Carbohydrate Metabolism I: Major Metabolic Pathways and Their Control

The carbohydrate economy of developing tomato fruit is determined by wholeplant source–sink relationships. However, the fate of the imported photoassimilate partitioned to the fruit sink is controlled by the carbohydrate metabolism of the fruit tissue. Within the Lycopersicon spp. there exists a broad range of genetic variability for fruit carbohydrate metabolism, such as sucrose accumulation and modified ratios of fructose to glucose in the mature fruit and increased starch synthesis in the immature fruit. Metabolic pathways of carbohydrate metabolism in tomatoes, as well as natural genetic variation in the metabolic pathways, will be described. The impact of sink carbohydrate metabolism on fruit non-structural carbohydrate economy will be discussed.

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Bifidobacterium breveUCC2003 Employs Multiple Transcriptional Regulators To Control Metabolism of Particular Human Milk Oligosaccharides

Applied and Environmental Microbiology ◽

10.1128/aem.02774-17 ◽

2018 ◽

Vol 84 (9) ◽

pp. e02774-17 ◽

Cited By ~ 7

Author(s):

Kieran James ◽

Mary O'Connell Motherway ◽

Christophe Penno ◽

Rebecca Louise O'Brien ◽

Douwe van Sinderen

Keyword(s):

Transcriptional Regulation ◽

Human Milk ◽

Carbohydrate Metabolism ◽

Metabolic Pathways ◽

Transcriptional Regulators ◽

Prototype Strain ◽

Regulatory Mechanisms ◽

Human Milk Oligosaccharides ◽

Content Type ◽

Bifidobacterium Breve

ABSTRACTBifidobacterial carbohydrate metabolism has been studied in considerable detail for a variety of both plant- and human-derived glycans, particularly involving the bifidobacterial prototype strainBifidobacterium breveUCC2003. We recently elucidated the metabolic pathways by which thehumanmilkoligosaccharide (HMO) constituents lacto-N-tetraose (LNT), lacto-N-neotetraose (LNnT) and lacto-N-biose (LNB) are utilized byB. breveUCC2003. However, to date, no work has been carried out on the regulatory mechanisms that control the expression of the genetic loci involved in these HMO metabolic pathways. In this study, we describe the characterization of three transcriptional regulators and the corresponding operator and associated (inducible) promoter sequences, with the latter governing the transcription of the genetic elements involved in LN(n)T/LNB metabolism. The activity of these regulators is dependent on the release of specific monosaccharides, which are believed to act as allosteric effectors and which are derived from the corresponding HMOs targeted by the particular locus.IMPORTANCEHuman milk oligosaccharides (HMOs) are a key factor in the development of the breastfed-infant microbiota. They function as prebiotics, selecting for a specific range of microbes, including a number of infant-associated species of bifidobacteria, which are thought to provide a range of health benefits to the infant host. While much research has been carried out on elucidating the mechanisms of HMO metabolism in infant-associated bifidobacteria, to date there is very little understanding of the transcriptional regulation of these pathways. This study reveals a multicomponent transcriptional regulation system that controls the recently identified pathways of HMO metabolism in the infant-associatedBifidobacterium breveprototype strain UCC2003. This not only provides insight into the regulatory mechanisms present in other infant-associated bifidobacteria but also provides an example of a network of sequential steps regulating microbial carbohydrate metabolism.

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Using Transcriptome Analysis to Screen for Key Genes and Pathways Related to Cytoplasmic Male Sterility in Cotton (Gossypium hirsutum L.)

International Journal of Molecular Sciences ◽

10.3390/ijms20205120 ◽

2019 ◽

Vol 20 (20) ◽

pp. 5120 ◽

Cited By ~ 2

Author(s):

Yuqing Li ◽

Tengfei Qin ◽

Chunyan Wei ◽

Jialiang Sun ◽

Tao Dong ◽

...

