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B R Bochner

Publications and source records attributed to B R Bochner.

At least 19 recordsLinked to original sources
PubMed2001

Phenotype microarrays for high-throughput phenotypic testing and assay of gene function.

The bacterium Escherichia coli is used as a model cellular system to test and validate a new technology called Phenotype MicroArrays (PMs). PM technology is a high-throughput technology for simultaneous testing of a large number of cellular phenotypes. It consists of preconfigured well arrays in which each well tests a different cellular phenotype and an automated instrument that continuously monitors and records the response of the cells in all wells of the arrays. For example, nearly 700 phenotypes of E. coli can be assayed by merely pipetting a cell suspension into seven microplate arrays. PMs can be used to directly assay the effects of genetic changes on cells, especially gene knock-outs. Here, we provide data on phenotypic analysis of six strains and show that we can detect expected phenotypes as well as, in some cases, unexpected phenotypes.

Escherichia coli↗
PubMed1995

Phenotypic characterisation of Acinetobacter strains of 13 DNA-DNA hybridisation groups by means of the biolog system.

A collection of 129 Acinetobacter strains belonging to DNA groups (genomic species) 1-14 (1-7 and 10-12 sensu Bouvet and Grimont; 8 and 13-14 sensu Tjernberg and Ursing) were investigated for their ability to oxidise 95 carbon sources in the Biolog system. The strain groupings obtained by cluster analysis with the Biolog software were compared with the results of DNA-DNA hybridisation studies. Strains of DNA groups 1 (A. calcoaceticus), 2 (A. baumannii), 3 and 13 were linked in one cluster, as were DNA groups 4 (A. haemolyticus) and 6, DNA groups 10 and 11, and DNA groups 8 (A. lwoffii) and 12 (A. radioresistens). Strains of DNA group 5 (A. junii) were grouped in a single cluster with one strain of DNA group 4. Strains of DNA groups 7 (A. johnsonii) and 14 formed separate clusters. With the exception of the linkage of DNA groups 8 and 12, these results correlated with classification of reference strains of the DNA groups by DNA-DNA hybridisation, but six strains of four different DNA groups were not allocated to the clusters of their respective DNA groups. In the case of DNA groups 4, 5, 6, 7, 10, 11 and 14, at least one carbon source oxidation test could be used to differentiate them from the other DNA groups.

Acinetobacter↗
PubMed1989

Sleuthing out bacterial identities.

Global phenotype analyses are now possible using a versatile redox chemistry that is readily automated with computerization and microplate technology.

Bacteria↗
PubMed1989

Periplasmic secretion of human growth hormone by Escherichia coli.

The gene coding for human growth hormone (hGH) was fused to the coding sequence for the signal peptide of a secreted Escherichia coli protein. STII heat-stable enterotoxin. This hybrid gene was expressed in E. coli. The signal peptide is properly processed and hGH is secreted in to the periplasmic space. In E. coli, some of the material made is proteolytically clipped or deamidated. The effect of culture conditions on the expression and secretion of hGH was studied and several important parameters were identified, including culture temperature and duration, cultivation pH, K+ levels, plasmid structure, and nutrient supplements. Alteration of culture conditions significantly improves the recovery yield and product quality of human growth hormone.

Culture Media↗
PubMed1986

Escherichia coli DnaK protein possesses a 5'-nucleotidase activity that is inhibited by AppppA.

AppppA and the DnaK protein have both been hypothesized to function in regulating the heat shock response of Escherichia coli. The proposals are that AppppA serves as a signal (alarmone) to turn on the heat shock response, whereas the DnaK protein is necessary to turn off the heat shock response. A simple model would be that the DnaK protein turns off the response by degrading AppppA. We disproved this model by demonstrating that the DnaK protein possesses a 5'-nucleotidase activity capable of degrading many cellular nucleotides but not AppppA. Although AppppA was not a substrate, it did inhibit the 5'-nucleotidase activity of the DnaK protein. This inhibition may be specific and have biological function since the mutant DnaK756 protein, which is defective in turning off the heat shock response, is partially desensitized to AppppA inhibition. These findings led us to consider other possible mechanisms for AppppA and the DnaK protein in heat shock regulation.

