Photosynthesis, Anatomy, and Metabolism as a Tool for Assessing Physiological Modulation in Five Native Species of the Brazilian Atlantic Forest.

The Brazilian Atlantic Forest, renowned for its exceptional species richness and high endemism, acts as a vital reservoir of terrestrial biodiversity, often referred to as a biodiversity hotspot. Consequently, there is an urgent need to restore this forest to safeguard certain species and to unravel the ecophysiological adaptations of others. This study aims to integrate some physiological parameters, including gas exchange and chlorophyll a fluorescence, with anatomical and metabolic techniques to elucidate how five different native species (Paubrasilia echinata, Chorisia glaziovii, Clusia nemorosa, Licania tomentosa, and Schinus terebinthifolius), each occupying distinct ecological niches, respond to seasonal variations in rainfall and their consequences. Our investigation has revealed that C. nemorosa and P. echinata exhibit robust mechanisms to mitigate the adverse effects of drought. In contrast, others demonstrate greater adaptability (e.g., S. terebinthifolia and C. glaziovii). In this context, exploring metabolic pathways has proven invaluable in comprehending the physiological strategies and their significance in species acclimatization. This study provides a comprehensive overview of the impact of water restrictions and their consequential effects on various species, defining the strategies each species uses to mitigate water privation during the dry season.

Key energy metabolisms in modern living microbialites from hypersaline Andean lagoons of the Salar de Atacama, Chile.

Microbialites are organosedimentary structures formed mainly due to the precipitation of carbonate minerals, although they can also incorporate siliceous, phosphate, ferric, and sulfate minerals. The minerals' precipitation occurs because of local chemical changes triggered by changes in pH and redox transformations catalyzed by the microbial energy metabolisms. Here, geochemistry, metagenomics, and bioinformatics tools reveal the key energy metabolisms of microbial mats, stromatolites and an endoevaporite distributed across four hypersaline lagoons from the Salar de Atacama. Chemoautotrophic and chemoheterotrophic microorganisms seem to coexist and influence microbialite formation. The microbialite types of each lagoon host unique microbial communities and metabolisms that influence their geochemistry. Among them, photosynthetic, carbon- and nitrogen- fixing and sulfate-reducing microorganisms appear to control the main biogeochemical cycles. Genes associated with non-conventional energy pathways identified in MAGs, such as hydrogen production/consumption, arsenic oxidation/reduction, manganese oxidation and selenium reduction, also contribute to support life in microbialites. The presence of genes encoding for enzymes associated with ureolytic processes in the Cyanobacteria phylum and Gammaproteobacteria class might induce carbonate precipitation in hypersaline environments, contributing to the microbialites formation. To the best of our knowledge, this is the first study characterizing metagenomically microbialites enriched in manganese and identifying metabolic pathways associated with manganese oxidation, selenium reduction, and ureolysis in this ecosystem, which suggests that the geochemistry and bioavailability of energy sources (As, Mn and Se) shapes the microbial metabolisms in the microbialites.

The impact of a story on learning ketone body metabolism.

Biochemistry is a core subject in the cross-disciplinary training on Biotechnology engineering courses. Metabolic pathways teaching has traditionally integrated hands-on laboratory experiences and traditional lectures, which detail a large number of reactions at a molecular level, their enzymes and regulation. The current scenario of Covid-19 outbreak have motivated the development of complementary tools that expand the horizon of metabolism teaching. In this study, we employed a story-based methodology to strengthen the metabolic pathways learning and to measure students' perception. Specifically, a peer-reviewed tale describing the ketone body metabolism was used during five semesters as a didactic strategy to teach this biochemical process. A questionnaire assessed the students' understanding and acceptance of the methodology (n = 83). Our findings showed that a high proportion of students (83.13%) were able to relate the story to the topics studied in the classroom (ketogenesis and ketolysis). On the other hand, they were satisfied and suggested that such methodology is effective and fun. In summary, most of the survey responses related to acceptance of story-based strategy ranged from 72% to 97%. Collectively, these results indicated that the story is appropriate to decomplex pathways, becoming a simple tool for driving motivation, learning and engagement of students. The narrative represents a bridge to connect the intriguing series of chemical reactions involved in the anabolism and degradation of 3-hydroxybutyrate (3-OHB), acetoacetate, and acetone with previously learned knowledge, emotions, and key concepts. In conclusion, the tale was useful to decode ketone body-related pathways and making metabolism learning more interesting and easier.

The growing field of immunometabolism and exercise: Key findings in the last 5 years.

