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Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp.

Kilaru A, Cao X, Dabbs PB, Sung HJ, Rahman MM, Thrower N, Zynda G, Podicheti R, Ibarra-Laclette E, Herrera-Estrella L, Mockaitis K, Ohlrogge JB - BMC Plant Biol. (2015)

Bottom Line: The accumulation of TAG, rich in oleic acid, was associated with higher transcript levels for a putative stearoyl-ACP desaturase and endoplasmic reticulum (ER)-associated acyl-CoA synthetases, during fruit development.The orthologs that are distinctively expressed in oil-rich mesocarp tissues of this basal angiosperm, such as WRI2, ER-associated acyl-CoA synthetases, and lipid-droplet associated proteins were also identified.This study provides a foundation for future investigations to increase oil-content and has implications for metabolic engineering to enhance storage oil content in nonseed tissues of diverse species.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37614, USA. kilaru@etsu.edu.

ABSTRACT

Background: The mechanism by which plants synthesize and store high amounts of triacylglycerols (TAG) in tissues other than seeds is not well understood. The comprehension of controls for carbon partitioning and oil accumulation in nonseed tissues is essential to generate oil-rich biomass in perennial bioenergy crops. Persea americana (avocado), a basal angiosperm with unique features that are ancestral to most flowering plants, stores ~ 70 % TAG per dry weight in its mesocarp, a nonseed tissue. Transcriptome analyses of select pathways, from generation of pyruvate and leading up to TAG accumulation, in mesocarp tissues of avocado was conducted and compared with that of oil-rich monocot (oil palm) and dicot (rapeseed and castor) tissues to identify tissue- and species-specific regulation and biosynthesis of TAG in plants.

Results: RNA-Seq analyses of select lipid metabolic pathways of avocado mesocarp revealed patterns similar to that of other oil-rich species. However, only some predominant orthologs of the fatty acid biosynthetic pathway genes in this basal angiosperm were similar to those of monocots and dicots. The accumulation of TAG, rich in oleic acid, was associated with higher transcript levels for a putative stearoyl-ACP desaturase and endoplasmic reticulum (ER)-associated acyl-CoA synthetases, during fruit development. Gene expression levels for enzymes involved in terminal steps to TAG biosynthesis in the ER further indicated that both acyl-CoA-dependent and -independent mechanisms might play a role in TAG assembly, depending on the developmental stage of the fruit. Furthermore, in addition to the expression of an ortholog of WRINKLED1 (WRI1), a regulator of fatty acid biosynthesis, high transcript levels for WRI2-like and WRI3-like suggest a role for additional transcription factors in nonseed oil accumulation. Plastid pyruvate necessary for fatty acid synthesis is likely driven by the upregulation of genes involved in glycolysis and transport of its intermediates. Together, a comparative transcriptome analyses for storage oil biosynthesis in diverse plants and tissues suggested that several distinct and conserved features in this basal angiosperm species might contribute towards its rich TAG content.

Conclusions: Our work represents a comprehensive transcriptome resource for a basal angiosperm species and provides insight into their lipid metabolism in mesocarp tissues. Furthermore, comparison of the transcriptome of oil-rich mesocarp of avocado, with oil-rich seed and nonseed tissues of monocot and dicot species, revealed lipid gene orthologs that are highly conserved during evolution. The orthologs that are distinctively expressed in oil-rich mesocarp tissues of this basal angiosperm, such as WRI2, ER-associated acyl-CoA synthetases, and lipid-droplet associated proteins were also identified. This study provides a foundation for future investigations to increase oil-content and has implications for metabolic engineering to enhance storage oil content in nonseed tissues of diverse species.

No MeSH data available.


