Although phosphine is ubiquitously present in anaerobic environments, little is known regarding the microbial community dynamics and metabolic pathways associated with phosphine formation in an anaerobic digestion system. This study investigated the production of phosphine in anaerobic digestion, with results indicating that phosphine production mainly occurred during logarithmic microbial growth. Dehydrogenase and hydrogen promoted the production of phosphine, with a maximum phosphine concentration of 300 mg/m3. The abundance of Ruminococcaceae and Escherichia was observed to promote phosphine generation. The analysis of metabolic pathways based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the MetaCyc pathway database revealed the highest relative abundance of replication and repair in genetic information processing; further, the cofactor, prosthetic group, electron carrier, and vitamin biosynthesis were observed to be closely related to phosphine formation. A phylogenetic tree was reconstructed based on the neighbor-joining method. The results indicated the clear evolutionary position of the isolated Pseudescherichia sp. SFM4 strain, adjacent to Escherichia, with a stable phosphate-reducing ability for a maximum phosphine concentration of 26 mg/m3. The response surface experiment indicated that the initial optimal conditions for phosphine production by SFM4 could be achieved with nitrogen, carbon, and phosphorus loads of 6.17, 300, and 10 mg/L, respectively, at pH 7.47. These results provide comprehensive insights into the dynamic changes in the microbial structure, isolated single bacterial strain, and metabolic pathways associated with phosphine formation. They also provide information on the molecular biology associated with phosphorus recycling.
- MeSH
- anaerobióza MeSH
- bioreaktory mikrobiologie MeSH
- Clostridiales genetika metabolismus MeSH
- dusík metabolismus MeSH
- Escherichia genetika metabolismus MeSH
- fosfáty metabolismus MeSH
- fosfiny analýza metabolismus MeSH
- fosfor metabolismus MeSH
- fylogeneze MeSH
- metabolické sítě a dráhy * genetika MeSH
- mikrobiota * MeSH
- odpadní vody mikrobiologie MeSH
- vodík metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Several studies indicated that antipsychotic treatment response and side effect manifestation can be different due to inter-individual variability in genetic variations. AIM OF THE STUDY: Here we perform a case-control study to explore a potential association between schizophrenia and variants within the antipsychotic drug molecular targets (DRD1, DRD2, DRD3, HTR2A, HTR6) and metabolizing enzymes (CYP2D6, COMT) genes in Armenian population including also analysis of their possible relationship with disease clinical symptoms. METHODS: A total of 18 SNPs was studied in patients with schizophrenia (n = 78) and healthy control subjects (n = 77) using MassARRAY genotyping. RESULTS: We found that two studied genetic variants, namely DRD2 rs4436578*C and HTR2A rs6314*A are underrepresented in the group of patients compared to healthy subjects. After the correction for multiple testing, the rs4436578*C variant remained significant while the rs6314*A reported borderline significance. No significant differences in minor allele frequencies for other studied variants were identified. Also, a relationship between the genotypes and age of onset as well as disease duration has been detected. CONCLUSIONS: The DRD2 rs4436578*C genetic variant might have protective role against schizophrenia, at least in Armenians.
- MeSH
- antipsychotika terapeutické užití MeSH
- cytochrom P-450 CYP2D6 genetika MeSH
- dopamin genetika metabolismus MeSH
- dospělí MeSH
- frekvence genu MeSH
- genetická predispozice k nemoci MeSH
- genetické asociační studie MeSH
- genotyp MeSH
- jednonukleotidový polymorfismus * MeSH
- katechol-O-methyltransferasa genetika MeSH
- lidé středního věku MeSH
- lidé MeSH
- metabolické sítě a dráhy genetika MeSH
- mladý dospělý MeSH
- receptory dopaminové genetika MeSH
- receptory serotoninové genetika MeSH
- schizofrenie farmakoterapie genetika MeSH
- senioři MeSH
- serotonin genetika metabolismus MeSH
- studie případů a kontrol MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.