This perspective review highlights the impact of physical exercise on immunometabolic responses in the past 5 years. Understanding immunometabolism as a part of immunological research is essential. Furthermore, the roles of both acute and chronic effects of physical exercise on health, aging, and chronic diseases in immunometabolic changes should be elaborated. In immune cells, ß2 adrenergic signaling stimulates the preferential mobilization of inflammatory phenotypes, such as CD16+ monocytes and CD8+ T cells, into the bloodstream after a physical exercise session. The mobilization of immune cells is closely related to the availability of energetic substrates for the cell and mechanisms associated with the uptake and oxidation of fatty acids and glucose. These cells, especially senescent T cells, are mobilized to the peripheral tissues and undergo apoptotic signaling, stimulating the creation of a "vacant space" where new cells will be matured and replaced in the circulation. This results in the upregulation of the expression and secretion of anti-inflammatory cytokines (IL-10 and IL-1ra), leading to increased regulatory immune cells that provide immunoregulatory properties. Thus, we suggest that a significant nutrient available to the cell will favor oxidative metabolism, augment ATP production, and consequently maintain the immune cells in their quiescent state, as well as promote rapid activation function. Therefore, based on the studies discussed in this perspective review, we highlight the importance of performing moderate-intensity continuous and high-intensity intermittent aerobic exercises, due to a higher magnitude of energetic demand and release of anti-inflammatory cytokines (IL-6 and IL-10).

In silico predictions of protein interactions between Zika virus and human host.

BACKGROUND: The ZIKA virus (ZIKV) belongs to the Flaviviridae family, was first isolated in the 1940s, and remained underreported until its global threat in 2016, where drastic consequences were reported as Guillan-Barre syndrome and microcephaly in newborns. Understanding molecular interactions of ZIKV proteins during the host infection is important to develop treatments and prophylactic measures; however, large-scale experimental approaches normally used to detect protein-protein interaction (PPI) are onerous and labor-intensive. On the other hand, computational methods may overcome these challenges and guide traditional approaches on one or few protein molecules. The prediction of PPIs can be used to study host-parasite interactions at the protein level and reveal key pathways that allow viral infection. RESULTS: Applying Random Forest and Support Vector Machine (SVM) algorithms, we performed predictions of PPI between two ZIKV strains and human proteomes. The consensus number of predictions of both algorithms was 17,223 pairs of proteins. Functional enrichment analyses were executed with the predicted networks to access the biological meanings of the protein interactions. Some pathways related to viral infection and neurological development were found for both ZIKV strains in the enrichment analysis, but the JAK-STAT pathway was observed only for strain PE243 when compared with the FSS13025 strain. CONCLUSIONS: The consensus network of PPI predictions made by Random Forest and SVM algorithms allowed an enrichment analysis that corroborates many aspects of ZIKV infection. The enrichment results are mainly related to viral infection, neuronal development, and immune response, and presented differences among the two compared ZIKV strains. Strain PE243 presented more predicted interactions between proteins from the JAK-STAT signaling pathway, which could lead to a more inflammatory immune response when compared with the FSS13025 strain. These results show that the methodology employed in this study can potentially reveal new interactions between the ZIKV and human cells.

Relationship Between Heart Rate, Oxygen Consumption, and Energy Expenditure in Futsal.

The primary aim of this study was to compare the measured oxygen consumption (Measured-VO2) in a simulated futsal game (S-Game) with the estimated oxygen consumption (Estimated-VO2) through a regression equation between heart rate (HR) and oxygen consumption (VO2) (HR-VO2) in treadmill running, and a secondary aim was to calculate the total energy expenditure (EE) in S-Game. Ten professional players (22.20 ± 3.22 years) were evaluated. HR-VO2 was determined individually in the continuous test on the treadmill (ContTest). The Measured-VO2 in S-Game was compared with the Estimated-VO2 in the ContTest. Alactic and lactic pathways were estimated by VO2. The Estimated-VO2 presented no statistically significant difference with the Measured-VO2, using the paired t-test (p = 0.38). However, the correlation between Estimated- and Measured-VO2 was very weak (r = -0.05), and it presented poor agreement (concordance correlation coefficient = -0.04). In addition, a Bland-Altman plot presented bias of -2.8 ml/kg/min and individual difference as large as 19 ml/kg/min. The HR-VO2 determined by the ContTest was not a good individual predictor of VO2. The high intensity and intermittent nature of the futsal game possibly caused dissociation in the HR-VO2 relationship. ContTest is not recommended for estimating VO2 and calculating individual EE in the futsal game. This is recommended only for the group mean. The total EE in S-Game was 13.10 ± 1.25 kcal.min-1 (10.81 ± 1.57 metabolic equivalents). The contributions from the metabolic pathways were as follows: aerobic (93%), alactic (5%), and lactic (2%).

