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The Amborella vacuolar processing enzyme family.

Poncet V, Scutt C, Tournebize R, Villegente M, Cueff G, Rajjou L, Balliau T, Zivy M, Fogliani B, Job C, de Kochko A, Sarramegna-Burtet V, Job D - Front Plant Sci (2015)

Bottom Line: Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013).Three genes were found to encode VPEs in the Amborella's genome.A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella.

View Article: PubMed Central - PubMed

Affiliation: Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des Plantes Montpellier, France.

ABSTRACT
Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs). In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013). In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella's genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations in New Caledonia.

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Gene duplication model for the β-type Amborella VPEs on scaffold 2. The two duplicated genes (AmTr_2.262-1 and AmTr_2.262-2) show 84.5 % similarity at the nucleotide sequence level and 98.8 % at the protein level. Top: The manual annotation of the two closely related VPE genes, AmTr_2.262-1 and AmTr_2.262-2, referred to 262-1 and 262-2, respectively and the gene encoding the pectinesterase/pectinesterase (AmTr_ 2.264). Bottom: In the framework of the Amborella Genome Project (2013) the EVidenceModeler (EVM) program (http://evidencemodeler.sourceforge.net) automatically annotated VPE genes within the region, leading to wrongly annotated, supernumerary and truncated genes.
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Figure 1: Gene duplication model for the β-type Amborella VPEs on scaffold 2. The two duplicated genes (AmTr_2.262-1 and AmTr_2.262-2) show 84.5 % similarity at the nucleotide sequence level and 98.8 % at the protein level. Top: The manual annotation of the two closely related VPE genes, AmTr_2.262-1 and AmTr_2.262-2, referred to 262-1 and 262-2, respectively and the gene encoding the pectinesterase/pectinesterase (AmTr_ 2.264). Bottom: In the framework of the Amborella Genome Project (2013) the EVidenceModeler (EVM) program (http://evidencemodeler.sourceforge.net) automatically annotated VPE genes within the region, leading to wrongly annotated, supernumerary and truncated genes.

Mentions: A shotgun proteomic analysis revealed 415 proteins from the isolated Amborella embryos (Villegente et al., unpublished results). In particular, this analysis confirmed the presence of three 11S globulin forms in the Amborella embryos, of which two contained canonical N-G VPE cleavage sites, while the third contained a variant cleavage site (N-V-I) (data not shown). This shotgun proteomic analysis also revealed the presence of two specific peptides (GIIINHPQGEDVYAGVPK and HQADVCHAYQLLLK) (Supplemental Table S1) matching with the amino acid sequences of Amborella VPE proteins encoded by sequences on the scaffold AmTr_v1.0_scaffold 00002, labeled 27.model.AmTr_v1.0_scaffold00002.262 and evm_27.model.AmTr_v1.0_scaffold00002.263 (Figure 1).


The Amborella vacuolar processing enzyme family.

Poncet V, Scutt C, Tournebize R, Villegente M, Cueff G, Rajjou L, Balliau T, Zivy M, Fogliani B, Job C, de Kochko A, Sarramegna-Burtet V, Job D - Front Plant Sci (2015)

Gene duplication model for the β-type Amborella VPEs on scaffold 2. The two duplicated genes (AmTr_2.262-1 and AmTr_2.262-2) show 84.5 % similarity at the nucleotide sequence level and 98.8 % at the protein level. Top: The manual annotation of the two closely related VPE genes, AmTr_2.262-1 and AmTr_2.262-2, referred to 262-1 and 262-2, respectively and the gene encoding the pectinesterase/pectinesterase (AmTr_ 2.264). Bottom: In the framework of the Amborella Genome Project (2013) the EVidenceModeler (EVM) program (http://evidencemodeler.sourceforge.net) automatically annotated VPE genes within the region, leading to wrongly annotated, supernumerary and truncated genes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4544213&req=5

Figure 1: Gene duplication model for the β-type Amborella VPEs on scaffold 2. The two duplicated genes (AmTr_2.262-1 and AmTr_2.262-2) show 84.5 % similarity at the nucleotide sequence level and 98.8 % at the protein level. Top: The manual annotation of the two closely related VPE genes, AmTr_2.262-1 and AmTr_2.262-2, referred to 262-1 and 262-2, respectively and the gene encoding the pectinesterase/pectinesterase (AmTr_ 2.264). Bottom: In the framework of the Amborella Genome Project (2013) the EVidenceModeler (EVM) program (http://evidencemodeler.sourceforge.net) automatically annotated VPE genes within the region, leading to wrongly annotated, supernumerary and truncated genes.
Mentions: A shotgun proteomic analysis revealed 415 proteins from the isolated Amborella embryos (Villegente et al., unpublished results). In particular, this analysis confirmed the presence of three 11S globulin forms in the Amborella embryos, of which two contained canonical N-G VPE cleavage sites, while the third contained a variant cleavage site (N-V-I) (data not shown). This shotgun proteomic analysis also revealed the presence of two specific peptides (GIIINHPQGEDVYAGVPK and HQADVCHAYQLLLK) (Supplemental Table S1) matching with the amino acid sequences of Amborella VPE proteins encoded by sequences on the scaffold AmTr_v1.0_scaffold 00002, labeled 27.model.AmTr_v1.0_scaffold00002.262 and evm_27.model.AmTr_v1.0_scaffold00002.263 (Figure 1).

Bottom Line: Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013).Three genes were found to encode VPEs in the Amborella's genome.A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella.

View Article: PubMed Central - PubMed

Affiliation: Institut de Recherche pour le Développement, UMR Diversité, Adaptation et Développement des Plantes Montpellier, France.

ABSTRACT
Most vacuolar proteins are synthesized on rough endoplasmic reticulum as proprotein precursors and then transported to the vacuoles, where they are converted into their respective mature forms by vacuolar processing enzymes (VPEs). In the case of the seed storage proteins, this process is of major importance, as it conditions the establishment of vigorous seedlings. Toward the goal of identifying proteome signatures that could be associated with the origin and early diversification of angiosperms, we previously characterized the 11S-legumin-type seed storage proteins from Amborella trichopoda, a rainforest shrub endemic to New Caledonia that is also the probable sister to all other angiosperms (Amborella Genome Project, 2013). In the present study, proteomic and genomic approaches were used to characterize the VPE family in this species. Three genes were found to encode VPEs in the Amborella's genome. Phylogenetic analyses showed that the Amborella sequences grouped within two major clades of angiosperm VPEs, indicating that the duplication that generated the ancestors of these clades occurred before the most recent common ancestor of living angiosperms. A further important duplication within the VPE family appears to have occurred in common ancestor of the core eudicots, while many more recent duplications have also occurred in specific taxa, including both Arabidopsis thaliana and Amborella. An analysis of natural genetic variation for each of the three Amborella VPE genes revealed the absence of selective forces acting on intronic and exonic single-nucleotide polymorphisms among several natural Amborella populations in New Caledonia.

No MeSH data available.


Related in: MedlinePlus