Keyword(s):

Fatty Acid ◽

Energy Metabolism ◽

Male Sterility ◽

Carbohydrate Metabolism ◽

Metabolic Pathways ◽

Amino Acid Metabolism ◽

Acid Metabolism ◽

Anther Development ◽

Gossypium Hirsutum L ◽

Key Genes

Cotton (Gossypium hirsutum L.) is one of the most important cash crops worldwide. Cytoplasmic male sterility (CMS) is an excellent breeding system for exploitation of heterosis, which has great potential to increase crop yields. To understand the molecular mechanism of CMS in cotton, we compared transcriptome, cytomorphological, physiological and bioinformatics data between the CMS line C2P5A and its maintainer line C2P5B. By using high-throughput sequencing technology, 178,166 transcripts were assembled and 2013 differentially expression genes (DEGs) were identified at three different stages of C2P5A anther development. In this study, we identified DEGs associated with reactive oxygen species (ROS), peroxisomes, aldehyde dehydrogenases (ALDH), cytochrome oxidase subunit VI, and cytochrome P450, and DEGs associated with tapetum development, Jojoba acyl-CoA reductase-related male sterility protein, basic helix-loop-helix (bHLH) and MYB transcription factors. The abnormal expression of one of these genes may be responsible for the CMS C2P5A line. In gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, DEGs were mainly related to carbohydrate metabolism, amino acid metabolism, transport and catabolism, and signal transduction. Carbohydrate metabolism provides energy for anther development, starch and sucrose metabolism, fatty acid biosynthesis and metabolism and ascorbate and aldarate metabolism. These results showed that numerous genes and multiple complex metabolic pathways regulate cotton anther development. Weighted correlation network analysis (WGCNA) indicated that three modules, ‘turquoise,’ ‘blue,’ and ‘green,’ were specific for the CMS C2P5A line. The ‘turquoise’ and ‘blue’ modules were mainly related to carbohydrate metabolism, amino acid metabolism, energy metabolism, peroxisomes, pyruvate metabolism as well as fatty acid degradation. The ‘green’ module was mainly related to energy metabolism, carbon metabolism, translation, and lipid metabolism. RNA-sequencing and WGCNA polymerization modules were screened for key genes and pathways related to CMS in cotton. This study presents a new perspective for further research into the metabolic pathways of pollen abortion in the CMS C2P5A line and also provides a theoretical basis for its breeding and production.

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Reconstruction of a generic genome-scale metabolic network for chicken: investigating network connectivity and finding potential biomarkers

10.1101/2021.07.22.453438 ◽

2021 ◽

Author(s):

Ehsan Salehabadi ◽

Ehsan Motamedian ◽

Seyed Abbas Shojaosadati

Keyword(s):

Carbohydrate Metabolism ◽

Metabolic Pathways ◽

Egg Production ◽

Genetic Manipulation ◽

Human Life ◽

Principal Component ◽

Metabolic Model ◽

Fat Cell ◽

Chicken Cell ◽

Genome Scale

Chicken is the first sequenced avian that has a crucial role in human life for its meat and egg production. Because of various metabolic disorders, study the metabolism of chicken cell is important. Herein, the first genome-scale metabolic model of a chicken cell named iES1300, consists of 2427 reactions, 2569 metabolites, and 1300 genes, was reconstructed manually based on databases. Interactions of metabolic genes for growth were examined for E. coli , S. cerevisiae , human, and chicken metabolic models. The results indicated robustness to genetic manipulation for iES1300 similar to the results for human. iES1300 was integrated with transcriptomics data using algorithms and Principal Component Analysis was applied to compare context-specific models of the normal, tumor, lean and fat cell lines. It was found that the normal model has notable metabolic flexibility in the utilization of various metabolic pathways, especially in metabolic pathways of the carbohydrate metabolism, compared to the others. It was also concluded that the fat and tumor models have similar growth metabolisms and the lean chicken model has a more active lipid and carbohydrate metabolism.

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6-Phosphogluconate Dehydrogenase Links Cytosolic Carbohydrate Metabolism to Protein Secretion

10.1101/480129 ◽

2018 ◽

Author(s):

Haoxin Li ◽

Maria Ericsson ◽

Bokang Rabasha ◽

Bogdan Budnik ◽

Bridget Wagner ◽

...

