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The synthesis of carbocyclic-ddA, a potent antiviral agent against hepatitis B, relies significantly on (1 R ,3 R)-3-hydroxycyclopentanemethanol as a key intermediate. To effectively produce this intermediate, our study employed a chemoenzymatic approach. The selection of appropriate biocatalysts was based on substrate similarity, leading us to adopt the CrS enoate reductase derived from Thermus scotoductus SA-01. Additionally, we developed an enzymatic system for NADH regeneration, utilising formate dehydrogenase from Candida boidinii. This system facilitated the efficient catalysis of (S)-4-(hydroxymethyl)cyclopent-2-enone, resulting in the formation of (3 R)-3-(hydroxymethyl) cyclopentanone. Furthermore, we successfully cloned, expressed, purified, and characterized the CrS enzyme in Escherichia coli. Optimal reaction conditions were determined, revealing that the highest activity occurred at 45 °C and pH 8.0. By employing 5 mM (S)-4-(hydroxymethyl)cyclopent-2-enone, 0.05 mM FMN, 0.2 mM NADH, 10 μM CrS, 40 μM formic acid dehydrogenase, and 40 mM sodium formate, complete conversion was achieved within 45 min at 35 °C and pH 7.0. Subsequently, (1 R ,3 R)-3-hydroxycyclopentanemethanol was obtained through a simple three-step chemical conversion process. This study not only presents an effective method for synthesizing the crucial intermediate but also highlights the importance of biocatalysts and enzymatic systems in chemoenzymatic synthesis approaches. [Display omitted] • New chemoenzymatic route for the synthesis of anti-hepatitis B drug intermediates. • Novel application of CrS enoate reductase from Thermus scotoductus SA-01. • The further application of (S)-4-(hydroxymethyl)cyclopent-2-enone. [ABSTRACT FROM AUTHOR]

[Display omitted] • Perturbing O-antigen ligation shortened the resuscitating lag phase. • Higher ATP levels of Δ rfaL VBNC cells promote resuscitation. • ATP consumption during lag phase was highly correlated with resuscitation efficiency. • ATP was utilized to activate the Handler and salvage pathways to synthesize NAD+. • VBNC cells using residual ATP recover metabolic activity, driving cells to exit dormancy. Entry into the viable but nonculturable (VBNC) state is a survival strategy adopted by bacteria to survive harsh environment. Although VBNC cells still have metabolic activity, they lose the ability to form colonies on nonselective culture media. Thus, conventional bacterial detection methods, such as plate counting, are unable to detect the presence of VBNC cells. When the environmental conditions are appropriate, VBNC cells can initiate resuscitation, posing a great risk to the safety of public health. The study of the VBNC resuscitation mechanism could provide new insights into the prevention and control of VBNC resuscitation. Uncovering the molecular mechanism of VBNC cell resuscitation by investigating the role of O-antigen ligase (RfaL) in inhibiting the resuscitation of Escherichia coli O157:H7 in the VBNC state. RfaL was screened and verified as a resuscitation inhibitor of VBNC Escherichia coli O157:H7 by detecting resuscitation curve and time-lapse microscopy. The mechanism of RfaL impacts VBNC E. coli resuscitation was investigated by detecting the single cell ATP content, metabolomic changes, NAD(H) content and new protein biosynthesis of WT and Δ rfaL at different stage of resuscitation. Mutation of rfaL , which encoded an O-antigen ligase, markedly shortened the resuscitating lag phase. Further studies indicated that Δ rfaL VBNC cells contained higher ATP levels, and ATP consumption during the resuscitating lag phase was highly correlated with resuscitation efficiency. Metabolomic analysis revealed that ATP was utilized to activate the Handler and salvage pathways to synthesize NAD+, balancing redox reactions to recover cell activity and promote cell resuscitation. Our findings revealed a strategy employed by VBNC cells for revival, that is, using residual ATP to primarily recover metabolic activity, driving cells to exit dormancy. The synthesis pathway of lipopolysaccharide (LPS) in rfaL null mutant was inhibited and could supply more ATP to synthesis NAD+ and promote resuscitation. [ABSTRACT FROM AUTHOR]

The sole known heme enzyme of the parasitic protist Giardia intestinalis is a flavohemoglobin (gFlHb) that acts as a nitric oxide dioxygenase (NOD) and protects the organism from the free radical nitric oxide. To learn more about the properties of this enzyme, we measured its nitric oxide dioxygenase, NADH oxidase, and cytochrome c reductase activities and compared these to the activities of the E. coli flavohemoglobin (Hmp). The turnover number for the NOD activity of gFlHb (23 s−1) is about two-thirds of that of Hmp (34 s−1) at pH 6.5 and 37 °C. The two enzymes differ in their sensitivity towards molecules that act as heme ligands. For both gFlHb and Hmp, inhibition with miconazole, a large imidazole ligand, is adequately described by simple competitive inhibition, with KI = 10 μM and 0.27 μM for gFlHb and Hmp, respectively. Inhibition plots with the small ligand imidazole were biphasic, which is consistent with previous experiments with carbon monoxide as a probe that show that the active site of flavohemoglobins exists in two conformations. Interestingly, the largest difference is observed with nitrite, which, like imidazole, also shows a biphasic inhibition plot; however, nitrite inhibits gFlHb at sub-millimolar concentrations while Hmp is not significantly affected. NADH oxidase activity measured under aerobic conditions in the absence of nitric oxide for Hmp was more than twice the activity of gFlHb. The addition of 1 mM hydrogen peroxide in these assays stimulated the NADH oxidase activity of gFlHb but not Hmp. Both enzymes had nearly identical cytochrome c reductase activities but the extent of the contribution of indirect reduction by flavohemoglobin-generated superoxide was much lower with gFlHb (4% SOD-inhibited) than with Hmp (17% SOD-inhibited). Although the active sites of the two enzymes share the same highly conserved residues that are important for catalysis, differences in the distal ligand binding site may account for these differences in activity and sensitivity towards NOD inhibitors. The differences observed in the NADH oxidase and cytochrome c reductase assays suggest that gFlHb may have evolved to protect the protist, which lacks both superoxide dismutase and catalase, from the damaging effects of superoxide by minimizing its production and from peroxide by actively reducing it. [ABSTRACT FROM AUTHOR]

Background: Dodecanedioic acid (DDA), a typical medium-chain dicarboxylic fatty acid with widespread applications, has a great synthetic value and a huge industrial market demand. Currently, a sustainable, eco-friendly and efficient process is desired for dodecanedioic acid production. Results: Herein, a multi-enzymatic cascade was designed and constructed for the production of DDA from linoleic acid based on the lipoxygenase pathway in plants. The cascade is composed of lipoxygenase, hydroperoxide lyase, aldehyde dehydrogenase, and unidentified double-bond reductase in E. coli for the main cascade reactions, as well as NADH oxidase for cofactor recycling. The four component enzymes involved in the cascade were co-expressed in E. coli, together with the endogenous double-bond reductase of E. coli. After optimizing the reaction conditions of the rate-limiting step, 43.8 g L− 1 d− 1 of DDA was obtained by a whole-cell one-pot process starting from renewable linoleic acid. Conclusions: Through engineering of the reaction system and co-expressing the component enzymes, a sustainable and eco-friendly DDA biosynthesis route was set up in E. coli, which afforded the highest space time yield for DDA production among the current artificial multi-enzymatic routes derived from the LOX-pathway, and the productivity achieved here ranks the second highest among the current research progress in DDA biosynthesis. [ABSTRACT FROM AUTHOR]

BACKGROUND: Many diseases may be caused by pathogens and oxidative stress resulting from carcinogens. Earlier studies have highlighted the antimicrobial and antioxidant effects of plant essential oils (EO). It is crucial to effectively utilize agricultural waste to achieve a sustainable agricultural economy and protect the environment. The present study aimed to evaluate the potential benefits of EO extracted from the discarded peels of Citrus depressa Hayata (CD) and Citrus microcarpa Bunge (CM), synonyms of Citrus deliciosa Ten and Citrus japonica Thunb, respectively. RESULTS: Gas chromatography‐mass spectrometry analysis revealed that the main compounds in CD‐EO were (R)‐(+)‐limonene (38.97%), γ‐terpinene (24.39%) and linalool (6.22%), whereas, in CM‐EO, the main compounds were (R)‐(+)‐limonene (48.00%), β‐pinene (13.60%) and γ‐terpinene (12.07%). CD‐EO exhibited inhibitory effects on the growth of common microorganisms, including Candida albicans, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. However, CM‐EO showed only inhibitory effects on E. coli. Furthermore, CD‐EO exhibited superior antioxidant potential, as demonstrated by its ability to eliminate 1,1‐diphenyl‐2‐picrylhydrazyl and 2,2′‐azinobis‐3‐ethylbenzthiazoline‐6‐sulfonate free radicals. Furthermore, CD‐EO at a concentration of 100 μg mL−1 significantly inhibited 12‐O‐tetradecanoylphorbol‐13‐acetate‐induced cancer transformation in mouse epidermal JB6 P+ cells (P < 0.05), possibly by up‐regulating protein expression of nuclear factor erythroid 2‐related factor 2 and its downstream antioxidant enzymes, such as NAD(P)H:quinone oxidoreductase 1, heme oxygenase‐1 and UGT1A. CONCLUSION: These findings suggest that CD‐EO exhibits inhibitory effects on pathogenic microorganisms, possesses antioxidant properties and has cancer chemopreventive potential. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

