Isolation and characterization of pyridoxine auxotrophs of Escherichia coli

Dempsey, Walter B. (University of Florida, Gainesville), and P. F. Pachler. Isolation and characterization of pyridoxine auxotrophs of Escherichia coli. J. Bacteriol. 91:642-645. 1966.-Pyridoxine auxotrophs of Escherichia coli B have been consistently produced by a modified penicillin enrichment method. This modified penicillin technique included a 6-hr growth period in the absence of any pyridoxine followed by a 2-hr treatment with penicillin at 1,000 units per ml. Penicillin was removed from these cultures by membrane filtration and the process was repeated. A minimum of three cycles was found necessary to isolate auxotrophs. Different phenotypes within the group of pyridoxine auxotrophs were distinguished by their responses to feeding with the various forms of pyridoxine, as well as by cross-feeding tests. Two auxotrophs were also differentiated by their frequency of reversion to prototrophy. Cross-feeding tests indicated that seven of the phenotypes fed in a linear sequence. These phenotypes had a very low frequency of reversion. The auxotrophs with a high frequency of reversion cross-fed in a linear sequence and fed the first five of the other seven auxotrophs. One of the auxotrophs isolated was a pyridoxal auxotroph.     

Differential Recovery of Auxotrophs After Penicillin Enrichment in Escherichia coli

Various auxotrophs are recovered from a penicillin enrichment cycle with differing efficiencies. Reconstruction experiments indicate that, under starvation conditions in the presence of penicillin, most auxotrophs undergo some death, whereas prolineless mutants are virtually immune to penicillin-induced killing.     

Penicillin formation by biochemical mutants of Penicillium chrysogenum and their spontaneous revertants

The capacity for the antibiotic production in the auxotrophs of Penicillium chrysogenum with various deficiency and their revertants was studied. It was found that the capacity for penicillin synthesis was impaired to various degrees in the majority of the auxotrophs. Variants with the penicillin production levels by 13--20 per cent higher than those in the initial prototrophic strain were isolated for the first time in selection of the eukaryotes with the method of obtaining highly active revertants from auxotrophs according to the scheme "prototroph-auxotroph-prototroph".     

Mutagenesis and Enrichment of Auxotrophs in Penicillium chrysogenum

An efficient method for isolation of auxotrophs of Penicillium chyrysogenum involving mutagenesis with ethyl methanesulfonate followed by enrichment with sodium pentachlorophenate was developed. The auxotroph frequencies obtained were 30 to 40%.     

Isolation of Spontaneously Derived Mutants of CAULOBACTER CRESCENTUS

Caulobacter crescentus has a penicillinase which precludes the use of penicillin for mutant enrichment. However, two other antibiotics, fosfomycin and D-cycloserine, can be enrich for C. crescentus mutants. In enrichment procedures for C. crescentus auxotrophs, spontaneously derived mutants occur at a frequency of 5-10% among the survivors of an enrichment procedure. Consequently, large numbers of mutants are readily obtained without any need for mutagenesis. These mutants are heterogeneous both with regard to the type of mutation and to the nutritional requirement. A similar procedure has been used to isolate temperature-sensitive mutants.     

Facilitated protoplasting in certain auxotrophic mutants of Corynebacterium glutamicum

Summary Auxotrophic mutants of Corynebacterium glutamicum strain ATCC 13 059 showed considerable variation in their ability to form protoplasts when treated with lysozyme and ethylene-diaminetetraacetic acid (EDTA) following growth in nutrient medium containing up to 2% glycine. The proportion of protoplasts formed by the parent strain was normally 10 to 15% whereas certain amino-acid auxotrophs formed protoplasts at much higher frequencies (>95%). There was no obvious correlation between the presence of specific auxotrophic markers or the number of rounds of mutagenesis and protoplasting ability. Strains which were most readily protoplasted were morphologically distinct from other auxotrophs and the parent strain but were similar to the parent strain in their sensitivity to lysozyme. However, isoleucine auxotrophs were more sensitive to penicillin G. All strains produced osmotically sensitive cells (lysed by dilution in water) after growth in glycine-containing media and lysozyme-EDTA treatment. These damaged cells could be distinguished from true protoplasts by their ability to recover on osmotically non-protective media if diluted in high osmotic pressure buffers. Protoplasts were regenerated on an osmotically protective medium (ET) in 48 to 72 h, at frequencies averaging 50–60%.     

