Sulfur Metabolism Research Articles

Molecular Influence of Resiniferatoxin on the Urinary Bladder Wall Based on Differential Gene Expression Profiling.

Resiniferatoxin (RTX) is a potent capsaicin analog used as a drug for experimental therapy to treat neurogenic disorders associated with enhanced nociceptive transmission, including lower urinary tract symptoms. The present study, for the first time, investigated the transcriptomic profile of control and RTX-treated porcine urinary bladder walls. We applied multistep bioinformatics and discovered 129 differentially expressed genes (DEGs): 54 upregulated and 75 downregulated. Metabolic pathways analysis revealed five significant Kyoto Encyclopedia of Genes and Genomes (KEGG) items ('folate biosynthesis', 'metabolic pathways', 'sulfur relay system', 'sulfur metabolism' and 'serotonergic synapse') that were altered after RTX intravesical administration. A thorough analysis of the detected DEGs indicated that RTX treatment influenced the signaling pathways regulating nerve growth, myelination, axon specification, and elongation. Many of the revealed DEGs are involved in the nerve degeneration process; however, some of them were implicated in the initiation of neuroprotective mechanisms. Interestingly, RTX intravesical installation was followed by changes in the expression of genes involved in synaptic plasticity and neuromodulation, including 5-HT, H2S, glutamate, and GABA transmission. The obtained results suggest that the toxin may exert a therapeutic, antinociceptive effect not only by acting on TRPV1 receptors.

Association of gut microbiota and SCFAs with finishing weight of Diannan small ear pigs.

Finishing weight is a key economic trait in the domestic pig industry. Evidence has linked the gut microbiota and SCFAs to health and production performance in pigs. Nevertheless, for Diannan small ear (DSE) pigs, a specific pig breed in China, the potential effect of gut microbiota and SCFAs on their finishing weight remains unclear. Herein, based on the data of the 16S ribosomal RNA gene and metagenomic sequencing analysis, we found that 13 OTUs could be potential biomarkers and 19 microbial species were associated with finishing weight. Among these, carbohydrate-decomposing bacteria of the families Streptococcaceae, Lactobacillaceae, and Prevotellaceae were positively related to finishing weight, whereas the microbial taxa associated with intestinal inflammation and damage exhibited opposite effects. In addition, interactions of these microbial species were found to be linked with finishing weight for the first time. Gut microbial functional annotation analysis indicated that CAZymes, such as glucosidase and glucanase could significantly affect finishing weight, given their roles in increasing nutrient absorption efficiency. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologies (KOs) and KEGG pathways analysis indicated that glycolysis/gluconeogenesis, phosphotransferase system (PTS), secondary bile acid biosynthesis, ABC transporters, sulfur metabolism, and one carbon pool by folate could act as key factors in regulating finishing weight. Additionally, SCFA levels, especially acetate and butyrate, had pivotal impacts on finishing weight. Finishing weight-associated species Prevotella sp. RS2, Ruminococcus sp. AF31-14BH and Lactobacillus pontis showed positive associations with butyrate concentration, and Paraprevotella xylaniphila and Bacteroides sp. OF04-15BH were positively related to acetate level. Taken together, our study provides essential knowledge for manipulating gut microbiomes to improve finishing weight. The underlying mechanisms of how gut microbiome and SCFAs modulate pigs' finishing weight required further elucidation.

Comparative Transcriptomics Reveal Metabolic Rather than Genetic Control of Divergent Antioxidant Metabolism in the Primary Root Elongation Zone of Water-Stressed Cotton and Maize.

Under water stress, the primary root elongation zones of cotton and maize exhibit both conserved and divergent metabolic responses, including variations in sulfur and antioxidant metabolism. To explore the relative importance of metabolic and genetic controls of these responses for each species, and the extent to which responses are mediated by similar gene expression networks within the framework of ortholog groups, comparative transcriptomics analyses were conducted under conditions of equivalent tissue water stress. Ortholog analysis revealed that 86% of the transcriptome response to water stress was phylogenetically unrelated between cotton and maize. Elevated transcript abundances for genes involved in abscisic acid (ABA) biosynthesis and signaling, as well as key enzymes that enable osmotic adjustment, were conserved between the species. In contrast, antioxidant responses, at least with regard to glutathione metabolism and anti-oxidative enzymes, did not exhibit such a transcript abundance adaptive signature. In particular, previously characterized differential responses of the glutathione and sulfur metabolic pathways between cotton and maize were not evident in the transcriptomic responses. The findings indicate that the antioxidant response in both species results from a metabolic acclimation to water stress, and thus represents an example of water stress-related metabolic plasticity.

Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland.

Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY,and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.

Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440.

The soil bacterium Pseudomonas putida KT2440 has been shown to produce selenium nanoparticles aerobically from selenite; however, the molecular actors involved in this process are unknown. Here, through a combination of genetic and analytical techniques, we report the first insights into selenite metabolism in this bacterium. Our results suggest that the reduction of selenite occurs through an interconnected metabolic network involving central metabolic reactions, sulphur metabolism, and the response to oxidative stress. Genes such as sucA, D2HGDH and PP_3148 revealed that the 2-ketoglutarate and glutamate metabolism is important to convert selenite into selenium. On the other hand, mutations affecting the activity of the sulphite reductase decreased the bacteria's ability to transform selenite. Other genes related to sulphur metabolism (ssuEF, sfnCE, sqrR, sqr and pdo2) and stress response (gqr, lsfA, ahpCF and sadI) were also identified as involved in selenite transformation. Interestingly, suppression of genes sqrR, sqr and pdo2 resulted in the production of selenium nanoparticles at a higher rate than the wild-type strain, which is of biotechnological interest. The data provided in this study brings us closer to understanding the metabolism of selenium in bacteria and offers new targets for the development of biotechnological tools for the production of selenium nanoparticles.

Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440

Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440

Brassinosteroids fine-tune secondary and primary sulfur metabolism through BZR1-mediated transcriptional regulation.

For adaptation to ever-changing environments, plants have evolved elaborate metabolic systems coupled to a regulatory network for optimal growth and defense. Regulation of plant secondary metabolic pathways such as glucosinolates (GSLs) by defense phytohormones in response to different stresses and nutrient deficiency has been intensively investigated, while how growth-promoting hormone balances plant secondary and primary metabolism has been largely unexplored. Here, we found that growth-promoting hormone brassinosteroid (BR) inhibits GSLs accumulation while enhancing biosynthesis of primary sulfur metabolites, including cysteine (Cys) and glutathione (GSH) both in Arabidopsis and Brassica crops, fine-tuning secondary and primary sulfur metabolism to promote plant growth. Furthermore, we demonstrate that of BRASSINAZOLE RESISTANT 1 (BZR1), the central component of BR signaling, exerts distinct transcriptional inhibition regulation on indolic and aliphatic GSL via direct MYB51 dependent repression of indolic GSL biosynthesis, while exerting partial MYB29 dependent repression of aliphatic GSL biosynthesis. Additionally, BZR1 directly activates the transcription of APR1 and APR2 which encodes rate-limiting enzyme adenosine 5'-phosphosulfate reductases in the primary sulfur metabolic pathway. In summary, our findings indicate that BR inhibits the biosynthesis of GSLs to prioritize sulfur usage for primary metabolites under normal growth conditions. These findings expand our understanding of BR promoting plant growth from a metabolism perspective.

DsrC is involved in fermentative growth and interacts directly with the FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough.

DsrC is a key protein in dissimilatory sulfur metabolism, where it works as co-substrate of the dissimilatory sulfite reductase DsrAB. DsrC has two conserved cysteines in a C-terminal arm that are converted to a trisulfide upon reduction of sulfite. In sulfate-reducing bacteria, DsrC is essential and previous works suggested additional functions beyond sulfite reduction. Here, we studied whether DsrC also plays a role during fermentative growth of Desulfovibrio vulgaris Hildenborough, by studying two strains where the functionality of DsrC is impaired by a lower level of expression (IPFG07) and additionally by the absence of one conserved Cys (IPFG09). Growth studies coupled with metabolite and proteomic analyses reveal that fermentation leads to lower levels of DsrC, but impairment of its function results in reduced growth by fermentation and a shift towards more fermentative metabolism during sulfate respiration. In both respiratory and fermentative conditions, there is increased abundance of the FlxABCD-HdrABC complex and Adh alcohol dehydrogenase in IPFG09 versus the wild type, which is reflected in higher production of ethanol. Pull-down experiments confirmed a direct interaction between DsrC and the FlxABCD-HdrABC complex, through the HdrB subunit. Dissimilatory sulfur metabolism, where sulfur compounds are used for energy generation, is a key process in the ecology of anoxic environments, and is more widespread among bacteria than previously believed. Two central proteins for this type of metabolism are DsrAB dissimilatory sulfite reductase and its co-substrate DsrC. Using physiological, proteomic and biochemical studies of Desulfovibrio vulgaris Hildenborough and mutants affected in DsrC functionality, we show that DsrC is also relevant for fermentative growth of this model organism and that it interacts directly with the soluble FlxABCD-HdrABC complex that links the NAD(H) pool with dissimilatory sulfite reduction.

