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PubMed2002

Biodegradation kinetics of aromatic hydrocarbon mixtures by pure and mixed bacterial cultures.

Microbial growth on pollutant mixtures is an important aspect of bioremediation and wastewater treatment. However, efforts to develop mathematical models for mixed substrate kinetics have been limited. Nearly all models group either the microbial population (as "biomass") or the chemical species (e.g., as biological oxygen demand). When individual chemical species are considered, most models assume either no interaction or that the nature of the interaction is competition for the same rate-limiting enzyme. And when individual microbial species are considered, simple competition for the growth substrate is the only interaction included. Here, we present results using Pseudomonas putida F1 and Burkholderia sp. strain JS150 growing individually and together on benzene, toluene, phenol, and their mixtures and compare mathematical models to describe these results. We demonstrate that the simple models do not accurately predict the outcome of these biodegradation experiments, and we describe the development of a new model for substrate mixtures, the sum kinetics with interaction parameters (SKIP) model. In mixed-culture experiments, the interactions between species were substrate dependent and could not be predicted by simple competition models. Together, this set of experimental and modeling results presents our current state of work in this area and identifies challenges for future modeling efforts.

Biodegradation, Environmental↗
PubMed2026

Implications of proteome allocation constraints for understanding interbacterial antagonism.

Bacteria live in dense communities where competition influences the composition and, therefore, the function of these communities. Beyond competing for resources, bacteria engage in antagonism by deploying a range of molecular weapon systems to inhibit and kill other bacteria. Investing in antagonism is expected to incur a fitness trade-off, but the nature of this trade-off at the level of molecular physiology remains underexplained. Applying recent advances about the physiological constraints faced by bacterial cells may help us better understand existing studies and design new investigations into interbacterial antagonism. Bacterial cells face two important constraints: a finite amount of protein and a maximum translation speed for ribosomes. As a result, the only way for a cell to grow faster is to allocate more of its finite proteome to synthesizing ribosomes. A cell choosing to attack competitors must therefore allocate some of its limited proteome budget to antagonistic proteins instead of other functions. Conversely, being attacked and resisting the effects of such attacks also require an investment of proteomic resources. The extent to which proteome allocation constraints influence bacterial physiology is not fully understood; consequently, how these constraints influence interbacterial antagonism has not been investigated. Here, I will discuss how proteome allocation constraints can re-contextualize our existing understanding of the costs of both deploying and resisting attacks and how investigation of these constraints may further our understanding of interbacterial antagonism.

Proteome↗
PubMed1984

Herbicide-quinone competition in the acceptor complex of photosynthetic reaction centers from Rhodopseudomonas sphaeroides: a bacterial model for PS-II-herbicide activity in plants.

A select group of herbicides that inhibit photosystem II also act at the acceptor side of the reaction center (RC) from the photosynthetic bacterium Rhodopseudomonas sphaeroides, with much the same relative specificity as in plants. These include the triazines and some phenolic compounds. The proposal that herbicides inhibit the electron transfer from the primary quinone (QA) to the secondary quinone (QB) by competing for the secondary quinone binding site--the B-site--[5], is tested here with terbutryn, the most potent of the triazines. Competition between terbutryn and ubiquinone (Q-10) was observed using the kinetics of the back-reaction as a measure of inhibition. The model includes binding equilibria before and after flash activation. The binding constants for the preflash (dark) equilibria, for reaction centers in 0.14% lauryl dimethylamine-N-oxide (LDAO), were KDi = 0.8 microM terbutryn, KDq = 2 microM Q-10; both are detergent-concentration dependent. After flash activation, binding equilibrium is not fully restored on the time scale of the back-reaction because terbutryn unbinds slowly. This gives rise to biphasic decay kinetics from which koff for terbutryn was estimated to be 3 sec-1. Titrations of the rate of the slow back reaction indicated that the post-flash equilibrium is less sensitive to inhibitor, in a manner that is independent of the much stronger binding of the semiquinone, Q-B, and indicative of a direct effect of the redox state of QA on the affinity of the B-site for ligands. However, the effects on KLi and KDq could not be separated: either KLi greater than KDi or KLq less than KDq. Some triazine-resistant mutants have been isolated and are described. All appear to be herbicide binding site mutants. Whole cells and photosynthetic membrane vesicles (chromatophores) exhibit a 10-50-fold increase in resistance to triazines due, in large part, to an increase in the rate of unbinding (koff). The modifications of the binding site appear to diminish the affinity of the B-site for ubiquinone as well as terbutryn. It is concluded that bacterial RCs are a useful model for the study of herbicide activity and specificity.

