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Phasin (PhaP), one of the polyhydroxyalkanoate granule-associated protein, enhances cell growth and polyhydroxybutyrate (PHB) biosynthesis by regulating the number and size of PHB granules. However, few studies have applied phasins to various PHB production conditions. In this study, we identified novel phasin genes from the genomic data of Arctic soil bacterium Pseudomonas sp. B14-6 and determined the role of phaP1 Ps under different PHB production conditions. Transmission electron microscopy and gel permeation chromatography revealed small PHB granules with high-molecular weight, while differential scanning calorimetry showed that the extracted PHB films had similar thermal properties. The phasin protein derived from Pseudomonas sp. B14-6 revealed higher PHB production and exhibited higher tolerance to several lignocellulosic biosugar-based inhibitors than the phasin protein of Ralstonia eutropha H16 in a recombinant Escherichia coli strain. The increased tolerance to propionate, temperature, and other inhibitors was attributed to the introduction of phaP1 Ps , which increased PHB production from lignocellulosic hydrolysate (2.39-fold) in the phaP1 Ps strain. However, a combination of phasin proteins isolated from two different sources did not increase PHB production. These findings suggest that phasin could serve as a powerful means to increase robustness and PHB production in heterologous strains. [ABSTRACT FROM AUTHOR]

Pectin, a diverse carbohydrate polymer in plants consists of a core of α-1,4-linked D-galacturonic acid units, includes a vast portion of fruit and agricultural wastes. Using the wastes to produce beneficial compounds is a new approach to control the negative environmental impacts of the accumulated wastes. In the present study, we report a pectinase producing bacterium Streptomyces hydrogenans YAM1 and evaluate antioxidative and anticancer effects of the oligosaccharides obtained from pectin degradation. The production of oligosaccharides due to pectinase activity was detected by thin layer chromatography (TLC) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Our results revealed that S. hydrogenans YAM1 can degrade pectin to unsaturated pectic oligo-galacturonic acids (POS) with approximately 93% radical scavenging activity in 20 mg/mL which it is more than 50% of the same concentration of pectin. Flow cytometric analysis revealed that MCF-7 cells viability decreased more than 32 and 92% following treatment with 6 and 20 mg/mL POS after 24 h, respectively. It is suggested that pectin degradation by S. hydrogenans YAM1 is not only a new approach to produce highly active compounds from fruit wastes, but also is an effective method to remove fibrous pollutants from different environments. [ABSTRACT FROM AUTHOR]

• Deep genome sequencing of H. socia CKY01 revealed 4627 genes with 64 % of GC content. • Genes aiding uptake, synthesis, and transport of osmolytes were identified. • Glutamate, proline and ectoine could enhance the growth of H.socia CKY01 in saline condition. • The strain produces polyhydroxybutyrate. Bacteria from the genus Halomonas hold promise in biotechnology as sources of salt-tolerant enzymes, biosurfactants, biopolymers, osmolytes, and as actors in bioremediation processes. In a previous work, we have identified Halomonas socia strain CKY01 having various hydrolase activities. Here, we aimed to study the survival strategies of marine bacteria. A deep genome sequencing study of H. socia CKY01 has revealed 4627 genes reaching 4,753,299 bp with 64 % of GC content. This strain produced polyhydroxybutyrate (PHB) having one gene clusters having phaC and phasin, and it has several genes responsible for the uptake, synthesis, and transport of the osmolytes such as betaine, choline, ectoine, carnitine, and proline in the bacterial genome. The addition of 60 mM glutamate, 60 mM proline and 60 mM ectoine enhanced growth 300.8 %, 294.2 % and 235.0 %, respectively, under 10 % saline conditions. In particular, ectoine and proline increased salt resistance and allowed cells to survive in more than 15 % NaCl. By combining experimental and genome sequencing data, we have investigated the importance of osmolytes on the survival of this Halomonas strain. [ABSTRACT FROM AUTHOR]

Polyhydroxyalkanoates (PHA), such as poly (3-hydroxybutyrate) (PHB), have emerged as potential alternatives to petroleum-based plastics and can be produced through the appropriate selection of marine bacteria that are already adapted to high salt and low temperature conditions without the requirement of antibiotic treatment. The present study, thus, aimed to screen and characterize thirteen PHA-producing microbial strains isolated from the Gwangalli beach in Busan, South Korea. Among them, Halomonas sp. YLGW01 produced the highest amount of PHB (94.6 ± 1.8% (w/w)) using fructose. Interestingly Halomonas sp. YLGW01 showed increase in cell size (8.39 ± 3.63 μm) with fructose as carbon source as compared to glucose (2.34 ± 0.44 μm). Fructose syrup was investigated as carbon source under unsterilized conditions and 95.26 ± 1.78% of PHB was produced. Overall, this strain showed the highest PHB contents in halotolerant bacteria. [ABSTRACT FROM AUTHOR]

Methicillin-resistant Staphylococcus aureus (MRSA) strains are distinct from general Staphylococcus strains with respect to the composition of the membrane, ability to form a thicker biofilm, and, importantly, ability to modify the target of antibiotics to evade their activity. The agr gene is an accessory global regulator of gram-positive bacteria that governs virulence or resistant mechanisms and therefore an important target for the control of resistant strains. However, the mechanism by which agr impacts resistance to β-lactam antibiotics remains unclear. In the present study, we found the Δagr mutant strain having higher resistance to high concentrations of β-lactam antibiotics such as oxacillin and ampicillin. To determine the influence of variation in the microenvironment of cells between the parental and mutant strains, fatty acid analysis of the supernatant, total lipids, and phospholipid fatty acids were compared. The Δagr mutant strain tended to produce fewer fatty acids and retained lower amounts of C16, C18 fatty acids in the supernatant. Phospholipid analysis showed a dramatic increase in the hydrophobic longer-chain fatty acids in the membrane. To target membrane, we applied several surfactants and found that sorbitan monolaurate (Span20) had a synergistic effect with oxacillin by decreasing biofilm formation and growth. These findings indicate that agr deletion allows for MRSA to resist antibiotics via several changes including constant expression of mecA, fatty acid metabolism, and biofilm thickening. [ABSTRACT FROM AUTHOR]

[Display omitted] • The phaP gene was first introduced for the purpose of enhancing hydrogen production. • Among engineering strain, the phaP strain exhibited the highest hydrogen production. • The introduction of phaP led to a decrease in the transcription of chaperone genes. • The introduction of phaP enhanced hydrogen production 2.6-fold compared to wild type. In this study, the goal was to enhance the tolerance of Clostridium acetobutylicum ATCC 824 to biomass-based inhibitory compounds for biohydrogen production and evaluate various known genes that enhance the production of biochemicals in various hosts. The introduction of phaP , the major polyhydroxyalkanoate granule-associated protein that has been reported as a chaperone-like protein resulted in increased tolerance to inhibitors and leads to higher levels of hydrogen production, cell growth, and glucose consumption in the presence of these inhibitors. It was observed that the introduction of phaP led to an increase in the transcription of the hydrogenase gene, whereas transcription of the chaperone functional genes decreased compared to the wild type. Finally, the introduction of phaP could significantly enhance biohydrogen production by 2.6-fold from lignocellulosic hydrolysates compared to that of wild type. These findings suggested that the introduction of phaP could enhance growth and biohydrogen production, even in non-polyhydroxyalkanoate-producing strains. [ABSTRACT FROM AUTHOR]

