Conformational requirement of signal sequences functioning in yeast: circular dichroism and 1H nuclear magnetic resonance studies of synthetic peptides

Recently, we have designed a series of simplified artificial signal sequences and have shown that a proline residue in the signal sequence plays an important role in the secretion of human lysozyme in yeast, presumably by altering the conformation of the signal sequence [Yamamoto, Y., Taniyama, Y., & Kikuchi, M. (1989) Biochemistry 28, 2728-2732]. To elucidate the conformational requirement of the signal sequence in more detail, functional and nonfunctional signal sequences connected to the N-terminal five residues of mature human lysozyme were chemically synthesized and their conformations in a lipophilic environment [aqueous trifluoroethanol (TFE) or sodium dodecyl sulfate micelles] analyzed by circular dichroism (CD) and 1H nuclear magnetic resonance (NMR) spectroscopy. The helix content of the peptides, including functional (L8, CL10) and nonfunctional (L8PL, L8PG, L8PL2) signal sequences, was estimated from CD spectra to be 40-50% and 60-70%, respectively, indicating that the helical structure is more abundant in the nonfunctional signal sequences. Two-dimensional NMR analyses in 50% TFE/H2O revealed that each peptide adopted a helical conformation throughout the sequence except for a few residues at the N- and C-termini. Furthermore, H-D exchange experiments indicated that the helical structure of the C-terminal region of the functional signal sequences (L8 and CL10) was less stable than that of the nonfunctional signal sequences (L8PL and L8PL2). On the basis of these results, a model was developed in which the functional signal sequence is inserted in the membrane with a helical conformation and the C-terminal helix unraveled in an extended conformational form through an interaction with the signal peptidase.

Enzymatic synthesis of pyrene-labeled polyphosphoinositides and their behavior in organic solvents and phosphatidylcholine bilayers

A method is reported for the synthesis of pyrene-labeled analogues of phosphatidylinositol 4-phosphate (Pyr-PIP) and phosphatidylinositol 4,5-biphosphate (Pyr-PIP2) from sn-2-(pyrenyl-decanoyl)phosphatidylinositol (Pyr-PI) using partially purified PI and PIP kinase preparations. Phosphorylation of Pyr-PI and Pyr-PIP was extensive (more than 50%) provided that the ATP concentration was high and that stabilizing agents such as sucrose and polyethylene glycol were present in the incubation medium. Pyr-PIP and Pyr-PIP2 were isolated by chromatography on immobilized neomycin. The identity of the products was established by thin-layer chromatography, UV-absorption spectroscopy, and spectrofluorometry. The pyrene excimer/monomer fluorescence technique revealed that, in contrast to Pyr-PI, Pyr-PIP and Pyr-PIP2 formed clusters in organic solvents. By use of the same technique for model membranes, it was shown that in phosphatidylcholine bilayers the collision frequency of the three fluorescent phosphoinositides decreased in the order PI greater than PIP greater than PIP2. Addition of Ca2+ at concentrations above 0.1 mM increased the collision frequency of Pyr-PIP2 and, to a much lesser extent, Pyr-PIP; Ca2+ had no effect on Pyr-PI.

The redox-cycling assay is not suited for the detection of pyrroloquinoline quinone in biological samples

Based on the results of the so-called redox-cycling assay it has been claimed that various common foods and beverages as well as mammalian body fluids and tissues contain substantial quantities (microM) of free PQQ [M. Paz et al. (1989) in: PQQ and Quinoproteins (J.A. Jongejan and J.A. Duine, eds.) Kluwer Academic Publishers, Dordrecht, pp. 131-143 and J. Killgore et al. (1989) Science 245, 850-852]. However, by investigating samples from such sources with a biological assay of nM sensitivity, we could not confirm these claims. Analysis of the samples with procedures that proved adequate for the detection of PQQ adducts and conjugates gave equally negative results. To account for the positive response in the redox-cycling assay, as opposed to the negative results obtained by other methods, a search was made for those substances in these samples that caused the false-positive reactions. It was found that a number of commonly occurring biochemicals like ascorbic and dehydroascorbic acid, riboflavin and to a lesser extent pyridoxal phosphate, gave a positive response in the redox-cycling assay. The amounts of these interfering substances that were determined in the samples by independent methods could well explain the response. In separate experiments it was found that the effect of PQQ added to biological samples was obscured over an appreciable range of concentrations. For these reasons it must be concluded that the redox-cycling assay is not suited for the detection of PQQ in these samples. Any claims that are based on the results of this method should be disregarded.

