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1.
Commun Biol ; 5(1): 1290, 2022 Nov 24.
Artigo em Inglês | MEDLINE | ID: mdl-36434094

RESUMO

Bacteria and Eucarya utilize the non-oxidative pentose phosphate pathway to direct the ribose moieties of nucleosides to central carbon metabolism. Many archaea do not possess this pathway, and instead, Thermococcales utilize a pentose bisphosphate pathway involving ribose-1,5-bisphosphate (R15P) isomerase and ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco). Intriguingly, multiple genomes from halophilic archaea seem only to harbor R15P isomerase, and do not harbor Rubisco. In this study, we identify a previously unrecognized nucleoside degradation pathway in halophilic archaea, composed of guanosine phosphorylase, ATP-dependent ribose-1-phosphate kinase, R15P isomerase, RuBP phosphatase, ribulose-1-phosphate aldolase, and glycolaldehyde reductase. The pathway converts the ribose moiety of guanosine to dihydroxyacetone phosphate and ethylene glycol. Although the metabolic route from guanosine to RuBP via R15P is similar to that of the pentose bisphosphate pathway in Thermococcales, the downstream route does not utilize Rubisco and is unique to halophilic archaea.


Assuntos
Ribose , Ribulose-Bifosfato Carboxilase , Ribulose-Bifosfato Carboxilase/genética , Ribulose-Bifosfato Carboxilase/metabolismo , Ribose/metabolismo , Pentoses/metabolismo , Archaea/genética , Archaea/metabolismo , Guanosina/metabolismo , Fosfatos
2.
Int J Mol Sci ; 23(20)2022 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-36293506

RESUMO

The accumulation of carotenoids in plants is a key nutritional quality in many horticultural crops. Although the structural genes encoding the biosynthetic enzymes are well-characterized, little is known regarding photoperiod-mediated carotenoid accumulation in the fruits of some horticultural crops. Herein, we performed physiological and transcriptomic analyses using two cucumber genotypes, SWCC8 (XIS-orange-fleshed and photoperiod-sensitive) and CC3 (white-fleshed and photoperiod-non-sensitive), established under two photoperiod conditions (8L/16D vs. 12L/12D) at four fruit developmental stages. Day-neutral treatments significantly increased fruit ß-carotene content by 42.1% compared to short day (SD) treatments in SWCC8 at 40 DAP with no significant changes in CC3. Day-neutral condition elevated sugar levels of fruits compared to short-day treatments. According to GO and KEGG analyses, the predominantly expressed genes were related to photosynthesis, carotenoid biosynthesis, plant hormone signaling, circadian rhythms, and carbohydrates. Consistent with ß-carotene accumulation in SWCC8, the day-neutral condition elevated the expression of key carotenoid biosynthesis genes such as PSY1, PDS, ZDS1, LYCB, and CHYB1 during later stages between 30 to 40 days of fruit development. Compared to SWCC8, CC3 showed an expression of DEGs related to carotenoid cleavage and oxidative stresses, signifying reduced ß-carotene levels in CC3 cucumber. Further, a WGCNA analysis revealed co-expression between carbohydrate-related genes (pentose-phosphatase synthase, ß-glucosidase, and trehalose-6-phosphatase), photoperiod-signaling genes (LHY, APRR7/5, FKF1, PIF3, COP1, GIGANTEA, and CK2) and carotenoid-biosynthetic genes, thus suggesting that a cross-talk mechanism between carbohydrates and light-related genes induces ß-carotene accumulation. The results highlighted herein provide a framework for future gene functional analyses and molecular breeding towards enhanced carotenoid accumulation in edible plant organs.


Assuntos
Celulases , Cucumis sativus , Frutas/química , Cucumis sativus/genética , Cucumis sativus/metabolismo , Transcriptoma , beta Caroteno/metabolismo , Regulação da Expressão Gênica de Plantas , Fotoperíodo , Reguladores de Crescimento de Plantas/metabolismo , Proteínas de Plantas/metabolismo , Trealose/metabolismo , Carotenoides/metabolismo , Monoéster Fosfórico Hidrolases/metabolismo , Pentoses/análise , Pentoses/metabolismo , Celulases/metabolismo
3.
JCI Insight ; 7(20)2022 10 24.
Artigo em Inglês | MEDLINE | ID: mdl-36278488

