Conversion of phosphoenolpyruvate to pyruvate in Thermoanaerobacterium saccharolyticum

Unveiling novel oxygen-dependent docosahexaenoic acid biosynthesis pathway in Crypthecodinium cohnii via dual-function △4-fatty acid desaturases

Crypthecodinium cohnii, a protist renowned for its high docosahexaenoic acid (DHA) production, has an unclear mechanism for converting docosapentaenoic acid (DPA) into DHA. This study employed transcriptomic analysis to investigate the effect of excessive oxygen limitation (EOL) on DHA biosynthesis, uncovering a novel oxygen-dependent pathway. The use of intermittent oxygen limitation (IOL) strategy significantly boosted DHA production. Five △4-fatty acid desaturase (FAD4) genes were identified, with CcFAD4_52534 exhibiting the highest catalytic efficiency and dual-functionality, converting eicosapentaenoic acid (EPA) to DPA, and subsequently to DHA. This study integrates transcriptomic insights, the discovery of the bifunctional CcFAD4_52534 enzyme, and the optimized IOL strategy, offering transformative potential for sustainable and high-yield DHA production through tailored genetic engineering in C. cohnii. This approach bridges ecological understanding with industrial innovation.

Comparative genomics reveals probable adaptations for xylose use in Thermoanaerobacterium saccharolyticum

Second-generation ethanol, a promising biofuel for reducing greenhouse gas emissions, faces challenges due to the inefficient metabolism of xylose, a pentose sugar. Overcoming this hurdle requires exploration of genes, pathways, and organisms capable of fermenting xylose. Thermoanaerobacterium saccharolyticum is an organism capable of naturally fermenting compounds of industrial interest, such as xylose, and understanding evolutionary adaptations may help to bring novel genes and information that can be used for industrial yeast, increasing production of current bio-platforms. This study presents a deep evolutionary study of members of the firmicutes clade, focusing on adaptations in Thermoanaerobacterium saccharolyticum that may be related to overall fermentation metabolism, especially for xylose fermentation. One highlight is the finding of positive selection on a xylose-binding protein of the xylFGH operon, close to the annotated sugar binding site, with this protein already being found to be expressed in xylose fermenting conditions in a previous study. Results from this study can serve as basis for searching for candidate genes to use in industrial strains or to improve Thermoanaerobacterium saccharolyticum as a new microbial cell factory, which may help to solve current problems found in the biofuels' industry.

Erythritol alters phosphotransferase gene expression and inhibits the in vitro growth of Staphylococcus coagulans isolated from canines with pyoderma

Staphylococcus coagulans (SC) belongs to a group of coagulase-positive staphylococci occasionally isolated from the skin lesions of dogs with pyoderma. We recently revealed that erythritol, a sugar alcohol, inhibited the growth of SC strain JCM7470. This study investigated the molecular mechanisms involved in this growth inhibition of JCM7470 by erythritol, and determine whether erythritol inhibits the growth of SC isolated from the skin of dogs with pyoderma. Comprehensive analysis of the gene expression of JCM7470 in the presence of erythritol revealed that erythritol upregulated the expression of glcB and ptsG genes, both of which encode phosphotransferase system (PTS) glucoside- and glucose-specific permease C, B, and A domains (EIICBA), respectively, associated with sugar uptake. Moreover, erythritol suppressed in vitro growth of all 27 SC strains isolated from the skin lesions of canine pyoderma, including 13 mecA gene-positive and 14 mecA gene-negative strains. Finally, the growth inhibition of the SC clinical isolates by erythritol was restored by the addition of glucose. In summary, we revealed that erythritol promotes PTS gene expression and suppresses the in vitro growth of SC clinical isolates from dogs with pyoderma. Restoration of the erythritol-induced growth inhibition by glucose suggested that glucose starvation may contribute to the growth inhibition of SC.

Erythritol alters gene transcriptome signatures, cell growth, and biofilm formation in Staphylococcus pseudintermedius

BACKGROUND

Erythritol was found to inhibit the growth of microorganisms. The present study aimed to demonstrate the growth inhibition of Staphylococcus pseudintermedius by erythritol and to define the changes in gene transcription signatures induced by erythritol. Changes in the gene transcription profiles were analysed by RNA sequencing and quantitative reverse transcription PCR. Gene ontology analysis was performed to assign functional descriptions to the genes.