Soil sulfur cycle bacteria and metabolites affected by soil depth and afforestation conditions in high-sulfur coal mining areas

This study aimed to clarify the changes in sulfur-driven microorganisms and sulfur metabolic pathways in the vertical soil profile during the restoration of different afforestation types. Soils of varying afforestation patterns (grassland, shrubland, woodland) in high‑sulfur coal mining areas (Gujiao City, China) were analysed to determine the characteristics of the sulfur distribution, microbial community structure, and sulfur metabolites in shallow (10 cm), middle (30 cm), and deep (50 cm) soils. Compared with the area without vegetation, the soil in the planted area had higher total soil S (5.1–58.6 %), Fe (37.5–67.4 %), and Cu (28.3–54.2 %); the content of these elements showed a consistent increase with depth. Afforestation resulted in increased pH by 0.8–1.3 pH units, organic carbon (1.6–2.9 times), total N (30.2–46.9 %), and available N (58.3–78.2 %) in the soil. Additionally, the electrical conductivity of the shallow soil in the three plant cover areas decreased by 78–82 %. The diversity of 16S bacterial showed that different afforestation types shaped the structure of specific microbial communities at different soil depths. Afforestation also showed a promotion of abundance of soil sulfur-related microorganisms (e.g., Desulfovibrio (0.8–34.2 %), Acidiferrobacter (0.3–32.8 %), Acidithiobacillus (1.2–21.7 %), and Thiomonas (0.6–15.6 %)). Plant cover induced the vertical spatial distribution pattern of sulfur metabolites in high-sulfur coal mines showing a shallow > middle > deep layer, and afforestation enhanced the transformation process of sulfur metabolites in shallow soil. The main metabolic pathways for soil sulfur metabolism involve sulfur-containing amino acids, such as cysteine and methionine metabolism, taurine, and hypotaurine. Interaction analysis indicated that Lysobacter, Luteimonas, and Leptospirillum made greater contributions to the changes in sulfur metabolites. The findings from this study suggest that the distribution of sulfur and soil properties in vertical depth soil of different afforestation types in high-sulfur coal mining areas recruit specific bacteria, which drive soil sulfur metabolic conversion and reestablishment of soil sulfur homeostasis, and the shallow layers of the soil were critical areas for turnover of sulfur metabolite. These results provide insights for understanding biochemical sulfur cycling in vertical soil depth under different afforestation models.

Denitrification performance and microbial community analysis of sulfur autotrophic denitrification filter for low-temperature treatment of landfill leachate

This study investigated the denitrification performance of sulfur autotrophic denitrification filter (SADF) in five low-temperature ranges (14.0–15.0 ℃, 13.1–13.9 °C, 12.0–13.0 °C, 10.1–11.9 °C and 8.8–9.8 °C) environments and the nitrogen removal contribution along the filter cells. Results showed that the average total nitrogen removal efficiency (TNRE) of the bioreactor were 90.06%, 88.49%, 86.61%, 85.71% and 74.54%, respectively. However, when the temperature was lower than 9.8 °C, the process of sulfur autotrophic denitrification was obviously inhibited, but the inhibition was slowed down after low-temperature acclimation. The bottom-filter layer (0–200 mm) contributed 50.54% of the nitrogen removal, which was the greatest. The middle- filter layer (400–600 mm), which was at 35.86%, was next. And the upper- filter layer (800–1200 mm) made the least contribution, at 13.60%. It was demonstrated by high-throughput sequencing that in addition to Thiobacillus, the genus Sulfurimonas was also found and its average relative abundance was comparable to the former (24.03% for Thiobacillus and 23.10% for Sulfurimonas). The results of microbial function prediction showed that sulfur and nitrogen metabolism played a key role in nitrogen removal. The study of substrate environmental variables showed that the key bacterial groups of nitrogen removal along the process were negatively correlated with total nitrogen (TN) and positively correlated with pH value.