- MeSH
- biologické modely MeSH
- chloroplasty genetika metabolismus MeSH
- dusičnany metabolismus MeSH
- dusík metabolismus MeSH
- metabolické sítě a dráhy genetika MeSH
- metabolomika metody MeSH
- mitochondrie genetika metabolismus MeSH
- molekulární evoluce MeSH
- mořská voda mikrobiologie MeSH
- proteomika metody MeSH
- regulace genové exprese MeSH
- rozsivky genetika metabolismus MeSH
- signální transdukce genetika MeSH
- stanovení celkové genové exprese metody MeSH
- uhlík metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Actinobacteria of the acI lineage are the most abundant microbes in freshwater systems, but there are so far no pure living cultures of these organisms, possibly because of metabolic dependencies on other microbes. This, in turn, has hampered an in-depth assessment of the genomic basis for their success in the environment. Here we present genomes from 16 axenic cultures of acI Actinobacteria. The isolates were not only of minute cell size, but also among the most streamlined free-living microbes, with extremely small genome sizes (1.2-1.4 Mbp) and low genomic GC content. Genome reduction in these bacteria might have led to auxotrophy for various vitamins, amino acids and reduced sulphur sources, thus creating dependencies to co-occurring organisms (the 'Black Queen' hypothesis). Genome analyses, moreover, revealed a surprising degree of inter- and intraspecific diversity in metabolic pathways, especially of carbohydrate transport and metabolism, and mainly encoded in genomic islands. The striking genotype microdiversification of acI Actinobacteria might explain their global success in highly dynamic freshwater environments with complex seasonal patterns of allochthonous and autochthonous carbon sources. We propose a new order within Actinobacteria ('Candidatus Nanopelagicales') with two new genera ('Candidatus Nanopelagicus' and 'Candidatus Planktophila') and nine new species.
- MeSH
- Actinobacteria klasifikace genetika izolace a purifikace MeSH
- biodiverzita MeSH
- DNA bakterií chemie MeSH
- fylogeneze MeSH
- genom bakteriální * MeSH
- metabolické sítě a dráhy genetika MeSH
- sladká voda mikrobiologie MeSH
- zastoupení bazí MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The obligate intracellular pathogen, Anaplasma phagocytophilum, is the causative agent of life-threatening diseases in humans and animals. A. phagocytophilum is an emerging tick-borne pathogen in the United States, Europe, Africa and Asia, with increasing numbers of infected people and animals every year. It is increasingly recognized that intracellular pathogens modify host cell metabolic pathways to increase infection and transmission in both vertebrate and invertebrate hosts. Recent reports have shown that amino acids are central to the host-pathogen metabolic interaction. In this study, a genome-wide search for components of amino acid metabolic pathways was performed in Ixodes scapularis, the main tick vector of A. phagocytophilum in the United States, for which the genome was recently published. The enzymes involved in the synthesis and degradation pathways of the twenty amino acids were identified. Then, the available transcriptomics and proteomics data was used to characterize the mRNA and protein levels of I. scapularis amino acid metabolic pathway components in response to A. phagocytophilum infection of tick tissues and ISE6 tick cells. Our analysis was focused on the interplay between carbohydrate and amino acid metabolism during A. phagocytophilum infection in ISE6 cells. The results showed that tick cells increase the synthesis of phosphoenolpyruvate (PEP) from tyrosine to control A. phagocytophilum infection. Metabolic pathway analysis suggested that this is achieved by (i) increasing the transcript and protein levels of mitochondrial phosphoenolpyruvate carboxykinase (PEPCK-M), (ii) shunting tyrosine into the tricarboxylic acid (TCA) cycle to increase fumarate and oxaloacetate which will be converted into PEP by PEPCK-M, and (iii) blocking all the pathways that use PEP downstream gluconeogenesis (i.e., de novo serine synthesis pathway (SSP), glyceroneogenesis and gluconeogenesis). While sequestering host PEP may be critical for this bacterium because it cannot actively carry out glycolysis to produce PEP, excess of this metabolite may be toxic for A. phagocytophilum. The present work provides a more comprehensive view of the major amino acid metabolic pathways involved in the response to pathogen infection in ticks, and provides the basis for further studies to develop novel strategies for the control of granulocytic anaplasmosis.
