Fast carbohydrate analysis via liquid chromatography coupled with ultra violet and electrospray ionization ion trap detection in 96-well format

Salmonella Typhimurium screen identifies shifts in mixed-acid fermentation during gut colonization

How enteric pathogens adapt their metabolism to a dynamic gut environment is not yet fully understood. To investigate how Salmonella enterica Typhimurium (S.Tm) colonizes the gut, we conducted an in vivo transposon mutagenesis screen in a gnotobiotic mouse model. Our data implicate mixed-acid fermentation in efficient gut-luminal growth and energy conservation throughout infection. During initial growth, the pathogen utilizes acetate fermentation and fumarate respiration. After the onset of gut inflammation, hexoses appear to become limiting, as indicated by carbohydrate analytics and the increased need for gluconeogenesis. In response, S.Tm adapts by ramping up ethanol fermentation for redox balancing and supplying the TCA cycle with α-ketoglutarate for additional energy. Our findings illustrate how S.Tm flexibly adapts mixed fermentation and its use of the TCA cycle to thrive in the changing gut environment. Similar metabolic wiring in other pathogenic Enterobacteriaceae may suggest a broadly conserved mechanism for gut colonization.

Comprehensive rheological analysis of structurally related acetan-like heteroexopolysaccharides from two Kozakia baliensis strains in surfactants and galactomannan blends

Natural biopolymers become increasingly attractive as bio-based alternatives to petrol-based rheological modifiers, especially in personal care applications. However, many polysaccharides exhibit undesired properties in cosmetic applications such as limited viscosifying characteristics, unpleasant sensory properties, or incompatibility with certain formulation compounds. Here, a comprehensive rheological analysis of non-decorated acetan-like heteroexopolysaccharides derived from two Kozakia baliensis strains was performed in selected surfactant formulations. The results were compared to native xanthan gum and a genetically engineered xanthan variant, Xan∆gumFGL, which lacks any acetyl- and pyruvyl moieties and whose rheological properties are unaffected by saline environments. All four polysaccharides displayed a highly similar rheological performance in the non-ionic surfactant lauryl glucoside, while the rheological properties differed in amphoteric and anionic surfactants cocamidopropyl betaine and sodium laureth sulfate due to minor changes in side chain composition. Polysaccharide precipitation was observed in the presence of the cationic surfactant. Nevertheless, the native heteroexopolysaccharide derived from K. baliensis LMG 27018 shows significant potential as a salt-independent rheological modifier compared to the genetically engineered Xan∆gumFGL variant. In addition, blends of heteroexopolysaccharides from K. baliensis and several galactomannans displayed synergistic effects which were comparable to native xanthan gum-galactomannan blends. This study shows that heteroexopolysaccharides of K. baliensis are capable of further extending the portfolio of bio-based rheological modifiers.

Uncovering the Molecular Composition and Architecture of the Bacillus subtilis Biofilm via Solid-State NMR Spectroscopy

The complex and dynamic compositions of biofilms, along with their sophisticated structural assembly mechanisms, endow them with exceptional capabilities to thrive in diverse conditions that are typically unfavorable for individual cells. Characterizing biofilms in their native state is significantly challenging due to their intrinsic complexities and the limited availability of noninvasive techniques. Here, we utilized solid-state nuclear magnetic resonance (NMR) spectroscopy to analyze Bacillus subtilis biofilms in-depth. Our data uncover a dynamically distinct organization within the biofilm: a dominant, hydrophilic, and mobile framework interspersed with minor, rigid cores of limited water accessibility. In these heterogeneous rigid cores, the major components are largely self-assembled. TasA fibers, the most robust elements, further provide a degree of mechanical support for the cell aggregates and some lipid vesicles. Notably, rigid cell aggregates can persist even without the major extracellular polymeric substance (EPS) polymers, although this leads to slight variations in their rigidity and water accessibility. Exopolysaccharides are exclusively present in the mobile domain, playing a pivotal role in its water retention property. Specifically, all water molecules are tightly bound within the biofilm matrix. These findings reveal a dual-layered defensive strategy within the biofilm: a diffusion barrier through limited water mobility in the mobile phase and a physical barrier posed by limited water accessibility in the rigid phase. Complementing these discoveries, our comprehensive, in situ compositional analysis is not only essential for delineating the sophisticated biofilm architecture but also reveals the presence of alternative genetic mechanisms for synthesizing exopolysaccharides beyond the known pathway.

Investigation of exopolysaccharide formation and its impact on anaerobic succinate production with Vibrio natriegens

