The family of Deg/HtrA proteases in plants
The family of Deg/HtrA proteases in plants
Loading...
Date
2012
Authors
Editors
Journal ISSN
Electronic ISSN
ISBN
Bibliographical data
Publisher
Series
URI (citable link)
DOI (citable link)
International patent number
Link to the license
EU project number
Project
Open Access publication
Collections
Title in another language
Publication type
Journal article
Publication status
Published in
BMC Plant Biology ; 12 (2012), 1. - 52. - eISSN 1471-2229
Abstract
Background
The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms from bacteria to human and vascular plants. In recent years, multiple deg/htrA protease genes were identified in various plant genomes. During genome annotations most proteases were named according to the order of discovery, hence the same names were sometimes given to different types of Deg/HtrA enzymes in different plant species. This can easily lead to false inference of individual protease functions based solely on a shared name. Therefore, the existing names and classification of these proteolytic enzymes does not meet our current needs and a phylogeny-based standardized nomenclature is required.
Results
Using phylogenetic and domain arrangement analysis, we improved the nomenclature of the Deg/HtrA protease family, standardized protease names based on their well-established nomenclature in Arabidopsis thaliana, and clarified the evolutionary relationship between orthologous enzymes from various photosynthetic organisms across several divergent systematic groups, including dicots, a monocot, a moss and a green alga. Furthermore, we identified a "core set" of eight proteases shared by all organisms examined here that might provide all the proteolytic potential of Deg/HtrA proteases necessary for a hypothetical plant cell.
Conclusions
In our proposed nomenclature, the evolutionarily closest orthologs have the same protease name, simplifying scientific communication when comparing different plant species and allowing for more reliable inference of protease functions. Further, we proposed that the high number of Deg/HtrA proteases in plants is mainly due to gene duplications unique to the respective organism.
The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms from bacteria to human and vascular plants. In recent years, multiple deg/htrA protease genes were identified in various plant genomes. During genome annotations most proteases were named according to the order of discovery, hence the same names were sometimes given to different types of Deg/HtrA enzymes in different plant species. This can easily lead to false inference of individual protease functions based solely on a shared name. Therefore, the existing names and classification of these proteolytic enzymes does not meet our current needs and a phylogeny-based standardized nomenclature is required.
Results
Using phylogenetic and domain arrangement analysis, we improved the nomenclature of the Deg/HtrA protease family, standardized protease names based on their well-established nomenclature in Arabidopsis thaliana, and clarified the evolutionary relationship between orthologous enzymes from various photosynthetic organisms across several divergent systematic groups, including dicots, a monocot, a moss and a green alga. Furthermore, we identified a "core set" of eight proteases shared by all organisms examined here that might provide all the proteolytic potential of Deg/HtrA proteases necessary for a hypothetical plant cell.
Conclusions
In our proposed nomenclature, the evolutionarily closest orthologs have the same protease name, simplifying scientific communication when comparing different plant species and allowing for more reliable inference of protease functions. Further, we proposed that the high number of Deg/HtrA proteases in plants is mainly due to gene duplications unique to the respective organism.
Summary in another language
Subject (DDC)
570 Biosciences, Biology
Keywords
Conference
Review
undefined / . - undefined, undefined. - (undefined; undefined)
Cite This
ISO 690
SCHUHMANN, Holger, Pitter F. HUESGEN, Iwona ADAMSKA, 2012. The family of Deg/HtrA proteases in plants. In: BMC Plant Biology. 12(1), 52. eISSN 1471-2229. Available under: doi: 10.1186/1471-2229-12-52BibTex
@article{Schuhmann2012famil-20449,
year={2012},
doi={10.1186/1471-2229-12-52},
title={The family of Deg/HtrA proteases in plants},
number={1},
volume={12},
journal={BMC Plant Biology},
author={Schuhmann, Holger and Huesgen, Pitter F. and Adamska, Iwona},
note={Article Number: 52}
}
RDF
<rdf:RDF
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bibo="http://purl.org/ontology/bibo/"
xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:void="http://rdfs.org/ns/void#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#" >
<rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/20449">
<dcterms:abstract xml:lang="eng">Background<br /><br /><br /><br />The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms from bacteria to human and vascular plants. In recent years, multiple deg/htrA protease genes were identified in various plant genomes. During genome annotations most proteases were named according to the order of discovery, hence the same names were sometimes given to different types of Deg/HtrA enzymes in different plant species. This can easily lead to false inference of individual protease functions based solely on a shared name. Therefore, the existing names and classification of these proteolytic enzymes does not meet our current needs and a phylogeny-based standardized nomenclature is required.<br /><br />Results<br /><br /><br /><br />Using phylogenetic and domain arrangement analysis, we improved the nomenclature of the Deg/HtrA protease family, standardized protease names based on their well-established nomenclature in Arabidopsis thaliana, and clarified the evolutionary relationship between orthologous enzymes from various photosynthetic organisms across several divergent systematic groups, including dicots, a monocot, a moss and a green alga. Furthermore, we identified a "core set" of eight proteases shared by all organisms examined here that might provide all the proteolytic potential of Deg/HtrA proteases necessary for a hypothetical plant cell.<br /><br />Conclusions<br /><br /><br /><br />In our proposed nomenclature, the evolutionarily closest orthologs have the same protease name, simplifying scientific communication when comparing different plant species and allowing for more reliable inference of protease functions. Further, we proposed that the high number of Deg/HtrA proteases in plants is mainly due to gene duplications unique to the respective organism.</dcterms:abstract>
<dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/20449/1/Schuhmann_etal_family.pdf"/>
<dc:contributor>Huesgen, Pitter F.</dc:contributor>
<dc:contributor>Schuhmann, Holger</dc:contributor>
<dcterms:issued>2012</dcterms:issued>
<void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
<dc:creator>Adamska, Iwona</dc:creator>
<dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/>
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2012-09-12T07:35:51Z</dc:date>
<dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
<dc:rights>terms-of-use</dc:rights>
<dc:contributor>Adamska, Iwona</dc:contributor>
<dc:creator>Huesgen, Pitter F.</dc:creator>
<dcterms:title>The family of Deg/HtrA proteases in plants</dcterms:title>
<dcterms:bibliographicCitation>BMC Plant Biology ; 12 (2012). - 52</dcterms:bibliographicCitation>
<dc:language>eng</dc:language>
<dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/20449/1/Schuhmann_etal_family.pdf"/>
<foaf:homepage rdf:resource="http://localhost:8080/"/>
<dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
<dc:creator>Schuhmann, Holger</dc:creator>
<dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2012-09-12T07:35:51Z</dcterms:available>
<bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/20449"/>
</rdf:Description>
</rdf:RDF>
Internal note
xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter
Examination date of dissertation
Method of financing
Comment on publication
Alliance license
Corresponding Authors der Uni Konstanz vorhanden
International Co-Authors
Bibliography of Konstanz
Yes