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Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana.

Hastwell AH, Gresshoff PM, Ferguson BJ - J. Exp. Bot. (2015)

Bottom Line: The soybean CLE pre-propeptide family was further analysed and separated into seven distinct groups based on structure, with groupings strongly associated with the CLE domain sequence and function.Transcriptional evidence was also used to provide further insight into the location and function of all CLE peptide-encoding members currently available in gene atlases for the three species.Taken together, this in-depth analysis helped to identify and categorize the complete CLE peptide families of soybean and common bean, established gene orthologues within the two legume species, and Arabidopsis, and provided a platform to help compare, contrast, and identify the function of critical CLE peptide hormones in plant development.

View Article: PubMed Central - PubMed

Affiliation: Centre for Integrative Legume Research, School of Agricultural and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.

No MeSH data available.


Related in: MedlinePlus

Multi-CLE domain pre-propeptides. (A) Multiple sequence alignment of the soybean and M. truncatula multi-CLE domain pre-propeptides, with putative 13 amino acid residue CLE domains highlighted by a red box. An additional CLE domain of MtCLE14 that is not detected in the two soybean pre-propeptides is underlined in red. Four MtCLE14 CLE domains are identical in sequence (CLE domains 2–5) while there are no 100% conserved 13 amino acid residue CLE domains in soybean. However, there are two fully conserved 12 residue CLE domains in GmCLE37b (CLE domains 1 and 2). (B) Phylogenetic tree of known multi-CLE domain-containing pre-propeptides of rice (Oryza sativa), potato cyst nematode (Globodera rostochiensis), MtCLE14 of M. truncatula, and the newly identified GmCLE27a and GmCLE37b of soybean, including AtCLV3 as an outgroup. The multi-CLE domain pre-propeptides identified here cluster separately from those that were previously identified. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.
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Figure 4: Multi-CLE domain pre-propeptides. (A) Multiple sequence alignment of the soybean and M. truncatula multi-CLE domain pre-propeptides, with putative 13 amino acid residue CLE domains highlighted by a red box. An additional CLE domain of MtCLE14 that is not detected in the two soybean pre-propeptides is underlined in red. Four MtCLE14 CLE domains are identical in sequence (CLE domains 2–5) while there are no 100% conserved 13 amino acid residue CLE domains in soybean. However, there are two fully conserved 12 residue CLE domains in GmCLE37b (CLE domains 1 and 2). (B) Phylogenetic tree of known multi-CLE domain-containing pre-propeptides of rice (Oryza sativa), potato cyst nematode (Globodera rostochiensis), MtCLE14 of M. truncatula, and the newly identified GmCLE27a and GmCLE37b of soybean, including AtCLV3 as an outgroup. The multi-CLE domain pre-propeptides identified here cluster separately from those that were previously identified. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.

Mentions: Genes encoding pre-propeptides that contain multi-CLE domains were also identified. This includes GmCLE37a and GmCLE37b, which have six possible CLE domains each (Fig. 4A). These were excluded from the alignment in Fig. 1 as they do not have the archetypical domain structure. There are only two identical CLE domains within the soybean multi-CLE domain pre-propeptides and they both occur in GmCLE37b (Fig. 4A). A multi-CLE domain-containing pre-propeptide previously reported in Medicago truncatula by Oelkers et al. (2008) was identified here as MtCLV3 (MtCLV3 was previously discovered by Chen et al., 2009, but was not reported to encode a multi-CLE domain). Although MtCLV3 encodes three CLE domains, only one is actually translated due to the presence of a previously undetected intron identified here. An additional pre-propeptide of M. truncatula, called MtCLE14, contains a multi-CLE domain with seven CLE peptide domains (Fig 4A; Mortier et al., 2011). MtCLE14 contains four identical 12 amino acid CLE domains in tandem, each followed by an asparagine residue (possible representing a 13th residue in the CLE peptide), and each preceded by the same two hydrophobic residues (Fig. 4A).


Genome-wide annotation and characterization of CLAVATA/ESR (CLE) peptide hormones of soybean (Glycine max) and common bean (Phaseolus vulgaris), and their orthologues of Arabidopsis thaliana.