One of the advantages of microbial synthesis of polyhydroxyalkanoates (PHAs) is the production of diverse polymers with different properties by the addition of different monomers, such as 3-hydroxybutyrate (3HB), 3-hydroxyvalerate (3HV), and 3-hydroxyhexanoate (3HHx). Considering the number of possible variables, terpolymers can have more variations than copolymers. In this study, we aimed to synthesize the terpolymer P(3HB- co -3HV- co -3HHx) from volatile fatty acids such as propionate and butyrate using the recombinant Ralstonia eutropha strain (Re2133/pCB81), containing deletions in the phaB1 , phaB2 , and phaB3 genes, and overexpression of synthetic PHA operon (phaC2 , phaA , phaJ). This strain produced terpolymers depending on the ratio of two different carbon sources, namely, propionic and butyric acids; however, wild type R. eutropha could not produce the same type of polymer. The incorporation of 3-hydroxyvalerate and 3-hydroxyhexanoate monomers was confirmed by gas chromatography and H-nuclear magnetic resonance spectroscopy, and the parameters affecting the terpolymer composition were obtained based on regression. In addition, the thermal analysis showed that this terpolymer has properties different from those of the copolymer, obtained from the same composition of volatile acids. Depending on the ratio of two volatile acids, the composition of the terpolymer can be regulated resulting in different properties. [ABSTRACT FROM AUTHOR]

• Rhodococcus sp. YHY01 can utilize volatile fatty acids as carbon source. • Acetate, butyrate and lactate play role in even number fatty acids synthesis. • Propionate directly involved in synthesis of odd carbon number fatty acids. • Higher biomass and fatty acid yield coefficient obtained with butyrate. • Food waste derived volatile fatty acids are a suitable feedstock for biodiesel production. Food waste-derived volatile fatty acids (VFAs) can act as a renewable feedstock for biodiesel production. In synthetic media, Rhodococcus sp. YHY01 was able to utilize various organic acids (acetate, butyrate, lactate, and propionate) as a carbon source. Butyrate was the optimal carbon source, having a minimum inhibitory effect on growth, and a maximum growth yield coefficient (Y x/s 0.288 g dcw/g butyrate) and fatty acid yield coefficient (Y f/s 0.206 g/g butyrate), compared to other organic acids (lactate, propionate, and acetate). Acetate, butyrate, and lactate mostly supported the production of fatty acids with an even number of carbons, whereas propionate enhanced the content of odd-numbered fatty acids. Response surface methodology (RSM) design study resulted in maximum biomass (2.8 g/L) and fatty acid yield (1.9 g/g) with acetate:butyrate:lactate (0.333:0.333:0.333) as a carbon source. Culture of Rhodococcus sp. YHY01 in media containing food waste-derived VFAs as the carbon source had a biomass (3.2 g dcw/L), fatty acid yield (2.2 g/L), and fatty acid accumulation (69% w/w) under nitrogen-limited condition. Biodiesel produced from food waste had an iodine value (IV, 37), cetane number (CN, 63), high heating value (HHV, 39), density (υ, 3.9), and viscosity (ρ, 0.868) that meet international standards. [ABSTRACT FROM AUTHOR]

Abstract A novel marine bacterium Arenibacter palladensis YHY2 isolated from Eastern Sea, South Korea revealed hydrolysing ability of crab chitin in shake flask and microbial fuel cell (MFC) systems. Under shake flask cultivation, strain YHY2 demonstrated 71.44 ± 1.90 U/ml chitinase activity with the microbial cell optical density (OD) 0.699 ± 0.021. High performance liquid chromatography (HPLC) results showed N-acetylglucosamine (GlcNAc) as the major by-product of chitin degradation. Furthermore, Ralstonia eutropha H16 which has carbon utilization limited to GlcNAc and fructose was co-cultivated with YHY2 to consume GlcNAc and accumulate polyhydroxyalkanoates (PHA). However, on co-cultivating strain YHY2 with H16 surprisingly showed higher production of chitinase (97.89 ± 2.72 U/ml) and GlcNAc (80.31 mg GlcNAc/g chitin) corresponding to the microbial cell OD (1.065 ± 0.005) at 120 h. In addition, marine strain YHY2 demonstrated biofilm formation, hence co-cultivation of strain YHY2 and H16 under MFC system was performed to check the electricity production. Maximum electricity current output density was 15.15 μA/cm2 at the initial stage and 10.72 μA/cm2 at 204 h. GlcNAc (196.34 mg GlcNAc/g chitin) was produced along with other metabolites like butyrate, acetate, lactate, and propionate in MFC system. The microbial cell biomass from MFC was analysed for PHA content showed 1.020 g/l of 3-polyhydroxybutyrate (PHB) and 0.198 g/l of 3-polyhydroxyvalerate (PHV) as the main components of PHA. Moreover, X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM) were performed to reveal changes in chitin before and after degradation. Thus, the exploitation of recalcitrant chitin biomass for simultaneous production of GlcNAc, electricity, and PHA in one-pot MFC system was the productive asset for sustainable development. Graphical abstract Image 1 Highlights • Coastal soil harbours Arenibacter palladensis YHY2 capable of hydrolysing chitin. • YHY2 produced electricity in MFC using chitin biomass as a sole source of carbon. • Co-cultivation of YHY2 with GlcNAc utilizing Ralstonia eutropha H16 accumulated PHA. • First report on one-pot bioconversion of chitin into electricity, GlcNAc and PHA. [ABSTRACT FROM AUTHOR]

With the continuous growth of the demand for eco-friendly alternatives to petroleum-based plastics, polyhydroxybutyrate (PHB) has emerged as a promising alternative because of its biodegradability. However, certain characteristics, such as its color, rigidity, and brittleness, have limited its range of applications. In this study, we investigated the in vivo coloring of PHB with indigo by combining the biosynthesis operons of PHB and indigo, which involved the use of tryptophan as the substrate for the biosynthesis of indigo. The heterologous and homologous tryptophanase genes converted tryptophan to indole, which was further oxidized to indoxyl by flavin monooxygenase (FMO), followed by spontaneous dimerization to indigo in the presence of oxygen. Different indigo-PHB films were obtained by controlling the concentration of tryptophan. Additionally, we investigated the mechanical properties of the indigo-PHB films using UTM analysis and found that their mechanical properties varied according to the amount of indigo incorporated into PHB. Notably, elongation at break in indigo-PHB film, which was produced using 10 mM of tryptophan resulting in a 1.1 mg indigo/g PHB content, significantly improved to 70 % compared to the 7.2 % observed in normal PHB films. Furthermore, indigo-PHB films were subjected to FE-SEM, GPC, and DSC analyses to identify differences, and it was observed that there was a decrease in T c and T g values, more obvious in T g value, in indigo PHB film with 1.1 mg indigo/g PHB content. Considering many approaches to improving PHB properties, our study showed the possibility of different changes in color and improved flexibility via the co-production of indigo and PHB. • We designed a system for the co-production of indigo and PHB using tryptophan as a substrate for indigo. • Different indigo-PHB films were obtained by adjusting the concentration of tryptophan. • Elongation at break in indigo PHB film with 1.1 mg indigo/g PHB significantly improved to 70% compared to the 7.2% observed in normal PHB films. • The existing issues with PHB, such as color, rigidity, and brittleness, could be addressed in indigo-PHB. • We expect that this approach can expand the use of PHAs in broader fields. [ABSTRACT FROM AUTHOR]

