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Journal ArticleDOI

PeroxiBase: A class III plant peroxidase database

01 Mar 2006-Phytochemistry (Phytochemistry)-Vol. 67, Iss: 6, pp 534-539
TL;DR: A new database (PeroxiBase) accessible through a web server with specific tools dedicated to facilitate query, classification and submission of peroxidase sequences is reported.
About: This article is published in Phytochemistry.The article was published on 2006-03-01 and is currently open access. It has received 85 citations till now.

Summary (2 min read)

1. Introduction

  • The homology between paralogs in a plant ranges from 30% to 100%, but very close orthologs exist, even between evolutionarily distant plants.
  • They are structurally related to other heme-containing 0031-9422/$ - see front matter 2006 Elsevier Ltd. Newly duplicated genes were likely conserved because they acquired new modes of expression, regulation or novel functions .
  • The large number of EST projects developed with more diverse plants will provide a better overview of peroxidase evolution throughout green plants.

2. Construction of the database

  • The database was constructed following two parallel procedures: one exhaustive and another more specific (Fig. 1).
  • The resulting hits are already treated data (assembled and translated sequences) with the risk of automatic compilation and translation.
  • The authors have then used AtPrx42 and OsPrx73, two sequences potentially related to an ancestral sequence (Passardi et al., 2004), for a second, more specific approach by scanning numerous public sources of plant ESTs and genome sequences in order to obtain a large collection of peroxidase-encoding sequences.
  • Low quality sequences are not included in TIGR consensus sequences due to the high sequence stringency TIGR uses.
  • In addition, as in numerous other genera, ESTs from Gossypium , Picea , Populus have been assembled by TIGR.

3. Web interface

  • The PeroxiBase web interface includes four main modules.
  • Each organism possesses a link with its taxonomic identity, also known as (ii) Organism.
  • Each file contains a direct link to the corresponding database (NCBI, TIGR, PGN, Sputnik) and to Swiss-Prot and DNA sequences when these entries exist.
  • In addition, numbers of ESTs, cellular localization and tissue type are all included.
  • Two BLAST searches can be performed against the whole peroxidase database (Altschul et al., 1997), BLASTp for protein sequence and BLASTx for nucleotide sequences, also known as (iii) BLAST.

4. Modelization of the number of class III isoforms evolution

  • Class III peroxidase encoding sequences and peroxidase activity are both absent from the green alga Chlamydomonas reinhardtii (Passardi et al., 2004).
  • The exhaustive data mining performed for the setup of the PeroxiBase confirms that the class III peroxidases are present in all land plants.
  • For some species the total EST count is low (less than 1000), yet several independent isoforms were identified.
  • A potential evolution of peroxidase gene numbers can be drawn up based on information concerning each species such as total EST count and number of unigenes with the following formula: (number of peroxidase encoding EST/ number of independent peroxidase encoding genes)/(number of total EST/number of unigenes).
  • Rosids, Asterids and Poales considered to be higher plants, show a high diversification rate value over 1.

5. Current status and future developments

  • The first goal of the PeroxiBase was to develop an efficient tool for the study of the evolution of a plant multigenic family.
  • The base currently consists of a core dataset containing over 2000 complete or partial peroxidase-encoding sequences from 125 organisms (Table 1), and it is still in constant evolution.
  • Continuous data mining will be performed until a putative complete analysis of the available sequences is achieved (EST and genomic sequences).
  • Information concerning the expression profile will also be updated and new features such as results of knock-out, knock-down or overexpression studies will be added when available.
  • The varied functions of peroxidases will be characterized and lead to a better understanding of plant growth, differentiation and interaction with the environment, and eventually to many exciting applications.

Acknowledgments

  • The authors thank Sonia Guimil for her critical reading.
  • The financial support of the Swiss National Science Foundation (Grant 31-068003.02) to C.P. and C.D. is gratefully acknowledged, N.B. is paid by the Office Cantonal de l’Emploi.

