scholarly journals Lokiarchaeon exhibits homoacetogenesis

2019 ◽  
Author(s):  
William D. Orsi ◽  
Aurèle Vuillemin ◽  
Paula Rodriguez ◽  
Ömer K. Coskun ◽  
Gonzalo V. Gomez-Saez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Host Cell ◽  
Extracellular Polymeric Substances ◽  
Carbon Fixation ◽  
Carbon Sources ◽  
Stable Isotope Probing ◽  
Organic Substrates ◽  
Sugar Fermentation ◽  
Expression Of Genes ◽  
Wide Range

AbstractThe proposed Asgard superphylum of Archaea comprises the closest archaeal relatives of eukaryotes, whose genomes hold clues pertaining to the nature host cell that acquired the mitochondrion at the origin of eukaryotes1-4. Genomes of the Asgard candidate Phylum ‘Candidatus Lokiarchaeota’ [Lokiarchaeon] suggest an acetogenic H2 –dependent lifestyle5 and mixotrophic capabilities6. However, data on the activity of Lokiarchaeon are currently lacking, and the ecology of the host cell that acquired the mitochondrion is debated4,7. Here, we show that in anoxic marine sediments underlying highly productive waters on the Namibian continental shelf Lokiarchaeon gene expression increases with depth below the seafloor, and was significantly different across a redox gradient spanning hypoxic to sulfidic conditions. Notably, Lokiarchaeon increased expression of genes involved in growth, carbohydrate metabolism, and the H2-dependent Wood-Ljungdahl (WLP) carbon fixation pathway under the most reducing (sulfidic) conditions. Quantitative stable isotope probing experiments revealed multiple populations of Lokiarchaeota utilizing both CO2 and diatomaceous extracellular polymeric substances (dEPS) as carbon sources over a 10-day incubation under anoxic conditions. This apparent anaerobic mixotrophic metabolism was consistent with the expression of Lokiarchaeon genes involved in transport and fermentation of sugars and amino acids. Remarkably, several Asgard populations were more enriched with 13C-dEPS compared to the community average, indicating a preference for dEPS as a growth substrate. The qSIP and gene expression data indicate a metabolism of “Candidatus Lokiarchaeota” similar to that of sugar fermenting homoacetogenic bacteria8, namely that Lokiarchaeon can couple fermentative H2 production from organic substrates with electron bifurcation and the autotrophic and H2-dependent WLP. Homoacetogenesis allows to access a wide range of substrates and relatively high ATP gain during acetogenic sugar fermentation8 thereby providing an ecological advantage for Lokiarchaeon in anoxic, energy limited settings.

Gene Expression Profile in the CML Cell Line K562 Treated with SKI-606, a Dual Inhibitor of Src/Abl Kinase.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 4870-4870
Author(s):  
Matteo Renzulli ◽  
Tiziana Grafone ◽  
Cristian Taccioli ◽  
Carolina Terragna ◽  
Frank Boschelli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Differential Expression ◽  
Signalling Pathways ◽  
Dual Inhibitor ◽  
Imatinib Resistance ◽  
Regulatory Pathways ◽  
Abl Kinase ◽  
Expression Of Genes ◽  
Wide Range

Abstract Although Imatinib represents the drug of choice for the treatment of Chronic Myeloid Leukemia (CML), new approaches to the treatment of CML remain a high priority in view of the continuing problems of Imatinib resistance. Previously (ASH 2004), we reported on the anti-proliferative and pro-apoptotic effects of the new drug, SKI-606, a potent Src/Abl kinase inhibitor, in blast crisis cell lines in vitro. Here we describe results of a transcriptional profiling study of SKI-606 activity in CML cells. Oligonucleotide microarray analysis using the Human 1A (V2) Oligo Microarrays of Agilent, containing more than 20,000 different genes was performed with untreated K562 cells and compared to the profile obtained from the same cells treated with 10 nM SKI-606 over a 48 h period. We labelled the amplified aRNA of the untreated cells with green (Cy3) dye and that of the treated with red (Cy5) dye, and also performed the reverse labeling experiment to confirm our data. Our approach to design comparisons utilizes a Lowess normalization and a filter followed by an analysis of variance (ANOVA) models to identify the genes with the greatest differential expression in the treated cells. We found identified 121 genes whose expression was modified by treatment with SKI-606. BCR-ABL activity results in activation of several downstream signalling pathways, including RAS/MAPK, PI3K/AKT and STAT pathways, which are implicated in mutagenic signalling and enhancement of survival. Our study showed that the expression of some genes involved in these regulatory pathways was altered by SKI-606. The greatest transcriptional changes (decreases or increases in gene expression of 2-fold or greater) were observed after 24h, while between 24 and 48h, the gene expression pattern stabilized. Ontological information concerning the cellular function of these transcripts suggests differential expression of genes associated with a wide range of cellular processes, including transcriptional regulation (CHAF1B, MRPL1, FLI1, FLN29 and CIR) and signal transduction (HRAS, ELMO, P114-RHO-GEF), among other functions. SKI-606 also modulates the expression of genes involved in cell cycle regulation such as MLLT7, a transcription factor that regulates the cell cycle through transcriptional activation of p27kip1. Our data also provide the first evidence that SKI-606 treatment is down-regulates apoptotic suppressor genes, such as LAMR1, RAC1 and DDB2. Interestingly, the component of the ubiquitin/proteasome pathway, FLJ12673, a subunit of the ubiquitin protein ligase complex, is downregulated by SKI-606 treatment. Currently, we are analyzing the most interesting modified genes to validate our data by Real Time PCR. Genome-wide expression-level analysis combined with biochemical studies of altered signalling pathways with cultured leukemia cells is expected to be a useful functional-genomic approach to more completely characterize the mechanism of action of this compound.

