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Characterization and transcript profiling of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum).

Pinzón-Latorre D, Deyholos MK - BMC Genomics (2013)

Bottom Line: PME activity may result in either rigidification or loosening of the cell wall, depending on the mode of demethylesterification.We found experimental evidence for the transcription of 77/105 LuPMEs and 83/95 LuPMEIs, and surveyed the transcript abundance of these in 12 different tissues and stages of development.The potential for functional redundancy was highlighted also by the phylogenetic analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada. deyholos@ualberta.ca.

ABSTRACT

Background: Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonans in the cell wall; their activity is regulated in part by pectin methylesterase inhibitors (PMEIs). PME activity may result in either rigidification or loosening of the cell wall, depending on the mode of demethylesterification. The activity of PMEs in the middle lamella is expected to affect intrusive elongation of phloem fibers, and their adhesion to adjacent cells. Length and extractability of phloem fibers are qualities important for their industrial uses in textiles and composites. As only three flax PMEs had been previously described, we were motivated to characterize the PME and PMEI gene families of flax.

Results: We identified 105 putative flax PMEs (LuPMEs) and 95 putative PMEIs (LuPMEIs) within the whole-genome assembly. We found experimental evidence for the transcription of 77/105 LuPMEs and 83/95 LuPMEIs, and surveyed the transcript abundance of these in 12 different tissues and stages of development. Six major monophyletic groups of LuPMEs could be defined based on the inferred relationships of flax genes and their presumed orthologs from other species. We searched the LuPMEs and LuPMEIs for conserved residues previously reported to be important for their tertiary structure and function. In the LuPMEs, the most highly conserved residues were catalytic residues while in the LuPMEIs, cysteines forming disulfude bridges between helices α2 and α3 were most highly conserved. In general, the conservation of critical residues was higher in the genes with evidence of transcript expression than in those for which no expression was detected.

Conclusions: The LuPMEs and LuPMEIs comprise large families with complex patterns of transcript expression and a wide range of physical characteristics. We observed that multiple PMEs and PMEIs are expressed in partially overlapping domains, indicative of several genes acting redundantly during most processes. The potential for functional redundancy was highlighted also by the phylogenetic analyses. We were able to identify a subset of PME and PMEIs that appeared particularly relevant to fiber development, which may provide a basis for the improvement of key traits in industrial feedstocks and a better understanding of the physiological roles of PMEs and PMEIs in general.

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Maximum likelihood dendrogram of PMEIs in flax and related species. Red: Linum usitatissimum; Purple: Manihot esculenta; Blue: Ricinus communis; Orange: Populus trichocarpa; Green: Arabidopsis thaliana. 100 bootstraps and 2 search-replicates (bootstrap values shown in Additional file5: Figure S3).
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Figure 10: Maximum likelihood dendrogram of PMEIs in flax and related species. Red: Linum usitatissimum; Purple: Manihot esculenta; Blue: Ricinus communis; Orange: Populus trichocarpa; Green: Arabidopsis thaliana. 100 bootstraps and 2 search-replicates (bootstrap values shown in Additional file5: Figure S3).

Mentions: To classify the predicted LuPMEs and LuPMEIs on the basis of amino acid sequence similarity and inferred evolutionary relationships, we aligned their amino acid sequences with predicted PMEs and PMEIs from four other angiosperms: cassava (Manihot esculenta), castor (Ricinus communis), poplar (Populus trichocarpa), and A. thaliana. These species were chosen because Arabidopsis is a well-characterized model organism, and castor, cassava, and poplar are in the same taxonomic order (Malpighiales) as flax, and whole-genome assemblies are available for each of these species. Following alignment, maximum likelihood phylogenetic trees for PMEs (Figure 9) and PMEIs (Figure 10) were constructed. Based on the groups defined by Louvet et al.[41] for Arabidopsis PMEs, the branch length, and the bootstrap values (Additional file4: Figure S2), six major monophyletic groups of PME could be defined (A, B, C, D, E, and F which correspond to groups 3, 1, 2, 1, 4, and 1 respectively in Louvet et al.[41]). Group A included five LuPMEs; three of them were Type-1 PME, and none of them had a cleavage recognition site. The PMEs in all the organisms of group B were Type-1 PMEs, and all the LuPMEs in this group had a cleavage recognition site, and a transmembrane domain, but no predicted signal peptide. Group C was composed of Type-1 and Type-2 PMEs. All of the Type-1 PMEs had a cleavage recognition site, and none of the Type-2 PMEs had either a signal peptide or transmembrane domain. Group D contained the previously described LuPME1, LuPME3, and LuPME5, we did not find any characteristic defining this group based on the parameters we described above (e.g. Table 1). The PMEs of all the species in group E were Type-2 PMEs. Finally group F contained PMEs of all the species analyzed except flax.


Characterization and transcript profiling of the pectin methylesterase (PME) and pectin methylesterase inhibitor (PMEI) gene families in flax (Linum usitatissimum).

