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Biosorption and biotransformation of fluoranthene by the white-rot fungus Pleurotus eryngii F032

Hadibarata T, Kristanti RA, Hamdzah M

Biotechnol Appl Biochem, 2014 Mar-Apr;61(2):126-33.
PMID: 24033877 DOI: 10.1002/bab.1155

Major concern about the presence of fluoranthene, which consists of four fused benzene rings, in the environment has been raised in the past few years due to its toxic, mutagenic, and persistent organic pollutant properties. In this study, we investigated the removal of fluoranthene under static and agitated conditions. About 89% fluoranthene was removed within 30 days under the agitated condition, whereas under the static condition, only 54% fluoranthene was removed. We further investigated the behavior and mechanism of fluoranthene biosorption and biotransformation by Pleurotus eryngii F032 to accelerate the elimination of fluoranthene. The optimum conditions for the elimination of fluoranthene by P. eryngii F032 included a temperature of 35 °C, pH 3, 0.2% inoculum concentration, and a C/N ratio of 16. Under these conditions at the initial fluoranthene concentration of 10 mg/L, more than 95% of fluoranthene was successfully removed within 30 days. Of those factors influencing the biodegradation of fluoranthene, salinity, glucose, and rhamnolipid content were of the greatest importance. Degradation metabolites identified using gas chromatography-mass spectrometry were 1-naphthalenecarboxylic acid and salicylic acid, suggesting possible metabolic pathways. Finally, it can be presumed that the major mechanism of fluoranthene elimination by white-rot fungi is to mineralize polycyclic aromatic hydrocarbons via biotransformation enzymes like laccase.

Matched MeSH terms: Metabolic Networks and Pathways
Identification of naphthalene metabolism by white rot fungus Armillaria sp. F022

Hadibarata T, Yusoff AR, Aris A, Kristanti RA

J Environ Sci (China), 2012;24(4):728-32.
PMID: 22894109

Armillaria sp. F022, a white rot fungus isolated from tropical rain forest (Samarinda, Indonesia) was used to biodegrade naphthalene in cultured medium. Transformation of naphthalene by Armillaria sp. F022 which is able to use naphthalene, a two ring-polycyclic aromatic hydrocarbon (PAH) as a source of carbon and energy was investigated. The metabolic pathway was elucidated by identifying metabolites, biotransformation studies and monitoring enzyme activities in cell-free extracts. The identification of metabolites suggests that Armillaria sp. F022 initiates its attack on naphthalene by dioxygenation at its C-1 and C-4 positions to give 1,4-naphthoquinone. The intermediate 2-hydroxybenzaldehyde and salicylic acid, and the characteristic of the meta-cleavage of the resulting diol were identified in the long-term incubation. A part from typical metabolites of naphthalene degradation known from mesophiles, benzoic acid was identified as the next intermediate for the naphthalene pathway of this Armillaria sp. F022. Neither phthalic acid, catechol and cis,cis-muconic acid metabolites were detected in culture extracts. Several enzymes (manganese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase) produced by Armillaria sp. F022 were detected during the incubation.

Matched MeSH terms: Metabolic Networks and Pathways
Model-assisted formate dehydrogenase-O (fdoH) gene knockout for enhanced succinate production in Escherichia coli from glucose and glycerol carbon sources

Mienda BS, Shamsir MS, Md Illias R

J Biomol Struct Dyn, 2016 Nov;34(11):2305-16.
PMID: 26510527 DOI: 10.1080/07391102.2015.1113387

Succinic acid is an important platform chemical that has broad applications and is been listed as one of the top twelve bio-based chemicals produced from biomass by the US Department of Energy. The metabolic role of Escherichia coli formate dehydrogenase-O (fdoH) under anaerobic conditions in relation to succinic acid production remained largely unspecified. Herein we report, what are to our knowledge, the first metabolic fdoH gene knockout that have enhanced succinate production using glucose and glycerol substrates in E. coli. Using the most recent E. coli reconstruction iJO1366, we engineered its host metabolism to enhance the anaerobic succinate production by deleting the fdoH gene, which blocked H(+) conduction across the mutant cell membrane for the enhanced succinate production. The engineered mutant strain BMS4 showed succinate production of 2.05 g l(-1) (41.2-fold in 7 days) from glycerol and .39 g l(-1) (6.2-fold in 1 day) from glucose. This work revealed that a single deletion of the fdoH gene is sufficient to increase succinate production in E. coli from both glucose and glycerol substrates.

