Primordial bioenergy sources: The two facets of adenosine triphosphate

Metabolite Profiling of Hydroponic Lettuce Roots Affected by Nutrient Solution Flow: Insights from Comprehensive Analysis Using Widely Targeted Metabolomics and MALDI Mass Spectrometry Imaging Approaches

Root morphology, an important determinant of nutrient absorption and plant growth, can adapt to various growth environments to promote survival. Solution flow under hydroponic conditions provides a mechanical stimulus, triggering adaptive biological responses, including altered root morphology and enhanced root growth and surface area to facilitate nutrient absorption. To clarify these mechanisms, we applied untargeted metabolomics technology, detecting 1737 substances in lettuce root samples under different flow rates, including 17 common differential metabolites. The abscisic acid metabolic pathway product dihydrophaseic acid and the amino and nucleotide sugar metabolism factor N-acetyl-d-mannosamine suggest that nutrient solution flow rate affects root organic acid and sugar metabolism to regulate root growth. Spatial metabolomics analysis of the most stressed root bases revealed significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways: "biosynthesis of cofactors" and "amino sugar and nucleotide sugar metabolism". Colocalization analysis of pathway metabolites revealed a flow-dependent spatial distribution, with higher flavin mononucleotide, adenosine-5'-diphosphate, hydrogenobyrinic acid, and D-glucosamine 6-phosphate under flow conditions, the latter two showing downstream-side enrichment. In contrast, phosphoenolpyruvate, 1-phospho-alpha-D-galacturonic acid, 3-hydroxyanthranilic acid, and N-acetyl-D-galactosamine were more abundant under no-flow conditions, with the latter two concentrated on the upstream side. As metabolite distribution is associated with function, observing their spatial distribution in the basal roots will provide a more comprehensive understanding of how metabolites influence plant morphology and response to environmental changes than what is currently available in the literature.

Optimizing Polyhydroxyalkanoate production using a novel Bacillus paranthracis isolate: A response surface methodology approach

Microorganisms have emerged as promising resources for producing economical and sustainable bioproducts like Polyhydroxyalkanoate (PHA), a biodegradable polymer that can replace synthetic plastics. In this study, we screened a novel isolate, Bacillus paranthracis RSKS-3 strain, to produce PHA from sewage water, identifying it using Whole Genome Sequence. This study represents the first report on optimizing PHA production using B. paranthracis RSKS-3, employing Design Expert 12.0 software. Our findings reveal that four factors (temperature, inoculum size, potassium dihydrogen phosphate, and magnesium sulfate) significantly affect PHA production in the Plackett-Burman design experiment. Through Response Surface Methodology, we optimized PHA production to 0.647 g/L with specific values for potassium dihydrogen phosphate (0.55 %), inoculum size (3 %), magnesium sulfate (0.055 %), and a temperature of 35 °C, in agreement with the predicted value of 0.630 g/L. This optimization resulted in a substantial 13.29-fold increase in PHA production from 0.34 g/L to 4.52 g/L, underscoring the promising role of B. paranthracis RSKS-3 in eco-friendly PHA production and advancing sustainable bioproduct development.

Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn (Zea mays L. var. everta): Insights from Proteomic and Metabolite Analysis

The expansion of agriculture and the need for sustainable practices drives breeders to develop plant varieties better adapted to abiotic stress such as nutrient deficiency, which negatively impacts yields. Phosphorus (P) is crucial for photosynthesis and plant growth, but its availability in the soil is often limited, hampering crop development. In this study, we examined the response of two popcorn inbred lines, L80 and P7, which have been characterized previously as P-use inefficient and P-use efficient, respectively, under low (stress) and high P (control) availability. Physiological measurements, proteomic analysis, and metabolite assays were performed to unravel the physiological and molecular responses associated with the efficient use of P in popcorn. We observed significant differences in protein abundances in response to the P supply between the two inbred lines. A total of 421 differentially expressed proteins (DEPs) were observed in L80 and 436 DEPs in P7. These proteins were involved in photosynthesis, protein biosynthesis, biosynthesis of secondary metabolites, and energy metabolism. In addition, flavonoids accumulated in higher abundance in P7. Our results help us understand the major components of P utilization in popcorn, providing new insights for popcorn molecular breeding programs.

