Limits...
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: Furthermore, we provide data that the recently identified PAMP-INDUCED SECRETED PEPTIDE (PIP) and PIP-LIKE (PIPL) peptides, which show similarity to the IDL and C-TERMINALLY ENCODED PEPTIDE (CEP) peptides, are not only involved in innate immune response in Arabidopsis but are also induced by abiotic stress.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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4526919&req=5

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).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4526919&req=5

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: Furthermore, we provide data that the recently identified PAMP-INDUCED SECRETED PEPTIDE (PIP) and PIP-LIKE (PIPL) peptides, which show similarity to the IDL and C-TERMINALLY ENCODED PEPTIDE (CEP) peptides, are not only involved in innate immune response in Arabidopsis but are also induced by abiotic stress.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