aminoacyl-tRNA Synthesis Research Articles

The amino acid composition of a protein influences its expression.

The quantity of each protein in a cell only is only partially correlated with its gene transcription rate. Independent influences on protein synthesis levels include mRNA sequence motifs, amino acyl-tRNA synthesis levels, elongation factor action, and protein susceptibility to degradation. Here we report that the amino acid composition of a protein can also influence its expression level in two distinct ways. The nutritional classification of amino acids in animals reflects their potential for scarcity-essential amino acids (EAA) are reliant on dietary supply, non-essential amino acids (NEAA) from internal biosynthesis, and conditionally essential amino acids (CEAA) from both. Accessing public proteomic datasets, we demonstrate that a protein's CEAA sequence composition is inversely correlated with expression-a correlation enhanced during rapid cellular proliferation-suggesting CEAA availability can limit translation. Similarly, proteins with the most extreme compositions of EAA are generally reduced in abundance. These latter proteins participate in biological systems such as taste and food-seeking behaviour, oxidative phosphorylation, and chemokine function, and so linking their expression to EAA availability may act as a homeostatic response to malnutrition. Protein composition can also influence general human phenotypes and disease susceptibility: stature proteins are enriched in CEAAs, and a curated dataset of over 700 cancer proteins is significantly under-represented in EAAs. We also show that individual amino acids can influence protein expression across all kingdoms of life and that this effect appears to be rooted in the unchanging structural and mRNA encoding features of each amino acid. Species-specific environmental survival pathways are shown to be enriched in proteins with individual amino acid compositions favouring higher expression. These two forms of amino acid-driven protein expression regulation promise new insights into systems biology, evolutionary studies, experimental research design, and public health intervention.

AMPK-mediated regulation of cardiac energy metabolism: Implications for thermotolerance in Argopecten irradians irradians

AMPK is a key regulator of metabolism in eukaryotes across various pathways related to energy regulation. Although extensive investigations of AMPK have been conducted in mammals and some model organisms, research on AMPK in scallops is comparatively limited. In this study, three AMPK family genes (AiAMPKα, AiAMPKβ and AiAMPKγ) in scallop Argopecten irradians irradians were identified through genome scanning. Structure prediction and phylogenetic analyses of AiAMPKs were performed to determine their structural features and evolutionary relationships. Spatiotemporal expression patterns of AiAMPKs at different developmental stages and in healthy adult tissues were analyzed to elucidate the function of AiAMPKs in bay scallops’ growth and development. The spatiotemporally specific expression of AiAMPKs implied their important roles in growth and development of bay scallops. Heat stress experiment was performed to determine the regulations of AiAMPKs in four kinds of thermosensitive tissues. Expression profiles revealed distinct molecular mechanisms of AiAMPKs in different tissues in response to heat stress: significant down-regulations in mobile hemocytes, but dominant up-regulations occurring in stationary gills, mantles and hearts. Functional verification including knock-down of AiAMPKα and inhibition of AiAMPK was separately conducted in the thermotolerant tissue heart at the post-transcription and translation levels. The thermotolerant index Arrhenius break temperature (ABT) showed a significant decrease and the rate-amplitude product (RAP) peaked earlier in the individuals after RNAi targeting AiAMPKα, displaying an earlier transition to anaerobic metabolism under heat stress, indicating an impairing ability of aerobic metabolism. After AiAMPK inhibition, widespread down-regulations of genes in key energy metabolism pathways, RNA polymerase II-mediated transcription, and aminoacyl-tRNA synthesis pathways were obviously observed, revealing the post-translational inhibition of AiAMPK hindered cardiac energy metabolism, basal transcription and translation. Overall, our findings provide evidences for exploring the molecular mechanisms of energy regulation in thermotolerant traits in bay scallops under ongoing global warming.