Vibrio natriegens is an emerging host for biotechnology due to its high growth and substrate consumption rates. In industrial processes typically fed-batch processes are applied to obtain high space-time yields. In this study, we established an aerobic glucose-limited fed-batch fermentation with the wild type (wt) of V. natriegens which yielded biomass concentrations of up to 28.4 gX  L-1 . However, we observed that the viscosity of the culture broth increased by a factor of 800 at the end of the cultivation due to the formation of 157 ± 20 mg exopolysaccharides (EPS) L-1 . Analysis of the genomic repertoire revealed several genes and gene clusters associated with EPS formation. Deletion of the transcriptional regulator cpsR in V. natriegens wt did not reduce EPS formation, however, it resulted in a constantly low viscosity of the culture broth and altered the carbohydrate content of the EPS. A mutant lacking the cps cluster secreted two-fold less EPS compared to the wt accompanied by an overall low viscosity and a changed EPS composition. When we cultivated the succinate producer V. natriegens Δlldh Δdldh Δpfl Δald Δdns::pycCg (Succ1) under anaerobic conditions on glucose, we also observed an increased viscosity at the end of the cultivation. Deletion of cpsR and the cps cluster in V. natriegens Succ1 reduced the viscosity five- to six-fold which remained at the same level observed at the start of the cultivation. V. natriegens Succ1 ΔcpsR and V. natriegens Succ1 Δcps achieved final succinate concentrations of 51 and 46 g L-1 with a volumetric productivity of 8.5 and 7.7 gSuc L-1  h-1 , respectively. Both strains showed a product yield of about 1.4 molSuc molGlc -1 , which is 27% higher compared with that of V. natriegens Succ1 and corresponds to 81% of the theoretical maximum.

Acetan-like heteropolysaccharide production by various Kozakia baliensis strains: Characterization and further insights

The family of Acetobacteraceae has demonstrated their ability to produce several heteropolysaccharides with a strong structural resemblance to xanthan gum. In this study, we assessed the potential of three isolates of K. baliensis as exopolysaccharide producers, namely K. baliensis SR-745, K. baliensis LMG 27018, and K. baliensis SR-1290. Among these, K. baliensis SR-745 was identified as the most promising candidate, exhibiting a final exopolysaccharide titer of 7.09 (± 0.50) g·L-1 and a productivity of 0.15 (± 0.01) g·L-1·h-1. Subsequent monomer analysis confirmed structural variations for the side chain composition of different strains. A molar subunit ratio of 6:1:1:1 (d-glucose: D-mannose: D-galactose: D-glucuronic acid) for EPS derived from K. baliensis SR-745 and of 3:1:3:1 for K. baliensis LMG 27018 was determined, while the exopolysaccharide produced by K. baliensis SR-1290 consisted of a major share of rhamnose. In-depth rheological polymer characterizations revealed high viscosity rates and predominantly elastic gel character, making polysaccharides of K. baliensis highly interesting for applications in the food and cosmetic industry. Further insights into the fundamental structure-function relationships of biopolymers were obtained by comparing exopolysaccharides derived from K. baliensis to a genetically engineered xanthan variant lacking acetyl and pyruvyl substitutions.

Rheological characterization of artificial paenan compositions produced by Paenibacillus polymyxa DSM 365

Microbial exopolysaccharides offer a sustainable alternative to petroleum-based rheological modifiers. Recent studies revealed that the heteroexopolysaccharide produced by Paenibacillus polymyxa is composed of three distinct biopolymers, referred to as paenan I, II and III. Using CRISPR-Cas9 mediated knock-out variants of glycosyltransferases, defined polysaccharide compositions were produced and rheologically characterized in detail. The high viscosity and gel-like character of the wildtype polymer is proposed to originate from the non-covalent interaction between a pyruvate residue of paenan I and the glucuronic acid found in the backbone of paenan III. Paenan II conveys thermostable properties to the exopolysaccharide mixture. In contrast to the wildtype polymer mixture, knock-out variants demonstrated significantly altered rheological behavior. Using the rheological characterization performed in this study, tailor-made paenan variants and mixtures can be generated to be utilized in a wide range of applications including thickening agents, coatings, or high-value biomedical materials.

Gene expression and metabolic activity of Streptococcus mutans during exposure to dietary carbohydrates glucose, sucrose, lactose, and xylitol

Recent RNA sequencing studies have given us a deeper insight into the cariogenic impact of carbohydrate sources in the bacterium Streptococcus mutans, the principal microbial agent in dental caries etiopathogenesis. The process of dental caries development is facilitated by the ability of this bacterium to ferment some carbohydrates into organic acids contributing to a pH decrease in the oral cavity and the demineralization of the hard tissues of the tooth. Furthermore, in dental caries progression, biofilm formation, which starts and ends with free planktonic cells, plays an important role and has several unique properties called virulence factors. The most cariogenic carbohydrate is sucrose, an easily metabolizable source of energy that induces the acidification and synthesis of glucans, forming typical bacterial cell clumps. We used multifaceted methodological approaches to compare the transcriptomic and metabolomic profiles of S. mutans growing in planktonic culture on preferred and nonpreferred carbohydrates and in fasting conditions. Streptococcus mutans in a planktonic culture with lactose produced the same pH drop as glucose and sucrose. By contrast, xylitol and lactose showed high effectiveness in regulating intracellular polysaccharide metabolism, cell wall structure, and overall virulence involved in the initial phase of biofilm formation and structure but with an opposite pattern compared with sucrose and glucose. Our results confirmed the recent findings that xylitol and lactose play a vital role in biofilm structure. However, they do not reduce its formation, which is related to the creation of a cariogenic environment.

