PeroxiBase: a powerful tool to collect and analyse peroxidase sequences from Viridiplantae.

Peroxidases are enzymes that are implicated in several biological processes and are detected in all living organisms. The increasing number of sequencing projects and the poor quality of annotation justified the creation of an efficient tool that was suitable for collecting and annotating the huge quantity of data. Started in 2004 to collect only class III peroxidases, PeroxiBase has undergone important updates since then and, currently, the majority of peroxidase sequences from all kingdoms of life is stored in the database. In addition, the web site (http://peroxibase.isb-sib.ch) provides a series of bioinformatics tools and facilities suitable for analysing these stored sequences. In particular, the high number of isoforms in each organism makes phylogenetic studies extremely useful to elucidate the complex evolution of these enzymes, not only within the plant kingdom but also between the different kingdoms. This paper provides a general overview of PeroxiBase, focusing on its tools and the stored data. The main goal is to give researchers some guidelines to extract classified and annotated sequences from the data base in a quick and easy way in order to perform alignments and phylogenetic analysis. The description of the database is accompanied by the updates we have recently carried out in order to improve its completeness and make it more user-friendly.

Phylogenetic distribution of catalase-peroxidases: are there patches of order in chaos?

Hydrogen peroxide features in many biological oxidative processes and must be continuously degraded enzymatically either via a catalatic or a peroxidatic mechanism. For this purpose ancestral bacteria evolved a battery of different heme and non-heme enzymes, among which heme-containing catalase-peroxidases (CP) are one of the most widespread representatives. They are unique since they can follow both H(2)O(2)-degrading mechanisms, the catalase activity being clearly dominant. With the fast increasing amount of genomic data available, we were able to perform an extensive search for CP and found almost 300 sequences covering a large range of microorganisms. Most of them were encoded by bacterial genomes, but we could also find some in eukaryotic organisms other than fungi, which has never been shown until now. Our screen also reveals that approximately 60% of the bacteria do not possess CP genes. Chaotic distribution among species and incongruous phylogenetic reconstruction indicated existence of numerous lateral gene transfers in addition to duplication events and regular speciation. The results obtained show an impressively complex gene transmission pattern, and give some new insights about the role of CP and the origin of life on earth. Finally, we propose for the first time bacterial candidates that may have participated in the transfer of CP from bacteria to eukaryotes.

PeroxiBase: the peroxidase database.

Peroxidases (EC 1.11.1.x), which are encoded by small or large multigenic families, are involved in several important physiological and developmental processes. Analyzing their evolution and their distribution among various phyla could certainly help to elucidate the mystery of their extremely widespread and diversified presence in almost all living organisms. PeroxiBase was originally created for the exhaustive collection of class III peroxidase sequences from plants (Bakalovic, N., Passardi, F., et al., 2006. PeroxiBase: a class III plant peroxidase database. Phytochemistry 67, 534-539). The extension of the class III peroxidase database to all proteins capable to reduce peroxide molecules appears as a necessity. Our database contains haem and non-haem peroxidase sequences originated from annotated or not correctly annotated sequences deposited in the main repositories such as GenBank or UniProt KnowledgeBase. This new database will allow obtaining a global overview of the evolution the protein families and superfamilies capable of peroxidase reaction. In this rapidly growing field, there is a need for continual updates and corrections of the peroxidase protein sequences. Following the lack of unified nomenclature, we also introduced a unique abbreviation for each different family of peroxidases. This paper thus aims to report the evolution of the PeroxiBase database, which is freely accessible through a web server (http://peroxibase.isb-sib.ch). In addition to new categories of peroxidases, new specific tools have been created to facilitate query, classification and submission of peroxidase sequences.

Morphological and physiological traits of three major Arabidopsis thaliana accessions.

Arabidopsis is currently the most studied organism in plant biology. Its short life cycle and small genome size have rendered it one of the principal model systems. Additionally, numerous large T-DNA insertion mutant collections are available. The advent of molecular biology and the completion of the Arabidopsis genome sequence have contributed to helping researchers discover a large variety of mutants identified for their phenotypes. Yet, it is important to consider that natural phenotypic variations exist and appear in natural ecotypes, differing greatly in several traits. Although there are a vast number of ecotypes available, only a few have been extensively studied, and some have been created in laboratories. In order to identify new phenotypic differences, we chose to study the differences observed between three ecotypes: Columbia (Col-0), Landsberg erecta (Laer-0) and Wassilewskija (Ws-0). Our research focuses on observable morphological traits throughout plant growth and development along the entire plant life cycle. We then attempted to shed some light on phenotypic discrepancies through the study of the class III peroxidase protein family, which is involved in many aspects of plant growth and tissue differentiation. Both morphological and molecular aspects reveal that there are major variations between ecotypes, hence indicating a possibly interesting heterotic effect in the F1 from crosses between different Arabidopsis ecotypes.

PeroxiBase: a class III plant peroxidase database.