Glutamine metabolism in fluorosis: Integrated metabolomics and transcriptomics analysis

ObjectiveTo identify the potential metabolic biomarkers of fluorosis and the pathogenesis of fluorosis. MethodsSprague Dawley rats in this study were randomly divided into fluoride exposure and control groups. In the fluoride exposure group, six offspring rats without dental fluorosis were defined as group A, and six offspring rats with dental fluorosis were defined as group C. Eight offspring rats in the control group were defined as group B. The metabolites in plasma were determined using GC–MS, with differential metabolites (DMs) identified using VIP > 1, and P < 0.05. Cluster analysis, KEGG pathway enrichment analysis and Receiver Operating Characteristic (ROC) analysis were subsequently performed. The DMs which were caused by fluoride exposure in the previous study were used to verify our results. The GSE70719 from GEO database were used to support this research at the mRNA level and in vitro experiment were selected to verify above results. ResultsThe 13 up-regulated and 4 down-regulated DMs were identified in the group A + C, the 18 up-regulated and 4 down-regulated DMs were identified in group A, and the 12 up-regulated and 2 down-regulated DMs were identified in group C. All groups showed enrichment in Aminoacyl-tRNA synthesis, D-glutamine and D-glutamate metabolism, Nitrogen metabolism, and Purine metabolism pathways. ROC analysis revealed that L-glutamine had excellent diagnostic ability for fluorosis (AUC > 0.85, P < 0.05). Changes in major DMs (L-glutamine, 4-hydroxyproline and L-alanine) were consistent with previous findings. Transcriptomic results showed the significant alteration of GLS gene in the fluoride exposure group. In vitro experiments confirmed decreased GLS and SLC1A5 genes expression. ConclusionL-glutamine emerges as a potential biomarker for fluorosis. Glutamine metabolism was involved in the pathogenesis of fluorosis.

Transcriptomic analysis reveals PC4's participation in thermotolerance of scallop Argopecten irradians irradians by regulating myocardial bioelectric activity

Rising ocean temperatures due to global warming pose a significant threat to the bay scallop aquaculture industry. Understanding the mechanisms of thermotolerance in bay scallops is crucial for developing thermotolerant breeds. Our prior research identified Arg0230340.1, part of the positive cofactor 4 (PC4) family, as a key gene associated with the thermotolerance index Arrhenius break temperature (ABT) in bay scallops. Further validation through RNA interference (RNAi) reinforced PC4's role in thermotolerance, offering a solid basis for investigating thermal response mechanisms in these scallops. In this study, we performed a comparative transcriptomic analysis on the temperature-sensitive hearts of bay scallops after siRNA-mediated RNAi targeting Arg0230340.1, to delve into the detailed molecular mechanism of PC4's participation in thermotolerance regulation. The analysis revealed that silencing Arg0230340.1 significantly reduced the expression of mitochondrial tRNA and rRNA, potentially affecting mitochondrial function and the heart's blood supply capacity. Conversely, the up-regulation of genes involved in energy metabolism, RNA polymerase II (RNAPII)-mediated basal transcription, and aminoacyl-tRNA synthesis pathways points to an intrinsic protective response, providing energy and substrates for damage repair and maintenance of essential functions under stress. GO and KEGG enrichment analyses indicated that the up-regulated genes were primarily associated with energy metabolism and spliceosome pathways, likely contributing to myocardial remodeling post-Arg0230340.1 knockdown. Down-regulated genes were enriched in ion channel pathways, particularly those for Na+, K+, and Ca2+ channels, whose dysfunction could disrupt normal myocardial bioelectric activity. The impaired cardiac performance resulting from RNAi targeting Arg0230340.1 reduced the cardiac workload in scallop hearts, thus affecting myocardial oxygen consumption and thermotolerance. We propose a hypothetical mechanism where PC4 down-regulation impairs cardiac bioelectric activity, leading to decreased thermotolerance in bay scallops, providing theoretical guidance for breeding thermotolerant scallop varieties and developing strategies for sustainable aquaculture in the face of long-term environmental changes.