CRISPR-Cas9 driven structural elucidation of the heteroexopolysaccharides from Paenibacillus polymyxa DSM 365

Paenibacillus polymyxa is a Gram-positive soil bacterium known for producing a wide range of exopolysaccharides. However, due to the biopolymer's complexity, structural elucidation has so far been inconclusive. Combinatorial knock-outs of glycosyltransferases were generated in order to separate distinct polysaccharides produced by P. polymyxa. Using a complementary analytical approach consisting of carbohydrate fingerprints, sequence analysis, methylation analysis as well as NMR spectroscopy, the structure of the repeating units of two additional heteroexopolysaccharides termed paenan I and paenan III were elucidated. Results for paenan I identified a trisaccharide backbone consisting of 1➔4-β-d-Glc, 1➔4-β-d-Man and a 1,3,4-branching β-d-Gal residue with a sidechain comprising of a terminal β-d-Gal^3,4-Pyr and 1➔3-β-d-Glc. For paenan III, results indicated a backbone consisting of 1➔3-β-d-Glc, 1,3,4-linked α-d-Man and 1,3,4-linked α-d-GlcA. NMR analysis indicated monomeric β-d-Glc and α-d-Man sidechains for the branching Man and GlcA residues respectively.

Analysis of the chemical composition of natural carbohydrates - An overview of methods

Natural carbohydrates are gaining importance over a wide spectrum of human activity due to their versatile functionalities. The properties of carbohydrates are currently used in many branches of industry and new possibilities of their utilization, like in medicine or materials science, are demonstrated systematically. The attractive properties of carbohydrates result from their chemical structure and ability to form macromolecules and derivatives. Each application of carbohydrate requires a knowledge of their chemical composition, which due to the number and differentiation of monosaccharides and their spatial forms is often challenging. This review presents an overview on sample preparation and the methods used for the determination of the fine chemical structure of natural carbohydrates. Most popular and reliable colorimetric, chromatographic and spectroscopic methods are presented with an emphasis on their pros and cons.

Structural Elucidation, Modification, and Structure-Activity Relationship of Polysaccharides in Chinese Herbs: A Review

Chinese herbal polysaccharides (CHPs) are natural polymers composed of monosaccharides, which are widely found in Chinese herbs and work as one of the important active ingredients. Its biological activity is attributed to its complex chemical structure with diverse spatial conformations. However, the structural elucidation is the foundation but a bottleneck problem because the majority of CHPs are heteropolysaccharides with more complex structures. Similarly, the studies on the relationship between structure and function of CHPs are even more scarce. Therefore, this review summarizes the structure-activity relationship of CHPs. Meanwhile, we reviewed the structural elucidation strategies and some new progress especially in the advanced structural analysis methods. The characteristics and applicable scopes of various methods are compared to provide reference for selecting the most efficient method and developing new hyphenated techniques. Additionally, the principle structural modification methods of CHPs and their effects on activity are summarized. The shortcomings, potential breakthroughs, and developing directions of the study of CHPs are discussed. We hope to provide a reference for further research and promote the application of CHPs.

Comparative study for analysis of carbohydrates in biological samples

This work presents a comparative study for the analysis of carbohydrates for four common chromatographic methods, each coupled to mass spectrometry. Supercritical fluid chromatography (SFC), hydrophilic interaction liquid chromatography (HILIC), reversed-phase liquid chromatography (RP-LC) and gas chromatography (GC) with detection by triple quadrupole mass spectrometer (QqQ-MS) are compared. It is shown that gas chromatography and reversed-phase liquid chromatography, each after derivatisation, are superior to the other two methods in terms of separation performance. Furthermore, comparing the different working modes of the mass spectrometer, it can be determined that a targeted analysis, i.e. moving from full scan to single ion monitoring (SIM) and multiple reaction monitoring (MRM), results in an improvement in the sensitivity as well as the repeatability of the method, which has deficiencies especially in the analysis using HILIC. Overall, RP-LC-MS in MRM after derivatisation with 1-phenyl-3-methyl-5-pyrazolone (PMP) proved to be the most suitable method in terms of separation performance, sensitivity and repeatability for the analysis of monosaccharides. Detection limits in the nanomolar range were achieved, which corresponds to a mass concentration in the low µg/L range. The applicability of this method to different biological samples was investigated with various herbal liquors, pectins and a human glycoprotein.

Structural elucidation of the fucose containing polysaccharide of Paenibacillus polymyxa DSM 365

Paenibacillus polymyxa is an avid producer of exopolysaccharides of industrial interest. However, due to the complexity of the polymer composition, structural elucidation of the polysaccharide remained unfeasible for a long time. By using a CRISPR-Cas9 mediated knock-out strategy, all single glycosyltransferases as well as the Wzy polymerases were individually deleted in the corresponding gene cluster for the first time. Thereby, it was observed that the main polymer fraction was completely suppressed (or deleted) and a pure minor fucose containing polysaccharide could be isolated, which was named paenan II. Applying this combinatorial approach, the monosaccharide composition, sequence and linkage pattern of this novel polymer was determined via HPLC-MS, GC-MS and NMR. Furthermore, we demonstrated that the knock-out of the glycosyltransferases PepQ, PepT, PepU and PepV as well as of the Wzy polymerase PepG led to the absence of paenan II, attributing those enzymes to the assembly of the repeating unit.