5'-Nucleotidase↗
PubMed1985

Toxicity of the pyrimidine biosynthetic pathway intermediate carbamyl aspartate in Salmonella typhimurium.

Growth of Salmonella typhimurium pyrC or pyrD auxotrophs was severely inhibited in media that caused derepressed pyr gene expression. No such inhibition was observed with derepressed pyrA and pyrB auxotrophs. Growth inhibition was not due to the depletion of essential pyrimidine biosynthetic pathway intermediates or substrates. This result and the pattern of inhibition indicated that the accumulation of the pyrimidine biosynthetic pathway intermediate carbamyl aspartate was toxic. This intermediate is synthesized by the sequential action of the first two enzymes of the pathway encoded by pyrA and pyrB and is a substrate for the pyrC gene product. It should accumulate to high levels in pyrC or pyrD mutants when expression of the pyrA and pyrB genes is elevated. The introduction of either a pyrA or pyrB mutation into a pyrC strain eliminated the observed growth inhibition. Additionally, a direct correlation was shown between the severity of growth inhibition of a pyrC auxotroph and the levels of the enzymes that synthesize carbamyl aspartate. The mechanism of carbamyl aspartate toxicity was not identified, but many potential sites of growth inhibition were excluded. Carbamyl aspartate toxicity was shown to be useful as a phenotypic trait for classifying pyrimidine auxotrophs and may also be useful for positive selection of pyrA or pyrB mutants. Finally, we discuss ways of overcoming growth inhibition of pyrC and pyrD mutants under derepressing conditions.

Aspartic Acid↗
PubMed1985

Mutations in the spoT gene of Salmonella typhimurium: effects on his operon expression.

The spoT gene of Salmonella typhimurium has been identified. Mutations in spoT map between gltC and pyrE at 79 min. The spoT1 mutant has elevated levels of guanosine 5'-diphosphate-3'-diphosphate (ppGpp) during steady-state growth and exhibits a slower than normal decay of ppGpp after reversal of amino acid starvation. The spoT1 mutation elevates his operon expression but is distinct from known his regulatory mutations. Elevated his operon expression in spoT mutants causes resistance to the histidine analogs, 1,2,4-triazole-3-alanine and 3-amino-1,2,4-triazole. These properties of spoT mutants allowed us to identify and characterize additional spoT mutants. Approximately 40% of these mutants are temperature sensitive for growth on minimal medium, suggesting that the spoT function is essential or that excessive accumulation of ppGpp is lethal.

Alcohol Oxidoreductases↗
PubMed1984

AppppA and related adenylylated nucleotides are synthesized as a consequence of oxidation stress.

AppppA , ApppGpp , AppppG , ApppG , and ApppA rapidly accumulate to high levels in Salmonella typhimurium following exposure to a variety of oxidizing agents, but not to a variety of other stresses. Among the agents inducing these adenylylated nucleotides are 1-chloro-2,4-dinitrobenzene, diamide, hydrogen peroxide, t-butyl hydroperoxide, N-ethyl maleimide, iodoacetamide, cadmium chloride, and a variety of quinones. Some of these oxidizing agents cause preferential synthesis of specific adenylylated nucleotides, e.g., N-ethyl maleimide induces ApppA and menadione induces ApppGpp . Our data, as well as other evidence in the literature, strongly suggest that oxidation stress is coupled to adenylylated nucleotide synthesis by aminoacyl-tRNA synthetases. Although adenylylated nucleotides are made by tRNA synthetases in vitro, their synthesis in vivo is not a simple consequence of inhibition of synthetase activity. Compounds that inhibit normal charging by aminoacyl-tRNA synthetases do not result in the synthesis of adenylylated nucleotides, nor do mutations in tRNA synthetase structural genes or tRNA structural, modifying, or processing genes. We propose that the family of adenylylated nucleotides are alarmones signaling the onset of oxidation stress, and that particular ones may be alarmones for specific oxidative stresses, e.g., ApppGpp for oxidative damage to amino acid biosynthesis.