Matched MeSH terms: Metabolic Networks and Pathways
Mini review: hydrogen and ethanol co-production from waste materials via microbial fermentation

Soo CS, Yap WS, Hon WM, Phang LY

World J Microbiol Biotechnol, 2015 Oct;31(10):1475-88.
PMID: 26185061 DOI: 10.1007/s11274-015-1902-6

The simultaneous production of hydrogen and ethanol by microorganisms from waste materials in a bioreactor system would establish cost-effective and time-saving biofuel production. This review aims to present the current status of fermentation processes producing hydrogen accompanied by ethanol as a co-product. We outlined the microbes used and their fundamental pathways for hydrogen and ethanol fermentation. Moreover, we discussed the exploitation of renewable and sustainable waste materials as promising feedstock and the limitations encountered. The low substrate bioconversion rate in hydrogen and ethanol co-production is regarded as the primary constraint towards the development of large scale applications. Thus, microbes with an enhanced capability have been generated via genetic manipulation to diminish the inefficiency of substrate consumption. In this review, other potential approaches to improve the performance of co-production through fermentation were also elaborated. This review will be a useful guide for the future development of hydrogen and ethanol co-production using waste materials.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext Variable Responses to Carbon Utilization between Planktonic and Biofilm Cells of a Human Carrier Strain of Salmonella enterica Serovar Typhi

Kalai Chelvam K, Yap KP, Chai LC, Thong KL

PLoS One, 2015;10(5):e0126207.
PMID: 25946205 DOI: 10.1371/journal.pone.0126207

Salmonella enterica serovar Typhi (S. Typhi) is a foodborne pathogen that causes typhoid fever and infects only humans. The ability of S. Typhi to survive outside the human host remains unclear, particularly in human carrier strains. In this study, we have investigated the catabolic activity of a human carrier S. Typhi strain in both planktonic and biofilm cells using the high-throughput Biolog Phenotype MicroArray, Minimum Biofilm Eradication Concentration (MBEC) biofilm inoculator (96-well peg lid) and whole genome sequence data. Additional strains of S. Typhi were tested to further validate the variation of catabolism in selected carbon substrates in the different bacterial growth phases. The analyzes of the carbon utilization data indicated that planktonic cells of the carrier strain, S. Typhi CR0044 could utilize a broader range of carbon substrates compared to biofilm cells. Pyruvic acid and succinic acid which are related to energy metabolism were actively catabolised in the planktonic stage compared to biofilm stage. On the other hand, glycerol, L-fucose, L-rhamnose (carbohydrates) and D-threonine (amino acid) were more actively catabolised by biofilm cells compared to planktonic cells. Notably, dextrin and pectin could induce strong biofilm formation in the human carrier strain of S. Typhi. However, pectin could not induce formation of biofilm in the other S. Typhi strains. Phenome data showed the utilization of certain carbon substrates which was supported by the presence of the catabolism-associated genes in S. Typhi CR0044. In conclusion, the findings showed the differential carbon utilization between planktonic and biofilm cells of a S. Typhi human carrier strain. The differences found in the carbon utilization profiles suggested that S. Typhi uses substrates mainly found in the human biliary mucus glycoprotein, gallbladder, liver and cortex of the kidney of the human host. The observed diversity in the carbon catabolism profiles among different S. Typhi strains has suggested the possible involvement of various metabolic pathways that might be related to the virulence and pathogenesis of this host-restricted human pathogen. The data serve as a caveat for future in-vivo studies to investigate the carbon metabolic activity to the pathogenesis of S. Typhi.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext The methanolic extract of Garcinia atroviridis (MeGa) reduces body weight and food intake, and improves lipid profiles by altering the lipid metabolism: a rat model