Seasonality and assembly of soil microbial communities in coastal salt marshes invaded by a perennial grass

Plant invasion profoundly changes the microbial-driven processes in the ecosystem; however, the seasonality of soil microbial communities and their assembly under plant invasion is poorly understood. In this study, coastal salt marshes with native Suaeda salsa (L.) Pall. and exotic Spartina alterniflora Loisel. in the Yellow River Estuary, North China, were selected, and soil bacterial and fungal communities and their seasonal variance were characterized by metabarcoding sequencing of the 16S rRNA gene and ITS2 regions, respectively. The importance of deterministic and stochastic processes in shaping bacterial and fungal seasonal assembly was explored by the null model. Results showed that soil microbes exhibited the lowest diversities in spring, while their diversity significantly improved in summer and autumn with the increase in organic carbon and nitrogen content in soils. Strong seasonal variances in microbial communities were observed, but plant invasion reduced the seasonal variation strength of soil bacteria. For the microbial assembly, the seasonal variability of soil bacterial community was mainly controlled by homogeneous selection, whereas soil fungal community was dominantly structured by stochastic processes. Among the selected variables, soil pH was the key abiotic factor driving the seasonal changes in bacteria and fungi. The microbial function annotation derived from taxonomy-based inference suggested that carbon metabolism was relatively stronger in spring, but nitrogen and sulfur metabolism increased evidently in summer and autumn, and the proportion of saprophytic fungi increased substantially after plant invasion. The seasonal turnover of bacterial and fungal groups were tightly associated with the seasonal variation in soil carbon and nitrogen contents. Collectively, these findings reveal the strong seasonal variability of different soil microbial constituents in plant-invaded coastal salt marshes and suggest the linkage between microbial community assembly and microbial-mediated functions in the context of plant invasions.

The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga.

The island of Hunga Tonga Hunga Ha'apai (HTHH) in the Kingdom of Tonga was formed by Surtseyan eruptions and persisted for 7 years before being obliterated by a massive volcanic eruption on 15 January 2022. Before it was destroyed, HTHH was an unparalleled natural laboratory to study primary succession on a newly formed landmass. We characterized the microbial communities found on the surface sediments of HTHH using a combination of quantitative PCR, marker gene sequencing, and shotgun metagenomic analyses. Contrary to expectations, photosynthetic cyanobacteria were not detected in these sediments, even though they are typically dominant in the earliest stages of primary succession in other terrestrial environments. Instead, our results suggest that the early sediment communities were composed of a diverse array of bacterial taxa, including trace gas oxidizers, anoxygenic photosynthesizers, and chemolithotrophs capable of metabolizing inorganic sulfur, with these bacteria likely sourced from nearby active geothermal environments. While the destruction of HTHH makes it impossible to revisit the site to conduct in situ metabolic measurements or observe how the microbial communities might have continued to change over time, our results do suggest that the early microbial colonizers have unique origins and metabolic capabilities. IMPORTANCE The volcanic island of Hunga Tonga Hunga Ha'apai in the Kingdom of Tonga represents a very rare example of new island formation and thus a unique opportunity to study how organisms colonize a new landmass. We found that the island was colonized by diverse microbial communities shortly after its formation in 2015, with these microbes likely originating from nearby geothermal environments. Primary succession in this system was distinct from that typically observed in other terrestrial environments, with the early microbial colonizers relying on unique metabolic strategies to survive on the surface of this newly formed island, including the capacity to generate energy via sulfur and trace gas metabolism.

Insights into the core bacterial consortia of root endophytes in two cultivated varieties of rice in West Bengal

