Structural Characterization of Glycerol Kinase from the Thermophilic Fungus Chaetomium thermophilum

Crystal structure of glycerol kinase from Trypanosoma cruzi, a potential molecular target in Chagas disease

Chagas disease is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. It bears a significant global health burden with limited treatment options, thus calling for the development of new and effective drugs. Certain trypanosomal metabolic enzymes have been suggested to be druggable and valid for subsequent inhibition. In this study, the crystal structure of glycerol kinase from T. cruzi, a key enzyme in glycerol metabolism in this parasite, is presented. Structural analysis allowed a detailed description of the glycerol binding pocket, while comparative assessment pinpointed a potential regulatory site which may serve as a target for selective inhibition. These findings advance the understanding of glycerol metabolism in eukaryotes and provide a solid basis for the future treatment of Chagas disease.

Anaerobic co-metabolic biodegradation of pharmaceuticals and personal care products driven by glycerol fermentation

Anaerobic digestion in two sequential phases, acidogenesis and methanogenesis, has been shown to be beneficial for enhancing the biomethane generation from wastewater. In this work, the application of glycerol (GOH) as a fermentation co-substrate during the wastewater treatment was evaluated on the biodegradation of different pharmaceuticals and personal care products (PPCPs). GOH co-digestion during acidogenesis led to a significant increase in the biodegradation of acetaminophen (from 78 to 89%), ciprofloxacin (from 25 to 46%), naproxen (from 73 to 86%), diclofenac (from 36 to 48%), ibuprofen (from 65 to 88%), metoprolol (from 45 to 59%), methylparaben (from 64 to 78%) and propylparaben (from 68 to 74%). The heterotrophic co-metabolism of PPCPs driven by glycerol was confirmed by the biodegradation kinetics, in which kbio (biodegradation kinetics constant) values increased from 0.18 to 2.11 to 0.27-3.60 L g-1-VSS d-1, for the operational phases without and with GOH, respectively. The assessment of metabolic pathways in each phase revealed that the prevalence of aromatic compounds degradation, metabolism of xenobiotics by cytochrome P450, and benzoate degradation routes during acidogenesis are key factors for the enzymatic mechanisms linked to the PPCPs co-metabolism. The phase separation of anaerobic digestion was effective in the PPCPs biodegradation, and the co-fermentation of glycerol provided an increase in the generation potential of biomethane in the system (energetic potential of 5.0 and 6.3 kJ g-1-CODremoved, without and with GOH, respectively). This study showed evidence that glycerol co-fermentation can exert a synergistic effect on the PPCPs removal during anaerobic digestion mediated by heterotrophic co-metabolism.

Oleic Acid Promotes the Biosynthesis of 10-Hydroxy-2-decenoic Acid via Species-Selective Remodeling of TAGs in Apis mellifera ligustica

This study aimed to assess the impact of oleic acid (OA) supplementation on the biosynthesis of 10-hydroxy-2-decenoic acid (10-HDA) in Apis mellifera ligustica. In experiment 1, varying concentrations of OA (2%, 4%, 6% and 8%) were added to an artificial diet for newly emerged bees reared in cages. Analysis of 10-HDA content and gene expression in the mandibular gland (MG) revealed that the 8% OA treatment had the greatest impact on promoting the synthesis of 10-HDA. Subsequent investigations utilized RNA-seq and lipidomics to characterize the molecular signature in the MG after feeding the 8% OA diet. Phosphatidylcholine (PC) and triacylglycerol (TAG) were found to be the predominant lipids in the MG of worker bees. A total of 154 TAGs were identified, with TAG (18:1-18:1-18:1) exhibiting the highest abundance, which increased by 1.5 times. The major TAG species contained palmitic acid (16:0) and oleic acid (18:1) in their structure, which was associated with fatty acid composition of diet. The increase in abundance of main TAGs may be attributed to the upregulation of glycerol-3-phosphate acyltransferase (Gpat) and glycerol kinase (GK) gene expression at the transcriptional level. The upregulation of differentially expressed genes (DEGs) related to carbohydrate metabolism may contribute to meeting the heightened metabolic demands of the MGs in worker bees. Royal jelly (RJ) samples from bee colonies fed with the 8% OA diet exhibited higher 10-HDA level than RJ collected from bee colonies fed with the artificial diet. These results indicate that 8% OA addition in the diet enhanced biosynthesis of 10-HDA in the mandibular gland, which was accompanied by significant and highly species-selective remodeling of TAGs.