Upgrading Mitochondria-Targeting Peptide-Based Nanocomplexes for Zebrafish In Vivo Compatibility Assays

The lack of effective delivery systems has slowed the development of mitochondrial gene therapy. Delivery systems based on cell-penetrating peptides (CPPs) like the WRAP (tryptophan and arginine-rich peptide) family conjugated with a mitochondrial targeting sequence (MTS) have emerged as adequate carriers to mediate gene expression into the mitochondria. In this work, we performed the PEGylation of WRAP/pDNA nanocomplexes and compared them with previously analyzed nanocomplexes such as (KH)9/pDNA and CpMTP/pDNA. All nanocomplexes exhibited nearly homogeneous sizes between 100 and 350 nm in different environments. The developed complexes were biocompatible and hemocompatible to both human astrocytes and lung smooth muscle cells, ensuring in vivo safety. The nanocomplexes displayed mitochondria targeting ability, as through transfection they preferentially accumulate into the mitochondria of astrocytes and muscle cells to the detriment of cytosol and lysosomes. Moreover, the transfection of these cells with MTS-CPP/pDNA complexes produced significant levels of mitochondrial protein ND1, highlighting their efficient role as gene delivery carriers toward mitochondria. The positive obtained data pave the way for in vivo research. Using confocal microscopy, the cellular internalization capacity of these nanocomplexes in the zebrafish embryo model was assessed. The peptide-based nanocomplexes were easily internalized into zebrafish embryos, do not cause harmful or toxic effects, and do not affect zebrafish's normal development and growth. These promising results indicate that MTS-CPP complexes are stable nanosystems capable of internalizing in vivo models and do not present associated toxicity. This work, even at an early stage, offers good prospects for continued in vivo zebrafish research to evaluate the performance of nanocomplexes for mitochondrial gene therapy.

Investigation of the Proton-Bound Dimer of Dihydrogen Phosphate and Formate Using Infrared Spectroscopy in Helium Droplets

Understanding the structural and dynamic properties of proton-bound complexes is crucial for elucidating fundamental aspects of chemical reactivity and molecular interactions. In this work, the proton-bound complex between dihydrogen phosphate and formate, and its deuterated counterparts, is investigated using IR action spectroscopy in helium droplets. Contrary to the initial expectation that the stronger phosphoric acid would donate a proton to formate, both experiment and theory show that all exchangeable protons are located in the phosphate moiety. The experimental spectra show good agreement with both scaled harmonic and VPT2 anharmonic calculations, indicating that anharmonic effects are small. Some H-bending modes of the nondeuterated complex are found to be sensitive to the helium environment. In the case of the partially deuterated complexes, the experiments indicate that internal dynamics leads to isomeric interconversion upon IR excitation.

Reflections on the Origin of Coded Protein Biosynthesis

The principle of continuity posits that some central features of primordial biocatalytic mechanisms should still be present in the genetically dependent pathway of protein synthesis, a crucial step in the emergence of life. Key bimolecular reactions of this process are catalyzed by DNA-dependent RNA polymerases, aminoacyl-tRNA synthetases, and ribosomes. Remarkably, none of these biocatalysts contribute chemically active groups to their respective reactions. Instead, structural and functional studies have demonstrated that nucleotidic α-phosphate and β-d-ribosyl 2' OH and 3' OH groups can help their own catalysis, a process which, consequently, has been called "substrate-assisted". Furthermore, upon binding, the substrates significantly lower the entropy of activation, exclude water from these catalysts' active sites, and are readily positioned for a reaction. This binding mode has been described as an "entropy trap". The combination of this effect with substrate-assisted catalysis results in reactions that are stereochemically and mechanistically simpler than the ones found in most modern enzymes. This observation is consistent with the way in which primordial catalysts could have operated; it may also explain why, thanks to their complementary reactivities, β-d-ribose and phosphate were naturally selected to be the central components of early coding polymers.