- MeSH
- aminokyseliny metabolismus MeSH
- Anaplasma phagocytophilum účinky léků genetika metabolismus patogenita MeSH
- anaplasmóza MeSH
- apoptóza MeSH
- bakteriální proteiny genetika metabolismus MeSH
- buněčné linie MeSH
- citrátový cyklus MeSH
- fosfoenolpyruvát metabolismus farmakologie MeSH
- fosfoenolpyruvátkarboxykinasa (závislá na ATP) metabolismus MeSH
- genom bakteriální MeSH
- glukoneogeneze MeSH
- glykolýza MeSH
- interakce hostitele a patogenu fyziologie MeSH
- klíště mikrobiologie MeSH
- kyselina oxaloctová metabolismus MeSH
- messenger RNA genetika MeSH
- metabolické sítě a dráhy genetika MeSH
- metabolismus sacharidů MeSH
- mitochondrie metabolismus MeSH
- proteomika metody MeSH
- serin metabolismus MeSH
- transkriptom MeSH
- tyrosin metabolismus MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The obligate intracellular pathogen, Anaplasma phagocytophilum, is the causative agent of human, equine, and canine granulocytic anaplasmosis and tick-borne fever (TBF) in ruminants. A. phagocytophilum has become an emerging tick-borne pathogen in the United States, Europe, Africa, and Asia, with increasing numbers of infected people and animals every year. It has been recognized that intracellular pathogens manipulate host cell metabolic pathways to increase infection and transmission in both vertebrate and invertebrate hosts. However, our current knowledge on how A. phagocytophilum affect these processes in the tick vector, Ixodes scapularis is limited. In this study, a genome-wide search for components of major carbohydrate metabolic pathways was performed in I. scapularis ticks for which the genome was recently published. The enzymes involved in the seven major carbohydrate metabolic pathways glycolysis, gluconeogenesis, pentose phosphate, tricarboxylic acid cycle (TCA), glyceroneogenesis, and mitochondrial oxidative phosphorylation and β-oxidation were identified. Then, the available transcriptomics and proteomics data was used to characterize the mRNA and protein levels of I. scapularis major carbohydrate metabolic pathway components in response to A. phagocytophilum infection of tick tissues and cultured cells. The results showed that major carbohydrate metabolic pathways are conserved in ticks. A. phagocytophilum infection inhibits gluconeogenesis and mitochondrial metabolism, but increases the expression of glycolytic genes. A model was proposed to explain how A. phagocytophilum could simultaneously control tick cell glucose metabolism and cytoskeleton organization, which may be achieved in part by up-regulating and stabilizing hypoxia inducible factor 1 alpha in a hypoxia-independent manner. The present work provides a more comprehensive view of the major carbohydrate metabolic pathways involved in the response to A. phagocytophilum infection in ticks, and provides the basis for further studies to develop novel strategies for the control of granulocytic anaplasmosis.
- MeSH
- Anaplasma phagocytophilum patogenita fyziologie MeSH
- anaplasmóza metabolismus MeSH
- buněčné linie MeSH
- citrátový cyklus genetika MeSH
- glukoneogeneze genetika MeSH
- glykolýza genetika MeSH
- interakce hostitele a patogenu genetika MeSH
- klíště enzymologie genetika metabolismus mikrobiologie MeSH
- metabolické sítě a dráhy genetika MeSH
- metabolismus sacharidů genetika MeSH
- mitochondrie genetika metabolismus MeSH
- pentózofosfátový cyklus genetika MeSH
- proteiny členovců chemie genetika metabolismus MeSH
- proteomika metody MeSH
- regulace genové exprese fyziologie MeSH
- sacharidy MeSH
- slinné žlázy mikrobiologie MeSH
- terciární struktura proteinů MeSH
- transkriptom genetika MeSH
- zvířata MeSH
- Check Tag
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Oxidative stress plays an important role in the pathogenesis of diabetes and its complications. The aim of this study was to examine the possible association between seven single nucleotide polymorphisms (SNPs) of the Trx2/TXNIP and TrxR2 genes encoding proteins involved in the thioredoxin antioxidant defence system and the risk of diabetic retinopthy (DR). DESIGN: Cross-sectional case-control study. PARTICIPANTS: A total of 802 Slovenian patients with Type 2 diabetes mellitus; 277 patients with DR and 525 with no DR were enrolled. METHODS: Patients genotypes of the SNPs; including rs8140110, rs7211, rs7212, rs4755, rs1548357, rs4485648 and rs5748469 were determined by the competitive allele specific PCR method. MAIN OUTCOME MEASURES: Each genotype of examined SNPs was regressed in a logistic model, assuming the co-dominant, dominant and the recessive models of inheritance with covariates of duration of diabetes, HbA1c, insulin therapy, total cholesterol and LDL cholesterol levels. RESULTS: In the present study, for the first time we identified an association between the rs4485648 polymorphism of the TrxR2 gene and DR in Caucasians with Type 2 DM. The estimated ORs of adjusted logistic regression models were found to be as follows: 4.4 for CT heterozygotes, 4.3 for TT homozygotes (co-dominant genetic model) and 4.4 for CT+TT genotypes (dominant genetic model). CONCLUSIONS: In our case-control study we were not able to demonstrate any association between rs8140110, rs7211, rs7212, rs4755, rs1548357, and rs5748469 and DR, however, our findings provide evidence that the rs4485648 polymorphism of the TrxR2 gene might exert an independent effect on the development of DR.
