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Journal of Bacteriology Jan 2020The species and were found to grow on d-ribose, d-xylose, and l-arabinose. Here, we report the discovery of a novel promiscuous oxidative pathway of pentose...
The species and were found to grow on d-ribose, d-xylose, and l-arabinose. Here, we report the discovery of a novel promiscuous oxidative pathway of pentose degradation based on genome analysis, identification and characterization of enzymes, transcriptional analysis, and growth experiments with knockout mutants. Together, the data indicate that in spp., d-ribose, d-xylose, and l-arabinose were degraded to α-ketoglutarate involving the following enzymes: (i) a promiscuous pentose dehydrogenase that catalyzed the oxidation of d-ribose, d-xylose, and l-arabinose; (ii) a promiscuous pentonolactonase that was involved in the hydrolysis of ribonolactone, xylonolactone, and arabinolactone; (iii) a highly specific dehydratase, ribonate dehydratase, which catalyzed the dehydration of ribonate, and a second enzyme, a promiscuous xylonate/gluconate dehydratase, which was involved in the conversion of xylonate, arabinonate, and gluconate. Phylogenetic analysis indicated that the highly specific ribonate dehydratase constitutes a novel sugar acid dehydratase family within the enolase superfamily; and (iv) finally, 2-keto-3-deoxypentanonate dehydratase and α-ketoglutarate semialdehyde dehydrogenase catalyzed the conversion of 2-keto-3-deoxypentanonate to α-ketoglutarate via α-ketoglutarate semialdehyde. We conclude that the expanded substrate specificities of the pentose dehydrogenase and pentonolactonase toward d-ribose and ribonolactone, respectively, and the presence of a highly specific ribonate dehydratase are prerequisites of the oxidative degradation of d-ribose in spp. This is the first characterization of an oxidative degradation pathway of d-ribose to α-ketoglutarate in archaea. The utilization and degradation of d-ribose in archaea, the third domain of life, have not been analyzed so far. We show that species utilize d-ribose, which is degraded to α-ketoglutarate via a novel oxidative pathway. Evidence is presented that the oxidative degradation of d-ribose involves novel promiscuous enzymes, pentose dehydrogenase and pentonolactonase, and a novel sugar acid dehydratase highly specific for ribonate. This is the first report of an oxidative degradation pathway of d-ribose in archaea, which differs from the canonical nonoxidative pathway of d-ribose degradation reported for most bacteria. The data contribute to our understanding of the unusual sugar degradation pathways and enzymes in archaea.
Topics: Arabinose; Archaea; Haloarcula; Oxidation-Reduction; Ribose; Xylose
PubMed: 31712277
DOI: 10.1128/JB.00608-19 -
Nature Metabolism Apr 2023
Topics: Pentoses; Oxidation-Reduction; Phosphates
PubMed: 37024755
DOI: 10.1038/s42255-021-00523-3 -
Environmental Microbiology Feb 2023The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently...
The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well-characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth-promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism (xylDXA) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism (araDXA). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.
Topics: Pentoses; Xylose; Arabinose; Pseudomonas putida; Oxidative Stress
PubMed: 36465038
DOI: 10.1111/1462-2920.16296 -
Systematic and Applied Microbiology Sep 2022Lactobacilli are dominant in zha-chili. This study provides a taxonomic characterization of five bacterial strains isolated from zha-chili in China. The cells were...
Characterization of two novel pentose-fermenting and GABA-producing species: Levilactobacillus tujiorum sp. nov. and Secundilactobacillus angelensis sp. nov. Isolated from a solid-state fermented zha-chili.
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 HBUAS51241, HBUAS51329, and HBUAS51416, C, Cω9c and C iso were the predominant cellular fatty acids; diphosphatidylglycerol (DPG), phosphatidylglycerol (DP), glycolipids (GL), and glycolipids (AL) were the major phospholipids. While for HBUAS51383 and HBUAS58055, C, Cω9c, C cyclo ω8c were the predominant cellular fatty acids; DPG, DP, GL, and AL were the major phospholipids. Strains HBUAS51241, 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 16381, Levilactobacillus parabrevis ATCC 53295, and Levilactobacillus fuyuanensis 244-4. Strains HBUAS51383 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 IWT5, Secundilactobacillus silagei JCM 19001, Secundilactobacillus pentosiphilus IWT25, Secundilactobacillus mixtipabuli IWT30, Secundilactobacillus odoratitofui DSM 19909, and Secundilactobacillus similis DSM 23365. 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 HBUAS51241 (=GDMCC 1.3022 = JCM 35241), and Secundilactobacillus angelensis sp. nov. whose type strain is HBUAS51383 (=GDMCC 1.3021 = JCM 35209).