RESUMO

Patients with the renal phosphate-wasting disease X-linked hypophosphatemia (XLH) and Hyp mice, the murine homolog of XLH, are characterized by loss-of-function mutations in phosphate-regulating endopeptidase homolog X-linked (PHEX), leading to excessive secretion of the bone-derived phosphotropic hormone FGF23. The mineralization defect in patients with XLH and Hyp mice is caused by a combination of hypophosphatemia and local accumulation of mineralization-inhibiting molecules in bone. However, the mechanism by which PHEX deficiency regulates bone cell metabolism remains elusive. Here, we used spatial metabolomics by employing matrix-assisted laser desorption/ionization (MALDI) Fourier-transform ion cyclotron resonance mass spectrometry imaging (MSI) of undecalcified bone cryosections to characterize in situ metabolic changes in bones of Hyp mice in a holistic, unbiased manner. We found complex changes in Hyp bone metabolism, including perturbations in pentose phosphate, purine, pyrimidine, and phospholipid metabolism. Importantly, our study identified an upregulation of several biochemical pathways involved in intra- and extracellular production of the mineralization inhibitor pyrophosphate in the bone matrix of Hyp mice. Our data emphasize the utility of MSI-based spatial metabolomics in bone research and provide holistic in situ insights as to how Phex deficiency-induced changes in biochemical pathways in bone cells are linked to impaired bone mineralization.


Assuntos
Raquitismo Hipofosfatêmico Familiar , Camundongos , Animais , Endopeptidase Neutra Reguladora de Fosfato PHEX/genética , Endopeptidase Neutra Reguladora de Fosfato PHEX/metabolismo , Difosfatos/metabolismo , Regulação para Cima , Osso Cortical/metabolismo , Fosfatos/metabolismo , Metabolômica , Purinas , Hormônios , Pirimidinas , Fosfolipídeos , Pentoses
4.
Front Immunol ; 13: 974648, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36275752

RESUMO

Background: Dysbiosis of the gut microbiota is closely related to chronic systemic inflammation and autoimmunity, playing an essential role in the pathogenesis of primary Sjögren's syndrome (pSS). Abnormalities in the proportions of blood T lymphocyte subtype, that is Th17/Treg, were detected in pSS patients. We aimed to determine the associations between gut microbiota and Th17/Treg in pSS. Method: 98 pSS patients and 105 healthy controls (NC) were enrolled between Dec 1, 2018, and Aug 31, 2019. The baseline information and clinical parameters on pSS patients and healthy controls were collected. 16S rRNA sequencing was performed to characterize the gut microbiome and identify gut microbes that are differentially abundant between patients and healthy controls. Lastly, associations between relative abundances of specific bacterial taxa in the gut and clinical outcome parameters were evaluated. Results: Patients with pSS show decreased gut microbial diversity and richness, decreased abundance of butyrate producing bacteria, such as Roseburia and Coprococcus, and increased abundance of other taxa, such as Eubacterium rectale and Roseburia inulinivorans. These bacteria are enriched with functions related to glycolytic and lipogenic, energy, substance, galactose, pentose metabolism pathways and glucuronate interconversions, decreased with functions related to peptidoglycan biosynthesis, pyrimidine metabolism pathways. An integrative analysis identified pSS-related specific bacterial taxa in the gut, for which the abundance of Eubacterium rectale is negatively correlated with Th17/Treg. Furthermore, the pathways of biosynthesis of secondary metabolites, biosynthesis of amino acids, peptidoglycan biosynthesis and pyrimidine, galactose, pentose, microbial metabolism in diverse environments, glyoxylate and dicarboxylate metabolism are associated with Treg or Th17/Treg. Conclusions: Primary Sjögren's syndrome could lead to decreased gut microbial diversity and richness of intestinal flora in patients. The proportions of Th17 and Treg cells induced by microbiota were predictive pSS manifestations and accounted for the pSS severity.


Assuntos
Síndrome de Sjogren , Células Th17 , Humanos , RNA Ribossômico 16S/genética , Galactose , Peptidoglicano , Bactérias/genética , Inflamação/complicações , Pirimidinas , Aminoácidos , Glioxilatos , Glucuronatos , Pentoses , Butiratos
5.
Biosci Rep ; 42(10)2022 10 28.
Artigo em Inglês | MEDLINE | ID: mdl-36196895

RESUMO

Sulfoquinovose (SQ, 6-deoxy-6-sulfo-D-glucose) is a sulfo-sugar with a ubiquitous distribution in the environment due to its production by plants and other photosynthetic organisms. Bacteria play an important role in degradation of SQ and recycling of its constituent sulfur and carbon. Since its discovery in 1963, SQ was noted to have a structural resemblance to glucose-6-phosphate and proposed to be degraded through a pathway analogous to glycolysis, termed sulfoglycolysis. Studies in recent years have uncovered an unexpectedly diverse array of sulfoglycolytic pathways in different bacteria, including one analogous to the Embden-Meyerhof-Parnas pathway (sulfo-EMP), one analogous to the Entner-Doudoroff pathway (sulfo-ED), and two involving sulfo-sugar cleavage by a transaldolase (sulfo-TAL) and transketolase (sulfo-TK), respectively, analogous to reactions in the pentose phosphate (PP) pathway. In addition, a non-sulfoglycolytic SQ degradation pathway was also reported, involving oxygenolytic C-S cleavage catalyzed by a homolog of alkanesulfonate monooxygenase (sulfo-ASMO). Here, we review the discovery of these new mechanisms of SQ degradation and lessons learnt in the study of new catabolic enzymes and pathways in bacteria.