Methods for Isolation of Auxotrophic Mutants of Methanobacterium ivanovii and Initial Characterization of Acetate Auxotrophs

To develop a biochemical genetic approach to understanding cell carbon synthesis or metabolic pathways in methanogens, Methanobacterium ivanovii was selected as a model organism for genetic manipulation studies. The organism displayed a colony size of 3 to 6 mm in less than 2 weeks and had a plating efficiency of about 90%, which made it suitable for replica plating. Mutagenesis and selection techniques were developed for selection of acetate auxotrophs. Chemical mutagenesis with ethyl methanesulfonate, followed by enrichment with bacitracin as a selective agent, resulted in stable acetate auxotrophs. M. ivanovii was very sensitive to UV, but UV-induced acetate auxotrophs were unstable and reverted within two to four transfers. The acetate auxotrophs were analyzed in relation to wild type for carbon monoxide dehydrogenase enzyme activity.     

Structural and ultrastructural changes in Mycobacterium rubrum cells exposed to penicillin

The action of penicillin taken at subbacterioscopic doses on Mycobacterium rubrum cells causes changes in the size and shape of the cells, in the structure of the cell wall, in the intracellular membrane systems and in functions associated with them, and in the structure of nucleoids whose DNA packing becomes more loose. If the antibiotic is added at bacteriostatic doses, the size and shape of the cells do not change, but peptidoglycan precursors being synthesized are not incorporated into the polymer and accumulate in the periplasm. DNA overspiralization in nucleoids is a non-specific reaction, which indicates that DNA is physiologically passive. DNA is isolated with a membrane from the cytoplasm in certain cells. It is possible that the resistance of cells against penicillin is associated with the capability of DNA to become inactive in physiological terms.     

The development of a negative selection system for the isolation of plant temperature-sensitive auxin auxotrophs

Summary A protocol has been developed for the negative selection of plant auxotrophs using the nucleoside analogues BUdR and FUdR. The protocol was optimised using nitrogen-starved protoplast-derived cells of Nicotiana plumbaginifolia to simulate auxotrophy. The present results represent a significant improvement over previous reports in that: 1) The background of colonies escaping BUdR/FUdR kill is low and reproducible. 2) The protocol was improved to the point where background survival was 0.03% for non-starved cultures and 0.09% for auxin-starved cultures. 3) It was shown that UV irradiation decreases BUdR sensitivity of dividing cells and that this is overcome by increased exposure to BUdR. 4) Application of the method to auxin-starved haploid protoplast-derived cell suspensions resulted, for the first time, in the selection of temperature-sensitive (ts) auxin auxotrophs. 5) It could be demonstrated, for the first time, that the method in practice enriches for auxotrophs, in this case by a factor of 10 for auxin auxotrophs and at least 60 for ts auxin auxotrophs.Abbreviations BUdR 5-bromodeoxyuridine - FUdR 5-fluoro-deoxyuridine - MNNG N-methyl-N-nitro-N-nitrosoguanidine - NAA 1-naphthaleneacetic acid - BAP 6-benzylamino-purine - CFE colony forming efficiency - PE plating efficiency - ts temperature sensitive     

Procedure for Isolating Mutants Defective in Metabolite Transport or Utilization

Mutants defective in uptake or utilization of a given metabolite can readily be obtained from facultative auxotrophs (for that metabolite) by penicillin enrichment under nonpermissive conditions in the presence of a low level of the required metabolite.     

Studies on the compaction of isolated nucleoids from Escherichia coli

The genomic DNA of Escherichia coli is contained in one or two compact bodies known as nucleoids. Isolation of typically shaped nucleoids requires control of DNA expansion, accomplished here by a modification of the polylysine-spermidine procedure. The ability to control expansion of in vitro nucleoids has application in nucleoid purification and in preparation of samples for high-resolution imaging, and may allow an increased resolution in gene localization studies. Polylysine of relatively low average molecular weight (approximately 3 kDa) is used to produce lysates containing nucleoids that are several-fold expanded relative to the sizes of in vivo nucleoids. These expanded forms can be converted to compact forms similar in dimensions to the cellular nucleoids by either a further addition of polylysine or by incubation of diluted lysates at 37 degrees C. The incubation at 37 degrees C is accompanied by autolytic degradation of most ribosomal RNA. Hyperchromism and circular dichroism spectra indicate that polylysine-DNA complexes are modified during the incubation. Compact forms of the nucleoid can be progressively reexpanded by exposure to salt solutions. Nucleoid compaction was similar in lysates made from rapidly or slowly growing cells or from cells that had been briefly treated with chloramphenicol to reduce linkages between DNA and cell envelope.     