Hastwell AH, Gresshoff PM, Ferguson BJ - J. Exp. Bot. (2015)

Multi-CLE domain pre-propeptides. (A) Multiple sequence alignment of the soybean and M. truncatula multi-CLE domain pre-propeptides, with putative 13 amino acid residue CLE domains highlighted by a red box. An additional CLE domain of MtCLE14 that is not detected in the two soybean pre-propeptides is underlined in red. Four MtCLE14 CLE domains are identical in sequence (CLE domains 2–5) while there are no 100% conserved 13 amino acid residue CLE domains in soybean. However, there are two fully conserved 12 residue CLE domains in GmCLE37b (CLE domains 1 and 2). (B) Phylogenetic tree of known multi-CLE domain-containing pre-propeptides of rice (Oryza sativa), potato cyst nematode (Globodera rostochiensis), MtCLE14 of M. truncatula, and the newly identified GmCLE27a and GmCLE37b of soybean, including AtCLV3 as an outgroup. The multi-CLE domain pre-propeptides identified here cluster separately from those that were previously identified. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Figure 4: Multi-CLE domain pre-propeptides. (A) Multiple sequence alignment of the soybean and M. truncatula multi-CLE domain pre-propeptides, with putative 13 amino acid residue CLE domains highlighted by a red box. An additional CLE domain of MtCLE14 that is not detected in the two soybean pre-propeptides is underlined in red. Four MtCLE14 CLE domains are identical in sequence (CLE domains 2–5) while there are no 100% conserved 13 amino acid residue CLE domains in soybean. However, there are two fully conserved 12 residue CLE domains in GmCLE37b (CLE domains 1 and 2). (B) Phylogenetic tree of known multi-CLE domain-containing pre-propeptides of rice (Oryza sativa), potato cyst nematode (Globodera rostochiensis), MtCLE14 of M. truncatula, and the newly identified GmCLE27a and GmCLE37b of soybean, including AtCLV3 as an outgroup. The multi-CLE domain pre-propeptides identified here cluster separately from those that were previously identified. The tree is shown with bootstrap confidence values expressed as a percentage from 1000 bootstrap replications.
Mentions: Genes encoding pre-propeptides that contain multi-CLE domains were also identified. This includes GmCLE37a and GmCLE37b, which have six possible CLE domains each (Fig. 4A). These were excluded from the alignment in Fig. 1 as they do not have the archetypical domain structure. There are only two identical CLE domains within the soybean multi-CLE domain pre-propeptides and they both occur in GmCLE37b (Fig. 4A). A multi-CLE domain-containing pre-propeptide previously reported in Medicago truncatula by Oelkers et al. (2008) was identified here as MtCLV3 (MtCLV3 was previously discovered by Chen et al., 2009, but was not reported to encode a multi-CLE domain). Although MtCLV3 encodes three CLE domains, only one is actually translated due to the presence of a previously undetected intron identified here. An additional pre-propeptide of M. truncatula, called MtCLE14, contains a multi-CLE domain with seven CLE peptide domains (Fig 4A; Mortier et al., 2011). MtCLE14 contains four identical 12 amino acid CLE domains in tandem, each followed by an asparagine residue (possible representing a 13th residue in the CLE peptide), and each preceded by the same two hydrophobic residues (Fig. 4A).

Bottom Line: The soybean CLE pre-propeptide family was further analysed and separated into seven distinct groups based on structure, with groupings strongly associated with the CLE domain sequence and function.Transcriptional evidence was also used to provide further insight into the location and function of all CLE peptide-encoding members currently available in gene atlases for the three species.Taken together, this in-depth analysis helped to identify and categorize the complete CLE peptide families of soybean and common bean, established gene orthologues within the two legume species, and Arabidopsis, and provided a platform to help compare, contrast, and identify the function of critical CLE peptide hormones in plant development.

View Article: PubMed Central - PubMed

Affiliation: Centre for Integrative Legume Research, School of Agricultural and Food Sciences, The University of Queensland, St Lucia, Brisbane, Queensland, 4072, Australia.

No MeSH data available.


Related in: MedlinePlus