The Impact of Lactobacillus delbrueckii Hepatic Metabolism in Post-Weaning Piglets

Lactobacillus delbrueckii garners interest for its contributions to gut microecological balance, diarrheal prevention and treatment, immune modulation, growth promotion, and meat quality enhancement in livestock. However, its impact on the gut microbiota and liver metabolism in weaned piglets is less documented. This study involved 80 Duroc-Landrace-Yorkshire weaned piglets aged 28 days, randomized into two groups with four replicates each and ten piglets per replicate. Over a 28-day period, the piglets were fed either a basal diet (control group) or the same diet supplemented with 0.1% Lactobacillus delbrueckii microcapsules (≥1.0 × 1010 CFU/g) (Lactobacillus delbrueckii group). The principal findings are as follows: During the initial phase of the experiment, supplementation with Lactobacillus delbrueckii increased the levels of L-phenylalanine and L-lysine in the liver while reducing the L-alanine levels, thereby enhancing the aminoacyl–tRNA synthesis pathway in weaned piglets. In the later phase, Lactobacillus delbrueckii supplementation boosted the liver arachidonic acid content, strengthening the arachidonic acid metabolic pathway in the piglets. The gut microbiota and their metabolites likely play a role in regulating these processes. These results indicate that, compared to the control group, Lactobacillus delbrueckii reduced weaning stress-induced liver damage and metabolic disorders, increased liver glycogen content, and enhanced liver antioxidant function by improving the metabolism of lipids and carbohydrates. Consequently, the liver functioned more healthily.

Evolution and variation in amide aminoacyl-tRNA synthesis.

The amide proteogenic amino acids, asparagine and glutamine, are two of the twenty amino acids used in translation by all known life. The aminoacyl-tRNA synthetases for asparagine and glutamine, asparaginyl-tRNA synthetase and glutaminyl tRNA synthetase, evolved after the split in the last universal common ancestor of modern organisms. Before that split, life used two-step indirect pathways to synthesize asparagine and glutamine on their cognate tRNAs to form the aminoacyl-tRNA used in translation. These two-step pathways were retained throughout much of the bacterial and archaeal domains of life and eukaryotic organelles. The indirect routes use non-discriminating aminoacyl-tRNA synthetases (non-discriminating aspartyl-tRNA synthetase and non-discriminating glutamyl-tRNA synthetase) to misaminoacylate the tRNA. The misaminoacylated tRNA formed is then transamidated into the amide aminoacyl-tRNA used in protein synthesis by tRNA-dependent amidotransferases (GatCAB and GatDE). The enzymes and tRNAs involved assemble into complexes known as transamidosomes to help maintain translational fidelity. These pathways have evolved to meet the varied cellular needs across a diverse set of organisms, leading to significant variation. In certain bacteria, the indirect pathways may provide a means to adapt to cellular stress by reducing the fidelity of protein synthesis. The retention of these indirect pathways versus acquisition of asparaginyl-tRNA synthetase and glutaminyl tRNA synthetase in lineages likely involves a complex interplay of the competing uses of glutamine and asparagine beyond translation, energetic costs, co-evolution between enzymes and tRNA, and involvement in stress response that await further investigation.

The role of tRNA identity elements in aminoacyl-tRNA editing.

The rules of the genetic code are implemented by the unique features that define the amino acid identity of each transfer RNA (tRNA). These features, known as "identity elements," mark tRNAs for recognition by aminoacyl-tRNA synthetases (ARSs), the enzymes responsible for ligating amino acids to tRNAs. While tRNA identity elements enable stringent substrate selectivity of ARSs, these enzymes are prone to errors during amino acid selection, leading to the synthesis of incorrect aminoacyl-tRNAs that jeopardize the fidelity of protein synthesis. Many error-prone ARSs have evolved specialized domains that hydrolyze incorrectly synthesized aminoacyl-tRNAs. These domains, known as editing domains, also exist as free-standing enzymes and, together with ARSs, safeguard protein synthesis fidelity. Here, we discuss how the same identity elements that define tRNA aminoacylation play an integral role in aminoacyl-tRNA editing, synergistically ensuring the correct translation of genetic information into proteins. Moreover, we review the distinct strategies of tRNA selection used by editing enzymes and ARSs to avoid undesired hydrolysis of correctly aminoacylated tRNAs.