Keyword(s):

Carbohydrate Metabolism ◽

Protein Secretion ◽

Metabolic Pathways ◽

Structural Integrity ◽

Computational Approach ◽

Cell Stress ◽

Phosphogluconate Dehydrogenase ◽

Genetic Suppression ◽

Cancer Cell Survival ◽

Chemical Inhibition

SUMMARYThe proteinaceous extracellular matrix (ECM) is vital for cancer cell survival, proliferation, migration, and differentiation. However, little is known regarding metabolic pathways required in the ECM secretion process. By using an unbiased computational approach, we searched for enzymes whose suppression may lead to disruptions in protein secretion. Here, we show that 6-phosphogluconate dehydrogenase (PGD), a cytosolic enzyme involved in carbohydrate metabolism, is required for endoplasmic reticulum (ER) structural integrity and protein secretion. Chemical inhibition or genetic suppression of its activity led to cell stress accompanied by significantly expanded ER volume and can be rescued by compensating glutathione supplies. Our results also suggest that this characteristic ER-dilation phenotype may be a general marker indicating increased ECM protein congestion inside cells and decreased secretion. Thus, PGD exemplifies a nexus of cytosolic carbohydrate metabolism and protein secretion.

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Major metabolic pathways for carbohydrate metabolism of voluntary skeletal muscle

American Journal of Physiology-Legacy Content ◽

10.1152/ajplegacy.1966.210.2.404 ◽

1966 ◽

Vol 210 (2) ◽

pp. 404-410 ◽

Cited By ~ 20

Author(s):

CH Beatty ◽

RD Peterson ◽

GM Basinger ◽

RM Bocek

Keyword(s):

Skeletal Muscle ◽

Carbohydrate Metabolism ◽

Metabolic Pathways

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Specific inhibition of Streptococcus bovis by endolysin LyJH307 supplementation shifts the rumen microbiota and metabolic pathways related to carbohydrate metabolism

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-021-00614-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Hanbeen Kim ◽

Tansol Park ◽

Inhyuk Kwon ◽

Jakyeom Seo

Keyword(s):

Carbohydrate Metabolism ◽

Metabolic Pathways ◽

Rumen Fluid ◽

Lactate Concentration ◽

Gas Production ◽

Lytic Activity ◽

Rumen Microbiota ◽

Functional Features ◽

Corn Grain

Abstract Background Endolysins, the bacteriophage-originated peptidoglycan hydrolases, are a promising replacement for antibiotics due to immediate lytic activity and no antibiotic resistance. The objectives of this study were to investigate the lytic activity of endolysin LyJH307 against S. bovis and to explore changes in rumen fermentation and microbiota in an in vitro system. Two treatments were used: 1) control, corn grain without LyJH307; and 2) LyJH307, corn grain with LyJH307 (4 U/mL). An in vitro fermentation experiment was performed using mixture of rumen fluid collected from two cannulated Holstein steers (450 ± 30 kg) and artificial saliva buffer mixed as 1:3 ratio for 12 h incubation time. In vitro dry matter digestibility, pH, volatile fatty acids, and lactate concentration were estimated at 12 h, and the gas production was measured at 6, 9, and 12 h. The rumen bacterial community was analyzed using 16S rRNA amplicon sequencing. Results LyJH307 supplementation at 6 h incubation markedly decreased the absolute abundance of S. bovis (approximately 70% compared to control, P = 0.0289) and increased ruminal pH (P = 0.0335) at the 12 h incubation. The acetate proportion (P = 0.0362) was significantly increased after LyJH307 addition, whereas propionate (P = 0.0379) was decreased. LyJH307 supplementation increased D-lactate (P = 0.0340) without any change in L-lactate concentration (P > 0.10). There were no significant differences in Shannon’s index, Simpson’s index, Chao1 estimates, and evenness (P > 0.10). Based on Bray-Curtis dissimilarity matrices, the LyJH307 affected the overall shift in microbiota (P = 0.097). LyJH307 supplementation induced an increase of 11 genera containing Lachnoclostridium, WCHB1–41, unclassified genus Selenomonadaceae, Paraprevotella, vadinBE97, Ruminococcus gauvreauii group, Lactobacillus, Anaerorhabdus furcosa group, Victivallaceae, Desulfuromonadaceae, and Sediminispirochaeta. The predicted functional features represented by the Kyoto Encyclopedia of Genes and Genomes pathways were changed by LyJH307 toward a decrease of carbohydrate metabolism. Conclusions LyJH307 caused a reduction of S. bovis and an increase of pH with shifts in minor microbiota and its metabolic pathways related to carbohydrate metabolism. This study provides the first insight into the availability of endolysin as a specific modulator for rumen and shows the possibility of endolysin degradation by rumen microbiota.