Acid helix-turn activator motif

A common sequence/structural motif pattern has been identified within the steroid/thyroid hormone receptors and other transcriptional activators using a new massively parallel symbolic learning assistant computer system. The pattern appears nearly diagnostic of transcription activation, including relative activation strength, among nuclear and DNA-binding prokaryotic proteins. In cases where mutation/deletion/chimeric studies have identified the activation domain, the pattern matches within that domain. These facts and the nature of the pattern itself strongly support the idea that the patterned domain is directly involved in a protein-protein transcription activation interaction.

[Determination of the benzo(a)pyrene content of microbial biomasses and protein feed]

A method for the fluorimetric determination of benzo(a)pyrene content is presented consisting of classical clean-up steps. The method was applied to microbial biomasses and different feed stuffs. The investigated yeasts grown on carbohydrates keep the limit of 5 ppb benzo(a)-pyrene recommended by the IUPAC. Yeast samples of the VEB Petrolchemisches Kombinat Schwedt grown on petroleum distillate have a constant quality with benzo(a)pyrene contents at 1 ppb. A selection of bacterial biomasses shows also contents less than 5 ppb. The benzo(a)pyrene contents of biomasses cultivated on liquid manure exceed the given limit.

Biotin analysis of commercial vitamin and other nutritional supplements

Because previous observations suggest that biotin may be present in vitamin preparations not labeled as containing biotin, we determined the biotin content of several over-the-counter vitamin and nutritional supplements said to contain biotin (group 1) and several in which biotin content was not specified (group 2). Biotin concentration was measured using the 125I-avidin assay which detects total avidin-binding substances. Water extracts were assayed for free biotin and acid hydrolysates were assayed for total biotin. The results of the 125I-avidin assay agreed with the stated biotin content for most vitamin and nutritional supplements in group 1. Biotin was the only avidin-binding substance in the preparations from group 1, based on reversed-phase chromatography. However, some vitamin and nutritional supplements in group 2 contained nutritionally significant amounts of biotin, particularly if the supplement contained liver or yeast extract. Total biotin was significantly higher than free biotin in one supplement; the difference was attributable to release of biotin rather than a biotin analog. We conclude that biotin may be present in some vitamin and nutritional supplements not labeled as containing biotin; biotin intake might be under-estimated if the subject is receiving a nutritional supplement containing extracts of liver or yeast.

Computer-controlled discontinuous rotating gel electrophoresis for separation of very large DNA molecules

The newly designed equipment for alternating field gel electrophoresis which permits the separation of very large DNA molecules and the simultaneous analysis of up to 35 samples is described. The field alternation is effected by intermittently rotating the submerged agarose gel by optitional angles. The time intervals between changes of position are controlled by a computer program driving a simple switching device which was designed to suit any technique using periodic switching or inversion of the electrical field. Because the electrophoresis unit provides an absolutely homogeneous electrical field, no distortion of migration lanes occurs and the resolution is very good. Moreover, by using a switching time interval gradient an almost perfect linear relationship between migration distances and molecule sizes in the range of about 100-1250 kilobase pairs is observed. In two-dimensional separations, different switching time programs for the first and second dimension allow maximum resolution of selected size ranges. Field inversion gel electrophoresis is possible as well. The performance of the method is demonstrated by comparing the chromosome sizes of different yeast strains.

SDS-PAGE protein patterns of yeasts from human sources

Protein patterns of Candida species and other yeasts have been studied by sodium dodecyl sulphate polyacrylamide gel electrophoresis. Although differences in patterns occur which tend to separate the species, variability between replicate samples is sometimes high. The method cannot be used for speciation of common yeasts from medical sources.

