scholarly journals Transcription of All amoC Copies Is Associated with Recovery of Nitrosomonas europaea from Ammonia Starvation

2007 ◽  
Vol 189 (11) ◽  
pp. 3935-3944 ◽  
Author(s):  
Paul M. Berube ◽  
Ram Samudrala ◽  
David A. Stahl
Keyword(s):  
Ammonia Oxidation ◽  
Transcriptional Response ◽  
Housekeeping Genes ◽  
Nitrosomonas Europaea ◽  
Primer Extension ◽  
Proximal Promoter ◽  
S1 Nuclease ◽  
Significant Difference ◽  
Genes Encoding ◽  
Ammonia Oxidizing Bacterium

ABSTRACT The chemolithotrophic ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to starvation conditions. The transcriptional response of N. europaea to ammonia addition following short- and long-term starvation was examined by primer extension and S1 nuclease protection analyses of genes encoding enzymes for ammonia oxidation (amoCAB operons) and CO2 fixation (cbbLS), a third, lone copy of amoC (amoC 3 ), and two representative housekeeping genes (glyA and rpsJ). Primer extension analysis of RNA isolated from growing, starved, and recovering cells revealed two differentially regulated promoters upstream of the two amoCAB operons. The distal σ70 type amoCAB promoter was constitutively active in the presence of ammonia, but the proximal promoter was only active when cells were recovering from ammonia starvation. The lone, divergent copy of amoC (amoC 3 ) was expressed only during recovery. Both the proximal amoC 1,2 promoter and the amoC 3 promoter are similar to gram-negative σE promoters, thus implicating σE in the regulation of the recovery response. Although modeling of subunit interactions suggested that a nonconservative proline substitution in AmoC3 may modify the activity of the holoenzyme, characterization of a ΔamoC 3 strain showed no significant difference in starvation recovery under conditions evaluated. In contrast to the amo transcripts, a delayed appearance of transcripts for a gene required for CO2 fixation (cbbL) suggested that its transcription is retarded until sufficient energy is available. Overall, these data revealed a programmed exit from starvation likely involving regulation by σE and the coordinated regulation of catabolic and anabolic genes.

scholarly journals Transcript Analysis of Multiple Copies ofamo (Encoding Ammonia Monooxygenase) and hao(Encoding Hydroxylamine Oxidoreductase) in Nitrosomonas europaea

2001 ◽  
Vol 183 (3) ◽  
pp. 1096-1100 ◽  
Author(s):  
Norman G. Hommes ◽  
Luis A. Sayavedra-Soto ◽  
Daniel J. Arp
Keyword(s):  
Nitrosomonas Europaea ◽  
Primer Extension ◽  
Transcript Analysis ◽  
Ammonia Monooxygenase ◽  
Transcription Start ◽  
Hydroxylamine Oxidoreductase ◽  
Transcription Start Sites ◽  
Promoter Sequences ◽  
Genes Encoding ◽  
Multiple Copies

ABSTRACT The genes encoding ammonia monooxygenase (amoCAB), hydroxylamine oxidoreductase (hao), and thec-type cytochrome c-554 (hcy) are present in multiple copies in the genome of Nitrosomonas europaea. The upstream regions of the two copies ofamoC, the three copies of hao, and one copy ofhcy were cloned and sequenced. Primer extension reactions were done to identify transcription start sites for these genes, as well as for amoA. Putative ς70 promoter sequences were found associated with all but one of the mapped transcription start sites. Primer extensions were done withamoC primers using RNA harvested from cells incubated with and without ammonium. The experiments suggested that N. europaea cells may be able to use different promoters in the presence and absence of ammonium.

scholarly journals Complete Genome Sequence of the Ammonia-Oxidizing Bacterium and Obligate Chemolithoautotroph Nitrosomonas europaea

2003 ◽  
Vol 185 (9) ◽  
pp. 2759-2773 ◽  
Author(s):  
Patrick Chain ◽  
Jane Lamerdin ◽  
Frank Larimer ◽  
Warren Regala ◽  
Victoria Lao ◽  
...  
Keyword(s):  
Inorganic Ions ◽  
Nitrosomonas Europaea ◽  
Ammonia Oxidizing Bacteria ◽  
Circular Chromosome ◽  
Gc Skew ◽  
Genes Encoding ◽  
Sequence Elements ◽  
Intergenic Regions ◽  
Obligate Chemolithoautotroph ◽  
Ammonia Oxidizing Bacterium

