Proteomics reveals an increase in the abundance of glycolytic and ethanolic fermentation enzymes in developing sugarcane culms during sucrose accumulation
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ABSTRACT:
ORGANISM(S): Saccharum Spp Plants
TISSUE(S): Plant
SUBMITTER: 
Thais Cataldi
PROVIDER: ST001879 | MetabolomicsWorkbench | Mon Jul 19 00:00:00 BST 2021
REPOSITORIES: MetabolomicsWorkbench
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Project description:Sugarcane established industrial crop providing sugar, ethanol and biomass-derived electricity around the world. Cane sugar content is an important, breeding target, but its improvement remains very slow in many breeding programmes. Biotechnology strategies to improve sucrose accumulation made little progress at crop level, mainly due to the limited understanding of its regulation. MiRNAs regulate many metabolic processes in plants. However, their roles and target genes associated with sugarcane sucrose accumulation remains unknown. Here, we conducted high-throughput sequencing of transcriptome, small RNAs and degradome of leaves and stem of two sugarcane genotypes with contrasting sucrose content from the early to late stages of sucrose accumulation stages, which provided more insights into miRNA-associated gene regulation during sucrose accumulation. Transcriptome analysis identified 18,722 differentially expressed genes (DEGs) between both genotypes during sucrose accumulation. The major DEGs identified were involved in starch and sucrose metabolism, and photosynthesis etc. miRNA sequencing identified 563 known and 281 novel miRNAs from both genotypes during sucrose accumulation. Of these, 311 miRNAs were differentially expressed.752 targets of 368 miRNAs (609 targets for 260 known miRNAs and 168 targets for 108 novel miRNAs) were identified by degradom sequencing.Several known and novel miRNAs and their target genes associated with sugar metabolism, sugar transport and sucrose storage were identified in this study.This new insight into the complex network of sucrose accumulation in sugarcane will help identify candidate targets for sucrose improvement in sugarcane through molecular means.
2021-12-30 | GSE188303 | GEO
Project description:Sugarcane is an economically important crop contributing to the world’s sugar and ethanol production with 80% and 40%, respectively. In recent years, the growing demands for sugar and ethanol production has prompted the necessity to increase sugarcane productivity through conventional breeding programs. However, sugarcane breeders have encountered several difficulties to raise productivity, mainly due to its complex genetics. Sugarcane has a polyploidy genome, with many varieties being aneuploidy. Today, the majority of the planted sugarcane cultivars are complex hybrids derived mainly from crosses between Saccharum officinarum and S. spontaneum. Therefore, proteomics can provide some insight into deciphering gene regulation and changes in carbon metabolism and sucrose accumulation in the culms at different stages of plant development. The aim of this work was to compare the quantitative changes of proteins in sugarcane culms, during plant growth and sucrose accumulation. Total proteins were isolated from both, juvenile and maturing internodes at three stages of plant development. Label free shotgun proteomics was used for protein profiling and quantification. The internodes 5 (I5) and 9 (I9) of 4, 7 and 10 month-old-plants (4M, 7M and 10M, respectively) were harvested and used for proteomic analyses. To mimic field conditions of sucrose accumulation during sugarcane maturation, we stopped watering 10M plants for 10 days. An average of 1130 proteins, unique and differentially expressed across all ages were identified and quantified. Proteins were categorized within 27 functional groups, related to biological process. The patterns of expression for some categories, such as cellular amino acids, metabolic processes, secondary metabolic processes and translation were down-regulated in the immature internode (I5-10M), while up-regulated in the mature I9-10M. We observed an increase in the abundance of several enzymes of the glycolytic pathway and isoforms of alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC), in the juvenile stages of development of I9. These changes in enzymes contents indicates that at the early stages of internode development, hypoxia is increasing the glycolytic and ethanolic fermentation pathways, in order to supply ATP for plant growth and NAD+ for mitochondrial respiration, which might be impaired by the low oxygen availability inside the culm.