Multifaceted roles of methylisothiazolinone intervention in sludge disintegration and acidogenic and methanogenic pathways for efficient carboxylate production during anaerobic fermentation

Anaerobic fermentation is a promising approach for sludge treatment, although it is frequently hindered by the tight structure of extracellular polymeric substances (EPS) and limited metabolic activities. This work firstly discovered that methylisothiazolinone (MIT, a commonly used antimicrobial agent in water treatment) effectively disintegrated the sludge structure and stimulated metabolic pathways, leading to efficient volatile fatty acids (VFAs) production. The presence of MIT (ranging from 10 to 40 mg/g TSS) contributed to the acidogenic process but strongly restrained the methanogenesis, and the distinct interfering effect is highly associated with the MIT dose. The VFAs accumulation reached a maximum of 1776.7 mg COD/L (5.2 times of control) but faced a complete inhibition of methanogenic activity at 40 mg/g TSS. Spectroscopic and molecular docking analysis revealed that MIT interacted with and disrupted the EPS (mainly proteins) structure by forming hydrogen bonds with N-H groups. This disruption facilitated the release of biodegradable organics, which served as fermentation substrates. Furthermore, the MIT-mediated improvement selectively enriched the hydrolytic-acidifying bacteria (i.e., Clostridium and Caloramator) and stimulated the associated metabolic functions, particularly in the uptake, hydrolysis, and metabolism of amino acids considering the high expressions of encoding genes (e.g., oppA, pepP, gdhA). However, methanogens' reproductive and metabolic abilities were suppressed due to their inefficient response and adaptation to MIT. This suppression was evident through downregulated genetic expressions involved in DNA replication and aminoacyl-tRNA synthesis. Consequently, a decline in methanogens abundance (e.g., Methanothrix, and Methanosarcina) and methanogenic activity occurred, impeding the consumption of VFAs. This work provided an innovative niche to promote resource recovery in the sludge anaerobic system and deciphered the underlying mechanisms at both biochemical interactive steps and microbial genetic traits.

Interplay of gene expression and regulators under salinity stress in gill of Labeo rohita

BackgroundLabeo rohita is the most preferred freshwater carp species in India. The concern of increasing salinity concentration in freshwater bodies due to climate change may greatly impact the aquatic environment. Gills are one of the important osmoregulatory organs and have direct contact with external environment. Hence, the current study is conducted to understand the gill transcriptomic response of L. rohita under hypersalinity environment.ResultsComprehensive analysis of differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs was performed in gills of L. rohita treated with 2, 4, 6 and 8ppt salinity concentrations. Networks of lncRNA-miRNA-mRNA revealed involvement of 20, 33, 52 and 61 differentially expressed lncRNAs, 11, 13, 26 and 21 differentially expressed miRNAs in 2, 4, 6 and 8ppt groups between control and treatment respectively. These lncRNA-miRNA pairs were regulating 87, 214, 499 and 435 differentially expressed mRNAs (DE mRNAs) in 2, 4, 6 and 8ppt treatments respectively. Functional analysis of these genes showed enrichment in pathways related to ion transportation and osmolyte production to cope with induced osmotic pressure due to high salt concentration. Pathways related to signal transduction (MAPK, FOXO and phosphatidylinositol signaling), and environmental information processing were also upregulated under hypersalinity. Energy metabolism and innate immune response pathways also appear to be regulated. Protein turnover was high at 8ppt as evidenced by enrichment of the proteasome and aminoacyl tRNA synthesis pathways, along with other enriched KEGG terms such as apoptosis, cellular senescence and cell cycle.ConclusionAltogether, the RNA-seq analysis provided valuable insights into competitive endogenous (lncRNA-miRNA-mRNA) regulatory network of L. rohita under salinity stress. L. rohita is adapting to the salinity stress by means of upregulating protein turnover, osmolyte production and removing the damaged cells using apoptotic pathway and regulating the cell growth and hence diverting the essential energy for coping with salinity stress.