Lim WF, Nasir SM, Teh LK, James RJ, Izhar MHM, Salleh MZ

Turk J Biol, 2020;44(6):437-448.
PMID: 33402870 DOI: 10.3906/biy-2005-2

Garcinia species are widely used for their slimming effects via increased fat burning and suppression of satiety. However, scientific evidence for the biological effects of Garcinia atroviridis (GA) is lacking. We investigated the phytochemical composition, safety profiles, and antioxidant and antiobesity effects of methanolic extracts of Garcinia atroviridis (MeGa) in obese female rats. Repeated dose toxicity studies were conducted according to the OECD guidelines. Upon sacrifice, haematological, biochemical, lipid profile, and serum-based metabolomics analyses were performed to evaluate metabolic expression changes and their related pathways. MeGa contains several phytochemical groups and GA fruit acids. MeGa was found to be nontoxic in both male and female rats with an oral lethal dose (LD50) of 2000 mg/kg. After 9 weeks of treatment, MeGa-treated obese rats had lower weight gain and better lipid profiles (cholesterol and triglyceride), which correlated with the altered metabolic pathways involved in the metabolism of lipid (glycerophospholipid) and biosynthesis of unsaturated fatty acid. In addition, MeGa caused differential metabolism pathways of arachidonic acid and tryptophan that affect the inflammatory response and suppression of appetite. We concluded that MeGa is safe, and its slimming effects are due to the differential metabolism of lipids.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency

Salleh SM, Mazzoni G, Løvendahl P, Kadarmideen HN

BMC Bioinformatics, 2018 Dec 17;19(1):513.
PMID: 30558534 DOI: 10.1186/s12859-018-2553-z

BACKGROUND: Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed efficiency could be included in the genomic selection of the best cows. The present study identified co-expression networks associated with high and low feed efficiency and their regulator genes in Danish Holstein and Jersey cows. RNA-sequencing data from Holstein and Jersey cows with high and low residual feed intake (RFI) and treated with two diets (low and high concentrate) were used. Approximately 26 million and 25 million pair reads were mapped to bovine reference genome for Jersey and Holstein breed, respectively. Subsequently, the gene count expressions data were analysed using a Weighted Gene Co-expression Network Analysis (WGCNA) approach. Functional enrichment analysis from Ingenuity® Pathway Analysis (IPA®), ClueGO application and STRING of these modules was performed to identify relevant biological pathways and regulatory genes.
RESULTS: WGCNA identified two groups of co-expressed genes (modules) significantly associated with RFI and one module significantly associated with diet. In Holstein cows, the salmon module with module trait relationship (MTR) = 0.7 and the top upstream regulators ATP7B were involved in cholesterol biosynthesis, steroid biosynthesis, lipid biosynthesis and fatty acid metabolism. The magenta module has been significantly associated (MTR = 0.51) with the treatment diet involved in the triglyceride homeostasis. In Jersey cows, the lightsteelblue1 (MTR = - 0.57) module controlled by IFNG and IL10RA was involved in the positive regulation of interferon-gamma production, lymphocyte differentiation, natural killer cell-mediated cytotoxicity and primary immunodeficiency.
CONCLUSION: The present study provides new information on the biological functions in liver that are potentially involved in controlling feed efficiency. The hub genes and upstream regulators (ATP7b, IFNG and IL10RA) involved in these functions are potential candidate genes for the development of new biomarkers. However, the hub genes, upstream regulators and pathways involved in the co-expressed networks were different in both breeds. Hence, additional studies are required to investigate and confirm these findings prior to their use as candidate genes.

Matched MeSH terms: Metabolic Networks and Pathways
Structure and function of the vacuolar Ccc1/VIT1 family of iron transporters and its regulation in fungi

Sorribes-Dauden R, Peris D, Martínez-Pastor MT, Puig S

Comput Struct Biotechnol J, 2020;18:3712-3722.
PMID: 33304466 DOI: 10.1016/j.csbj.2020.10.044

Iron is an essential micronutrient for most living beings since it participates as a redox active cofactor in many biological processes including cellular respiration, lipid biosynthesis, DNA replication and repair, and ribosome biogenesis and recycling. However, when present in excess, iron can participate in Fenton reactions and generate reactive oxygen species that damage cells at the level of proteins, lipids and nucleic acids. Organisms have developed different molecular strategies to protect themselves against the harmful effects of high concentrations of iron. In the case of fungi and plants, detoxification mainly occurs by importing cytosolic iron into the vacuole through the Ccc1/VIT1 iron transporter. New sequenced genomes and bioinformatic tools are facilitating the functional characterization, evolution and ecological relevance of metabolic pathways and homeostatic networks across the Tree of Life. Sequence analysis shows that Ccc1/VIT1 homologs are widely distributed among organisms with the exception of animals. The recent elucidation of the crystal structure of a Ccc1/VIT1 plant ortholog has enabled the identification of both conserved and species-specific motifs required for its metal transport mechanism. Moreover, recent studies in the yeast Saccharomyces cerevisiae have also revealed that multiple transcription factors including Yap5 and Msn2/Msn4 contribute to the expression of CCC1 in high-iron conditions. Interestingly, Malaysian S. cerevisiae strains express a partially functional Ccc1 protein that renders them sensitive to iron. Different regulatory mechanisms have been described for non-Saccharomycetaceae Ccc1 homologs. The characterization of Ccc1/VIT1 proteins is of high interest in the development of biofortified crops and the protection against microbial-derived diseases.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext Global metabolomics profiling of colorectal cancer in Malaysian patients