Generation and characterization of U937-TR: a platform cell line for inducible gene expression in human macrophages

Parasitology ◽  
2020 ◽  
Vol 147 (13) ◽  
pp. 1524-1531
Author(s):  
Cristian Camilo Galindo ◽  
Carlos Arturo Clavijo-Ramírez
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Molecular Mechanisms ◽  
Expression System ◽  
Precise Control ◽  
Expression Of Genes ◽  
Wide Range ◽  
Monocytes And Macrophages

AbstractMonocytes and macrophages are involved in a wide range of biological processes and parasitic diseases. The characterization of the molecular mechanisms governing such processes usually requires precise control of the expression of genes of interest. We implemented a tetracycline-controlled gene expression system in the U937 cell line, one of the most used in vitro models for the research of human monocytes and macrophages. Here we characterized U937-derived cell lines in terms of phenotypic (morphology and marker expression) and functional (capacity for phagocytosis and for Leishmania parasite hosting) changes induced by phorbol-12-myristate-13-acetate (PMA). Finally, we provide evidence of tetracycline-inducible and reversible Lamin-A gene silencing of the PMA-differentiated U937-derived cells.

scholarly journals Comprehensive Transcriptomic Analysis for Developing Seeds of a Synthetic Brassica Hexaploid

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1141
Author(s):  
Zhengyi Liu ◽  
Ruihua Wang ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Mature Stage ◽  
Developing Seeds ◽  
Expression Of Genes ◽  
Wide Range ◽  
Transcription Factor Genes ◽  
Range Of Functions ◽  
Paternal Parent ◽  
Resistance To Stress ◽  
Morphological Differences

Polyploidization is a universal phenomenon in plants and plays a crucial role in evolution. In this study, the transcriptomes of developing seeds of a synthetic Brassica hexaploid and its parents (B. rapa and B. carinata) were analyzed to find the gene expression changes in hexaploid seeds. There were 3166 and 3893 DEGs between the Brassica hexaploid and its parents at the full-size stage and mature stage, respectively, most of which were upregulated in hexaploid seeds compared to its parents. At the mature stage, the hexaploid seeds showed a greater difference from its parents. These DEGs had a wide range of functions, which may account for the physiological and morphological differences between the Brassica hexaploid and its parents. The KEGG pathway analysis revealed that hexaploid seeds had higher levels of expression of genes involved in metabolic pathways, RNA transport and biosynthesis of secondary metabolites, and the expression levels in the photosynthesis-related pathways were significantly higher than those in B. rapa. Transgressive expression was the main non-additive expression pattern of the Brassica hexaploid. The gene expression difference between the Brassica hexaploid and its paternal parent was more significant than that with its maternal parent, which may be due in part to the cytoplasmic and maternal effects. Moreover, transcription factor genes, such as G2-like, MYB and mTERF, were highly expressed in hexaploid seeds, possibly promoting their resistance to stress. Our results may provide valuable insights into the adaptation mechanisms of polyploid plants.

scholarly journals Pasteurella multocida Gene Expression in Response to Iron Limitation

2001 ◽  
Vol 69 (6) ◽  
pp. 4109-4115 ◽  
Author(s):  
Michael L. Paustian ◽  
Barbara J. May ◽  
Vivek Kapur
Keyword(s):  
Gene Expression ◽  
Pasteurella Multocida ◽  
Molecular Mechanisms ◽  
Iron Acquisition ◽  
Expression Profiles ◽  
Growth Conditions ◽  
Whole Genome ◽  
Altered Expression ◽  
Expression Of Genes ◽  
Wide Range