Promoting the healing of methicillin-resistant Staphylococcus aureus-infected wound by a multi-target antimicrobial AIEgen of 6-Aza-2-thiothymine-decorated gold nanoclusters

The use of conventional antibiotic therapies is in question owing to the emergence of drug-resistant pathogenic bacteria. Therefore, novel, highly efficient antibacterial agents to effectively overcome resistant bacteria are urgently needed. Accordingly, in this work, we described a novel class luminogen of 6-Aza-2-thiothymine-decorated gold nanoclusters (ATT-AuNCs) with aggregation-induced emission property that possessed potent antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA). Scanning electron microscopy was performed to investigate the interactions between ATT-AuNCs and MRSA. In addition, ATT-AuNCs exhibited excellent ROS generation efficiency and could effectively ablate MRSA via their internalization to the cells. Finally, tandem mass tag-labeling proteome analysis was carried out to investigate the differential expression proteins in MRSA strains. The results suggested that ATT-AuNCs killed MRSA cells through altering the expression of multiple target proteins involved in DNA replication, aminoacyl-tRNA synthesis, peptidoglycan and arginine biosynthesis metabolism. Parallel reaction monitoring technique was further used for the validation of these proteome results. ATT-AuNCs could also be served as a wound-healing agent and accelerate the healing process. Overall, we proposed ATT-AuNCs could serve as a robust antimicrobial aggregation-induced emission luminogen (AIEgen) that shows the ability to alter the activities of multiple targets for the elimination of drug-resistant bacteria.

The Effect of Xanthium strumarium Root Extracts on Growth Inhibition of Epithelial Ovarian Cancer SK-OV-3 Cell Line: A Metabolomics-Based Study

Background: Epithelial ovarian cancer (EOC) is a deadly gynecological cancer among women worldwide. Ministering ovarian cancer with classic chemotherapy medications can cause various side effects. Thus, in recent years, the anticancer potential of medicinal plants has been noticed in complementary cancer treatment due to their high efficacy and low toxicity. The anti-proliferative potential of Xanthium strumarium leaf and seed extract against several cancer cell lines was reported; however, there is no report on the effect of its root so far. Objectives: In this study, the antitumor effect of X. strumarium root extract was evaluated on the SK-OV-3 ovarian cancer cell line, and metabolic alterations were identified. Methods: Cancer cells were cultured and ministered with different concentrations of ethanolic root extract. The antitumor effect of the root extract was determined by MTT assay, and cell metabolites was extracted. Finally, the metabolome profile was characterized and analyzed by 1H NMR-based metabolomics. Results: The IC50 value of the root extract of X. Strumarium was 30 µg/mL after 48 hours, which exhibited anticancer activity against SK-OV-3 ovarian cancer cells. Aminoacyl-tRNA synthesis, glycerolipid metabolism, fatty acid biosynthesis, and biotin metabolism were the most affected metabolic pathways involved in the growth inhibition of cancer cells. Conclusions: In the current study, the ethanolic root extract of X. Strumarium reveals antitumor activity against SK-OV-3 ovarian cancer cells and could affect vital metabolic pathways.

A comparative metabolomic study of Camellia oleifera fruit under light and temperature stress

ABSTRACT Camellia oleifera（C. oleifera）is one of the four main woody oils of the world. Research on improving the productivity of C. oleifera has focused on the growth process, with much less research on the mechanism of lipid accumulation post-ripening. The present study analyzed the metabolism of C. oleifera fruit under light and temperature stress and identified the primary and secondary metabolites of C. oleifera fruit using UPLC-MS. A total of 878 metabolites were detected, including 152 primary metabolites and 726 secondary metabolites, with a total of 32 core differential metabolites analyzed using a Venn diagram. After KEGG database matching, the differential metabolites were mainly enriched in the aminoacyl-tRNA synthesis pathway, the arginine and proline metabolism pathway and other pathways. Light and temperature stresses may have induced the expression of abscisic acid, arginase, and synthesized upstream substances to increase the accumulation of oils, squalene and sterols.