Topics: Bacterial Typing Techniques; Base Composition; Carbon; Cardiolipins; Catalase; DNA, Bacterial; Fatty Acids; Glycolipids; Nucleic Acid Hybridization; Pentoses; Phospholipids; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; gamma-Aminobutyric Acid
PubMed: 35834933
DOI: 10.1016/j.syapm.2022.126344 -
Journal of Biomedical Materials... Dec 2022There remains a need for stiffer collagen hydrogels for tissue engineering and disease modeling applications. Pre-glycation, or glycation of collagen in solution prior...
There remains a need for stiffer collagen hydrogels for tissue engineering and disease modeling applications. Pre-glycation, or glycation of collagen in solution prior to gelation, has been shown to increase the mechanics of collagen hydrogels while maintaining high viability of encapsulated cells. The stiffness of glycated collagen gels can be increased by increasing the collagen concentration, sugar concentration, and glycation time. However, previous studies on pre-glycation of collagen have used low collagen concentrations and/or low sugar concentrations and have not investigated the effect of glycation time. Therefore, the objective of this study was to determine the effects of pre-glycation with high sugar concentrations (up to 500 mM) and extended glycation times (up to 21 days) on high concentration collagen (8 mg/ml). The addition of sugar to the collagen and the formation of advanced glycation end products (AGEs) were quantified. The ability to gel successfully and rheological properties were determined and correlated with biochemical characterizations. Successful collagen gelation and rheological properties of pre-glycated collagen were found to be strongly dependent on the ratio of added sugars to added AGEs with high ratios impairing gelation and low ratios resulting in optimal storage moduli. There is likely a competing effect during pre-glycation of the formation of AGEs resulting in crosslinking of collagen and the formation of Amadori intermediates acting to increase collagen solubility. Overall, this study shows that collagen glycation can be optimized by increasing the formation of AGEs while maintaining a low ratio of added sugar to added AGEs.
Topics: Collagen; Glycation End Products, Advanced; Glycosylation; Hydrogels; Ribose
PubMed: 36183358
DOI: 10.1002/jbm.a.37431 -
Organic & Biomolecular Chemistry Oct 2017One of the possible synthetic routes to pentoses is the formose reaction pathway from C1 and C2 carbon sources, but preferential ribose generation in a one-pot reaction...
One of the possible synthetic routes to pentoses is the formose reaction pathway from C1 and C2 carbon sources, but preferential ribose generation in a one-pot reaction without any control of conditions has not been reported. We have tested a one-pot pentose formation and analyzed the products and mechanism in the reaction, using H-NMR and mass spectrometry. Hydroxyapatite (HAp), which consists of phosphate and calcium ions, worked continuously for cross-aldol reactions and Lobry de Bruyn-van Ekenstein transformations to yield ribose from formaldehyde and glycolaldehyde. The continuous reaction proceeds in one pot in hot water only in the presence of a HAp catalyst, without any fine pH control or any complicated condition control at each reaction step. Ribose production by HAp may be a reason why a pentose backbone was incorporated into nucleic acids in the prebiotic world.
Topics: Catalysis; Durapatite; Molecular Structure; Pentoses
PubMed: 28952648
DOI: 10.1039/c7ob02051a -
Preparative Biochemistry & Biotechnology May 2018Butyric acid (CHCOOH) is an important chemical that is widely used in foodstuffs along with in the chemical and pharmaceutical industries. The bioproduction of butyric...
Butyric acid (CHCOOH) is an important chemical that is widely used in foodstuffs along with in the chemical and pharmaceutical industries. The bioproduction of butyric acid through large-scale fermentation has the potential to be more economical and efficient than petrochemical synthesis. In this paper, the metabolic pathways involved in the production of butyric acid from Clostridium tyrobutyricum using hexose and pentose as substrates are investigated, and approaches to enhance butyric acid production through genetic modification are discussed. Finally, bioreactor modifications (including fibrous bed bioreactor, inner disk-shaped matrix bioreactor, fibrous matrix packed in porous levitated sphere carriers), low-cost feedstocks, and special treatments (including continuous fermentation with cell recycling, extractive fermentation with solvent, using different artificial electron carriers) intended to improve the feasibility of commercial butyric acid bioproduction are summarized.
