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The IDA/IDA-LIKE and PIP/PIP-LIKE gene families in Arabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide.

Vie AK, Najafi J, Liu B, Winge P, Butenko MA, Hornslien KS, Kumpf R, Aalen RB, Bones AM, Brembu T - J. Exp. Bot. (2015)

Bottom Line: Here we present three novel members of the IDL subfamily and show that two of them are strongly and rapidly induced by different biotic and abiotic stresses.Expression patterns of the IDA/IDL and PIP/PIPL genes were analysed using in silico data, qRT-PCR and GUS promoter lines.Transcriptomic responses to PIPL3 peptide treatment suggested a role in regulation of biotic stress responses and cell wall modification.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.

No MeSH data available.


Related in: MedlinePlus

The IDA/IDL and PIP/PIPL peptide families. (A) Protein alignment based on full-length sequences of the IDA/IDL/PIP/PIPL proteins. The green box indicates the SP, the blue box indicates the C-terminal putative peptide ligand motif and the red box indicates the second ligand motif identified in PIP2, PIP3 and PIPL1. The conserved arginine following the predicted SP is marked by a red diamond. The SGPS and GxGH motifs are indicated by red and brown bars below the alignment, respectively. (B) Schematic representation of the proteins in the IDA/IDL and PIP/PIPL peptide families. Grey boxes (marked with ‘sp’) represent the SP sequences identified by SignalP 4.1, orange boxes (marked with ‘var’) indicates a variable region with little homology, and red boxes represents the conserved, C-terminal EPIP domain known to be the active part of the IDA peptide indicated by the conserved core motif SGPS. The IDA and IDL proteins possess a C-terminal, variable sequence (i). This non-conserved sequence is not found among the PIP/PIPLs (ii). PIP2, PIP3 and PIPL1 contain two tandem SPGS motifs (iii).
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Figure 1: The IDA/IDL and PIP/PIPL peptide families. (A) Protein alignment based on full-length sequences of the IDA/IDL/PIP/PIPL proteins. The green box indicates the SP, the blue box indicates the C-terminal putative peptide ligand motif and the red box indicates the second ligand motif identified in PIP2, PIP3 and PIPL1. The conserved arginine following the predicted SP is marked by a red diamond. The SGPS and GxGH motifs are indicated by red and brown bars below the alignment, respectively. (B) Schematic representation of the proteins in the IDA/IDL and PIP/PIPL peptide families. Grey boxes (marked with ‘sp’) represent the SP sequences identified by SignalP 4.1, orange boxes (marked with ‘var’) indicates a variable region with little homology, and red boxes represents the conserved, C-terminal EPIP domain known to be the active part of the IDA peptide indicated by the conserved core motif SGPS. The IDA and IDL proteins possess a C-terminal, variable sequence (i). This non-conserved sequence is not found among the PIP/PIPLs (ii). PIP2, PIP3 and PIPL1 contain two tandem SPGS motifs (iii).

Mentions: Six members of the IDA gene family have been identified in Arabidopsis to date: IDA and IDL1 to IDL5. All members of the IDA gene family are intronless and encode small proteins (<110 amino acids) characterized by an N-terminal secretory SP, a variable region and a C-terminal, conserved region (Butenko et al., 2003). Through database searches, three new IDL genes were found (Table 1; Fig. 1A; Supplementary Dataset S1). In addition, we identified 11 genes with similarity to the IDLs. During preparation of this paper an article was published presenting these genes as a family encoding secreted PAMP-INDUCED PEPTIDES (PIPs) and PIP-LIKE (PIPL) peptides (Hou et al., 2014) (Table 1; Fig. 1A; Supplementary Dataset S1). For all members the N-terminal SP contains a stretch of aliphatic residues typical of secreted proteins (Fig. 1A, green box). This motif is followed by a conspicuously conserved arginine residue (Fig. 1A, red diamond). The C-terminal is characterized by the conserved core motif S(G,A,V)PS (hereafter called the SGPS motif) conserved in both IDLs and PIP/PIPLs (Fig. 1A, blue box). The SGPS motif in IDL proteins is followed by four highly conserved residues [(R/K)(R/K)HN] followed by up to 13 additional less conserved residues (Fig. 1A, Bi). The PIP/PIPL proteins lack the variable region C-terminal to the SGPS motif that is found for the IDL proteins (Fig. 1A, Bii, iii). Three of the PIP/PIPLs (PIP2, PIP3 and PIPL1) contain two SPGS motifs in a tandem orientation at the C-terminal (Fig. 1A, Biii), as identified by Hou et al. (2014).


