The complete genome sequence of Escherichia coli K-12.

The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.

The histone demethylase KDM4B regulates peritoneal seeding of ovarian cancer.

Epithelial ovarian cancer (EOC) has poor prognosis and rapid recurrence because of widespread dissemination of peritoneal metastases at diagnosis. Multiple pathways contribute to the aggressiveness of ovarian cancer, including hypoxic signaling mechanisms. In this study, we have determined that the hypoxia-inducible histone demethylase KDM4B is expressed in ∼60% of EOC tumors assayed, including primary and matched metastatic tumors. Expression of KDM4B in tumors is positively correlated with expression of the tumor hypoxia marker CA-IX, and is robustly induced in EOC cell lines exposed to hypoxia. KDM4B regulates expression of metastatic genes and pathways, and loss of KDM4B increases H3K9 trimethylation at the promoters of target genes like LOXL2, LCN2 and PDGFB. Suppressing KDM4B inhibits ovarian cancer cell invasion, migration and spheroid formation in vitro. KDM4B also regulates seeding and growth of peritoneal tumors in vivo, where its expression corresponds to hypoxic regions. This is the first demonstration that a Jumonji-domain histone demethylase regulates cellular processes required for peritoneal dissemination of cancer cells, one of the predominant factors affecting prognosis of EOC. The pathways regulated by KDM4B may present novel opportunities to develop combinatorial therapies to improve existing therapies for EOC patients.

Mechanism-based inhibition of thioredoxin reductase by antitumor quinoid compounds.

Quinoids undergo metabolism by a number of flavoenzymes. Reactive species formed during the metabolism of some quinoids might be anticipated to inhibit flavoenzyme activity. Several quinoids have been tested for their ability to inhibit rat liver thioredoxin reductase (TR). The antitumor quinones diaziquone and doxorubicin, and the quinoneimine 2,6-dichloroindophenol, were found to be inhibitors of the reduction of 5,5'-dithiobis-2-nitrobenzoic acid (DTNB) by TR. The inhibition was most marked after incubation of the quinoid with NADPH and the enzyme for 60 min before adding DTNB, with Ki values of 0.5 microM for diaziquone, 0.5 microM for doxorubicin, and 0.07 microM for 2,6-dichloroindophenol. The three quinoids all produced a time-dependent and first order loss of TR activity. There was formation of electron spin resonance-detectable semiquinoid free radicals upon incubation of diaziquone, doxorubicin and 2,6-dichloroindophenol with TR and NADPH under anaerobic conditions. Oxygen radicals formed by redox cycling of the quinoids did not make a major contribution to the inhibition of TR by the quinoids, as shown by the absence of significant reversal of the inhibition by anaerobic incubation conditions and the lack of effect of the oxygen radical scavengers dimethyl sulfoxide, superoxide dismutase and catalase. It was not possible to demonstrate NADPH-dependent covalent binding of radiolabeled diaziquone or doxorubicin to the TR apoprotein. It is possible that the quinoids bind noncovalently to the enzyme apoprotein, or bind to the FAD prosthetic group. The results of the study suggest that some antitumor quinoids are mechanism-based inhibitors of TR showing metabolism- and time-dependent irreversible inhibition of enzyme activity.

Inhibition of cellular thioredoxin reductase by diaziquone and doxorubicin. Relationship to the inhibition of cell proliferation and decreased ribonucleotide reductase activity.

The flavoenzyme thioredoxin reductase (TR) is an important enzyme for many aspects of cellular function. The antitumor quinones diaziquone and doxorubicin have been shown to produce a time- and concentration-dependent inhibition of TR when incubated for up to 24 hr with intact A204 human rhabdomyosarcoma cells. There was a positive correlation between the inhibition of TR and the inhibition of cell colony formation measured 7 days later for diaziquone (r = 0.84, P less than 0.01), and for doxorubicin (r = 0.87, P less than 0.01). 2,6-Dichloroindophenol, which in previous studies was shown to be a good inhibitor of TR in vitro, was a poor inhibitor of TR in intact A204 cells and there was no significant correlation with inhibition of colony formation. The activity of ribonucleotide reductase, which catalyzes the first unique step of DNA synthesis and which obtains its reducing equivalents from TR through thioredoxin, was decreased in diaziquone- and doxorubicin treated A204 cells. We suggest that the inhibition of TR by some antitumor quinones leading to a decreased activity of TR and, consequently, a decreased activity of thioredoxin-dependent enzymes including ribonucleotide reductase may contribute to the growth inhibitory activity of these quinones.

Spectrum and prognostication of KIT and PDGFRA mutation in gastrointestinal stromal tumors.