2,5-Dimethylpyrazine (2,5-DMP) is important pharmaceutical raw material and food flavoring agent. Recently, engineering microbes to produce 2,5-DMP has become an attractive alternative to chemical synthesis approach. In this study, metabolic engineering strategies were used to optimize the modified Escherichia coli BL21 (DE3) strain for efficient synthesis of 2,5-DMP using L-threonine dehydrogenase (EcTDH) from Escherichia coli BL21, NADH oxidase (EhNOX) from Enterococcus hirae, aminoacetone oxidase (ScAAO) from Streptococcus cristatus and L-threonine transporter protein (EcSstT) from Escherichia coli BL21, respectively. We further optimized the reaction conditions for synthesizing 2,5-DMP. In optimized conditions, the modified strain can convert L-threonine to obtain 2,5-DMP with a yield of 2897.30 mg/L. Therefore, the strategies used in this study contribute to the development of high-level cell factories for 2,5-DMP. [ABSTRACT FROM AUTHOR]

The occurrence of NAD+ as a non-canonical RNA cap has been demonstrated in diverse organisms. TIR domain-containing proteins present in all kingdoms of life act in defense responses and can have NADase activity that hydrolyzes NAD+. Here, we show that TIR domain-containing proteins from several bacterial and one archaeal species can remove the NAM moiety from NAD-capped RNAs (NAD-RNAs). We demonstrate that the deNAMing activity of AbTir (from Acinetobacter baumannii) on NAD-RNA specifically produces a cyclic ADPR-RNA, which can be further decapped in vitro by known decapping enzymes. Heterologous expression of the wild-type but not a catalytic mutant AbTir in E. coli suppressed cell propagation and reduced the levels of NAD-RNAs from a subset of genes before cellular NAD+ levels are impacted. Collectively, the in vitro and in vivo analyses demonstrate that TIR domain-containing proteins can function as a deNAMing enzyme of NAD-RNAs, raising the possibility of TIR domain proteins acting in gene expression regulation. Toll/interleukin-1 receptor domain-containing proteins can catabolize NAD+. Here, Wang et al show that these proteins can also function as NAD-RNA decapping enzymes by releasing the NAM moiety from the NAD-RNA, resulting in the regulation of gene expression. [ABSTRACT FROM AUTHOR]

The Escherichia coli TetR-related transcriptional regulator RutR is involved in the coordination of pyrimidine and purine metabolism. Here we report that lysine acetylation modulates RutR function. Applying the genetic code expansion concept, we produced site-specifically lysine-acetylated RutR proteins. The crystal structure of lysine-acetylated RutR reveals how acetylation switches off RutR-DNA-binding. We apply the genetic code expansion concept in E. coli in vivo revealing the consequences of RutR acetylation on the transcriptional level. We propose a model in which RutR acetylation follows different kinetic profiles either reacting non-enzymatically with acetyl-phosphate or enzymatically catalysed by the lysine acetyltransferases PatZ/YfiQ and YiaC. The NAD+-dependent sirtuin deacetylase CobB reverses enzymatic and non-enzymatic acetylation of RutR playing a dual regulatory and detoxifying role. By detecting cellular acetyl-CoA, NAD+ and acetyl-phosphate, bacteria apply lysine acetylation of transcriptional regulators to sense the cellular metabolic state directly adjusting gene expression to changing environmental conditions. The mechanisms underlying adaptation of bacteria to changing environmental conditions remain poorly understood. Here, the authors show bacteria using lysine acetylation of transcriptional regulators to adjust gene expression to changing conditions. [ABSTRACT FROM AUTHOR]

Synthetic autotrophy is a promising avenue to sustainable bioproduction from CO2. Here, we use iterative laboratory evolution to generate several distinct autotrophic strains. Utilising this genetic diversity, we identify that just three mutations are sufficient for Escherichia coli to grow autotrophically, when introduced alongside non-native energy (formate dehydrogenase) and carbon-fixing (RuBisCO, phosphoribulokinase, carbonic anhydrase) modules. The mutated genes are involved in glycolysis (pgi), central-carbon regulation (crp), and RNA transcription (rpoB). The pgi mutation reduces the enzyme's activity, thereby stabilising the carbon-fixing cycle by capping a major branching flux. For the other two mutations, we observe down-regulation of several metabolic pathways and increased expression of native genes associated with the carbon-fixing module (rpiB) and the energy module (fdoGH), as well as an increased ratio of NADH/NAD+ - the cycle's electron-donor. This study demonstrates the malleability of metabolism and its capacity to switch trophic modes using only a small number of genetic changes and could facilitate transforming other heterotrophic organisms into autotrophs. [ABSTRACT FROM AUTHOR]

Tyrosol (4-hydroxyphenylethanol) is a phenolic compound used in the pharmaceutical and chemical industries. However, current supply methods, such as extraction from natural resources and chemical synthesis, have disadvantages from the viewpoint of cost and environmental protection. Here, we developed a tyrosol-producing Escherichia coli cell factory from a high-tyrosine-producing strain by expressing selected tyrosine decarboxylase-, tyramine oxidase (TYO)-, and medium-chain dehydrogenase/reductase (YahK)-encoding genes. The genes were controlled by the strong T7 promoter and integrated into the chromosome because of the advantages over plasmid-based systems. The strain produced a melanin-like pigment as a by-product, which is suggested to be formed from 4-hydroxyphenylacetaldehyde (a TYO product/YahK substrate). By using a culture medium containing a high concentration of glycerol, which was reported to enhance NADH supply required for YahK activity, the final titer of tyrosol reached 2.42 g/L in test tube-scale cultivation with a concomitant decrease in the amount of pigment. These results indicate that chromosomally integrated and T7 promoter-controlled gene expression system in E. coli is useful for high production of heterologous enzymes and might be applied for industrial production of useful compounds including tyrosine and tyrosol. [Display omitted] [ABSTRACT FROM AUTHOR]

Cofactor imbalance obstructs the productivities of meta-bolically engineered cells. Herein, we employed a minimally perturbing system, xylose reductase and lactose (XR/lactose), to increase the levels of a pool of sugar phosphates which are connected to the biosynthesis of NAD(P)H, FAD, FMN, and ATP in Escherichia coli. The XR/lactose system could increase the amounts of the precursors of these cofactors and was tested with three different metabolically engineered cell systems (fatty alcohol biosynthesis, bioluminescence light generation, and alkane biosynthesis) with different cofactor demands. Productivities of these cells were increased 2-4-fold by the XR/lactose system. Untargeted metabolomic analysis revealed different metabolite patterns among these cells, demonstrating that only metabolites involved in relevant cofactor biosynthesis were altered. The results were also confirmed by transcriptomic analysis. Another sugar reducing system (glucose dehydrogenase) could also be used to increase fatty alcohol production but resulted in less yield enhancement than XR. This work demonstrates that the approach of increasing cellular sugar phosphates can be a generic tool to increase in vivo cofactor generation upon cellular demand for synthetic biology. [ABSTRACT FROM AUTHOR]

Utilizing anaerobic metabolisms for the production of biotechnologically relevant products presents potential advantages, such as increased yields and reduced energy dissipation. However, lower energy dissipation may indicate that certain reactions are operating closer to their thermodynamic equilibrium. While stoichiometric analyses and genetic modifications are frequently employed in metabolic engineering, the use of thermodynamic tools to evaluate the feasibility of planned interventions is less documented. In this study, we propose a novel metabolic engineering strategy to achieve an efficient anaerobic production of poly-(R)-3-hydroxybutyrate (PHB) in the model organism Escherichia coli. Our approach involves re-routing of two-thirds of the glycolytic flux through non-oxidative glycolysis and coupling PHB synthesis with NADH re-oxidation. We complemented our stoichiometric analysis with various thermodynamic approaches to assess the feasibility and the bottlenecks in the proposed engineered pathway. According to our calculations, the main thermodynamic bottleneck are the reactions catalyzed by the acetoacetyl-CoA β-ketothiolase (EC 2.3.1.9) and the acetoacetyl-CoA reductase (EC 1.1.1.36). Furthermore, we calculated thermodynamically consistent sets of kinetic parameters to determine the enzyme amounts required for sustaining the conversion fluxes. In the case of the engineered conversion route, the protein pool necessary to sustain the desired fluxes could account for 20% of the whole cell dry weight. [ABSTRACT FROM AUTHOR]