ABSTRACT Pasteurella multocida is the causative agent of a wide range of diseases in avian and mammalian hosts. Gene expression in response to low iron conditions was analyzed in P. multocida using whole-genome microarrays. The analysis shows that the expression of genes involved in energy metabolism and electron transport generally decreased 2.1- to 6-fold while that of genes used for iron binding and transport increased 2.1- to 7.7-fold in P. multocida during the first 2 h of growth under iron-limiting conditions compared with controls. Notably, 27% of the genes with significantly altered expression had no known function, illustrating the limitations of using publicly available databases to identify genes involved in microbial metabolism and pathogenesis. Taken together, the results of our investigations demonstrate the utility of whole-genome microarray analyses for the identification of genes with altered expression profiles during varying growth conditions and provide a framework for the detailed analysis of the molecular mechanisms of iron acquisition and metabolism in P. multocida and other gram-negative bacteria.

scholarly journals Regulation of Autotrophic CO2 Fixation in the Archaeon Thermoproteus neutrophilus

2010 ◽  
Vol 192 (20) ◽  
pp. 5329-5340 ◽  
Author(s):  
W. Hugo Ramos-Vera ◽  
Valérie Labonté ◽  
Michael Weiss ◽  
Julia Pauly ◽  
Georg Fuchs
Keyword(s):  
Carbon Fixation ◽  
Protein A ◽  
Carbon Sources ◽  
Fumarate Hydratase ◽  
Central Carbon Metabolism ◽  
Gene Organization ◽  
Fumarate Reductase ◽  
Organic Substrates ◽  
Autotrophic Co2 Fixation ◽  
Whole Cells

ABSTRACT Thermoproteus neutrophilus, a hyperthermophilic, chemolithoautotrophic, anaerobic crenarchaeon, uses a novel autotrophic CO2 fixation pathway, the dicarboxylate/hydroxybutyrate cycle. The regulation of the central carbon metabolism was studied on the level of whole cells, enzyme activity, the proteome, transcription, and gene organization. The organism proved to be a facultative autotroph, which prefers organic acids as carbon sources that can easily feed into the metabolite pools of this cycle. Addition of the preferred carbon sources acetate, pyruvate, succinate, and 4-hydroxybutyrate to cultures resulted in stimulation of the growth rate and a diauxic growth response. The characteristic enzyme activities of the carbon fixation cycle, fumarate hydratase, fumarate reductase, succinyl coenzyme A (CoA) synthetase, and enzymes catalyzing the conversion of succinyl-CoA to crotonyl-CoA, were differentially downregulated in the presence of acetate and, to a lesser extent, in the presence of other organic substrates. This regulation pattern correlated well with the differential expression profile of the proteome as well as with the transcription of the encoding genes. The genes encoding phosphoenolpyruvate (PEP) carboxylase, fumarate reductase, and four enzymes catalyzing the conversion of succinyl-CoA to crotonyl-CoA are clustered. Two putative operons, one comprising succinyl-CoA reductase plus 4-hydroxybutyrate-CoA ligase genes and the other comprising 4-hydroxybutyryl-CoA dehydratase plus fumarate reductase genes, were divergently transcribed into leaderless mRNAs. The promoter regions were characterized and used for isolating DNA binding proteins. Besides an Alba protein, a 18-kDa protein characteristic for autotrophic Thermoproteales that bound specifically to the promoter region was identified. This system may be suitable for molecular analysis of the transcriptional regulation of autotrophy-related genes.

Diversity and metabolic potentials of As(III)-oxidizing bacteria in activated sludge

2021 ◽  
Author(s):  
Rui Xu ◽  
Duanyi Huang ◽  
Xiaoxu Sun ◽  
Miaomiao Zhang ◽  
Dongbo Wang ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Activated Sludge ◽  
Extracellular Polymeric Substances ◽  
Carbon Fixation ◽  
Stable Isotope Probing ◽  
Synthetic Wastewater ◽  
Contaminated Water ◽  
Natural Environments ◽  
Genes Encoding ◽  
Treatment Facilities

