Limits...
Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins.

Demina IV, Persson T, Santos P, Plaszczyca M, Pawlowski K - PLoS ONE (2013)

Bottom Line: Root and nodule libraries representing the 3'-ends of cDNAs were subjected to high-throughput parallel 454 sequencing.The evaluation revealed 406 differentially regulated genes, 295 of which (72.7%) could be assigned a function based on homology.The D. glomerata members of this defensin subgroup contain an acidic C-terminal domain that was never found in plant defensins before.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, Stockholm University, Stockholm, Sweden.

ABSTRACT
Actinorhizal root nodule symbioses are very diverse, and the symbiosis of Datisca glomerata has previously been shown to have many unusual aspects. In order to gain molecular information on the infection mechanism, nodule development and nodule metabolism, we compared the transcriptomes of D. glomerata roots and nodules. Root and nodule libraries representing the 3'-ends of cDNAs were subjected to high-throughput parallel 454 sequencing. To identify the corresponding genes and to improve the assembly, Illumina sequencing of the nodule transcriptome was performed as well. The evaluation revealed 406 differentially regulated genes, 295 of which (72.7%) could be assigned a function based on homology. Analysis of the nodule transcriptome showed that genes encoding components of the common symbiosis signaling pathway were present in nodules of D. glomerata, which in combination with the previously established function of SymRK in D. glomerata nodulation suggests that this pathway is also active in actinorhizal Cucurbitales. Furthermore, comparison of the D. glomerata nodule transcriptome with nodule transcriptomes from actinorhizal Fagales revealed a new subgroup of nodule-specific defensins that might play a role specific to actinorhizal symbioses. The D. glomerata members of this defensin subgroup contain an acidic C-terminal domain that was never found in plant defensins before.

Show MeSH

Related in: MedlinePlus

Defensin amino acid sequence alignment.The amino acid sequences of the mature peptides of DgDEF1 and DgDEF2 are compared with the sequences of four mature defensin peptides of the A3 class, a defensin from Arabidopsis halleri (AhPDF1.4; GenBank accession no. AY961379.1), the Antifungal Protein 1 from Raphanus sativus seeds (RsAFP1) [55], a defensin from D. merckii (AMP1) [53] and the aluminum-induced tobacco protein (NtPit1) [52]. Gaps to optimize the alignment were introduced using the program ClustalW (EMBL), and the editor GeneDoc was used to present the alignment [89]. Identical amino acids at conserved positions are labeled by inverse print, whereas positions without full amino acid conservation are shaded in gray. Asterisks mark the cysteine residues conserved in the defensins from plants other than D. glomerata. All negatively charged amino acids in the unique C-terminal domains of DgDEF1 and DgDEF1 are marked by bold print and underlined.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3756986&req=5

pone-0072442-g001: Defensin amino acid sequence alignment.The amino acid sequences of the mature peptides of DgDEF1 and DgDEF2 are compared with the sequences of four mature defensin peptides of the A3 class, a defensin from Arabidopsis halleri (AhPDF1.4; GenBank accession no. AY961379.1), the Antifungal Protein 1 from Raphanus sativus seeds (RsAFP1) [55], a defensin from D. merckii (AMP1) [53] and the aluminum-induced tobacco protein (NtPit1) [52]. Gaps to optimize the alignment were introduced using the program ClustalW (EMBL), and the editor GeneDoc was used to present the alignment [89]. Identical amino acids at conserved positions are labeled by inverse print, whereas positions without full amino acid conservation are shaded in gray. Asterisks mark the cysteine residues conserved in the defensins from plants other than D. glomerata. All negatively charged amino acids in the unique C-terminal domains of DgDEF1 and DgDEF1 are marked by bold print and underlined.

Mentions: Dgc156, a 639 bp cDNA, encodes a protein of altogether 120 amino acids with a molecular weight of 13.77 kDa. According to Euk-mPLoc 2.0 (http://www.csbio.sjtu.edu.cn/bioinf/euk-multi-2/)[48], the protein localizes to the apoplast; according to SignalP [49], the first 26 amino acids represent the signal peptide, resulting in a mature protein of 94 amino acids, a molecular weight of 11.44 kDa and an IEP of 5.79. The amino acid sequence shows homology with defensins; accordingly, the protein was termed DgDEF1. Plant defensins are small basic apoplastic proteins of typically 45–55 amino acids and a net positive charge, with eight cysteine residues that form four disulfide bridges [50]. It should be pointed out that the net negative charge and the acidic IEP of DgDEF1 are due to the acidic C-terminal domain comprising 40 amino acids; the N-terminal defensin domain does indeed have a net positive charge and an alkaline IEP (Figure 1).


Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins.

Demina IV, Persson T, Santos P, Plaszczyca M, Pawlowski K - PLoS ONE (2013)

Defensin amino acid sequence alignment.The amino acid sequences of the mature peptides of DgDEF1 and DgDEF2 are compared with the sequences of four mature defensin peptides of the A3 class, a defensin from Arabidopsis halleri (AhPDF1.4; GenBank accession no. AY961379.1), the Antifungal Protein 1 from Raphanus sativus seeds (RsAFP1) [55], a defensin from D. merckii (AMP1) [53] and the aluminum-induced tobacco protein (NtPit1) [52]. Gaps to optimize the alignment were introduced using the program ClustalW (EMBL), and the editor GeneDoc was used to present the alignment [89]. Identical amino acids at conserved positions are labeled by inverse print, whereas positions without full amino acid conservation are shaded in gray. Asterisks mark the cysteine residues conserved in the defensins from plants other than D. glomerata. All negatively charged amino acids in the unique C-terminal domains of DgDEF1 and DgDEF1 are marked by bold print and underlined.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3756986&req=5

pone-0072442-g001: Defensin amino acid sequence alignment.The amino acid sequences of the mature peptides of DgDEF1 and DgDEF2 are compared with the sequences of four mature defensin peptides of the A3 class, a defensin from Arabidopsis halleri (AhPDF1.4; GenBank accession no. AY961379.1), the Antifungal Protein 1 from Raphanus sativus seeds (RsAFP1) [55], a defensin from D. merckii (AMP1) [53] and the aluminum-induced tobacco protein (NtPit1) [52]. Gaps to optimize the alignment were introduced using the program ClustalW (EMBL), and the editor GeneDoc was used to present the alignment [89]. Identical amino acids at conserved positions are labeled by inverse print, whereas positions without full amino acid conservation are shaded in gray. Asterisks mark the cysteine residues conserved in the defensins from plants other than D. glomerata. All negatively charged amino acids in the unique C-terminal domains of DgDEF1 and DgDEF1 are marked by bold print and underlined.
Mentions: Dgc156, a 639 bp cDNA, encodes a protein of altogether 120 amino acids with a molecular weight of 13.77 kDa. According to Euk-mPLoc 2.0 (http://www.csbio.sjtu.edu.cn/bioinf/euk-multi-2/)[48], the protein localizes to the apoplast; according to SignalP [49], the first 26 amino acids represent the signal peptide, resulting in a mature protein of 94 amino acids, a molecular weight of 11.44 kDa and an IEP of 5.79. The amino acid sequence shows homology with defensins; accordingly, the protein was termed DgDEF1. Plant defensins are small basic apoplastic proteins of typically 45–55 amino acids and a net positive charge, with eight cysteine residues that form four disulfide bridges [50]. It should be pointed out that the net negative charge and the acidic IEP of DgDEF1 are due to the acidic C-terminal domain comprising 40 amino acids; the N-terminal defensin domain does indeed have a net positive charge and an alkaline IEP (Figure 1).

Bottom Line: Root and nodule libraries representing the 3'-ends of cDNAs were subjected to high-throughput parallel 454 sequencing.The evaluation revealed 406 differentially regulated genes, 295 of which (72.7%) could be assigned a function based on homology.The D. glomerata members of this defensin subgroup contain an acidic C-terminal domain that was never found in plant defensins before.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, Stockholm University, Stockholm, Sweden.

ABSTRACT
Actinorhizal root nodule symbioses are very diverse, and the symbiosis of Datisca glomerata has previously been shown to have many unusual aspects. In order to gain molecular information on the infection mechanism, nodule development and nodule metabolism, we compared the transcriptomes of D. glomerata roots and nodules. Root and nodule libraries representing the 3'-ends of cDNAs were subjected to high-throughput parallel 454 sequencing. To identify the corresponding genes and to improve the assembly, Illumina sequencing of the nodule transcriptome was performed as well. The evaluation revealed 406 differentially regulated genes, 295 of which (72.7%) could be assigned a function based on homology. Analysis of the nodule transcriptome showed that genes encoding components of the common symbiosis signaling pathway were present in nodules of D. glomerata, which in combination with the previously established function of SymRK in D. glomerata nodulation suggests that this pathway is also active in actinorhizal Cucurbitales. Furthermore, comparison of the D. glomerata nodule transcriptome with nodule transcriptomes from actinorhizal Fagales revealed a new subgroup of nodule-specific defensins that might play a role specific to actinorhizal symbioses. The D. glomerata members of this defensin subgroup contain an acidic C-terminal domain that was never found in plant defensins before.

Show MeSH
Related in: MedlinePlus