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The characterization of a set of amber mutants of bacteriophage T5.

A collection of amber mutants of bacteriophage T5 was analysed using an in vivo complementation test and assigned to 21 complementation groups. The incomplete phage structures produced by T5 amber mutant infection of the non-permissive host were examined. The mutants were allocated to four phenotypic types, as defined by an in vitro complementation test: those which produced functional heads, H; those which produced functional tails, T; those which produced inactive heads and functional tails, HI + T; and those which did not synthesize either heads or tails, 0. Functional heads and inactive heads were indistinguishable in shape and size in the electron microscope. Four different patterns of DNA metabolism were observed when different amber mutants were grown under non-permissive conditions. They were the wild-type pattern (D+) in which host DNA degradation was followed by synthesis of phage DNA, host DNA degradation without phage DNA synthesis (D0), neither host DNA degradation nor phage DNA synthesis (DD0) and host DNA degradation with slight DNA synthesis (DS). Upon infection of the non-permissive host with representatives of different complementation groups of mutants either normal lysis occurred or bacterial growth ceased without subsequent lysis. The phenotypic characteristics of the amber mutants were used for partial elucidation of the functions of the affected genes.

Bacteriolysis↗

Suppression of amber and ochre mutants in Salmonella typhimurium by a mutant F'-1-gal factor carrying an ochre suppressor gene.

A Salmonella typhimurium strain was given the amber mutation hisC527 by transduction, made galactose-negative by mutation, then infected with the F'-1-gal factor. Of 107 spontaneous and mutagen-induced histidine-independent mutants tested, 3 proved to result from suppressor mutations within the F' factor. The mutant F' factors, when transferred to S. typhimurium and E. coli auxotrophs, suppressed amber and ochre but not UGA or missense mutants, and are inferred to carry ochre suppressor genes. Attempts to isolate an F' amber suppressor mutant were unsuccessful. A suppressor F' factor was transferred to 14 rough mutants which had been isolated from LT2 hisC527 (amber) by selection for resistance to phage P22.c2. One rough mutant was partly suppressed, as shown by its acquisition of O agglutinability and by alterations in its phage resistance pattern. Phage P22h grown on the suppressed mutant contransduced its rf. gene with cysE(+) and with pyrE(+), and the affected locus is inferred to be rfaL. Both the original and the mutant F' factors conferred resistance to the rough-specific phage Br60, which is therefore "female-specific."

Bacteriophages↗

Isolation and characterization of amber mutations in gene dnaA of escherichia coli K-12.

Amber mutants with defects in the dnaA gene of Escherichia coli K-12 were isolated after localized mutagenesis of the tna-dnaA region of the chromosome. We isolated 36 mutants defective in the initiation of deoxyribonucleic acid replication as determined by their dependence upon integrative suppression by a P2 sig5 prophage. Three of the 36 mutants were shown to contain amber mutations through the use of a temperature-sensitive amber suppressor. These mutations, which mapped between gyrB and tna, were characterized genetically and biochemically as amber mutations in dnaA.

Bacterial Proteins↗

Plasmid-located pathogenicity determinants of Serratia entomophila, the causal agent of amber disease of grass grub, show similarity to the insecticidal toxins of Photorhabdus luminescens.

Serratia entomophila and Serratia proteamaculans cause amber disease in the grass grub Costelytra zealandica (Coleoptera: Scarabaeidae), an important pasture pest in New Zealand. Larval disease symptoms include cessation of feeding, clearance of the gut, amber coloration, and eventual death. A 115-kb plasmid, pADAP, identified in S. entomophila is required for disease causation and, when introduced into Escherichia coli, enables that organism to cause amber disease. A 23-kb fragment of pADAP that conferred disease-causing ability on E. coli and a pADAP-cured strain of S. entomophila was isolated. Using insertion mutagenesis, the pathogenicity determinants were mapped to a 17-kb region of the clone. Sequence analysis of the 17-kb region showed that the predicted products of three of the open reading frames (sepA, sepB, and sepC) showed significant sequence similarity to components of the insecticidal toxin produced by the bacterium Photorhabdus luminescens. Transposon insertions in sepA, sepB, or sepC completely abolished both gut clearance and cessation of feeding on the 23-kb clone; when recombined back into pADAP, they abolished gut clearance but not cessation of feeding. These results suggest that SepA, SepB, and SepC together are sufficient for amber disease causation by S. entomophila and that another locus also able to exert a cessation-of-feeding effect is encoded elsewhere on pADAP.