Mechanism of trehalose-enhanced metabolism of heterotrophic nitrification-aerobic denitrification community under high-salt stress

Heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria are aerobic microorganisms that can remove nitrogen under high-salt conditions, but their performance in practical applications are not satisfactory. As a compatible solute, trehalose helps microorganisms to cope with high salt stress by participating in the regulation of cellular osmotic pressure, and plays an important role in promoting the nitrogen removal efficiency of microbial populations in the high-salt environment. We investigated the mechanism of exogenous-trehalose-enhanced metabolism of HN-AD community under high-salt stress by starting up a membrane aerobic biofilm reactor (MABR) to enrich HN-AD bacteria, and designed a C150 experimental group with 150 μmol/L trehalose addition and a C0 control group without trehalose. The reactor performance and the community structure showed that NH4+-N, total nitrogen (TN) and chemical oxygen demand (COD) removal efficiency were increased by 29.7%, 28.0% and 29.1%, respectively. The total relative abundance of salt-tolerant HN-AD bacteria (with Acinetobacter and Pseudofulvimonas as the dominant genus) in the C150 group reached 66.8%, an 18.2% increase compared with that of the C0 group. This demonstrated that trehalose addition promoted the enrichment of salt-tolerant HN-AD bacteria in the high-salt environment to enhance the nitrogen removal performance of the system. In-depth metabolomics analysis showed that the exogenous trehalose was utilized by microorganisms to improve proline synthesis to increase resistance to high-salt stress. By regulating the activity of cell proliferation signaling pathways (cGMP-PKG, PI3K-Akt), phospholipid metabolism pathway and aminoacyl-tRNA synthesis pathway, the abundances of phosphoethanolamine, which was one of the glycerophospholipid metabolites, and purine and pyrimidine were up-regulated to stimulate bacterial aggregation and cell proliferation to promote the growth of HN-AD bacteria in the high-salt environment. Meanwhile, the addition of trehalose accelerated the tricarboxylic acid (TCA) cycle, which might provide more electron donors and energy to the carbon and nitrogen metabolisms of HN-AD bacteria and promote the nitrogen removal performance of the system. These results may facilitate using HN-AD bacteria in the treatment of high-salt and high-nitrogen wastewater.

Hepatic transcriptome analysis reveals the metabolic strategies of largemouth bass (Micropterus salmoides) under different dissolved oxygen condition

Dissolved oxygen (DO) affects aquatic animals at a fundamental level so that the differences in its metabolic strategies under prolonged hypoxic conditions need an urgent exploration. In this experiment, largemouth bass (Micropterus salmoides) were chronically exposed (6 weeks) to severe hypoxia (S-HYP, DO: 2.0 ± 0.4 mg/L) and mild hypoxia (M-HYP, DO: 5.1 ± 0.4 mg/L). Compared to the control group (CON, DO:8.4 ± 0.4 mg/L), 1196 and 232 differentially expressed genes (DEGs) were obtained in S-HYP and M-HPY groups via transcriptome analysis, respectively. In S-HYP, lipolysis was promoted while anabolism was blocked. Meanwhile, significantly less fat droplet area was observed in the liver histology of S-HYP. Additionally, the cell cycle also responded to hypoxia, being blocked in the G1 phase with the suspension of DNA replication process. In M-HYP, the processing of protein in the endoplasmic reticulum and the synthesis of various aminoacyl t-RNA were inhibited, and a novel balance of the urea cycle might be established in the biosynthesis of arginine. The key DEGs involved in the above metabolic pathways, such as atgl, cpt1, arg1, etc., were validated by Q-PCR yielding results consistent with transcriptome data. This study indicates that the largemouth bass is prone to increase the proportion of lipid as an energy supply to adapt to the reprogramming of energy metabolism, while reducing the rate of cell proliferation to adapt to chronic severe hypoxia. This is also an undescribed observation in fish liver metabolism that largemouth bass may transform the synthesis and processing strategies of protein when exposed to chronic mild hypoxia.