Experimental determination of Escherichia coli biomass composition for constraint-based metabolic modeling

Genome-scale metabolic models (GEMs) are mathematical representations of metabolism that allow for in silico simulation of metabolic phenotypes and capabilities. A prerequisite for these predictions is an accurate representation of the biomolecular composition of the cell necessary for replication and growth, implemented in GEMs as the so-called biomass objective function (BOF). The BOF contains the metabolic precursors required for synthesis of the cellular macro- and micromolecular constituents (e.g. protein, RNA, DNA), and its composition is highly dependent on the particular organism, strain, and growth condition. Despite its critical role, the BOF is rarely constructed using specific measurements of the modeled organism, drawing the validity of this approach into question. Thus, there is a need to establish robust and reliable protocols for experimental condition-specific biomass determination. Here, we address this challenge by presenting a general pipeline for biomass quantification, evaluating its performance on Escherichia coli K-12 MG1655 sampled during balanced exponential growth under controlled conditions in a batch-fermentor set-up. We significantly improve both the coverage and molecular resolution compared to previously published workflows, quantifying 91.6% of the biomass. Our measurements display great correspondence with previously reported measurements, and we were also able to detect subtle characteristics specific to the particular E. coli strain. Using the modified E. coli GEM iML1515a, we compare the feasible flux ranges of our experimentally determined BOF with the original BOF, finding that the changes in BOF coefficients considerably affect the attainable fluxes at the genome-scale.

Systematic optimization of exopolysaccharide production by Gluconacetobacter sp. and use of (crude) glycerol as carbon source

The usage of polysaccharides as biodegradable polymers is of growing interest in the context of a sustainable and ecofriendly economy. For this, the production of exopolysaccharides (EPS) by Gluconacetobacter sp. was investigated. Glycerol as carbon source revealed to be beneficial compared to glucose. In addition, pure glycerol could be substituted by a crude glycerol waste stream from biodiesel production. Systematic analysis of the peptone and phosphate concentrations in glycerol-based media indicated a strong effect of peptone. Optimized parameters resulted in a titer of 25.4 ± 2.4 g/L EPS with a productivity of 0.46 ± 0.04 g*(L*h)^-1. With decreasing peptone, a variation in the monomer ratios was observed. An accompanying change in molecular size distribution indicated the production of two different polysaccharides. Intensified analysis revealed the main polysaccharide to be composed of glucose (Glc), galactose (Gal), mannose (Man) and glucuronic acid (GlcA), and the minor polysaccharide of Gal, Man, ribose (Rib).

Progress in the pretreatment and analysis of carbohydrates in food: An update since 2013

Carbohydrates in foods and other matrices plays vital roles in their diverse biological functions. Carbohydrates serve not only as functional substances but also as structural materials, such as components of membranes, and participate in cellular recognition. The fact that carbohydrates are indispensable has contributed to the need for pretreatment and analytical methods to be developed for their characterization. The aim of this review is to provide a comprehensive overview of carbohydrate pretreatment and determination methods in various matrices. The pretreatment methods include simple and more developed approaches (e.g., solid phase extraction, supercritical fluid extraction, and different microextraction methods, among others). The analytical methods include those by liquid chromatography (including high-performance anion-exchange chromatography), capillary electrophoresis, gas chromatography and supercritical fluid chromatography, and others. Different pretreatment methods and determination approaches are updated, compared, and discussed. Moreover, we discuss and compare the strengths and weaknesses of different methods and suggest their future prospects.

Characterization of polysaccharides from different species of brown seaweed using saccharide mapping and chromatographic analysis

Brown seaweed polysaccharides (BSPs) are one of the primary active components from brown seaweed that has a range of pharmaceutical and biomedical applications. However, the quality control of BSPs is a challenge due to their complicated structure and macromolecule. In this study, saccharide mapping based on high-performance liquid chromatography (HPLC), multi-angle laser light scattering, viscometer, and refractive index detector (HPSEC-MALLS-Vis-RID), and Fourier transform infrared (FT-IR) were used to discriminate the polysaccharides from nine different species of brown algae (BA1-9). The results showed that BSPs were composed of β-D-glucans and β-1,3-1,4-glucan linkages. The molecular weight, radius of gyration, and intrinsic viscosity of BSPs were ranging from 1.718 × 10⁵ Da to 6.630 × 10⁵ Da, 30.2 nm to 51.5 nm, and 360.99 mL/g to 865.52 mL/g, respectively. Moreover, α values of BSPs were in the range of 0.635 to 0.971, which indicated a rigid rod chain conformation. The antioxidant activities of BSPs exhibited substantial radical scavenging activities against DPPH (1,1-diphenyl-2-picrylhydrazyl) and ABTS (2, 2'-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid) radicals, which indicated that the use of BSPs might be a potential approach for antioxidant supplements. Thus, this study gives insights about the structure-function relationship of BSPs, which will be beneficial to improve the quality of polysaccharides derived from marine algae.