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Specific inhibition of Streptococcus bovis by endolysin LyJH307 supplementation shifts the rumen microbiota and metabolic pathways related to carbohydrate metabolism

10.21203/rs.3.rs-269499/v1 ◽

2021 ◽

Author(s):

Han Been KIM ◽

Tansol Park ◽

Inhyuk Kwon ◽

Jakyeom Seo

Keyword(s):

Carbohydrate Metabolism ◽

Metabolic Pathways ◽

Dry Matter ◽

Lytic Activity ◽

Streptococcus Bovis ◽

Rumen Microbiota ◽

Ruminal Ph ◽

Functional Features ◽

Corn Grain

Abstract Background: Ruminal acidosis negatively affects the animal production and performances of high-performance cattle by abnormal balancing of the rumen microbiota, which caused significant economic damage to farmers. Endolysins, the bacteriophage-originated peptidoglycan hydrolases, are a promising replacement of antibiotics due to their immediate lytic activity and no evidence of antibiotic resistance. The objectives of this study were to investigate the lytic activity of Streptococcus bovis specific endolysin LyJH307 against S. bovis and explore changes in rumen fermentation and microbiota in an in vitro system. Treatments consisted of corn grain with protein elution buffer and corn grain with endolysin LyJH307 (LyJH307, 0.2% of dietary dry matter). The rumen bacterial community was analyzed using 16S rRNA amplicon sequencing, followed by the prediction of microbial functional features by using PICRUSt2.Results: Endolysin LyJH307 supplementation at 6 h incubation time markedly decreased the absolute abundance of S. bovis (approximately 70%) and increased ruminal pH at the end of the incubation. There were no significant changes in gas production, in vitro dry matter degradability, and total volatile fatty acid production. The acetate proportion was significantly increased after LyJH307 addition, whereas propionate was decreased, thereby inducing an increase of acetate to propionate ratio in LyJH307. LyJH307 supplementation increased D-lactate without any change in L-lactate concentration. Among the alpha diversity indices, there were no significant differences in Shannon’s index, Simpson’s index, Chao1 estimates, and evenness. Based on Bray-Curtis dissimilarity matrices, the LyJH307 affected the overall shift in ruminal microbiota. Endolysin LyJH307 supplementation induced an increase of 11 genera containing Lachnoclostridium, WCHB1-41, unclassified genus Selenomonadaceae, Paraprevotella, vadinBE97, Ruminococcus gauvreauii group, Lactobacillus, Anaerorhabdus furcosa group, Victivallaceae, Desulfuromonadaceae, and Sediminispirochaeta. The predicted functional features represented by the Kyoto Encyclopedia of Genes and Genomes pathways were changed by LyJH307 toward a decrease of carbohydrate metabolism.Conclusions: Endolysin LyJH307 caused a reduction of S. bovis and an increase of ruminal pH with concomitant shifts in minor rumen microbiota and its metabolic pathways related to carbohydrate metabolism. This study provides the first insight into the availability of endolysin as a specific modulator for rumen and shows the possibility of endolysin degradation by rumen microbiota.