Release of compact nucleoids with characteristic shapes from Escherichia coli

The genomic DNA of bacteria is contained in one or a few compact bodies known as nucleoids. We describe a simple procedure that retains the general shape and compaction of nucleoids from Escherichia coli upon cell lysis and nucleoid release from the cell envelope. The procedure is a modification of that used for the preparation of spermidine nucleoids (nucleoids released in the presence of spermidine) (T. Kornberg, A. Lockwood, and A. Worcel, Proc. Natl. Acad. Sci. USA 71:3189--3193, 1974). Polylysine is added to prevent the normal decompaction of nucleoids which occurs upon cell lysis. Nucleoids retained their characteristic shapes in lysates of exponential-phase cells or in lysates of cells treated with chloramphenicol or nalidixate to alter nucleoid morphology. The notably unstable nucleoids of rifampin-treated cells were obtained in compact, stable form in such lysates. Nucleoids released in the presence of polylysine were easily processed and provided well-defined DNA fluorescence and phase-contrast images. Uniform populations of nucleoids retaining characteristic shapes could be isolated after formaldehyde fixation and heating with sodium dodecyl sulfate.     

Envelope-associated nucleoid from Caulobacter crescentus stalked and swarmer cells.

Envelope-associated nucleoids have been isolated from Caulobacter crescentus by using a modification of the procedure of T. Kornberg et al. (Proc. Natl. Acad. Sci. U.S.A. 71:3189-3193, 1974). The development of a Ludox density gradient procedure has permitted preparation of large quantities of synchronous cells. The sedimentation coefficients of the envelope-associated nucleoids of stalked and swarmer cells, prepared under conditions of equivalent cell lysis, were 3,000S and greater than 6,000S respectively. Small differences in the relative amounts of deoxyribonucleic acid, ribonucleic acid, and protein in stalked and swarmer cell envelope-associated nucleoids could not account for the large differences in sedimentation behavior. These characteristic sedimentation coefficients were retained in mixing experiments.     

Quantitative assessment of the mutagenic effect of ethyl methanesulfonate inMicrococcus glutamicus

Micrococcus glutamicus ATCC 13032, a glutamic acid-excreting organism, was mutated by treating a 6–8 h old culture with 0.2m ethyl methanesulfonate (EMS) in a phosphate buffer of pH 7.6 for 150 min. The auxotrophs isolated showed varied patterns of extracellular amino acids, 38 isolates excreted lysine up to 1–2 mg/ml but most lost their excretion potency in subsequent fermentation trials although they remained auxotrophic. Most of the auxotrophs showed a requirement for amino acids.     

Activity of penicillin acylase from E. coli in the reversed-micelle system AOT--H2O--octane

The behavior of a penicillin acylase from E. coli was studied in the reversed-micelle system AOT--H2O--octane. Kinetic studies of the enzymatic hydrolysis of the m-carboxy-p-nitroanilide of phenylacetic acid, titration of the penicillin acylase active site with an irreversible specific inhibitor (phenylmethylsulfonyl fluoride), sedimentation analysis at different hydration degrees, and chemical modification showed that the enzyme loses no more than 20% of its initial activity during 3-4 h in the reversed-micelle systems of different hydration degrees and retains its catalytically active structure.     

Characterization of Escherichia coli nucleoids released by osmotic shock

Nucleoids were isolated by osmotic shock from Escherichia coli spheroplasts at relatively low salt concentrations and in the absence of detergents. Sucrose-protected cells, made osmotically sensitive by growth in the presence of ampicillin or by digestion with low lysozyme concentrations (50-5 μg/ml), were shocked by 100-fold dilution of the sucrose buffer. Liberated nucleoids stained with 4',6-diamidino-2-phenylindole dihydrochloride hydrate (DAPI), the dimeric cyanine dye TOTO-1, or fluorescent DNA-binding protein appeared as cloud-like structures, in the absence of phase contrast. Because UV-irradiation disrupted the DAPI-stained nucleoids within 5-10 s, they were imaged by time-lapse microscopy with exposure times less than 2 s. The volume of nucleoids isolated from ampicillin- or low-lysozyme spheroplasts and minimally exposed to UV (<2 s) was on average ～42 μm(3). Lysozyme at concentrations above 1 μg/ml in the lysate compacted the nucleoids. Treatment with protease E or K (20-200 μg/ml) and sodium dodecyl sulfate (SDS; 0.001-0.01%) caused a twofold volume increase and showed a granular nucleoid at the earliest UV-exposure; the expansion could be reversed with 50 μM ethidium bromide, but not with chloroquine. While DNase (1 μg/ml) caused a rapid disruption of the nucleoids, RNase (0.1-400 μg/ml) had no effect. DAPI-stained nucleoids treated with protease, SDS or DNase consisted of granular substructures at the earliest exposure similar to UV-disrupted nucleoids obtained after prolonged (>4 s) UV irradiation. We interpret the measured volume in terms of a physical model of the nucleoid viewed as a branched DNA supercoil crosslinked by adhering proteins into a homogeneous network.     