2021-09-09 | PXD027410 | Pride
Project description:In C4 sugarcane (Saccharum spp. hybrids), photosynthetic activity has been shown to be regulated by the demand for carbon from sink tissues. There is evidence, from other plant species, that sink-limitation of photosynthesis is facilitated by sugar-signaling mechanisms in the leaf that affect photosynthesis through regulation of gene expression. In this work, we manipulated leaf sugar levels by cold-girdling leaves (5oC) for 80 h to examine the mechanisms whereby leaf sugar accumulation affects photosynthetic activity and assess whether signaling mechanisms reported for other species operate in sugarcane. During this time, sucrose and hexose concentrations above the girdle increased by 77% and 81%, respectively. Conversely, leaf photosynthetic activity (A) and electron transport rates (ETR) decreased by 66% and 54%, respectively. Quantitative expression profiling by means of an Affymetrix GeneChip Sugarcane Genome Array was used to identify genes responsive to cold-girdling (56 h). A number of genes (74) involved in primary and secondary metabolic pathways were identified as being differentially expressed. Decreased expression of genes related to photosynthesis and increased expression of genes involved in assimilate partitioning, cell wall synthesis, phosphate metabolism and stress were observed. Furthermore four probe sets homologous to trehalose 6-phosphate phosphatase (TPP; EC 5.3.1.1) and trehalose 6-phosphate synthase (TPS; EC 2.4.1.15) were up- and down-regulated, respectively, indicating a possible role for trehalose 6-phosphate (T6P) as a putative sugar-sensor in sugarcane leaves.
2008-07-01 | GSE11934 | GEO
Project description:In C4 sugarcane (Saccharum spp. hybrids), photosynthetic activity has been shown to be regulated by the demand for carbon from sink tissues. There is evidence, from other plant species, that sink-limitation of photosynthesis is facilitated by sugar-signaling mechanisms in the leaf that affect photosynthesis through regulation of gene expression. In this work, we manipulated leaf sugar levels by cold-girdling leaves (5oC) for 80 h to examine the mechanisms whereby leaf sugar accumulation affects photosynthetic activity and assess whether signaling mechanisms reported for other species operate in sugarcane. During this time, sucrose and hexose concentrations above the girdle increased by 77% and 81%, respectively. Conversely, leaf photosynthetic activity (A) and electron transport rates (ETR) decreased by 66% and 54%, respectively. Quantitative expression profiling by means of an Affymetrix GeneChip Sugarcane Genome Array was used to identify genes responsive to cold-girdling (56 h). A number of genes (74) involved in primary and secondary metabolic pathways were identified as being differentially expressed. Decreased expression of genes related to photosynthesis and increased expression of genes involved in assimilate partitioning, cell wall synthesis, phosphate metabolism and stress were observed. Furthermore four probe sets homologous to trehalose 6-phosphate phosphatase (TPP; EC 5.3.1.1) and trehalose 6-phosphate synthase (TPS; EC 2.4.1.15) were up- and down-regulated, respectively, indicating a possible role for trehalose 6-phosphate (T6P) as a putative sugar-sensor in sugarcane leaves. Twelve month-old field grown Saccharum spp. (L.) hybrid cv. N19 (N19) cultivated at Mount Edgecombe, KwaZulu-Natal (SASRI) were used in the study, which was conducted in November, 2006. Plants were grown on a 5 x 15 m plot located on a north-east facing slope with a gradient of ca. 10o. Cold-girdles were attached to sugarcane leaves (n=4) for a period of 56 h prior to harvest. The girdle consisted of 0.75 cm (diameter) soft plastic tubing, firmly clamped around each leaf, approximately 30 cm from the leaf base. Cooled water maintained at 5oC was then pumped through the tubing using a Grant LTD6G cooling bath (Grant Instruments, Barrington, Cambridge, UK). At harvest, leaf samples were immediately frozen in liquid nitrogen (–196oC) and subsequently milled in an A11 Basic Analysis Mill (IKA, Staufen, Germany). Ground leaf tissue was stored at –80oC in 50 ml centrifuge tubes prior to analysis.
2008-07-01 | E-GEOD-11934 | biostudies-arrayexpress
Project description:Sweet sorghum has emerged as a promising source of bioenergy mainly due to its high biomass and high soluble sugar yield in stems. Studies have shown that loss-of-function Dry locus alleles have been selected during sweet sorghum domestication, and decapitation can further boost sugar accumulation in sweet sorghum, indicating that the potential for improving sugar yields is yet to be fully realized. To maximize sugar accumulation, it is essential to gain a better understanding of the mechanism underlying the massive accumulation of soluble sugars in sweet sorghum stems in addition to the Dry locus. We performed a transcriptomic analysis upon decapitation of near-isogenic lines for mutant (d, juicy stems, and green leaf midrib) and functional (D, dry stems and white leaf midrib) alleles at the Dry locus. Our analysis revealed that decapitation suppressed photosynthesis in leaves, but accelerated starch metabolic processes in stems. SbbHLH093 negatively correlates with sugar levels supported by genotypes (DD vs. dd), treatments (control vs. decapitation), and developmental stage post anthesis (3d vs.10d). D locus gene SbNAC074A and other programmed cell death-related genes were downregulated by decapitation, while sugar transporter-encoding gene SbSWEET1A was induced. Both SbSWEET1A and Invertase 5 were detected in phloem companion cells by RNA in situ assay. Loss of the SbbHLH093 homolog, AtbHLH093, in Arabidopsis led to a sugar accumulation increase. This study provides new insights into sugar accumulation enhancement in bioenergy crops, which can be potentially achieved by reducing reproductive sink strength and enhancing phloem unloading.