Binding, Competitive↗
PubMedDate not supplied

Mechanism of beta-lactamase inhibition: differences between sulbactam and other inhibitors.

Three different types of beta-lactamases--TEM-2 type penicillinase, a typical cephalosporinase of Citrobacter freundii, and a Proteus vulgaris cephalosporinase with broad substrate range--were studied to determine the inactivation and reactivation kinetics for beta-lactamase inhibitors of these enzymes. Sulbactam, cloxacillin sulfone, clavulanic acid, imipenem, and aztreonam were evaluated. On the basis of the kinetic parameters a minimum scheme for the inactivation of these beta-lactamases by each compound was proposed, and the difference in the features of each of these as progressive and competitive inhibitors were evaluated. The relationship between the kinetic parameters and the synergistic effects of the inhibitors in combination with traditional beta-lactam antibiotics on the bacterial strains producing these beta-lactamases was examined. A close relationship between the synergistic effect, expressed as the FIC index, and a proposed parameter, TN x Ki/Km, was demonstrated. The results of this analysis suggest that sulbactam is a beta-lactamase inhibitor applicable to a wide range of beta-lactamase types.

Anti-Bacterial Agents↗
PubMed1987

Phosphonamidate inhibitors of human neutrophil collagenase.

A series of phosphonamidates has been synthesized and shown to inhibit human neutrophil collagenase. The compounds all have sequences patterned after the cleavage site in the alpha 1(I) chain of type I collagen, except that the carbonyl group of the Gly residue in subsite P1 has been replaced by a P(= O)(OH) group (abbreviated GlyP). As the central GlyP-Leu unit is lengthened in the N- and C-terminal directions, in accordance with the cleavage sequence found in collagen, inhibition is systematically improved. The best inhibitor is Cbz-GlyP-Leu-Ala-Gly, which inhibits competitively with a KI value of 14 microM. These phosphonamidates are thought to be acting as transition-state analogues.

Binding, Competitive↗
PubMed1999

Molecular mechanism of VanHst, an alpha-ketoacid dehydrogenase required for glycopeptide antibiotic resistance from a glycopeptide producing organism.

The vancomycin resistance enzyme VanH is an alpha-ketoacid dehydrogenase that stereospecifically reduces pyruvate to D-lactate, which is required for the synthesis of the depsipeptide D-alanine-D-lactate. This compound then forms an integral part of the bacterial cell wall replacing the vancomycin target dipeptide D-alanine-D-alanine, thus the presence of VanH is essential for glycopeptide resistance. In this work, the VanH homologue from the glycopeptide antibiotic producing organism Streptomyces toyocaensis NRRL 15009, VanHst, has been overexpressed in Escherichia coli and purified, and its substrate specificity and mechanism were probed by steady-state kinetic methods and site-directed mutagenesis. The enzyme is highly efficient at pyruvate reduction with kcat/Km = 1.3 x 10(5) M-1 s-1 and has a more restricted alpha-ketoacid substrate specificity than VanH from vancomycin resistant enterococci (VRE). Conversely, VanHst shows no preference between NADH and NADPH while VanH from VRE prefers NADPH. The kinetic mechanism for VanHst was determined using product and dead-end inhibitors to be ordered BiBi with NADH binding first followed by pyruvate and products leaving in the order D-lactate, NAD+. Site-directed mutagenesis indicated that Arg237 plays a role in pyruvate binding and catalysis and that His298 is a candidate for an active-site proton donor. Glu266, which has been suggested to modulate the pKa of the catalytic His in other D-lactate dehydrogenases, was found to fulfill a similar role in VanHst, lowering a pKa value of kcat/Km nearly 2 units. These results now provide the framework for additional structure and inhibitor design work on the VanH family of antibiotic resistance enzymes.

Anti-Bacterial Agents↗
PubMed2000

Immunization with f-Met peptides induces immune reactivity against Mycobacterium tuberculosis.