Genetic analysis of Acinetobacter calcoaceticus proline auxotrophs.

Twenty-six Acinetobacter calcoaceticus proline auxotrophs were isolated after ethyl methane sulfonate mutagenesis. Studies using the efficient transformation system of this organism indicate that the mutations comprise therr genetically distinct groups.     

Nature of conformational restrictions in nuclear superhelical DNA from thymus lymphocytes

The lymphocyte nucleoids of mouse thymus contain about 40% of rapidly labelled nuclear RNA, about 9% of total intracellular protein and all nuclear DNA. Relaxation of superhelical DNA after thymocyte nucleoids treatment with pronase or RNAase suggests that non-histone proteins and/or RNAs are involved in conformational restrictions in the superhelical domains of cell DNAs. Thymocyte nucleoids proteins are represented by two groups of nonhistone proteins with molecular weights of 50 000-60 000 and 75 000-85 000. An essential role in the appearance of conformational restrictions in thymocyte superhelical DNA belongs to disulfide bonds.     

Isolation and Characterization of a Phosphatidylethanolamine-Deficient Mutant of Bacillus subtilis

A mutant of Bacillus subtilis ATCC 6051 deficient in phosphatidylethanolamine, an important membrane lipid, was isolated by a combination of nitrosoguanidine mutagenesis and penicillin concentration of auxotrophs employing phosphatidylethanolamine as a supplement. The mutant was compared to the parent strain with regard to lipid composition, growth, osmotic fragility, and staining character and differed substantially in each category. In addition to scant amounts of phosphatidylethanolamine, the mutant contained phosphatidylglycerol, cardiolipin, lysyl phosphatidylglycerol, and diglucosyldiglyceride, though in amounts differing from those found in the parent strain. The mutant was unable to grow appreciably on synthetic media, had enhanced osmotic fragility of protoplasts, and resisted decolorization in staining.     

Folding of prokaryotic DNA. Isolation and characterization of nucleoids from Bacillus licheniformis

Intact and fast-sedimenting nucleoids of Bacillus licheniformis were isolated under low-salt conditions and without addition of detergents, polyamines or Mg2+. These nucleoids were partially unfolded by treatment with RNase and completely unfolded by treatments that disrupt protein-DNA interactions, like incubation with proteinase K, 0.1% sodium dodecyl sulphate and high ionic strength. Ethidium bromide intercalation studies on RNase-treated, proteinase-K-treated and non-treated nucleoids in combination with sedimentation analysis of DNase-I-treated nucleoids revealed that DNA is organized in independent, negatively supertwisted domains. In contrast to the DNA organization in bacterial nucleoids, isolated under high-salt conditions and in the presence of detergents (Stonington & Pettijohn, 1971; Worcel & Burgi, 1972), the domains of supertwisted DNA in the low-salt-isolated nucleoids studied here are restrained by protein-DNA interactions. A major role for nascent RNA in restraining supertwisted DNA was not observed. The superhelix density of B. licheniformis nucleoids calculated from the change of the sedimentation coefficient upon ethidium bromide intercalation, was of the same order of magnitude as that of other bacterial nucleoids and eukaryotic chromosomes, isolated under high-salt conditions: namely, -0.150 (corrected to standard conditions: 0.2 M-NaCl, 37 degrees C; Bauer, 1978). Electron microscopy of spread nucleoids showed relaxed DNA and regions of condensed DNA. Spreading in the presence of 100 micrograms ethidium bromide per ml revealed only condensed structures, indicating that nucleoids are intact. From spreadings of proteinase-K-treated nucleoids we infer that supertwisted DNA and the protein-DNA interactions, responsible for restraining the superhelical DNA conformation, are localized in the regions of condensed DNA.