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Project description:Regulation of intracellular sugar homeostasis is maintained by regulation of activities of sugar import and export proteins residing at the tonoplast. We show here that the EARLY RESPONSE TO DEHYDRATION6-LIKE4 protein, being the closest homolog to the proton/glucose symporter ERDL6, resides in the vacuolar membrane. Gene expression and subcellular fractionation studies indicated that ERDL4 was involved in fructose allocation across the tonoplast. Overexpression of ERDL4 increased total sugar levels in leaves, due to a concomitantly induced stimulation of TST2 expression, coding for the major vacuolar sugar loader. This conclusion is supported by the finding that tst1-2 knockout lines overexpressing ERDL4 lack increased cellular sugar levels. ERDL4 activity contributing to the coordination of cellular sugar homeostasis is also indicated by two further observations. Firstly, ERDL4 and TST genes exhibit an opposite regulation during a diurnal rhythm, and secondly, the ERDL4 gene is markedly expressed during cold acclimation representing a situation in which TST activity needs to be upregulated. Moreover, ERDL4-overexpressing plants show larger size of rosettes and roots, a delayed flowering time and increased total seed yield. Consistently, erdl4 knock-out plants show impaired cold acclimation and freezing tolerance along with reduced plant biomass. In summary, we show that modification of cytosolic fructose levels influences plant organ development and stress tolerance.
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2024-01-26 | PXD047578 | Pride
Project description:The physiology of ethanologenic Escherichia coli grown anaerobically in alkaline-pretreated plant hydrolysates is not well studied. To gain insight into how E. coli responds to such hydrolysates, we studied an E. coli K-12 ethanologen fermenting a hydrolysate prepared from corn stover pre-treated by ammonia fiber expansion. Despite the high sugar content (~6% glucose, 3% xylose) and relatively low toxicity of this hydrolysate, E. coli ceased growth long before glucose was depleted. Nevertheless, the cells remained metabolically active and continued conversion of glucose to ethanol until all glucose was consumed. Gene expression profiling revealed complex and changing patterns of metabolic physiology and cellular stress responses throughout the different stages of growth. During the exponential and transition phases of growth, high cell maintenance and stress response costs were mitigated, in part, by free amino acids available in the hydrolysate media. However, after the majority of amino acids were depleted from the media cells entered stationary phase and ATP derived from glucose fermentation was consumed entirely by the demands of cell maintenance in the hydrolysate. Comparative gene expression profiling and metabolic modeling of the ethanologen suggested that the high energetic cost of mitigating osmotic, lignotoxin and ethanol stress collectively limits growth, sugar utilization rates and ethanol yields in alkaline-pretreated lignocellulosic hydrolysates. 38 samples in total. 24 samples were derived from biological replicate fermentations of alkaline-pretreated cornstover hydrolysate (12 datapoint time-series per fermentation). The remaining samples were obtained from fermentations conducted in defined media (Glucose Minimal Media (GMM, n=7), Synthetic Hydrolysate media (SynH, n=7)).
2012-06-17 | E-GEOD-35049 | biostudies-arrayexpress
Project description:Transcripts libraries were prepared from three sugarcane genotypes with high-sugar (HS), medium-sugar (MS) or low-sugar (LS) content that were treated with ethylene or H2O. The libraries were sequenced with the Illumina paired-end HiSeq platform.Transcriptomic analyses have identified about 160,000 unigenes of which 86000 annotated genes were classified into functional groups associated with carbohydrate metabolism, signaling, localization, transport, hydrolysis, growth, catalytic activity, membrane and storage, suggesting the structural and functional specification, including sucrose accumulation, occurring in maturing internodes. About 25,000 genes were differentially expressed between all genotypes and treatments combined. Genotype had a dominant effect on differential gene expression than ethylene treatment. Sucrose and starch metabolism genes were more responsive to ethylene treatment in low-sugar genotype. Ethylene caused differential gene expression of many stress-related transcription factors, carbohydrate metabolism, hormone metabolism and epigenetic modification. Ethylene-induced expression of ethylene-responsive transcription factors, cytosolic acid- and cell wall-bound invertases, and ATPase was more pronounced in low- than in high-sugar genotype, suggesting an ethylene-stimulated sink activity and consequent increased sucrose accumulation in low-sugar genotype.
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