Clickable Photoreactive ATP-Affinity Probe for Global Profiling of ATP-Binding Proteins

Adenosine triphosphate (ATP) is the major energy carrier in organisms, and there are many cellular proteins that can bind to ATP. Among these proteins, kinases are key regulators in several cell signaling processes, and aberrant kinase signaling contributes to the development of many human diseases, including cancer. Hence, small-molecule kinase inhibitors have been successfully used for the treatment of various diseases. Since the ATP-binding pockets are similar for many kinases, it is very important to evaluate the selectivity of different kinase inhibitors. We report here a clickable ATP photoaffinity probe for the global profiling of ATP-binding proteins. After incubating the protein lysate with the ATP probe followed by ultraviolet (UV) irradiation, ATP-binding proteins were labeled with an alkyne handle for subsequent biotin conjugation through click chemistry. Labeled proteins were enriched with streptavidin beads, digested with trypsin, and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). More than 400 ATP-binding proteins, including approximately 200 kinases, could be identified in a single LC-MS/MS run in the data-dependent acquisition mode. We then applied this method to the analysis of targets of three selected ATP-competitive kinase inhibitors. We were able to successfully identify some of their reported target proteins from label-free quantification results and validated the results using Western blot analyses. Together, we developed a clickable ATP photoaffinity probe for proteome-wide profiling of ATP-binding proteins and demonstrated that this chemoproteomic method is amenable to high-throughput target identification of kinase inhibitors.

Metal/ADP Complexes Promote Phosphorylation of Ribonucleotides

Under enzyme catalysis, adenosine triphosphate (ATP) transfers a phosphoryl group to canonical ribonucleotide diphosphates (NDPs) to form ribonucleotide triphosphates (NTPs), the direct biosynthetic precursors to RNA. However, it remains unclear whether the phosphorylation of NDPs could have occurred in water before enzymes existed and why an adenosine derivative, rather than another canonical NTP, typically performs this function. Here, we show that adenosine diphosphate (ADP) in the presence of Fe3+ or Al3+ promotes phosphoryl transfer from acetyl phosphate to all canonical NDPs to produce their corresponding NTP in water at room temperature and in the absence of enzymes. No other NDPs were found to promote phosphorylation, giving insight into why adenosine derivatives specifically became used for this purpose in biology. The metal-ADP complexes also promote phosphoryl transfer to ribonucleoside monophosphates (NMPs) to form a mixture of the corresponding NDPs and NTPs, albeit less efficiently. This work represents a rare example in which a single nucleotide carries out a function critical to biology without enzymes. ADP-metal complexes may have played an important role in nucleotide phosphorylation in prebiotic chemistry.

Allosteric probe initiated triple signal recycles for sensitive analysis of adenosine triphosphate (ATP)

Adenosine triphosphate (ATP) is closely associated with a variety of pathophysiological process, providing energy for cell activities. However, it remains a huge challenge to develop a simple and sensitive ATP detection method. Herein, we describe an ultrasensitive approach for ATP detection by using an elegantly designed allosteric probe to bind with targets and to induce DNAzyme assisted triple signal recycles. To establish the approach, the allosteric probe is designed with three functional parts to bind with target ATP, to induce signal recycles and to assist chain extension. After recognition of ATP by allosteric probe, the triple signal recycles are initiated, including (i) released ATP-allosteric probe complex unfolds H1 probe, constituting the first signal recycle; (ii) DNAzyme based cleavage induces the second signal recycle; and (iii) chain extension induced release of ATP is the third signal recycle. Through a series of experiments, the approach exhibits a favorable ATP detection performance and shows a high anti-interference ability, indicating a potential application value in early diagnosis of diseases.

Progesterone Reduces ATP-Induced Pyroptosis of SH-SY5Y Cells

Aim

To investigate the mechanism of progesterone inhibiting the scorch death of SH-SY5Y cells induced by exogenous adenosine triphosphate (ATP).

Methods

SH-SY5Y cells with good logarithmic growth were used in the experiment. The cells were randomly divided into 5 groups: normal control group, DMSO group, BBG group, ATP group, and ATP+progesterone group. The cell survival rate of each group was measured by CCK-8 method. The expressions of P2X7 receptor, caspase-1, caspase-11, and IL-1β were detected by western blotting.

Results

(1) After SH-SY5Y cells were treated with ATP at different concentrations (1, 3, 6, and 9 mmol/L) for 2 hours, the cell survival rate decreased in a concentration-dependent manner compared with the normal blank group. The results showed that the optimal lethal concentration of ATP was 6 mmol/L. SH-SY5Y cells were preincubated with progesterone at different concentrations (3, 10, 30, and 100 nmol/L) for 30 minutes and then incubated with 6 mmol/L ATP. The cell survival rate of this group was significantly improved (P < 0.01). The optimal concentration of progesterone to improve cell survival and inhibit cell death was 30 nmol/L. (2) Compared to the control group, there was no significant difference (P > 0.05) in P2X7 receptor, caspase-1, caspase-11, and IL-1β with the DMSO group (0.001% DMSO, 24 h) and BBG group (bbg1 mmol/L, 24 h). (3) In the ATP group, the expression of P2X7 receptor and caspase-1 (the key protein of classical cell death pathway) increased significantly (P < 0.01), which was related to inflammatory factor IL-1β with consistent performance (P < 0.01). There was no significant change in caspase-11 (the key protein of nonclassical focal death pathway) (P > 0.05). (4) The expression of P2X7 receptor, caspase-1, and inflammatory factor IL-1β in the progesterone+ATP group was significantly downregulated (P < 0.01). There was no significant change in caspase-11 (P > 0.05).