In order to address the challenges associated with antibiotic resistance by bacteria, two new complexes, Ni(II) and Zn(II), have been synthesized using the conventional method based on Schiff base ligand (E)-2-((5-bromothiazol-2-yl) imino) methyl) phenol. The Schiff base ligand (HL) was synthesized using salicylaldehyde and 5-(4-bromophenyl)thiazol-2-amine in both traditional and efficient, ecologically friendly, microwave-assisted procedures. The ligand and its complexes were evaluated by elemental analyses, FTIR spectroscopy, UV-Vis spectroscopy, nuclear magnetic resonance (NMR), thermogravimetric analysis (TGA) and magnetic susceptibility. The ligand and its complexes were tested for antibacterial activity against three Gram-positive bacteria (Staphylococcus aureus ATCC 25923, Methicillin-resistant Staphylococcus aureus ATCC 43300 and Enterococcus faecalis ATCC 29212) and three Gram-negative bacteria (Pseudomonas aeruginosa ATCC 27853, Escherichia coli ATCC 25922 and Klebsiella pneumoniae ATCC 700603). The findings demonstrate the potent activity of the ligand and its complexes against selective bacteria but the Ni(II) complex with MIC values ranging from 1.95 to 7.81 µg/mL outperformed all other compounds, including the widely used antibiotic Streptomycin. Furthermore, the docking study provided evidence supporting the validity of the antimicrobial results, since the Ni complex showed superior binding affinity against to E. coli NAD synthetase, which had a docking score (−7.61 kcal/mol). [ABSTRACT FROM AUTHOR]

NAD-dependent malic enzymes catalyze NAD reduction to NADH while converting malate to pyruvate and CO 2. In this study, NAD was reduced to NADH by MaeA, NAD-dependent malic enzyme from Escherichia coli , when fumarate was used as substrate. This suggested that MaeA catalyzed the conversion of fumarate to malate and then malate to pyruvate. The K 0.5 value for fumarate was determined as 13 mM, different from previously characterized fumarases in Escherichia coli. Fumarate inhibited the malic enzyme activity of MaeA where NAD reduction to NADH was examined in the presence of malate as substrate. Human ME2, an NAD-dependent malic enzyme, also converted NAD to NADH in the presence of fumarate, suggesting that the duplex activity as fumarase and malic enzyme might be conserved in various NAD-dependent malic enzymes. MaeB, NADP-dependent malic enzyme from Escherichia coli , did not reduce NADP to NADPH in the presence of fumarate, suggesting the fumarase activities of MaeA and ME2 were specific. • NAD-dependent malic enzymes, MaeA and ME2, catalyze the reduction of NAD to NADH in the presence of fumarate. • In addition to as malic enzymes, MaeA and ME2 may function as fumarases. • Fumarate also acts an allosteric inhibitor for MaeA. [ABSTRACT FROM AUTHOR]

As a life-essential coenzyme, nicotinamide adenine dinucleotide (NAD+) has been explored for more than a century. In Saccharomyces, the natural NAD+de novo biosynthetic pathway initiating from tryptophan has been well elucidated. To bypass this stringently controlled natural pathway in yeast, an economical C3N pathway that was developed in Escherichia coli previously was constructed in Saccharomyces as a short detour for de novo NAD+ biosynthesis. After the functional expressions of the C3N genes were identified in Saccharomyces cerevisiae BY4741 by in vitro enzymatic assays, the C3N module was introduced into an NAD+ auxotrophic S. cerevisiae strain BY01, in which the BNA2 gene encoding tryptophan 2,3-dioxygenase was inactivated. The efficient NAD+ synthesis via the C3N pathway was confirmed by both plate assays and fermentation analysis. The applicability of the C3N pathway in cofactor engineering was tested by introducing it into S. cerevisiae BY4741, which improved the cellular NAD(H) level considerably. Consequently, this study proved that the de novo NAD+ biosynthetic pathway can be replaced by an artificial pathway in yeast, which paves a way to design more promising schemes in eukaryotes for rational manipulation of the cellular NAD(H) levels. [ABSTRACT FROM AUTHOR]

1-Decanol has great value in the pharmaceutical and fragrance industries and plays an important role in the chemical industry. In this study, we engineered Escherichia coli to selectively synthesize 1-decanol by using enzymes of the core reverse β-oxidation (rBOX) pathway and termination module with overlapping chain-length specificity. Through screening for acyl-CoA reductase termination enzymes and proper regulation of rBOX pathway expression, a 1-decanol titer of 1.4 g/L was achieved. Further improvements were realized by engineering pyruvate dissimilation to ensure the generation of NADH through pyruvate dehydrogenase (PDH) and reducing byproduct synthesis via a tailored YigI thioesterase knockout, increasing 1-decanol titer to 1.9 g/L. The engineered strain produced about 4.4 g/L 1-decanol with a yield of 0.21 g/g in 36 h in a bi-phasic fermentation that used a dodecane overlay to increase 1-decanol transport and reduce its toxicity. Adjustment of pathway expression (varying inducer concentration) and cell growth (oxygen availability) enabled 1-decanol production at 6.1 g/L (0.26 g/g yield) and 10.05 g/L (0.2 g/g yield) using rich medium in shake flasks and bioreactor, respectively. Remarkably, the use of minimal medium resulted in 1-decanol production with 100% specificity at 2.8 g/L (0.14 g/g yield) and a per cell mass yield higher than rich medium. These 1-decanol titers, yields and purity are at least 10-fold higher than others reported to date and the engineered strain shows great potential for industrial production. Taken together, our findings suggest that using rBOX pathway and termination enzymes of proper chain-length specificity in combination with optimal chassis engineering should be an effective approach for the selective production of alcohols. • Selective production of 1-decanol was achieved using the reverse β-oxidation (rBOX) pathway. • 1-Decanol titers, yields and purity are at least 10-fold higher than others reported to date. • rBOX and termination enzymes of proper chain-length specificity in combination with optimal chassis engineering enable selective production of alcohols. [ABSTRACT FROM AUTHOR]

The ubiquitous coexistence of the redox cofactors NADH and NADPH is widely considered to facilitate an efficient operation of cellular redox metabolism. However, it remains unclear what shapes the NAD(P)H specificity of specific redox reactions. Here, we present a computational framework to analyze the effect of redox cofactor swaps on the maximal thermodynamic potential of a metabolic network and use it to investigate key aspects of redox cofactor redundancy in Escherichia coli. As one major result, our analysis suggests that evolved NAD(P)H specificities are largely shaped by metabolic network structure and associated thermodynamic constraints enabling thermodynamic driving forces that are close or even identical to the theoretical optimum and significantly higher compared to random specificities. Furthermore, while redundancy of NAD(P)H is clearly beneficial for thermodynamic driving forces, a third redox cofactor would require a low standard redox potential to be advantageous. Our approach also predicts trends of redox-cofactor concentration ratios and could facilitate the design of optimal redox cofactor specificities. NADH and NADPH are redox cofactors coexisting in all living cells. Here, the authors present a computational study suggesting that evolved NAD(P)H reaction specificities in E. coli are largely shaped by metabolic network structure enabling maximal thermodynamic driving forces close to the theoretical optimum. [ABSTRACT FROM AUTHOR]

Escherichia coli has been engineered for L-malate production via aerobic cultivation. However, the maximum yield obtained through this mode is inferior to that of anaerobic fermentation due to massive amounts of CO2 emissions. Here, we aim to address this issue by reducing CO2 emissions of recombinant E. coli during aerobic L-malate production. Our findings indicated that NADH oxidation and ATP-synthesis-related genes were down-regulated with 2 g/L of YE during aerobic cultivations of E. coli E23, as compared to 5 g/L of YE. Then, E23 was engineered via the knockout of nuoA and the introduction of the nonoxidative glycolysis (NOG) pathway, resulting in a reduction of NAD+ and ATP supplies. The results demonstrate that E23 (ΔnuoA, NOG) exhibited decreased CO2 emissions, and it produced 21.3 g/L of L-malate from glucose aerobically with the improved yield of 0.43 g/g. This study suggests that a restricted NAD+ and ATP supply can prompt E. coli to engage in incomplete oxidization of glucose, leading to the accumulation of metabolites instead of utilizing them in cellular respiration. [ABSTRACT FROM AUTHOR]