Novel Prokaryotic CRISPR-Cas12a-Based Tool for Programmable Transcriptional Activation and Repression

Transcriptional perturbation using inactivated CRISPR-nucleases (dCas) is a common method in eukaryotic organisms. While rare examples of dCas9-based tools for prokaryotes have been described, multiplexing approaches are limited due to the used effector nuclease. For the first time, a dCas12a derived tool for the targeted activation and repression of genes was developed. Therefore, a previously described SoxS activator domain was linked to dCas12a to enable the programmable activation of gene expression. A proof of principle of transcriptional regulation was demonstrated on the basis of fluorescence reporter assays using the alternative host organism Paenibacillus polymyxa as well as Escherichia coli. Single target and multiplex CRISPR interference targeting the exopolysaccharide biosynthesis of P. polymyxa was shown to emulate polymer compositions of gene knockouts. The simultaneous expression of 11 gRNAs targeting multiple lactate dehydrogenases and a butanediol dehydrogenase resulted in decreased lactate formation, as well as an increased butanediol production in microaerobic fermentation processes. Even though Cas12a is more restricted in terms of its genomic target sequences compared to Cas9, its ability to efficiently process its own guide RNAs in vivo makes it a promising tool to orchestrate sophisticated genetic reprogramming of bacterial cells or to screen for engineering targets in the genome. The developed tool will accelerate metabolic engineering efforts in the alternative host organism P. polymyxa and might be also applied for other bacterial cell factories.

Fucoidan Characterization: Determination of Purity and Physicochemical and Chemical Properties

Fucoidans are marine sulfated biopolysaccharides that have heterogenous and complicated chemical structures. Various sugar monomers, glycosidic linkages, molecular masses, branching sites, and sulfate ester pattern and content are involved within their backbones. Additionally, sources, downstream processes, and geographical and seasonal factors show potential effects on fucoidan structural characteristics. These characteristics are documented to be highly related to fucoidan potential activities. Therefore, numerous chemical qualitative and quantitative determinations and structural elucidation methods are conducted to characterize fucoidans regarding their physicochemical and chemical features. Characterization of fucoidan polymers is considered a bottleneck for further biological and industrial applications. Consequently, the obtained results may be related to different activities, which could be improved afterward by further functional modifications. The current article highlights the different spectrometric and nonspectrometric methods applied for the characterization of native fucoidans, including degree of purity, sugar monomeric composition, sulfation pattern and content, molecular mass, and glycosidic linkages.

Rheological characterization of Porphyridium sordidum and Porphyridium purpureum exopolysaccharides

Porphyridium exopolysaccharides (EPSs), which contain sulfate and methyl groups, have a similar potential for use in multiple industrial applications as macroalgae counterparts but lack detailed characterization. For this reason, we produced 0.21 g L^-1 of P. sordidum EPS and 0.17 g L^-1P. purpureum EPS, followed by a thorough rheological characterization in respect to their differences in monomer composition, sulfate concentrations and methyl patterns. Furthermore, the effect of NaCl and CaCl₂ was evaluated, and the effect of high salinity media on the rheological properties of the biopolymers was analyzed. Both Porphyridium EPSs show a remarkable stability at high temperature and under the effect of mono- and divalent cations, and high salinity cultivation medium, which was evidenced by the rheological properties of the EPS. This feature is not displayed by many carbohydrate polymers, making it possible to enrich current applications in which EPS are used.

Rapid Analysis of Monosaccharides in Sub-milligram Plant Samples Using Liquid Chromatography-Mass Spectrometry Assisted by Post-column Derivatization

Monosaccharides play important roles in plant growth and development, and their biofunctions are closely related to their endogenous contents. Therefore, the determination of monosaccharides is beneficial for the further study of monosaccharide biofunction. In this work, we developed a liquid chromatography-mass spectrometry analytical method assisted by a post-column derivatization technique (LC-PCD-MS) for the fast and automatic determination of 16 monosaccharides in samples. Post-column chemical derivatization of monosaccharides was performed by a reaction of monosaccharides with 4-benzylaminobenzeneboronic acid (4-PAMBA) through boronate ester formation in a three-way connector. 4-PAMBA worked as a derivatization reagent to improve the selectivity and sensitivity of monosaccharide detection by MS. The developed LC-PCD-MS method integrates LC separation, chemical derivatization, and MS detection in one run, thus greatly reducing the analysis time for each sample. The limits of detection and limits of quantification for 16 monosaccharides were in the range of 0.002-0.1 and 0.007-0.5 ng/mL, respectively. Good linearity was obtained from the linear regression, with a determination coefficient (R²) ranging from 0.9928 to 1.0000. The relative recoveries were in the range of 80.7-117.8%, with the intra- and interday relative standard deviations less than 19.7 and 16.5%, respectively, indicating good accuracy and acceptable reproducibility of the method. Finally, the method was successfully applied to investigate the spatial and temporal distribution of 16 monosaccharides in the developing flower and germinating seed of Arabidopsis thaliana.

Overall Nutritional and Sensory Profile of Different Species of Australian Wattle Seeds (Acacia spp.): Potential Food Sources in the Arid Semi-Arid Regions

Wattle seed (Acacia spp.) is a well-known staple food within indigenous communities in Australia. A detailed investigation of the overall nutritional and sensory profile of four abundant and underutilized Acacia species-A. coriacea, A. cowleana, A. retinodes and A. sophorae-were performed. Additionally, molecular weight of protein extracts from the wattle seeds (WS) was determined. The seeds are rich in protein (23-27%) and dietary fibre (33-41%). Relatively high fat content was found in A. cowleana (19.3%), A. sophorae (14.8%) and A. retinodes (16.4%) with oleic acid being the predominant fatty acid. The seeds contained high amounts of essential amino acids (histidine, lysine, valine, isoleucine and leucine). A. coriacea is rich in iron (43 mg/kg), potassium (10 g/kg) and magnesium (1.7 g/kg). Pentose (xylose/arabinose), glucose, galactose and galacturonic acids were the major sugars found in the four species. Raw seeds from A. sophorae, A. retinodes and A. coriacea have the highest protein molecular weight, between 50-90 kDa, 80 kDa and 50-55 kDa, respectively. There was variation in the sensory profile of the WS species. This study showed that the four WS species have good nutritional value and could be included in human diet or used in food formulations.

