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Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays.

Ghorbani S, Lin YC, Parizot B, Fernandez A, Njo MF, Van de Peer Y, Beeckman T, Hilson P - J. Exp. Bot. (2015)

Bottom Line: Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication.The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms.A similar approach can be implemented in different species for the study of a wide range of developmental programmes.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.

No MeSH data available.


Flow chart of the pipeline for SSP family assembly. See Materials and Methods for details.
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Figure 1: Flow chart of the pipeline for SSP family assembly. See Materials and Methods for details.

Mentions: To benchmark SSP identification algorithms, the preproprotein primary sequences of signalling peptides known or suspected to be involved in root development (identified first in Arabidopsis in most cases) were collected. These include: CEP, CLAVATA3 (CLV3/CLE), GOLVEN/ROOT GROWTH FACTOR/CLE-LIKE (GLV/RGF/CLEL), IDA, PSK, PLANT PEPTIDE CONTAINING SULFATED TYROSINE (PSY), and additional cysteine-rich peptides (Table 1; Supplementary Table 3). In total, 195 Arabidopsis protein sequences were collected from these known secretory peptide families. Most of these short preproproteins contain an amino (N)-terminal signal peptide and a conserved carboxyl (C)-terminal end that is cleaved off to yield the mature signal. This latter sequence corresponds to the secreted bioactive portion of the peptide hormones shown in multiple cases to act as a ligand of leucine-rich repeat-receptor-like kinase (LRR-RLK) membrane proteins (Benková and Hejátko, 2009; Butenko et al., 2009; Murphy et al., 2012). The successive stages of the analytical pipeline aimed at identifying SSPs are explained below and summarized in Fig. 1.


Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays.

Ghorbani S, Lin YC, Parizot B, Fernandez A, Njo MF, Van de Peer Y, Beeckman T, Hilson P - J. Exp. Bot. (2015)

Flow chart of the pipeline for SSP family assembly. See Materials and Methods for details.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4526923&req=5

Figure 1: Flow chart of the pipeline for SSP family assembly. See Materials and Methods for details.
Mentions: To benchmark SSP identification algorithms, the preproprotein primary sequences of signalling peptides known or suspected to be involved in root development (identified first in Arabidopsis in most cases) were collected. These include: CEP, CLAVATA3 (CLV3/CLE), GOLVEN/ROOT GROWTH FACTOR/CLE-LIKE (GLV/RGF/CLEL), IDA, PSK, PLANT PEPTIDE CONTAINING SULFATED TYROSINE (PSY), and additional cysteine-rich peptides (Table 1; Supplementary Table 3). In total, 195 Arabidopsis protein sequences were collected from these known secretory peptide families. Most of these short preproproteins contain an amino (N)-terminal signal peptide and a conserved carboxyl (C)-terminal end that is cleaved off to yield the mature signal. This latter sequence corresponds to the secreted bioactive portion of the peptide hormones shown in multiple cases to act as a ligand of leucine-rich repeat-receptor-like kinase (LRR-RLK) membrane proteins (Benková and Hejátko, 2009; Butenko et al., 2009; Murphy et al., 2012). The successive stages of the analytical pipeline aimed at identifying SSPs are explained below and summarized in Fig. 1.

Bottom Line: Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication.The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms.A similar approach can be implemented in different species for the study of a wide range of developmental programmes.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.

No MeSH data available.