Pinzón-Latorre D, Deyholos MK - BMC Genomics (2013)

Maximum likelihood dendrogram of PMEIs in flax and related species. Red: Linum usitatissimum; Purple: Manihot esculenta; Blue: Ricinus communis; Orange: Populus trichocarpa; Green: Arabidopsis thaliana. 100 bootstraps and 2 search-replicates (bootstrap values shown in Additional file5: Figure S3).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4008260&req=5

Figure 10: Maximum likelihood dendrogram of PMEIs in flax and related species. Red: Linum usitatissimum; Purple: Manihot esculenta; Blue: Ricinus communis; Orange: Populus trichocarpa; Green: Arabidopsis thaliana. 100 bootstraps and 2 search-replicates (bootstrap values shown in Additional file5: Figure S3).
Mentions: To classify the predicted LuPMEs and LuPMEIs on the basis of amino acid sequence similarity and inferred evolutionary relationships, we aligned their amino acid sequences with predicted PMEs and PMEIs from four other angiosperms: cassava (Manihot esculenta), castor (Ricinus communis), poplar (Populus trichocarpa), and A. thaliana. These species were chosen because Arabidopsis is a well-characterized model organism, and castor, cassava, and poplar are in the same taxonomic order (Malpighiales) as flax, and whole-genome assemblies are available for each of these species. Following alignment, maximum likelihood phylogenetic trees for PMEs (Figure 9) and PMEIs (Figure 10) were constructed. Based on the groups defined by Louvet et al.[41] for Arabidopsis PMEs, the branch length, and the bootstrap values (Additional file4: Figure S2), six major monophyletic groups of PME could be defined (A, B, C, D, E, and F which correspond to groups 3, 1, 2, 1, 4, and 1 respectively in Louvet et al.[41]). Group A included five LuPMEs; three of them were Type-1 PME, and none of them had a cleavage recognition site. The PMEs in all the organisms of group B were Type-1 PMEs, and all the LuPMEs in this group had a cleavage recognition site, and a transmembrane domain, but no predicted signal peptide. Group C was composed of Type-1 and Type-2 PMEs. All of the Type-1 PMEs had a cleavage recognition site, and none of the Type-2 PMEs had either a signal peptide or transmembrane domain. Group D contained the previously described LuPME1, LuPME3, and LuPME5, we did not find any characteristic defining this group based on the parameters we described above (e.g. Table 1). The PMEs of all the species in group E were Type-2 PMEs. Finally group F contained PMEs of all the species analyzed except flax.

Bottom Line: PME activity may result in either rigidification or loosening of the cell wall, depending on the mode of demethylesterification.We found experimental evidence for the transcription of 77/105 LuPMEs and 83/95 LuPMEIs, and surveyed the transcript abundance of these in 12 different tissues and stages of development.The potential for functional redundancy was highlighted also by the phylogenetic analyses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada. deyholos@ualberta.ca.

ABSTRACT

Background: Pectin methylesterases (PMEs) catalyze the demethylesterification of homogalacturonans in the cell wall; their activity is regulated in part by pectin methylesterase inhibitors (PMEIs). PME activity may result in either rigidification or loosening of the cell wall, depending on the mode of demethylesterification. The activity of PMEs in the middle lamella is expected to affect intrusive elongation of phloem fibers, and their adhesion to adjacent cells. Length and extractability of phloem fibers are qualities important for their industrial uses in textiles and composites. As only three flax PMEs had been previously described, we were motivated to characterize the PME and PMEI gene families of flax.

Results: We identified 105 putative flax PMEs (LuPMEs) and 95 putative PMEIs (LuPMEIs) within the whole-genome assembly. We found experimental evidence for the transcription of 77/105 LuPMEs and 83/95 LuPMEIs, and surveyed the transcript abundance of these in 12 different tissues and stages of development. Six major monophyletic groups of LuPMEs could be defined based on the inferred relationships of flax genes and their presumed orthologs from other species. We searched the LuPMEs and LuPMEIs for conserved residues previously reported to be important for their tertiary structure and function. In the LuPMEs, the most highly conserved residues were catalytic residues while in the LuPMEIs, cysteines forming disulfude bridges between helices α2 and α3 were most highly conserved. In general, the conservation of critical residues was higher in the genes with evidence of transcript expression than in those for which no expression was detected.

Conclusions: The LuPMEs and LuPMEIs comprise large families with complex patterns of transcript expression and a wide range of physical characteristics. We observed that multiple PMEs and PMEIs are expressed in partially overlapping domains, indicative of several genes acting redundantly during most processes. The potential for functional redundancy was highlighted also by the phylogenetic analyses. We were able to identify a subset of PME and PMEIs that appeared particularly relevant to fiber development, which may provide a basis for the improvement of key traits in industrial feedstocks and a better understanding of the physiological roles of PMEs and PMEIs in general.

Show MeSH
Related in: MedlinePlus