Amir Hashim NA, Ab-Rahim S, Wan Ngah WZ, Nathan S, Ab Mutalib NS, Sagap I, et al.

Bioimpacts, 2021;11(1):33-43.
PMID: 33469506 DOI: 10.34172/bi.2021.05

Introduction:
The serum metabolomics approach has been used to identify metabolite biomarkers that can diagnose colorectal cancer (CRC) accurately and specifically. However, the biomarkers identified differ between studies suggesting that more studies need to be performed to understand the influence of genetic and environmental factors. Therefore, this study aimed to identify biomarkers and affected metabolic pathways in Malaysian CRC patients.
Methods:
Serum from 50 healthy controls and 50 CRC patients were collected at UKM Medical Centre. The samples were deproteinized with acetonitrile and untargeted metabolomics profile determined using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOFMS, Agilent USA). The data were analysed using Mass Profiler Professional (Agilent, USA) software. The panel of biomarkers determined were then used to identify CRC from a new set of 20 matched samples.
Results:
Eleven differential metabolites were identified whose levels were significantly different between CRC patients compared to normal controls. Based on the analysis of the area under the curve, 7 of these metabolites showed high sensitivity and specificity as biomarkers. The use of the 11 metabolites on a new set of samples was able to differentiate CRC from normal samples with 80% accuracy. These metabolites were hypoxanthine, acetylcarnitine, xanthine, uric acid, tyrosine, methionine, lysoPC, lysoPE, citric acid, 5-oxoproline, and pipercolic acid. The data also showed that the most perturbed pathways in CRC were purine, catecholamine, and amino acid metabolisms.
Conclusion:
Serum metabolomics profiling can be used to identify distinguishing biomarkers for CRC as well as to further our knowledge of its pathophysiological mechanisms.

Matched MeSH terms: Metabolic Networks and Pathways
Novel antimicrobial development using genome-scale metabolic model of Gram-negative pathogens: a review

Chung WY, Zhu Y, Mahamad Maifiah MH, Shivashekaregowda NKH, Wong EH, Abdul Rahim N

J Antibiot (Tokyo), 2021 02;74(2):95-104.
PMID: 32901119 DOI: 10.1038/s41429-020-00366-2

Antimicrobial resistance (AMR) threatens the effective prevention and treatment of a wide range of infections. Governments around the world are beginning to devote effort for innovative treatment development to treat these resistant bacteria. Systems biology methods have been applied extensively to provide valuable insights into metabolic processes at system level. Genome-scale metabolic models serve as platforms for constraint-based computational techniques which aid in novel drug discovery. Tools for automated reconstruction of metabolic models have been developed to support system level metabolic analysis. We discuss features of such software platforms for potential users to best fit their purpose of research. In this work, we focus to review the development of genome-scale metabolic models of Gram-negative pathogens and also metabolic network approach for identification of antimicrobial drugs targets.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext Reduced Expression of Glycerol-3-phosphate dehydrogenase (Gpdh) in Drosophila melanogaster pasha mutants Suggests A miRNA-dependency in Its Regulation

