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Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study.

Joët T, Laffargue A, Salmona J, Doulbeau S, Descroix F, Bertrand B, de Kochko A, Dussert S - New Phytol. (2009)

Bottom Line: However, to date, little information is available regarding dicot seeds with a transient perisperm and a persistent, copious endosperm.Coffea arabica is the subject of increasing genomic research and is a model for nonorthodox albuminous dicot seeds of tropical origin. * The aim of this study was to reconstruct the metabolic pathways involved in the biosynthesis of the main coffee seed storage compounds, namely cell wall polysaccharides, triacylglycerols, sucrose, and chlorogenic acids.For this purpose, we integrated transcriptomic and metabolite analyses, combining real-time RT-PCR performed on 137 selected genes (of which 79 were uncharacterized in Coffea) and metabolite profiling. * Our map-drawing approach derived from model plants enabled us to propose a rationale for the peculiar traits of the coffee endosperm, such as its unusual fatty acid composition, remarkable accumulation of chlorogenic acid and cell wall polysaccharides. * Comparison with the developmental features of exalbuminous seeds described in the literature revealed that the two seed types share important regulatory mechanisms for reserve biosynthesis, independent of the origin and ploidy level of the storage tissue.

View Article: PubMed Central - PubMed

Affiliation: IRD, UMR DIA-PC, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France. joet@ird.fr

ABSTRACT
* The genomic era facilitates the understanding of how transcriptional networks are interconnected to program seed development and filling. However, to date, little information is available regarding dicot seeds with a transient perisperm and a persistent, copious endosperm. Coffea arabica is the subject of increasing genomic research and is a model for nonorthodox albuminous dicot seeds of tropical origin. * The aim of this study was to reconstruct the metabolic pathways involved in the biosynthesis of the main coffee seed storage compounds, namely cell wall polysaccharides, triacylglycerols, sucrose, and chlorogenic acids. For this purpose, we integrated transcriptomic and metabolite analyses, combining real-time RT-PCR performed on 137 selected genes (of which 79 were uncharacterized in Coffea) and metabolite profiling. * Our map-drawing approach derived from model plants enabled us to propose a rationale for the peculiar traits of the coffee endosperm, such as its unusual fatty acid composition, remarkable accumulation of chlorogenic acid and cell wall polysaccharides. * Comparison with the developmental features of exalbuminous seeds described in the literature revealed that the two seed types share important regulatory mechanisms for reserve biosynthesis, independent of the origin and ploidy level of the storage tissue.

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Mapping of transcripts and metabolites associated with sucrose metabolism throughout coffee (Coffea arabica) seed development. Metabolite profiles are in gray boxes and gene expression profiles are in white boxes. Dashed lines indicate multistep pathways. AGPP, ADP-glucose pyrophosphorylase; CWIN, cell wall invertase; FK, fructokinase; HK, hexokinase; INV, invertase; PFK, phosphofructokinase, PGMc and PGMp, cytosolic and plastidial phosphoglucomutase, respectively; PGI, phosphoglucose isomerase; PK, pyruvate kinase; SPP, sucrose phosphate phosphatase; SPS, sucrose phosphate synthase; SS, starch synthase; SUSY, sucrose synthase; UGPP, UDP-glucose pyrophosphorylase.
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fig02: Mapping of transcripts and metabolites associated with sucrose metabolism throughout coffee (Coffea arabica) seed development. Metabolite profiles are in gray boxes and gene expression profiles are in white boxes. Dashed lines indicate multistep pathways. AGPP, ADP-glucose pyrophosphorylase; CWIN, cell wall invertase; FK, fructokinase; HK, hexokinase; INV, invertase; PFK, phosphofructokinase, PGMc and PGMp, cytosolic and plastidial phosphoglucomutase, respectively; PGI, phosphoglucose isomerase; PK, pyruvate kinase; SPP, sucrose phosphate phosphatase; SPS, sucrose phosphate synthase; SS, starch synthase; SUSY, sucrose synthase; UGPP, UDP-glucose pyrophosphorylase.

Mentions: Total lipids were extracted from 300 mg samples of freeze-dried powder using a modified Folch method (Folchet al., 1957) as described in Laffargue et al. (2007). Fatty acid methyl esters (FAMEs) were prepared according to the ISO-5509 standard, and GC analyses of FAMEs were performed as previously described (Laffargueet al., 2007). Sugars were extracted and measured by high-performance anion exchange chromatography coupled with pulsed amperometric detection (Dionex Chromatography Co., Sunnyvale, CA, USA) as described elsewhere (Dussertet al., 2006). The seed content in CWP was estimated by measuring the defatted alcohol insoluble residue (DAIR) using the method developed by Redgwell et al. (2003). Chlorogenic acids were extracted as described in Bertrand et al. 2003 and then analyzed using the HPLC conditions employed previously (Bertrandet al., 2008). All metabolites were analyzed in triplicate (from three different extractions) using a completely random experimental design. Estimation of CWP throughout seed development allowed us to report lipids, free sugars and CGA contents on a corrected dry mass basis (cDM = DM/(100 – DAIR content) × 100, Figs 2–6) giving a better estimate of these compounds at the intracellular level.


Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study.