Amino Acid Sequence↗

The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read-through amber codons.

Three different methyltransferases initiate methanogenesis from trimethylamine (TMA), dimethylamine (DMA) or monomethylamine (MMA) by methylating different cognate corrinoid proteins that are subsequently used to methylate coenzyme M (CoM). Here, genes encoding the DMA and TMA methyltransferases are characterized for the first time. A single copy of mttB, the TMA methyltransferase gene, was cotranscribed with a copy of the DMA methyltransferase gene, mtbB1. However, two other nearly identical copies of mtbB1, designated mtbB2 and mtbB3, were also found in the genome. A 6.8-kb transcript was detected with probes to mttB and mtbB1, as well as to mtbC and mttC, encoding the cognate corrinoid proteins for DMA:CoM and TMA:CoM methyl transfer, respectively, and with probes to mttP, encoding a putative membrane protein which might function as a methylamine permease. These results indicate that these genes, found on the chromosome in the order mtbC, mttB, mttC, mttP, and mtbB1, form a single transcriptional unit. A transcriptional start site was detected 303 or 304 bp upstream of the translational start of mtbC. The MMA, DMA, and TMA methyltransferases are not homologs; however, like the MMA methyltransferase gene, the genes encoding the DMA and TMA methyltransferases each contain a single in-frame amber codon. Each of the three DMA methyltransferase gene copies from Methanosarcina barkeri contained an amber codon at the same position, followed by a downstream UAA or UGA codon. The C-terminal residues of DMA methyltransferase purified from TMA-grown cells matched the residues predicted for the gene products of mtbB1, mtbB2, or mtbB3 if termination occurred at the UAA or UGA codon rather than the in-frame amber codon. The mttB gene from Methanosarcina thermophila contained a UAG codon at the same position as the M. barkeri mttB gene. The UAG codon is also present in mttB transcripts. Thus, the genes encoding the three types of methyltransferases that initiate methanogenesis from methylamine contain in-frame amber codons that are suppressed during expression of the characterized methyltransferases.

Amino Acid Sequence↗

Nonsense suppression in a multiauxotrophic derivative of Escherichia coli 15T-: identification and consequences of an amber triplet in the deoxyribomutase gene.

Previously, arginine revertants of Escherichia coli WWU, a derivative of E. coli 15T(-), have been subdivided by two independent methods: (i) the streak morphology on nutrient agar, and (ii) the pattern of phage growth using amber and ochre mutants of bacteriophage T4. In the first assay, revertants were subdivided into two classes according to the appearance of streaks after incubation on nutrient agar, a thick, even line of growth defining normal revertants and a thin, irregular line defining aberrant revertants. In the second assay, revertants were classified by the suppressors they contained. The present work demonstrates that revertants containing an amber suppressor show the aberrant morphology and are also able to catabolize thymidine for energy and carbon. This is in contrast to the parent WWU containing no suppressor, which shows a normal morphology and cannot utilize thymidine as an energy source. Revertants containing no suppressor, isolated specifically for their ability to catabolize thymidine, show an aberrant morphology. Together, these results indicate that the aberrant morphology results from suppression of an amber triplet in a gene of the thymidine catabolic pathway. Enzyme assays show the amber triplet to be in the gene specifying deoxyribomutase. It is suggested that the aberrant arginine revertants are analogous to high thymine-requiring mutants and that, in general, high and low thymine-requiring mutants differ from one another in their ability to catabolize deoxyribose-1-phosphate.

Arginine↗

Effect of mutation to streptomycin resistance on amber suppressor genes.