Assuntos
Glucose-6-Fosfato , Transaldolase , Transaldolase/metabolismo , Transcetolase/metabolismo , Bactérias/metabolismo , Glicólise , Enxofre/metabolismo , Glucose/metabolismo , Carbono , Alcanossulfonatos , Oxigenases de Função Mista/metabolismo , Fosfatos , Pentoses
6.
Microbiol Spectr ; 10(5): e0189922, 2022 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-36197290

RESUMO

Maintaining the health of seafarers is a difficult task during long-term voyages. Little is known about the corresponding changes in the gut microbiome-host interaction. This study recruited 30 seafarers undertaking a 6-month voyage and analyzed their gut microbiota using 16S rRNA gene sequencing. Fecal untargeted metabolomics analysis was performed using liquid chromatography-mass spectrometry. Significant changes in the composition of the gut microbiota and an increased ratio of Firmicutes/Bacteroidetes at the end (day 180) of the 6-month voyage, relative to the start (day 0), were observed. At the genus level, the abundances of Holdemanella and Plesiomonas were significantly increased, while the abundance of Bacteroides was decreased. Predicted microbial functional analysis revealed significant decreases in folate biosynthesis and biotin metabolism. Furthermore, 20 differential metabolites within six differentially enriched human metabolic pathways (including arginine biosynthesis, lysine degradation, phenylalanine metabolism, sphingolipid metabolism, pentose and glucuronate interconversions, and glycine, serine, and threonine metabolism) were identified by comparing the fecal metabolites at day 0 and day 180. Spearman correlation analysis revealed close relationships between the 14 differential microbiota members and the six differential fecal metabolites that might affect specific human metabolic pathways. This study adopted a multi-omics approach and provides potential targets for maintaining the health of seafarers during long-term voyages. These findings are worthy of more in-depth exploration in future studies. IMPORTANCE Maintaining the health of seafarers undertaking long-term voyages is a difficult task. Apart from the alterations in the gut microbiome and fecal metabolites after a long-term voyage, our study also revealed that 20 differential metabolites within six differentially enriched human metabolic pathways are worthy of attention. Moreover, we found close relationships between the 14 differential microbiota members and the six differential fecal metabolites that might impact specific human metabolic pathways. Accordingly, preventative measures, such as adjusting the gut microbiota by decreasing potential pathobionts or increasing potential probiotics as well as offsetting the decrease in B vitamins and beneficial metabolites (e.g., d-glucuronic acid and citrulline) via dietary adjustment or nutritional supplements, might improve the health of seafarers during long-term sea voyages. These findings provide valuable clues about gut microbiome-host interactions and propose potential targets for maintaining the health of seafarers engaged in long-term sea voyages.


Assuntos
Microbioma Gastrointestinal , Complexo Vitamínico B , Humanos , Microbioma Gastrointestinal/genética , RNA Ribossômico 16S/genética , Complexo Vitamínico B/análise , Citrulina/análise , Biotina , Lisina/análise , Metabolômica/métodos , Fezes , Pentoses/análise , Glucuronatos/análise , Glicina/análise , Ácido Glucurônico , Serina/análise , Fenilalanina/análise , Esfingolipídeos/análise , Treonina/análise , Arginina/análise , Ácido Fólico/análise
7.
Genes (Basel) ; 13(10)2022 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-36292652

RESUMO

The content of metal ions in fruits is inseparable from plant intake of trace elements and health effects in the human body. To understand metal ion content in the fruit and pericarp of melon (Cucumis melo L.) and the candidate genes responsible for controlling this process, we analyzed the metal ion content in distinct parts of melon fruit and pericarp and performed RNA-seq. The results showed that the content of metal ions in melon fruit tissue was significantly higher than that in the pericarp. Based on transcriptome expression profiling, we found that the fruit and pericarp contained elevated levels of DEGs. GO functional annotations included cell surface receptor signaling, signal transduction, organic substance metabolism, carbohydrate derivative binding, and hormone-mediated signaling pathways. KEGG pathways included pectate lyase, pentose and glucuronate interconversions, H+-transporting ATPase, oxidative phosphorylation, plant hormone signal transduction, and MAPK signaling pathways. We also analyzed the expression patterns of genes and transcription factors involved in hormone biosynthesis and signal transduction. Using weighted gene co-expression network analysis (WGCNA), a co-expression network was constructed to identify a specific module that was significantly correlated with the content of metal ions in melon, after which the gene expression in the module was measured. Connectivity and qRT-PCR identified five candidate melon genes, LOC103501427, LOC103501539, LOC103503694, LOC103504124, and LOC107990281, associated with metal ion content. This study provides a theoretical basis for further understanding the molecular mechanism of heavy metal ion content in melon fruit and peel and provides new genetic resources for the study of heavy metal ion content in plant tissues.