OBJECTIVE: To determine whether synthetic peptides containing an amino terminal formyl-methionine residue and corresponding to the sequence of several proteins produced by Mycobacterium tuberculosis, would elicit an immune response in mice. DESIGN: Peptides corresponding to the amino termini of 8 M. tuberculosis proteins and initiating with formyl methionine residues were synthesized. The ability of these peptides to bind to the mouse non-classical MHC class I molecule H-2M3a was determined by flow microfluorimetry. These peptides were used to pulse dendritic cells that were then injected into normal mice. These mice were subsequently challenged with aerosolized M. tuberculosis and, 30 days later, the number of viable bacteria in the lungs was determined. RESULTS: Four of the 8 synthetic peptides bound to H-2M3a and stabilized its expression on the cell surface. Injection of mice with dendritic cells pulsed with H-2M3a binding peptides elicited non-MHC restricted cytotoxic T lymphocytes that killed peptide pulsed target cells and macrophages infected with M. tuberculosis. Immunization of mice with syngeneic dendritic cells pulsed in vitro with 2 of these peptides led to retardation of the growth of M. tuberculosis following aerosol challenge. CONCLUSION: Peptides that bind to non-polymorphic class I molecules can elicit immune reactivity directed towards M. tuberculosis.

Animals↗
PubMed2002

In vivo selection of spectinomycin-binding RNAs.

The folding of even short RNA molecules in a random library can produce a huge number of possible macromolecular structures. Using this principle, we have designed selections to seek non-coding RNA transcripts capable of interfering with specific macromolecules such as transcription factors in living bacterial cells. Here we show that such selections can uncover an unexpected class of RNAs. In the present case, we report short RNA transcripts whose expression confers bacterial resistance to the antibiotic spectinomycin. We provide evidence that such RNAs cause drug resistance by direct antibiotic binding, demonstrating a class of spectinomycin-specific functional molecular decoys built from RNA.

Anti-Bacterial Agents↗
PubMed1998

Development of a rapid method for quantitative evaluation of Mycobacterium tuberculosis growth based on competitive polymerase chain reaction.

A competitive polymerase chain reaction (cPCR) assay for the quantitative evaluation of Mycobacterium tuberculosis growth was developed based on co-amplification of genomic DNA and a modified DNA fragment derived from a well-conserved region of the 16S rRNA gene. There was a good correlation between the number of DNA copies in the sample, indicated by competitive PCR, and the number of colony forming units determined by conventional culture methods.

Antitubercular Agents↗
PubMed1992

Short-term effects of rhizosphere microorganisms on fe uptake from microbial siderophores by maize and oat.

Effects of rhizosphere microorganisms on Fe uptake by oat (Avena sativa) and maize (Zea mays) were studied in short-term (10 h) nutrient solution experiments. Fe was supplied either as microbial siderophores (pseudobactin [PSB] or ferrioxamine B [FOB]) or as phytosiderophores obtained as root exudates from barley (epi-3-hydroxy-mugineic acid [HMA]) under varied population densities of rhizosphere microorganisms (axenic, uninoculated, or inoculated with different microorganism cultures). When maize was grown under axenic conditions and supplied with FeHMA, Fe uptake rates were 100 to 300 times higher compared to those in plants supplied with Fe siderophores. Fe from both sources was taken up without the involvement of an extracellular reduction process. The supply of FeHMA enhanced both uptake rate and translocation rate to the shoot (more than 60% of the total uptake). However, increased density of microorganisms resulted in a decrease in Fe uptake rate (up to 65%), presumably due to microbial degradation of the FeHMA. In contrast, when FeFOB or FePSB was used as the Fe source, increased population density of microorganisms enhanced Fe uptake. The enhancement of Fe uptake resulted from the uptake of FeFOB and FePSB by microorganisms adhering to the rhizoplane or living in the free space of cortical cells. The microbial apoplastic Fe pool was not available for root to shoot transport or, thus, for utilization by the plants. These results, in addition to the low uptake rate under axenic conditions, are in contrast to earlier hypotheses suggesting the existence of a specific uptake system for Fe siderophores in higher plants. The bacterial siderophores PSB and FOB were inefficient as Fe sources for plants even when supplied by stem injection. It was concluded that microorganisms are involved in degradation processes of microbial siderophores, as well as in competition for Fe with higher plants.

Journal Article↗
PubMed1984

Comparison of fortimicins with other aminoglycosides and effects on bacterial ribosome and protein synthesis.