RESULTS

Erythritol inhibited S. pseudintermedius growth in a dose-dependent manner. We then performed a transcriptome analysis of S. pseudintermedius with and without 5% (w/w) erythritol exposure to validate the mechanism of growth inhibition. We revealed that erythritol induced up-regulation of three genes (ptsG, ppdK, and ppdkR) that are related to the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). Glucose supplementation restored the up-regulation of the PTS-related genes in response to erythritol. In addition, erythritol down-regulated eleven genes that are located in a single pur-operon and inhibited biofilm formation of S. pseudintermedius.

CONCLUSIONS

These findings indicated that erythritol antagonistically inhibits PTS-mediated glucose uptake, thereby exerting a growth inhibitory effect on S. pseudintermedius. Moreover, erythritol inhibits the 'de novo' IMP biosynthetic pathway that may contribute to biofilm synthesis in S. pseudintermedius.

Pyrophosphate as allosteric regulator of ATP-phosphofructokinase in Clostridium thermocellum and other bacteria with ATP- and PPi-phosphofructokinases

The phosphofructokinase (Pfk) reaction represents one of the key regulatory points in glycolysis. While most organisms encode for Pfks that use ATP as phosphoryl donor, some organisms also encode for PP_i-dependent Pfks. Despite this central role, the biochemical characteristics as well as the physiological role of both Pfks is often not known. Clostridium thermocellum is an example of a microorganism that encodes for both Pfks, however, only PP_i-Pfk activity has been detected in cell-free extracts and little is known about the regulation and function of both enzymes. In this study, the ATP- and PP_i-Pfk of C. thermocellum were purified and biochemically characterized. No allosteric regulators were found for PP_i-Pfk amongst common effectors. With fructose-6-P, PP_i, fructose-1,6-bisP, and P_i PP_i-Pfk showed high specificity (K_M < 0.62 mM) and maximum activity (V_max > 156 U mg^-1). In contrast, ATP-Pfk showed much lower affinity (K_0.5 of 9.26 mM) and maximum activity (14.5 U mg^-1) with fructose-6-P. In addition to ATP, also GTP, UTP and ITP could be used as phosphoryl donors. The catalytic efficiency with GTP was 7-fold higher than with ATP, suggesting that GTP is the preferred substrate. The enzyme was activated by NH₄⁺, and pronounced inhibition was observed with GDP, FBP, PEP, and especially with PP_i (K_i of 0.007 mM). Characterization of purified ATP-Pfks originating from eleven different bacteria, encoding for only ATP-Pfk or for both ATP- and PP_i-Pfk, identified that PP_i inhibition of ATP-Pfks could be a common phenomenon for organisms with a PP_i-dependent glycolysis.

Effects of biochar addition towards the treatment of blackwater in anaerobic dynamic membrane bioreactor (AnDMBR): Comparison among room temperature, mesophilic and thermophilic conditions

Effects of biochar addition on the performance of anaerobic dynamic membrane bioreactor (AnDMBR) under different temperatures for blackwater treatment was investigated. When the organic load ratios (OLR) was 1.0 g COD/L·d, the specific methane yield for the three biochar-amended reactors were 125.7, 148.0 and 182.3 mLCH₄/g COD_removed, respectively. Compare to those digesters without biochar participation, the methane production in the thermophilic reactor with biochar increased by 12% while the other two digesters increased by 6-10%. An analysis of membrane filtration resistance showed a reduction in total resistance (R_t) of 6.2 × 10¹¹-7.3 × 10¹¹ m^-1 when biochar was added to the three reactors. The thermophilic reactors with biochar increased the relative abundance of Methanothermobacter and promoted gene expression of metabolic pathways related to hydrolysis, acid production and methane production. Overall, biochar showed great potential as an inexpensive conductive material to increase methane production with reduced membrane fouling in AnDMBR systems.

Upgrade the high-load anaerobic digestion and relieve acid stress through the strategy of side-stream micro-aeration: biochemical performances, microbial response and intrinsic mechanisms

In high-load anaerobic digestion such as in kitchen waste, side-stream micro-aeration (SMA) shows excellent operational performance to direct micro-aeration (DMA). It immediately restores the acidification to stability. Methanogenic performance remained stable when organic load ratios (OLR) was further increased to 5.5 g VS/L. Enhanced enzyme activity, microbial aggregation, and proliferation of bacteria and archaea were observed in SMA. The results indicates that SMA enriched Methanosaeta (relative abundance exceeded 93%) and induced the change of the main methanogenic pathway to acetoclastic methanogenesis. Mechanisms was further explored by using metagenomic analysis, and the results show SMA avoids mass formation of ROS (reactive oxygen species) by cycling the aerated slurry, and retains benefits of trace O₂ on material and energic metabolism, which poses great application potentials and deserves further investigation.

