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The family of Deg/HtrA proteases in plants.

Schuhmann H, Huesgen PF, Adamska I - BMC Plant Biol. (2012)

Bottom Line: Therefore, the existing names and classification of these proteolytic enzymes does not meet our current needs and a phylogeny-based standardized nomenclature is required.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.Further, we proposed that the high number of Deg/HtrA proteases in plants is mainly due to gene duplications unique to the respective organism.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Physiology and Biochemistry, University of Konstanz, Universitätsstr, 10, 78457, Konstanz, Germany.

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.

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Maximum likelihood phylogenetic tree of Deg/HtrA proteases in selected plant species. Following plant species were investigated: Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Physcomitrella patens, Chlamydomonas reinhardtii, and the cyanobacterium Synechocystis sp. PCC6803. Phylogenetic tree labeled labeled with the new names as suggested by this study. Filled circles indicated a bootstrap support (100 replicates) of > 90%, empty circles indicate a bootstrap support of > 70%. Additionally, the domain arrangement representative for proteases from each group is indicated. Deg/HtrA proteases from clade I contain one protease domain (oval shapes) and one PDZ domain (diamonds), with the exception of Deg5 proteases, which possess a protease domain only. Proteases from clade II contain an additional PDZ domain, clade III gathers proteases with one active (oval shape) and one inactive (discontinous oval shape) protease domain and four PDZ domains, whereas enzymes from clade IV contain a single protease domain, which is shifted toward the C-terminus.
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Figure 1: Maximum likelihood phylogenetic tree of Deg/HtrA proteases in selected plant species. Following plant species were investigated: Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Physcomitrella patens, Chlamydomonas reinhardtii, and the cyanobacterium Synechocystis sp. PCC6803. Phylogenetic tree labeled labeled with the new names as suggested by this study. Filled circles indicated a bootstrap support (100 replicates) of > 90%, empty circles indicate a bootstrap support of > 70%. Additionally, the domain arrangement representative for proteases from each group is indicated. Deg/HtrA proteases from clade I contain one protease domain (oval shapes) and one PDZ domain (diamonds), with the exception of Deg5 proteases, which possess a protease domain only. Proteases from clade II contain an additional PDZ domain, clade III gathers proteases with one active (oval shape) and one inactive (discontinous oval shape) protease domain and four PDZ domains, whereas enzymes from clade IV contain a single protease domain, which is shifted toward the C-terminus.

Mentions: The Deg/HtrA proteases investigated here form four distinct clades (Figure 1; see Addtional file 4 for a tree containing the original gene model names), similar to an earlier study that included Deg/HtrA proteases from evolutionarily very distant taxa and only a few plant orthologs [7]. Clade I is further split into two subgroups, where subgroup IA includes orthologs of Deg1, Deg5 and Deg8 (Figure 1, Addtional file 4). Subgroup IB comprises the prokaryotic (cyanobacterial) Deg/HtrA proteases, and one protease each from the land plants A. thaliana (AtDeg14, Table 1), P. trichocarpa (PtDeg14, Table 2), O. sativa (OsDeg14, originally called OsDegP12, Table 3) and P. patens (PpDeg14, Table 4). Notably, the Deg14 protease is missing in the green alga C. reinhardti (Table 5).


The family of Deg/HtrA proteases in plants.

Schuhmann H, Huesgen PF, Adamska I - BMC Plant Biol. (2012)

Maximum likelihood phylogenetic tree of Deg/HtrA proteases in selected plant species. Following plant species were investigated: Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Physcomitrella patens, Chlamydomonas reinhardtii, and the cyanobacterium Synechocystis sp. PCC6803. Phylogenetic tree labeled labeled with the new names as suggested by this study. Filled circles indicated a bootstrap support (100 replicates) of > 90%, empty circles indicate a bootstrap support of > 70%. Additionally, the domain arrangement representative for proteases from each group is indicated. Deg/HtrA proteases from clade I contain one protease domain (oval shapes) and one PDZ domain (diamonds), with the exception of Deg5 proteases, which possess a protease domain only. Proteases from clade II contain an additional PDZ domain, clade III gathers proteases with one active (oval shape) and one inactive (discontinous oval shape) protease domain and four PDZ domains, whereas enzymes from clade IV contain a single protease domain, which is shifted toward the C-terminus.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473262&req=5

Figure 1: Maximum likelihood phylogenetic tree of Deg/HtrA proteases in selected plant species. Following plant species were investigated: Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Physcomitrella patens, Chlamydomonas reinhardtii, and the cyanobacterium Synechocystis sp. PCC6803. Phylogenetic tree labeled labeled with the new names as suggested by this study. Filled circles indicated a bootstrap support (100 replicates) of > 90%, empty circles indicate a bootstrap support of > 70%. Additionally, the domain arrangement representative for proteases from each group is indicated. Deg/HtrA proteases from clade I contain one protease domain (oval shapes) and one PDZ domain (diamonds), with the exception of Deg5 proteases, which possess a protease domain only. Proteases from clade II contain an additional PDZ domain, clade III gathers proteases with one active (oval shape) and one inactive (discontinous oval shape) protease domain and four PDZ domains, whereas enzymes from clade IV contain a single protease domain, which is shifted toward the C-terminus.
Mentions: The Deg/HtrA proteases investigated here form four distinct clades (Figure 1; see Addtional file 4 for a tree containing the original gene model names), similar to an earlier study that included Deg/HtrA proteases from evolutionarily very distant taxa and only a few plant orthologs [7]. Clade I is further split into two subgroups, where subgroup IA includes orthologs of Deg1, Deg5 and Deg8 (Figure 1, Addtional file 4). Subgroup IB comprises the prokaryotic (cyanobacterial) Deg/HtrA proteases, and one protease each from the land plants A. thaliana (AtDeg14, Table 1), P. trichocarpa (PtDeg14, Table 2), O. sativa (OsDeg14, originally called OsDegP12, Table 3) and P. patens (PpDeg14, Table 4). Notably, the Deg14 protease is missing in the green alga C. reinhardti (Table 5).

Bottom Line: Therefore, the existing names and classification of these proteolytic enzymes does not meet our current needs and a phylogeny-based standardized nomenclature is required.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.Further, we proposed that the high number of Deg/HtrA proteases in plants is mainly due to gene duplications unique to the respective organism.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant Physiology and Biochemistry, University of Konstanz, Universitätsstr, 10, 78457, Konstanz, Germany.

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.

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Related in: MedlinePlus