ABSTRACT Nitrosomonas europaea (ATCC 19718) is a gram-negative obligate chemolithoautotroph that can derive all its energy and reductant for growth from the oxidation of ammonia to nitrite. Nitrosomonas europaea participates in the biogeochemical N cycle in the process of nitrification. Its genome consists of a single circular chromosome of 2,812,094 bp. The GC skew analysis indicates that the genome is divided into two unequal replichores. Genes are distributed evenly around the genome, with ∼47% transcribed from one strand and ∼53% transcribed from the complementary strand. A total of 2,460 protein-encoding genes emerged from the modeling effort, averaging 1,011 bp in length, with intergenic regions averaging 117 bp. Genes necessary for the catabolism of ammonia, energy and reductant generation, biosynthesis, and CO2 and NH3 assimilation were identified. In contrast, genes for catabolism of organic compounds are limited. Genes encoding transporters for inorganic ions were plentiful, whereas genes encoding transporters for organic molecules were scant. Complex repetitive elements constitute ca. 5% of the genome. Among these are 85 predicted insertion sequence elements in eight different families. The strategy of N. europaea to accumulate Fe from the environment involves several classes of Fe receptors with more than 20 genes devoted to these receptors. However, genes for the synthesis of only one siderophore, citrate, were identified in the genome. This genome has provided new insights into the growth and metabolism of ammonia-oxidizing bacteria.

scholarly journals Structure of the human sialophorin (CD43) gene. Identification of features atypical of genes encoding integral membrane proteins

1990 ◽  
Vol 270 (3) ◽  
pp. 569-576 ◽  
Author(s):  
C S Shelley ◽  
E Remold-O'Donnell ◽  
F S Rosen ◽  
A S Whitehead
Keyword(s):  
Transcription Initiation ◽  
Alternative Polyadenylation ◽  
Housekeeping Genes ◽  
Initiation Site ◽  
S1 Nuclease ◽  
Dna Structures ◽  
Repeat Sequences ◽  
Extracellular Region ◽  
Genes Encoding ◽  
Polyadenylation Signals

A human sialophorin (CD43) specific genomic clone was isolated, and a 6.5 kb fragment containing the 4.6 kb sialophorin gene was sequenced. The promoter region contains no TATA or CAAT boxes, but is highly enriched in G and C nucleotides and contains short repeat sequences similar to those found in the promoters of ‘housekeeping’ genes. S1-nuclease protection and primer-extension experiments established that the sialophorin gene has two major transcription initiation sites. There is a single intron of 378 bp that interrupts the sequence specifying the mRNA 5′ untranslated region. The gene is therefore unusual in that the discrete extracellular, transmembrane and intracellular regions of the protein, including repeat sequences in the extracellular region, are not encoded by separate exons. Utilization of alternative polyadenylation signals was previously shown to generate two sialophorin mRNAs of 1.9 and 4.3 kb, which differ in the length of their 3′ untranslated regions. Sequence analysis of the gene establishes that a single polyadenylation signal 2301 bp downstream of the first major transcription initiation site and five overlapping polyadenylation signals beginning a further 2290 bp downstream define the 3′ termini of the 1.9 and 4.3 kb mRNA species respectively. The gene contains potential Z-DNA structures, Aly sequences, and elements that may be involved in regulating mRNA stability.

scholarly journals Loss of Ammonia Monooxygenase Activity in Nitrosomonas europaea upon Exposure to Nitrite

1998 ◽  
Vol 64 (10) ◽  
pp. 4098-4102 ◽  
Author(s):  
Lisa Y. Stein ◽  
Daniel J. Arp
Keyword(s):  
Ammonia Oxidation ◽  
Nitrosomonas Europaea ◽  
Ammonia Monooxygenase ◽  
Oxidation Activity ◽  
Monooxygenase Activity ◽  
Nitrite Toxicity ◽  
Acidic Conditions ◽  
Ammonia Oxidizing Bacterium ◽  
Aerobic And Anaerobic ◽  
Unique Mechanism