Introduction: Antibiotic persistence (subpopulation tolerance) occurs when a subpopulation of antibiotic sensitive cells survives prolonged exposure to a bactericidal concentration of an antibiotic, and is capable of regrowth once the antibiotic is removed. This phenomenon has been shown to contribute to prolonged treatment duration, infection recurrence, and accelerated development of genetic resistance. Currently, there are no biomarkers which would allow for segregation of these antibiotic-tolerant cells from the bulk population prior to antibiotic exposure, limiting research on this phenomenon to retrograde analyses. However, it has been previously shown that persisters often have a dysregulated intracellular redox homeostasis, warranting its investigation as a potential marker for antibiotic tolerance. Furthermore, it is currently unknown whether another antibiotic tolerant subpopulation - viable but non-culturable cells (VBNCs), are simply persisters with extreme lag phase, or are formed through separate pathways. VBNCs similarly to persisters remain viable following antibiotic exposure, however, are not capable of regrowth in standard conditions. Methods: In this article we employed an NADH:NAD+ biosensor (Peredox) to investigate NADH homeostasis of ciprofloxacin-tolerant E. coli cells on a singlecell level. [NADH:NAD+] was used as a proxy for measuring intracellular redox homeostasis and respiration rate. Results and Discussion: First, we demonstrated that ciprofloxacin exposure results in a high number of VBNCs, several orders of magnitude higher than persisters. However, we found no correlation in the frequencies of persister and VBNC subpopulations. Ciprofloxacin-tolerant cells (persisters & VBNCs) were actively undergoing respiration, although at a significantly lower rate on average when compared to the bulk population. We also noted significant heterogeneity on a single-cell level within the subpopulations, however were unable to segregate persisters from VBNCs based on these observations alone. Finally, we showed that in the highly-persistent strain of E. coli, E. coli HipQ, ciprofloxacin-tolerant cells have a significantly lower [NADH:NAD+] ratio than tolerant cells of its parental strain, providing further link between disturbed NADH homeostasis and antibiotic tolerance. [ABSTRACT FROM AUTHOR]

S-Adenosyl-L-methionine (SAM) and S -adenosyl-L-homocysteine (SAH) are important biochemical intermediates. SAM is the major methyl donor for diverse methylation reactions in vivo. The SAM to SAH ratio serves as a marker of methylation capacity. Stable isotope-labeled SAM and SAH are used to measure this ratio with high sensitivity. SAH hydrolase (EC 3.13.2.1; SAHH), which reversibly catalyzes the conversion of adenosine and L-homocysteine to SAH, is used to produce labeled SAH. To produce labeled SAH with high efficiency, we focused on the SAHH of Pyrococcus horikoshii OT3, a thermophilic archaeon. We prepared recombinant P. horikoshii SAHH using Escherichia coli and investigated its enzymatic properties. Unexpectedly, the optimum temperature and thermostability of P. horikoshii SAHH were much lower than its optimum growth temperature. However, addition of NAD+ to the reaction mixture shifted the optimum temperature of P. horikoshii SAHH to a higher temperature, suggesting that NAD + stabilizes the structure of the enzyme. [ABSTRACT FROM AUTHOR]

The use of enzymes in biochemical processes is of interest due to their ability to work under mild conditions while attaining high reaction rates. A limitation in the use of enzymes such as oxidoreductases on a large scale lies with their requirement for costly cofactors, e.g. NAD+, in stoichiometric quantities. Cofactor regeneration mechanisms using bienzymatic recycling systems is an attractive way to increase productivity and efficiency. The thermophilic enzyme aldehyde dehydrogenase (ALDHTt) was immobilized directly from E. coli cell lysate, containing the expressed enzyme, onto Ni2+ activated Sepharose®. The system displayed a rate of conversion of approx. 63% NAD+ with reuse achievable for up to 5 cycles and residual activity of the enzyme upon storage of 93% after 7 days. L -Lactate dehydrogenase was immobilized in a second reactor module downstream of ALDHTtvia two different methods, electrochemical entrapment in poly(3,4-ethylenedioxypyrrole) (PEDOP) and covalent attachment on glyoxyl agarose. Both reactors allowed for up to 100% conversion of NADH, however LDH@agarose proved superior in terms of reuse and storage. LDH@agarose displayed no reduction in activity after 6 cycles of use and retained 98% activity following 56 days storage. A coupled reactor containing immobilized ALDHTt–LDH was operated with the substrates hexanal, benzaldehyde, terephthalaldehyde and p-tolualdehyde. A particular advantage of the system is its ability to preferentially oxidise a single aldehyde group in substrates containing two aldehyde functional groups. The reactor demonstrated efficient cofactor regeneration under continual operation for up 24 h, with enhanced product yields. [ABSTRACT FROM AUTHOR]

Bacterial biofilm is a major contributor to the persistence of infection and the limited efficacy of antibiotics. Antibiofilm molecules that interfere with the biofilm lifestyle offer a valuable tool in fighting bacterial pathogens. Ellagic acid (EA) is a natural polyphenol that has shown attractive antibiofilm properties. However, its precise antibiofilm mode of action remains unknown. Experimental evidence links the NADH:quinone oxidoreductase enzyme WrbA to biofilm formation, stress response, and pathogen virulence. Moreover, WrbA has demonstrated interactions with antibiofilm molecules, suggesting its role in redox and biofilm modulation. This work aims to provide mechanistic insights into the antibiofilm mode of action of EA utilizing computational studies, biophysical measurements, enzyme inhibition studies on WrbA, and biofilm and reactive oxygen species assays exploiting a WrbA-deprived mutant strain of Escherichia coli. Our research efforts led us to propose that the antibiofilm mode of action of EA stems from its ability to perturb the bacterial redox homeostasis driven by WrbA. These findings shed new light on the antibiofilm properties of EA and could lead to the development of more effective treatments for biofilm-related infections. [ABSTRACT FROM AUTHOR]

Allitol and gluconic acid (GA) are important industrial compounds that are preferably produced via bio-production processes. In this research, d -psicose-3-epimerase (DPEase), glucose dehydrogenase (GDH), and ribitol dehydrogenase (RDH) were heterologously expressed in Escherichia coli , realizing the co-production of allitol and GA. Compared to the loss of carbon flux from formate dehydrogenase (FDH), glucose dehydrogenase can produce GA while generating NAD(H). The recombinant strain Ec/pA d -pR rg boosted NADH production to 2.4 μmol/gDCW, 118% higher than with the control strain. Under the optimized conditions, 12.0 g/L allitol and 14.8 g/L GA were produced from 25 g/L d -fructose and 20 g/L d -glucose; i.e., 66.7% and 66.3% higher yields compared to the case of fermentation without optimization, respectively. Furthermore, 42.7 g/L allitol and 56.2 g/L GA can be obtained from pretreated molasses (containing 139.2 g/L d -fructose and 149.1 g/L d -glucose). This work provides a practicable strategy for industrial and efficient co-production of allitol and GA from a cheap raw substrate. [Display omitted] • Co-production of GA improves the economy of allitol production. • d -Glucose used as cosubstrate for NADH regeneration facilitated allitol production. • 12.0 g allitol and 14.8 g GA were produced from 25 g d -fructose and 20 g d -glucose. • Up to 42.7 g/L allitol and 56.2 g/L GA were produced from pretreated molasses. [ABSTRACT FROM AUTHOR]

Escherichia coli NfsB has been studied extensively for its potential for cancer gene therapy by reducing the prodrug CB1954 to a cytotoxic derivative. We have previously made several mutants with enhanced activity for the prodrug and characterised their activity in vitro and in vivo. Here, we determine the X-ray structure of our most active triple and double mutants to date, T41Q/N71S/F124T and T41L/N71S. The two mutant proteins have lower redox potentials than wild-type NfsB, and the mutations have lowered activity with NADH so that, in contrast to the wild-type enzyme, the reduction of the enzyme by NADH, rather than the reaction with CB1954, has a slower maximum rate. The structure of the triple mutant shows the interaction between Q41 and T124, explaining the synergy between these two mutations. Based on these structures, we selected mutants with even higher activity. The most active one contains T41Q/N71S/F124T/M127V, in which the additional M127V mutation enlarges a small channel to the active site. Molecular dynamics simulations show that the mutations or reduction of the FMN cofactors of the protein has little effect on its dynamics and that the largest backbone fluctuations occur at residues that flank the active site, contributing towards its broad substrate range. [ABSTRACT FROM AUTHOR]