Three classes of nonidentical streptomycin-resistant mutations were distinguished in Escherichia coli by their effect on the efficiency of suppression by an amber suppressor gene, sup E. The first class of mutation caused a strong restriction in efficiency of suppression of an amber codon in various cistrons of phage lambda and in an alkaline phosphatase structural gene of E. coli. The second class caused weak restriction, and the third class caused no restriction. The restrictive effect of the streptomycin resistance mutation of the first class on the sup E gene was reduced by addition of streptomycin. This mutation had little effect on efficiencies of suppression by amber suppressor genes sup D and sup F. Analyses on the alkaline phosphatase formed in the suppressor strain indicated that mutation to restrictive streptomycin resistance causes a reduction in translation of the amber codon in the alkaline phosphatase structural gene.

Alkaline Phosphatase↗

Application of AMBER in single- and dual-energy digital imaging: improvement in noise level and display dynamic range.

The combination of computed radiography (CR) and advanced multiple beam equalization radiography (AMBER) was evaluated for both single- and dual-energy chest radiography. The improved signal-to-noise ratio found with CR and AMBER resulted in a better visualization of structures in the mediastinum and basal lung than that found with CR alone. For the central lung, no improvement was seen. Because of the compressed dynamic range with CR and AMBER, contrast on hard copies and video monitors could be high without a sacrifice in image latitude. Dual-energy images showed a considerably lower noise level. The combined use of AMBER and CR promises to overcome the dynamic range limitations of digital displays while improving signal-to-noise ratio.

Artifacts↗

An amber suppressor of Escherichia coli strain KO1.

The suppression characteristics of Escherichia coli strain KO1 have been investigated. The growth patterns of nonsense mutants of RNA (GA and f2) and DNA (lambda and T4) phages suggested that KO1 carried an amber, but not ochre or opal suppressors. The comparison of KO1 with previously identified amber suppressors indicated that KO1 differed from su1, su3 and su6 in its suppression pattern. KO1 and su2 shared some properties in common, for instance, their ability to suppress GA amber mutants with one exception (amN20) and the restriction of suppression capacity by the strr mutation. However, the suppression efficiency of KO1 (48%) was about three times that of su2 (18%). A possibility that KO1 contained a new amber suppressor is discussed.

Coliphages↗

Mitochondrial assembly in respiration-deficient mutants of Saccharomyces cerevisiae. IV. Effects of nuclear amber suppressors on the accumulation of a mitochondrially made subunit of cytochrome c oxidase.

Earlier studies from this laboratory have shown that cytochrome c oxidase from bakers' yeast contains seven subunits, three of which are made in the mitochondrion (Mason, T. L., and Schatz, G. (1973) J. Biol. Chem. 248, 1355). Moreover, a cytochrome c oxidase-less yeast mutant (pet 494-1) was isolated which lacked one of the mitochondrially made subunits (Ebner, E., Mason, T. L., and Schatz, G. (1973) J. Biol. Chem. 248, 5369). Surprisingly, the mutated gene was localized in the nucleus. The results presented here demonstrate that this mutant phenotype can be suppressed by nuclear amber suppressors which affect translation on cytoplasmic ribosomes. This fact was established by two methods, (a) By constructing pet 494-1 strains possessing various amber and ochre markers, isolating respiring revertants from these strains, and demonstrating co-reversion of the amber (but not of the ochre) markers. (b) By coupling the pet 494-1 allele with the well characterized amber suppressor gene SUP 4-3. These data show that suppressor genes located on nuclear chromosomes may control the accumulation of a mitochondrially synthesized polypeptide. The present results also allow some tentative conclusions about the mechanism of the pet 494 mutation. Because it is highly unlikely that the cytoplasmic and the mitochondrial translation system share a common suppressor, the pet 494 locus probably does not code for the missing mitochondrially made subunit, but for a cytoplasmically made protein. This as yet unidentified protein seems to control the synthesis or the integration of the mitochondrially made subunit. Nuclear suppressor genes may thus be useful tools for studying the role of cytoplasmic protein synthesis in mitochondrial formation.

Alleles↗

[The Kodak AMBER imaging system--a new approach to lung imaging].