Fortimicins are bicyclic aminoglycoside antibiotics that contain a fortamine moiety instead of the deoxystreptamine found in other aminoglysides. Fortimicin A had a bactericidal effect on Escherichia coli and Staphylococcus epidermidis and was found to inhibit protein synthesis in vivo. In vitro, fortimicin A inhibited polyuridylic acid-directed phenylalanine polymerization and induced misreading, as shown by leucine incorporation. In contrast, fortimicin B had no effect on either polymerization or misreading. In assays programmed with natural mRNA, only a weak polymerization inhibition effect was observed with fortimicin A, whereas a strong stimulation was seen in the presence of fortimicin B. Both fortimicins A and B inhibited dissociation of 70S ribosomes into their subunits and neither was able to displace [3H]dihydrostreptomycin, [3H]tobramycin, or [3H]gentamicin from their respective binding sites on the 70S particle.

Aminoglycosides↗
PubMed1991

Outer membranes are competitive inhibitors of Escherichia coli O157:H7 adherence to epithelial cells.

Escherichia coli of serotype O157:H7 are Vero cytotoxin-producing enteric pathogens that have been associated recently with sporadic cases and outbreaks of hemorrhagic colitis and with the hemolytic-uremic syndrome. Adherence of many enteropathogenic bacteria to mucosal surfaces is a critical step in the pathogenesis of diarrheal disease. We showed previously that adherence of E. coli O157:H7 strain CL-56 to epithelial cells in vitro is inhibited by outer membranes. In this study we examined whether outer membranes from a series of E. coli O157:H7 strains mediated competitive inhibition of bacterial binding to epithelial cells grown in tissue culture. We also determined which constituents of the outer membrane mediated inhibition of CL-56 adherence. Binding of six O157:H7 strains to HEp-2 cells was determined by quantitating the number of adherent bacteria in the presence and absence of outer membranes which were extracted from each strain with N-lauroyl sarcosinate (1.7%, wt/vol). After separation of outer membranes by gel electrophoresis, four bands (94, 40, 36, and 30 kDa) were collected by electroelution. Immune sera were raised in rabbits to each of the four eluted bands. Outer membrane extracts from each of the six O157:H7 strains inhibited binding of homologous organisms to the HEp-2 cells. At dilutions which did not cause bacterial agglutination, antiserum raised against the 94-kDa outer membrane protein showed maximal inhibition of bacterial adherence (17.0 +/- 7.3% adherence of control levels). Growth of bacteria in iron-depleted broth did not affect their binding to HEp-2 cells, suggesting that iron-regulated outer membranes were not involved. Fluid accumulation in ileal ligated loops of rabbits in response to E. coli O157:H7 challenge was diminished following both parenteral immunization with outer membranes extracted from the homologous strain and coincubation of organisms with immune serum which contained antibodies to outer membrane extracts. These data indicate that outer membranes are competitive inhibitors of E. coli O157:H7 adherence. Specific constituents of the outer membrane may function as bacterial attachment factors (i.e., adhesins) for E. coli O157:H7 adherence to epithelial cell surfaces.

Actins↗
PubMed1998

Comparison of the ABI 7700 system (TaqMan) and competitive PCR for quantification of IS6110 DNA in sputum during treatment of tuberculosis.

Mycobacterium tuberculosis can persist in sputum for long periods of time after the initiation of antituberculosis chemotherapy. The purpose of this study was to determine whether quantitative estimates of M. tuberculosis DNA in sputum correlate with the numbers of viable bacilli and thus measure the therapeutic response of patients during treatment. Two methods of M. tuberculosis DNA quantification were examined by using DNA isolated from sputum specimens serially collected during the course of chemotherapy. A competitive PCR assay was compared to an automated system of real-time quantification with the ABI Prism 7700 Sequence Detection System (TaqMan). The ABI 7700 system uses standard PCR in conjunction with a fluorogenic probe in which the intensity of fluorescence is proportional to the amount of target DNA present. The results showed that both PCR systems are reproducible and accurate. The amounts of M. tuberculosis DNA quantified in sputum corresponded well with the numbers of acid-fast bacilli (AFB) counted by microscopy. Before initiation of antituberculosis therapy, measures of AFB, M. tuberculosis DNA, and cultivable bacilli were similar, suggesting that quantification of DNA is a good method for measuring the initial bacillary load. However, the rate of disappearance of both AFB and M. tuberculosis DNA did not correlate with the decline in cultivable bacilli in the specimen; therefore, these tests are not appropriate for monitoring treatment efficacy.

Antitubercular Agents↗
PubMed2000

Eap1p, a novel eukaryotic translation initiation factor 4E-associated protein in Saccharomyces cerevisiae.