Assuntos
Cucumis melo , Cucurbitaceae , Metais Pesados , Oligoelementos , Humanos , Cucumis melo/genética , Cucurbitaceae/genética , Reguladores de Crescimento de Plantas/metabolismo , Oligoelementos/metabolismo , Metais Pesados/toxicidade , Metais Pesados/metabolismo , Fatores de Transcrição/metabolismo , Hormônios , Pentoses/metabolismo , Glucuronatos/metabolismo , ATPases Translocadoras de Prótons/metabolismo , Receptores de Superfície Celular/metabolismo
8.
Int J Mol Sci ; 23(19)2022 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-36232348

RESUMO

The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, 'Goldrich' and 'Santa Rosa'. KEEG and protein-protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in 'Goldrich' and 'Santa Rosa', respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in 'Goldrich' and 'Santa Rosa', respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process.


Assuntos
Quitinases , Prunus armeniaca , Prunus domestica , Antioxidantes/metabolismo , Quitinases/metabolismo , Ciclopropanos , Etilenos , Ferredoxinas/metabolismo , Frutas/genética , Frutas/metabolismo , Galactose/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Glucuronatos/metabolismo , Glutarredoxinas/genética , Ácidos Indolacéticos/metabolismo , Compostos Organofosforados , Pentoses/metabolismo , Complexo de Proteína do Fotossistema I/metabolismo , Reguladores de Crescimento de Plantas/metabolismo , Reguladores de Crescimento de Plantas/farmacologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Prunus armeniaca/genética , Prunus domestica/genética
9.
Nat Commun ; 13(1): 5243, 2022 09 06.
Artigo em Inglês | MEDLINE | ID: mdl-36068201

RESUMO

Methanol is a liquid with high energy storage capacity that holds promise as an alternative substrate to replace sugars in the biotechnology industry. It can be produced from CO2 or methane and its use does not compete with food and animal feed production. However, there are currently only limited biotechnological options for the valorization of methanol, which hinders its widespread adoption. Here, we report the conversion of the industrial platform organism Escherichia coli into a synthetic methylotroph that assimilates methanol via the energy efficient ribulose monophosphate cycle. Methylotrophy is achieved after evolution of a methanol-dependent E. coli strain over 250 generations in continuous chemostat culture. We demonstrate growth on methanol and biomass formation exclusively from the one-carbon source by 13C isotopic tracer analysis. In line with computational modeling, the methylotrophic E. coli strain optimizes methanol oxidation by upregulation of an improved methanol dehydrogenase, increasing ribulose monophosphate cycle activity, channeling carbon flux through the Entner-Doudoroff pathway and downregulating tricarboxylic acid cycle enzymes. En route towards sustainable bioproduction processes, our work lays the foundation for the efficient utilization of methanol as the dominant carbon and energy resource.


Assuntos
Escherichia coli , Metanol , Carbono/metabolismo , Escherichia coli/genética , Engenharia Metabólica , Metanol/metabolismo , Pentoses
10.
Infect Immun ; 90(9): e0023922, 2022 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-35938858

RESUMO

Nitrate metabolism is an adaptation mechanism used by many bacteria for survival in anaerobic environments. As a by-product of inflammation, nitrate is used by the intestinal bacterial pathogens to enable gut infection. However, the responses of bacterial respiratory pathogens to nitrate are less well understood. Actinobacillus pleuropneumoniae is an important bacterial respiratory pathogen of swine. Previous studies have suggested that adaptation of A. pleuropneumoniae to anaerobiosis is important for infection. In this work, A. pleuropneumoniae growth and pathogenesis in response to the nitrate were investigated. Nitrate significantly promoted A. pleuropneumoniae growth under anaerobic conditions in vitro and lethality in mice. By using narQ and narP deletion mutants and single-residue-mutated complementary strains of ΔnarQ, the two-component system NarQ/P was confirmed to be critical for nitrate-induced growth, with Arg50 in NarQ as an essential functional residue. Transcriptome analysis showed that nitrate upregulated multiple energy-generating pathways, including nitrate metabolism, mannose and pentose metabolism, and glycerolipid metabolism via the regulation of NarQ/P. Furthermore, narQ, narP, and its target gene encoding the nitrate reductase Nap contributed to the pathogenicity of A. pleuropneumoniae. The Nap inhibitor tungstate significantly reduced the survival of A. pleuropneumoniae in vivo, suggesting that Nap is a potential drug target. These results give new insights into how the respiratory pathogen A. pleuropneumoniae utilizes the alternative electron acceptor nitrate to overcome the hypoxia microenvironment, which can occur in the inflammatory or necrotic infected tissues.