Gene expression pattern for select pathways (Additional file 1: Table S3). a Schematic of the pathways involved in conversion of sucrose to triacylglycerol (TAG). b The distribution of transcripts among the six pathways. c The number of reads per kilobase per million mapped reads (RPKM) per protein in each pathway. Multiple protein isoforms or subunits of a multi-protein complex were considered as a single protein and their transcripts were summed (Additional file 1: Table S3). The data are average transcript levels of five developing stages of mesocarp with error bars representing their standard deviation
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Fig2: Gene expression pattern for select pathways (Additional file 1: Table S3). a Schematic of the pathways involved in conversion of sucrose to triacylglycerol (TAG). b The distribution of transcripts among the six pathways. c The number of reads per kilobase per million mapped reads (RPKM) per protein in each pathway. Multiple protein isoforms or subunits of a multi-protein complex were considered as a single protein and their transcripts were summed (Additional file 1: Table S3). The data are average transcript levels of five developing stages of mesocarp with error bars representing their standard deviation

Mentions: The conversion of sucrose to TAG involves degradation of sucrose, generation of pyruvate in the plastid, which involves glycolysis, pentose phosphate pathway and plastid transporters, fatty acid synthesis in the plastid and TAG assembly in the ER (Fig. 2a). These six metabolic pathways require expression of over 200 genes (Additional file 1: Table S3). In avocado mesocarp, about 45 % of the transcripts corresponded to genes involved in glycolysis and 34 % to those in plastidial fatty acid biosynthesis (Fig. 2b). The analyses we undertook were designed to discover conserved functions in lipid biosynthesis and regulation in avocado, without regard to separation of close paralogs or allelic transcripts in the RNA datasets. Therefore, multiple transcripts encoding for genes of the same protein family or protein complex were summed and represented as RPKM/protein (Additional file 1: Table S3). More detailed analyses using whole genome assemblies will aid in further gene family member resolution. Overall, the average RPKM/protein, based on conserved protein annotation, across the five developmental stages of the mesocarp, were also abundant for those genes involved in glycolysis or the generation of pyruvate and subsequently fatty acid synthesis (Additional file 1: Table S3; Fig. 2c).Fig. 2


Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp.

Kilaru A, Cao X, Dabbs PB, Sung HJ, Rahman MM, Thrower N, Zynda G, Podicheti R, Ibarra-Laclette E, Herrera-Estrella L, Mockaitis K, Ohlrogge JB - BMC Plant Biol. (2015)

Gene expression pattern for select pathways (Additional file 1: Table S3). a Schematic of the pathways involved in conversion of sucrose to triacylglycerol (TAG). b The distribution of transcripts among the six pathways. c The number of reads per kilobase per million mapped reads (RPKM) per protein in each pathway. Multiple protein isoforms or subunits of a multi-protein complex were considered as a single protein and their transcripts were summed (Additional file 1: Table S3). The data are average transcript levels of five developing stages of mesocarp with error bars representing their standard deviation
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4537532&req=5

Fig2: Gene expression pattern for select pathways (Additional file 1: Table S3). a Schematic of the pathways involved in conversion of sucrose to triacylglycerol (TAG). b The distribution of transcripts among the six pathways. c The number of reads per kilobase per million mapped reads (RPKM) per protein in each pathway. Multiple protein isoforms or subunits of a multi-protein complex were considered as a single protein and their transcripts were summed (Additional file 1: Table S3). The data are average transcript levels of five developing stages of mesocarp with error bars representing their standard deviation
Mentions: The conversion of sucrose to TAG involves degradation of sucrose, generation of pyruvate in the plastid, which involves glycolysis, pentose phosphate pathway and plastid transporters, fatty acid synthesis in the plastid and TAG assembly in the ER (Fig. 2a). These six metabolic pathways require expression of over 200 genes (Additional file 1: Table S3). In avocado mesocarp, about 45 % of the transcripts corresponded to genes involved in glycolysis and 34 % to those in plastidial fatty acid biosynthesis (Fig. 2b). The analyses we undertook were designed to discover conserved functions in lipid biosynthesis and regulation in avocado, without regard to separation of close paralogs or allelic transcripts in the RNA datasets. Therefore, multiple transcripts encoding for genes of the same protein family or protein complex were summed and represented as RPKM/protein (Additional file 1: Table S3). More detailed analyses using whole genome assemblies will aid in further gene family member resolution. Overall, the average RPKM/protein, based on conserved protein annotation, across the five developmental stages of the mesocarp, were also abundant for those genes involved in glycolysis or the generation of pyruvate and subsequently fatty acid synthesis (Additional file 1: Table S3; Fig. 2c).Fig. 2