Ribosome binding to eukaryotic mRNA is a multistep process which is mediated by the cap structure [m(7)G(5')ppp(5')N, where N is any nucleotide] present at the 5' termini of all cellular (with the exception of organellar) mRNAs. The heterotrimeric complex, eukaryotic initiation factor 4F (eIF4F), interacts directly with the cap structure via the eIF4E subunit and functions to assemble a ribosomal initiation complex on the mRNA. In mammalian cells, eIF4E activity is regulated in part by three related translational repressors (4E-BPs), which bind to eIF4E directly and preclude the assembly of eIF4F. No structural counterpart to 4E-BPs exists in the budding yeast, Saccharomyces cerevisiae. However, a functional homolog (named p20) has been described which blocks cap-dependent translation by a mechanism analogous to that of 4E-BPs. We report here on the characterization of a novel yeast eIF4E-associated protein (Eap1p) which can also regulate translation through binding to eIF4E. Eap1p shares limited homology to p20 in a region which contains the canonical eIF4E-binding motif. Deletion of this domain or point mutation abolishes the interaction of Eap1p with eIF4E. Eap1p competes with eIF4G (the large subunit of the cap-binding complex, eIF4F) and p20 for binding to eIF4E in vivo and inhibits cap-dependent translation in vitro. Targeted disruption of the EAP1 gene results in a temperature-sensitive phenotype and also confers partial resistance to growth inhibition by rapamycin. These data indicate that Eap1p plays a role in cell growth and implicates this protein in the TOR signaling cascade of S. cerevisiae.

Amino Acid Sequence↗
PubMedDate not supplied

Effect of combined application of methyl isothiocyanate and chloropicrin on their transformation.

Combining several soil fumigants to increase the broad spectrum of pest control is a common fumigation practice in current production agriculture. In this study, we investigated the effect of combined application of chloropicrin and methyl isothiocyanate (MITC) on their transformations and persistence in the environment. In aqueous solution, no direct reaction between MITC and chloropicrin occurred and relatively slow rates of hydrolysis of these compounds were observed in aquatic environments free of suspended solids. The transformation of chloropicrin, however, was accelerated in aqueous solution with MITC because of a reduction reaction with bisulfide (HS(-)), which is a by-product of MITC hydrolysis. In soil, when fumigants were applied simultaneously, the degradation of MITC was suppressed under the bi-fumigant application due to the inhibition of soil microbial activity and a possible abiotic competition with chloropicrin for a limited number of reaction sites on the surface of soil particles. However, the degradation rate of chloropicrin was significantly enhanced in the bi-fumigant soil system, which was primarily attributed to the reaction of chloropicrin and HS(-). Two sequential application approaches were developed to investigate the feasibility of the combined application of metam sodium (parent compound of MITC) and chloropicrin in soil and assess their potential effects on environmental fate. For both application sequences, the degradation of chloropicrin was accelerated and that of MITC, as a major breakdown product of metam sodium, was inhibited in soil.

Chemical Warfare Agents↗
PubMed2002

Detection and quantification of expression of amoA by competitive reverse transcription-pCR.

Ammonia oxidation by chemolithoautotrophic ammonia-oxidizing bacteria is an important step in the biological nitrogen removal process. The first conversion step, the oxidation of ammonia to hydroxylamine is catalyzed by ammonia monooxygenase (AMO). To investigate the activity of ammonia oxidation, mRNA (designated as amoA) encoding a subunit of AMO was quantified by competitive reverse transcription (RT)-PCR. As a result, it was possible to detect and quantify amoA expression in cultured Nitrosomonas europaea and even complex microbial communities such as nitrifying bacterial aggregates by competitive RT-PCR. It was estimated that amoA concentration in cultured N. europaea was 2.3 x 10(8) copies x ml(-1). Additionally, it was calculated that the copy number of amoA in nitrifying bacterial aggregates was 1.0 x 10(12) copies x ml(-1) (5.1 x 10(10) copies x mg(-1)-dry weight). On the other hand, amoA expression in the natural activated sludge in a household Gappei-Johkaso was undetectable, whereas 16S rRNA of ammonia-oxidizing bacteria was detected by RT-PCR. Then, four days cultivation of this sludge in inorganic artificial wastewater resulted in increasing amoA expression to a quantifiable amount by competitive RT-PCR. In conclusion, the competitive RT-PCR was effective to investigate the expression of amoA as an indicator of ammonia oxidation activity by autotrophic ammonia-oxidizing bacteria.

Ammonia↗