Ralstonia eutropha is a well-known microbe reported for polyhydroxyalkonate (PHA) production, and unable to utilize sucrose as carbon source. Two strains, Ralstonia eutropha H16 and Ralstonia eutropha 5119 were co-cultured with sucrose hydrolyzing microbes ( Bacillus subtilis and Bacillus amyloliquefaciens ) for PHA production . Co-culture of B. subtilis:R. eutropha 5119 (BS:RE5) resulted in best PHA production (45% w/w dcw). Optimization of the PHA production process components through response surface resulted in sucrose: NH 4 Cl: B. subtilis : R. eutropha (3.0:0.17:0.10:0.190). Along with the hydrolysis of sucrose, B. subtilis also ferments sugars into organic acid (propionic acid), which acts as a precursor for HV monomer unit. Microbial consortia of BS:RE5 when cultured in optimized media led to the production of poly(3-hydroxybutyrate- co -3-hydroxyvalerate) (P(3HB- co -3HV) with 66% w/w of dcw having 16 mol% HV fraction . This co-culture strategy overcomes the need for metabolic engineering of R. eutropha for sucrose utilization, and addition of precursor for copolymer production. [ABSTRACT FROM AUTHOR]

To reduce the furfural toxicity for biochemical production in E. coli , a new strategy was successfully applied by supplying NAD(P)H through the nicotine amide salvage pathway. To alleviate the toxicity, nicotinamide salvage pathway genes were overexpressed in recombinant, isobutanol-producing E. coli . Gene expression of pncB and nadE respectively showed increased tolerance to furfural among these pathways. The combined expression of pncB and nadE was the most effective in increasing the tolerance of the cells to toxic aldehydes. By comparing noxE - and fdh -harbouring strains, the form of NADH, rather than NAD + , was the major effector of furfural tolerance. Overall, this study is the application of the salvage pathway to isobutanol production in the presence of furfural, and this system seems to be applicable to alleviate furfural toxicity in the production of other biochemical. [ABSTRACT FROM AUTHOR]

Cadaverine, a five-carbon diamine (1,5-diaminopentane), can be made by fermentation or direct bioconversion and plays an important role as a building block of polyamides. Lysine decarboxylase (CadA) transforms L-lysine to cadaverine and pyridoxal 5′-phosphate (PLP) can increases conversion rate and yield as a cofactor. Biotransformation of cadaverine using whole Escherichia coli cells that overexpress the lysine decarboxylase has many merits, such as the rapid conversion of l -lysine to cadaverine, possible application of high concentration reactions up to the molar level, production of less byproduct and potential reuse of the enzyme by immobilization. However, the supply of PLP, which is a cofactor of lysine decarboxylase, is the major bottleneck in this system. Therefore, we initiated our study on PLP precursors and PLP-related enzymes and discovered that pyridoxal (PL) can be a viable alternative to supply PLP. Among various PLP systems examined, pyridoxal kinase (PdxY) showed the highest conversion of PL to PLP, resulting in more than 60% conversion of l -lysine to cadaverine with lysine decarboxylase. When the reaction with 0.4 M l -lysine, 0.2 mM PL and more whole cells was performed, it resulted in an 80% conversion yield. Furthermore, when barium-alginate immobilization was applied, it showed a 90% conversion yield in 1 h with PL, suggesting that it is compatible with developed whole-cell systems without a direct supply of exogenous PLP. [ABSTRACT FROM AUTHOR]

Biomass is normally processed using acidic or basic catalysts, which both have their drawbacks. One suitable alternative is the application of hydrolytic enzymes that can convert biomass into simpler molecules, which can be fermented and processed into biofuel. Hydrolytic enzymes include proteases, lipases, amylases, cellulases, mannanases, chitinases, and xylanases. To discover sources of these enzymes, 19 halophilic strains of microorganisms that are significantly resistant to high salt concentrations were analyzed. The objective of this research was to identify halophilic microorganisms that produce the target enzymes with high activities, and to characterize these enzymes according to their salt tolerances. The results obtained indicated that Pseudolateromonas phenolica, Micrococcus luteus, Pseudoalteromonas peptidolytica, Halomonas socia, Marinobacter maritimus, and Exiguobacterium aurantiacum strain 2 produced the highest protease, lipase, amylase, cellulase, mannanase, chitinase, and xylanase relative activities, respectively. Except for protease from P. phenolica, all the enzymes tested for salt resistance either maintained or increased their activities with increasing NaCl concentration. [ABSTRACT FROM AUTHOR]

The effect of various biomass derived inhibitors (i.e. furfural, hydroxymethylfurfural (HMF), vanillin, 4-hydroxy benzaldehyde (4-HB) and acetate) was investigated for fatty acid accumulation in Rhodococcus sp. YHY 01. Rhodococcus sp. YHY01 was able to utilize acetate, vanillin, and 4-HB for biomass production and fatty acid accumulation. The IC 50 value for furfural (3.1 mM), HMF (3.2 mM), vanillin (2.0 mM), 4-HB (2.7 mM) and acetate (3.7 mM) was calculated. HMF and vanillin affect fatty acid composition and increase saturated fatty acid content. Rhodococcus sp. YHY 01 cultured with empty fruit bunch hydrolysate (EFBH) as the main carbon source resulted in enhanced biomass (20%) and fatty acid productivity (37%), in compression to glucose as a carbon source. Overall, this study showed the beneficial effects of inhibitory molecules on growth and fatty acid production, and support the idea of biomass hydrolysate utilization for biodiesel production by avoiding complex efforts to remove inhibitory compounds. [ABSTRACT FROM AUTHOR]

Cytochrome P450 monooxygenases (CYP) are a superfamily of heme-thiolate proteins which catalyze the incorporation of oxygen atoms into substrates. Here, a self-sufficient CYP102A from Streptomyces cattleya (CYP102A_scat) was cloned, produced recombinantly in Escherichia coli strain BL21 (DE3), and the characteristic features were investigated. However, unlike other self-sufficient CYP102A enzymes that have been reported, CYP102A_scat was found to be able to catalyze intracellular hydroxylation of indole molecules with 3-C specific regioselectivity. Consequently, E. coli strains producing CYP102A_scat could synthesize approximately 1.0 g/L of indigo in LB media. Optimization of indigo synthesis was investigated through additional feeding of indole precursors such as glucose, l -tryptophan, and indole. Indigo production reached up to 3.8 ± 0.1 g/L by adding 20 μM of extracellular indole and 0.2 mM of l -tryptophan to the LB media. To our knowledge, this is a record and the highest yield achieved so far. [ABSTRACT FROM AUTHOR]

Arctic psychrotrophic bacterium Pseudomonas sp. PAMC 28620 was found to produce a distinctive medium-chain-length polyhydroxyalkanoate (MCL-PHA) copolymer when grown on structurally unrelated carbon sources including glycerol. The maximum MCL-PHA copolymer yield was obtained about 52.18 ± 4.12% from 7.95 ± 0.66 g/L of biomass at 144 h of fermentation when 3% glycerol was used as sole carbon and energy source during the laboratory-scale bioreactor process. Characterization of the copolymer was carried out using fourier transform infrared spectroscopy (FTIR), gas chromatography–mass spectrometry (GC–MS), proton ( 1 H) and carbon ( 13 C) nuclear magnetic resonance spectroscopy (NMR), gel permeation chromatography (GPC), differential scanning calorimeter (DSC) and thermo-gravimetric analysis (TGA). The copolymer produced by Pseudomonas sp. PAMC 28620 consisting of four PHA monomers and identified as 3-hydroxyoctanoate (3HO), 3-hydroxydecanoate (3HD), 3-hydroxydodecanoate (3HDD) and 3-hydroxytetradecanoate (3HTD). An average molecular weight of the copolymer was found approximately 30.244 kDa with polydispersity index (PDI) value of 2.05. Thermal analysis showed the produced MCL-PHA copolymer to be low-crystalline (43.73%) polymer with great thermal stability, having the thermal decomposition temperature of 230 °C–280 °C, endothermic melting temperature ( T m ) of 172.84 °C, glass transition ( T g ) temperature of 3.99 °C, and apparent melting enthalpy fusion (Δ H m ) about 63.85 J g −1 . [ABSTRACT FROM AUTHOR]