On the relations between the elemental surface composition of yeasts and bacteria and their charge and hydrophobicity

The elemental surface composition of eleven microorganisms was determined by X-ray photoelectron spectroscopy. Bacteria could be distinguished from yeasts by higher nitrogen and phosphate concentrations. Overall physico-chemical properties, electrical charge and hydrophobicity, were also investigated: the former by electrophoretic mobility measurements, the latter by contact angle and by hydrophobic interaction chromatography. Phosphate plays the major role in determining the surface electrostatic charge. A correlation is observed between the N/P atomic concentration ratio and the electrostatic charge. In bacteria, hydrophobicity is directly related to concentration of carbon in hydrocarbon form and inversely related to oxygen concentration or to the N/P ratio. For yeasts, a positive correlation is found between hydrophobicity and the N/P ratio, pointing at the role of proteins in determining the hydrophobicity.

The determination of selenomethionine in selenium yeast by cyanogen bromide gas chromatography

A new method for the determination of bonded selenomethionine in selenium yeast by gas chromatography is established. Bonded selenomethionine is rapidly and precisely determined by measuring CH3SeCN released during the reaction of selenoprotein with CNBr (CNBr-GC method). Conditions for the reaction and chromatography are described. The results of CNBr-GC are compared with those obtained by acid hydrolysis/ion exchange chromatography. This new method has the advantage of being accurate, sensitive and selective.

Glutathione and glutathione metabolizing enzymes in yeasts

Total glutathione content, glutathione peroxidase, glutathione transferase and glutathione reductase activities have been measured in 12 species of yeasts. All the strains tested contained glutathione, though in different amounts, as well as the above mentioned enzymes. To discriminate between the selenium-dependent and the selenium-independent form, glutathione peroxidase activity has been measured with both H2O2 and cumene hydroperoxide. Rhodotorula glutinis appeared to be the only strain in which the selenium-dependent form was not found, but this yeast exhibited the highest level of selenium-independent glutathione peroxide activity as compared to the other strains.

NAD(P)H-dependent 6'-deoxychalcone synthase activity in Glycyrrhiza echinata cells induced by yeast extract

The crude extract prepared from Glycyrrhiza echinata cells treated with yeast extract catalyzed the formation of liquiritigenin (5-deoxyflavanone) and isoliquiritigenin (6'-deoxychalcone) in addition to naringenin (5-hydroxyflavanone) when incubated with 4-coumaroyl-CoA and malonyl-CoA in the presence of high concentrations (0.1 mM or higher) of NADPH. Incubation without NADPH, or with low concentrations (0.01 mM or lower), gave only naringenin as a reaction product. With NADH (1 mM), the major product was naringenin accompanied by a small quantity of liquiritigenin. The initial product of the assay with 1 mM NADPH was isoliquiritigenin, indicating a reaction catalyzed by 6'-deoxychalcone synthase (DOCS). Subsequent formation of liquiritigenin was attributed to the presence of chalcone isomerase in the crude extract. The results constitute the first demonstration in vitro of DOCS activity which, in G. echinata cells and other leguminous plants, is involved in the biosynthesis of retrochalcone and 5-deoxyisoflavonoid-derived phytoalexins.

[Quantitative evaluation of storage substances (lipids and glycogen) in resting yeast cells on replicas obtained by freeze etching]

A method is proposed for evaluating the intracellular quantity of storage substances (lipids and glycogen) in dormant cells, on the basis of a stereological analysis of the electron-microscopic image of cross-sectioned freeze-etched cells.

A simple method for extraction of DNA from fungi and yeasts with anhydrous hydrogen fluoride

A novel method is described for the extraction of DNAs from fungi and yeasts. Anhydrous hydrogen fluoride (HF) selectively cleaves their cell walls under mild conditions (for 5 min at 0 degrees C), enabling the effective extraction of DNAs from organisms with a cell wall. A possible mechanism for this method concerning the selective cleavage of O-glycosidic linkages in cell walls has been described previously [(1977) Anal. Biochem. 82,289-309]. The extracted DNA is intact: in fact, the yeast DNA is directly applicable for restriction analysis and transformation of Escherichia coli.

Purification of elongation factor 2 from human placenta and evidence of its fragmentation patterns in various eukaryotic sources

While preparing human placenta elongation factor 2 (EF-2), whose purification and some molecular properties are reported, we noticed the presence of numerous protein fractions which did not have EF-2 activity, but were ADP-ribosylated by diphtheria toxin in the presence of NAD+. All these proteins, like EF-2, were selectively retained by a heparin-Sepharose column, which we used as an affinity-chromatography step. This was also observed when EF-2 was prepared, by this purification step, from other sources, i.e. ox liver and two species of yeasts. In order to assess whether these proteins were a degradation product of EF-2, independent proteins or a mixture of both, they were analysed by subjecting them, after [14C]ADP-ribosylation, to exhaustive trypsinolysis. Only one radioactive peptide was found, thus suggesting that those proteins originate from EF-2 by some proteolytic process. Our findings indicate that this proteolysis does not occur after cell disruption, but is more or less active in the intact cell, depending on the system considered.

