PeroxiBase: A class III plant peroxidase database

Abstract

Class III plant peroxidases (EC 1.11.1.7), which are encoded by multigenic families in land plants, are involved in several important physiological and developmental processes. Their varied functions are not yet clearly determined, but their characterization will certainly lead to a better understanding of plant growth, differentiation and interaction with the environment, and hence to many exciting applications. Since there is currently no central database for plant peroxidase sequences and many plant sequences are not deposited in the EMBL/GenBank/DDBJ repository or the UniProt KnowledgeBase, this prevents researchers from easily accessing all peroxidase sequences. Furthermore, gene expression data are poorly covered and annotations are inconsistent. In this rapidly moving field, there is a need for continual updating and correction of the peroxidase superfamily in plants. Moreover, consolidating information about peroxidases will allow for comparison of peroxidases between species and thus significantly help making correlations of function, structure or phylogeny. We report a new database (PeroxiBase) accessible through a web server (http://peroxidase.isb-sib.ch) with specific tools dedicated to facilitate query, classification and submission of peroxidase sequences. Recent developments in the field of plant peroxidase are also mentioned.

An anionic class III peroxidase from zucchini may regulate hypocotyl elongation through its auxin oxidase activity

“…Exhaustive data mining has been performed to detect APRX othologs. Two isoforms with 70-86% identity were identiWed in C. melo and C. sativus (Bakalovic et al 2006). The Cucurbitaceae APRX homologues formed a well supported branch clearly separated from other species peroxidases (Fig.…”

“…In previous studies the identiWcation and isolation of an anionic peroxidase (initially named APRX and also named CpPrx01 based on the nomenclature of the Peroxibase, Bakalovic et al 2006) from the apoplast of zucchini was reported. APRX mRNA accumulated strongly in hypocotyls (Carpin et al 1999) particularly in the elongation area (Dunand et al 2002).…”

Purification and characterization of a peroxidase present in xilopodium exsudates of umbu plants (Spondias tuberosa A.)

“…Plant peroxidases belong to the class III of peroxidases and form a large multigenic family with molecular weights varying from 30 up to 150 kDa (Bakalovic et al, 2006;Cosio and Dunand, 2008). Class III peroxidases have variable domain but conserved motifs position in the structures; it is due to the catalytic function preservation, associated always to presence of a heme group with an iron ion interaging with histidine and phenylalanine amino acids residues in conservaed position (Veitch, 2006).…”

Age-related resistance to Fusarium oxysporum f. sp. cepae and associated enzymatic changes in seedlings of Allium cepa and A. fistulosum

“…The high versatility of isoperoxidases allows them to be involved in a range of physiological and developmental processes (Passardi et al, 2005;Bakalovic et al, 2006). Among these, class III peroxidases (EC 1.11.1.7) can play a role in defence against pathogens by involvement in physiological responses, specific resistance responses, or induction during pathogenesis as a response to damage (Neale et al, 1990;Dowd & Johnson, 2005;Silvar et al, 2008).…”