Biodiesel, an alternative to petroleum oil has gained significant attention from the research community because of its high energy content and good compatibility with existing engine systems. It can be produced from many different sources, such as animals, plants, and microbes. In this study, we demonstrated the overproduction of fatty acid methyl esters (FAMEs) using a synthetic consortium of manA mutant Streptomyces coelicolor with Ralstonia eutropha . The synthetic consortium of S. coelicolor Δ manA : R. eutropha produced 114 mg/L fatty acids, which is 124% higher than the amount produced using S. coelicolor alone. Overall, the fatty acids produced by the consortia S. coelicolor Δ manA : R. eutropha were composed of medium chain fatty acid (MCFA): long chain fatty acid (LCFA): very long chain fatty acid (VLCFA) in 8.75: 91.0: 0.25 proportion, and contained 75% saturated and 25% unsaturated fatty acids, which resulted in FAMEs with better cetane number (65) and oxidation stability (76 h) than the fatty acids produced by one strain alone. Nile red staining and subsequent fluorescence spectroscopy revealed S. coelicolor Δ manA as good candidate for triacylglycerol (TAG) accumulation. Phospholipid-derived fatty acids (PLFA) analysis of consortia shows that S. coelicolor Δ manA and R. eutropha synergistically support each other’s growth. The results suggest that the synthetic consortium provides an approach for biodiesel production along with improved quality. [ABSTRACT FROM AUTHOR]

The aberrant glycosylation profile on the surface of cancer cells has been recognized for its potential diagnostic value towards assessing tumor progression. In this study, we initially investigate N-glycan profiles on the surface of normal (HPDE) and cancerous (Capan-1, Panc-1, and MIA PaCa-2) pancreatic cell lines, which are from different sites of pancreatic tumor. The enzymatically deglycosylated total N-glycans are permethylated via a quantitative solid-phase method and then analyzed by using MALDI-TOF MS and MALDI-QIT-TOF MS. We demonstrate that the level of high-mannose type glycans is higher among Capan-1 cells—pancreatic cancer cells that have metastasized to the liver—than that observed among Panc-1 and MIA PaCa-2 cells—pancreatic cancer cells from the pancreas duct head and tail regions, respectively. Furthermore, the relative abundance of highly-branched sialyted N-glycans is significantly up-regulated on Panc-1 and MIA PaCa-2 pancreatic cancer cells compared to that of normal HPDE pancreas cells. Taken together, these results indicate that specific N-glycosylation profile changes in pancreatic cancer cells can be used to not only distinguish between normal and cancerous cells but also provide more information on their location and metastatic potential. [ABSTRACT FROM AUTHOR]

Aliphatic diamines have been used as chemical reagents for the monomers of polyamides ( i.e. , Nylon 46, Nylon 510, Nylon 66, Nylon 610 and so on), and can be made from lysine, arginine or ornithine by the metabolism of microbes through decarboxylases. However, the conventional derivatization methods for the HPLC-based quantitative analysis of aliphatic diamines exhibit poor sensitivity and efficiency for the monitoring of enzyme activity. In this study, a chemical derivatization method using diethyl ethoxymethylenemalonate (DEEMM) was applied to monitor lysine decarboxylase activity for the production of cadaverine by measuring the levels of intracellular and secreted lysine and cadaverine. The calibration graphs for the determination of 2,4-diaminobutyrate, 2,6-diaminopimelic acid, ornithine, arginine, lysine, 1,3-diaminopropane, putrescine dihydrochloride, cadaverine, hexamethylenediamine, and 1,7-diaminoheptane were measured by the highly sensitive method using DEEMM, and a linear relationship was observed for each dimaine compound, with limits of detection up to 0.001 mM. Application of this method will be useful for the sensitive monitoring of lysine decarboxylase reactions through the detection of substrates containing amine groups and products with diamines using HPLC and a UV detector. [ABSTRACT FROM AUTHOR]

Glycan immobilization and epitope recognition on a solid support is useful for functional glycoproteomics and analysis of protein-protein interactions. However, the lack of high-throughput experimental methods for the examination of cell-glycan interactions means that identifying glycan-binding cells remains a challenge. Herein, we describe a tool which enables the screening of glycanbinding cells that specifically recognize the glycan epitopes released from the membrane glycoproteins of cells and tissues. Biotinylated pig kidney N-glycans were immobilized on streptavidin-conjugated solid supports and then incubated with human immune cell lines. U937 cells discriminated between the α-galactose (α-Gal) and non-Gal pig N-glycans on the solid support. This screening strategy could aid exploration of cell-protein or cell-cell interactions. [ABSTRACT FROM AUTHOR]

To increase algal growth in treated livestock waste water, we designed a culture system targeting symbiotic bacteria. Microbacterium sp. HJ1 is a symbiotic bacteria associated with Chlorella vulgaris , which was found to increase the growth rate when controlled by nitrogen addition. The validated analysis model for nitrogen source mixture was used to analyze the growth and final pH of Microbacterium sp. HJ1, in different compositions of nitrogen sources, by elucidating the functions of each nitrogen ions such as NO 3 − , NO 2 − , and NH 4 + . By modifying the growth medium made from treated livestock waste water with additional nitrogen source, we were able to increase dry cell weight (DCW) of C. vulgaris by 65.7% and chlorophyll a contents by 78.8%. This is an example of an indirect method to increase algal biomass by changing the population of symbiotic bacteria, and it is the practical application of positive effects from symbiotic bacteria to the host. [ABSTRACT FROM AUTHOR]

[Display omitted] • Sphingobium yanoikuyae BBL01 has the capacity to produce biopolymer. • Plant biomass pretreatment resulted in biosugar and side products. • Side products affect carbon source utilization, growth, EPS, and PHA production. • Low C/N ratio promotes EPS production while high C/N favors PHA accumulation. • Biochar detoxified pine hydrolysate coproduce EPS (2.83 g/L) and PHA (40.8 %). Sphingobium yanoikuyae BBL01 can produce exopolysaccharides (EPS) and polyhydroxyalkanoates (PHAs). The effect of side products (furfural, hydroxymethylfurfural (HMF), vanillin, and acetate) produced during pretreatment of biomass was evaluated on S. yanoikuyae BBL01. It was observed that a certain concentration range (0.01–0.03 %) of these compounds can improve growth, EPS production, and polyhydroxybutyrate (PHB) accumulation. The addition of HMF increases glucose and xylose utilization while other side products have a negative effect. The C/N of 5 favors EPS production (3.24 ± 0.05 g/L), while a higher C/N ratio of 30 promotes PHB accumulation (38.7 ± 0.08 % w/w), when commercial sugar is used as a carbon source. Pine biomass-derived biochar was able to remove 40 ± 2.1 % of total phenolic. Various biomass hydrolysates were evaluated and the use of detoxified pine biomass hydrolysate (DPH) as a carbon source resulted in the higher coproduction of EPS (2.83 ± 0.03 g/L) and PHB (40.8 ± 2.4 % w/w). [ABSTRACT FROM AUTHOR]

We established a 'seize-and-release' purification method to eliminate polyhexose contaminants for a highly sensitive glycan profiling. Pig liver membrane lysates were pretreated with sodium dodecyl sulfate (SDS) surfactant and subsequently dialyzed to remove polyhexose contaminants. From the purified membrane glycoproteins, glycans were released and identified by mass spectrometry. As a result, we clearly obtained N- and O-glycan profiles of a pig liver, which were not achieved without any pre-treatments. This technique demonstrates a powerful approach for enhancing the sensitivity of MS-based glycan profiling. [ABSTRACT FROM AUTHOR]

