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World Journal of Microbiology &... Oct 2022Xylitol (CHO), an amorphous sugar alcohol of crystalline texture has received great interest on the global market due to its numerous applications in different... (Review)
Review
Xylitol (CHO), an amorphous sugar alcohol of crystalline texture has received great interest on the global market due to its numerous applications in different industries. In addition to its high anticariogenic and sweetening properties, characteristics such as high solubility, stability and low glycemic index confer xylitol its fame in the food and odontological industries. Moreover, it also serves as a building-block in the production of polymers. As a result of the harmful effects of the chemical production of xylitol, the biotechnological means of producing this polyol have evolved over the decades. In contrast to the high consumption of energy, long periods of purification, specialized equipment and high production cost encountered during its chemical synthesis, the biotechnological production of xylitol offers advantages both to the economy and the environment. Non-Saccharomyces yeast strains, also termed as nonconventional, possess the inherent capacity to utilize D-xylose as a sole carbon source, unlike Saccharomyces species.
Topics: Xylitol; Xylose; Biotechnology; Saccharomyces cerevisiae; Sugar Alcohols; Fermentation
PubMed: 36306036
DOI: 10.1007/s11274-022-03437-8 -
Angewandte Chemie (International Ed. in... May 2024The world in which we live is homochiral. The ribose units that form the backbone of DNA and RNA are all D-configured and the encoded amino acids that comprise the...
The world in which we live is homochiral. The ribose units that form the backbone of DNA and RNA are all D-configured and the encoded amino acids that comprise the proteins of all living species feature an all-L-configuration at the α-carbon atoms. The homochirality of α-amino acids is essential for folding of the peptides into well-defined and functional 3D structures and the homochirality of D-ribose is crucial for helix formation and base-pairing. The question of why nature uses only encoded L-α-amino acids is not understood. Herein, we show that an RNA-peptide world, in which peptides grow on RNAs constructed from D-ribose, leads to the self-selection of homo-L-peptides, which provides a possible explanation for the homo-D-ribose and homo-L-amino acid combination seen in nature.
Topics: Peptides; RNA; Ribose; Stereoisomerism; Amino Acids
PubMed: 38407532
DOI: 10.1002/anie.202319235 -
Biotechnology Advances 2021Xylan is the most abundant hemicellulose in nature and as such it is a huge source of renewable carbon. Its bioconversion requires a battery of xylanolytic enzymes. Of... (Review)
Review
Xylan is the most abundant hemicellulose in nature and as such it is a huge source of renewable carbon. Its bioconversion requires a battery of xylanolytic enzymes. Of them the most important are the endo-β-1,4-xylanases which depolymerize the polysaccharide into smaller fragments. Most of the xylanases are members of glycoside hydrolase (GH) families 10 and 11, although they are classified in some other GH families. The relatively new xylanases of GH30 are of special interest. Initially, they appeared to be specific glucuronoxylanases, however, other specificities were found later among prokaryotic and in particular eukaryotic enzymes. This review gives an overview of the substrate and product specificities observed for the GH30 xylanases characterized to date. An emphasis is given to the structure-activity relationship in order to explain how minor differences in catalytic centre and its vicinity can alter catalytic properties from the endoxylanase into the reducing end xylose releasing exoxylanase or into the non-reducing end xylobiohydrolase. Biotechnological potential of the GH30 xylanases is also considered.