Root endophytes are considered to be one of the potent environment-friendly substitutes for chemical fertilizers, as they possess an ability to induce crosstalk inside the hosts for growth promotion, nitrogen fixation, phosphate solubilization and iron sequestration. This study aimed to explore and evaluate the key root endophytic bacterial consortia of two widely cultivated varieties of rice (Oryza sativa L.), cv. ‘Saraswati’ (OS01) and cv. ‘Kunti’ (OS04). Detailed comparative metagenome data were generated for endophytes of OS01 and OS04 and the species richness was calculated. OS01 showed higher endophyte species richness than OS04, with alpha diversity values of 3.10 and 2.40, respectively. Bacillus, Magnetospirillum, Methanocystis, Desulfomicrobium and Pantoea were identified as common endophyte members for both cultivars. Solibacillus, Paenibacillus, Candidatus, and Melospira were unique members of OS01, and Herbaspirillum, Pandoraea, Anabaenopsis for OS04. Considerable occurrence of nitrogen fixing bacteria and methanogenic bacteria in the cultivars confirmed biological nitrogen fixation, which can contribute to plant development. Core homeotic pathways of amino acid biosynthesis and carbon metabolism were also reflected in endophytes from both cultivars, indicating a supportive environment for microorganisms. Sulfur metabolism pathways were likewise predicted to be active in the niche under study, which may be attributed as a response to arsenic stress. Furthermore, the most abundant genera identified may potentially serve as crucial consortium candidates for host plant development and contribute to better yield in a sustainable manner.

Characterization of cadmium accumulation mechanism between eggplant (Solanum melongena L.) cultivars.

Excessive cadmium (Cd) accumulation in vegetables due to farmland pollution constitutes a serious threat to human health. Eggplant has a tendency to accumulate Cd. To investigate the mechanism of the differences in Cd accumulation levels between high-Cd (BXGZ) and low-Cd (MYQZ) eggplant cultivar, physiological and biochemical indicators and mRNA expression of eggplant were examined using photosynthetic apparatus, biochemical test kits, Fourier transform infrared (FTIR) spectroscopy and transcriptome sequencing, etc. The results of biochemical test kits and FTIR revealed that MYQZ enhanced pectin methylesterase (PME) activity, and lignin and pectin content in the root cell wall, which was associated with the upregulation of PME, cinnamyl-alcohol dehydrogenase and peroxidase (PODs). Higher levels of cysteine and glutathione (GSH) contents and upregulation of genes associated with sulfur metabolism, as well as higher expression of ATP-binding cassette transporters (ABCs), cation exchangers (CAX) and metal tolerance proteins (MTPs) were observed in MYQZ. In BXGZ, the higher stomatal density and stomatal aperture as well as higher levels of Ca2+ binding protein-1 (PCaP1) and aquaporins and lower levels of A2-type cyclins (CYCA2-1) are consistent with an enhanced transpiration rate in BXGZ. Furthermore, a more developed root system was shown to be associated with higher levels of auxin response factor (ARF19), GATA transcription factors (GATA4, 5 and 11) and auxin efflux carrier component (PIN5) in BXGZ. In conclusion, highly active PME, and higher levels of lignin and pectin in MYQZ are expected to reduce Cd toxicity, while Cd translocation can be inhibited with the help of ABC and other Cd transporters. As for BXGZ, the uptake and translocation of Cd were enhanced by the developed root system and stronger transpiration.

Isolation and Characterization of A Novel Iron–Sulfur Oxidizing Bacterium Acidithiobacillus Ferrooxidans YQ-N3 and its Applicability in Coal Biodesulfurization

Acidithiobacillus ferrooxidans is a chemotrophic, aerobic, acidophilic, and Gram-negative bacterium that plays a key role in iron and sulfur cycling and has a wide range of applications in the industrial field. A novel A. ferrooxidans strain, hereinafter referred to as strain “YQ-N3”, was isolated from sediments of a river polluted by acid mine drainage (AMD) of an abandoned mine in Shanxi, China. The whole genome sequencing results revealed that A. ferrooxidans YQ-N3 has a 3,217,720 bp genome, which is comprised of one circular chromosome and five circular plasmids (Plasmid A, Plasmid B, Plasmid C, Plasmid D, Plasmid E). Plasmid E, a new plasmid, had not been annotated in the reference database. A. ferrooxidans YQ-N3 had a close evolutionary relationship with A. ferrooxidans ATCC23270 and A. ferridurans JCM18981 and exhibited higher similarity in its genomic structure with A. ferrooxidans ATCC23270. Multiple genes related to environmental resistance and iron and sulfur metabolism were predicted from its genome. A. ferrooxidans YQ-N3 can remarkably increase the oxidation rate of Fe2+ and S0 and enhance the hydrophilicity of S0, which was supported by functional gene analysis and laboratory experiments. The biological desulfurization experiment demonstrated that A. ferrooxidans YQ-N3 can reduce the sulfur content in coal by removing pyrite sulfur and organic sulfur.