ABSTRACT Nitrosomonas europaea, an obligate ammonia-oxidizing bacterium, lost an increasing amount of ammonia oxidation activity upon exposure to increasing concentrations of nitrite, the primary product of ammonia-oxidizing metabolism. The loss of activity was specific to the ammonia monooxygenase (AMO) enzyme, as confirmed by a decreased rate of NH4 +-dependent O2consumption, some loss of active AMO molecules observed by polypeptide labeling with 14C2H2, the protection of activity by substrates of AMO, and the requirement for copper. The loss of AMO activity via nitrite occurred under both aerobic and anaerobic conditions, and more activity was lost under alkaline than under acidic conditions except in the presence of large concentrations (20 mM) of nitrite. These results indicate that nitrite toxicity in N. europaea is mediated by a unique mechanism that is specific for AMO.

scholarly journals The Early Transcriptional Response of Human Granulocytes to Infection with Candida albicans Is Not Essential for Killing but Reflects Cellular Communications

2006 ◽  
Vol 75 (3) ◽  
pp. 1493-1501 ◽  
Author(s):  
Chantal Fradin ◽  
Abigail L. Mavor ◽  
Günther Weindl ◽  
Martin Schaller ◽  
Karin Hanke ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Mononuclear Cells ◽  
De Novo ◽  
Transcriptional Response ◽  
Mononuclear Leukocytes ◽  
General Notion ◽  
Genes Encoding ◽  
Global Transcriptional Profile ◽  
Life Threatening ◽  
Systemic Infections

ABSTRACT Candida albicans is a polymorphic opportunistic fungus that can cause life-threatening systemic infections following hematogenous dissemination in patients susceptible to nosocomial infection. Neutrophils form part of the innate immune response, which is the first line of defense against microbes and is particularly important in C. albicans infections. To compare the transcriptional response of leukocytes exposed to C. albicans, we investigated the expression of key cytokine genes in polymorphonuclear and mononuclear leukocytes after incubation with C. albicans for 1 h. Isolated mononuclear cells expressed high levels of genes encoding proinflammatory signaling molecules, whereas neutrophils exhibited much lower levels, similar to those observed in whole blood. The global transcriptional profile of neutrophils was examined by using an immunology-biased human microarray to determine whether different morphological forms or the viability of C. albicans altered the transcriptome. Hyphal cells appeared to have the broadest effect, although the most strongly induced genes were regulated independently of morphology or viability. These genes were involved in proinflammatory cell-cell signaling, cell signal transduction, and cell growth. Generally, genes encoding known components of neutrophil granules showed no upregulation at this time point; however, lactoferrin, a well-known candidacidal peptide, was secreted by neutrophils. Addition to inhibitors of RNA or protein de novo synthesis did not influence the killing activity within 30 min. These results support the general notion that neutrophils do not require gene transcription to mount an immediate and direct attack against microbes. However, neutrophils exposed to C. albicans express genes involved in communication with other immune cells.

scholarly journals Transcriptomic Responses in the Bloom-Forming Cyanobacterium Microcystis Induced during Exposure to Zooplankton

2016 ◽  
Vol 83 (5) ◽  
Author(s):  
Matthew J. Harke ◽  
Jennifer G. Jankowiak ◽  
Brooke K. Morrell ◽  
Christopher J. Gobler
Keyword(s):  
Secondary Metabolites ◽  
Daphnia Pulex ◽  
Transcriptional Response ◽  
Extracellular Polysaccharides ◽  
Gas Vesicles ◽  
Transcriptomic Response ◽  
Content Type ◽  
Genes Encoding ◽  
Transcriptomic Responses ◽  
Shock Proteins

ABSTRACT The bloom-forming, toxic cyanobacterium Microcystis synthesizes multiple secondary metabolites and has been shown to deter zooplankton grazing. However, the biochemical and/or molecular basis by which Microcystis deters zooplankton remains unclear. This global transcriptomic study explored the response of Microcystis to direct and indirect exposures to multiple densities of two cladoceran grazers, Daphnia pulex and D. magna. Higher densities of both daphnids significantly reduced Microcystis cell densities and elicited a stronger transcriptional response in Microcystis. While many putative grazer deterrence genes (encoding microcystin, aeruginosin, cyanopeptolin, and microviridin) were largely unaffected by zooplankton, transcripts for heat shock proteins (hsp) increased in abundance. Beyond metabolites and hsp, large increases in the abundances of transcripts from photosynthetic processes were observed, evidencing energy acquisition pathways were stimulated by grazing. In addition, transcripts of genes associated with the production of extracellular polysaccharides and gas vesicles significantly increased in abundance. These genes have been associated with colony formation and may have been invoked to deter grazers. Collectively, this study demonstrates that daphnid grazers induce a significant transcriptomic response in Microcystis, suggesting this cyanobacterium upregulates specific biochemical pathways to adapt to predation. IMPORTANCE This work explores the transcriptomic responses of Microcystis aeruginosa following exposure to grazing by two cladocerans, Daphnia magna and D. pulex. Contrary to previous hypotheses, Microcystis did not employ putative grazing deterrent secondary metabolites in response to the cladocerans, suggesting they may have other roles within the cell, such as oxidative stress protection. The transcriptional metabolic signature during intense grazing was largely reflective of a growth and stress response, although increasing abundances of transcripts encoding extracellular polysaccharides and gas vesicles were potentially related to predator avoidance.