p -Hydroxyacetophenone (p -HAP) and its glucoside picein are plant-derived natural products that have been extensively used in chemical, pharmaceutical and cosmetic industries owing to their antioxidant, antibacterial and antiseptic activities. However, the natural biosynthetic pathways for p -HAP and picein have yet been resolved so far, limiting their biosynthesis in microorganisms. In this study, we design and construct a biosynthetic pathway for de novo production of p -HAP and picein from glucose in E. coli. First, screening and characterizing pathway enzymes enable us to successfully establish functional biosynthetic pathway for p -HAP production. Then, the rate-limiting step in the pathway caused by a reversible alcohol dehydrogenase is completely eliminated by modulating intracellular redox cofactors. Subsequent host strain engineering via systematic increase of precursor supplies enables production enhancement of p -HAP with a titer of 1445.3 mg/L under fed-batch conditions. Finally, a novel p -HAP glucosyltransferase capable of generating picein from p -HAP is identified and characterized from a series of glycosyltransferases. On this basis, de novo biosynthesis of picein from glucose is achieved with a titer of 210.7 mg/L under fed-batch conditions. This work not only demonstrates a microbial platform for p -HAP and picein synthesis, but also represents a generalizable pathway design strategy to produce value-added compounds. • Establishing biosynthetic pathway for de novo biosynthesis of p -HAP and picein. • Modulating intracellular redox cofactors to eliminate reverse side reaction of a dehydrogenase. • Achieving de novo production of p -HAP at 1445.3 mg/L in a fed-batch fermenter. • Identifying a novel p-HAP glucosyltransferase allows de novo bio-production of picein. [ABSTRACT FROM AUTHOR]

Hydroxytyrosol, a phenolic compound derived from olives, is conducive to human health and is widely used in food additives and cosmetic industries due to its significant antioxidant activity and cancer prevention properties. In this research, we designed and constructed a nearly irreversible and efficient bio-catalysis cascade reaction for hydroxytyrosol production from L-3,4-dihydroxy-phenylalanine. The recombinant Escherichia coli cells were constructed by co-expressing L -amino acid deaminase from Cosenzaea myxofaciens , α-keto acid decarboxylase from Proteus mirabilis , aldehyde reductase from Escherichia coli (DE3) and glucose dehydrogenase from Bacillus subtilis. The glucose dehydrogenase catalyzed the dehydrogenation of co-substrate (glucose) to achieve the regeneration of NADH, which was an indispensable reductant for producing hydroxytyrosol. Subsequently, the expression of these enzymes was coordinated using a strategy of combining two different compatible plasmids. Finally, the production of hydroxytyrosol reached at 55.53 mM (8.55 g/L) within 6 h under the optimum biotransformation conditions. [Display omitted] ● Designing a novel multi-enzyme cascade system for synthesis of hydroxytyrosol. ● Construction of a nearly irreversible hydroxytyrosol biosynthetic pathway. ● A hydroxytyrosol production level of 8.55 g/L was achieved using the three-step biotransformation. [ABSTRACT FROM AUTHOR]

• Assemble AuNPs and hydrogenase to construct membraneless organelles for photocatalysis. • Efficient H 2 production through direct electron transfer between hydrogenase and AuNPs. • The membraneless organelle approach provides high selectivity and specificity for H 2 formation. The emergence of semiartificial photosynthesis holds great promise for improving light energy capture and conversion efficiency. However, achieving high product specificity and selectivity in semiartificial photosynthetic systems remains a challenge. In this study, we employed genetic engineering techniques to construct a membraneless organelle in E. coli , serving as the photoreaction carrier. The self-assembly of photosensitizers and hydrogenase within the carrier has successfully established a semiartificial photosynthetic model characterized by high product specificity and selectivity. In this model system, electrons were directly transferred to hydrogenase upon AuNPs light excitation in membraneless organelle, eliminating the need for additional electron mediators and bypassing the use of intracellular NADH/NAD+ as a reducing agent to avoid byproduct formation. The semiartificial photosynthetic system demonstrated an 11782-fold and 40-fold increase in hydrogen production compared to bare AuNPs and the empty vector E. coli hybrid system, respectively. This membraneless organelle holds the potential to robustly support the specific synthesis of high-energy-density, value-added compounds through solar energy conversion. [ABSTRACT FROM AUTHOR]

L-Phosphinothricin (L-PPT) is the active compound of a broad-spectrum herbicide. In this study, we biosynthesized L-PPT via the asymmetric reduction of 2-carboxy-4-(hydroxymethylphosphoryl) butyric acid (PPO) using a whole-cell biocatalyst. Glutamate dehydrogenase from Pseudomonas moorei (Pm GluDH), Glucose dehydrogenase from Exiguobacterium sibiricum (Es GDH) and NAD kinase from Corynebacterium glutamicum (Cg NADK) were coexpressed in E. coli , significantly increasing the catalytic efficiency by regenerating more NADPH to promote PPO reduction. Following the optimization of balancing the co-expression of the three enzymes in pETDuet-1 and pCDFDuet-1, the coexpressing strain increases in the intracellular NADP(H) concentration to 54.9 μmol/g DCW, which was 3.8-fold higher than the control. The co-expression system exhibited optimal activity at a temperature of 35°C, pH 7.5, and the glucose to PPO molar ratio of 1.4:1. In a 30 L bioconversion system the final concentration and productivity of L-PPT reached 79.8 g/L (>99% ee) and 1440 g/(L·d), respectively. These results will contribute to the industrial biological production of L-PPT. • NAD kinase enhances NADPH regeneration and increases intracellular NADP(H) levels. • Regulate protein expression by optimizing gene copy number in co-expression systems. • E. coli GluDH-GDH-NADK strain effectively synthesized L-PPT at 30 L scale. [ABSTRACT FROM AUTHOR]

Icariin (ICA) is a naturally occurring phytochemical agent primarily extracted from Epimedium Brevicornum Maxim (Family Berberidaceae) with a broad spectrum of bioactivities. Endometritis is a uterine disease that causes enormous losses in the dairy industry worldwide. In this study, anti-inflammatory and anti-oxidant properties of ICA were investigated against lipopolysaccharide (LPS)-induced endometritis in mice to investigate possible underlying molecular mechanisms. Sixty heathy female Kunming mice were randomly assigned to four groups (n = 15), namely control, LPS, LPS + ICA, and ICA groups. The endometritis was induced by intrauterine infusion of 50 µL of LPS (1 mg/mL). After 24 h of onset of LPS-induced endometritis, ICA groups were injected thrice by ICA intraperitoneally six hours apart. Histopathological examination, enzyme linked immunosorbent assay (ELISA), real time quantitative polymerase chain reaction (RT-qPCR), western blotting, and immunohistochemistry were used in this study. Histological alterations revealed that ICA markedly mitigated uterine tissue injury caused by LPS. The results showed that the ICA inhibited the production of pro-inflammatory cytokines (IL-1ß, IL-6, and TNF-α) and boosted the production of anti-inflammatory cytokines (IL-10). Additionally, ICA modulated the expression of malondialdehyde (MDA), reactive oxygen species (ROS), superoxide dismutase 1 (SOD1), catalase (CAT), and glutathione peroxidase 1 (Gpx1) induced by LPS. The administration of ICA significantly (p < 0.05) improved the mRNA and protein expression of Toll-like receptor (TLR) 4. The western blotting and ELISA finding revealed that the ICA repressed LPS-triggered NF-κB pathway activation. Moreover, ICA improved the antioxidant defense system via activation of the Nrf2 pathway. The results revealed that ICA up-regulated the mRNA and protein expression of Nuclear erythroid-2-related factor (Nrf2), NAD(P)H: quinone oxidoreductase 1 (NQO1), heme oxygenase-1 (HO-1), and glutamate-cysteine ligase catalytic subunit (GCLC) under LPS exposure. Conclusively, our findings strongly suggested that ICA protects endometritis caused by LPS by suppressing TLR4-associated NF-κB and Nrf2 pathways. Altogether, these innovative findings may pave the way for future studies into the therapeutic application of ICA to protect humans and animals against endometritis. [ABSTRACT FROM AUTHOR]

As an important metabolic intermediate, 2-ketoisovalerate has significant potential in the pharmaceutical and biofuel industries. However, a low output through microbial fermentation inhibits its industrial application. The microbial production of 2-ketoisovalerate is representative whereby redox imbalance is generated with two molecules of NADH accumulated and an extra NADPH required to produce one 2-ketoisovalerate from glucose. To achieve efficient 2-ketoisovalerate production, metabolic engineering strategies were evaluated in Escherichia coli. After deleting the competing routes, overexpressing the key enzymes for 2-ketoisovalerate production, tuning the supply of NADPH, and recycling the excess NADH through enhancing aerobic respiration, a 2-ketoisovalerate titer and yield of 46.4 g/L and 0.644 mol/ mol glucose, respectively, were achieved. To reduce the main by-product of isobutanol, the activity and expression of acetolactate synthase were modified. Additionally, a protein degradation tag was fused to pyruvate dehydrogenase (PDH) to curtail the conversion of pyruvate precursor into acetyl-CoA and the generation of NADH. The resulting strain, 050TY/pCTSDTQ487S-RBS55, was initially incubated under aerobic conditions to attain sufficient cell mass and then transferred to a microaerobic condition to degrade PDH and inhibit the remaining activity of PDH. Intracellular redox imbalance was relieved with titer, productivity and yield of 2-ketoisovalerate improved to 55.8 g/L, 2.14 g/L h and 0.852 mol/mol glucose. These results revealed metabolic engineering strategies for the production of a redox-imbalanced fermentative metabolite with high titer, productivity, and yield. [ABSTRACT FROM AUTHOR]