Assuntos
Infecções por Actinobacillus , Actinobacillus pleuropneumoniae , Actinobacillus pleuropneumoniae/genética , Actinobacillus pleuropneumoniae/metabolismo , Animais , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica , Manose/metabolismo , Camundongos , Nitrato Redutases/genética , Nitrato Redutases/metabolismo , Nitratos/metabolismo , Pentoses/metabolismo , Suínos , Virulência
11.
J Chem Inf Model ; 62(17): 4122-4133, 2022 09 12.
Artigo em Inglês | MEDLINE | ID: mdl-36036609

RESUMO

To develop a realistic electrostatic model that allows for the anisotropy of the atomic electron density, high-rank atomic multipole moments computed by quantum chemical calculations have been studied extensively. However, it is hard to process huge RNA systems only relying on quantum chemical calculations due to its highly computational cost. In this study, we employ five machine learning methods of Gaussian process regression with automatic relevance determination (ARDGPR), Kriging, radial basis function neural networks, Bagging, and generalized regression neural network to predict atomic multipole moments. Atom-atom electrostatic interaction energies are subsequently computed using the predicted atomic multipole moments in the pilot system pentose of RNA. Here, the performance of the five methods is compared in terms of both the multipole moment prediction errors and the electrostatic energy prediction errors. For the predicted high-rank multipole moments of the four elements (O, C, N, and H) in capped pentose, ARDGPR and Kriging consistently outperform the other three methods. Therefore, the multipole moments predicted by the two best methods of ARDGPR and Kriging are then used to predict electrostatic interaction energy of each pentose. Finally, the absolute average energy errors of ARDGPR and Kriging are 1.83 and 4.33 kJ mol-1, respectively. Compared to Kriging, the ARDGPR method achieves a 58% decrease in the absolute average energy error. These satisfactory results demonstrated that the ARDGPR method with the strong feature extraction ability can predict the electrostatic interaction energy of pentose in RNA correctly and reliably.


Assuntos
Pentoses , RNA , Aprendizado de Máquina , Distribuição Normal , Eletricidade Estática
12.
Redox Biol ; 54: 102379, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35779441

RESUMO

The Pentose Phosphate Pathway (PPP), a metabolic offshoot of the glycolytic pathway, provides protective metabolites and molecules essential for cell redox balance and survival. Transketolase (TKT) is the critical enzyme that controls the extent of "traffic flow" through the PPP. Here, we explored the role of TKT in maintaining the health of the human retina. We found that Müller cells were the primary retinal cell type expressing TKT in the human retina. We further explored the role of TKT in human Müller cells by knocking down its expression in primary cultured Müller cells (huPMCs), isolated from the human retina (11 human donors in total), under light-induced oxidative stress. TKT knockdown and light stress reduced TKT enzymatic activities and the overall metabolic activities of huPMCs with no detectable cell death. TKT knockdown restrained the PPP traffic flow, reduced the expression of NAD(P)H Quinone Dehydrogenase 1 (NQO1), impaired the antioxidative response of NRF2 to light stress and aggravated the endoplasmic reticulum (ER) stress. TKT knockdown also inhibited overall glucose intake, reduced expression of Dihydrolipoamide dehydrogenase (DLD) and impaired the energy supply of the huPMCs. In summary, Müller cell-mediated TKT activity plays a critical protective role in the stressed retina. Knockdown of TKT disrupted the PPP and impaired overall glucose utilisation by huPMCs and rendered huPMCs more vulnerable to light stress by impairing energy supply and antioxidative NRF2 responses.