The exposure range of X-ray films is often too small for objects with large absorption differences. This holds true also for wide latitude films. The large absorption differences can be equalized with the Kodak AMBER Imaging System by means of local exposure control. The AMBER System is a variation of the slit technique, where the narrowly collimated beam is divided into 21 beam segments the intensity of which is controlled in relation to the absorption in the object. This results in radiographs which are well exposed in the lung parenchyma and the mediastinum. An AMBER System has been routinely used for chest radiography in the Klinikum Mannheim since April 1990. The radiographs with the AMBER-Systems show an improved image quality especially in the mediastinum and the thorax wall resulting in a gain in diagnostic information.

Humans↗

[Effect of mutations in Escherichia coli genes PolAm RecA, RecB and RecC on the frequency of genetic recombination in amber-mutants involving the early genes of bacteriophage T4].

Effects of mutations in genes PolA, RecA, RecB and RecC of Escherichia coli on the recombination frequencies between rII markers of T4 have been studied in conditions of partial inhibition of some early functions. It was found that the presence of the mutations in genes PolA or RecA decreased significantly the recombination frequency of phage amber mutant in the gene 43 (DNA polymerase), increased it in the case of amber mutation in the gene 46 (exonuclease) and had no effect on the recombination of amber mutants in genes 30, 32, 33, 41, 42, 45, 44, 52. None of the amber mutants studied changed recombination frequencies in the presence of the mutations in genes RecB or RecC. Possible mechanisms of some of the effects observed are discussed.

Coliphages↗

Stability of ampicillin trihydrate suspension in amber plastic oral syringes.

The stability of ampicillin trihydrate oral suspension stored in amber plastic oral syringes was studied. Commercially available ampicillin trihydrate powder for oral suspension was reconstituted according to manufacturer's instructions and drawn into 5-mL amber polypropylene plastic oral syringes. The syringes were divided into groups and stored at -20, 4, 25, 60, or 80 degrees C. Powder from two additional lots was similarly reconstituted and packaged and stored at 80 degrees C only to assess interlot variability. Immediately after reconstitution and at specified times during storage, three syringes at each storage temperature were removed and their contents analyzed for ampicillin trihydrate concentration by a spectrophotometric assay. Samples stored at frozen (-20 degrees C) or refrigerated (4 degrees C) temperature retained at least 90% of the initial ampicillin concentration throughout the 47-day study period. Samples stored at room temperature retained at least 90% of the initial ampicillin concentration for 30 days and exhibited an apparent zero-order degradation rate. Samples stored at heated temperatures (60 and 80 degrees C) exhibited an apparent first-order degradation process, with the concentration of ampicillin decreasing to less than 90% of initial concentration within two hours. Reconstituted ampicillin trihydrate powder for oral suspension is stable for at least 30 days when stored at room, refrigerated, or frozen temperature in the amber plastic oral syringes studied. The expiration dates recommended by the manufacturer for ampicillin trihydrate suspension stored in its original container can also be used for reconstituted suspension stored in these amber plastic syringes.

Ampicillin↗

[The AMBER thoracic imaging system in routine diagnosis].

After installation of an Amber lung x-ray imaging system the range of application of this technique was registered for two months. Additionally the image quality for structures of the lung parenchyma and mediastinum were proved and dose measurements were performed. 50.6% (772) patients from a total of 1525 could be x-rayed by the Amber imaging system. Related to all people able to stand 73.6% from 1049 patients were examined with the Amber system. Most of the imaging figures of merit specified by the German national physician board were accomplished, besides the fact that 1/3 of the p.a. radiographs were cut off at the side because of the small size of the film. The excellent image of pleuro-mediastinal structures was proofed quantitatively by counting the pleuro-mediastinal lines and comparing the results with standard radiographs. Measuring the exposure at entrance point we obtained nearly the same values for the Amber system using a screen-film combination with a speed of 400 and conventional radiographs (40-120 mu Gy; 21 pat.).

Evaluation Studies as Topic↗

DNA changes in tissues entrapped in plant resins (the precursors of amber).