Distribution of immunoreactive glia maturation factor-like molecule in organs and tissues

Using the monoclonal antibody G2-09 raised against bovine glia maturation factor (GMF), we screened various rat organs and tissues for GMF-like immunoreactivity. In the adult animal, with the exception of the heart, GMF was found exclusively in the nervous system, with the cerebellum exhibiting higher specific activity than other brain regions. The nature of the immunoactivity in the heart is presently unclear. None of the body fluids collected from humans, including serum and cerebrospinal fluid, possessed detectable GMF immunoactivity. A phylogenetic comparison revealed the presence of GMF in the brain of al vertebrates studied, from fish to primates. GMF was absent from bacteria and yeast. An ontogenetic study on rats showed the highest GMF level in the fetal brain, with a gradual but steady decrease after birth. However, a substantial amount of GMF persisted even in older animals. GMF was localized in astrocytes and Bergmann glia in the rat brain, using immunostaining at the light microscopic level.

Intensity and anisotropy decays of the Wye base of yeast tRNA(Phe) as measured by frequency-domain fluorometry

The intensity and anisotropy decays of Wye base fluorescence from yeast tRNA(Phe) were determined by frequency-domain fluorometry. The intensity decay is at least a double exponential in the presence and absence of Mg2+, but the multi-exponential character of the decay is more pronounced in the absence of Mg2+. The anisotropy decay displays components due to overall tRNA rotational diffusion and to local torsional motions. The amplitude of the local motion is decreased 2-fold by the presence of Mg2+. The results are broadly consistent with a more homogeneous environment for the Wye base in the presence of Mg2+.

Orthogonal-field-alternation gel electrophoresis banding patterns of DNA from yeasts

Chromosomal DNAs from various yeast species were separated by orthogonal-field-alternation gel electrophoresis (OFAGE). To this end we developed a spheroplasting and lysis method to obtain intact DNA from both ascomycetous and basidiomycetous yeasts. The OFAGE banding patterns of 22 ascomycetous and four basidiomycetous yeast strains were compared. The strains represented species from the genera: Brettanomyces, Candida, Cryptococcus, Filobasidiella, Geotrichum, Hansenula, Kluyveromyces, Pachysolen, Pichia, Rhodosporidium, Rhodotorula, Saccharomyces, Saccharomycodes, Saccharomycopsis, Schizosaccharomyces and Zygosaccharomyces. Variations occurred in the number of bands and their positions in the gel, not only among strains of different genera but also among species from the same genus and even between varieties of the same species. The ascomycetous yeasts, with the exception of Saccharomyces cerevisiae, only showed one to five bands of DNA larger than 1000 kilobase pairs (kb) in general none smaller. The patterns of the four basidiomycetous yeasts revealed also a few large DNA bands but in addition one to six bands ranging in size from 500 to 1000 kb, with the exception of a single smaller chromosome in Rhodotorula mucilaginosa. From the OFAGE banding patterns of strains studied here it appears that in Sacch. cerevisiae the partitioning of DNA over chromosomes is unique. But rather than the large number of chromosomes, the presence of four chromosomes with less than 500 kb of DNA is characteristic for Sacch. cerevisiae.

Homologous ribosomal proteins in bacteria, yeast, and humans

We describe sequences of two human ribosomal proteins, S14 and S17, and messenger RNAs that encode them. cDNAs were used as molecular hybridization probes to recognize complementary genes in rodent, Drosophila, and yeast chromosomal DNAs. Human ribosomal protein sequences are compared to analogous Chinese hamster, yeast, and bacterial genes. Our observations suggest that some ribosomal protein genes have been conserved stringently in the several phylogenetic lines examined. These genes apparently were established early in evolution and encode products that are fundamental to the translational apparatus. Other ribosomal protein genes examined, although similar enough to heterologous DNA sequences to indicate their structural relationships, appear to have diverged substantially during evolution, probably reflecting adaptations to different genetic environments.