Assuntos
Fator 2 Relacionado a NF-E2 , Transcetolase , Células Ependimogliais/metabolismo , Glucose/metabolismo , Humanos , Fator 2 Relacionado a NF-E2/genética , Fator 2 Relacionado a NF-E2/metabolismo , Via de Pentose Fosfato , Pentoses , Fosfatos , Transcetolase/genética , Transcetolase/metabolismo
13.
New Phytol ; 236(2): 350-356, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-35860861

RESUMO

The Calvin-Benson-Bassham (CBB) cycle is arguably the most important pathway on earth, capturing CO2 from the atmosphere and converting it into organic molecules, providing the basis for life on our planet. This cycle has been intensively studied over the 50 yr since it was elucidated, and it is highly conserved across nature, from cyanobacteria to the largest of our land plants. Eight out of the 11 enzymes in this cycle catalyse the regeneration of ribulose-1-5 bisphosphate (RuBP), the CO2 acceptor molecule. The potential to manipulate RuBP regeneration to improve photosynthesis has been demonstrated in a number of plant species, and the development of new technologies, such as omics and synthetic biology provides exciting future opportunities to improve photosynthesis and increase crop yields.


Assuntos
Dióxido de Carbono , Cianobactérias , Dióxido de Carbono/metabolismo , Cianobactérias/metabolismo , Pentoses , Fotossíntese , Plantas/metabolismo , Ribulose-Bifosfato Carboxilase/metabolismo
14.
Front Public Health ; 10: 902445, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35801241

RESUMO

This study analyzed the differences in subtypes and characteristics of advanced lung adenocarcinoma (LUAD) patients based on the pentose phosphate metabolic pathway-related long non-coding RNAs (lncRNAs), along with their potential regulatory mechanisms. Using the expression profiling and corresponding clinical information of LUAD patients from Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA). Differential pathway scores between normal and tumor samples from TCGA were identified by rank-sum tests. Pearson correlation coefficients between pentose phosphate scores of the pentose phosphate samples and lncRNAs of the corresponding datasets were calculated. Next, the clusterProfiler software package was used for functional annotation. Clustering of pentose phosphate-related lncRNAs from LUAD samples categorized two molecular subtypes (C1, and C2). C1 was associated with a lower pentose phosphate score and a good prognosis; the C2 showed a higher pentose phosphate score and was related to poorer prognoses. The C2 was markedly associated with energy metabolic pathways. The expression of most immune cells were markedly higher in C1 subtype. Some crucial immune checkpoints, including CTLA4, CD274, and CD47, were also significantly upregulated in C1 subtype, leading to a higher score of clinical effect on the C1 subtype. Finally, one TF, BACH1, was found to be significantly upregulated in C1 subtypes; the pathways activated by this TF may be associated with tumor progression and poor prognoses. LUAD typing based on pentose phosphate metabolic pathway-related lncRNAs was confirmed. Differences in characteristics between C1 and C2 subtypes improved the current LUAD detection and treatment.


Assuntos
Adenocarcinoma , Neoplasias Pulmonares , RNA Longo não Codificante , Adenocarcinoma/genética , Adenocarcinoma/patologia , Regulação Neoplásica da Expressão Gênica , Humanos , Pulmão/patologia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Pentoses , Fosfatos/metabolismo , Prognóstico , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo
15.
Astrobiology ; 22(8): 981-991, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35833833

RESUMO

The formose reaction has been a leading hypothesis for the prebiotic synthesis of sugars such as ribose for many decades but tends to produce complex mixtures of sugars and often tars. Channeling the formose reaction towards the synthesis of biologically useful sugars such as ribose has been a holy grail of origins-of-life research. Here, we tested the hypothesis that a simple, prebiotically plausible phosphorylating agent, acetyl phosphate, could direct the formose reaction towards ribose through phosphorylation of intermediates in a manner resembling gluconeogenesis and the pentose phosphate pathway. We did indeed find that addition of acetyl phosphate to a developing formose reaction stabilized pentoses, including ribose, such that after 5 h of reaction about 10-fold more ribose remained compared with control runs. But mechanistic analyses using liquid chromatography-mass spectrometry showed that, far from being directed towards ribose by phosphorylation, the formose reaction was halted by the precipitation of Ca2+ ions as phosphate minerals such as apatite and hydroxyapatite. Adding orthophosphate had the same effect. Phosphorylated sugars were only detected below the limit of quantification when adding acetyl phosphate. Nonetheless, our findings are not strictly negative. The sensitivity of the formose reaction to geochemically reasonable conditions, combined with the apparent stability of ribose under these conditions, serves as a valuable constraint on possible pathways of sugar synthesis at the origin of life.