Najat Dzaki, Ghows Azzam

Trop Life Sci Res, 2019;30(2):191-200.
MyJurnal

In Drosophila, the Glycerol-3-phosphate dehydrogenase (Gpdh) enzyme plays an active role in many pathways, including the glycerol metabolic pathway and the alphaglycerophosphate cycle. It is also important for ethanol metabolism, as well as flight muscle development. Recent years have exposed small RNAs as a major posttranscriptional regulator of multiple metabolic-pathway genes. Of the many kinds of these RNAs at work, micro RNAs (miRNAs) are the most widely implicated and well understood. However, the roles they may play in regulating Gpdh has never been shown in any model organism. In this study, a pasha-mutant D. melanogaster strain was found to express only 25% of the Gpdh levels typical of their wild type counterparts. Such mutants lack the ability to produce pasha, a protein integral during miRNA-processing, and as a consequence do not produce mature miRNAs. As miRNA-centric regulation often culminates in the depletion of their targets, the concurrent downregulation of Gpdh observed in their absence here therefore alludes to two possibilities: one, that rather than being explicitly bound and repressed by miRNAs, Gpdh expression relies on their action upon an upstream Gpdh-antagonist; or two, that Gpdh may come under the regulation of another class of miRNA-like elements called mirtrons, which do not require pasha to be processed into their functional form. The preliminary findings in this study further highlights the imperative nature of miRNAs in regulating metabolic processes and subsequently, ensuring proper organismal development and its continued survival.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext De novo sequencing, assembly and analysis of eight different transcriptomes from the Malayan pangolin

Mohamed Yusoff A, Tan TK, Hari R, Koepfli KP, Wee WY, Antunes A, et al.

Sci Rep, 2016 09 13;6:28199.
PMID: 27618997 DOI: 10.1038/srep28199

Pangolins are scale-covered mammals, containing eight endangered species. Maintaining pangolins in captivity is a significant challenge, in part because little is known about their genetics. Here we provide the first large-scale sequencing of the critically endangered Manis javanica transcriptomes from eight different organs using Illumina HiSeq technology, yielding ~75 Giga bases and 89,754 unigenes. We found some unigenes involved in the insect hormone biosynthesis pathway and also 747 lipids metabolism-related unigenes that may be insightful to understand the lipid metabolism system in pangolins. Comparative analysis between M. javanica and other mammals revealed many pangolin-specific genes significantly over-represented in stress-related processes, cell proliferation and external stimulus, probably reflecting the traits and adaptations of the analyzed pregnant female M. javanica. Our study provides an invaluable resource for future functional works that may be highly relevant for the conservation of pangolins.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

Rosli R, Amiruddin N, Ab Halim MA, Chan PL, Chan KL, Azizi N, et al.

PLoS One, 2018;13(4):e0194792.
PMID: 29672525 DOI: 10.1371/journal.pone.0194792

Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext Computational prediction of changes in brain metabolic fluxes during Parkinson's disease from mRNA expression

Supandi F, van Beek JHGM

PLoS One, 2018;13(9):e0203687.
PMID: 30208076 DOI: 10.1371/journal.pone.0203687

BACKGROUND: Parkinson's disease is a widespread neurodegenerative disorder which affects brain metabolism. Although changes in gene expression during disease are often measured, it is difficult to predict metabolic fluxes from gene expression data. Here we explore the hypothesis that changes in gene expression for enzymes tend to parallel flux changes in biochemical reaction pathways in the brain metabolic network. This hypothesis is the basis of a computational method to predict metabolic flux changes from post-mortem gene expression measurements in Parkinson's disease (PD) brain.
RESULTS: We use a network model of central metabolism and optimize the correspondence between relative changes in fluxes and in gene expression. To this end we apply the Least-squares with Equalities and Inequalities algorithm integrated with Flux Balance Analysis (Lsei-FBA). We predict for PD (1) decreases in glycolytic rate and oxygen consumption and an increase in lactate production in brain cortex that correspond with measurements (2) relative flux decreases in ATP synthesis, in the malate-aspartate shuttle and midway in the TCA cycle that are substantially larger than relative changes in glucose uptake in the substantia nigra, dopaminergic neurons and most other brain regions (3) shifts in redox shuttles between cytosol and mitochondria (4) in contrast to Alzheimer's disease: little activation of the gamma-aminobutyric acid shunt pathway in compensation for decreased alpha-ketoglutarate dehydrogenase activity (5) in the globus pallidus internus, metabolic fluxes are increased, reflecting increased functional activity.
CONCLUSION: Our method predicts metabolic changes from gene expression data that correspond in direction and order of magnitude with presently available experimental observations during Parkinson's disease, indicating that the hypothesis may be useful for some biochemical pathways. Lsei-FBA generates predictions of flux distributions in neurons and small brain regions for which accurate metabolic flux measurements are not yet possible.