α,ω‐Dicarboxylic acids are valuable precursors in various chemical industries and have recently been produced using biotechnological methods to overcome the limitations of chemical synthesis. Nonanedioic acid, decanedioic acid, undecanedioic acid, and dodecanedioic acid have been produced at high concentrations from ω‐hydroxycarboxylic acids using engineered biocatalysts. However, no study has been attempted on the efficient production of pentadecanedioic acid. Here, the production of pentadecanedioic acid from 15‐hydroxypentadecanoic acid was carried out with alcohol dehydrogenases (ADHs), aldehyde dehydrogenases (ALDHs), and NAD(P)H oxidases, including NAD(P)H flavin oxidoreductase (NFO), that used a co‐factor regeneration system, derived from several species and expressed in Escherichia coli. Among the enzymes, Kangiella koreensis ADH (KkADH), Geobacillus kaustophilus ALDH (GkALDH), and Deinococcus radiodurans NFO (DrNFO) were selected because they had the highest activity. E. coli expressing pRSF‐DrNFO and pACYC‐KkADH/GkALDH as the best distribution of three genes in two plasmids was used as a biocatalyst to produce pentadecanedioic acid. The optimal conditions for producing pentadecanedioic acid from 15‐hydroxypentadecanoic acid by the biocatalyst were pH 8.0, 35°C, 5% (v/v) methanol, 40 g L−1 cells, and 60 mM 15‐hydroxypentadecanoic acid with agitation at 250 rpm. Under these optimized conditions, 57.4 mM pentadecanedioic acid was produced after 3 h, with a molar yield of 95.6% and a productivity of 19.1 mM h−1. The molar yield and concentration of pentadecanedioic acid showed the highest values among the reported biotechnological production of pentadecanedioic acid. [ABSTRACT FROM AUTHOR]

In all living organisms, adenosine triphosphate (ATP) and NAD(H) represent universal molecular currencies for energy and redox state, respectively, and are thus widely applicable molecular proxies for an organism's viability and activity. To this end, corresponding luciferase-based assays in combination with a microplate reader were established with the marine model bacterium Phaeobacter inhibens DSM 17395 (Escherichia coli K12 served as reference). Grey multiwell plates best balanced sensitivity and crosstalk, and optimal incubation times were 5 min and 30 min for the ATP and NAD(H) assay, respectively, together allowing limits of detection of 0.042, 0.470 and 0.710 nM for ATP, NAD+, and NADH, respectively. Quenching of bacterial cell samples involved Tris-EDTA-DTAB and bicarbonate base-DTAB for ATP and NAD(H) assays, respectively. The ATP and NAD(H) yields determined for P. inhibens DSM 17395 at ¼ ODmax were found to reside well within the range previously reported for E. coli and other bacteria, e.g., 3.28 µmol ATP (g cellsdry)−1. Thus, the here described methods for luciferase-based determination of ATP/NAD(H) pools open a promising approach to investigate energy and redox states in marine (environmental) bacteria. [ABSTRACT FROM AUTHOR]

This study explored the genetic engineering of Escherichia coli for hydrogen (H 2) production. In E. coli W3110, the introduction of NAD+-reducing [NiFe]-hydrogenase from Cupriavidus necator , combined with the inactivation of three endogenous [NiFe]-hydrogenases, exhibited not only H 2 production but also H 2 uptake based on exogenous hydrogenase. Although the H 2 production ability was much lower than the H 2 uptake ability, inactivation of the ethanol, lactate, and succinate production pathways resulted in a marked increase in H 2 production, demonstrating the bidirectional hydrogenase function in vivo depending on NADH/NAD+. Unexpectedly, H 2 production was completely repressed under conditions for high expression of exogenous hydrogenase. Furthermore, the introduction of the heterologous enzyme markedly repressed the endogenous H 2 production ability of E. coli W3110 but not the HST02. These in vivo behaviors largely correlated with in vitro hydrogenase activity suggested complicated interactions between the native and nonnative functional expression of [NiFe]-hydrogenases. • Hydrogenase is heterologously expressed and bidirectionally functions in vivo. • Optimization is critical for functional expression of heterologous hydrogenase. • Exogenous hydrogenase differentially influences endogenous ones depending on hosts. [ABSTRACT FROM AUTHOR]

Sequence-based screening has been widely applied in the discovery of novel microbial enzymes. However, majority of the sequences in the genomic databases were annotated using computational approaches and lacks experimental characterization. Hence, the success in obtaining the functional biocatalysts with improved characteristics requires an efficient screening method that considers a wide array of factors. Recombinant expression of microbial enzymes is often hampered by the undesirable formation of inclusion body. Here, we present a systematic in silico screening method to identify the proteins expressible in soluble form and with the desired biological properties. The screening approach was adopted in the recombinant expression of dimethyl sulfide (DMS) monooxygenase in Escherichia coli. DMS monooxygenase, a two-component enzyme consisting of DmoA and DmoB subunits, was used as a model protein. The success rate of producing soluble and active DmoA is 71% (5 out of 7 genes). Interestingly, the soluble recombinant DmoA enzymes exhibited the NADH:FMN oxidoreductase activity in the absence of DmoB (second subunit), and the cofactor FMN, suggesting that DmoA is also an oxidoreductase. DmoA originated from Janthinobacterium sp. AD80 showed the maximum NADH oxidation activity (maximum reaction rate: 6.6 µM/min; specific activity: 133 µM/min/mg). This novel finding may allow DmoA to be used as an oxidoreductase biocatalyst for various industrial applications. The in silico gene screening methodology established from this study can increase the success rate of producing soluble and functional enzymes while avoiding the laborious trial and error involved in the screening of a large pool of genes available. Key points: • A systematic gene screening method was demonstrated. • DmoA is also an oxidoreductase capable of oxidizing NADH and reducing FMN. • DmoA oxidizes NADH in the absence of external FMN. [ABSTRACT FROM AUTHOR]

Hydrogenase-mediated reduction of flavin mononucleotide by H2 is exploited to enable cleaner application of nitroreductase enzymes for reduction of aromatic nitro functional groups. This turns the overall reaction into a biocatalytic hydrogenation. Use of flavincontaining nitroreductases in industrial biotechnology typically relies upon NADH or NADPH as reductant, together with glucose dehydrogenase and glucose as a regeneration system for the reduced nicotinamide cofactor, with 3 equivalents of the carbon-intensive glucose required for a single 6-electron nitro to amine conversion. We show here that reduced flavin mononucleotide is an alternative reductant for nitroreductases, and by combining this with H2-driven recycling of reduced flavin, we avoid glucose, thereby enabling atom-efficient biocatalytic nitro reductions. We compare this biocatalytic system, via green chemistry metrics, to existing strategies for biocatalytic nitro-group reductions, particularly with respect to replacing glucose with H2 gas.We take steps towards demonstrating industrial viability: we report an overexpression system for E. coli hydrogenase 1, giving a 12-fold improvement in enzyme yield; we show a reaction in which the hydrogenase exhibits > 26,000 enzyme turnovers; and we demonstrate reasonable solvent tolerance of the hydrogenase and flavin reduction system which would enable reaction intensification. [ABSTRACT FROM AUTHOR]

Synthetic biology has boosted the rapid development on using non-methylotrophy as chassis for value added chemicals production from one-carbon feedstocks, such as methanol and formic acid. The one-carbon dissimilation pathway can provide more NADH than monosaccharides including glucose, which is conducive for reductive chemicals production, such as succinic acid. In this study, the one-carbon dissimilation pathway was introduced in E. coli Suc260 to enhance the succinic acid production capability. Through the rational construction of methanol dissimilation pathway, the succinic acid yield was increased from 0.91 to 0.95 g/g with methanol and sodium formate as auxiliary substrates in anaerobic fed-batch fermentation. Furthermore, the metabolic flux of by-product pyruvate was redirected to succinic acid together with the CO2 fixation. Finally, through the immobilization on a specially designed glycosylated membrane, E. coli cells are more resistant to adverse environments, and the final yield of succinic acid was improved to 0.98 g/g. This study proved the feasibility of endowing producers with methanol dissimilation pathway to enhance the production of reductive metabolites. [ABSTRACT FROM AUTHOR]