On the sequence homology of the ribosomal proteins, Escherichia coli S11, yeast rp59 and Chinese hamster S14

A strong sequence homology was found among the ribosomal proteins of the different species, S11 of Escherichia coli, rp59 of Saccharomyces cerevisiae and S14 of Chinese hamster ovary cell. The significance of this series of highly conserved proteins is discussed.

A small-scale five-hour procedure for isolating multiple samples of CsCl-purified DNA: application to isolations from mammalian, insect, higher plant, algal, yeast, and bacterial sources

A rapid and simple procedure is described for obtaining CsCl-purified DNA from multiple small samples of cells or tissue. The DNA is recovered in a high-molecular-weight form (greater than or equal to 50 kb) that is readily cleaved with restriction enzymes. Sufficient quantities of DNA (10-50 micrograms) are recovered to allow multiple analyses by Southern blotting and most cloning procedures. The isolation procedure involves addition of intact cells or powders of frozen tissues directly to a simple lysis buffer containing detergent (sodium dodecyl sulfate or sodium sarcosinate) and high concentrations of EDTA. Ultra-high-speed centrifugation of CsCl gradients allows the isolation of DNA from 10 different samples in as little as 5 h. Applications are described for mammalian cells (HeLa cells), insect tissues (Drosophila melanogaster adults and pupa, Manduca sexta pupa, and Musca domestica pupa), higher plant tissues (Vicia faba leaves and meristems), algal cells (walled and wall-less Chlamydomonas reinhardi), yeast cells (Saccharomyces cerevisiae), and bacterial cells (Escherichia coli spheroplasts for preparation of both chromosomal and plasmid DNA). The procedure can be scaled up with larger sample sizes and longer centrifugation times to provide bulk quantities of DNA.

[The chemical composition of "zymosans" from yeasts]

The chemical composition of "Zymosanes" (complex cell-wall-polysaccharides), prepared by different methods from Baker's yeast, were analyzed by classical and modern techniques, e.g. GLC and TLC. They are very complex natural products consisting of a basic structure of polysaccharides, which proteins and different lipids are bound to. Higher purified zymosanes seem to be free from nucleic acids and do not contain sialic acid.

[Primary and spatial structure of tRNA]

The recent achievements in studying of structure of tRNA are considered in the present paper. A brief analysis of the new methods for sequencing tRNA was carried out. Due to the development of these methods about 300 tRNA primary structures have been determined. Comparison of the primary tRNA structures gives us the possibility to divide them into seven classes: prokaryotic initiator tRNAs and eukaryotic initiator tRNAs; prokaryotic elongator tRNAs and eukaryotic elongator tRNAs; archaebacterial tRNAs; and mitochondrial tRNAs of lower and higher eukaryotes. Structural properties of the tRNAs of each of these classes are discussed. The second part of the paper is devoted to the three-dimensional structure of tRNA. Recent data in this field obtained by X-ray crystallographic technique as well as by high-resolution NMR and chemical modification methods are reviewed.

[Thallium in wine--trace element vinogram of thallium]

The ultra trace element Thallium is regularly found in very low quantities in wine, in red wines with 0.2 micrograms T1/1 about twice as much as in white wines. Certain hints the origin and behaviour of such low T1-contents can be derived from additional investigations (soil, location, fertilizer, influence of wine making). A correlation between T1 and K is known, but above that it can be shown, that similarly to Rb certain parts of the grape (grape, flesh, peel) are richer in T1 and that thereby the higher content of T1 in red wines can be explained. Slightly higher T1-levels are found in wines which grow next to cement plants or on abandoned mines. The Anodic Stripping Voltammetry in EDTA-containing base solution has proved effective for the determination of very low levels in the investigated samples. Wine and similar samples are decomposed with H2SO4-H2O2. After extraction as T1(III) bromide Thallium is measured by anodic-stripping-voltammetry. The preceding separation of T1 from soil samples or the like is achieved by evaporation analysis.