Matched MeSH terms: Metabolic Networks and Pathways
Biodegradation of poly (vinyl alcohol) by an orychophragmus rhizosphere-associated fungus Penicillium brevicompactum OVR-5, and its proposed PVA biodegradation pathway

Mohamed H, Shah AM, Nazir Y, Naz T, Nosheen S, Song Y

World J Microbiol Biotechnol, 2021 Dec 06;38(1):10.
PMID: 34866162 DOI: 10.1007/s11274-021-03197-x

In recent years, the utilisation of endophytes has emerged as a promising biological treatment technology for the degradation of plastic wastes such as biodegradation of synthetic plastics. This study, therefore, aimed to explore and extensively screen endophytic fungi (from selected plants) for efficient in vitro polyvinyl alcohol (PVA) biodegradation. In total, 76 endophytic fungi were isolated and cultivated on a PVA screening agar medium. Among these fungi, 10 isolates showed potential and were subsequently identified based on phenotypical characteristics, ITS ribosomal gene sequences, and phylogenetic analyses. Four strains exhibited a maximum level of PVA-degradation in the liquid medium when cultivated for 10 days at 28 °C and 150 rpm. These strains showed varied PVA removal rates of 81% (Penicillium brevicompactum OVR-5), 67% (Talaromyces verruculosus PRL-2), 52% (P. polonicum BJL-9), and 41% (Aspergillus tubingensis BJR-6) respectively. The most promising PVA biodegradation isolate 'OVR-5', with an optimal pH at 7.0 and optimal temperature at 30 °C, produced lipase, manganese peroxidase, and laccase enzymes. Based on analyses of its metabolic intermediates, as identified with GC-MS, we proposed the potential PVA degradation pathway of OVR-5. Biodegradation results were confirmed through scanning electron microscopy and Fourier transform infrared spectroscopy. This study provides the first report on an endophytic P. brevicompactum strain (associated with Orychophragmus violaceus) that has a great ability for PVA degradation providing more insight on potential fungus-based applications in plastic waste degradation.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses

Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, et al.

Sci Rep, 2016 09 19;6:33660.
PMID: 27641516 DOI: 10.1038/srep33660

Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext Metabolite profiling, antioxidant, and α-glucosidase inhibitory activities of germinated rice: nuclear-magnetic-resonance-based metabolomics study

Pramai P, Abdul Hamid NA, Mediani A, Maulidiani M, Abas F, Jiamyangyuen S

J Food Drug Anal, 2018 01;26(1):47-57.
PMID: 29389588 DOI: 10.1016/j.jfda.2016.11.023

In an attempt to profile the metabolites of three different varieties of germinated rice, specifically black (GBR), red, and white rice, a 1H-nuclear-magnetic-resonance-based metabolomics approach was conducted. Multivariate data analysis was applied to discriminate between the three different varieties using a partial least squares discriminant analysis (PLS-DA) model. The PLS model was used to evaluate the relationship between chemicals and biological activities of germinated rice. The PLS-DA score plot exhibited a noticeable separation between the three rice varieties into three clusters by PC1 and PC2. The PLS model indicated that α-linolenic acid, γ-oryzanol, α-tocopherol, γ-aminobutyric acid, 3-hydroxybutyric acid, fumaric acid, fatty acids, threonine, tryptophan, and vanillic acid were significantly correlated with the higher bioactivities demonstrated by GBR that was extracted in 100% ethanol. Subsequently, the proposed biosynthetic pathway analysis revealed that the increased quantities of secondary metabolites found in GBR may contribute to its nutritional value and health benefits.

Matched MeSH terms: Metabolic Networks and Pathways
Degradation and transformation of anthracene by white-rot fungus Armillaria sp. F022

Hadibarata T, Zubir MM, Rubiyatno, Chuang TZ, Yusoff AR, Salim MR, et al.