Biological arsenite (As(III)) oxidation is an important process in the removal of toxic arsenic (As) from contaminated water. However, the diversity and metabolic potentials of As(III)-oxidizing bacteria (AOBs) responsible for As(III) oxidation in wastewater treatment facilities are not well documented. In this study, two groups of bioreactors inoculated with activated sludge were operated under anoxic or oxic conditions to treat As-containing synthetic wastewater. Batch tests of inoculated sludges from the bioreactors further indicated that microorganisms could use nitrate or oxygen as electron acceptors to stimulate biological As(III) oxidation, suggesting the potentials of this process in wastewater treatment facilities. In addition, DNA-based stable isotope probing (DNA-SIP) was performed to identify the putative AOBs in the activated sludge. Bacteria associated with Thiobacillus were identified as nitrate-dependent AOBs, while bacteria associated with Hydrogenophaga were identified as aerobic AOBs in activated sludge. Metagenomic binning reconstructed a number of high-quality metagenome-assembled genomes (MAGs) associated with the putative AOBs. Functional genes encoding for As resistance, As(III) oxidation, denitrification, and carbon fixation were identified in these MAGs, suggesting their potentials for chemoautotrophic As(III) oxidation. In addition, the presence of genes encoding secondary metabolite biosynthesis and extracellular polymeric substance metabolism in these MAGs may facilitate the proliferation of these AOBs in activated sludge and enhance their capacity for As(III) oxidation. Importance AOBs play an important role in the removal of toxic arsenic from wastewater. Most of the AOBs have been isolated from natural environments. However, knowledge regarding the structure and functional roles of As(III)-oxidizing communities in wastewater treatment facilities are not well documented. The combination of DNA-SIP and metagenomic binning provides an opportunity to elucidate the diversity of in situ AOBs community inhabited the activated sludges. In this study, the putative AOBs responsible for As(III) oxidation in wastewater treatment facilities were identified, and their metabolic potentials including As(III) oxidation, denitrification, carbon fixation, secondary metabolites biosynthesis, and extracellular polymeric substances metabolisms were investigated. This observation provides an understanding of anoxic and/or oxic AOBs during the A(III) oxidation process in wastewater treatment facilities, which may contribute to the removal of As from contaminated water.

scholarly journals Differential Effects of Epinephrine, Norepinephrine, and Indole on Escherichia coli O157:H7 Chemotaxis, Colonization, and Gene Expression

2007 ◽  
Vol 75 (9) ◽  
pp. 4597-4607 ◽  
Author(s):  
Tarun Bansal ◽  
Derek Englert ◽  
Jintae Lee ◽  
Manjunath Hegde ◽  
Thomas K. Wood ◽  
...  
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Biofilm Formation ◽  
Signaling Molecules ◽  
Signal Molecules ◽  
Autoinducer 2 ◽  
Expression Of Genes ◽  
Wide Range ◽  
Host Cell Surface

ABSTRACT During infection in the gastrointestinal tract, enterohemorrhagic Escherichia coli (EHEC) O157:H7 is exposed to a wide range of signaling molecules, including the eukaryotic hormones epinephrine and norepinephrine, and bacterial signal molecules such as indole. Since these signaling molecules have been shown to be involved in the regulation of phenotypes such as motility and virulence that are crucial for EHEC infections, we hypothesized that these molecules also govern the initial recognition of the large intestine environment and attachment to the host cell surface. Here, we report that, compared to indole, epinephrine and norepinephrine exert divergent effects on EHEC chemotaxis, motility, biofilm formation, gene expression, and colonization of HeLa cells. Using a novel two-fluorophore chemotaxis assay, it was found that EHEC is attracted to epinephrine and norepinephrine while it is repelled by indole. In addition, epinephrine and norepinephrine also increased EHEC motility and biofilm formation while indole attenuated these phenotypes. DNA microarray analysis of surface-associated EHEC indicated that epinephrine/norepinephrine up-regulated the expression of genes involved in surface colonization and virulence while exposure to indole decreased their expression. The gene expression data also suggested that autoinducer 2 uptake was repressed upon exposure to epinephrine/norepinephrine but not indole. In vitro adherence experiments confirmed that epinephrine and norepinephrine increased attachment to epithelial cells while indole decreased adherence. Taken together, these results suggest that epinephrine and norepinephrine increase EHEC infection while indole attenuates the process.

scholarly journals The Kaposi's sarcoma-associated herpesvirus ORF57 protein: a pleurotropic regulator of gene expression

2006 ◽  
Vol 34 (5) ◽  
pp. 705-710 ◽  
Author(s):  
P. Malik ◽  
E.C. Schirmer
Keyword(s):  
Gene Expression ◽  
Host Cell ◽  
Nuclear Export ◽  
Kaposi's Sarcoma ◽  
Immune Cell ◽  
Kaposi’S Sarcoma ◽  
Nucleocytoplasmic Transport ◽  
Wide Range ◽  
Kaposi's Sarcoma Associated Herpesvirus ◽  
Kaposi’S Sarcoma Associated Herpesvirus

Herpesviridae comprises over 120 viruses infecting a wide range of vertebrates including humans and livestock. Herpesvirus infections typically produce dermal lesions or immune cell destruction, but can also lead to oncogenesis, especially with KSHV (Kaposi's sarcoma-associated herpesvirus). All herpesviruses are nuclear replicating viruses that subvert cellular processes such as nucleocytoplasmic transport for their advantage. For virus replication to take over the cell and produce lytic infection requires that virus gene expression outpace that of the host cell. KSHV ORF57 (open reading frame 57) appears to play a major role in this by (i) serving as a nuclear export receptor to carry intronless viral mRNAs out of the nucleus and (ii) inhibiting expression of intron-containing host mRNAs. As most of the virally encoded mRNAs are intronless compared with host cell mRNAs, these two mechanisms are critical to overcoming host gene expression.

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