Testing Anti-Biofilm Polymeric Surfaces: Where to Start?

Present day awareness of biofilm colonization on polymeric surfaces has prompted the scientific community to develop an ever-increasing number of new materials with anti-biofilm features. However, compared to the large amount of work put into discovering potent biofilm inhibitors, only a small number of papers deal with their validation, a critical step in the translation of research into practical applications. This is due to the lack of standardized testing methods and/or of well-controlled in vivo studies that show biofilm prevention on polymeric surfaces; furthermore, there has been little correlation with the reduced incidence of material deterioration. Here an overview of the most common methods for studying biofilms and for testing the anti-biofilm properties of new surfaces is provided.

A Bifunctional UDP-Sugar 4-Epimerase Supports Biosynthesis of Multiple Cell Surface Polysaccharides in Sinorhizobium meliloti

Sinorhizobium meliloti produces multiple extracellular glycans, including among others, lipopolysaccharides (LPS), and the exopolysaccharides (EPS) succinoglycan (SG) and galactoglucan (GG). These polysaccharides serve cell protective roles. Furthermore, SG and GG promote the interaction of S. meliloti with its host Medicago sativa in root nodule symbiosis. ExoB has been suggested to be the sole enzyme catalyzing synthesis of UDP-galactose in S. meliloti (A. M. Buendia, B. Enenkel, R. Köplin, K. Niehaus, et al. Mol Microbiol 5:1519-1530, 1991, https://doi.org/10.1111/j.1365-2958.1991.tb00799.x). Accordingly, exoB mutants were previously found to be affected in the synthesis of the galactose-containing glycans LPS, SG, and GG and consequently, in symbiosis. Here, we report that the S. meliloti Rm2011 uxs1-uxe-apsS-apsH1-apsE-apsH2 (SMb20458-63) gene cluster directs biosynthesis of an arabinose-containing polysaccharide (APS), which contributes to biofilm formation, and is solely or mainly composed of arabinose. Uxe has previously been identified as UDP-xylose 4-epimerase. Collectively, our data from mutational and overexpression analyses of the APS biosynthesis genes and in vitro enzymatic assays indicate that Uxe functions as UDP-xylose 4- and UDP-glucose 4-epimerase catalyzing UDP-xylose/UDP-arabinose and UDP-glucose/UDP-galactose interconversions, respectively. Overexpression of uxe suppressed the phenotypes of an exoB mutant, evidencing that Uxe can functionally replace ExoB. We suggest that under conditions stimulating expression of the APS biosynthesis operon, Uxe contributes to the synthesis of multiple glycans and thereby to cell protection, biofilm formation, and symbiosis. Furthermore, we show that the C₂H₂ zinc finger transcriptional regulator MucR counteracts the previously reported CuxR-c-di-GMP-mediated activation of the APS biosynthesis operon. This integrates the c-di-GMP-dependent control of APS production into the opposing regulation of EPS biosynthesis and swimming motility in S. meliloti IMPORTANCE Bacterial extracellular polysaccharides serve important cell protective, structural, and signaling roles. They have particularly attracted attention as adhesives and matrix components promoting biofilm formation, which significantly contributes to resistance against antibiotics. In the root nodule symbiosis between rhizobia and leguminous plants, extracellular polysaccharides have a signaling function. UDP-sugar 4-epimerases are important enzymes in the synthesis of the activated sugar substrates, which are frequently shared between multiple polysaccharide biosynthesis pathways. Thus, these enzymes are potential targets to interfere with these pathways. Our finding of a bifunctional UDP-sugar 4-epimerase in Sinorhizobium meliloti generally advances the knowledge of substrate promiscuity of such enzymes and specifically of the biosynthesis of extracellular polysaccharides involved in biofilm formation and symbiosis in this alphaproteobacterium.

Screening of c-di-GMP-Regulated Exopolysaccharides in Host Interacting Bacteria

Bacterial exopolysaccharides (EPS) often confer a survival advantage by protecting the cell against abiotic and biotic stresses, including host defensive factors. They are also main components of the extracellular matrix involved in cell-cell recognition, surface adhesion and biofilm formation. Biosynthesis of a growing number of EPS has been reported to be regulated by the ubiquitous second messenger c-di-GMP, which promotes the transition to a biofilm mode of growth in an intimate association with the eukaryotic host. Here we describe a strategy based on the combination of an approach to artificially increase the intracellular level of c-di-GMP in virtually any gram-negative bacteria with a high throughput screening (HTS) for the identification of monosaccharide composition and carbohydrate fingerprinting of novel EPS, or modified variants, that can be involved in host-bacteria interactions.

