic linkage analysis of stable QTLs in Gossypium hirsutum RIL population revealed function of GhCesA4 in fiber development.Journal of advanced research · 2024Article
- Toxin Homology Domain in Plant Type 2 Prolyl 4-Hydroxylases Acts as a Golgi Localization Domain.Cells · 2024Article
- Do Arabinogalactan Proteins Occur in the Transfer Cells ofInternational journal of molecular sciences · 2024Article
- Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (International journal of molecular sciences · 2024Article
- Cell Wall Microdomains in the External Glands ofInternational journal of molecular sciences · 2024Article
- Developing an SNP dataset for efficiently evaluating soybean germplasm resources using the genome sequencing data of 3,661 soybean accessions.BMC genomics · 2024Article
- The plant cell wall-dynamic, strong, and adaptable-is a natural shapeshifter.The Plant cell · 2024Review
- The cellular and molecular basis of the spur development inHorticulture research · 2024Article
116 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hydroxyproline-rich glycoproteins (HRGPs) are a superfamily of plant cell wall proteins that function in diverse aspects of plant growth and development. This superfamily consists of three members: hyperglycosylated arabinogalactan proteins (AGPs), moderately glycosylated extensins (EXTs), and lightly glycosylated proline-rich proteins (PRPs). Hybrid and chimeric versions of HRGP molecules also exist. In order to "mine" genomic databases for HRGPs and to facilitate and guide research in the field, the BIO OHIO software program was developed that identifies and classifies AGPs, EXTs, PRPs, hybrid HRGPs, and chimeric HRGPs from proteins predicted from DNA sequence data. This bioinformatics program is based on searching for biased amino acid compositions and for particular protein motifs associated with known HRGPs. HRGPs identified by the program are subsequently analyzed to elucidate the following: (1) repeating amino acid sequences, (2) signal peptide and glycosylphosphatidylinositol lipid anchor addition sequences, (3) similar HRGPs via Basic Local Alignment Search Tool, (4) expression patterns of their genes, (5) other HRGPs, glycosyl transferase, prolyl 4-hydroxylase, and peroxidase genes coexpressed with their genes, and (6) gene structure and whether genetic mutants exist in their genes. The program was used to identify and classify 166 HRGPs from Arabidopsis (Arabidopsis thaliana) as follows: 85 AGPs (including classical AGPs, lysine-rich AGPs, arabinogalactan peptides, fasciclin-like AGPs, plastocyanin AGPs, and other chimeric AGPs), 59 EXTs (including SP(5) EXTs, SP(5)/SP(4) EXTs, SP(4) EXTs, SP(4)/SP(3) EXTs, a SP(3) EXT, "short" EXTs, leucine-rich repeat-EXTs, proline-rich extensin-like receptor kinases, and other chimeric EXTs), 18 PRPs (including PRPs and chimeric PRPs), and AGP/EXT hybrid HRGPs.
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