Abstract: To identify more effective but less toxic compositions of organic solvent mixtures for biodiesel production from Chlorella vulgaris, 15 different organic solvents were examined and compared for their power of lipid extraction from algal biomass. When solvents were individually examined, methanol showed the best efficiency for the extraction of fatty acids, followed by dichloromethane. Although chloroform resulted in yields which were equal to or greater than those of other solvents, it showed a very low fatty acid content and a high level of unknown impurities when analyzed by gas-chromatography (GC). Furthermore, solvent mixtures were applied in order to determine the optimal composition for a high lipid extraction efficiency, using chloroform, methanol and dichloromethane. Through comparison of compositions using the Bligh and Dyers method, the best composition was to be methanol:dichloromethane (1:1). Our findings resulted in a 25% increase of lipid extraction yield, together with C16, C16:2, C18:2 as major components from C. vulgaris. [Copyright &y& Elsevier]

Abstract: In the process of evaluating the growth of Streptomyces coelicolor on rich media such as blood agar, we found that S. coelicolor a non-pathogenic, well-known antibiotic producer had the ability to grow and produce a prominent hemolytic zone. By comparing the growth with an agarase gene mutant of S. coelicolor, a similar prominent hemolytic zone was found to develop due to the organism's hemolytic activity. After the confirmation of hemolytic activity from S. coelicolor, the genome was searched for hemolysin-coding genes; consequently, SCO1782, SCO2534, and SCO3882 were identified, whose products were annotated as a putative, membrane, and hypothetical proteins, respectively. Functional characterization of all the recombinant proteins expressed in Escherichia coli BL21(DE3) revealed that only SCO1782 exhibited hemolytic activity. This S. coelicolor protein, designated as S-hemolysin, showed sequence similarity toward hemolysins from Brachyspira hyodysenteriae (35%) and Mycobacterium tuberculosis (62%). Recombinant hemolysin exhibited activity against sheep blood erythrocytes and cytolytic activity against human fibroblast cells. Deletion of SCO1782 resulted in complete loss of hemolysin activity in S. coelicolor. [Copyright &y& Elsevier]

Several reports state that three architectural units, including integration host factor, leucyl aminopeptidase (PepA), and purine regulator, are involved in transcriptional process with RNA polymerase in Escherichia coli. Similarly, Streptomyces species possess the same structural units. We previously identified a protein, Streptomyces integration host factor (sIHF), involved in antibiotic production and sporulation. Subsequently, the function of PepA (SCO2179) was examined in detail. PepA is highly conserved among various Streptomyces spp., but it has not yet been characterized in Streptomyces coelicolor. While it is annotated as a putative leucyl aminopeptidase because it contains a peptidase M17 superfamily domain, this protein did not exhibit leucyl aminopeptidase activity. SCO2179 deletion mutant showed increased actinorhodin production and sporulation, as well as more distinct physiological differences, particularly when cultured on N-acetylglucosamine (GlcNAc) minimal media. The results of two-dimensional gel analysis and reverse transcription PCR showed that the SCO2179 deletion increased protein and mRNA levels of ftsZ, ssgA, and actinorhodin (ACT)-related genes such as actII- ORF4, resulting in increased actinorhodin production and spore formation in minimal media containing GlcNAc. [ABSTRACT FROM AUTHOR]

γ-Butyrolactones in Streptomyces are well recognized as bacterial hormones, and they affect secondary metabolism of Streptomyces. γ-Butyrolactone receptors are considered important regulatory proteins, and various γ-butyrolactone synthases and receptors have been reported in Streptomyces. Here, we characterized a new regulator, SCO0608, that interacted with SCB1 (γ-butyrolactone of Streptomyces coelicolor) and bound to the scbR/A and adpA promoters. The SCO0608 protein sequences are not similar to those of any known γ-butyrolactone binding proteins in Streptomyces such as ScbR from S. coelicolor or ArpA from Streptomyces griseus. Interestingly, SCO0608 functions as a repressor of antibiotic biosynthesis and spore formation in R5 complex media. We showed the existence of another type of γ-butyrolactone receptor in Streptomyces, and this SCO0608 was named ScbR-like γ-butyrolactone binding regulator (SlbR) in S. coelicolor. [ABSTRACT FROM AUTHOR]

Abstract: This study presents a microfluidic approach for the rapid analysis of bacterial chemotaxis in response to chemical gradients. The diffusional mixing of laminar flow continuously generates a stable chemical gradient in a microfluidic device. For the proof of concept, we have investigated the effects of the attractant peptone and repellent trichloroethylene (TCE) on chemotactic responses of wild type Pseudomonas aeruginosa PAO1 and chemotactic mutant PC4. The microfluidic method clearly demonstrates that P. aeruginosa PAO1 is attracted to peptone and repelled from TCE, whereas PC4 shows non-chemotactic behavior. In addition, the analysis of PAO1 chemotaxis on 20 amino acids revealed the effective concentration range of each amino acid as a chemoeffector. Not only does the microfluidic approach facilitate the quantitative information of chemotaxis, which gives an insight into understanding the mechanism of P. aeruginosa motility, but it also provides a useful tool for the rapid monitoring of bacterial chemotaxis in a reproducible experimental manner. [ABSTRACT FROM AUTHOR]

Abstract: We present a robust, fully automatable technology platform that includes computer software for the detailed analysis of low femtomoles of N-linked sugars released from glycoproteins. Features include (i) sample immobilization in 96-well plates, glycan release, and fluorescent labeling; (ii) quantitative HPLC analysis, including monosaccharide sequence, linkage, and arm-specific information for charged and neutral glycans; (iii) automatic structural assignment of peaks from HPLC profiles via web-based software that accesses our database (GlycoBase) of more than 350 N-glycan structures, including 117 present in the human serum glycome; and (iv) software (autoGU) that progressively analyzes data from exoglycosidase digestions to produce a refined list of final structures. The N-glycans from a plate of 96 samples can be released and purified in 2 or 3 days and profiled in 2 days. This strategy can be used for (i) identification and screening of disease biomarkers and (ii) monitoring the production of therapeutic glycoproteins, allowing optimization of production conditions. This technology is also suitable for preparing released glycans for other analytical techniques. Here we demonstrate its application to rheumatoid arthritis using 5 μl of patient serum. [Copyright &y& Elsevier]

Abstract: For the rapid identification of functional activity of unknown genes from a sequence database, a new method based on in vitro protein synthesis combined with mass spectrometry was developed. To discriminate their subtle enzymatic activity, in vitro synthesized and one-step purified lipolytic enzymes, such as lipA and lipB from Bacillus subtilis and an unknown protein ybfF from Escherichia coli, were reacted with a mixture of triglycerides with different carbon chain lengths. Using direct matrix-assisted laser desorption/ionization mass spectrometry (MALDI–MS) analysis of reaction product, all three enzymes were revealed to have strong esterase activity rather than true lipase activity, which has no reactivity on long-chain fatty acids such as triolein. These results were also confirmed by classical color assay using p-nitrophenyl butyrate (pNPB) and p-nitrophenyl palmitate (pNPP) as representative lipolytic substrates. [Copyright &y& Elsevier]

We have successfully produced a recombinant human matrix metalloproteinase 9 (hMMP9) antigen with high yield and purity and used it to generate a hybridoma cell-culture-based monoclonal anti-hMMP9 antibody. We selected the most effective antibody for binding antigens and successfully identified its nucleotide sequence. The entire antigen and antibody developmental procedures described herein can be a practical approach for producing large amounts of monoclonal antibodies against hMMP9 and other antigens of interest. Additionally, the nucleotide sequence information of the anti-hMMP9 monoclonal antibody revealed herein will be useful for the generation of recombinant antibodies or antibody fragments against hMMP9. ● A soluble recombinant hMMP9 was produced with high yield and purity. ● Hybridoma cell-culture-based monoclonal anti-hMMP9 antibodies were generated. ● Most effective monoclonal antibody for binding antigen was selected and its nucleotide sequence was identified. [ABSTRACT FROM AUTHOR]