Imprints of PGPB association on the metabolic dynamism of Piper nigrum

ABSTRACT Endophytes are endosymbiotic microorganisms that coexist within different plant species which assist the host in multifarious ways without causing any detrimental effects on the plant well-being. The current study is focused on the bacterial isolates found in the Piper nigrum in vitro culture in the basal MS medium. The growth of these bacterial isolates even after repeated surface sterilization of the explant concludes the nature of these isolates as endophytes and these isolates were identified as Pantoea sp., Luteibacter sp., Herbaspirillum sp., and Agrobacterium sp. through 16srRNA. The endophytes were tested for their potential to aid plant development by assessing the production of Indoleacetic Acid, Ammonia, Hydrogen Cyanide, 1-aminocyclopropane-1-carboxylic acid deaminase, Siderophore, fixation of Nitrogen, solubilization of Phosphate, heavy metal and salt tolerance. Pantoea sp. and Herbaspirillum sp. were found tolerant against salt and heavy metal stress respectively. Based on plant growth promotion assays, Pantoea sp. and Agrobacterium sp. were further selected for metabolomic profiling. The results indicated the effects of isolates on primary and secondary metabolite biogenesis, aminoacyl-tRNA synthesis and amino acid metabolic pathways. The profiling of important metabolites linked to crop development, revealing its metabolic mechanism of plant growth promoting activities facilitated through selected Plant Growth Promoting Bacteria.

Longitudinal Metabolomics and Lipidomics Analyses Reveal Alterations Associated with Envenoming by Bothrops asper and Daboia russelii in an Experimental Murine Model.

Longitudinal metabolomics and lipidomics analyses were carried out on the blood plasma of mice injected intramuscularly with venoms of the viperid species Bothrops asper or Daboia russelii. Blood samples were collected 1, 3, 6, and 24 h after venom injection, and a control group of non-envenomed mice was included. Significant perturbations in metabolomics and lipidomics were observed at 1, 3, and 6 h, while values returned close to those of control mice by 24 h, hence reflecting a transient pattern of metabolic disturbance. Both venoms induced significant changes in amino acids, as well as in several purines and pyrimidines, and in some metabolites of the tricarboxylic acid cycle. KEGG analysis of metabolic pathways that showed those with the greatest change included aminoacyl tRNA synthesis and amino acid biosynthesis and metabolism pathways. With regard to lipid metabolism, there was an increase in triglycerides and some acyl carnitines and a concomitant drop in the levels of some phospholipids. In addition, envenomed mice had higher levels of cortisol, heme, and some oxidative stress markers. The overall pattern of metabolic changes in envenomed mice bears similarities with the patterns described in several traumatic injuries, thus underscoring a metabolic response/adaptation to the injurious action of the venoms.

Phenotype microarray analysis reveals the biotransformation of Fusarium oxysporum f.sp. lycopersici influenced by Bacillus subtilis PBE-8 metabolites.

Herein, Bacillus subtilis PBE-8's biocontrol efficacy was evaluated through physiological and metabolic approaches against Fusarium oxysporum f.sp. lycopersici (FOL). The study elaborates on PBE-8's cell-free filtrate (CFF) antifungal activity through mycelial growth inhibition, metabolite profiling, and substrates utilization patterns. Additionally, under different CFF concentrations, reduction in spore count (94%-55%), biomass (50%), and cytoplasmic bulbous protrusions in mycelia were also observed. Furthermore, the effect of bacterial CFF on FOL metabolism was confirmed through GC-MS. CFF suppresses the concentration of aliphatic amino acids like L-valine, L-leucine, L-Isoleucine, glycine, and fatty acids such as linoleic acid and α- linolenic acid during the co-culturing conditions, which are essential for pathogenicity and resistance against host's systemic acquired resistance. The phenotype microarray assay revealed that CFF-treated FOL shows phenotype loss in 507 (56.58%) out of 896 substrates. Among 507, twenty-seven substrates showed significant phenotype loss, among which four substrates such as L-glutamic acid, L-glutamine, ammonia, and L-arginine are common in different crucial metabolic pathways of FOL, like alanine, aspartate, and glutamate metabolism, arginine and proline, carbon metabolism, arginine biosynthesis, nitrogen metabolism, amino-acyl tRNA synthesis, and biosynthesis of amino acids. The results suggest that PBE-8 CFF has certain antifungal metabolites that hinder the fungal metabolic pathways.

Integrated Metagenomic and Metaproteomic Analyses Unravel Ammonia Toxicity to Active Methanogens and Syntrophs, Enzyme Synthesis, and Key Enzymes in Anaerobic Digestion.