Substrate scope of a dehydrogenase from Sphingomonas species A1 and its potential application in the synthesis of rare sugars and sugar derivatives

Rare sugars and sugar derivatives that can be obtained from abundant sugars are of great interest to biochemical and pharmaceutical research. Here, we describe the substrate scope of a short‐chain dehydrogenase/reductase from Sphingomonas species A1 (SpsADH) in the oxidation of aldonates and polyols. The resulting products are rare uronic acids and rare sugars respectively. We provide insight into the substrate recognition of SpsADH using kinetic analyses, which show that the configuration of the hydroxyl groups adjacent to the oxidized carbon is crucial for substrate recognition. Furthermore, the specificity is demonstrated by the oxidation of d‐sorbitol leading to l‐gulose as sole product instead of a mixture of d‐glucose and l‐gulose. Finally, we applied the enzyme to the synthesis of l‐gulose from d‐sorbitol in an in vitro system using a NADH oxidase for cofactor recycling. This study shows the usefulness of exploring the substrate scope of enzymes to find new enzymatic reaction pathways from renewable resources to value‐added compounds.

Tailor-made exopolysaccharides-CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa

Application of state-of-the-art genome editing tools like CRISPR-Cas9 drastically increase the number of undomesticated micro-organisms amenable to highly efficient and rapid genetic engineering. Adaptation of these tools to new bacterial families can open up entirely new possibilities for these organisms to accelerate as biotechnologically relevant microbial factories, also making new products economically competitive. Here, we report the implementation of a CRISPR-Cas9 based vector system in Paenibacillus polymyxa, enabling fast and reliable genome editing in this host. Homology directed repair allows for highly efficient deletions of single genes and large regions as well as insertions. We used the system to investigate the yet undescribed biosynthesis machinery for exopolysaccharide (EPS) production in P. polymyxa DSM 365, enabling assignment of putative roles to several genes involved in EPS biosynthesis. Using this simple gene deletion strategy, we generated EPS variants that differ from the wild-type polymer not only in terms of monomer composition, but also in terms of their rheological behavior. The developed CRISPR-Cas9 mediated engineering approach will significantly contribute to the understanding and utilization of socially and economically relevant Paenibacillus species and extend the polymer portfolio.

Revisiting monosaccharide analysis - quantitation of a comprehensive set of monosaccharides using dynamic multiple reaction monitoring

A rapid method for the quantitation of sixteen neutral and acidic monosaccharides, from both animal and plant sources was developed using ultra-high performance liquid chromatography triple quadrupole mass spectrometry (UHPLC/QqQ-MS) in dynamic multiple reaction monitoring (dMRM) mode. Monosaccharides including three pentoses (ribose, xylose, arabinose), two deoxyhexoses (rhamnose, fucose), five hexoses (fructose, mannose, allose, glucose, galactose), two hexuronic acids (glucuronic acid, galacturonic acid), and two N-acetyl-hexosamines (GlcNAc, GalNAc), were derivatized with 1-phenyl-3-methyl-5-pyrazolone (PMP), while underivatized sialic acids, Neu5Ac and Neu5Gc, were simultaneously analyzed with a 10-minute run. With the optimized UHPLC conditions, baseline separations of the isomers were achieved. The sensitivity and calibration ranges of this method were determined. The limits of detection were between femtomoles and attomoles with linear ranges spanning four to six orders of magnitude and coefficients of variation (CVs) ≤7.2%. Spiking experiments performed on a pooled fecal sample demonstrated the high accuracy of this method even when applied to samples with complicated matrices. The validated method was applied to fecal samples from an infant transitioning from breast milk to weaning foods. Major milk monosaccharides including galactose, fucose, glucose, GlcNAc, and Neu5Ac were found to be the most abundant components in the feces of milk-fed infants. PMP-derivatives of nine other monosaccharides including apiose, lyxose, altrose, talose, gulose, glucosamine, galactosamine, mannosamine, and N-acetylmannosamine (ManNAc) were also tested and could be added to the quantitation method depending on the need. The speed and sensitivity of the method makes it readily adaptable to rapid throughput analysis of monosaccharides in biological samples.

Recent Liquid Chromatographic Approaches and Developments for the Separation and Purification of Carbohydrates

Carbohydate purification remains a bottleneck in securing analytical standards from natural sources or by chemical or enzymatic synthesis. This review highlights the scope and remaining limitations of recent approaches and methods development in liquid chromatography for robust and higher-throughput carbohydrate separation and isolation.

The hypoglycemic and antioxidant effects of polysaccharides from the petioles and pedicels of Euryale ferox Salisb. on alloxan-induced hyperglycemic mice

The present study investigated the potential hypoglycemic and antioxidant effects of polysaccharides extracted from the petioles and pedicels of Euryale ferox Salisb. (EFPP) on alloxan-induced hyperglycemic mice.