• Sphingobium yanoikuyae BBL01 was isolated from marine habitat. • Strain able to produce a heteropolysaccharides i.e., 2.63 ± 0.02 g/L EPS. • Exopolysaccharide was composed of seven different monosaccharides units. • Exopolysaccharide was thermally stable up to 233 °C. • EPS showed emulsifying, flocculating, and metal chelating activity. In the present study , an exopolysaccharide (EPS)-producing bacterial strain was isolated from the Eastern Sea (Sokcho Beach) of South Korea and identified as Sphingobium yanoikuyae BBL01. Media optimization was performed using response surface design, and a yield of 2.63 ± 0.02 g/L EPS was achieved. Purified EPS produced using lactose as the main carbon source was analyzed by GC–MS and found to be composed of α-D-xylopyranose (28.6 ± 2.0%), β-D-glucopyranose (21.0 ± 1.6%), α-D-mannopyranose (18.5 ± 1.2%), β- d -mannopyranose (13.1 ± 1.4%), β-D-xylopyranose (10.2 ± 2.1%), α- d -talopyranose (5.9 ± 1.1%), and β- d -galacturonic acid (2.43 ± 0.8%). Interestingly, different carbon sources (glucose, galactose, glycerol, lactose, sucrose, and xylose) showed no effect on EPS monomer composition, with a slight change in the mass percentage of various monosaccharides. Purified EPS was stable up to 233 °C, indicating its possible suitability as a thickening and gelling agent for food-related applications. EPS also showed considerable emulsifying, flocculating, free-radical scavenging, and metal-complexion activity, suggesting various biotechnological applications. [ABSTRACT FROM AUTHOR]

• Lignocellulose is an abundantly available recalcitrant raw material. • Pretreatment is required to convert it into free sugars. • Pretreatment generates various byproducts having negative effects on microbes. • Hydrolysate requires detoxification before being subjected to fermentation. Lignocellulosic biomass is an inexpensive renewable source that can be used to produce biofuels and bioproducts. The recalcitrance nature of biomass hampers polysaccharide accessibility for enzymes and microbes. Several pretreatment methods have been developed for the conversion of lignocellulosic biomass into value-added products. However, these pretreatment methods also produce a wide range of secondary compounds, which are inhibitory to enzymes and microorganisms. The selection of an effective and efficient pretreatment method discussed in the review and its process optimization can significantly reduce the production of inhibitory compounds and may lead to enhanced production of fermentable sugars and biochemicals. Moreover, evolutionary and genetic engineering approaches are being used for the improvement of microbial tolerance towards inhibitors. Advancements in pretreatment and detoxification technologies may help to increase the productivity of lignocellulose-based biorefinery. In this review, we discuss the recent advancements in lignocellulosic biomass pretreatment technologies and strategies for the removal of inhibitors. [ABSTRACT FROM AUTHOR]

Incessant depletion of non-renewable energy sources has gained attention to search for new biological systems to transform organic biomass into electricity using microbial fuel cell (MFC). The main approach of the existing study was to develop a single step process to produce electrical energy from underutilized chitin biomass. Halophilic bacterium Bacillus circulans BBL03 isolated from anodic biofilm showed higher electricity production (26.508 μAcm2) in a natural seawater medium fed with 1.0% chitin. Maximum chitinase activity (94.24 ± 4.2 U mL−1) and N -acetylglucosamine (GlcNAc) production (136.30 ± 2.8 mg g−1 chitin) were achieved at 48 h. Prominent metabolites detected in chitin hydrolysis were lactate, formate, acetate, propionate, and butyrate. Furthermore, cyclic voltammetry (CV) studies revealed the possibility of direct electron transfer by anodic biofilm to anode without any external redox mediators. Polarization and coulombic efficiency (CE) analysis showed maximum power density (P D) 1.742 mWcm2 and 47% CE using 1% chitin as a substrate. Alteration in crystallinity and functional group on chitin were analysed using FTIR and XRD. Therefore, natural seawater-chitin powered MFCs could be a cheap asset for longer electricity production. Unlabelled Image • Electroactive Bacillus circulans BBL03 was isolated from sea salt harvesting area. • BBL03 produced electricity in natural seawater using 1% chitin as a carbon source • GlcNAc and intermediate metabolites of degradation acted as electron donors in MFC. • Cost-effective asset for longer electricity production in a single step process. [ABSTRACT FROM AUTHOR]

Engineered human cardiac tissues have been utilized for various biomedical applications, including drug testing, disease modeling, and regenerative medicine. However, the applications of cardiac tissues derived from human pluripotent stem cells are often limited due to their immaturity and lack of functionality. Therefore, in this study, we establish a perfusable culture system based on in vivo-like heart microenvironments to improve human cardiac tissue fabrication. The integrated culture platform of a microfluidic chip and a three-dimensional heart extracellular matrix enhances human cardiac tissue development and their structural and functional maturation. These tissues are comprised of cardiovascular lineage cells, including cardiomyocytes and cardiac fibroblasts derived from human induced pluripotent stem cells, as well as vascular endothelial cells. The resultant macroscale human cardiac tissues exhibit improved efficacy in drug testing (small molecules with various levels of arrhythmia risk), disease modeling (Long QT Syndrome and cardiac fibrosis), and regenerative therapy (myocardial infarction treatment). Therefore, our culture system can serve as a highly effective tissue-engineering platform to provide human cardiac tissues for versatile biomedical applications., (© 2024. The Author(s).)

Butyrate-producing bacteria play a key role in human health, and recent studies have triggered interest in their development as next-generation probiotics. However, there remains limited knowledge not only on the identification of high-butyrate-producing bacteria in the human gut but also in the metabolic capacities for prebiotic carbohydrates and their interaction with the host. Herein, it was discovered that Roseburia intestinalis produces higher levels of butyrate and digests a wider variety of prebiotic polysaccharide structures compared with other human major butyrate-producing bacteria (Eubacterium rectale, Faecalibacterium prausnitzii, and Roseburia hominis). Moreover, R. intestinalis extracts upregulated the mRNA expression of tight junction proteins (TJP1, OCLN, and CLDN3) in human intestinal epithelial cells more than other butyrate-producing bacteria. R. intestinalis was cultured with human intestinal epithelial cells in the mimetic intestinal host-microbe interaction coculture system to explore the health-promoting effects using multiomics approaches. Consequently, it was discovered that live R. intestinalis only enhances purine metabolism and the oxidative pathway, increasing adenosine triphosphate levels in human intestinal epithelial cells, but that heat-killed bacteria had no effect. Therefore, this study proposes that R. intestinalis has potentially high value as a next-generation probiotic to promote host intestinal health., (© 2023 Wiley-VCH GmbH.)

Antibiotic-induced gut microbiota disruption constitutes a major risk factor for Clostridioides difficile infection (CDI). Further, antibiotic therapy, which is the standard treatment option for CDI, exacerbates gut microbiota imbalance, thereby causing high recurrent CDI incidence. Consequently, probiotic-based CDI treatment has emerged as a long-term management and preventive option. However, the mechanisms underlying the therapeutic effects of probiotics for CDI remain uninvestigated, thereby creating a knowledge gap that needs to be addressed. To fill this gap, we used a multiomics approach to holistically investigate the mechanisms underlying the therapeutic effects of probiotics for CDI at a molecular level. We first screened Bifidobacterium longum owing to its inhibitory effect on C. difficile growth, then observed the physiological changes associated with the inhibition of C. difficile growth and toxin production via a multiomics approach. Regarding the mechanism underlying C. difficile growth inhibition, we detected a decrease in intracellular adenosine triphosphate (ATP) synthesis due to B. longum -produced lactate and a subsequent decrease in (deoxy)ribonucleoside triphosphate synthesis. Via the differential regulation of proteins involved in translation and protein quality control, we identified B. longum -induced proteinaceous stress. Finally, we found that B. longum suppressed the toxin production of C. difficile by replenishing proline consumed by it. Overall, the findings of the present study expand our understanding of the mechanisms by which probiotics inhibit C. difficile growth and contribute to the development of live biotherapeutic products based on molecular mechanisms for treating CDI., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Jo, Jeon, Song, Lee, Kwon, Park, Kim, Kim, Baek, Kwon, Kim, Yang and Kim.)

