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Organic & Biomolecular Chemistry Apr 2020S-Glycosides are important tools for the elucidation of specific protein-carbohydrate interactions and can significantly aid structural and functional studies of...
S-Glycosides are important tools for the elucidation of specific protein-carbohydrate interactions and can significantly aid structural and functional studies of carbohydrate-active enzymes, as they are often inert or act as enzyme inhibitors. In this context, this work focuses on the introduction of an S-linkage into arabinoxylan oligosaccharides (AXs) in order to obtain a small collection of synthetic tools for the study of AXs degrading enzymes. The key step for the introduction of the S-glycosidic linkage involved anomeric thiol S-alkylation of an orthogonally protected l-arabinopyranoside triflate. The resulting S-linked disaccharide was subsequently employed in a series of glycosylation reactions to obtain a selectively protected tetrasaccharide. This could be further elaborated through chemoselective deprotection and glycosylation reactions to introduce branching l-arabinofuranosides.
Topics: Arabinose; Cross-Linking Reagents; Disaccharides; Glycosides; Glycosylation; Oligosaccharides; Sulfhydryl Compounds; Xylans
PubMed: 32206767
DOI: 10.1039/d0ob00470g -
Bioresource Technology May 2020Alpha-L-arabinofuranoside arabinofuranohydrolase (ARA), more commonly known as alpha-L-arabinofuranosidase (E.C. number 3.2.1.55), is a hydrolytic enzyme, catalyzing the... (Review)
Review
Alpha-L-arabinofuranoside arabinofuranohydrolase (ARA), more commonly known as alpha-L-arabinofuranosidase (E.C. number 3.2.1.55), is a hydrolytic enzyme, catalyzing the cleavage of alpha-L-arabinose by acting on the non-reducing ends of alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)- and/or (1,5)-linked arabinoxylans and arabinogalactans. ARA functions as debranching enzyme removing arabinose substituents from arabinoxylan and arabinoxylooligomers, thereby, boosting the hydrolysis of arabinoxylan fraction of hemicellulose and improving bioconversion of lignocellulosic biomass. Previously, comprehensive information on this enzyme has not been reviewed thoroughly. Therefore, the main aim of this review is to highlight the important properties of this interesting enzyme, microorganisms used for its production, and enhanced production using genetic engineering approach. An account on synergism with other biomass hydrolyzing enzymes and various industrial applications of this enzyme has also been provided along with an outlook on further research and development.
Topics: Arabinose; Biomass; Glycoside Hydrolases; Hydrolysis; Substrate Specificity; Xylans
PubMed: 32089440
DOI: 10.1016/j.biortech.2020.123019 -
Biochemical Society Transactions Dec 2019The recruitment of the furanosidic scaffold of ribose as the crucial step for nucleotides and then for nucleic acids synthesis is presented. Based on the view that the... (Review)
Review
The recruitment of the furanosidic scaffold of ribose as the crucial step for nucleotides and then for nucleic acids synthesis is presented. Based on the view that the selection of molecules to be used for relevant metabolic purposes must favor structurally well-defined molecules, the inadequacy of ribose as a preferential precursor for nucleotides synthesis is discussed. The low reliability of ribose in its furanosidic hemiacetal form must have played ab initio against the choice of d-ribose for the generation of d-ribose-5-phosphate, the fundamental precursor of the ribose moiety of nucleotides. The latter, which is instead generated through the 'pentose phosphate pathway' is strictly linked to the affordable and reliable pyranosidic structure of d-glucose.
Topics: Biochemical Phenomena; Furans; Pentose Phosphate Pathway; Reproducibility of Results; Ribose
PubMed: 31697320
DOI: 10.1042/BST20190749 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Oct 2018One of the requirements for increasing the economic profitability on the large-scale production of second-generation ethanol and other bio-chemicals using lignocellulose... (Review)
Review
One of the requirements for increasing the economic profitability on the large-scale production of second-generation ethanol and other bio-chemicals using lignocellulose biomass as raw materials is efficient hexose and pentose utilization. Saccharomyces cerevisiae, the traditional ethanol producer, is an attractive chassis cell due to its robustness towards harsh environmental conditions and inherent advantages. But S. cerevisiae cannot utilize pentose. The precision construction of suitable strains for second-generation bio-ethanol production has been taken for more than three decades based on the principle of metabolic engineering and synthetic biology. The resulting strains have improved significantly co-fermentation of glucose and xylose. Recently, much attentions have been focused on sugar transport, which is one of the limiting but formerly ignored step for ethanol production from both glucose and xylose, to get the desired state that different sugars could efficiently delivered by their individual specific transporters. In this paper, the progress on sugar transporters of S. cerevisiae was reviewed, and the research status of xylose and/or L-arabinose metabolic engineering in S. cerevisiae were also presented.