Topics: Bioreactors; Biosynthetic Pathways; Butyric Acid; Clostridium tyrobutyricum; Equipment Design; Fermentation; Genetic Engineering; Hexoses; Industrial Microbiology; Mutation; Pentoses
PubMed: 29561227
DOI: 10.1080/10826068.2018.1452257 -
Scientific Reports Mar 2022Urinary free-glycans are promising markers of disease. In this study, we attempted to identify novel tumor markers by focusing on neutral free-glycans in urine....
Urinary free-glycans are promising markers of disease. In this study, we attempted to identify novel tumor markers by focusing on neutral free-glycans in urine. Free-glycans extracted from the urine of normal subjects and cancer patients with gastric, colorectal, pancreatic and bile duct were fluorescently labeled with 2-aminopyridine. Profiles of these neutral free-glycans constructed using multidimensional high performance liquid chromatography separation were compared between normal controls and cancer patients. The analysis identified one glycan in the urine of cancer patients with a unique structure, which included a pentose residue. To reveal the glycan structure, the linkage fashion, monosaccharide species and enantiomer of the pentose were analyzed by high performance liquid chromatography and mass spectrometry combined with several chemical treatments. The backbone of the glycan was a monoantennary complex-type free-N-glycan containing β1,4-branch. The pentose residue was attached to the antennal GlcNAc and released by α1,3/4-L-fucosidase. Intriguingly, the pentose residue was consistent with D-arabinose. Collectively, this glycan structure was determined to be Galβ1-4(D-Araβ1-3)GlcNAcβ1-4Manα1-3Manβ1-4GlcNAc-PA. Elevation of D-arabinose-containing free-glycans in the urine of cancer patients was confirmed by selected reaction monitoring. This is the first study to unequivocally show the occurrence of a D-arabinose-containing oligosaccharide in human together with its detailed structure.
Topics: Arabinose; Chromatography, High Pressure Liquid; Glycoside Hydrolases; Humans; Neoplasms; Oligosaccharides; Polysaccharides
PubMed: 35318379
DOI: 10.1038/s41598-022-08790-0 -
Biochimica Et Biophysica Acta. Gene... Mar 2019Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life... (Review)
Review
Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). In that case one catalytic subunit acts at various RNA sites, the specificity is provided by base pairing of the sno(s)RNA guide with the target RNA. In this review we compile available information on 2'-OH ribose methylation in different RNAs, enzymatic machineries involved in their biosynthesis and dynamics, as well as on the physiological functions of these modified residues.
Topics: Animals; Humans; Methyltransferases; RNA; RNA Processing, Post-Transcriptional; Ribose
PubMed: 30572123
DOI: 10.1016/j.bbagrm.2018.11.009 -
International Journal of Molecular... Nov 2023Salt stress has a considerable impact on the development and growth of plants. The soil is currently affected by salinisation, a problem that is becoming worse every...
Salt stress has a considerable impact on the development and growth of plants. The soil is currently affected by salinisation, a problem that is becoming worse every year. This means that a significant amount of salt-tolerant plant material needs to be added. has aesthetically pleasing leaves, unique flowers, and a remarkable tolerance to salt. In this study, RNA-seq technology was used to sequence and analyse the transcriptome of the root of seedlings subjected to 200 mM NaCl treatment for 12, 24, and 48 h. In total, 12 seedling root transcriptome libraries were constructed. At the three time points of salt treatment compared with the control, 3888, 1907, and 1479 differentially expressed genes (DEGs) were identified, respectively. Various families of transcription factors (TFs), mainly AP2, MYB, and bHLH, were identified and might be linked to salt tolerance. Gene Ontology (GO) analysis of DEGs revealed that the structure and composition of the cell wall and cytoskeleton may be crucial in the response to salt stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs showed a significant enrichment of the pentose and glucuronate interconversion pathway, which is associated with cell wall metabolism after 24 and 48 h of salt treatment. Based on GO and KEGG analyses of DEGs, the pentose and glucuronate interconversion pathway was selected for further investigation. AP2, MYB, and bHLH were found to be correlated with the functional genes in this pathway based on a correlation network. This study provides the groundwork for understanding the key pathways and gene networks in response to salt stress, thereby providing a theoretical basis for improving salt tolerance in .
Topics: Salt Tolerance; Aquilegia; Gene Expression Regulation, Plant; Gene Expression Profiling; Transcriptome; Seedlings; Glucuronates; Pentoses; Salinity
PubMed: 38003641
DOI: 10.3390/ijms242216450