Correlating the transcriptome, proteome, and metabolome in the environmental adaptation of a hyperthermophile.

We have performed a comprehensive characterization of global molecular changes for a model organism Pyrococcus furiosus using transcriptomic (DNA microarray), proteomic, and metabolomic analysis as it undergoes a cold adaptation response from its optimal 95 to 72 degrees C. Metabolic profiling on the same set of samples shows the down-regulation of many metabolites. However, some metabolites are found to be strongly up-regulated.

The human gastric pathogen Helicobacter pylori has a potential acetone carboxylase that enhances its ability to colonize mice.

Background: Helicobacter pylori colonizes the human stomach and is the etiological agent of peptic ulcer disease. All three H. pylori strains that have been sequenced to date contain a potential operon whose products share homology with the subunits of acetone carboxylase (encoded by acxABC) from Xanthobacter autotrophicus strain Py2 and Rhodobacter capsulatus strain B10.

Direct analysis of the extracellular proteome from two strains of Helicobacter pylori.

Helicobacter pylori extracellular proteins are of interest because of possible roles in pathogenesis, host recognition, and vaccine development. We utilized a unique approach by growing two strains (including one nonsequenced strain) in a defined serum-free medium and directly analyzing the proteins present in the culture supernatants by LC-MS/MS. Over 125 proteins were identified in the extracellular proteomes of two H.

Interaction between the Helicobacter pylori accessory proteins HypA and UreE is needed for urease maturation.

Several accessory proteins are required for the maturation of two nickel-containing enzymes in the gastric pathogen Helicobacter pylori. These two enzymes are hydrogenase and urease. Among the accessory/maturation proteins, the nickel-binding HypA protein has been previously shown to be required for the full activity of both the hydrogenase and the urease enzymes, while another nickel-binding protein, UreE, is known to be solely involved in the urease maturation process.

Peptide transport in Helicobacter pylori: roles of dpp and opp systems and evidence for additional peptide transporters.

Despite research into the nutritional requirements of Helicobacter pylori, little is known regarding its use of complex substrates, such as peptides. Analysis of genome sequences revealed putative ABC-type transporter genes for dipeptide (dppABCDF) and oligopeptide (oppABCD) transport. Genes from each system were PCR amplified, cloned, and disrupted by cassette insertion either individually (dppA, dppB, dppC, oppA, oppB, and oppC) or to create double mutants (dppA oppA, dppB oppB, dppB dppC, and oppB oppC).

Defining genes in the genome of the hyperthermophilic archaeon Pyrococcus furiosus: implications for all microbial genomes.

The original genome annotation of the hyperthermophilic archaeon Pyrococcus furiosus contained 2,065 open reading frames (ORFs). The genome was subsequently automatically annotated in two public databases by the Institute for Genomic Research (TIGR) and the National Center for Biotechnology Information (NCBI). Remarkably, more than 500 of the originally annotated ORFs differ in size in the two databases, many very significantly.

In vitro reconstitution of an NADPH-dependent superoxide reduction pathway from Pyrococcus furiosus.

A scheme for the detoxification of superoxide in Pyrococcus furiosus has been previously proposed in which superoxide reductase (SOR) reduces (rather than dismutates) superoxide to hydrogen peroxide by using electrons from reduced rubredoxin (Rd). Rd is reduced with electrons from NAD(P)H by the enzyme NAD(P)H:rubredoxin oxidoreductase (NROR). The goal of the present work was to reconstitute this pathway in vitro using recombinant enzymes.

Cold shock of a hyperthermophilic archaeon: Pyrococcus furiosus exhibits multiple responses to a suboptimal growth temperature with a key role for membrane-bound glycoproteins.

The hyperthermophilic archaeon, Pyrococcus furiosus, was grown on maltose near its optimal growth temperature, 95 degrees C, and at the lower end of the temperature range for significant growth, 72 degrees C. In addition, cultures were shocked by rapidly dropping the temperature from 95 to 72 degrees C. This resulted in a 5-h lag phase, during which time little growth occurred.

Rubrerythrin from the hyperthermophilic archaeon Pyrococcus furiosus is a rubredoxin-dependent, iron-containing peroxidase.

Rubrerythrin was purified by multistep chromatography under anaerobic, reducing conditions from the hyperthermophilic archaeon Pyrococcus furiosus. It is a homodimer with a molecular mass of 39.2 kDa and contains 2.