Multimodal deep learning as a next challenge in nutrition research: tailoring fermented dairy products based on cytidine diphosphate-diacylglycerol synthase-mediated lipid metabolism

Deep learning is evolving in nutritional epidemiology to address challenges including precise nutrition and data-driven disease modeling. Fermented dairy products consumption as the implementation of specific dietary priority contributes to a lower risk of all-cause mortality, cardiovascular disease, and obesity. Various lipid types play different roles in cardiometabolic health and fermentation process changes the lipid profile in dairy products. Leveraging the power of multiple biological datasets can provide mechanistic insights into how proteins impact lipid pathways, and establish connections among fermentation-lipid biomarkers-protein. The recent leap of deep learning has been performed in food category recognition, agro-food freshness detection, and food flavor prediction and regulation. The proposed multimodal deep learning method includes four steps: (i) Forming data matrices based on data generated from different omics layers. (ii) Decomposing high-dimensional omics data according to self-attention mechanism. (iii) Constructing View Correlation Discovery Network to learn the cross-omics correlations and integrate different omics datasets. (iv) Depicting a biological network for lipid metabolism-centered quantitative multi-omics data analysis. Relying on the cytidine diphosphate-diacylglycerol synthase-mediated lipid metabolism regulates the glycerophospholipid composition of fermented dairy effectively. Innovative processing strategies including ohmic heating and pulsed electric field improve the sensory qualities and nutritional characteristics of the products.

Glycerol metabolism supports oral commensal interactions

During oral biofilm development, interspecies interactions drive species distribution and biofilm architecture. To understand what molecular mechanisms determine these interactions, we used information gained from recent biogeographical investigations demonstrating an association of corynebacteria with streptococci. We previously reported that Streptococcus sanguinis and Corynebacterium durum have a close relationship through the production of membrane vesicle and fatty acids leading to S. sanguinis chain elongation and overall increased fitness supporting their commensal state. Here we present the molecular mechanisms of this interspecies interaction. Coculture experiments for transcriptomic analysis identified several differentially expressed genes in S. sanguinis. Due to its connection to fatty acid synthesis, we focused on the glycerol-operon. We further explored the differentially expressed type IV pili genes due to their connection to motility and biofilm adhesion. Gene inactivation of the glycerol kinase glpK had a profound impact on the ability of S. sanguinis to metabolize C. durum secreted glycerol and impaired chain elongation important for their interaction. Investigations on the effect of type IV pili revealed a reduction of S. sanguinis twitching motility in the presence of C. durum, which was caused by a decrease in type IV pili abundance on the surface of S. sanguinis as determined by SEM. In conclusion, we identified that the ability to metabolize C. durum produced glycerol is crucial for the interaction of C. durum and S. sanguinis. Reduced twitching motility could lead to a closer interaction of both species, supporting niche development in the oral cavity and potentially shaping symbiotic health-associated biofilm communities.

Expression and characterisation of human glycerol kinase: the role of solubilising agents and molecular chaperones

BACKGROUND

Glycerol kinase (GK; EC 2.7.1.30) facilitates the entry of glycerol into pathways of glucose and triglyceride metabolism and may play a potential role in Type 2 diabetes mellitus (T2DM). However, the detailed regulatory mechanisms and structure of the human GK are unknown.