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Citations
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Journal ArticleDOI
TL;DR: A number of aspects regarding the origin and evolution of lignin biosynthesis during land plant evolution are discussed, including the establishment of its monomer biosynthetic scaffold, potential precursors to the lIGNin polymer, as well as the emergence of the polymerization machinery and regulatory system.
Abstract: Contents Summary 273 I. Introduction 273 II. Emergence of the monolignol biosynthetic scaffold 274 III. Occurrence and elaboration of lignification in tracheophytes 280 IV. Concluding remarks 282 Acknowledgements 282 References 282 Summary Lignin, a phenolic polymer derived mainly from hydroxycinnamyl alcohols, is ubiquitously present in tracheophytes. The development of lignin biosynthesis has been considered to be one of the key factors that allowed land plants to flourish in terrestrial ecosystems. Lignin provides structural rigidity for tracheophytes to stand upright, and strengthens the cell wall of their water-conducting tracheary elements to withstand the negative pressure generated during transpiration. In this review, we discuss a number of aspects regarding the origin and evolution of lignin biosynthesis during land plant evolution, including the establishment of its monomer biosynthetic scaffold, potential precursors to the lignin polymer, as well as the emergence of the polymerization machinery and regulatory system. The accumulated knowledge on the topic, as summarized here, provides us with an evolutionary view on how this complex metabolic system emerged and developed.

611 citations

Journal ArticleDOI
TL;DR: The complex relationships and evolutionary rates of this gene family suggest that basal glutathione peroxidase classes, present in all kingdoms, have originated from independent evolutionary events such as gene duplication, gene losses, lateral gene transfer among invertebrates and vertebrates or plants.
Abstract: Glutathione peroxidases (EC 1.11.1.9 and EC 1.11.1.12) catalyze the reduction of H(2)O(2) or organic hydroperoxides to water or corresponding alcohols using reduced glutathione. Some glutathione peroxidase isozymes have a selenium-dependent glutathione peroxidase activity and present a selenocysteine encoded by the opal TGA codon. In the present study, insights into the evolution of the whole glutathione peroxidase gene family were obtained after a comprehensive phylogenetic analysis using the improved number of glutathione peroxidase sequences recorded in the PeroxiBase database (http://peroxidase.isb-sib.ch/index.php). The identification of a common ancestral origin for the diverse glutathione peroxidase clusters was not possible. The complex relationships and evolutionary rates of this gene family suggest that basal glutathione peroxidase classes, present in all kingdoms, have originated from independent evolutionary events such as gene duplication, gene losses, lateral gene transfer among invertebrates and vertebrates or plants. In addition, the present study also emphasizes the possibility of some members being submitted to strong selective forces that probably dictated functional convergences of taxonomically distant groups.

430 citations

Journal ArticleDOI
TL;DR: This review presents the current knowledge on the ROS signals and their role during plant-microorganism interactions and reports the characterisation of ROS producing and scavenging systems from plants and from microorganisms during interactions.
Abstract: Reactive Oxygen Species (ROS) are continuously produced as a result of aerobic metabolism or in response to biotic and abiotic stresses. ROS are not only toxic by-products of aerobic metabolism, but are also signalling molecules involved in several developmental processes in all organisms. Previous studies have clearly shown that an oxidative burst often takes place at the site of attempted invasion during the early stages of most plant-pathogen interactions. Moreover, a second ROS production can be observed during certain types of plant-pathogen interactions, which triggers hypersensitive cell death (HR). This second ROS wave seems absent during symbiotic interactions. This difference between these two responses is thought to play an important signalling role leading to the establishment of plant defense. In order to cope with the deleterious effects of ROS, plants are fitted with a large panel of enzymatic and non-enzymatic antioxidant mechanisms. Thus, increasing numbers of publications report the characterisation of ROS producing and scavenging systems from plants and from microorganisms during interactions. In this review, we present the current knowledge on the ROS signals and their role during plant-microorganism interactions.