The IDA/IDA-LIKE and PIP/PIP-LIKE gene families in Arabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the PIPL3 peptide.

Vie AK, Najafi J, Liu B, Winge P, Butenko MA, Hornslien KS, Kumpf R, Aalen RB, Bones AM, Brembu T - J. Exp. Bot. (2015)

The IDA/IDL and PIP/PIPL peptide families. (A) Protein alignment based on full-length sequences of the IDA/IDL/PIP/PIPL proteins. The green box indicates the SP, the blue box indicates the C-terminal putative peptide ligand motif and the red box indicates the second ligand motif identified in PIP2, PIP3 and PIPL1. The conserved arginine following the predicted SP is marked by a red diamond. The SGPS and GxGH motifs are indicated by red and brown bars below the alignment, respectively. (B) Schematic representation of the proteins in the IDA/IDL and PIP/PIPL peptide families. Grey boxes (marked with ‘sp’) represent the SP sequences identified by SignalP 4.1, orange boxes (marked with ‘var’) indicates a variable region with little homology, and red boxes represents the conserved, C-terminal EPIP domain known to be the active part of the IDA peptide indicated by the conserved core motif SGPS. The IDA and IDL proteins possess a C-terminal, variable sequence (i). This non-conserved sequence is not found among the PIP/PIPLs (ii). PIP2, PIP3 and PIPL1 contain two tandem SPGS motifs (iii).
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Related In: Results  -  Collection

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Figure 1: The IDA/IDL and PIP/PIPL peptide families. (A) Protein alignment based on full-length sequences of the IDA/IDL/PIP/PIPL proteins. The green box indicates the SP, the blue box indicates the C-terminal putative peptide ligand motif and the red box indicates the second ligand motif identified in PIP2, PIP3 and PIPL1. The conserved arginine following the predicted SP is marked by a red diamond. The SGPS and GxGH motifs are indicated by red and brown bars below the alignment, respectively. (B) Schematic representation of the proteins in the IDA/IDL and PIP/PIPL peptide families. Grey boxes (marked with ‘sp’) represent the SP sequences identified by SignalP 4.1, orange boxes (marked with ‘var’) indicates a variable region with little homology, and red boxes represents the conserved, C-terminal EPIP domain known to be the active part of the IDA peptide indicated by the conserved core motif SGPS. The IDA and IDL proteins possess a C-terminal, variable sequence (i). This non-conserved sequence is not found among the PIP/PIPLs (ii). PIP2, PIP3 and PIPL1 contain two tandem SPGS motifs (iii).
Mentions: Six members of the IDA gene family have been identified in Arabidopsis to date: IDA and IDL1 to IDL5. All members of the IDA gene family are intronless and encode small proteins (<110 amino acids) characterized by an N-terminal secretory SP, a variable region and a C-terminal, conserved region (Butenko et al., 2003). Through database searches, three new IDL genes were found (Table 1; Fig. 1A; Supplementary Dataset S1). In addition, we identified 11 genes with similarity to the IDLs. During preparation of this paper an article was published presenting these genes as a family encoding secreted PAMP-INDUCED PEPTIDES (PIPs) and PIP-LIKE (PIPL) peptides (Hou et al., 2014) (Table 1; Fig. 1A; Supplementary Dataset S1). For all members the N-terminal SP contains a stretch of aliphatic residues typical of secreted proteins (Fig. 1A, green box). This motif is followed by a conspicuously conserved arginine residue (Fig. 1A, red diamond). The C-terminal is characterized by the conserved core motif S(G,A,V)PS (hereafter called the SGPS motif) conserved in both IDLs and PIP/PIPLs (Fig. 1A, blue box). The SGPS motif in IDL proteins is followed by four highly conserved residues [(R/K)(R/K)HN] followed by up to 13 additional less conserved residues (Fig. 1A, Bi). The PIP/PIPL proteins lack the variable region C-terminal to the SGPS motif that is found for the IDL proteins (Fig. 1A, Bii, iii). Three of the PIP/PIPLs (PIP2, PIP3 and PIPL1) contain two SPGS motifs in a tandem orientation at the C-terminal (Fig. 1A, Biii), as identified by Hou et al. (2014).

Bottom Line: Here we present three novel members of the IDL subfamily and show that two of them are strongly and rapidly induced by different biotic and abiotic stresses.Expression patterns of the IDA/IDL and PIP/PIPL genes were analysed using in silico data, qRT-PCR and GUS promoter lines.Transcriptomic responses to PIPL3 peptide treatment suggested a role in regulation of biotic stress responses and cell wall modification.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.

No MeSH data available.


Related in: MedlinePlus