While lignocellulose is a promising source of renewable sugars for microbial fermentations, the presence of inhibitory compounds in typical lignocellulosic feedstocks, such as furfural, has hindered their utilisation. In Escherichia coli, a major route of furfural toxicity is the depletion of NADPH pools due to its use as a substrate by the YqhD enzyme that reduces furfural to its less toxic alcohol form. Here, we examine the potential of exploiting benzyl alcohol dehydrogenases as an alternative means to provide this same catalytic function but using the more abundant reductant NADH, as a strategy to increase the capacity for furfural removal. We determine the biochemical properties of three of these enzymes, from Pseudomonas putida, Acinetobacter calcoaceticus, and Burkholderia ambifaria, which all demonstrate furfural reductase activity. Furthermore, we show that the P. putida and B. ambifaria enzymes are able to provide substantial increases in furfural tolerance in vivo, by allowing more rapid conversion to furfuryl alcohol and resumption of growth. The study demonstrates that methods to seek alternative cofactor dependent enzymes can improve the intrinsic robustness of microbial chassis to feedstock inhibitors. [ABSTRACT FROM AUTHOR]

A novel arabitol dehydrogenase (ArDH) gene was cloned from a bacterium named Aspergillus nidulans and expressed heterologously in Escherichia coli. The purified ArDH exhibited the maximal activity in pH 9.5 Tris-HCl buffer at 40 °C, showed Km and Vmax of 1.2 mg/mL and 9.1 U/mg, respectively. The ArDH was used to produce the L-xylulose and coupled with the NADH oxidase (Nox) for the regeneration of NAD+. In further optimization, a high conversion of 84.6% in 8 hours was achieved under the optimal conditions: 20 mM of xylitol, 100 µM NAD+ in pH 9.0 Tris-HCl buffer at 30 °C. The results indicated the coupling system with cofactor regeneration provides a promising approach for L-xylulose production from xylitol. [ABSTRACT FROM AUTHOR]

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key enzyme in the central metabolism of microbial cells. GAPDHs differ in cofactor specificity and use NAD+, NADP+, or both cofactors, reducing them to NADH and NADPH, respectively. Sufficient NADPH supply is one of the critical factors required for synthesis of the amino acids l-lysine, l-threonine, and l-proline in industrially important Escherichia coli-based producer strains. E. coli cells have NAD+-dependent glycolytic GAPDH. One reasonable approach to increase NADPH formation in cells is to change the specificity of the GAPDH from NAD+ to NADP+. In this study, we modified the cofactor specificity of E. coli GAPDH by amino acid substitutions at positions 34, 188 and 189. Several mutant enzymes with dual NAD+/NADP+ cofactor specificity were obtained, and their kinetic parameters were determined. Overexpression of the genes encoding the resulting mutant GAPDHs with dual cofactor specificity in cells of l-lysine-, l-threonine-, and l-proline-producing E. coli strains led to a marked increase in the accumulation of the corresponding amino acid in the culture medium. This effect was more pronounced when cultivating on xylose as a carbon source. Other possible applications of the mutant enzymes are discussed. [ABSTRACT FROM AUTHOR]

[Display omitted] • C. glutamicum exhibited higher formate tolerance than E. coli. • Systematic metabolic engineering enabled C. glutamicum to assimilate formate. • Metabolic model revealed bottlenecks in formate assimilation metabolism. • 13C-tracer revealed the pattern of formate assimilation in C. glutamicum. Formate as an ideal mediator between the physicochemical and biological realms can be obtained from electrochemical reduction of CO 2 and used to produce bio-chemicals. Yet, limitations arise when employing natural formate-utilizing microorganisms due to restricted product range and low biomass yield. This study presents a breakthrough: engineered Corynebacterium glutamicum strains (L2-L4) through modular engineering. L2 incorporates the formate-tetrahydrofolate cycle and reverse glycine cleavage pathway, L3 enhances NAD(P)H regeneration, and L4 reinforces metabolic flux. Metabolic modeling elucidates C1 assimilation, guiding strain optimization for co-fermentation of formate and glucose. Strain L4 achieves an OD 600 of 0.5 and produces 0.6 g/L succinic acid. 13C-labeled formate confirms C1 assimilation, and further laboratory evolution yields 1.3 g/L succinic acid. This study showcases a successful model for biologically assimilating formate in C. glutamicum that could be applied in C1-based biotechnological production, ultimately forming a formate-based bioeconomy. [ABSTRACT FROM AUTHOR]

The asymmetric reduction of α , β -unsaturated compounds conjugated with electron-withdrawing group by ene-reductases (ERs) is a valuable method for the synthesis of enantiopure chiral compounds. This study introduced an ER from Corynebacterium casei (Cc ER) which was heterologously expressed in Escherichia coli BL21(DE3), and the purified recombinant Cc ER was characterized for its biocatalytic properties. Cc ER exhibited the highest specific activity at 40 °C and pH 6.5, and showcased appreciable stability below 40 °C over a pH range of 6.0–7.0. The enzyme displayed high resistance to methanol. Cc ER accepted NADH or NADPH as a cofactor and exhibited a broad substrate spectrum towards α , β -unsaturated compounds. It achieved complete conversion of 2-cyclohexen-1-one and good performance for stereoselective reduction of (R)-carvone (conversion 98 %, diastereoselectivity 96 %). This study highlights the robustness and potential of Cc ER. [ABSTRACT FROM AUTHOR]

The coupling of PHB generation with NADH reoxidation is required to generate PHB as a fermentation product. A fundamental trait to accomplish this feature is to express a functional NADH-preferring acetoacetyl-CoA reductase, engaged in PHB accumulation. One way to obtain such a reductase is by engineering the cofactor preference of the acetoacetyl-CoA reductase encoded by the phaB1 gene from Cupriavidus necator (AARCn1). Aiming to have a deeper understanding of the structural determinants of the cofactor preference in AARCn1, and to obtain an NADH-preferring acetoacetyl-CoA reductase derived from this protein, some engineered enzymes were expressed, purified and kinetically characterized, together with the parental AARCn1. One of these engineered enzymes, Chimera 5, experimentally showed a selectivity ratio ((kcat/KM)NADH/(kcat/KM)NADPH) ≈ 18, which is 160 times higher than the selectivity ratio experimentally observed in the parental AARCn1. A thermodynamic-kinetic approach was employed to estimate the cofactor preference and flux capacity of Chimera 5 under physiological conditions. According to this approach, Chimera 5 could prefer NADH over NADPH between 25 and 150 times. Being a derivative of AARCn1, Chimera 5 should be readily functional in Escherichia coli and C. necator. Moreover, with the expected expression level, its activity should be enough to sustain PHB accumulation fluxes similar to the fluxes previously observed in these biotechnologically relevant cell factories. [ABSTRACT FROM AUTHOR]

During the light‐dependent reaction of photosynthesis, green plants couple photoinduced cascades of redox reactions with transmembrane proton translocations to generate reducing equivalents and chemical energy in the form of NADPH (nicotinamide adenine dinucleotide phosphate) and ATP (adenosine triphosphate), respectively. We mimic these basic processes by combining molecular ruthenium polypyridine‐based photocatalysts and inverted vesicles derived from Escherichia coli. Upon irradiation with visible light, the interplay of photocatalytic nicotinamide reduction and enzymatic membrane‐located respiration leads to the simultaneous formation of two biologically active cofactors, NADH (nicotinamide adenine dinucleotide) and ATP, respectively. This inorganic‐biologic hybrid system thus emulates the cofactor delivering function of an active chloroplast. [ABSTRACT FROM AUTHOR]

Summary: Most microorganisms can metabolize glycerol when external electron acceptors are available (i.e. under respiratory conditions). However, few can do so under fermentative conditions owing to the unique redox constraints imposed by the high degree of reduction of glycerol. Here, we utilize in silico analysis combined with in vivo genetic and biochemical approaches to investigate the fermentative metabolism of glycerol in Escherichia coli. We found that E. coli can achieve redox balance at alkaline pH by reducing protons to H2, complementing the previously reported role of 1,2‐propanediol synthesis under acidic conditions. In this new redox balancing mode, H2 evolution is coupled to a respiratory glycerol dissimilation pathway composed of glycerol kinase (GK) and glycerol‐3‐phosphate (G3P) dehydrogenase (G3PDH). GK activates glycerol to G3P, which is further oxidized by G3PDH to generate reduced quinones that drive hydrogenase‐dependent H2 evolution. Despite the importance of the GK‐G3PDH route under alkaline conditions, we found that the NADH‐generating glycerol dissimilation pathway via glycerol dehydrogenase (GldA) and phosphoenolpyruvate (PEP)‐dependent dihydroxyacetone kinase (DHAK) was essential under both alkaline and acidic conditions. We assessed system‐wide metabolic impacts of the constraints imposed by the PEP dependency of the GldA‐DHAK route. This included the identification of enzymes and pathways that were not previously known to be involved in glycerol metabolisms such as PEP carboxykinase, PEP synthetase, multiple fructose‐1,6‐bisphosphatases and the fructose phosphate bypass. [ABSTRACT FROM AUTHOR]