A review on the enzymes and metabolites identified by mass spectrometry from bacteria and microalgae involved in the degradation of high molecular weight PAHs.

High molecular weight PAHs (HMW PAHs) are dangerous pollutants widely distributed in the environment. The use of microorganisms represents an important tool for HMW PAHs bioremediation, so, the understanding of their biochemical pathways facilitates the development of biodegradation strategies. For this reason, the potential role of species of microalgae, bacteria, and microalga-bacteria consortia in the degradation of HMW PAHs is discussed. The identification of their metabolites, mostly by GC-MS and LC-MS, allows a better approach to the enzymes involved in the key steps of the metabolic pathways of HMW PAHs biodegradation. So, this review intends to address the proteomic research on enzyme activities and their involvement in regulating essential biochemical functions that help bacteria and microalgae in the biodegradation processes of HMW PAHs. It is noteworthy that, given that to the best of our knowledge, this is the first review focused on the mass spectrometry identification of the HMW PAHs metabolites; whereby and due to the great concern of the presence of HMW PAHs in the environment, this material could help the urgency of developing new bioremediation methods. The elucidation of the metabolic pathways of persistent pollutant degrading microorganisms should lead to a better knowledge of the enzymes involved, which could contribute to a very ecological route to the control of environmental contamination in the future.

Bioengineering potato plants to produce benzylglucosinolate for improved broad-spectrum pest and disease resistance.

In traditional, small-scale agriculture in the Andes, potatoes are frequently co-cultivated with the Andean edible tuber Tropaeolum tuberosum, commonly known as mashua, which is believed to exert a pest and disease protective role due to its content of the phenylalanine-derived benzylglucosinolate (BGLS). We bioengineered the production of BGLS in potato by consecutive generation of stable transgenic events with two polycistronic constructs encoding for expression of six BGLS biosynthetic genes from Arabidopsis thaliana. First, we integrated a polycistronic construct coding for the last three genes of the pathway (SUR1, UGT74B1 and SOT16) into potato driven by the cauliflower mosaic virus 35S promoter. After identifying the single-insertion transgenic event with the highest transgene expression, we stacked a second polycistronic construct coding for the first three genes in the pathway (CYP79A2, CYP83B1 and GGP1) driven by the leaf-specific promoter of the rubisco small subunit from chrysanthemum. We obtained transgenic events producing as high as 5.18 pmol BGLS/mg fresh weight compared to the non-transgenic potato plant producing undetectable levels of BGLS. Preliminary bioassays suggest a possible activity against Phytophthora infestans, causing the late blight disease and Premnotrypes suturicallus, referred to as the Andean potato weevil. However, we observed altered leaf morphology, abnormally thick and curlier leaves, reduced growth and tuber production in five out of ten selected transgenic events, which indicates that the expression of BGLS biosynthetic genes has an undesirable impact on the potato. Optimization of the expression of the BGLS biosynthetic pathway in potato is required to avoid alterations of plant development.

Unraveling biogeochemical phosphorus dynamics in hyperarid Mars-analogue soils using stable oxygen isotopes in phosphate.

With annual precipitation less than 20 mm and extreme UV intensity, the Atacama Desert in northern Chile has long been utilized as an analogue for recent Mars. In these hyperarid environments, water and biomass are extremely limited, and thus, it becomes difficult to generate a full picture of biogeochemical phosphate-water dynamics. To address this problem, we sampled soils from five Atacama study sites and conducted three main analyses-stable oxygen isotopes in phosphate, enzyme pathway predictions, and cell culture experiments. We found that high sedimentation rates decrease the relative size of the organic phosphorus pool, which appears to hinder extremophiles. Phosphoenzyme and pathway prediction analyses imply that inorganic pyrophosphatase is the most likely catalytic agent to cycle P in these environments, and this process will rapidly overtake other P utilization strategies. In these soils, the biogenic δ18 O signatures of the soil phosphate (δ18 OPO4 ) can slowly overprint lithogenic δ18 OPO4 values over a timescale of tens to hundreds of millions of years when annual precipitation is more than 10 mm. The δ18 OPO4 of calcium-bound phosphate minerals seems to preserve the δ18 O signature of the water used for biogeochemical P cycling, pointing toward sporadic rainfall and gypsum hydration water as key moisture sources. Where precipitation is less than 2 mm, biological cycling is restricted and bedrock δ18 OPO4 values are preserved. This study demonstrates the utility of δ18 OPO4 values as indicative of biogeochemical cycling and hydrodynamics in an extremely dry Mars-analogue environment.