Assuntos
Pentoses , Ribose , Espectrometria de Massas , Pentoses/química , Fosfatos , Ribose/química , Açúcares
16.
Syst Appl Microbiol ; 45(5): 126344, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-35834933

RESUMO

Lactobacilli are dominant in zha-chili. This study provides a taxonomic characterization of five bacterial strains isolated from zha-chili in China. The cells were Gram-positive, facultative anaerobic, non-spore-forming, flagella-free, catalase-negative, heterofermentative, pentose-fermenting, and gamma-aminobutyric acid (GABA)-producing rods. For HBUAS51241T, HBUAS51329, and HBUAS51416, C16:0, C18:1ω9c and C19:0 iso were the predominant cellular fatty acids; diphosphatidylglycerol (DPG), phosphatidylglycerol (DP), glycolipids (GL), and glycolipids (AL) were the major phospholipids. While for HBUAS51383T and HBUAS58055, C16:0, C18:1ω9c, C19:0 cyclo ω8c were the predominant cellular fatty acids; DPG, DP, GL, and AL were the major phospholipids. Strains HBUAS51241T, HBUAS51329, and HBUAS51416 showed 98.1-99.1% 16S rRNA gene sequence similarity, 80.2-81.4% ANI, 87.7-90.0% AAI, and 23.8-32.8% digital DDH to their closest related type strains Levilactobacillus hammesii DSM 16381T, Levilactobacillus parabrevis ATCC 53295T, and Levilactobacillus fuyuanensis 244-4T. Strains HBUAS51383T and HBUAS58055 showed 98.7-99.5% 16S rRNA gene sequence similarity, 75.4-81.4% ANI, 75.5-89.1% AAI, and 19.7-24.0% digital DDH to their closest related type strains Secundilactobacillus silagincola IWT5T, Secundilactobacillus silagei JCM 19001T, Secundilactobacillus pentosiphilus IWT25T, Secundilactobacillus mixtipabuli IWT30T, Secundilactobacillus odoratitofui DSM 19909T, and Secundilactobacillus similis DSM 23365T. The central carbon metabolism pathways for the five strains were summarizeded. Based on the phenotypic, chemotaxonomic, and genomic data, we propose two novel species Levilactobacillus tujiorum sp. nov. whose type strain is HBUAS51241T (=GDMCC 1.3022T = JCM 35241T), and Secundilactobacillus angelensis sp. nov. whose type strain is HBUAS51383T (=GDMCC 1.3021T = JCM 35209T).


Assuntos
Cardiolipinas , Pentoses , Técnicas de Tipagem Bacteriana , Composição de Bases , Carbono , Catalase/genética , DNA Bacteriano/genética , Ácidos Graxos/análise , Glicolipídeos , Hibridização de Ácido Nucleico , Fosfolipídeos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ácido gama-Aminobutírico/genética
17.
Biol Reprod ; 107(4): 1084-1096, 2022 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-35835585

RESUMO

Roles of fructose in elongating ovine conceptuses are poorly understood, despite it being the major hexose sugar in fetal fluids and plasma throughout gestation. Therefore, we determined if elongating ovine conceptuses utilize fructose via metabolic pathways for survival and development. Immunohistochemical analyses revealed that trophectoderm and extra-embryonic endoderm express ketohexokinase and aldolase B during the peri-implantation period of pregnancy for conversion of fructose into fructose-1-phosphate for entry into glycolysis and related metabolic pathways. Conceptus homogenates were cultured with 14C-labeled glucose and/or fructose under oxygenated and hypoxic conditions to assess contributions of glucose and fructose to the pentose cycle (PC), tricarboxylic acid cycle, glycoproteins, and lipid synthesis. Results indicated that both glucose and fructose contributed carbons to each of these pathways, except for lipid synthesis, and metabolized to pyruvate and lactate, with lactate being the primary product of glycolysis under oxygenated and hypoxic conditions. We also found that (1) conceptuses preferentially oxidized glucose over fructose (P < 0.05); (2) incorporation of fructose and glucose at 4 mM each into the PC by Day 16 conceptus homogenates was similar in the presence or absence of glucose, but incorporation of glucose into the PC was enhanced by the presence of fructose (P < 0.05); (3) incorporation of fructose into the PC in the absence of glucose was greater under oxygenated conditions (P < 0.01); and (4) incorporation of glucose into the PC under oxygenated conditions was greater in the presence of fructose (P = 0.05). These results indicate that fructose is an important metabolic substrate for ovine conceptuses.