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CarbMetSim:A discrete-event simulator for carbohydrate metabolism in humans

10.1101/491019 ◽

2018 ◽

Author(s):

Mukul Goyal ◽

Buket Aydas ◽

Husam Ghazaleh ◽

Sanjay Rajasekharan

Keyword(s):

Insulin Resistance ◽

Blood Glucose ◽

Blood Glucose Level ◽

Carbohydrate Metabolism ◽

Glucose Level ◽

Metabolic Pathways ◽

Discrete Event ◽

Human Beings ◽

Average Impact ◽

The Impact

AbstractThis paper describesCarbMetSim, adiscrete-eventsimulator that tracks the blood glucose level of a person in response to a timed sequence of diet and exercise activities.CarbMetSimimplements broader aspects of carbohydrate metabolism in human beings with the objective of capturing the average impact of various diet/exercise activities on the blood glucose level. Key organs (stomach, intestine, portal vein, liver, kidney, muscles, adipose tissue, brain and heart) are implemented to the extent necessary to capture their impact on the production and consumption of glucose. Key metabolic pathways (glucose oxidation, glycolysisandgluconeogenesis) are accounted for in the operation of different organs. The impact of insulin and insulin resistance on the operation of various organs and pathways is captured in accordance with published research.CarbMetSimprovides broad flexibility to configure the insulin production ability, the average flux along various metabolic pathways and the impact of insulin resistance on different aspects of carbohydrate metabolism. The simulator does not yet have a detailed implementation of protein and lipid metabolism.

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Metabolic Flux Hierarchy Prioritizes the Entner-Doudoroff Pathway for Carbohydrate Co-Utilization inPseudomonas protegensPf-5

10.1101/402073 ◽

2018 ◽

Cited By ~ 1

Author(s):

Rebecca A. Wilkes ◽

Caroll M. Mendonca ◽

Ludmilla Aristilde

Keyword(s):

Metabolic Network ◽

Carbohydrate Metabolism ◽

Metabolic Pathways ◽

Metabolic Flux ◽

Gene Annotation ◽

Central Carbon Metabolism ◽

Flux Analysis ◽

Environmental Matrices ◽

Fructose 1,6 Bisphosphate ◽

Kinase Phosphorylation

ABSTRACTThe genetic characterization ofPseudomonas protegensPf-5 was recently completed. However, the inferred metabolic network structure has not yet been evaluated experimentally. Here we employed13C-tracers and quantitative flux analysis to investigate the intracellular network for carbohydrate metabolism. Similar to otherPseudomonasspecies,P. protegensPf-5 relied primarily on the Entner-Doudoroff (ED) pathway to connect initial glucose catabolism to downstream metabolic pathways. Flux quantitation determined that, in lieu of the direct phosphorylation of glucose by glucose kinase, phosphorylation of oxidized products of glucose (gluconate and 2-ketogluconate) towards the ED pathway accounted for over 90% of consumed glucose and greater than 35% of consumed glucose was secreted as gluconate and 2-ketogluconate. Consistent with the lack of annotated pathways for the initial catabolism of pentoses and galactose inP. protegensPf-5, only glucose was assimilated into intracellular metabolites in the presence of xylose, arabinose, or galactose. However, when glucose was fed simultaneously with fructose or mannose, co-uptake of the hexoses was evident but glucose was preferred over fructose (3 to 1) and over mannose (4 to 1). Despite gene annotation of mannose catabolism toward fructose 6-phosphate, metabolite labeling patterns revealed that mannose-derived carbons specifically entered central carbon metabolism via fructose-1,6-bisphosphate, similarly to fructose catabolism. Remarkably, carbons from mannose and fructose were found to cycle backward through the upper Emden-Meyerhof-Parnas pathway to feed into the ED pathway. Therefore, the operational metabolic network for processing carbohydrates inP. protegensPf-5 prioritizes flux through the ED pathway to channel carbons to downstream metabolic pathways.IMPORTANCESpecies of thePseudomonasgenus thrive in various nutritional environments and have strong biocatalytic potential due to their diverse metabolic capabilities. Carbohydrate substrates are ubiquitous both in environmental matrices and in feedstocks for engineered bioconversion. Here we investigated the metabolic network for carbohydrate metabolism inP. protegensPf-5. Metabolic flux quantitation revealed the relative involvement of different catabolic routes in channeling carbohydrate carbons through the network. We also uncovered that mannose catabolism was similar to fructose catabolism, despite the gene annotation of two different pathways in the genome. Elucidation of the constitutive metabolic network inP. protegensis important for understanding its innate carbohydrate processing, thus laying the foundation for targeting metabolic engineering of this untappedPseudomonasspecies.

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