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 with specific tools dedicated to facilitate query, classification and submission of peroxidase sequences. Recent developments in the field of plant peroxidase are also mentioned.

Performing the paradoxical: how plant peroxidases modify the cell wall.

Since their appearance in the first land plants, genes encoding class III peroxidases have been duplicated many times during evolution and now compose a large multigene family. The reason for these many genes is elusive, and we are still searching for the specific function of every member of the family. Nevertheless, our current understanding implicates peroxidases as key players during the whole life cycle of a plant, and particularly in cell wall modifications, in roles that can be antagonistic depending on the developmental stage. This diversity of functions derives in part from two possible catalytic cycles of peroxidases involving the consumption or release of H(2)O(2) and reactive oxygen species (e.g. O(2)(-), H(2)O(2), OH).

The class III peroxidase multigenic family in rice and its evolution in land plants.

Plant peroxidases (class III peroxidases, E.C. 1.11.1.7) are secreted glycoproteins known to be involved in the mechanism of cell elongation, in cell wall construction and differentiation, and in the defense against pathogens. They usually form large multigenic families in angiosperms. The recent completion of rice (Oryza sativa japonica c.v. Nipponbare) genome sequencing allowed drawing up the full inventory of the genes encoding class III peroxidases in this plant. We found 138 peroxidase genes distributed among the 12 rice chromosomes. In contrast to several other gene families studied so far, peroxidase genes are twice as numerous in rice as in Arabidopsis. This large number of genes results from various duplication events that were tentatively traced back using a phylogenetic tree based on the alignment of conserved amino acid sequences. We also searched for peroxidase encoding genes in the major phyla of plant kingdom. In addition to gymnosperms and angiosperms, sequences were found in liverworts, mosses and ferns, but not in unicellular green algae. Two rice and one Arabidopsis peroxidase genes appeared to be rather close to the only known sequence from the liverwort Marchantia polymorpha. The possible relationship of these peroxidases with the putative ancestor of peroxidase genes is discussed, as well as the connection between the development of the class III peroxidase multigenic family and the emergence of the first land plants.

Prokaryotic origins of the non-animal peroxidase superfamily and organelle-mediated transmission to eukaryotes.

Members of the superfamily of plant, fungal, and bacterial peroxidases are known to be present in a wide variety of living organisms. Extensive searching within sequencing projects identified organisms containing sequences of this superfamily. Class I peroxidases, cytochrome c peroxidase (CcP), ascorbate peroxidase (APx), and catalase peroxidase (CP), are known to be present in bacteria, fungi, and plants, but have now been found in various protists. CcP sequences were detected in most mitochondria-possessing organisms except for green plants, which possess only ascorbate peroxidases. APx sequences had previously been observed only in green plants but were also found in chloroplastic protists, which acquired chloroplasts by secondary endosymbiosis. CP sequences that are known to be present in prokaryotes and in Ascomycetes were also detected in some Basidiomycetes and occasionally in some protists. Class II peroxidases are involved in lignin biodegradation and are found only in the Homobasidiomycetes. In fact class II peroxidases were identified in only three orders, although degenerate forms were found in different Pezizomycota orders. Class III peroxidases are specific for higher plants, and their evolution is thought to be related to the emergence of the land plants. We have found, however, that class III peroxidases are present in some green algae, which predate land colonization. The presence of peroxidases in all major phyla (except vertebrates) makes them powerful marker genes for understanding the early evolutionary events that led to the appearance of the ancestors of each eukaryotic group.

Two cell wall associated peroxidases from Arabidopsis influence root elongation.

Two class III peroxidases from Arabidopsis, AtPrx33 and Atprx34, have been studied in this paper. Their encoding genes are mainly expressed in roots; AtPrx33 transcripts were also found in leaves and stems. Light activates the expression of both genes in seedlings. Transformed seedlings producing AtPrx33-GFP or AtPrx34-GFP fusion proteins under the control of the CaMV 35S promoter exhibit fluorescence in the cell walls of roots, showing that the two peroxidases are localized in the apoplast, which is in line with their affinity for the Ca(2+)-pectate structure. The role they can play in cell wall was investigated using (1) insertion mutants that have suppressed or reduced expression of AtPrx33 or AtPrx34 genes, respectively, (2) a double mutant with no AtPrx33 and a reduced level of Atprx34 transcripts, (3) a mutant overexpressing AtPrx34 under the control of the CaMV 35S promoter. The major phenotypic consequences of these genetic manipulations were observed on the variation of the length of seedling roots. Seedlings lacking AtPrx33 transcripts have shorter roots than the wild-type controls and roots are still shorter in the double mutant. Seedlings overexpressing AtPrx34 exhibit significantly longer roots. These modifications of root length are accompanied by corresponding changes of cell length. The results suggest that AtPrx33 and Atprx34, two highly homologous Arabidopsis peroxidases, are involved in the reactions that promote cell elongation and that this occurs most likely within cell walls.