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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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LuPME transcript expression in various tissues. Venn diagram showing the number of LuPMEs detected in phloem-fiber containing tissues (A) and in tissue systems (B) ECP: early cortical peels. LCP: late cortical peels. EF: early fibers. LF: late fibers. RT: reproductive tissues. VS: Vascular tissues at shoot. R: Root . LSL: Leaves and senescent leaves.
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Figure 4: LuPME transcript expression in various tissues. Venn diagram showing the number of LuPMEs detected in phloem-fiber containing tissues (A) and in tissue systems (B) ECP: early cortical peels. LCP: late cortical peels. EF: early fibers. LF: late fibers. RT: reproductive tissues. VS: Vascular tissues at shoot. R: Root . LSL: Leaves and senescent leaves.

Mentions: We also identified PMEs and PMEIs whose transcript abundance was correlated with phloem fiber development. The transcript expression of 11 PMEs and 20 PMEIs was detected in EF, while 15 PMEs and 26 PMEIs were expressed in LF (Figure 2). 15 PMEI were expressed in both EF and LF while only one PME was expressed in both of these stages. Nine PMEs and five PMEIs were detected in EF but not LF, and conversely 13 PME and 12 PMEI were detected in LF and not EF. In general there were more PMEIs expressed in the fibers. Specifically there were more PMEIs expressed in the LF than in the EF, which might indicate that the inhibitory activity of the PMEIs is low at early stages of fiber development (i.e. EF stage), when fibers actively synthesize secondary cell walls, and demethylesterification of the newly synthesized homogalacturonan is required. However, when the cell wall deposition ceases, in the late fiber stage, PMEIs are expressed, and so the PME activity diminishes. Seven PMEs and three PMEI were expressed in the shoot apex (SA), but not in any other of the stem vascular tissues. Moreover, nine PMEs and six PMEIs were expressed in the early cortical (ECP) peel, but not the late cortical peel (LCP), and three PMEs and nine PMEIs were expressed in late cortical peel but not early cortical peel (Figures 4A and5A). 13 PMEs and 14 PMEIs were found only in reproductive tissues; and three PMEs and two PMEI were found only in vascular tissues (Figures 4B and5B). Seven PMEs and six PMEIs showed specific transcript expression in only one tissue/organ; these transcripts were detected in flower buds (four PMEs and two PMEIs), flowers (one PMEI), bolls (one of each), xylem (one PMEI), roots (one PMEI), late cortical peel (one PME), and shoot apex (one PME). Two of these might be important for phloem fiber development: LuPME71, which was detected only in LCP, a fiber containing tissue where secondary cell wall deposition and maturation is taking place, and LuPME102, only detected in the SA, where intrusive growth takes place (Figure 2A-B).


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)

LuPME transcript expression in various tissues. Venn diagram showing the number of LuPMEs detected in phloem-fiber containing tissues (A) and in tissue systems (B) ECP: early cortical peels. LCP: late cortical peels. EF: early fibers. LF: late fibers. RT: reproductive tissues. VS: Vascular tissues at shoot. R: Root . LSL: Leaves and senescent leaves.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: LuPME transcript expression in various tissues. Venn diagram showing the number of LuPMEs detected in phloem-fiber containing tissues (A) and in tissue systems (B) ECP: early cortical peels. LCP: late cortical peels. EF: early fibers. LF: late fibers. RT: reproductive tissues. VS: Vascular tissues at shoot. R: Root . LSL: Leaves and senescent leaves.
Mentions: We also identified PMEs and PMEIs whose transcript abundance was correlated with phloem fiber development. The transcript expression of 11 PMEs and 20 PMEIs was detected in EF, while 15 PMEs and 26 PMEIs were expressed in LF (Figure 2). 15 PMEI were expressed in both EF and LF while only one PME was expressed in both of these stages. Nine PMEs and five PMEIs were detected in EF but not LF, and conversely 13 PME and 12 PMEI were detected in LF and not EF. In general there were more PMEIs expressed in the fibers. Specifically there were more PMEIs expressed in the LF than in the EF, which might indicate that the inhibitory activity of the PMEIs is low at early stages of fiber development (i.e. EF stage), when fibers actively synthesize secondary cell walls, and demethylesterification of the newly synthesized homogalacturonan is required. However, when the cell wall deposition ceases, in the late fiber stage, PMEIs are expressed, and so the PME activity diminishes. Seven PMEs and three PMEI were expressed in the shoot apex (SA), but not in any other of the stem vascular tissues. Moreover, nine PMEs and six PMEIs were expressed in the early cortical (ECP) peel, but not the late cortical peel (LCP), and three PMEs and nine PMEIs were expressed in late cortical peel but not early cortical peel (Figures 4A and5A). 13 PMEs and 14 PMEIs were found only in reproductive tissues; and three PMEs and two PMEI were found only in vascular tissues (Figures 4B and5B). Seven PMEs and six PMEIs showed specific transcript expression in only one tissue/organ; these transcripts were detected in flower buds (four PMEs and two PMEIs), flowers (one PMEI), bolls (one of each), xylem (one PMEI), roots (one PMEI), late cortical peel (one PME), and shoot apex (one PME). Two of these might be important for phloem fiber development: LuPME71, which was detected only in LCP, a fiber containing tissue where secondary cell wall deposition and maturation is taking place, and LuPME102, only detected in the SA, where intrusive growth takes place (Figure 2A-B).

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