PMID- 27769192
OWN - NLM
STAT- MEDLINE
DCOM- 20170921
LR  - 20240326
IS  - 1471-2229 (Electronic)
IS  - 1471-2229 (Linking)
VI  - 16
IP  - 1
DP  - 2016 Oct 21
TI  - Bioinformatic Identification and Analysis of Hydroxyproline-Rich Glycoproteins in 
      Populus trichocarpa.
PG  - 229
LID - 229
AB  - BACKGROUND: 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). RESULTS: 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. CONCLUSIONS: 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.
FAU - Showalter, Allan M
AU  - Showalter AM
AUID- ORCID: 0000-0003-0775-4991
AD  - Department of Environmental and Plant Biology, Molecular and Cellular Biology 
      Program, Ohio University, 504 Porter Hall, Athens, OH, 45701-2979, USA. 
      showalte@ohio.edu.
FAU - Keppler, Brian D
AU  - Keppler BD
AD  - Department of Environmental and Plant Biology, Molecular and Cellular Biology 
      Program, Ohio University, 504 Porter Hall, Athens, OH, 45701-2979, USA.
FAU - Liu, Xiao
AU  - Liu X
AD  - Department of Environmental and Plant Biology, Molecular and Cellular Biology 
      Program, Ohio University, 504 Porter Hall, Athens, OH, 45701-2979, USA.
FAU - Lichtenberg, Jens
AU  - Lichtenberg J
AD  - Russ College of Engineering and Technology, Center for Intelligent, Distributed 
      and Dependable Systems, Ohio University, Athens, OH, 45701-2979, USA.
FAU - Welch, Lonnie R
AU  - Welch LR
AD  - Russ College of Engineering and Technology, Center for Intelligent, Distributed 
      and Dependable Systems, Ohio University, Athens, OH, 45701-2979, USA.
LA  - eng
PT  - Journal Article
DEP - 20161021
PL  - England
TA  - BMC Plant Biol
JT  - BMC plant biology
JID - 100967807
RN  - 0 (Glycoproteins)
RN  - 0 (Plant Proteins)
RN  - RMB44WO89X (Hydroxyproline)
SB  - IM
MH  - Amino Acid Sequence
MH  - Computational Biology
MH  - Glycoproteins/analysis/chemistry/*genetics/metabolism
MH  - Hydroxyproline/metabolism
MH  - Plant Proteins/analysis/chemistry/*genetics/metabolism
MH  - Populus/*genetics/metabolism
PMC - PMC5073881
OTO - NOTNLM
OT  - Arabinogalactan-protein
OT  - Bioinformatics
OT  - Extensin
OT  - Hydroxyproline-rich glycoprotein
OT  - Plant cell wall
OT  - Poplar
OT  - Populus trichocarpa
OT  - Proline-rich protein
EDAT- 2016/10/23 06:00
MHDA- 2017/09/22 06:00
PMCR- 2016/10/21
CRDT- 2016/10/23 06:00
PHST- 2016/04/26 00:00 [received]
PHST- 2016/09/29 00:00 [accepted]
PHST- 2016/10/23 06:00 [pubmed]
PHST- 2017/09/22 06:00 [medline]
PHST- 2016/10/23 06:00 [entrez]
PHST- 2016/10/21 00:00 [pmc-release]
AID - 10.1186/s12870-016-0912-3 [pii]
AID - 912 [pii]
AID - 10.1186/s12870-016-0912-3 [doi]
PST - epublish
SO  - BMC Plant Biol. 2016 Oct 21;16(1):229. doi: 10.1186/s12870-016-0912-3.