Multi-omics eco-surveillance of complex legacy contamination with a locally adapted estuarine invertebrate

Complex legacy contamination from human use is a major issue for estuaries globally. In particular, contamination of water and sediments with bioavailable metals/metalloids, in addition to other industrial contaminants, such as hydrocarbons. Yet, understanding of complex toxicity and local adaptation in field exposed, non-model, invertebrate communities is limited. Herein, we apply multi-omics (metabolomics, lipidomics, proteomics) coupled to traditional sediment quality analyses, to better characterise molecular and cellular responses necessary for application to monitoring, as an eco-surveillance tool. Using these approaches, we characterise functional phenotypes of a sediment associated invertebrate (sipunculid), from an estuary exposed to complex legacy contamination (metals: Zn, Hg, Cd, Pb, Cu, As; and polycyclic aromatic hydrocarbons, PAHs). We sampled individuals at a range of exposure sites, highly (NTB5), moderately (NTB13), and lesser-influenced reference sites. Size differences were observed in sampled individuals between sites, with smaller individuals collected from NTB13. Analysis of environmental variables that correlated with change in the metabolite data revealed that the metabolism of smaller individuals at medium exposure NTB13 was highly differentiated by sediment concentrations of Hg, despite higher concentrations at more exposed NTB5. Functional phenotypes of these smaller individuals were characterised by sulphur and aromatic amino acid metabolism, increases in oxidised intermediates, upregulation of protein responses to oxidative stress, and melanin synthesis, and saturation of membrane and storage of lipids; in addition to the metabolism of naphthalene (PAH). Such widespread change was not observed in the metabolite and lipid profiles of larger individuals at high exposure NTB5, suggesting possible differences in effects between sites may also be associated with size (developmental stage, or age) and/or PAH exposure. This study serves to further understanding of differing modes of toxicity and local adaptation to multiple contaminants, and drivers of functional change in a complex estuary environment.

Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow.

A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text. We present a text mining workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) from literature databases (e.g., PubMed and PMC). This semi-automatic workflow is built with the Named Entity Recognition (NER) method and Convolutional Neural Network (CNN) model. With PubMed and PMCID as inputs, the workflow identified 227 genes belonging to several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment and biological network analysis was performed using UniprotKB and STRING-DB, respectively. The GO analysis showed that metal ion binding, sulfur binding, and electron transport were among the principal molecular functions. Furthermore, the biological network analysis generated three interlinked clusters containing genes involved in metal ion binding, cellular respiration, and electron transfer, which suggests the involvement of the extracted gene set in biocorrosion. Finally, the dataset was validated through manual curation, yielding a similar set of genes as our workflow; among these, hysB and hydA, and sat and dsrB were identified as the metal ion binding and sulfur metabolism genes, respectively. The identified genes were mapped with the pangenome of 63 SRB genomes that yielded the distribution of these genes across 63 SRB based on the amino acid sequence similarity and were further categorized as core and accessory gene families. SRB's role in biocorrosion involves the transfer of electrons from the metal surface via a hydrogen medium to the sulfate reduction pathway. Therefore, genes encoding hydrogenases and cytochromes might be participating in removing hydrogen from the metals through electron transfer. Moreover, the production of corrosive sulfide from the sulfur metabolism indirectly contributes to the localized pitting of the metals. After the corroboration of text mining results with SRB biocorrosion mechanisms, we suggest that the text mining framework could be utilized for genes/proteins extraction and significantly reduce the manual curation time.

Technical note: simultaneous determination of amino thiols in pig tissue by ultra-high performance liquid chromatography with fluorescence detection.

