Limits...
Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation.

Tuttle JR, Nah G, Duke MV, Alexander DC, Guan X, Song Q, Chen ZJ, Scheffler BE, Haigler CH - BMC Genomics (2015)

Bottom Line: Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90.Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA.The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA. jrtuttle@ncsu.edu.

ABSTRACT

Background: The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G. hirsutum cv Deltapine 90. When grown in parallel, the two types of fiber developed similarly except for prolonged fiber elongation in the G. barbadense cultivar. The data were collected from isolated fibers between 10 to 28 days post anthesis (DPA) representing: primary wall synthesis to support elongation; transitional cell wall remodeling; and secondary wall cellulose synthesis, which was accompanied by continuing elongation only in G. barbadense fiber.

Results: Of 206 identified fiber metabolites, 205 were held in common between the two genotypes. Approximately 38,000 transcripts were expressed in the fiber of each genotype, and these were mapped to the reference set and interpreted by homology to known genes. The developmental changes in the transcriptomes and the metabolomes were compared within and across genotypes with several novel implications. Transitional cell wall remodeling is a distinct stable developmental stage lasting at least four days (18 to 21 DPA). Expression of selected cell wall related transcripts was similar between genotypes, but cellulose synthase gene expression patterns were more complex than expected. Lignification was transcriptionally repressed in both genotypes. Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90. Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA.

Conclusions: The parallel data on deep-sequencing transcriptomics and non-targeted metabolomics for two genotypes of single-celled cotton fiber showed that a discrete developmental stage of transitional cell wall remodeling occurs before secondary wall cellulose synthesis begins. The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length.

No MeSH data available.


Four clusters of Gb and Gh fiber metabolites included three that were similar between genotypes. Metabolites with changes in concentration during fiber development (p ≤ 0.05) were clustered. The x-axis is as defined for Fig. 2. The y-axis is the scaled imputed mean value of metabolite concentration standardized to mean = 0 and standard deviation = 1. Color coding is as described in Fig. 2
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4482290&req=5

Fig3: Four clusters of Gb and Gh fiber metabolites included three that were similar between genotypes. Metabolites with changes in concentration during fiber development (p ≤ 0.05) were clustered. The x-axis is as defined for Fig. 2. The y-axis is the scaled imputed mean value of metabolite concentration standardized to mean = 0 and standard deviation = 1. Color coding is as described in Fig. 2

Mentions: Fuzzy C-means clustering revealed four major patterns of change in metabolite concentrations, with only three clusters being similar between genotypes (Fig. 3). Below we interpret the metabolite clusters by reference to metabolites with >10-fold concentration changes across DPA in both Gh and Gb fiber. Cluster ‘a-metabolites’ have higher concentration at 10 to 15 DPA with similar lower concentrations observed in both genotypes at 18 to 28 DPA. This cluster contains fucosterol (3β-Hydroxy-5,24(28)-stigmastadiene, Additional file 16). Phytosterols help to structure plasma membrane lipid domains that contain sphingolipids, which are derived from precursor phytosphingosine (4-D-Hydroxysphinganine) [50]. Phytosphingosine was in the ‘a’ or ‘c’ metabolite clusters in Gb or Gh fiber, but, like fucosterol, it occurred in high concentration at 10 DPA in both genotypes. Possibly, fucosterol and phytosphingosine are related to the organization of the plasma membrane to support high-rate elongation. The overall dissimilar Cluster ‘b-metabolites’ (Gb) and Cluster ‘c-metabolites’ (Gh) each contained linoleamide, with high concentration at 15 DPA in both genotypes. Linoleamide is derived from linoleic (18:2) fatty acid and modulates calcium levels in animal cells [51]. These two clusters (with 30 or 35 metabolites in Gb or Gh fiber) share the feature of lower metabolite concentrations at 28 DPA. About half of the molecules are held in common, including many fatty acids that could relate to building plasma membranes to support elongation. However one-third of the metabolites in Gb Cluster ‘b-metabolites’ have peak concentrations at 15 DPA, with potential functional consequences still to be determined. Cluster ‘d-metabolites’ are low at 18 to 21 DPA during transitional cell wall remodeling, but none showed >10-fold change across DPA in both genotypes. The biological context of this cluster will be discussed below as part of defining the transition stage. Cluster ‘e-metabolites’ have highest concentrations at 28 DPA in both genotypes and include: methyl-beta-glucopyranoside, raffinose, and the four nucleotide-2’,3’-cyclic monophosphates. The synthesis of methyl-beta-glucopyranoside may serve to detoxify methanol arising from pectin methylesterase activity during SCW synthesis [25, 52–54]. Raffinose is a sucrose-derived oligosaccharide that can act as an antioxidant to protect against oxidative stress, as well as exerting other protective effects [55]; see further discussion on ROS management below. The nucleotide-2’,3’-cyclic monophosphates are intermediate products of RNase activity that may signify increased nuclease activity in the initial stages of fiber cell death [56].Fig. 3


Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation.