277 citations

Journal ArticleDOI
TL;DR: The evolution of the PeroxiBase database is reported, which is freely accessible through a web server, and new specific tools have been created to facilitate query, classification and submission of peroxidase sequences.

196 citations

Journal ArticleDOI
TL;DR: The presence of proteins known to be related to cell wall extension after growth arrest showed that these proteins may play other roles in cell walls, highlighting the CWP dynamics that takes place between the two developmental stages.
Abstract: Cell elongation in plants requires addition and re-arrangements of cell wall components. Even if some protein families have been shown to play roles in these events, a global picture of proteins present in cell walls of elongating cells is still missing. A proteomic study was performed on etiolated hypocotyls of Arabidopsis used as model of cells undergoing elongation followed by growth arrest within a short time. Two developmental stages (active growth and after growth arrest) were compared. A new strategy consisting of high performance cation exchange chromatography and mono-dimensional electrophoresis was established for separation of cell wall proteins. This work allowed identification of 137 predicted secreted proteins, among which 51 had not been identified previously. Apart from expected proteins known to be involved in cell wall extension such as xyloglucan endotransglucosylase-hydrolases, expansins, polygalacturonases, pectin methylesterases and peroxidases, new proteins were identified such as proteases, proteins related to lipid metabolism and proteins of unknown function. This work highlights the CWP dynamics that takes place between the two developmental stages. The presence of proteins known to be related to cell wall extension after growth arrest showed that these proteins may play other roles in cell walls. Finally, putative regulatory mechanisms of protein biological activity are discussed from this global view of cell wall proteins.

186 citations

References
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TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Abstract: The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSIBLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

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Journal ArticleDOI
14 Dec 2000-Nature
TL;DR: This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
Abstract: The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.

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Additional excerpts

  • ...Keywords: Database; Multigenic family; Evolution; Phylogeny; Peroxidases...

    [...]

Journal ArticleDOI
05 Apr 2002-Science
TL;DR: A draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp.indica, by whole-genome shotgun sequencing is produced, with a large proportion of rice genes with no recognizable homologs due to a gradient in the GC content of rice coding sequences.
Abstract: We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC-content of rice coding sequences.

4,064 citations

Journal Article
01 Jan 2002-Science
TL;DR: A draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing was presented in this paper.
Abstract: We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.

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Journal ArticleDOI
TL;DR: This review will discuss the factors that can influence this delicate balance in plant peroxidases, which can prevent biological and chemical attacks by raising physical barriers or by counterattacking with a large production of ROS.
Abstract: Plant peroxidases (class III peroxidases) are present in all land plants. They are members of a large multigenic family. Probably due to this high number of isoforms, and to a very heterogeneous regulation of their expression, plant peroxidases are involved in a broad range of physiological processes all along the plant life cycle. Due to two possible catalytic cycles, peroxidative and hydroxylic, peroxidases can generate reactive oxygen species (ROS) (•OH, HOO•), polymerise cell wall compounds, and regulate H2O2 levels. By modulating their activity and expression following internal and external stimuli, peroxidases are prevalent at every stage of plant growth, including the demands that the plant meets in stressful conditions. These multifunctional enzymes can build a rigid wall or produce ROS to make it more flexible; they can prevent biological and chemical attacks by raising physical barriers or by counterattacking with a large production of ROS; they can be involved in a more peaceful symbiosis. They are finally present from the first hours of a plant’s life until its last moments. Although some functions look paradoxical, the whole process is probably regulated by a fine-tuning that has yet to be elucidated. This review will discuss the factors that can influence this delicate balance.

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"PeroxiBase: A class III plant perox..." refers background in this paper

  • ...The high number of isoenzymes and their remarkable catalytic versatility allow them to be involved in a broad range of physiological and developmental processes all along the plant life cycle (Passardi et al., 2005)....

    [...]

Frequently Asked Questions (1)
Q1. What are the contributions mentioned in the paper "Peroxibase: a class iii plant peroxidase database" ?

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. The authors 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. Furthermore, gene expression data are poorly covered and annotations are inconsistent.