Adenine Nucleotides↗
PubMed1983

Diadenosine 5',5"'-P1,P4-tetraphosphate and related adenylylated nucleotides in Salmonella typhimurium.

Salmonella typhimurium LT2 rapidly accumulates high levels of a family of five adenylylated nucleotides following exposure to a bacteriostatic quinone, 6-amino-7-chloro-5,8-dioxoquinoline. These compounds have been analyzed using our recently described two-dimensional thin layer chromatographic method. The five dinucleotides, which cannot be detected in exponentially growing cells, have been identified as diadenosine 5',5"'-P1,P4-tetraphosphate (AppppA), ApppGpp (guanosine 3'-diphosphate-5'-adenosine-5'-(P1,P3-triphosphate)), AppppG (adenosine 5'-guanosine-5'-(P1,P4-tetraphosphate)), ApppG (adenosine 5'-guanosine-5'-(P1,P3-triphosphate)), and ApppA (diadenosine 5',5"'-P1,P3-triphosphate). AppppA has been previously detected in vitro as an enzymatic product of aminoacyl-tRNA synthetases and in vivo at submicromolar levels in eucaryotic cells. The induced intracellular concentration of AppppA and the other adenylylated nucleotides in S. typhimurium is approximately 100-fold higher than that found in eucaryotic cells. We propose that these dinucleotides are alarmones, regulatory molecules signaling a particular metabolic stress.

Adenine Nucleotides↗
PubMed1983

Sensitive fluorographic detection of 3H and 14C on chromatograms using methyl anthranilate as a scintillant.

Methyl anthranilate is a simple, sensitive, and inexpensive liquid scintillant for fluorographic detection of weak beta-emitting isotopes on chromatograms. Detection of tritium is enhanced 1000-fold compared to autoradiography in a 24-h exposure. Since methyl anthranilate is a viscous liquid, it is easily applied as an even coating which subsequently solidifies at the low temperature (-80 degrees C) used for fluorography. Of several liquid scintillants tested, methyl anthranilate was most effective, followed by 9-ethyl fluorene, methyl salicylate, and 1-methyl naphthalene. The efficiency of 1-methyl naphthalene could be raised to the level of methyl anthranilate by the addition of a small amount (0.5%) of 2,5-diphenyloxazole (PPO).

Autoradiography↗
PubMed1983

AppppA, heat-shock stress, and cell oxidation.

Salmonella typhimurium LT2 induces a set of heat-shock proteins analogous to those found previously in Escherichia coli. These are virtually the only proteins synthesized after a temperature shift from 28 degrees C to 50 degrees C. Using a two-dimensional thin-layer chromatographic system developed to resolve adenylylated nucleotides, we have found that S. typhimurium and E. coli accumulate P1,P4-diadenosine-5'-tetraphosphate (AppppA), P1-(adenosine-5')-P3-(guanosine-3'-diphosphate-5')-triphosphate (ApppGpp), P1-(adenosine-5')-P4-(guanosine-5')-tetraphosphate (AppppG), P1-(adenosine-5')-P3-(guanosine-5')-triphosphate (ApppG), and P1,P3-diadenosine-5'-triphosphate (ApppA) after heat shock. These same adenylylated nucleotides accumulate after exposure to ethanol, an agent also known to induce the heat-shock response in a variety of cells. AppppA, ApppGpp, AppppG, ApppG, and ApppA were previously shown to accumulate under conditions of oxidation stress. We proposed that these adenylylated nucleotides may be alarmones--i.e., regulatory molecules, alerting cells to the onset of oxidation stress. The finding that these dinucleotides accumulate in response to heat shock suggests that oxidation and heat shock have a common physiological effect on cells. We hypothesize that these dinucleotides signal the onset of these stresses and trigger the "heat-shock response."

Adenine Nucleotides↗
PubMed1982

Complete analysis of cellular nucleotides by two-dimensional thin layer chromatography.