Topics: Endo-1,4-beta Xylanases; Glycoside Hydrolases; Substrate Specificity; Xylans; Xylose
PubMed: 33548454
DOI: 10.1016/j.biotechadv.2021.107704 -
Applied Microbiology and Biotechnology May 2023One of the critical steps of the biotechnological production of xylitol from lignocellulosic biomass is the deconstruction of the plant cell wall. This step is crucial... (Review)
Review
One of the critical steps of the biotechnological production of xylitol from lignocellulosic biomass is the deconstruction of the plant cell wall. This step is crucial to the bioprocess once the solubilization of xylose from hemicellulose is allowed, which can be easily converted to xylitol by pentose-assimilating yeasts in a microaerobic environment. However, lignocellulosic toxic compounds formed/released during plant cell wall pretreatment, such as aliphatic acids, furans, and phenolic compounds, inhibit xylitol production during fermentation, reducing the fermentative performance of yeasts and impairing the bioprocess productivity. Although the toxicity of lignocellulosic inhibitors is one of the biggest bottlenecks of the biotechnological production of xylitol, most of the studies focus on how much xylitol production is inhibited but not how and where cells are affected. Understanding this mechanism is important in order to develop strategies to overcome lignocellulosic inhibitor toxicity. In this mini-review, we addressed how these inhibitors affect both yeast physiology and metabolism and consequently xylose-to-xylitol bioconversion. In addition, this work also addresses about cellular adaptation, one of the most relevant strategies to overcome lignocellulosic inhibitors toxicity, once it allows the development of robust and tolerant strains, contributing to the improvement of the microbial performance against hemicellulosic hydrolysates toxicity. KEY POINTS: • Impact of lignocellulosic inhibitors on the xylitol production by yeasts • Physiological and metabolic alterations provoked by lignocellulosic inhibitors • Cell adaptation as an efficient strategy to improve yeast's robustness.
Topics: Saccharomyces cerevisiae; Xylitol; Xylose; Lignin; Fermentation
PubMed: 37039848
DOI: 10.1007/s00253-023-12495-3 -
The New Phytologist Oct 2022The Calvin-Benson-Bassham (CBB) cycle is arguably the most important pathway on earth, capturing CO from the atmosphere and converting it into organic molecules,... (Review)
Review
The Calvin-Benson-Bassham (CBB) cycle is arguably the most important pathway on earth, capturing CO 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 CO 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.
Topics: Carbon Dioxide; Cyanobacteria; Pentoses; Photosynthesis; Plants; Ribulose-Bisphosphate Carboxylase
PubMed: 35860861
DOI: 10.1111/nph.18394 -
Food Research International (Ottawa,... Jul 2021Presently, because of the extraordinary roles and potential applications, rare sugars turn into a focus point for countless researchers in the field of carbohydrates.... (Review)
Review
Presently, because of the extraordinary roles and potential applications, rare sugars turn into a focus point for countless researchers in the field of carbohydrates. l-ribose and l-ribulose are rare sugars and isomers of each other. This aldo and ketopentose are expensive but can be utilized as an antecedent for the manufacturing of various rare sugars and l-nucleoside analogue. The bioconversion approach turns into an excellent alternative method to l-ribulose and l-ribose production, as compared to the complex and lengthy chemical methods. The basic purpose of this research was to describe the importance of rare sugars in various fields and their easy production by using enzymatic methods. l-Ribose isomerase (L-RI) is an enzyme discovered by Tsuyoshi Shimonishi and Ken Izumori in 1996 from Acinetobacter sp. strain DL-28. L-RI structure was cupin-type-β-barrel shaped with a catalytic site between two β-sheets surrounded by metal ions. The crystal structures of the L-RI showed that it contains a homotetramer structure. Current review have concentrated on the sources, characteristics, applications, conclusions and future prospects including the potentials of l-ribose isomerase for the commercial production of l-ribose and l-ribulose. The MmL-RIse and CrL-RIse have the potential to produce the l-ribulose up to 32% and 31%, respectively. The CrL-RIse is highly stable as compared to other L-RIs. The results explained that the L-RIs have great potential in the production of rare sugars especially, l-ribose and l-ribulose, while the immobilization technique can enhance its functionality and properties. The present study precises the applications of L-RIs acquired from various sources for l-ribose and l-ribulose production.
Topics: Aldose-Ketose Isomerases; Pentoses; Ribose
PubMed: 34112412
DOI: 10.1016/j.foodres.2021.110409 -
Communications Biology Jan 2024Our previous work has shown that D-ribose (RIB)-induced depressive-like behaviors in mice. However, the relationship between variations in RIB levels and depression as...
