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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.


Conserved SSP C-terminal sequences. Consensus sequences are represented for previously uncharacterized families. Conserved protein residues are higher in the HMM profile (see Supplementary Table 2 for cluster [c#] and family [f#] content).
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Figure 3: Conserved SSP C-terminal sequences. Consensus sequences are represented for previously uncharacterized families. Conserved protein residues are higher in the HMM profile (see Supplementary Table 2 for cluster [c#] and family [f#] content).

Mentions: In addition, the manual curation of previously unreported consensus sequences revealed conspicuous patterns commonly observed in known signalling peptide families. For example, a tyrosine residue was found in the conserved motif in multiple families (e.g., f131, f409, f919; Fig. 3). Such a tyrosine residue is known to be sulfated in the GLV, PSK, and PSY mature signalling peptides, where it is also preceded by an aspartic acid residue. Its presence and its post-translational modification are crucial for bioactivity (Komori et al., 2009; Matsuzaki et al., 2010; Whitford et al., 2012). The conserved motifs often end at or very near the last C-terminal residue of the precursor protein and contain one or several proline residues that might act as hinges when the peptide ligand binds to its receptor (Fig. 3). Together, these observations indicate that the global de novo sequence search method used in this study provides valuable hints about unrecognized bona fide SSPs.


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)

Conserved SSP C-terminal sequences. Consensus sequences are represented for previously uncharacterized families. Conserved protein residues are higher in the HMM profile (see Supplementary Table 2 for cluster [c#] and family [f#] content).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 3: Conserved SSP C-terminal sequences. Consensus sequences are represented for previously uncharacterized families. Conserved protein residues are higher in the HMM profile (see Supplementary Table 2 for cluster [c#] and family [f#] content).
Mentions: In addition, the manual curation of previously unreported consensus sequences revealed conspicuous patterns commonly observed in known signalling peptide families. For example, a tyrosine residue was found in the conserved motif in multiple families (e.g., f131, f409, f919; Fig. 3). Such a tyrosine residue is known to be sulfated in the GLV, PSK, and PSY mature signalling peptides, where it is also preceded by an aspartic acid residue. Its presence and its post-translational modification are crucial for bioactivity (Komori et al., 2009; Matsuzaki et al., 2010; Whitford et al., 2012). The conserved motifs often end at or very near the last C-terminal residue of the precursor protein and contain one or several proline residues that might act as hinges when the peptide ligand binds to its receptor (Fig. 3). Together, these observations indicate that the global de novo sequence search method used in this study provides valuable hints about unrecognized bona fide SSPs.

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.