fra-1: a serum-inducible, cellular immediate-early gene that encodes a fos-related antigen

1988 ◽  
Vol 8 (5) ◽  
pp. 2063-2069 ◽  
Author(s):  
D R Cohen ◽  
T Curran
Keyword(s):  
Regulatory Protein ◽  
Transcriptional Response ◽  
Early Gene ◽  
Immediate Early ◽  
Cdna Clones ◽  
Protein Synthesis Inhibitors ◽  
Amino Acid Homology ◽  
Serum Stimulation ◽  
Fos Protein ◽  
Genes Encoding

A set of proteins antigenically related to the c-fos protein (Fos) are induced by serum in fibroblasts. To isolate cDNA clones of genes encoding such proteins, a lambda gt11 expression cDNA library constructed from serum-stimulated rat fibroblasts was screened with antibodies raised against a hydrophilic region (amino acids 127 to 152) of Fos. One of the positive clones identified, termed fra-1 (Fos-related antigen) was characterized. It encoded a protein that shared several regions of extensive amino acid homology with Fos (including the region that showed similarity to both the yeast GCN4 regulatory protein and the protein encoded by the jun oncogene), although its nucleotide sequence was considerably diverged from that of the c-fos gene. Only a subset of the agents and conditions that activated c-fos also induced fra-1. Induction of fra-1 expression following serum stimulation was delayed compared with that of c-fos. However, like c-fos, fra-1 was induced rapidly by serum in the presence of protein synthesis inhibitors. Thus, a family of Fos-related, inducible genes are involved in the cellular immediate-early transcriptional response to extracellular stimuli.

Organization of the Ly-5 gene

1988 ◽  
Vol 8 (11) ◽  
pp. 4889-4895
Author(s):  
Y Saga ◽  
J S Tung ◽  
F W Shen ◽  
T C Pancoast ◽  
E A Boyse
Keyword(s):  
Alternative Splicing ◽  
Primer Extension ◽  
Alternative Exon ◽  
Chromosome 1 ◽  
Cdna Clones ◽  
S1 Nuclease ◽  
Protein Coding ◽  
Cell Lineages ◽  
Transmembrane Glycoprotein

A single Ly-5 gene is known to generate a variety of transmembrane glycoprotein isoforms that distinguish various cell lineages and stages of differentiation within the hematopoietic developmental compartment of the mouse. Systems homologous to Ly-5 are known in rats and in humans. The complete exon-intron organization of the Ly-5 gene is described in this report. The Ly-5 gene occupies about 120 kilobases of chromosome 1 and comprises 34 exons, of which 32 (Ex-3 to Ex-34) are protein coding. Ex-1, Ex-2, and parts of Ex-3 and Ex-34 are untranslated. In all cDNA clones examined, either Ex-1 or Ex-2 was represented, but not both, implying that Ex-1 and Ex-2 in Ly-5 mRNA may be mutually exclusive. Primer extension and S1 nuclease protection mapping were used to identify initiation (cap) sites for transcription. The finding of putative cap sites for Ex-1 and Ex-2, and of corresponding TATA-like sequences, suggests the presence of two promoters. In both Ex-1+ and Ex-2+ cDNA clones the next exon is Ex-3, which has a translation-initiating codon. The intron between Ex-3 and Ex-4 is unusually long, about 50 kilobases. Evidence is given that Ex-5, like Ex-6 and Ex-7 (studied previously), is another alternative exon that is selectively programmed, alone or together with Ex-6 or Ex-7 or both, to generate actual or potential Ly-5 isoforms by alternative splicing.

scholarly journals Transcriptional Regulation and Organization of thedcuA and dcuB Genes, Encoding Homologous Anaerobic C4-Dicarboxylate Transporters inEscherichia coli

