title: Bioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in Populus trichocarpa.
abstract: 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). 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).
  
  
  
  The 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.
  
  
  
  The 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.
authors: Department of Environmental and Plant Biology, Molecular and Cellular Biology Program, Ohio University, 504 Porter Hall, Athens, OH, 45701-2979, USA. showalte@ohio.edu.
authors: Allan M
authors: 0000-0003-0775-4991
authors: AM
authors: Showalter
authors: Department of Environmental and Plant Biology, Molecular and Cellular Biology Program, Ohio University, 504 Porter Hall, Athens, OH, 45701-2979, USA.
authors: Brian D
authors: BD
authors: Keppler
authors: Department of Environmental and Plant Biology, Molecular and Cellular Biology Program, Ohio University, 504 Porter Hall, Athens, OH, 45701-2979, USA.
authors: Xiao
authors: X
authors: Liu
authors: Russ College of Engineering and Technology, Center for Intelligent, Distributed and Dependable Systems, Ohio University, Athens, OH, 45701-2979, USA.
authors: Jens
authors: J
authors: Lichtenberg
authors: Russ College of Engineering and Technology, Center for Intelligent, Distributed and Dependable Systems, Ohio University, Athens, OH, 45701-2979, USA.
authors: Lonnie R
authors: LR
authors: Welch
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology; D006023:Glycoproteins / Q000032:analysis / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D006909:Hydroxyproline / Q000378:metabolism; D010940:Plant Proteins / Q000032:analysis / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D032107:Populus / Q000235:genetics* / Q000378:metabolism
chemical_list: D006023:Glycoproteins; D010940:Plant Proteins; D006909:Hydroxyproline
keywords: Arabinogalactan-protein; Bioinformatics; Extensin; Hydroxyproline-rich glycoprotein; Plant cell wall; Poplar; Populus trichocarpa; Proline-rich protein