Physicochemical and Biological Characterization of Fucoidan from Fucus vesiculosus Purified by Dye Affinity Chromatography

A comparative study concerning the physicochemical, monomeric composition and biological characters among different fucoidan fractions is presented. Common purification techniques for fucoidan usually involve many steps. During these steps, the important structural features might be affected and consequently alter its biological activities. Three purified fractions were derived from Fucus vesiculosus water extract which, afterwards, were purified by a recently-developed dye affinity chromatography protocol. This protocol is based on dye-sulfated polysaccharide interactions. The first two fractions were obtained from crude precipitated fucoidan at different pH values of the adsorption phase: pH 1 and 6. This procedure resulted in fucoidan_1 and 6 fractions. The other, third, fraction: fucoidan_M, however, was obtained from a buffered crude extract at pH 1, eliminating the ethanol precipitation step. All of the three fractions were then further evaluated. Results revealed that fucoidan_M showed the highest sulfur content (S%), 12.11%, with the lowest average molecular weight, 48 kDa. Fucose, galactose, and uronic acid/glucose dimers were detected in all fractions, although, xylose was only detected in fucoidan_1 and 6. In a concentration of 10 µg·mL(-1), Fucoidan_6 showed the highest heparin-like anticoagulant activity and could prolong the APTT and TT significantly to 66.03 ± 2.93 and 75.36 ± 1.37 s, respectively. In addition, fucoidan_M demonstrated the highest potency against HSV-1 with an IC50 of 2.41 µg·mL(-1). The technique proved to be a candidate for fucoidan purifaction from its crude extract removing the precipitation step from common purification protocols and produced different fucoidan qualities resulted from the different incubation conditions with the immobilized thiazine toluidine blue O dye.

Automated Modular High Throughput Exopolysaccharide Screening Platform Coupled with Highly Sensitive Carbohydrate Fingerprint Analysis

Many microorganisms are capable of producing and secreting exopolysaccharides (EPS), which have important implications in medical fields, food applications or in the replacement of petro-based chemicals. We describe an analytical platform to be automated on a liquid handling system that allows the fast and reliable analysis of the type and the amount of EPS produced by microorganisms. It enables the user to identify novel natural microbial exopolysaccharide producers and to analyze the carbohydrate fingerprint of the corresponding polymers within one day in high-throughput (HT). Using this platform, strain collections as well as libraries of strain variants that might be obtained in engineering approaches can be screened. The platform has a modular setup, which allows a separation of the protocol into two major parts. First, there is an automated screening system, which combines different polysaccharide detection modules: a semi-quantitative analysis of viscosity formation via a centrifugation step, an analysis of polymer formation via alcohol precipitation and the determination of the total carbohydrate content via a phenol-sulfuric-acid transformation. Here, it is possible to screen up to 384 strains per run. The second part provides a detailed monosaccharide analysis for all the selected EPS producers identified in the first part by combining two essential modules: the analysis of the complete monomer composition via ultra-high performance liquid chromatography coupled with ultra violet and electrospray ionization ion trap detection (UHPLC-UV-ESI-MS) and the determination of pyruvate as a polymer substituent (presence of pyruvate ketal) via enzymatic oxidation that is coupled to a color formation. All the analytical modules of this screening platform can be combined in different ways and adjusted to individual requirements. Additionally, they can all be handled manually or performed with a liquid handling system. Thereby, the screening platform enables a huge flexibility in order to identify various EPS.

Bacterial Glycosyltransferases: Challenges and Opportunities of a Highly Diverse Enzyme Class Toward Tailoring Natural Products

The enzyme subclass of glycosyltransferases (GTs; EC 2.4) currently comprises 97 families as specified by CAZy classification. One of their important roles is in the biosynthesis of disaccharides, oligosaccharides, and polysaccharides by catalyzing the transfer of sugar moieties from activated donor molecules to other sugar molecules. In addition GTs also catalyze the transfer of sugar moieties onto aglycons, which is of great relevance for the synthesis of many high value natural products. Bacterial GTs show a higher sequence similarity in comparison to mammalian ones. Even when most GTs are poorly explored, state of the art technologies, such as protein engineering, domain swapping or computational analysis strongly enhance our understanding and utilization of these very promising classes of proteins. This perspective article will focus on bacterial GTs, especially on classification, screening and engineering strategies to alter substrate specificity. The future development in these fields as well as obstacles and challenges will be highlighted and discussed.

Methods to identify the unexplored diversity of microbial exopolysaccharides

Microbial exopolysaccharides (EPS) are a structurally very diverse class of molecules. A number of them have found their application in rather diverging fields that extend from medicine, food, and cosmetics on the one side to construction, drilling, and chemical industry on the other side. The analysis of microbial strains for their competence in polysaccharide production has therefore been a major issue in the past, especially in the search for new polysaccharide variants among natural strain isolates. Concerning the fact that nearly all microbes carry the genetic equipment for the production of polysaccharides under specific conditions, the naturally provided EPS portfolio seems to be still massively underexplored. Therefore, there is a need for high throughput screening techniques capable of identifying novel variants of bacterial EPS with properties superior to the already described ones, or even totally new ones. A great variety of different techniques has been used in screening approaches for identifying microorganisms that are producing EPS in substantial amounts. Mucoid growth is often the method of choice for visual identification of EPS producing strains. Depending on the thickening characteristics of the polysaccharide, observation of viscosity in culture broth can also be an option to evaluate EPS production. Precipitation with different alcohols represents a common detection, isolation, and purification method for many EPS. A more quantitative approach is found in the total carbohydrate content analysis, normally determined, e.g., by phenol-sulfuric-acid-method. In addition, recently a new and reliable method for the detailed analysis of the monomeric composition and the presence of rare sugars and sugar substitutions has become available, which could give a first hint of the polymer structure of unknown EPS. This minireview will compare available methods and novel techniques and discuss their benefits and disadvantages.