There have been many reports characterizing DNA from amber, which is a fossil version of plant resin. Here we report an investigation of the effects of plant resin (from Pseudotsuga menziesii) and drying conditions on the preservation of DNA in biological tissues. We examined the degree of degradation of the DNA by agarose gel electrophoresis of extracted DNA, by polymerase chain reaction, and by DNA sequencing. The plant resin alone appeared to cause little or no damage to DNA. Tissue immersed in plant resin that dried rapidly (exposed to sunlight) contained DNA with little apparent damage. Tissue immersed in the resin that was dried slowly (in shade without sunlight) contained DNA with some degradation (3.5% nucleotide changes). The tissue that was immersed in the resin that was constantly hydrated (by immersion in water) yielded DNA that was severely damaged (50-62% nucleotide changes). Transversions outnumbered transitions in these samples by a ratio of 1.4 : 1. A piece of Baltic amber immersed in water for 5 days appeared to be impervious to the water. Thus amber inclusions that initially dried rapidly have the potential to yield undamaged DNA. Those that dried slowly may contain damaged DNA and may be unsuitable for phylogenetic and other studies.

Amber↗

Problems of reproducibility--does geologically ancient DNA survive in amber-preserved insects?

Apparently ancient DNA has been reported from amber-preserved insects many millions of years old. Rigorous attempts to reproduce these DNA sequences from amber- and copal-preserved bees and flies have failed to detect any authentic ancient insect DNA. Lack of reproducibility suggests that DNA does not survive over millions of years even in amber, the most promising of fossil environments.

Amber↗

Extinction and biogeography in the Caribbean: new evidence from a fossil riodinid butterfly in Dominican amber.

We describe a new species of extinct riodinid butterfly, Voltinia dramba, from Oligo-Miocene Dominican amber (15-25 Myr ago). This appears to be the first butterfly to be taxonomically described from amber, and the first adult riodinid fossil. The series of five specimens represents probably the best-preserved fossil record for any lepidopteran. The phenomenon of extant Voltinia females ovipositing on arboreal epiphytes probably explains the discovery of multiple female V. dramba specimens in amber. Voltinia dramba appears to be one of many extinct butterfly species on Hispaniola. The northwestern Mexican distribution of the explicitly hypothesized sister species, the extant V. danforthi, supports the hypothesis that V. dramba reached Hispaniola by the 'proto-Greater Antillean arc', dating the divergence of V. dramba and V. danforthi to 40-50 Myr ago. This date is contemporaneous with the oldest known butterfly fossils, and implies a more ancient date of origin for many of the higher-level butterfly taxa than is often conceded.

Amber↗

Characterization of an amber mutation in the structural gene for ribosomal protein L15, which impairs the expression of the protein export gene, secY, in Escherichia coli.

We have previously described a temperature-sensitive mutant, ts215, which is defective in protein secretion. Complementation studies indicated that the mutation was located at the distal part of the spc ribosomal protein operon and the gene secY is required for efficient protein secretion. We now report a more complete genetic and biochemical analysis of the ts215 mutant. These studies revealed that the ts215 mutant has an amber mutation in the gene rp10 for ribosomal protein L15, which is located upstream and adjacent to secY. The amber mutation exerts a polar effect on secY causing a defect in protein secretion. These conclusions were supported by the following observations. The mutant strain carries a phi 80 prophage containing a temperature-sensitive suppressor, supFts6. The strain contains decreased amounts of L15 and is suppressible by a temperature-independent nonsense suppressor. In addition, L15 contains an extra tyrosine residue when suppressed by supF. DNA sequence analysis revealed the presence of a single base change in rp10 resulting in an amber codon at the 38th codon of L15. The mutant phenotype is complemented by a plasmid carrying only the secY gene under lac promoter control. The mutant cells complemented by secY can grow and synthesize proteins at normal rates and abundances at 42 degrees C, despite the fact that their ribosomes contain barely detectable levels of L15. These results indicate that ribosomal protein L15 is dispensable for protein synthesis and cell growth. In contrast, the decreased level of expression of the secY gene leads to defective protein secretion and defective cell growth.

Electrophoresis, Polyacrylamide Gel↗