title: Bioinformatic Identification and Analysis of Extensins in the Plant Kingdom.
abstract: Extensins (EXTs) are a family of plant cell wall hydroxyproline-rich glycoproteins (HRGPs) that are implicated to play important roles in plant growth, development, and defense. Structurally, EXTs are characterized by the repeated occurrence of serine (Ser) followed by three to five prolines (Pro) residues, which are hydroxylated as hydroxyproline (Hyp) and glycosylated. Some EXTs have Tyrosine (Tyr)-X-Tyr (where X can be any amino acid) motifs that are responsible for intramolecular or intermolecular cross-linkings. EXTs can be divided into several classes: classical EXTs, short EXTs, leucine-rich repeat extensins (LRXs), proline-rich extensin-like receptor kinases (PERKs), formin-homolog EXTs (FH EXTs), chimeric EXTs, and long chimeric EXTs. To guide future research on the EXTs and understand evolutionary history of EXTs in the plant kingdom, a bioinformatics study was conducted to identify and classify EXTs from 16 fully sequenced plant genomes, including Ostreococcus lucimarinus, Chlamydomonas reinhardtii, Volvox carteri, Klebsormidium flaccidum, Physcomitrella patens, Selaginella moellendorffii, Pinus taeda, Picea abies, Brachypodium distachyon, Zea mays, Oryza sativa, Glycine max, Medicago truncatula, Brassica rapa, Solanum lycopersicum, and Solanum tuberosum, to supplement data previously obtained from Arabidopsis thaliana and Populus trichocarpa. A total of 758 EXTs were newly identified, including 87 classical EXTs, 97 short EXTs, 61 LRXs, 75 PERKs, 54 FH EXTs, 38 long chimeric EXTs, and 346 other chimeric EXTs. Several notable findings were made: (1) classical EXTs were likely derived after the terrestrialization of plants; (2) LRXs, PERKs, and FHs were derived earlier than classical EXTs; (3) monocots have few classical EXTs; (4) Eudicots have the greatest number of classical EXTs and Tyr-X-Tyr cross-linking motifs are predominantly in classical EXTs; (5) green algae have no classical EXTs but have a number of long chimeric EXTs that are absent in embryophytes. Furthermore, phylogenetic analysis was conducted of LRXs, PERKs and FH EXTs, which shed light on the evolution of three EXT classes.
authors.affiliation: Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, United States of America.|Molecular and Cellular Biology Program, Ohio University, Athens, Ohio, United States of America.
authors.forename: Xiao
authors.initials: X
authors.lastname: Liu
authors.affiliation: Russ College of Engineering and Technology, Center for Intelligent, Distributed and Dependable Systems, Ohio University, Athens, Ohio, United States of America.
authors.forename: Richard
authors.initials: R
authors.lastname: Wolfe
authors.affiliation: Molecular and Cellular Biology Program, Ohio University, Athens, Ohio, United States of America.|Russ College of Engineering and Technology, Center for Intelligent, Distributed and Dependable Systems, Ohio University, Athens, Ohio, United States of America.
authors.forename: Lonnie R
authors.initials: LR
authors.lastname: Welch
authors.affiliation: Department of Biology, Skidmore College, Saratoga Springs, New York, United States of America.
authors.forename: David S
authors.initials: DS
authors.lastname: Domozych
authors.affiliation: Botany and Plant Science and Ryan Institute for Environmental, Marine, and Energy Research, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
authors.forename: Zoë A
authors.initials: ZA
authors.lastname: Popper
authors.affiliation: Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, United States of America.|Molecular and Cellular Biology Program, Ohio University, Athens, Ohio, United States of America.
authors.forename: Allan M
authors.initials: AM
authors.lastname: Showalter
mesh_terms: D020418:Algal Proteins / Q000145:classification / Q000235:genetics; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D029681:Arabidopsis Proteins / Q000145:classification / Q000235:genetics; D005075:Biological Evolution; D019295:Computational Biology; D018745:Genome, Plant; D006023:Glycoproteins / Q000145:classification* / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification* / Q000235:genetics; D010944:Plants / Q000145:classification; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity
chemical_list: D020418:Algal Proteins; D029681:Arabidopsis Proteins; D006023:Glycoproteins; D010940:Plant Proteins; C005488:extensin protein, plant