Objectives: S100A8 is highly expressed in several inflammatory and oncological conditions. To address the current lack of a reliable and sensitive detection method for S100A8, we generated a monoclonal antibody with a high binding affinity to human S100A8 to enable early disease diagnosis., Results: A soluble recombinant S100A8 protein with a high yield and purity was produced using Escherichia coli. Next, mice were immunized with recombinant S100A8 to obtain anti-human S100A8 monoclonal antibodies using hybridoma technology. Lastly, the high binding activity of the antibody was confirmed and its sequence was identified., Conclusions: This method, including the production of antigens and antibodies, will be useful for the generation of hybridoma cell lines that produce anti-S100A8 monoclonal antibodies. Moreover, the sequence information of the antibody can be used to develop a recombinant antibody for use in various research and clinical applications., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)

Direct cardiac reprogramming has emerged as a promising therapeutic approach for cardiac regeneration. Full chemical reprogramming with small molecules to generate cardiomyocytes may be more amenable than genetic reprogramming for clinical applications as it avoids safety concerns associated with genetic manipulations. However, challenges remain regarding low conversion efficiency and incomplete cardiomyocyte maturation. Furthermore, the therapeutic potential of chemically induced cardiomyocytes (CiCMs) has not been investigated. Here, we report that a three-dimensional microenvironment reconstituted with decellularized heart extracellular matrix can enhance chemical reprogramming and cardiac maturation of fibroblasts to cardiomyocytes. The resultant CiCMs exhibit elevated cardiac marker expression, sarcomeric organization, and improved electrophysiological features and drug responses. We investigated the therapeutic potential of CiCMs reprogrammed in three-dimensional heart extracellular matrix in a rat model of myocardial infarction. Our platform can facilitate the use of CiCMs for regenerative medicine, disease modeling, and drug screening.

Methicillin-resistant Staphylococcus aureus (MRSA), one of the most well-known human pathogens, houses many virulence factors and regulatory proteins that confer resistance to diverse antibiotics. Although they have been investigated intensively, the correlations among virulence factors, regulatory proteins and antibiotic resistance are still elusive. We aimed to identify the most significant global MRSA regulator by concurrently analyzing protein-binding and several promoters under same conditions and at the same time point. DNA affinity capture assay (DACA) was performed with the promoters of mecA , sarA , and sarR , all of which significantly impact survival of MRSA. Here, we show that SarA protein binds to all three promoters. Consistent with the previous reports, ΔsarA mutant exhibited weakened antibiotic resistance to oxacillin and reduced biofilm formation. Additionally, production and activity of many virulence factors such as phenol-soluble modulins (PSM), α-hemolysin, motility, staphyloxanthin, and other related proteins were decreased. Comparing the sequence of SarA with that of clinical strains of various lineages showed that all sequences were highly conserved, in contrast to that observed for AgrA, another major regulator of virulence and resistance in MRSA. We have demonstrated that SarA regulates antibiotic resistance and the expression of various virulence factors. Our results warrant that SarA could be a leading target for developing therapeutic agents against MRSA infections.

Polyhydroxybutyrate (PHB) is a bio-based, biodegradable and biocompatible plastic that has the potential to replace petroleum-based plastics. Lignocellulosic biomass is a promising feedstock for industrial fermentation to produce bioproducts such as polyhydroxybutyrate (PHB). However, the pretreatment processes of lignocellulosic biomass lead to the generation of toxic byproducts, such as furfural, 5-HMF, vanillin, and acetate, which affect microbial growth and productivity. In this study, to reduce furfural toxicity during PHB production from lignocellulosic hydrolysates, we genetically engineered Cupriavidus necator NCIMB 11599, by inserting the nicotine amide salvage pathway genes pncB and nadE to increase the NAD(P)H pool. We found that the expression of pncB was the most effective in improving tolerance to inhibitors, cell growth, PHB production and sugar consumption rate. In addition, the engineered strain harboring pncB showed higher PHB production using lignocellulosic hydrolysates than the wild-type strain. Therefore, the application of NAD salvage pathway genes improves the tolerance of Cupriavidus necator to lignocellulosic-derived inhibitors and should be used to optimize PHB production., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Clostridioides difficile is a gram-positive anaerobic bacterium that causes antibiotic-associated infections in the gut. C. difficile infection develops in the intestine of a host with an imbalance of the intestinal microbiota and, in severe cases, can lead to toxic megacolon, intestinal perforation, and even death. Despite its severity and importance, however, the lack of a model to understand host-pathogen interactions and the lack of research results on host cell effects and response mechanisms under C. difficile infection remain limited. Here, we developed an in vitro anaerobic-aerobic C. difficile infection model that enables direct interaction between human gut epithelial cells and C. difficile through the Mimetic Intestinal Host-Microbe Interaction Coculture System. Additionally, an integrative multiomics approach was applied to investigate the biological changes and response mechanisms of host cells caused by C. difficile in the early stage of infection. The C. difficile infection model was validated through the induction of disaggregation of the actin filaments and disruption of the intestinal epithelial barrier as the toxin-mediated phenotypes following infection progression. In addition, an upregulation of stress-induced chaperones and an increase in the ubiquitin proteasomal pathway were identified in response to protein stress that occurred in the early stage of infection, and downregulation of proteins contained in the electron transfer chain and ATP synthase was observed. It has been demonstrated that host cell energy metabolism is inhibited through the glycolysis of Caco-2 cells and the reduction of metabolites belonging to the TCA cycle. Taken together, our C. difficile infection model suggests a new biological response pathway in the host cell induced by C. difficile during the early stage of infection at the molecular level under anaerobic-aerobic conditions. Therefore, this study has the potential to be applied to the development of future therapeutics through basic metabolic studies of C. difficile infection., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Kwon, Jo, Song, Lee, Jeon, Park, Kim, Baek, Kim, Kwon, Kim, Yang and Kim.)

Methicillin-resistant Staphylococcus aureus (MRSA) is a pathogenic bacterium that causes severe diseases in humans. For decades, MRSA has acquired substantial resistance against conventional antibiotics through regulatory adaptation, thereby posing a challenge for treating MRSA infection. One of the emerging strategies to combat MRSA is the combinatory use of antibacterial agents. Based on the dramatic change in phospholipid fatty acid (PLFA) composition of MRSA in previous results, this study investigated branched-chain amino acid derivatives (precursors of fatty acid synthesis of cell membrane) and discovered the antimicrobial potency of D-norvaline. The compound, which can act synergistically with oxacillin, is among the three leucine-tRNA synthetase inhibitors with high potency to inhibit MRSA cell growth and biofilm formation. PLFA analysis and membrane properties revealed that D-norvaline decreased the overall amount of PLFA, increasing the fluidity and decreasing the hydrophobicity of the bacterial cell membrane. Additionally, we observed genetic differences to explore the response to D-norvaline. Furthermore, deletion mutants and clinically isolated MRSA strains were treated with D-norvaline. The study revealed that D-norvaline, with low concentrations of oxacillin, was effective in killing several MRSA strains. In summary, our findings provide a new combination of aminoacyl-tRNA synthetase inhibitor D-norvaline and oxacillin, which is effective against MRSA.