Tuttle JR, Nah G, Duke MV, Alexander DC, Guan X, Song Q, Chen ZJ, Scheffler BE, Haigler CH - BMC Genomics (2015)

Four clusters of Gb and Gh fiber metabolites included three that were similar between genotypes. Metabolites with changes in concentration during fiber development (p ≤ 0.05) were clustered. The x-axis is as defined for Fig. 2. The y-axis is the scaled imputed mean value of metabolite concentration standardized to mean = 0 and standard deviation = 1. Color coding is as described in Fig. 2
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4482290&req=5

Fig3: Four clusters of Gb and Gh fiber metabolites included three that were similar between genotypes. Metabolites with changes in concentration during fiber development (p ≤ 0.05) were clustered. The x-axis is as defined for Fig. 2. The y-axis is the scaled imputed mean value of metabolite concentration standardized to mean = 0 and standard deviation = 1. Color coding is as described in Fig. 2
Mentions: Fuzzy C-means clustering revealed four major patterns of change in metabolite concentrations, with only three clusters being similar between genotypes (Fig. 3). Below we interpret the metabolite clusters by reference to metabolites with >10-fold concentration changes across DPA in both Gh and Gb fiber. Cluster ‘a-metabolites’ have higher concentration at 10 to 15 DPA with similar lower concentrations observed in both genotypes at 18 to 28 DPA. This cluster contains fucosterol (3β-Hydroxy-5,24(28)-stigmastadiene, Additional file 16). Phytosterols help to structure plasma membrane lipid domains that contain sphingolipids, which are derived from precursor phytosphingosine (4-D-Hydroxysphinganine) [50]. Phytosphingosine was in the ‘a’ or ‘c’ metabolite clusters in Gb or Gh fiber, but, like fucosterol, it occurred in high concentration at 10 DPA in both genotypes. Possibly, fucosterol and phytosphingosine are related to the organization of the plasma membrane to support high-rate elongation. The overall dissimilar Cluster ‘b-metabolites’ (Gb) and Cluster ‘c-metabolites’ (Gh) each contained linoleamide, with high concentration at 15 DPA in both genotypes. Linoleamide is derived from linoleic (18:2) fatty acid and modulates calcium levels in animal cells [51]. These two clusters (with 30 or 35 metabolites in Gb or Gh fiber) share the feature of lower metabolite concentrations at 28 DPA. About half of the molecules are held in common, including many fatty acids that could relate to building plasma membranes to support elongation. However one-third of the metabolites in Gb Cluster ‘b-metabolites’ have peak concentrations at 15 DPA, with potential functional consequences still to be determined. Cluster ‘d-metabolites’ are low at 18 to 21 DPA during transitional cell wall remodeling, but none showed >10-fold change across DPA in both genotypes. The biological context of this cluster will be discussed below as part of defining the transition stage. Cluster ‘e-metabolites’ have highest concentrations at 28 DPA in both genotypes and include: methyl-beta-glucopyranoside, raffinose, and the four nucleotide-2’,3’-cyclic monophosphates. The synthesis of methyl-beta-glucopyranoside may serve to detoxify methanol arising from pectin methylesterase activity during SCW synthesis [25, 52–54]. Raffinose is a sucrose-derived oligosaccharide that can act as an antioxidant to protect against oxidative stress, as well as exerting other protective effects [55]; see further discussion on ROS management below. The nucleotide-2’,3’-cyclic monophosphates are intermediate products of RNase activity that may signify increased nuclease activity in the initial stages of fiber cell death [56].Fig. 3

Bottom Line: Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90.Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA.The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length.

View Article: PubMed Central - PubMed

Affiliation: Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA. jrtuttle@ncsu.edu.

ABSTRACT

Background: The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G. hirsutum cv Deltapine 90. When grown in parallel, the two types of fiber developed similarly except for prolonged fiber elongation in the G. barbadense cultivar. The data were collected from isolated fibers between 10 to 28 days post anthesis (DPA) representing: primary wall synthesis to support elongation; transitional cell wall remodeling; and secondary wall cellulose synthesis, which was accompanied by continuing elongation only in G. barbadense fiber.

Results: Of 206 identified fiber metabolites, 205 were held in common between the two genotypes. Approximately 38,000 transcripts were expressed in the fiber of each genotype, and these were mapped to the reference set and interpreted by homology to known genes. The developmental changes in the transcriptomes and the metabolomes were compared within and across genotypes with several novel implications. Transitional cell wall remodeling is a distinct stable developmental stage lasting at least four days (18 to 21 DPA). Expression of selected cell wall related transcripts was similar between genotypes, but cellulose synthase gene expression patterns were more complex than expected. Lignification was transcriptionally repressed in both genotypes. Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90. Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA.

Conclusions: The parallel data on deep-sequencing transcriptomics and non-targeted metabolomics for two genotypes of single-celled cotton fiber showed that a discrete developmental stage of transitional cell wall remodeling occurs before secondary wall cellulose synthesis begins. The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length.

No MeSH data available.