Tertiary structure of tRNAPhe. A possible correlation between the structural functional unit of this tRNA and its exonic sequence

It has been shown recently [Go (1981) Nature (London) 291, 90-92; Blake (1983) Trends Biochem Sci. 8, 11-13] that the exonic regions of the genes of proteins haemoglobin, lysozyme and immunoglobin correspond closely to the compactly folded structural units. Despite the absence of classical domain structures in tRNA compared with those found in several proteins, close inspection of certain features in the distance maps obtained for yeast tRNAPhe using the conformationally equivalent heminucleotide scheme reveals that a similar situation might also be present in ribonucleic acids such as tRNA species and the exonic sequences of their genes. Also it seems possible that certain segments of yeast tRNAPhe may be characterized as possessing a domain-like character, and this seems to provide stereochemical support for possible conservation of L-shape structure for tRNA species lacking the entire dihydrouridine arm such as those found in mitochondria.

Phenylalanine transfer RNA: molecular dynamics simulation

Yeast phenylalanine transfer RNA was subjected to a 12-picosecond molecular dynamics simulation. The principal features of the x-ray crystallographic analysis are reproduced, and the amplitudes of atomic displacements appear to be determined by the degree of exposure of the atoms. An analysis of the hydrogen bonds shows a correlation between the average length of a bond and the fluctuation in that length and reveals a rocking motion of bases in Watson-Crick guanine X cytosine base pairs. The in-plane motions of the bases are generally of larger amplitude than the out-of-plane motions, and there are correlations in the motions of adjacent bases.

Chemical changes in cell wall structure of five strains of Paracoccidioides brasiliensis

Differences in cell wall structure of Paracoccidioides brasiliensis strains isolated from localized or disseminated cases of paracoccidioidomycosis and from soil emphasize the importance of standardization if results obtained in different laboratories are to be compared.

Molecular aspects of fungal dimorphism

The approach to this article will be the review of experimental developments achieved in recent years in the fields of biochemistry, molecular biology, ultrastructure, etc. and that have suggested models and hypothesis in order to understand the regulation of the molecular mechanisms involved in fungal differentiation. Since fungal dimorphism has been seen by many investigators as a useful model of differentiation in eukaryotic systems, and also because of the prevalence of dimorphism among human pathogenic fungi, we have considered relevant to review the work done in Mucor, but also in dimorphic pathogenic fungi such as Paracoccidioides brasiliensis, Histoplasma capsulatum, Candida albicans, Blastomyces dermatitidis, and Sporothrix Schenckii. From this point of view, the involvements of cyclic nucleotides, nucleic acid polymerases, synthesis of macromolecules, synthesis of cell wall and less studied factors will be reviewed.

[Determination of free and bound ergosterol in microorganisms]

A method for the quantitative determination of free and esterified ergosterol in lipid fractions from biomasses grown on hydrocarbons as sole carbon source is described. Column chromatography was used for the fractionation of lipids. Esterified ergosterol was determined in the benzene fraction and free ergosterol in the methanol fraction by known methods.

[Two-dimensional polyacrylamide gel electrophoresis in the study of yeast mitochondrial transfer RNA]

An improved system of tRNA fractionation by two-dimensional polyacrylamide electrophoresis with high resolution power and also methods of visualization and identification of fractioned tRNAs are given. The system was used for studying mitochondrial tRNAs and their precursors.

Role of RNA structure in splicing: excision of the intervening sequence in yeast tRNA3leu is dependent on the formation of a D stem

A substitution mutant of the yeast tRNA3leu gene results in the sequence change of GCC to AAA at positions 10, 11, and 12 in the noncoding strand. The ability to form a D stem is lost. Transcription in the heterologous Xenopus germinal vesicle system is not drastically affected, but splicing of the tRNA precursor does not occur. To determine whether this effect is caused by the change in sequence or the change in conformation we constructed two new mutants. In one, mutation results in the sequence change of GGC to TTT at positions 24, 25, and 26. The ability to form a D stem is lost; transcription is unaffected, but excision of the intron does not occur. The other, a double mutant, is characterized by both substitutions described above, and the ability to form a D stem is retained. The precursor derived from the double mutant is accurately spliced in X. laevis germinal vesicle extracts, therefore excision of the intervening sequence appears to depend on the formation of a D stem.