1998 ◽  
Vol 180 (24) ◽  
pp. 6586-6596 ◽  
Author(s):  
Paul Golby ◽  
David J. Kelly ◽  
John R. Guest ◽  
Simon C. Andrews
Keyword(s):  
Degradation Products ◽  
Single Copy ◽  
Northern Blotting ◽  
Primer Extension ◽  
Receptor Protein ◽  
Primary Role ◽  
Homologous Proteins ◽  
Dicarboxylate Transport ◽  
Genes Encoding ◽  
A Minor

ABSTRACT The dcuA and dcuB genes ofEscherichia coli encode homologous proteins that appear to function as independent and mutually redundant C4-dicarboxylate transporters during anaerobiosis. ThedcuA gene is 117 bp downstream of, and has the same polarity as, the aspartase gene (aspA), whiledcuB is 77 bp upstream of, and has the same polarity as, the anaerobic fumarase gene (fumB). To learn more about the respective roles of the dcu genes, the environmental and regulatory factors influencing their expression were investigated by generating and analyzing single-copy dcuA- anddcuB-lacZ transcriptional fusions. The results show thatdcuA is constitutively expressed whereas dcuBexpression is highly regulated. The dcuB gene is strongly activated anaerobically by FNR, repressed in the presence of nitrate by NarL, and subject to cyclic AMP receptor protein (CRP)-mediated catabolite repression. In addition, dcuB is strongly induced by C4-dicarboxylates, suggesting thatdcuB is under the control of an uncharacterized C4-dicarboxylate-responsive gene regulator. Northern blotting confirmed that dcuA (and aspA) is expressed under both aerobic and anaerobic conditions and thatdcuB (and fumB) is induced anaerobically. Major monocistronic transcripts were identified for aspA anddcuA, as well as a minor species possibly corresponding to an aspA-dcuA cotranscript. Five major transcripts were observed for dcuB and fumB: monocistronic transcripts for both fumB and dcuB; adcuB-fumB cotranscript; and two transcripts, possibly corresponding to dcuB-fumB and fumB mRNA degradation products. Primer extension analysis revealed independent promoters for aspA, dcuA, and dcuB, but surprisingly no primer extension product could be detected forfumB. The expression of dcuB is entirely consistent with a primary role for DcuB in mediating C4-dicarboxylate transport during anaerobic fumarate respiration. The precise physiological purpose of DcuA remains unclear.

scholarly journals Cometabolism of Trihalomethanes by Nitrosomonas europaea

2005 ◽  
Vol 71 (12) ◽  
pp. 7980-7986 ◽  
Author(s):  
David G. Wahman ◽  
Lynn E. Katz ◽  
Gerald E. Speitel
Keyword(s):  
Drinking Water ◽  
Rate Constants ◽  
Degradation Kinetics ◽  
Drinking Water Treatment ◽  
Nitrosomonas Europaea ◽  
Ammonia Nitrogen ◽  
Degradation Rates ◽  
Ammonia Oxidizing Bacterium ◽  
Treated Drinking Water ◽  
Bromine Substitution

ABSTRACT The ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718) was shown to degrade low concentrations (50 to 800 μg/liter) of the four trihalomethanes (trichloromethane [TCM], or chloroform; bromodichloromethane [BDCM]; dibromochloromethane [DBCM]; and tribromomethane [TBM], or bromoform) commonly found in treated drinking water. Individual trihalomethane (THM) rate constants ( \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(k_{1_{THM}}\) \end{document} ) increased with increasing THM bromine substitution, with TBM > DBCM > BDCM > TCM (0.23, 0.20, 0.15, and 0.10 liters/mg/day, respectively). Degradation kinetics were best described by a reductant model that accounted for two limiting reactants, THMs and ammonia-nitrogen (NH3-N). A decrease in the temperature resulted in a decrease in both ammonia and THM degradation rates with ammonia rates affected to a greater extent than THM degradation rates. Similarly to the THM degradation rates, product toxicity, measured by transformation capacity (Tc ), increased with increasing THM bromine substitution. Because both the rate constants and product toxicities increase with increasing THM bromine substitution, a water's THM speciation will be an important consideration for process implementation during drinking water treatment. Even though a given water sample may be kinetically favored based on THM speciation, the resulting THM product toxicity may not allow stable treatment process performance.

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