Metabolic energy conservation for fermentative product formation

Microbial production of bulk chemicals and biofuels from carbohydrates competes with low-cost fossil-based production. To limit production costs, high titres, productivities and especially high yields are required. This necessitates metabolic networks involved in product formation to be redox-neutral and conserve metabolic energy to sustain growth and maintenance. Here, we review the mechanisms available to conserve energy and to prevent unnecessary energy expenditure. First, an overview of ATP production in existing sugar-based fermentation processes is presented. Substrate-level phosphorylation (SLP) and the involved kinase reactions are described. Based on the thermodynamics of these reactions, we explore whether other kinase-catalysed reactions can be applied for SLP. Generation of ion-motive force is another means to conserve metabolic energy. We provide examples how its generation is supported by carbon-carbon double bond reduction, decarboxylation and electron transfer between redox cofactors. In a wider perspective, the relationship between redox potential and energy conservation is discussed. We describe how the energy input required for coenzyme A (CoA) and CO2 binding can be reduced by applying CoA-transferases and transcarboxylases. The transport of sugars and fermentation products may require metabolic energy input, but alternative transport systems can be used to minimize this. Finally, we show that energy contained in glycosidic bonds and the phosphate-phosphate bond of pyrophosphate can be conserved. This review can be used as a reference to design energetically efficient microbial cell factories and enhance product yield.

Metabolic Fluxes of Nitrogen and Pyrophosphate in Chemostat Cultures of Clostridium thermocellum and Thermoanaerobacterium saccharolyticum

Clostridium thermocellum and Thermoanaerobacterium saccharolyticum were grown in cellobiose-limited chemostat cultures at a fixed dilution rate. C. thermocellum produced acetate, ethanol, formate, and lactate. Surprisingly, and in contrast to batch cultures, in cellobiose-limited chemostat cultures of T. saccharolyticum, ethanol was the main fermentation product. Enzyme assays confirmed that in C. thermocellum, glycolysis proceeds via pyrophosphate (PP_i)-dependent phosphofructokinase (PFK), pyruvate-phosphate dikinase (PPDK), as well as a malate shunt for the conversion of phosphoenolpyruvate (PEP) to pyruvate. Pyruvate kinase activity was not detectable. In T. saccharolyticum, ATP but not PP_i served as cofactor for the PFK reaction. High activities of both pyruvate kinase and PPDK were present, whereas the activities of a malate shunt enzymes were low in T. saccharolyticum In C. thermocellum, glycolysis via PP_i-PFK and PPDK obeys the equation glucose + 5 NDP + 3 PP_i → 2 pyruvate + 5 NTP + P_i (where NDP is nucleoside diphosphate and NTP is nucleoside triphosphate). Metabolic flux analysis of chemostat data with the wild type and a deletion mutant of the proton-pumping pyrophosphatase showed that a PP_i-generating mechanism must be present that operates according to ATP + P_i → ADP + PP_i Both organisms also produced significant amounts of amino acids in cellobiose-limited cultures. It was anticipated that this phenomenon would be suppressed by growth under nitrogen limitation. Surprisingly, nitrogen-limited chemostat cultivation of wild-type C. thermocellum revealed a bottleneck in pyruvate oxidation, as large amounts of pyruvate and amino acids, mainly valine, were excreted; up to 50% of the nitrogen consumed was excreted again as amino acids.IMPORTANCE This study discusses the fate of pyrophosphate in the metabolism of two thermophilic anaerobes that lack a soluble irreversible pyrophosphatase as present in Escherichia coli but instead use a reversible membrane-bound proton-pumping enzyme. In such organisms, the charging of tRNA with amino acids may become more reversible. This may contribute to the observed excretion of amino acids during sugar fermentation by Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Calculation of the energetic advantage of reversible pyrophosphate-dependent glycolysis, as occurs in Clostridium thermocellum, could not be properly evaluated, as currently available genome-scale models neglect the anabolic generation of pyrophosphate in, for example, polymerization of amino acids to protein. This anabolic pyrophosphate replaces ATP and thus saves energy. Its amount is, however, too small to cover the pyrophosphate requirement of sugar catabolism in glycolysis. Consequently, pyrophosphate for catabolism is generated according to ATP + P_i → ADP + PP_i.