Folia Microbiol (Praha), 2013 Sep;58(5):385-91.
PMID: 23307571 DOI: 10.1007/s12223-013-0221-2

Characterization of anthracene metabolites produced by Armillaria sp. F022 was performed in the enzymatic system. The fungal culture was conducted in 100-mL Erlenmeyer flask containing mineral salt broth medium (20 mL) and incubated at 120 rpm for 5-30 days. The culture broth was then centrifuged at 10,000 rpm for 45 min to obtain the extract. Additionally, the effect of glucose consumption, laccase activity, and biomass production in degradation of anthracene were also investigated. Approximately, 92 % of the initial concentration of anthracene was degraded within 30 days of incubation. Dynamic pattern of the biomass production was affected the laccase activity during the experiment. The biomass of the fungus increased with the increasing of laccase activity. The isolation and characterization of four metabolites indicated that the structure of anthracene was transformed by Armillaria sp. F022 in two routes. First, anthracene was oxidized to form anthraquinone, benzoic acid, and second, converted into other products, 2-hydroxy-3-naphthoic acid and coumarin. Gas chromatography-mass spectrometry analysis also revealed that the molecular structure of anthracene was transformed by the action of the enzyme, generating a series of intermediate compounds such as anthraquinone by ring-cleavage reactions. The ligninolytic enzymes expecially free extracellular laccase played an important role in the transformation of anthracene during degradation period.

Matched MeSH terms: Metabolic Networks and Pathways
Fulltext (1) H NMR Metabolic Profiling of Biofluids from Rats with Gastric Mucosal Lesion and Electroacupuncture Treatment

Xu J, Cheng KK, Yang Z, Wang C, Shen G, Wang Y, et al.

Evid Based Complement Alternat Med, 2015;2015:801691.
PMID: 26170882 DOI: 10.1155/2015/801691

Gastric mucosal lesion (GML) is a common gastrointestinal disorder with multiple pathogenic mechanisms in clinical practice. In traditional Chinese medicine (TCM), electroacupuncture (EA) treatment has been proven as an effective therapy for GML, although the underlying healing mechanism is not yet clear. Here, we used proton nuclear magnetic resonance- ((1)H NMR-) based metabolomic method to investigate the metabolic perturbation induced by GML and the therapeutic effect of EA treatment on stomach meridian (SM) acupoints. Clear metabolic differences were observed between GML and control groups, and related metabolic pathways were discussed by means of online metabolic network analysis toolbox. By comparing the endogenous metabolites from GML and GML-SM groups, the disturbed pathways were partly recovered towards healthy state via EA treated on SM acupoints. Further comparison of the metabolic variations induced by EA stimulated on SM and the control gallbladder meridian (GM) acupoints showed a quite similar metabolite composition except for increased phenylacetylglycine, 3,4-dihydroxymandelate, and meta-hydroxyphenylacetate and decreased N-methylnicotinamide in urine from rats with EA treated on SM acupoints. The current study showed the potential application of metabolomics in providing further insight into the molecular mechanism of acupuncture.

Matched MeSH terms: Metabolic Networks and Pathways
Temporal proteomic profiling of Chlamydia trachomatis-infected HeLa-229 human cervical epithelial cells

Tan GM, Lim HJ, Yeow TC, Movahed E, Looi CY, Gupta R, et al.

Proteomics, 2016 05;16(9):1347-60.
PMID: 27134121 DOI: 10.1002/pmic.201500219

Chlamydia trachomatis is the leading causative agent of bacterial sexually transmitted infections worldwide which can lead to female pelvic inflammatory disease and infertility. A greater understanding of host response during chlamydial infection is essential to design intervention technique to reduce the increasing incidence rate of genital chlamydial infection. In this study, we investigated proteome changes in epithelial cells during C. trachomatis infection by using an isobaric tags for relative and absolute quantitation (iTRAQ) labeling technique coupled with a liquid chromatography-tandem mass spectrometry (LC-MS(3) ) analysis. C. trachomatis (serovar D, MOI 1)-infected HeLa-229 human cervical carcinoma epithelial cells (at 2, 4 and 8 h) showed profound modifications of proteome profile which involved 606 host proteins. MGST1, SUGP2 and ATXN10 were among the top in the list of the differentially upregulated protein. Through pathway analysis, we suggested the involvement of eukaryotic initiation factor 2 (eIF2) and mammalian target of rapamycin (mTOR) in host cells upon C. trachomatis infection. Network analysis underscored the participation of DNA repair mechanism during C. trachomatis infection. In summary, intense modifications of proteome profile in C. trachomatis-infected HeLa-229 cells indicate complex host-pathogen interactions at early phase of chlamydial infection.

Matched MeSH terms: Metabolic Networks and Pathways/genetics

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