Whole-Transcriptome Profiling in Developing Tubers of the Jerusalem Artichoke
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PROVIDER: PRJNA549527 | ENA |
REPOSITORIES: ENA
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Project description:Helianthus tuberosus L., known as the Jerusalem Artichoke, is a hexaploid plant species, adapted to low nutrient soils, that accumulates high levels of inulin in its tubers. Inulin is a fructose-based polysaccharide used either as dietary fiber or for the production of bioethanol. Key enzymes involved in inulin biosynthesis are well known. However, the gene networks underpinning tuber development and inulin accumulation in H. tuberous remain elusive. To fill this gap, we selected 6,365 ESTs from a H. tuberosus library to set up a microarray platform and record their expression across three tuber developmental stages, when rhizomes start enlarging (T0), at maximum tuber elongation rate (T3) and at tuber physiological maturity (Tm), in “VR” and “K8-HS142”clones. The former was selected as an early tuberizing, the latter as a late-tuberizing clone. We quantified inulin and starch levels, and q-RT PCR confirmed the expression of key genes accounting for inulin biosynthesis. The microarray analysis revealed that the differences in morphological and physiological traits between tubers of the two clones are genetically determined since T0 and that is relatively low the number of differentially expressed ESTs across the stages shared between the clones (93). The expression of ESTs for sucrose:sucrose 1-fructosyltransferase (1-SST) and fructan:fructan 1-fructosyltransferase (1-FFT), the two critical genes for fructans polymerization, resulted to be temporarily synchronized and mirror the progress of inulin accumulation and stretching. The expression of ESTs for starch biosynthesis was insignificant throughout the developmental stages of the clones in line with the negligible level of starch into their mature tubers, where inulin was the dominant polysaccharide. Overall, our study disclosed candidate genes underpinning the development and storage of carbohydrates in the tubers of two H. tuberosus clones. A model according to which the steady state levels of 1-SST and 1-FFT transcripts are developmentally controlled and might represent a limiting factor for inulin accumulation has been provided. Our finding may have significant repercussions for breeding clones with improved levels of inulin for food and chemical industry.
2020-01-13 | GSE132955 | GEO
Project description:Six isolates of bacteria associated with fermentation of jerusalem artichoke.
| PRJEB86987 | ENA
Project description:Jerusalem artichoke (JA) tubers are an important bio-economy developing crop because of its invaluable bioproducts in both food and biofuel aspects. However, the molecular mechanism of its tuberization, and the differences among different cultivars have been little studied to date. Here, we conducted a comparative proteome profiling of the JA tubers of three different cultivars including PJA, DJA, and HJA, showing phenotypic characteristics. Tuber epidermal pigmentation and underground tuberization habit were different phenological characters in the three cultivars and inulin content was also a physiological character exceptionally DJA regardless of the similar level of total carbohydrate amount. We identified a total of 420 proteins in the tubers and out of 114 showed significantly modulated among the cultivars. GO classification of the DEPs revealed biosynthesis amino acid and carbohydrate metabolic enzymes were differentially expressed in the three cultivar tubers. Integrated physiological inulin content and the biosynthetic protein expression levels among the cultivars suggest that Sucrose:sucrose 1-fructosyltransferase (1-SST) prioritizes inulin biosynthesis rather than rate-limiting enzyme fructan:fructan 1-fructosyltransferases (1-FFT). Furthermore, we confirmed the relationship between transcript-protein expression levels was in discord within inulin biosynthesis enzymes 1-SST and 1-FFT with the terms in previous RT-qPCR results using the same tubers. Our data represent the first report that comparative proteome profiling in JA tubers among the different cultivars and provides the metabolic and molecular basis for understanding carbohydrate metabolism in storage tuber tissue.
2019-05-29 | PXD010835 | Pride
Project description:Helianthus tuberosus strain:Purple Jerusalem artichoke (PJA) Transcriptome or Gene expression
| PRJNA258432 | ENA
Project description:Helianthus tuberosus L., known as the Jerusalem artichoke, is a hexaploid plant species, adapted to low-nutrient soils, that accumulates high levels of inulin in its tubers. Inulin is a fructose-based polysaccharide used either as dietary fiber or for the production of bioethanol. Key enzymes involved in inulin biosynthesis are well known. However, the gene networks underpinning tuber development and inulin accumulation in H. tuberous remain elusive. To fill this gap, we selected 6,365 expressed sequence tags (ESTs) from an H. tuberosus library to set up a microarray platform and record their expression across three tuber developmental stages, when rhizomes start enlarging (T0), at maximum tuber elongation rate (T3), and at tuber physiological maturity (Tm), in "VR" and "K8-HS142"clones. The former was selected as an early tuberizing and the latter as a late-tuberizing clone. We quantified inulin and starch levels, and qRT-PCR confirmed the expression of critical genes accounting for inulin biosynthesis. The microarray analysis revealed that the differences in morphological and physiological traits between tubers of the two clones are genetically determined since T0 and that is relatively low the number of differentially expressed ESTs across the stages shared between the clones (93). The expression of ESTs for sucrose:sucrose 1-fructosyltransferase (1-SST) and fructan:fructan 1-fructosyltransferase (1-FFT), the two critical genes for fructans polymerization, resulted to be temporarily synchronized and mirror the progress of inulin accumulation and stretching. The expression of ESTs for starch biosynthesis was insignificant throughout the developmental stages of the clones in line with the negligible level of starch into their mature tubers, where inulin was the dominant polysaccharide. Overall, our study disclosed candidate genes underpinning the development and storage of carbohydrates in the tubers of two H. tuberosus clones. A model according to which the steady-state levels of 1-SST and 1-FFT transcripts are developmentally controlled and might represent a limiting factor for inulin accumulation has been provided. Our finding may have significant repercussions for breeding clones with improved levels of inulin for food and chemical industry.