Our previous work has shown that D-ribose (RIB)-induced depressive-like behaviors in mice. However, the relationship between variations in RIB levels and depression as well as potential RIB participation in depressive disorder is yet unknown. Here, a reanalysis of metabonomics data from depressed patients and depression model rats is performed to clarify whether the increased RIB level is positively correlated with the severity of depression. Moreover, we characterize intestinal epithelial barrier damage, gut microbial composition and function, and microbiota-gut-brain metabolic signatures in RIB-fed mice using colonic histomorphology, 16 S rRNA gene sequencing, and untargeted metabolomics analysis. The results show that RIB caused intestinal epithelial barrier impairment and microbiota-gut-brain axis dysbiosis. These microbial and metabolic modules are consistently enriched in peripheral (fecal, colon wall, and serum) and central (hippocampus) glycerophospholipid metabolism. In addition, three differential genera (Lachnospiraceae_UCG-006, Turicibacter, and Akkermansia) and two types of glycerophospholipids (phosphatidylcholine and phosphatidylethanolamine) have greater contributions to the overall correlations between differential genera and glycerophospholipids. These findings suggest that the disturbances of gut microbiota by RIB may contribute to the onset of depressive-like behaviors via regulating glycerophospholipid metabolism, and providing new insight for understanding the function of microbiota-gut-brain axis in depression.
Topics: Humans; Animals; Mice; Rats; Brain-Gut Axis; Ribose; Lipid Metabolism; Gastrointestinal Microbiome; Glycerophospholipids
PubMed: 38195757
DOI: 10.1038/s42003-023-05759-1 -
Chemical Reviews Oct 2022Fluorinated carbohydrates have found many applications in the glycosciences. Typically, these contain fluorination at a single position. There are not many applications... (Review)
Review
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.
Topics: Fluorine; Carbohydrates; Hexoses; Pentoses; Monosaccharides; Nucleosides; Sialic Acids; Carbon
PubMed: 35613331
DOI: 10.1021/acs.chemrev.2c00086 -
Bioresource Technology Oct 2021The production of chemicals and fuels from lignocellulosic biomass has great potential industrial applications due to its economic feasibility and environmental... (Review)
Review
The production of chemicals and fuels from lignocellulosic biomass has great potential industrial applications due to its economic feasibility and environmental attractiveness. However, the utilized microorganisms must be able to use all the sugars present in lignocellulosic hydrolysates, especially xylose, the second most plentiful monosaccharide on earth. Yarrowia lipolytica is a good candidate for producing various valuable products from biomass, but this yeast is unable to catabolize xylose efficiently. The development of metabolic engineering facilitated the application of Y. lipolytica as a platform for the bioconversion of xylose into various value-added products. Here, we reviewed the research progress on natural xylose-utilization pathways and their reconstruction in Y. lipolytica. The progress and emerging trends in metabolic engineering of Y. lipolytica for producing chemicals and fuels are further introduced. Finally, challenges and future perspectives of using lignocellulosic hydrolysate as substrate for Y. lipolytica are discussed.
Topics: Biomass; Metabolic Engineering; Xylose; Yarrowia
PubMed: 34320765
DOI: 10.1016/j.biortech.2021.125484 -
Journal of Bacteriology Jul 2019genetics has rapidly advanced in recent years thanks to the development of tools for allelic replacement and transposon mutagenesis. In this issue, Müh extend the...
genetics has rapidly advanced in recent years thanks to the development of tools for allelic replacement and transposon mutagenesis. In this issue, Müh extend the genetics toolbox by developing a CRISPRi strategy for gene silencing in (U.Müh, A. G. Pannullo, D. S. Weiss, and C. D. Ellermeier, 2019, J Bacteriol 201:e00711-18. . https://doi.org/10.1128/JB.00711-18). The authors demonstrate the tunability and robustness of their CRISPRi system, highlight its utility in studying essential gene function, and discuss exciting new possibilities for dissecting physiology.
Topics: Clostridioides difficile; Clustered Regularly Interspaced Short Palindromic Repeats; Gene Expression; Plasmids; Xylose
PubMed: 30833354
DOI: 10.1128/JB.00089-19