Matrigel, a mouse tumor extracellular matrix protein mixture, is an indispensable component of most organoid tissue culture. However, it has limited the utility of organoids for drug development and regenerative medicine due to its tumor-derived origin, batch-to-batch variation, high cost, and safety issues. Here, we demonstrate that gastrointestinal tissue-derived extracellular matrix hydrogels are suitable substitutes for Matrigel in gastrointestinal organoid culture. We found that the development and function of gastric or intestinal organoids grown in tissue extracellular matrix hydrogels are comparable or often superior to those in Matrigel. In addition, gastrointestinal extracellular matrix hydrogels enabled long-term subculture and transplantation of organoids by providing gastrointestinal tissue-mimetic microenvironments. Tissue-specific and age-related extracellular matrix profiles that affect organoid development were also elucidated through proteomic analysis. Together, our results suggest that extracellular matrix hydrogels derived from decellularized gastrointestinal tissues are effective alternatives to the current gold standard, Matrigel, and produce organoids suitable for gastrointestinal disease modeling, drug development, and tissue regeneration., (© 2022. The Author(s).)

Ever since bioplastics were globally introduced to a wide range of industries, the disposal of used products made with bioplastics has become an issue inseparable from their application. Unlike petroleum-based plastics, bioplastics can be completely decomposed into water and carbon dioxide by microorganisms in a relatively short time, which is an advantage. However, there is little information on the specific degraders and accelerating factors for biodegradation. To elucidate a new strain for biodegrading poly-3-hydroxybutyrate (PHB), we screened out one PHB-degrading bacterium, Microbulbifer sp. SOL03, which is the first reported strain from the Microbulbifer genus to show PHB degradation activity, although Microbulbifer species are known to be complex carbohydrate degraders found in high-salt environments. In this study, we evaluated its biodegradability using solid- and liquid-based methods in addition to examining the changes in physical properties throughout the biodegradation process. Furthermore, we established the optimal conditions for biodegradation with respect to temperature, salt concentration, and additional carbon and nitrogen sources; accordingly, a temperature of 37°C with the addition of 3% NaCl without additional carbon sources, was determined to be optimal. In summary, we found that Microbulbifer sp. SOL03 showed a PHB degradation yield of almost 97% after 10 days. To the best of our knowledge, this is the first study to investigate the potent bioplastic degradation activity of Microbulbifer sp., and we believe that it can contribute to the development of bioplastics from application to disposal.

Faecalibacterium prausnitzii , a major commensal bacterium in the human gut, is well known for its anti-inflammatory effects, which improve host intestinal health. Although several studies have reported that inulin, a well-known prebiotic, increases the abundance of F. prausnitzii in the intestine, the mechanism underlying this effect remains unclear. In this study, we applied liquid chromatography tandem mass spectrometry (LC-MS/MS)-based multiomics approaches to identify biological and enzymatic mechanisms of F. prausnitzii involved in the selective digestion of inulin. First, to determine the preference for dietary carbohydrates, we compared the growth of F. prausnitzii in several carbon sources and observed selective growth in inulin. In addition, an LC-MS/MS-based intracellular proteomic and metabolic profiling was performed to determine the quantitative changes in specific proteins and metabolites of F. prausnitzii when grown on inulin. Interestingly, proteomic analysis revealed that the putative proteins involved in inulin-type fructan utilization by F. prausnitzii , particularly β-fructosidase and amylosucrase were upregulated in the presence of inulin. To investigate the function of these proteins, we overexpressed bfrA and ams, genes encoding β-fructosidase and amylosucrase, respectively, in Escherichia coli, and observed their ability to degrade fructan. In addition, the enzyme activity assay demonstrated that intracellular fructan hydrolases degrade the inulin-type fructans taken up by fructan ATP-binding cassette transporters. Furthermore, we showed that the fructose uptake activity of F. prausnitzii was enhanced by the fructose phosphotransferase system transporter when inulin was used as a carbon source. Intracellular metabolomic analysis indicated that F. prausnitzii could use fructose, the product of inulin-type fructan degradation, as an energy source for inulin utilization. Taken together, this study provided molecular insights regarding the metabolism of F. prauznitzii for inulin, which stimulates the growth and activity of the beneficial bacterium in the intestine., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Park, Song, Lee, Jo, Lee, Jeon, Kwon, Kim, Baek, Kim, Yang, Kim and Kim.)

Community-associated Methicillin-Resistant Staphylococcus aureus (CA-MRSA) is notorious as a leading cause of soft tissue infections. Despite several studies on the Agr regulator, the mechanisms of action of Agr on the virulence factors in different strains are still unknown. To reveal the role of Agr in different CA-MRSA, we investigated the LACΔ agr mutant and the MW2Δ agr mutant by comparing LAC (USA300), MW2 (USA400), and Δ agr mutants. The changes of Δ agr mutants in sensitivity to oxacillin and several virulence factors such as biofilm formation, pigmentation, motility, and membrane properties were monitored. LACΔ agr and MW2Δ agr mutants showed different oxacillin sensitivity and biofilm formation compared to the LAC and MW2 strains. Regardless of the strain, the motility was reduced in Δ agr mutants. And there was an increase in the long chain fatty acid in phospholipid fatty acid composition of Δ agr mutants. Other properties such as biofilm formation, pigmentation, motility, and membrane properties were different in both Δ agr mutants. The Agr regulator may have a common role like the control of motility and straindependent roles such as antibiotic resistance, biofilm formation, change of membrane, and pigment production. It does not seem easy to control all MRSA by targeting the Agr regulator only as it showed strain-dependent behaviors.

Brain organoids derived from human pluripotent stem cells provide a highly valuable in vitro model to recapitulate human brain development and neurological diseases. However, the current systems for brain organoid culture require further improvement for the reliable production of high-quality organoids. Here, we demonstrate two engineering elements to improve human brain organoid culture, (1) a human brain extracellular matrix to provide brain-specific cues and (2) a microfluidic device with periodic flow to improve the survival and reduce the variability of organoids. A three-dimensional culture modified with brain extracellular matrix significantly enhanced neurogenesis in developing brain organoids from human induced pluripotent stem cells. Cortical layer development, volumetric augmentation, and electrophysiological function of human brain organoids were further improved in a reproducible manner by dynamic culture in microfluidic chamber devices. Our engineering concept of reconstituting brain-mimetic microenvironments facilitates the development of a reliable culture platform for brain organoids, enabling effective modeling and drug development for human brain diseases., (© 2021. The Author(s).)

Tyrian purple, mainly composed of 6,6'-dibromoindigo (6BrIG), is an ancient dye extracted from sea snails and was recently demonstrated as a biocompatible semiconductor material. However, its synthesis remains limited due to uncharacterized biosynthetic pathways and the difficulty of regiospecific bromination. Here, we introduce an effective 6BrIG production strategy in Escherichia coli using tryptophan 6-halogenase SttH, tryptophanase TnaA and flavin-containing monooxygenase MaFMO. Since tryptophan halogenases are expressed in highly insoluble forms in E. coli, a flavin reductase (Fre) that regenerates FADH 2 for the halogenase reaction was used as an N-terminal soluble tag of SttH. A consecutive two-cell reaction system was designed to overproduce regiospecifically brominated precursors of 6BrIG by spatiotemporal separation of bromination and bromotryptophan degradation. These approaches led to 315.0 mg l -1 6BrIG production from tryptophan and successful synthesis of regiospecifically dihalogenated indigos. Furthermore, it was demonstrated that 6BrIG overproducing cells can be directly used as a bacterial dye.