Bottom Line: The accumulation of TAG, rich in oleic acid, was associated with higher transcript levels for a putative stearoyl-ACP desaturase and endoplasmic reticulum (ER)-associated acyl-CoA synthetases, during fruit development.The orthologs that are distinctively expressed in oil-rich mesocarp tissues of this basal angiosperm, such as WRI2, ER-associated acyl-CoA synthetases, and lipid-droplet associated proteins were also identified.This study provides a foundation for future investigations to increase oil-content and has implications for metabolic engineering to enhance storage oil content in nonseed tissues of diverse species.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37614, USA. kilaru@etsu.edu.

ABSTRACT

Background: The mechanism by which plants synthesize and store high amounts of triacylglycerols (TAG) in tissues other than seeds is not well understood. The comprehension of controls for carbon partitioning and oil accumulation in nonseed tissues is essential to generate oil-rich biomass in perennial bioenergy crops. Persea americana (avocado), a basal angiosperm with unique features that are ancestral to most flowering plants, stores ~ 70 % TAG per dry weight in its mesocarp, a nonseed tissue. Transcriptome analyses of select pathways, from generation of pyruvate and leading up to TAG accumulation, in mesocarp tissues of avocado was conducted and compared with that of oil-rich monocot (oil palm) and dicot (rapeseed and castor) tissues to identify tissue- and species-specific regulation and biosynthesis of TAG in plants.

Results: RNA-Seq analyses of select lipid metabolic pathways of avocado mesocarp revealed patterns similar to that of other oil-rich species. However, only some predominant orthologs of the fatty acid biosynthetic pathway genes in this basal angiosperm were similar to those of monocots and dicots. The accumulation of TAG, rich in oleic acid, was associated with higher transcript levels for a putative stearoyl-ACP desaturase and endoplasmic reticulum (ER)-associated acyl-CoA synthetases, during fruit development. Gene expression levels for enzymes involved in terminal steps to TAG biosynthesis in the ER further indicated that both acyl-CoA-dependent and -independent mechanisms might play a role in TAG assembly, depending on the developmental stage of the fruit. Furthermore, in addition to the expression of an ortholog of WRINKLED1 (WRI1), a regulator of fatty acid biosynthesis, high transcript levels for WRI2-like and WRI3-like suggest a role for additional transcription factors in nonseed oil accumulation. Plastid pyruvate necessary for fatty acid synthesis is likely driven by the upregulation of genes involved in glycolysis and transport of its intermediates. Together, a comparative transcriptome analyses for storage oil biosynthesis in diverse plants and tissues suggested that several distinct and conserved features in this basal angiosperm species might contribute towards its rich TAG content.

Conclusions: Our work represents a comprehensive transcriptome resource for a basal angiosperm species and provides insight into their lipid metabolism in mesocarp tissues. Furthermore, comparison of the transcriptome of oil-rich mesocarp of avocado, with oil-rich seed and nonseed tissues of monocot and dicot species, revealed lipid gene orthologs that are highly conserved during evolution. The orthologs that are distinctively expressed in oil-rich mesocarp tissues of this basal angiosperm, such as WRI2, ER-associated acyl-CoA synthetases, and lipid-droplet associated proteins were also identified. This study provides a foundation for future investigations to increase oil-content and has implications for metabolic engineering to enhance storage oil content in nonseed tissues of diverse species.

No MeSH data available.