Topics: Arabinose; Biological Transport; Biomass; Ethanol; Fermentation; Glucose; Industrial Microbiology; Lignin; Metabolic Engineering; Monosaccharide Transport Proteins; Pentoses; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Xylose
PubMed: 30394022
DOI: 10.13345/j.cjb.180031 -
Bioprocess and Biosystems Engineering May 2019Industrial production of lignocellulosic ethanol requires a microorganism utilizing both hexose and pentose, and tolerating inhibitors. In this study, a...
Industrial production of lignocellulosic ethanol requires a microorganism utilizing both hexose and pentose, and tolerating inhibitors. In this study, a hydrolysate-cofermenting Saccharomyces cerevisiae strain was obtained through one step in vivo DNA assembly of pentose-metabolizing pathway genes, followed by consecutive adaptive evolution in pentose media containing acetic acid, and direct screening in biomass hydrolysate media. The strain was able to coferment glucose and xylose in synthetic media with the respective maximal specific rates of glucose and xylose consumption, and ethanol production of 3.47, 0.38 and 1.62 g/g DW/h, with an ethanol titre of 41.07 g/L and yield of 0.42 g/g. Industrial wheat straw hydrolysate fermentation resulted in maximal specific rates of glucose and xylose consumption, and ethanol production of 2.61, 0.54 and 1.38 g/g DW/h, respectively, with an ethanol titre of 54.11 g/L and yield of 0.44 g/g. These are among the best for wheat straw hydrolysate fermentation through separate hydrolysis and cofermentation.
Topics: Biomass; Ethanol; Glucose; Hydrolysis; Lignin; Saccharomyces cerevisiae; Triticum; Xylose
PubMed: 30820665
DOI: 10.1007/s00449-019-02090-0 -
Applied and Environmental Microbiology Oct 2023have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon...
have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimize biomass conversion to fuels and chemicals. The CCR functioning in M2, a strain capable of consuming both hexose and pentose sugars as well as aromatic compounds, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 co-utilized sugars and aromatic compounds simultaneously; however, during cultivation with glucose and aromatic compounds (coumarate and ferulate) mixture, intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis revealed that glucose exerted stronger repression than xylose on the aromatic catabolic proteins. Key glucose (Eda) and xylose (XylX) catabolic proteins were also identified at lower abundance during cultivation with aromatic compounds implying simultaneous catabolite repression by sugars and aromatic compounds. Reduction of expression via CRISPRi led to faster growth and glucose and -coumarate uptake in the CRISPRi strains compared to the control, while no difference was observed on xylose+-coumarate. The increased abundances of Eda and amino acid biosynthesis proteins in the CRISPRi strain further supported these observations. Lastly, small RNAs (sRNAs) sequencing results showed that CrcY and CrcZ homologues levels in M2, previously identified in strains, were lower under strong CCR (glucose+-coumarate) condition compared to when repression was absent (-coumarate or glucose only).IMPORTANCEA newly isolated strain, M2, can utilize both hexose and pentose sugars as well as aromatic compounds making it a promising host for the valorization of lignocellulosic biomass. Pseudomonads have developed a regulatory strategy, carbon catabolite repression, to control the assimilation of carbon sources in the environment. Carbon catabolite repression may impede the simultaneous and complete metabolism of sugars and aromatic compounds present in lignocellulosic biomass and hinder the development of an efficient industrial biocatalyst. This study provides insight into the cellular physiology and proteome during mixed-substrate utilization in M2. The phenotypic and proteomics results demonstrated simultaneous catabolite repression in the sugar-aromatic mixtures, while the CRISPRi and sRNA sequencing demonstrated the potential role of the gene and small RNAs in carbon catabolite repression.
Topics: Sugars; Catabolite Repression; Xylose; Pseudomonas putida; Glucose; Hexoses; Pentoses; Carbon
PubMed: 37724856
DOI: 10.1128/aem.00852-23 -
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