- MeSH
- diabetes mellitus 2. typu komplikace genetika MeSH
- diabetická retinopatie genetika MeSH
- genetická predispozice k nemoci MeSH
- genetické asociační studie MeSH
- jednonukleotidový polymorfismus MeSH
- lidé středního věku MeSH
- lidé MeSH
- metabolické sítě a dráhy genetika MeSH
- mitochondriální proteiny genetika MeSH
- mitochondrie genetika metabolismus MeSH
- průřezové studie MeSH
- rizikové faktory MeSH
- senioři MeSH
- studie případů a kontrol MeSH
- thioredoxinreduktasa 2 genetika MeSH
- thioredoxiny genetika metabolismus MeSH
- transportní proteiny genetika MeSH
- Check Tag
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
An arsenate susceptibility test was performed with transformed and cultured Escherichia coli DH5α cells, which carried recombinant DNA of full-length arsenic (ars) operon, namely a putative membrane permease, ArsP; a transcriptional repressor, ArsR; an arsenate reductase, ArsC; and an arsenical-resistance membrane transporter, Acr3, from the Japanese urease-positive thermophilic Campylobacter lari (UPTC) CF89-12. The E. coli DH5α transformant showed reduced susceptibility to arsenate (~1536 μg/mL), compared to the control. Thus, these ars four-genes from the UPTC CF89-12 strain cells could confer a reduced susceptibility to arsenate in the transformed and E. coli DH5α cells. E. coli transformants with truncated ars operons, acr3 (acr3) and arsC-acr3 (∆arsC-acr3), of the ars operon, showed an MIC value of 384 μg/mL (~384 μg/mL), similar to the E. coli cells which carried the pGEM-T vector (control). Reverse transcription PCR confirmed in vivo transcription of recombinant full-length ars operon and deletion variants (∆acr3 and ∆arsC-acr3) in the transformed E. coli cells.
- MeSH
- arsen metabolismus toxicita MeSH
- Campylobacter lari účinky léků genetika metabolismus MeSH
- Escherichia coli genetika metabolismus MeSH
- metabolické sítě a dráhy genetika MeSH
- mikrobiální testy citlivosti MeSH
- operon * MeSH
- polymerázová řetězová reakce s reverzní transkripcí MeSH
- stanovení celkové genové exprese MeSH
- transformace genetická MeSH
- Publikační typ
- časopisecké články MeSH
This review aims at comparing some historical data with the current situation in the study of biogenesis of natural compounds, antibiotics in the first place. Biogenesis of tetracyclines and cycloheximide and related compounds serves as example. Examples of molecular biological and bioinformatics methods used in the study of antibiotic biogenesis are described both in terms of its historical aspects and the current knowledge.
- MeSH
- antibakteriální látky biosyntéza metabolismus MeSH
- dějiny 20. století MeSH
- dějiny 21. století MeSH
- metabolické sítě a dráhy genetika MeSH
- objevování léků dějiny MeSH
- výpočetní biologie MeSH
- Check Tag
- dějiny 20. století MeSH
- dějiny 21. století MeSH
- Publikační typ
- časopisecké články MeSH
- historické články MeSH
- přehledy MeSH
To clarify the pathway of anaerobic sulfur oxidation coupled with dissimilatory ferric iron reduction in Acidithiobacillus ferrooxidans strain CCM 4253 cells, we monitored their energy metabolism gene transcript profiles. Several genes encoding electron transporters involved in aerobic iron and sulfur respiration were induced during anaerobic growth of ferrous iron-grown cells. Most sulfur metabolism genes were either expressed at the basal level or their expression declined. However, transcript levels of genes assumed to be responsible for processing of elemental sulfur and other sulfur intermediates were elevated at the beginning of the growth period. In contrast, genes with predicted functions in formation of hydrogen sulfide and sulfate were significantly repressed. The main proposed mechanism involves: outer membrane protein Cyc2 (assumed to function as a terminal ferric iron reductase); periplasmic electron shuttle rusticyanin; c4-type cytochrome CycA1; the inner membrane cytochrome bc1 complex I; and the quinone pool providing connection to the sulfur metabolism machinery, consisting of heterodisulfide reductase, thiosulfate:quinone oxidoreductase and tetrathionate hydrolase. However, an alternative mechanism seems to involve a high potential iron-sulfur protein Hip, c4-type cytochrome CycA2 and inner membrane cytochrome bc1 complex II. Our results conflict with findings regarding the type strain, indicating strain- or phenotype-dependent pathway variation.