Salmonella enterica Optimizes Metabolism After Addition of Acyl-Homoserine Lactone Under Anaerobic Conditions.

Acyl-homoserine lactones (AHLs) are quorum sensing (QS) signaling molecules that mediate cell-to-cell communication in Gram-negative bacteria. Salmonella does not produce AHL, however, it can recognize AHLs produced by other species through SdiA protein modulating important cellular functions. In this work, the influence of the N-dodecanoyl-DL-homoserine lactone (C12-HSL) on glucose consumption, metabolic profile, and gene expression of Salmonella throughout the cultivation time in Tryptic Soy Broth (TSB) under anaerobic conditions was evaluated. Analysis of the supernatant culture in high-performance liquid chromatography (HPLC) revealed lower glucose uptake after 4 and 6 h of the addition of C12-HSL. Gas chromatography-mass spectrometry (GC-MS) based analysis of the intracellular metabolites revealed C12-HSL perturbation in the abundance levels of metabolites related to the metabolic pathways of glycerolipids, purines, amino acids, and aminoacyl-tRNA biosynthesis. The real-time quantitative PCR (RT-qPCR) indicated that Salmonella increase expression of genes associated with nucleoside degradation and quantification of metabolites supported the induction of pentose phosphate pathway to ensure growth under lower glucose consumption. The obtained data suggest an important role of C12-HSL in the optimization of metabolism at a situation of high population densities.

New Insights on the Effect of TNF Alpha Blockade by Gene Silencing in Noise-Induced Hearing Loss.

Noise exposure represents the second most common cause of acquired sensorineural hearing loss and we observed that tumor necrosis factor α (TNFα) was involved in this context. The effect of Tnfα gene silencing on the expression profile related to the TNFα metabolic pathway in an experimental model of noise-induced hearing loss had not previously been studied. METHODS: Single ears of Wistar rats were pretreated with Tnfα small interfering RNA (siRNA) by trans-tympanic administration 24 h before they were exposed to white noise (120 dBSPL for three hours). After 24 h of noise exposure, we analyzed the electrophysiological threshold and the amplitude of waves I, II, III, and IV in the auditory brain response click. In addition, qRT-PCR was performed to evaluate the TNFα metabolic pathway in the ears submitted or not to gene silencing. RESULTS: Preservation of the electrophysiological threshold and the amplitude of waves was observed in the ears submitted to gene silencing compared to the ears not treated. Increased anti-apoptotic gene expression and decreased pro-apoptotic gene expression were found in the treated ears. CONCLUSION: Our results allow us to suggest that the blockade of TNFα by gene silencing was useful to prevent noise-induced hearing loss.

Role of Muscarinic Acetylcholine Receptors in Breast Cancer: Design of Metronomic Chemotherapy.

BACKGROUND: muscarinic acetylcholine receptors (mAChRs) have attracted interest as targets for therapeutic interventions in different illnesses like Alzheimer´s disease, viral infections and different tumors. Regarding the latter, many authors have studied each subtype of mAChRs, which seem to be involved in the progression of distinct types of malignancies. METHODS: We carefully revised research literature focused on mAChRs expression and signaling as well as in their involvement in cancer progression and treatment. The characteristics of screened papers were described using the mentioned conceptual framework. RESULTS: Muscarinic antagonists and agonists have been assayed for the treatment of tumors established in lung, brain and breast with beneficial effects. We described an up-regulation of mAChRs in mammary tumors and the lack of expression in non-tumorigenic breast cells and normal mammary tissues. We and others demonstrated that muscarinic agonists can trigger anti-tumor actions in a dose-dependent manner on tumors originated in different organs like brain or breast. At pharmacological concentrations, they exert similar effects to traditional chemotherapeutic agents. Metronomic chemotherapy refers to the administration of anti-cancer drugs at low doses with short intervals among them, and it is a different regimen applied in cancer treatment reducing malignant growth and angiogenesis, and very low incidence of adverse effects. CONCLUSION: The usage of subthreshold concentrations of muscarinic agonists combined with conventional chemotherapeutic agents could be a promising tool for breast cancer therapy.