We describe methods for the complete analysis of cellular nucleotides from as few as 10(6) 32Pi-labeled cells in a simple 2-day experiment. Nucleotides are extracted with acid, neutralized, and resolved by two-dimensional thin layer chromatography on polyethyleneimine cellulose. In the first dimension the nucleotides are separated based on the negative charge of their phosphate groups (i.e. cyclic, mono-, di, and triphosphates) and in the second dimension on their content of nucleobases (i.e. Ura, Cyt, Thy, Gua, and Ade). Because the separation is logical, one can predict the chromatographic migration of most nucleotides. By running standards we have determined the chromatographic location of over 90 biologically important nucleotides, nucleotide derivatives, and modified nucleotides from tRNA. We also developed a set of enzymatic and chemical methods to be used in conjunction with the chromatographic separations for verifying the identity of nucleotides and characterizing novel nucleotides. In this paper we use these methods to analyze and inventory the nucleotide content of Salmonella typhimurium in balanced log phase growth. Other potential uses of the method are also described.

5'-Nucleotidase↗
PubMed1982

ZTP (5-amino 4-imidazole carboxamide riboside 5'-triphosphate): a proposed alarmone for 10-formyl-tetrahydrofolate deficiency.

Starvation of Salmonella typhimurium for folate in six different ways triggers the intracellular accumulation of a novel ribotide, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate (ZTP). Numerous other starvations not involving folate do not cause ZTP to accumulate. We propose that ZTP is an alarmone for C-1-folate deficiency and present evidence that it is formed from ZMP, an intermediate in purine biosynthesis. ZMP accumulates rapidly in cells when 10-formyl-tetrahydrofolate, a substrate for ZMP transformylase, is depleted. We review previous evidence that Z-ribotides may be involved in physiological processes in many types of cells, including sporulation of Bacillus subtilis. We also discuss the implications of ZTP synthesis for chemotherapy and other pharmacological uses of antifolates and analogs of Z-ribosides.

Aminoimidazole Carboxamide↗
PubMed1980

Positive selection for loss of tetracycline resistance.

A simple technique has been devised that allows direct plate selection of tetracycline-sensitive clones from a predominantly tetracycline-resistant population. The technique is especially useful in genetic methodologies based on the use of tetracycline resistance transposons, such as Tn10. Potential uses of the method include selection of deletion mutants, fine-structure mapping, generalized mapping, construction of multiply marked strains, elimination of tetracycline resistance transposons and plasmids and cloning. The technique is based on our finding that tetracycline-resistant cells are hypersensitive to lipophilic chelating agents, such as fusaric acid. This finding supports the contention that certain metal ions critically facilitate tetracycline uptake and leads us to suggest possible molecular mechanisms for tetracycline resistance.

Carboxylic Acids↗
PubMed1979

Inhibition of growth by imidazol(on)e propionic acid: evidence in vivo for coordination of histidine catabolism with the catabolism of other amino acids.

Imidazole propionic acid (ipa), a gratuitous inducer of the histidine-utilization (hut) system in Salmonella typhimurium, inhibits the organism's growth on succinate minimal medium. Induction of the hut system is necessary, but not sufficient, to cause inhibition. A study of the ability of single amino acids to relieve ipa-restricted growth suggests that insufficient glutamate is the cause of slow growth. The inhibition of growth by imidazolone propionic acid (iopa), an intermediate in the catabolism of histidine to glutamate, is similar to that by ipa. Studies using 2, 3, 5-triphenyl tetrazolium chloride plates to examine amino acid catabolism suggest that accumulation of ipa or iopa leads to inactivation of aspartate amino-transferase (AAT). This interpretation is supported by studies of an Escherichia coli mutant lacking AAT. The mutant grows poorly on succinate minimal medium, and the poor growth is relieved by the same amino acids that relieve ipa- and iopa-restricted growth. These and other findings are discussed in terms of coordination of the histidine-utilization system with enzymatic activities involved in the catabolism of other amino acids.

Amino Acid Oxidoreductases↗