Assuntos
Frutose-Bifosfato Aldolase , Frutose , Animais , Feminino , Frutoquinases , Glucose , Lactatos , Lipídeos , Pentoses , Gravidez , Piruvatos , Ovinos , Carneiro Doméstico
18.
Appl Microbiol Biotechnol ; 106(12): 4587-4606, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35708749

RESUMO

The transport of substrates across the cell membrane plays an essential role in nutrient assimilation by yeasts. The establishment of an efficient microbial cell factory, based on the maximum use of available carbon sources, can generate new technologies that allow the full use of lignocellulosic constituents. These technologies are of interest because they could promote the formation of added-value products with economic feasibility. In silico analyses were performed to investigate gene sequences capable of encoding xylose transporter proteins in the Candida tropicalis genome. The current study identified 11 putative transport proteins that have not yet been functionally characterized. A phylogenetic tree highlighted the potential C. tropicalis xylose-transporter proteins CtXUT1, CtXUT4, CtSTL1, CtSTL2, and CtGXT2, which were homologous to previously characterized and reported xylose transporters. Their expression was quantified through real-time qPCR at defined times, determined through a kinetic analysis of the microbial growth curve in the absence/presence of glucose supplemented with xylose as the main carbon source. The results indicated different mRNA expression levels for each gene. CtXUT1 mRNA expression was only found in the absence of glucose in the medium. Maximum CtXUT1 expression was observed in intervals of the highest xylose consumption (21 to 36 h) that corresponded to consumption rates of 1.02 and 0.82 g/L/h in the formulated media, with xylose as the only carbon source and with glucose addition. These observations indicate that CtXUT1 is an important xylose transporter in C. tropicalis. KEY POINTS: • Putative xylose transporter proteins were identified in Candida tropicalis; • The glucose concentration in the cultivation medium plays a key role in xylose transporter regulation; • The transporter gene CtXUT1 has an important role in xylose consumption by Candida tropicalis.


Assuntos
Candida tropicalis , Xilose , Candida tropicalis/genética , Candida tropicalis/metabolismo , Carbono/metabolismo , Proteínas de Transporte/genética , Biologia Computacional , Fermentação , Expressão Gênica , Glucose/metabolismo , Cinética , Proteínas de Membrana Transportadoras/genética , Proteínas de Membrana Transportadoras/metabolismo , Pentoses/metabolismo , Filogenia , RNA Mensageiro/metabolismo , Xilitol , Xilose/metabolismo
19.
Appl Biochem Biotechnol ; 194(10): 4852-4866, 2022 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-35670905

RESUMO

L-ribulose, a kind of high-value rare sugar, could be utilized to manufacture L-form sugars and antiviral drugs, generally produced from L-arabinose as a substrate. However, the production of L-ribulose from L-arabinose is limited by the equilibrium ratio of the catalytic reaction, hence, it is necessary to explore a new biological enzymatic method to produce L-ribulose. Ribose-5-phosphate isomerase (Rpi) is an enzyme that can catalyze the reversible isomerization between L-ribose and L-ribulose, which is of great significance for the preparation of L-ribulose. In order to obtain highly active ribose-5-phosphate isomerase to manufacture L-ribulose, ribose-5-phosphate isomerase A (OsRpiA) from Ochrobactrum sp. CSL1 was engineered based on structural and sequence analyses. Through a rational design strategy, a triple-mutant strain A10T/T32S/G101N with 160% activity was acquired. The enzymatic properties of the mutant were systematically investigated, and the optimum conditions were characterized to achieve the maximum yield of L-ribulose. Kinetic analysis clarified that the A10T/T32S/G101N mutant had a stronger affinity for the substrate and increased catalytic efficiency. Furthermore, molecular dynamics simulations indicated that the binding of the substrate to A10T/T32S/G101N was more stable than that of wild type. The shorter distance between the catalytic residues of A10T/T32S/G101N and L-ribose illuminated the increased activity. Overall, the present study provided a solid basis for demonstrating the complex functions of crucial residues in RpiAs as well as in rare sugar preparation.


Assuntos
Aldose-Cetose Isomerases , Ochrobactrum , Aldose-Cetose Isomerases/metabolismo , Antivirais , Arabinose/metabolismo , Cinética , Ochrobactrum/genética , Ochrobactrum/metabolismo , Pentoses , Ribose
20.
Chem Rev ; 122(20): 15503-15602, 2022 10 26.
Artigo em Inglês | MEDLINE | ID: mdl-35613331

RESUMO

Fluorinated carbohydrates have found many applications in the glycosciences. Typically, these contain fluorination at a single position. There are not many applications involving polyfluorinated carbohydrates, here defined as monosaccharides in which more than one carbon has at least one fluorine substituent directly attached to it, with the notable exception of their use as mechanism-based inhibitors. The increasing attention to carbohydrate physical properties, especially around lipophilicity, has resulted in a surge of interest for this class of compounds. This review covers the considerable body of work toward the synthesis of polyfluorinated hexoses, pentoses, ketosugars, and aminosugars including sialic acids and nucleosides. An overview of the current state of the art of their glycosidation is also provided.


Assuntos
Carboidratos , Flúor , Hexoses , Pentoses , Monossacarídeos , Nucleosídeos , Ácidos Siálicos , Carbono
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