Sulfur amino acid nutrition and metabolism are linked to animal disease. While validated methods for the determination of amino thiol levels in plasma or serum are available, there is a dearth of validated methods for their measurement in tissue. A robust and reproducible ultra-high performance liquid chromatography method has been validated for the simultaneous determination of concentrations of cysteine (Cys), cysteinylglycine (CysGly), homocysteine (Hcys), γ-glutamylcysteine (γ-GluCys), and glutathione (GSH) in pig tissue. Tissue was homogenized and deproteinized with trichloroacetic acid. Amino thiols in the acid-soluble fraction of the tissue homogenate were reduced with tris-(2-carboxyethyl)-phosphine hydrochloride and derivatized with 4-(aminosulfonyl)-7-fluoro-2,1,3-benzoxadiazole (ABD-F). Amino thiols were resolved under reversed-phase gradient conditions on a Waters Acquity BEH C18 column (1.7 µm, 2.1 mm × 100 mm) within 4.5 min and detected with fluorescence. The peak area ratio of analyte to 2-mercaptopropionylglycine internal standard, added to external calibration standards and samples, was used to develop linear calibration curves. Linear calibrations were performed over the range of 15-1,500 nmol/g for Cys, CysGly, Hcys, and γ-GluCys and 150-15,000 nmol/g for GSH. Linearity, lower limit of detection, lower limit of quantitation, accuracy, precision, sample stability, and carryover were evaluated. We demonstrate excellent linearity for all analytes within their respective concentration range (r2 > 0.99) and excellent recovery of amino thiols from spiked samples (mean ± SD across tissues; Cys, 100.0 ± 2.2%; CysGly, 95.4 ± 5.1%; Hcys, 96.6 ± 2.0%; γ-GluCys, 102.2 ± 2.7%; and GSH, 100.6 ± 3.3%). The intra-day and inter-day precisions did not exceed 5% and 10%, respectively. Repeated freezing and thawing of tissue homogenate did not affect measured amino thiol concentrations, ABD-labeled amino thiols were stable for 1 wk after derivatization, and there was no sample carryover across consecutive injections. We confirm the identity of each ABD-labeled amino thiol with Orbitrap mass spectrometry. Finally, we apply the method to the determination of amino thiol concentrations in liver and jejunum tissues in newly weaned pigs and show that despite elevated Cys and maintained GSH concentrations in liver, both γ-GluCys and GSH decline in jejunum of weaned pigs.

Transcriptome Analysis and Physiological Responses of Economic Macroalga Gracilariopsis lemaneiformis under Sulfate Deficiency

Sulfur is an essential macronutrient for the growth of all photosynthetic organisms and plays important roles in different metabolic pathways. However, sulfur metabolism and its related research on macroalgae with important ecological value is rather limited. In this study, marine ecological valued macroalga Gracilariopsis lemaneiformis was used to study the general physiological responses and transcriptome profiling under the sulfate deficiency. The relative growth rate of algae under sulfate deficiency was statistically significantly lower than that of control after 6 days. However, no significant differences were observed in the pigments content and Fv/Fm value, indicating that the photosynthesis was not obviously affected under the sulfate deficiency. Furthermore, the significantly increased soluble protein and carbohydrate contents, and indistinctively differentially expressed sulfate transporter/permease (ST) and ATP sulfurylase (ATPS) genes suggesting that G. lemaneiformis cells did not use sulfur from internal protein and carbohydrate pools but utilize stored sulfur from vacuole to satisfy their nutritional requirements during the sulfate deficiency. Transcriptome data showed that most annotated differentially expressed genes (DEGs) were down-regulated under the sulfate deficiency, including a large proportion of genes involved in the pathway of sulfur metabolism. Therefore, it was concluded that the pathway of sulfur metabolism was suppressed under the sulfate deficiency in G. lemaneiformis. The results and analysis in this study provide a comprehensive understanding for the physiological and molecular response of G. lemaneiformis to sulfate deficiency.

Mice kidney biometabolic process analysis after cantharidin exposure using widely-targeted metabolomics combined with network pharmacology.

Cantharidin (CTD) is a principal bioactive component of traditional Chinese medicine Mylabris used in cancer treatment. However, CTD clinical application is limited due to nephrotoxicity, and the mechanism is unknown. The present study used widely-targeted metabolomics, network pharmacology, and cell experiments to investigate the nephrotoxicity mechanism after CTD exposure. In mice exposed to CTD, serum creatinine and urea nitrogen levels increased with renal injury. Then, 74 differential metabolites were detected, including 51 up-regulated and 23 down-regulated metabolites classified as amino acids, small peptides, fatty acyl, arachidonic acid metabolite, organic acid, and nucleotides. Sixteen metabolic pathways including tyrosine, sulfur, and pyrimidine metabolism were all disrupted in the kidney. Furthermore, network pharmacology revealed that 258 metabolic targets, and pathway enrichment indicated that CTD could activate oxidative phosphorylation and oxidative stress (OS). Subsequently, HK-2cell experiments demonstrated that CTD could reduce superoxide dismutase while increasing malondialdehyde levels. In conclusion, after CTD exposure, biometabolic processes may be disrupted with renal injury in mice, resulting in oxidative phosphorylation and OS.