METHODS

The human GK gene was cloned into the pET-24a(+) vector and over-expressed in Escherichia coli BL21 (DE3). Since the protein was expressed as inclusion bodies (IBs), various culture parameters and solubilising agents were used but they did not produce bioactive His-GK; however, co-expression of His-GK with molecular chaperones, specifically pKJE7, achieved expression of bioactive His-GK. The overexpressed bioactive His-GK was purified using coloumn chromatography and characterised using enzyme kinetics.

RESULTS

The overexpressed bioactive His-GK was purified apparently to homogeneity (∼295-fold) and characterised. The native His-GK was a dimer with a monomeric molecular weight of ∼55 kDa. Optimal enzyme activity was observed in TEA buffer (50 mM) at 7.5 pH. K+ (40 mM) and Mg2+ (2.0 mM) emerged as prefered metal ions for His-GK activity with specific activity 0.780 U/mg protein. The purified His-GK obeyed standard Michaelis-Menten kinetics with Km value of 5.022 µM (R2=0.927) for its substrate glycerol; whereas, that for ATP and PEP was 0.767 mM (R2=0.928) and 0.223 mM (R2=0.967), respectively. Other optimal parameters for the substrate and co-factors were also determined.

CONCLUSION

The present study demonstrates that co-expression of molecular chaperones assists with the expression of bioactive human GK for its characterisation.

Scattering-based Light Microscopy: From Metal Nanoparticles to Single Proteins

Our ability to detect, image, and quantify nanoscopic objects and molecules with visible light has undergone dramatic improvements over the past few decades. While fluorescence has historically been the go-to contrast mechanism for ultrasensitive light microscopy due to its superior background suppression and specificity, recent developments based on light scattering have reached single-molecule sensitivity. They also have the advantages of universal applicability and the ability to obtain information about the species of interest beyond its presence and location. Many of the recent advances are driven by novel approaches to illumination, detection, and background suppression, all aimed at isolating and maximizing the signal of interest. Here, we review these developments grouped according to the basic principles used, namely darkfield imaging, interferometric detection, and surface plasmon resonance microscopy.

Transcriptome Variations in Verticillium dahliae in Response to Two Different Inorganic Nitrogen Sources

The fungus Verticillium dahliae causes vascular wilt disease on hundreds of plant species. The main focus of the research to control this fungus has been aimed at infection processes such as penetration peg formation and effector secretion, but the ability of the fungus to acquire and utilize nutrients are often overlooked and may hold additional potential to formulate new disease control approaches. Little is known about the molecular mechanisms of nitrogen acquisition and assimilation processes in V. dahliae. In this present study, RNA sequencing and gene expression analysis were used to examine differentially expressed genes in response to the different nitrogen sources, nitrate and ammonium, in V. dahliae. A total of 3244 and 2528 differentially expressed genes were identified in response to nitrate and ammonium treatments, respectively. The data indicated nitrate metabolism requires additional energy input while ammonium metabolism is accompanied by reductions in particular cellular processes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of DEGs during nitrate metabolism revealed that many of the genes encoded those involved in protein biosynthetic and metabolic processes, especially ribosome and RNA polymerase biosynthesis, but also other processes including transport and organonitrogen compound metabolism. Analysis of DEGs in the ammonium treatment indicated that cell cycle, oxidoreductase, and certain metabolic activities were reduced. In addition, DEGs participating in the utilization of both nitrate and ammonium were related to L-serine biosynthesis, energy-dependent multidrug efflux pump activity, and glycerol transport. We further showed that the mutants of three differentially expressed transcription factors (VdMcm1, VdHapX, and VDAG_08640) exhibited abnormal phenotypes under nitrate and ammonium treatment compared with the wild type strain. Deletion of VdMcm1 displayed slower growth when utilizing both nitrogen sources, while deletion of VdHapX and VDAG_08640 only affected nitrate metabolism, inferring that nitrogen assimilation required regulation of bZIP transcription factor family and participation of cell cycle. Taken together, our findings illustrate the convergent and distinctive regulatory mechanisms between preferred (ammonium) and alternative nitrogen (nitrate) metabolism at the transcriptome level, leading to better understanding of inorganic nitrogen metabolism in V. dahliae.