Conclusion

Certain dose of progesterone can inhibit the focal death of SH-SY5Y cells induced by extracellular high concentration ATP. It can reduce the expression of P2X7 receptor, inhibit the conduction pathway of cell death, reduce the release of inflammatory factor IL-1β, and improve cell survival.

Protocells: Milestones and Recent Advances

The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.

Sublethal effects of tolfenpyrad on the development, reproduction, and predatory ability of Chrysoperla sinica

The lacewing, Chrysoperla sinica, is a predaceous insect that is important in crop pest management. Chemical pesticides have adversely impacted predaceous insect species. Here we studied the effect of tolfenpyrad on C. sinica. The acute toxicity of tolfenpyrad to the second-instar larvae was determined and indicated that tolfenpyrad is a medium-risk insecticide. Sublethal concentrations (LC₁₀, LC₂₀, and LC₃₀) of tolfenpyrad had effects on the development, reproduction, and predatory ability of C. sinica. When the second-instar larvae of C. sinica were exposed to sublethal concentrations of tolfenpyrad, the activities of protective enzymes, such as superoxide dismutase, peroxidase, and catalase, and detoxification enzymes, including carboxylesterase, glutathione-S-transferase, and P450 monooxygenases, were increased with exposure time. The second-instar larvae of C. sinica exposed to sublethal concentrations of tolfenpyrad exhibited an oxidative stress response that increased the levels of malondialdehyde and reactive oxygen species (ROS). Within 48-120 h after treatment, the contents of mitochondrial respiratory chain complex I and adenosine triphosphate in the second-instar larvae were decreased. This resulted in an imbalance between the production and clearance of ROS and caused cellular damage.

The Complex Roles of Adenosine Triphosphate in Bioenergetics

ATP is generally defined as the "energy currency" of the cell. Its phosphoanhydride P-O bonds are often considered to be "high energy" linkages that release free energy when broken, and its hydrolysis is described as "strongly exergonic". However, breaking bonds cannot release energy and ATP hydrolysis in motor and active transport proteins is not "strongly exergonic". So, the relevance of ATP resides elsewhere. As important as the nucleotide are the proteins that undergo functionally relevant conformational changes upon both ATP binding and release of ADP and inorganic phosphate. ATP phosphorylates proteins for signaling, active transport, and substrates in condensation reactions. The ensuing dephosphorylation has different consequences in each case. In signaling and active transport the phosphate group is hydrolyzed whereas in condensation reactions the phosphoryl fragment acts as a dehydrating agent. As it will be discussed in this article, ATP does much more than simply contribute free energy to biological processes.

Part-time cancers and role of melatonin in determining their metabolic phenotype

This brief review describes the association of the endogenous pineal melatonin rhythm with the metabolic flux of solid tumors, particularly breast cancer. It also summarizes new information on the potential mechanisms by which endogenously-produced or exogenously-administered melatonin impacts the metabolic phenotype of cancer cells. The evidence indicates that solid tumors may redirect their metabolic phenotype from the pathological Warburg-type metabolism during the day to the healthier mitochondrial oxidative phosphorylation on a nightly basis. Thus, they function as cancer cells only during the day and as healthier cells at night, that is, they are only part-time cancerous. This switch to oxidative phosphorylation at night causes cancer cells to exhibit a reduced tumor phenotype and less likely to rapidly proliferate or to become invasive or metastatic. Also discussed is the likelihood that some solid tumors are especially aggressive during the day and much less so at night due to the nocturnal rise in melatonin which determines their metabolic state. We further propose that when melatonin is used/tested in clinical trials, a specific treatment paradigm be used that is consistent with the temporal metabolic changes in tumor metabolism. Finally, it seems likely that the concurrent use of melatonin in combination with conventional chemotherapies also would improve cancer treatment outcomes.