Background: As a kind of rare sugar alcohol, allitol has important application values in food and medication. In addition, it can be used as a key substrate to produce other D/L-rare sugars. Allitol can be effectively produced by the resting-cell biotransformation method. Results: Two recombinant Escherichia coli strains, one simultaneously expressing ribitol dehydrogenase (RDH) and formate dehydrogenase (FDH) in fusion (fusion expression strain for short) and the other expressing the above two enzymes individually (individual expression strain for short), were respectively constructed and used for allitol bioproduction. The produced allitol was confirmed by HPLC, mass spectrometry, and polarimetry. The individual expression strain had higher activity, which produced 58.5 g/L allitol from 90 g/L D-allulose (also named D-psicose) in 1 h with an allitol productivity of 58.5 g/L/h under optimized conditions. Conclusions: The constructed individual expression strain had the highest allitol productivity among the reports. The production process developed in this study was simple, highly efficient, and had the potential for mass production of allitol. [ABSTRACT FROM AUTHOR]

Short-chain esters have broad utility as flavors, fragrances, solvents, and biofuels. Controlling selectivity of ester microbial biosynthesis has been an outstanding metabolic engineering problem. In this study, we enabled the de novo fermentative microbial biosynthesis of butyryl-CoA-derived designer esters (e.g., butyl acetate, ethyl butyrate, butyl butyrate) in Escherichia coli with controllable selectivity. Using the modular design principles, we generated the butyryl-CoA-derived ester pathways as exchangeable production modules compatible with an engineered chassis cell for anaerobic production of designer esters. We designed these modules derived from an acyl-CoA submodule (e.g., acetyl-CoA, butyryl-CoA), an alcohol submodule (e.g., ethanol, butanol), a cofactor regeneration submodule (e.g., NADH), and an alcohol acetyltransferase (AAT) submodule (e.g., ATF1, SAAT) for rapid module construction and optimization by manipulating replication (e.g., plasmid copy number), transcription (e.g., promoters), translation (e.g., codon optimization), pathway enzymes, and pathway induction conditions. To further enhance production of designer esters with high selectivity, we systematically screened various strategies of protein solubilization using protein fusion tags and chaperones to improve the soluble expression of multiple pathway enzymes. Finally, our engineered ester-producing strains could achieve 19-fold increase in butyl acetate production (0.64 g/L, 96% selectivity), 6-fold increase in ethyl butyrate production (0.41 g/L, 86% selectivity), and 13-fold increase in butyl butyrate production (0.45 g/L, 54% selectivity) as compared to the initial strains. Overall, this study presented a generalizable framework to engineer modular microbial platforms for anaerobic production of butyryl-CoA-derived designer esters from renewable feedstocks. • Developed a generalizable framework to engineer a modular microbial platform for anaerobic production of designer esters. • Engineered the de novo modular fermentative pathways for selective biosynthesis of butyryl-CoA-derived esters in E. coli. • Manipulated replication, transcription, and (post)translation to tune the metabolic fluxes of the ester production modules. • Implemented various protein solubilization strategies on aggregate-prone pathway enzymes for selective ester production. • Demonstrated modular microbial biosynthesis of butyryl-CoA-derived esters from glucose with high (up to >96%) selectivity. [ABSTRACT FROM AUTHOR]

Microbial-based bio-refining seeks to replace fossil-based chemical industry with reduced capital cost and lower environmental concern. However, current metabolic engineering practices suffer from intensive CO2 emission and limited yield ceiling via hardwired native biochemical infrastructures. Herein, via a highly-efficient 1,3-butanediol pathway, we demonstrate a new approach of tunable hybrid carbon metabolism coordination for carbon-efficient bioproduction in engineered Escherichia coli. The approach fine-tunes a phosphoketolase-mediated non-oxidative glycolysis based on computational analysis to accommodate the output NAD(P)H/acetyl-CoA stoichiometries from sugar breakdown to downstream pathway demands, raising the theoretical pathway yields of acetyl-CoA-derived products to their upper limits. As a proof-of-concept demonstration, coordination of hybrid carbon metabolism enables the highest titer to date of 3-hydroxybutyrate from glucose (51.13 g l−1) in bioreactor-based fed-batch cultivation, with a yield (1.13 mol mol−1) reaching 113% of the theoretical maximum from native metabolism. Further combination of carbon metabolism coordination and a novel 3-hydroxybutyrate-responsive dynamic control circuit for fatty acid pathway repression affords the highest titer and yield to date of 1,3-butanediol (22.66 g l−1, 0.80 mol mol−1) from glucose. This work demonstrates a generalizable approach for carbon-efficient microbial production through a hybrid and tunable biochemical infrastructure. [ABSTRACT FROM AUTHOR]

L-Rhamnose and L-fucose are the two main 6-deoxyhexoses Escherichia coli can use as carbon and energy sources. Deoxyhexose metabolism leads to the formation of lactaldehyde, whose fate depends on oxygen availability. Under anaerobic conditions, lactaldehyde is reduced to 1,2-propanediol, whereas under aerobic conditions, it should be oxidized into lactate and then channeled into the central metabolism. However, although this all-or-nothing view is accepted in the literature, it seems overly simplistic since propanediol is also reported to be present in the culture medium during aerobic growth on L-fucose. To clarify the functioning of 6-deoxyhexose sugar metabolism, a quantitative metabolic analysis was performed to determine extra- and intracellular fluxes in E. coli K-12 MG1655 (a laboratory strain) and in E. coli Nissle 1917 (a human commensal strain) during anaerobic and aerobic growth on L-rhamnose and L-fucose. As expected, lactaldehyde is fully reduced to 1,2-propanediol under anoxic conditions, allowing complete reoxidation of the NADH produced by glyceraldehyde-3-phosphate-dehydrogenase. We also found that net ATP synthesis is ensured by acetate production. More surprisingly, lactaldehyde is also primarily reduced into 1,2-propanediol under aerobic conditions. For growth on L-fucose, 13C-metabolic flux analysis revealed a large excess of available energy, highlighting the need to better characterize ATP utilization processes. The probiotic E. coli Nissle 1917 strain exhibits similar metabolic traits, indicating that they are not the result of the K-12 strain's prolonged laboratory use. [ABSTRACT FROM AUTHOR]

Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I from Escherichia coli is among the best functionally characterized complexes, but its structure remains unknown, hindering further studies to understand the enzyme coupling mechanism. Here, we describe the single particle cryo-electron microscopy (cryo-EM) structure of the entire catalytically active E. coli complex I reconstituted into lipid nanodiscs. The structure of this mesophilic bacterial complex I displays highly dynamic connection between the peripheral and membrane domains. The peripheral domain assembly is stabilized by unique terminal extensions and an insertion loop. The membrane domain structure reveals novel dynamic features. Unusual conformation of the conserved interface between the peripheral and membrane domains suggests an uncoupled conformation of the complex. Considering constraints imposed by the structural data, we suggest a new simple hypothetical coupling mechanism for the molecular machine. [ABSTRACT FROM AUTHOR]

Objectives: Alteration of the cofactor specificity of acrylyl-CoA reductase (AcuI) catalyzing the NAD(P)H-dependent reduction of acrylyl-CoA to propionyl-CoA is often desirable for designing of artificial metabolic pathways of various appointments. Results: Several variants of AcuIs from Escherichia coli K-12 with multiple amino acid substitutions to alter the cofactor preference were obtained by site directed mutagenesis and the modified enzymes as His6-tagged proteins were characterized. The simultaneous substitutions of arginine-180, arginine-198 and serine-178 residues by alanine in the enzyme pocket sequence as well as other amino acid changes decreased both NADPH- and NADH-dependent activities in comparison to the wild-type enzyme. The replacement of serine-156 by glutamic acid decreased NADPH-dependent activity at least 7000-fold but NADH-dependent activity only by threefold. The replacement of serine-156 by aspartic acid decreased NADPH-dependent activity 70-fold with fair preservation of activity and specificity to NADH. Conclusions: These results demonstrated a relevance of Asp156 in the interaction of AcuI from E. coli K-12 with NADH as a coenzyme. These findings may provide reference information for shifting coenzyme specificity of acrylyl-CoA reductases. [ABSTRACT FROM AUTHOR]