| S-EPMC7046554 | biostudies-literature
Project description:The present research investigates a ‘medicinal’ plant Jerusalem artichoke (abbreviated as JA) (Helianthus tuberosus L.) tuber proteome with an aim to unravel its proteome using a high-throughput proteomics technique. Although JA has been historically know to the Native Americans, it was brought back and spread to Europe by the colonists and in the late 19th century early 20th century it began to regain importance including its use for health and as a folk remedy for diabetes. In Japan (referred to as ‘kiku-imo’) its cultivation became popular mostly for health-related benefits such as reducing the blood sugar level. The group of (Genboku Takahashi et al.) has been working on the cultivation and utilization of kiku-imo tuber as a traditional/alternative medicine in daily life, and thus the research progressed to deeply look into the protein components through proteomics as very less is known about the proteome of the tubers, especially in relation to its importance as a functional food in treating diseases health conditions like diabetes. Using three commercially processed JA tuber products we used total protein extraction on the powdered samples in conjunction with label-free quantitate proteomic approach (mass spectrometry) to identify for the first time a comprehensive protein list for the JA tuber. A total of 2967 high‐confidence proteins were identified and categorized into different protein classes through bioinformatics. We have discussed these proteins especially in relation to their association with health and disease regulatory metabolism.
2022-02-21 | PXD030744 | Pride
Project description:To better understand the mechanism of inherent salt resistance in Jerusalem artichoke (Helianthus tuberosus L.), physiological and metabolic responses of tubers at the initiation stage of sprouting under different salt stress levels were evaluated in the present study. As a result, 28 metabolites were identified using proton nuclear magnetic resonance (1H-NMR) spectroscopy. Jerusalem artichoke tubers showed minor changes in metabolic response under moderate salt stress when they had not yet sprouted, where metabolism was downregulated at the start of sprouting and then upregulated significantly after plants became autotrophic. However, mild and severe salt stress levels caused different metabolic response patterns. In addition, the accumulation of fructose and sucrose was enhanced by moderate salt stress, while glucose was highly consumed. Aspartate and asparagine showed accelerated accumulation in sprouting Jerusalem artichoke tubers that became autotrophic, suggesting the enhancement of photosynthesis by moderate salt stress.
| S-EPMC7323981 | biostudies-literature
Project description:This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers. Keywords: Reference design
2008-02-13 | GSE10483 | GEO
Project description:An increase in inulin and plant-protein based nutraceutical demand ultimately puts pressure on available resources. Therefore, there is a need to prospect for supplementary feedstocks and sustainable ways to exploit them. The aim of this study was to explore the technical feasibility of sequential extraction of inulin and protein from Jerusalem artichoke tubers and understand the interrelationships between processes and product functional properties. The response surface methodology was used to determine the optimal parameters for sequential extraction. Protein functional properties analysis was done to identify the effects of the extraction process. The extraction approach adopted in this study was preceded by mechanical pressing of the tuber to yield a protein-rich juice. However, only 40.8% of the protein was recovered from the juice, therefore a subsequent solvent extraction step followed to extract the residual protein and inulin retained in the solids. Selective extraction was achieved when protein was solubilised in the first step of solvent extraction. The overall protein and inulin yields from pressing and both sequential extraction steps were 71.88 and 67.6%, respectively. The inulin yields were substantially higher than the maximum overall yields when inulin extraction, from the pressed tuber, was performed first thus improving yields from 57.3 to 67.6%. Consequently, mechanical pressing improved the overall protein yield. Sequential extraction resulted in an inulin extract with minimal protein contamination compared to the conventional method. Therefore, sequential extraction was efficient in yielding extracts with reduced impurities and good functional properties.
| S-EPMC7016075 | biostudies-literature
Project description:The rate of hyperglycaemia in people around the world is increasing at an alarming rate at present, and innovative methods of alleviating hyperglycaemia are needed. The effects of Jerusalem artichoke inulin on hyperglycaemia, liver-related genes and the intestinal microbiota in mice fed a high-fat diet (HFD) and treated with streptozotocin (STZ) to induce hyperglycaemia were investigated. Inulin-treated hyperglycaemic mice had decreased average daily food consumption, body weight, average daily water consumption and relative liver weight and blood concentrations of TAG, total cholesterol, HDL-cholesterol and fasting blood glucose. Liver-related gene expressions in hyperglycaemic (HFD-fed and STZ-treated) compared with control mice showed eighty-four differentially expressed genes (forty-nine up-regulated and thirty-five down-regulated). In contrast, hyperglycaemic mice treated with inulin had twenty-two differentially expressed genes compared with control ones. Using Illumina high-throughput sequencing technology, the rarefaction and the rank abundance curves as well as the α diversity indices showed the treatment-induced differences in bacterial diversity in intestine. The linear discriminant analysis of effect size showed that the inulin treatment improved intestinal microbiota; in particular, it significantly increased the number of Bacteroides in the intestine of mice. In conclusion, inulin is potentially an effective functional food for the prevention and/or treatment of hyperglycaemia.
| S-EPMC7015883 | biostudies-literature