Joët T, Laffargue A, Salmona J, Doulbeau S, Descroix F, Bertrand B, de Kochko A, Dussert S - New Phytol. (2009)

Mapping of transcripts and metabolites associated with sucrose metabolism throughout coffee (Coffea arabica) seed development. Metabolite profiles are in gray boxes and gene expression profiles are in white boxes. Dashed lines indicate multistep pathways. AGPP, ADP-glucose pyrophosphorylase; CWIN, cell wall invertase; FK, fructokinase; HK, hexokinase; INV, invertase; PFK, phosphofructokinase, PGMc and PGMp, cytosolic and plastidial phosphoglucomutase, respectively; PGI, phosphoglucose isomerase; PK, pyruvate kinase; SPP, sucrose phosphate phosphatase; SPS, sucrose phosphate synthase; SS, starch synthase; SUSY, sucrose synthase; UGPP, UDP-glucose pyrophosphorylase.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2713855&req=5

fig02: Mapping of transcripts and metabolites associated with sucrose metabolism throughout coffee (Coffea arabica) seed development. Metabolite profiles are in gray boxes and gene expression profiles are in white boxes. Dashed lines indicate multistep pathways. AGPP, ADP-glucose pyrophosphorylase; CWIN, cell wall invertase; FK, fructokinase; HK, hexokinase; INV, invertase; PFK, phosphofructokinase, PGMc and PGMp, cytosolic and plastidial phosphoglucomutase, respectively; PGI, phosphoglucose isomerase; PK, pyruvate kinase; SPP, sucrose phosphate phosphatase; SPS, sucrose phosphate synthase; SS, starch synthase; SUSY, sucrose synthase; UGPP, UDP-glucose pyrophosphorylase.
Mentions: Total lipids were extracted from 300 mg samples of freeze-dried powder using a modified Folch method (Folchet al., 1957) as described in Laffargue et al. (2007). Fatty acid methyl esters (FAMEs) were prepared according to the ISO-5509 standard, and GC analyses of FAMEs were performed as previously described (Laffargueet al., 2007). Sugars were extracted and measured by high-performance anion exchange chromatography coupled with pulsed amperometric detection (Dionex Chromatography Co., Sunnyvale, CA, USA) as described elsewhere (Dussertet al., 2006). The seed content in CWP was estimated by measuring the defatted alcohol insoluble residue (DAIR) using the method developed by Redgwell et al. (2003). Chlorogenic acids were extracted as described in Bertrand et al. 2003 and then analyzed using the HPLC conditions employed previously (Bertrandet al., 2008). All metabolites were analyzed in triplicate (from three different extractions) using a completely random experimental design. Estimation of CWP throughout seed development allowed us to report lipids, free sugars and CGA contents on a corrected dry mass basis (cDM = DM/(100 – DAIR content) × 100, Figs 2–6) giving a better estimate of these compounds at the intracellular level.

Bottom Line: However, to date, little information is available regarding dicot seeds with a transient perisperm and a persistent, copious endosperm.Coffea arabica is the subject of increasing genomic research and is a model for nonorthodox albuminous dicot seeds of tropical origin. * The aim of this study was to reconstruct the metabolic pathways involved in the biosynthesis of the main coffee seed storage compounds, namely cell wall polysaccharides, triacylglycerols, sucrose, and chlorogenic acids.For this purpose, we integrated transcriptomic and metabolite analyses, combining real-time RT-PCR performed on 137 selected genes (of which 79 were uncharacterized in Coffea) and metabolite profiling. * Our map-drawing approach derived from model plants enabled us to propose a rationale for the peculiar traits of the coffee endosperm, such as its unusual fatty acid composition, remarkable accumulation of chlorogenic acid and cell wall polysaccharides. * Comparison with the developmental features of exalbuminous seeds described in the literature revealed that the two seed types share important regulatory mechanisms for reserve biosynthesis, independent of the origin and ploidy level of the storage tissue.

View Article: PubMed Central - PubMed

Affiliation: IRD, UMR DIA-PC, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France. joet@ird.fr

ABSTRACT
* The genomic era facilitates the understanding of how transcriptional networks are interconnected to program seed development and filling. However, to date, little information is available regarding dicot seeds with a transient perisperm and a persistent, copious endosperm. Coffea arabica is the subject of increasing genomic research and is a model for nonorthodox albuminous dicot seeds of tropical origin. * The aim of this study was to reconstruct the metabolic pathways involved in the biosynthesis of the main coffee seed storage compounds, namely cell wall polysaccharides, triacylglycerols, sucrose, and chlorogenic acids. For this purpose, we integrated transcriptomic and metabolite analyses, combining real-time RT-PCR performed on 137 selected genes (of which 79 were uncharacterized in Coffea) and metabolite profiling. * Our map-drawing approach derived from model plants enabled us to propose a rationale for the peculiar traits of the coffee endosperm, such as its unusual fatty acid composition, remarkable accumulation of chlorogenic acid and cell wall polysaccharides. * Comparison with the developmental features of exalbuminous seeds described in the literature revealed that the two seed types share important regulatory mechanisms for reserve biosynthesis, independent of the origin and ploidy level of the storage tissue.

Show MeSH