During anaerobic digestion, the active microbiome synthesizes enzymes by transcription and translation, and then enzymes catalyze multistep bioconversions of substrates before methane being produced. However, little information is available on how ammonia affects truly active microbes containing the expressed enzymes, enzyme synthesis, and key enzymes. In this study, an integrated metagenomic and metaproteomic investigation showed that ammonia suppressed not only the obligate acetotrophic methanogens but also the syntrophic propionate and butyrate oxidation taxa and their assistant bacteria (genus Desulfovibrio), which declined the biotransformations of propionate and butyrate → acetate → methane. Although the total population of the hydrolyzing and acidifying bacteria was not affected by ammonia, the bacteria with ammonia resistance increased. Our study also revealed that ammonia restrained the enzyme synthesis process by inhibiting the RNA polymerase (subunits A' and D) during transcription and the ribosome (large (L3, L12, L13, L22, and L25) and small (S3, S3Ae, and S7) ribosomal subunits) and aminoacyl-tRNA synthesis (aspartate-tRNA synthetase) in translation. Further investigation suggested that methylmalonyl-CoA mutase, acetyl-CoA C-acetyltransferase, and CH3-CoM reductase, which regulate propionate and butyrate oxidation and acetoclastic methanation, were significantly downregulated by ammonia. This study provides intrinsic insights into the fundamental mechanisms of how ammonia inhibits anaerobic digestion.

Comparative study on antibacterial mechanism of shikimic acid and quinic acid against Staphylococcus aureus through transcriptomic and metabolomic approaches

Shikimic acid (SA) and quinic acid (QA), widely found in many natural plants, have been reported to exhibit prominent antibacterial activity in our previous studies. In this study, their inhibitory mechanism against Staphylococcus aureus was comparatively investigated for the first time by combined transcriptomic and metabolomic analyses. Bioinformatic analysis results revealed SA and QA had remarkably different action mechanism against S. aureus at multi-targets and multi-pathways. These two organic acids disturbed oxidative phosphorylation pathway, and changed glycerophospholipids and fatty acids levels to interfere with the membrane fluidity. Besides, only SA affected the normal functions of potassium channel and calcium channel. After penetrated cell membrane, SA and QA influenced the ribosome functions and aminoacyl-tRNA synthesis, thus disordering the protein synthesis. Furthermore, SA interfered with the pyruvate metabolic pathways, while QA damaged the synthesis of l-lysine and peptidoglycan to inhibit cell wall synthesis and cell division. This study lays theoretical foundations for the application of SA and QA as novel natural antibacterial agents in foods.

1H-NMR metabolomics response to a realistic diet contamination with the mycotoxin deoxynivalenol: Effect of probiotics supplementation

Low-level contamination of food and feed by deoxynivalenol (DON) is unavoidable.We investigated the effects of subclinical treatment with DON, and supplementation with probiotic yeast Saccharomyces cerevisiae boulardii I1079 as a preventive strategy in piglets.Thirty-six animals were randomly assigned to either a control diet, a diet contaminated with DON (3 mg/kg), a diet supplemented with yeast (4 × 109 CFU/kg), or a DON-contaminated diet supplemented with yeast, for four weeks. Plasma and tissue samples were collected for biochemical analysis,1H-NMR untargeted metabolomics, and histology.DON induced no significant modifications in biochemical parameters. However, lesion scores were higher and metabolomics highlighted alterations of amino acid and 2-oxocarboxylic acid metabolism. Administering yeast affected aminoacyl-tRNA synthesis and amino acid and glycerophospholipid metabolism. Yeast supplementation of piglets exposed to DON prevented histological alterations, and partial least square discriminant analysis emphasised similarity between the metabolic profiles of their plasma and that of the control group. The effect on liver metabolome remained marginal, indicating that the toxicity of the mycotoxin was not eliminated.These findings show that the 1H-NMR metabolomics profile is a reliable biomarker to assess subclinical exposure to DON, and that supplementation with S. cerevisiae boulardii increases the resilience of piglets to this mycotoxin.