Cloning and expression analysis of three critical triterpenoid pathway genes in Osmanthus fragrans

Background: Osmanthus fragrans is an important ornamental tree and has been widely planted in China because of its pleasant aroma, which is mainly due to terpenes. The monoterpenoid and sesquiterpenoid metabolic pathways of sweet osmanthus have been well studied. However, these studies were mainly focused on volatile small molecule compounds. The molecular regulation mechanism of synthesis of large molecule compounds (triterpenoids) remains unclear. Squalene synthase (SQS), squalene epoxidase (SQE), and beta-amyrin synthase (BETA-AS) are three critical enzymes of the triterpenoid biosynthesis pathway. Results: In this study, the full-length cDNA and gDNA sequences of OfSQS, OfSQE, and OfBETA-AS were isolated from sweet osmanthus. Phylogenetic analysis suggested that OfSQS and OfSQE had the closest relationship with Sesamum indicum, and OfBETA-AS sequence shared the highest similarity of 99% with that of Olea europaea. The qRT-PCR analysis revealed that the three genes were highly expressed in flowers, especially OfSQE and OfBETA-AS, which were predominantly expressed in the flowers of both "Boye" and "Rixiang" cultivars, suggesting that they might play important roles in the accumulation of triterpenoids in flowers of O. fragrans. Furthermore, the expression of OfBETA-AS in the two cultivars was significantly different during all the five flowering stages; this suggested that OfBETA-AS may be the critical gene for the differences in the accumulation of triterpenoids. Conclusion: The evidence indicates that OfBETA-AS could be the key gene in the triterpenoid synthesis pathway, and it could also be used as a critical gene resource in the synthesis of essential oils by using bioengineered bacteria.

Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions.

Proteiniphilum saccharofermentans str. M3/6T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, ß-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6T, 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6T and its closest described relative P. acetatigenes str. DSM 18083T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars.

The completely annotated genome and comparative genomics of the Peptoniphilaceae bacterium str. ING2-D1G, a novel acidogenic bacterium isolated from a mesophilic biogas reactor.

The strictly anaerobic Peptoniphilaceae bacterium str. ING2-D1G (=DSM 28672=LMG 28300) was isolated from a mesophilic laboratory-scale completely stirred tank biogas reactor (CSTR) continuously co-digesting maize silage, pig and cattle manure. Based on 16S rRNA gene sequence comparison, the closest described relative to this strain is Peptoniphilus obesi ph1 showing 91.2% gene sequence identity. The most closely related species with a validly published name is Peptoniphilus indolicus DSM 20464T whose 16S rRNA gene sequence is 90.6% similar to the one of strain ING2-D1G. The genome of the novel strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding anaerobic digestion of biomass. The strain harbors a circular chromosome with a size of 1.6 Mb that contains 1466 coding sequences, 53 tRNA genes and 4 ribosomal RNA (rrn) operons. The genome carries a 28,261bp prophage insertion comprising 47 phage-related coding sequences. Reconstruction of fermentation pathways revealed that strain ING2-D1G encodes all enzymes for hydrogen, lactate and acetate production, corroborating that it is involved in the acido- and acetogenic phase of the biogas process. Comparative genome analyses of Peptoniphilaceae bacterium str. ING2-D1G and its closest relative Peptoniphilus obesi ph1 uncovered rearrangements, deletions and insertions within the chromosomes of both strains substantiating a divergent evolution. In addition to genomic analyses, a physiological and phenotypic characterization of the novel isolate was performed. Grown in Brain Heart Infusion Broth with added yeast extract, cells were spherical to ovoid, catalase- and oxidase-negative and stained Gram-positive. Optimal growth occurred between 35 and 37°C and at a pH value of 7.6. Fermentation products were acetate, butanoate and carbon dioxide.

Evaluation of the leishmanicidal and cytotoxic effects of inhibitors for microorganism metabolic pathway enzymes.

Chemotherapy for leishmaniosis a neglected parasitic disease, is based on few drugs, which are toxic and present resistance issues. Efforts for the development of new therapies are essential for the control of leishmaniasis. Metabolic pathway enzymes are promising targets for new drugs against parasites. The search for effective drugs against key enzymes can take advantage of the similarities between metabolic pathways in different microorganisms trypanosomatids Trypanosoma cruzi and Leishmania and fungus Saccharomyces cerevisiae. In this report, leishmanicidal activity of the metabolic pathway enzymes inhibitors (IDs) of dihydroorotate dehydrogenase (DHODH), glyceraldehyde 3-phosphate dehydrogenase and cruzain-cysteine protease from T. cruzi and scitalona-desidratase, adenosine deaminase, succinate dehydrogenase complex II and hydroxynaphthalene reductase from S. cerevisiae was performed on Leishmania amazonensis extracellular promastigotes and amastigotes within macrophages. The most promising compound, ID195, which is a DHODH inhibitor was toxic against promastigotes and was selective for amastigotes over host cells.

Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp: ONBA-17 and deduction on its metabolic pathway

A previously reported o-nitrobenzaldehyde (ONBA) degrading bacterium Pseudomonas sp. ONBA-17 was further identified and characterized. Based on results of DNA base composition and DNA-DNA hybridization, the strain was identified as P. putida. Its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. Higher removal rate was achieved under shaking conditions. All tested ONBA with different initial concentrations could be completely degraded within 5 d. In addition, degradative enzyme(s) involved was confirmed as intra-cellular distributed and constitutively expressed. Effects of different compounds on relative activity of degradative enzyme(s) within cell-free extract were also evaluated. Finally, 2-nitrobenzoic acid and 2, 3-dihydroxybenzoic acid were detected as metabolites of ONBA degradation by P. putida ONBA-17, and relevant metabolic pathway was preliminary proposed. This study might help with future research in better understanding of nitroaromatics biodegradation.

Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp: ONBA-17 and deduction on its metabolic pathway

A previously reported o-nitrobenzaldehyde (ONBA) degrading bacterium Pseudomonas sp. ONBA-17 was further identified and characterized. Based on results of DNA base composition and DNA-DNA hybridization, the strain was identified as P. putida. Its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. Higher removal rate was achieved under shaking conditions. All tested ONBA with different initial concentrations could be completely degraded within 5 d. In addition, degradative enzyme(s) involved was confirmed as intra-cellular distributed and constitutively expressed. Effects of different compounds on relative activity of degradative enzyme(s) within cell-free extract were also evaluated. Finally, 2-nitrobenzoic acid and 2, 3-dihydroxybenzoic acid were detected as metabolites of ONBA degradation by P. putida ONBA-17, and relevant metabolic pathway was preliminary proposed. This study might help with future research in better understanding of nitroaromatics biodegradation.

Further characterization of o-nitrobenzaldehyde degrading bacterium Pseudomonas sp. ONBA-17 and deduction on its metabolic pathway.

A previously reported o-nitrobenzaldehyde (ONBA) degrading bacterium Pseudomonas sp. ONBA-17 was further identified and characterized. Based on results of DNA base composition and DNA-DNA hybridization, the strain was identified as P. putida. Its degradation effect enhanced with increase of inoculum amount and no lag phase was observed. Higher removal rate was achieved under shaking conditions. All tested ONBA with different initial concentrations could be completely degraded within 5 d. In addition, degradative enzyme(s) involved was confirmed as intra-cellular distributed and constitutively expressed. Effects of different compounds on relative activity of degradative enzyme(s) within cell-free extract were also evaluated. Finally, 2-nitrobenzoic acid and 2, 3-dihydroxybenzoic acid were detected as metabolites of ONBA degradation by P. putida ONBA-17, and relevant metabolic pathway was preliminary proposed. This study might help with future research in better understanding of nitroaromatics biodegradation.

Expression analysis in response to drought stress in soybean: Shedding light on the regulation of metabolic pathway genes.

Metabolomics analysis of wild type Arabidopsis thaliana plants, under control and drought stress conditions revealed several metabolic pathways that are induced under water deficit. The metabolic response to drought stress is also associated with ABA dependent and independent pathways, allowing a better understanding of the molecular mechanisms in this model plant. Through combining an in silico approach and gene expression analysis by quantitative real-time PCR, the present work aims at identifying genes of soybean metabolic pathways potentially associated with water deficit. Digital expression patterns of Arabidopsis genes, which were selected based on the basis of literature reports, were evaluated under drought stress condition by Genevestigator. Genes that showed strong induction under drought stress were selected and used as bait to identify orthologs in the soybean genome. This allowed us to select 354 genes of putative soybean orthologs of 79 Arabidopsis genes belonging to 38 distinct metabolic pathways. The expression pattern of the selected genes was verified in the subtractive libraries available in the GENOSOJA project. Subsequently, 13 genes from different metabolic pathways were selected for validation by qPCR experiments. The expression of six genes was validated in plants undergoing drought stress in both pot-based and hydroponic cultivation systems. The results suggest that the metabolic response to drought stress is conserved in Arabidopsis and soybean plants.