AIMS: Recent studies reported various mutation rates in gastrointestinal stromal tumors (GISTs) and inconsistent prognostic value of mutation in GIST patients. Our purpose was to analyze the frequency and spectrum of KIT and PDFGRA in a large series study and to determine if the presence of mutation and mutation type serve as prognostic factors in GIST patients. METHODS: A total of 134 GISTs were subjected to mutation analysis of KIT (exons 9, 11, 13, and 17) and PDGFRA (exons 10, 12, 14, and 18). Clinicopathologic characteristics and survivals were correlated to KIT mutation. RESULTS: Approximately 69% of GISTs had KIT/PDGFRA mutation in Taiwanese GIST patients, with 99% of mutations occurred in KIT and 1% occurred in PDGFRA. Mutation rate was significantly increased in GISTs with mitotic counts >5 per 50 high power fields (chi(2) test, p=0.045). However, KIT mutations, regardless of the location (exons 9 versus 11) and type (missense, insertion, and deletion, including deletion specifically involving codons 557 and 558) of mutation, were not significantly associated with poor progression-free survivals. Comparing the overall survival in imatinib-treated patients, there was no significant difference between patients with exon 11 mutation and those with exon 9 mutation (p=0.473). CONCLUSIONS: GISTs were commonly associated with KIT mutation, but rarely associated with PDGFRA mutation in Taiwan. The presence of KIT mutation and mutation type was not significant prognostic factors in GIST patients without imatinib treatment, suggesting that there is no need to stratify GIST patients by mutation status in clinical trials of targeted therapy.

Inhibition of thioredoxin reductase (E.C. 1.6.4.5.) by antitumor quinones.

Thioredoxin reductase (TR) is a widely distributed flavoenzyme that provides reduced thioredoxin, a dithiol hydrogen donor for protein disulfide reduction and for the reduction of ribonucleotides to deoxyribonucleotides, the first unique step of DNA synthesis. Antitumor quinones were found to exhibit time- and concentration-dependent inhibition of purified rat liver TR that requires the presence of NADPH. Diaziquone initially shows competitive inhibition of the enzyme with 5,5'-dithiobis 2-nitrobenzoic acid as substrate with a Ki of 7.5 microM, which becomes non-competitive after 1 hour incubation with NADPH with a Ki of 0.5 microM. Doxorubicin shows non-competitive inhibition both initially and after 1 hr incubation with NADPH, with Ki values of 10 microM and 0.5 microM, respectively. Electron spin resonance spectroscopy showed the formation of semiquinone free radicals by TR incubated under anaerobic conditions with doxorubicin or diaziquone and NADPH. Redox cycling and formation of oxygen radicals does not play a major role in the inhibition of TR by antitumor quinones as shown by the minor effect on inhibition of removing O2, and the lack of effect of superoxide dismutase and catalase. Diaziquone causes time- and concentration-dependent inhibition of TR activity in intact A204 human rhabdomyosarcoma cells that is associated with growth inhibition. The results suggest that inhibition of TR by antitumor quinones could contribute to their growth inhibitory properties.

Bayesian phylogenetic inference via Markov chain Monte Carlo methods.

We derive a Markov chain to sample from the posterior distribution for a phylogenetic tree given sequence information from the corresponding set of organisms, a stochastic model for these data, and a prior distribution on the space of trees. A transformation of the tree into a canonical cophenetic matrix form suggests a simple and effective proposal distribution for selecting candidate trees close to the current tree in the chain. We illustrate the algorithm with restriction site data on 9 plant species, then extend to DNA sequences from 32 species of fish. The algorithm mixes well in both examples from random starting trees, generating reproducible estimates and credible sets for the path of evolution.

Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T.

We determined the complete genome sequence of Shigella flexneri serotype 2a strain 2457T (4,599,354 bp). Shigella species cause >1 million deaths per year from dysentery and diarrhea and have a lifestyle that is markedly different from those of closely related bacteria, including Escherichia coli. The genome exhibits the backbone and island mosaic structure of E. coli pathogens, albeit with much less horizontally transferred DNA and lacking 357 genes present in E. coli. The strain is distinctive in its large complement of insertion sequences, with several genomic rearrangements mediated by insertion sequences, 12 cryptic prophages, 372 pseudogenes, and 195 S. flexneri-specific genes. The 2457T genome was also compared with that of a recently sequenced S. flexneri 2a strain, 301. Our data are consistent with Shigella being phylogenetically indistinguishable from E. coli. The S. flexneri-specific regions contain many genes that could encode proteins with roles in virulence. Analysis of these will reveal the genetic basis for aspects of this pathogenic organism's distinctive lifestyle that have yet to be explained.

Shotgun optical maps of the whole Escherichia coli O157:H7 genome.

We have constructed NheI and XhoI optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies.

Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.

The bacterium Escherichia coli O157:H7 is a worldwide threat to public health and has been implicated in many outbreaks of haemorrhagic colitis, some of which included fatalities caused by haemolytic uraemic syndrome. Close to 75,000 cases of O157:H7 infection are now estimated to occur annually in the United States. The severity of disease, the lack of effective treatment and the potential for large-scale outbreaks from contaminated food supplies have propelled intensive research on the pathogenesis and detection of E. coli O157:H7 (ref. 4). Here we have sequenced the genome of E. coli O157:H7 to identify candidate genes responsible for pathogenesis, to develop better methods of strain detection and to advance our understanding of the evolution of E. coli, through comparison with the genome of the non-pathogenic laboratory strain E. coli K-12 (ref. 5). We find that lateral gene transfer is far more extensive than previously anticipated. In fact, 1,387 new genes encoded in strain-specific clusters of diverse sizes were found in O157:H7. These include candidate virulence factors, alternative metabolic capacities, several prophages and other new functions--all of which could be targets for surveillance.