Abstract
BackgroundHydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This superfamily contains three members: the highly glycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). Chimeric and hybrid HRGPs, however, also exist. A bioinformatics approach is employed here to identify and classify AGPs, EXTs, PRPs, chimeric HRGPs, and hybrid HRGPs from the proteins predicted by the completed genome sequence of poplar (Populus trichocarpa). This bioinformatics approach is based on searching for biased amino acid compositions and for particular protein motifs associated with known HRGPs with a newly revised and improved BIO OHIO 2.0 program. Proteins detected by the program are subsequently analyzed to identify the following: 1) repeating amino acid sequences, 2) signal peptide sequences, 3) glycosylphosphatidylinositol lipid anchor addition sequences, and 4) similar HRGPs using the Basic Local Alignment Search Tool (BLAST).ResultsThe program was used to identify and classify 271 HRGPs from poplar including 162 AGPs, 60 EXTs, and 49 PRPs, which are each divided into various classes. This is in contrast to a previous analysis of the Arabidopsis proteome which identified 162 HRGPs consisting of 85 AGPs, 59 EXTs, and 18 PRPs. Poplar was observed to have fewer classical EXTs, to have more fasciclin-like AGPs, plastocyanin AGPs and AG peptides, and to contain a novel class of PRPs referred to as the proline-rich peptides.ConclusionsThe newly revised and improved BIO OHIO 2.0 bioinformatics program was used to identify and classify the inventory of HRGPs in poplar in order to facilitate and guide basic and applied research on plant cell walls. The newly identified poplar HRGPs can now be examined to determine their respective structural and functional roles, including their possible applications in the areas plant biofuel and natural products for medicinal or industrial uses. Additionally, other plants whose genomes are sequenced can now be examined in a similar way using this bioinformatics program which will provide insight to the evolution of the HRGP family in the plant kingdom.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0912-3) contains supplementary material, which is available to authorized users.
Highlights
Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development
Because a single amino acid change in the consensus sequence would result in a particular fasciclin-like AGPs (FLAs) not being identified, the additional 26 FLAs were identified with BLAST searches
Five Plastocyanin AGPs (PAGs) were identified with the 50 % PAST search, but 34 others were identified that fall below the 50 % PAST threshold with BLAST searches
Summary
Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development This superfamily contains three members: the highly glycosylated arabinogalactan-proteins (AGPs), the moderately glycosylated extensins (EXTs), and the lightly glycosylated proline-rich proteins (PRPs). Certain families of HRGPs, the AGPs, are modified with a C-terminal glycosylphosphatidylinositol (GPI) membrane anchor, which tethers the protein to the outer leaflet of plasma membrane and allows the rest of the glycoprotein to extend toward the cell wall in the periplasm [11,12,13] These characteristic amino acid sequences and sequence features allow for the effective identification and classification of HRGPs from proteomic databases by bioinformatic approaches involving biased amino acid composition searches and/or HRGP amino acid motif searches [14,15,16,17]. Newman and Cooper [18] utilized another bioinformatic approach involving searching for proline-rich tandem repeats to identify numerous HRGPs as well as other proteins in a variety of plant species
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