Binding of yeast tRNAPhe anticodon arm to Escherichia coli 30 S ribosomes

A 15-nucleotide fragment of RNA having the sequence of the anticodon arm of yeast tRNAPhe was constructed using T4 RNA ligase. The stoichiometry and binding constant of this oligomer to poly(U)-programmed 30 S ribosomes was found to be identical to that of deacylated tRNAPhe. The anticodon arm and tRNAPhe also compete for the same binding site on the ribosome. These data indicate that the interaction of tRNAPhe with poly(U)-programmed 30 S ribosomes is primarily a result of contacts in the anticodon arm region and not with other parts of the transfer RNA. Since similar oligomers which cannot form a stable helical stem do not bind ribosomes, a clear requirement for the entire anticodon arm structure is demonstrated.

Codon-induced transfer RNA association. A property of transfer RNA involved in its adaptor function?

It is shown by equilibrium sedimentation that the binding of cognate codons to tRNAPhe (yeast), tRNAPhe (Escherichia coli), tRNALys, tRNAfMet and of the wobble codon UUU to tRNAPhe (yeast) induces dimerization of codon transfer RNA complexes. Analysis of the sedimentation profiles with a quantitative evaluation of the coupling between sedimentation and association equilibrium provides dimerization constants in the range from 1 X 10(4) to 6 X 10(4) M-1. These results on various tRNAs from different organisms suggest that the codon-induced tRNA association is a general phenomenon. Probably the codon-induced tRNA association facilitates the aminoacyl transfer reaction.

Synthesis of the 5'-half molecule of yeast alanine tRNA

In this paper, we report the synthesis of the 5'-half molecule of yeast alanine tRNA (tRNAAlay) by ligating three oligonucleotide fragments corresponding to the nucleotide sequences 1-13, 14-22 and 23-35 respectively under the catalysis of T4 RNA ligase (Fig. 1). Because of the high purity of the oligonucleotide fragments and the excellent quality of T4RNA ligase and polynucleotide kinase we prepared, the isolation steps were simplified and the overall yields were much higher. The ligating yield of the docosamer (IV) was 75%, that of the pentatriacontamer (V), 90%, and the isolated yield of the final product was 21% calculated on the basis of the tridecamer (III) used in the first reaction. Under the action of T4 RNA ligase the synthetic 5'-half molecule was joined with the natural 3'-half molecule forming a semi-synthetic tRNAAlay, which possessed the biological activities of both accepting (3H)-alanine and incorporating it into proteins. The correctness of the structure of the synthetic 5'-half molecule was verified by both chemical analysis and biological activity assay.

Assay of biological activity of synthetic yeast alanine transfer RNA (tRNAAlay)

The biological activity of the synthetic tRNAAlay was studied with an extremely sensitive method. tRNAAlay accepted alanine in the presence of rat liver aminoacyl-tRNAAlay-synthetase (this was called the accepting activity). The aminoacylated tRNAAlay was conveniently precipitated by ethanol with good recovery. The efficiency of transferring alanine from the aminoacylated tRNAAlay into the protein was determined in in vitro rabbit reticulocyte lysate cell-free protein-synthesizing system (this was called the incorporation activity). Both accepting and incorporation activities could be determined in one assay with only 5-7 pmoles of tRNAAlay either in ligation mixture or in purified form. Our results show that the accepting activities of the synthetic products were 51.6-65.6% and 91.3-106.0% of that of natural and reconstituted natural tRNAAlay respectively. The efficiency of the incorporation of alanine in the aminoacylated tRNAAlay into the protein was 61.6-63.1%, corresponding to 90.6-91.7% and 97.2-115.8% of that of the natural and the reconstituted natural tRNAAlay respectively.

Total synthesis of yeast alanine transfer ribonucleic acid

By a combination of chemical and enzymatic methods, small oligonucleotides with lengths varying from 2 to 8 nucleotides were synthesized from mononucleotides. The small oligonucleotides were then ligated with T4 RNA ligase into six large oligonucleotides (9 to 19 nucleotides long) which were further ligated to form two half molecules with 35 and 41 nucleotides respectively. Finally, the two synthetic half molecules were annealed and ligated to obtain the whole molecule of yeast alanine tRNA (tRNAAlay). Prior to this, two semi-syntheses were performed, i.e. ligation of the synthetic 5'-half molecule with the natural 3'-half molecule and that of the natural 5'-half molecule with the synthetic 3'-half molecule. Both the semi-synthetic tRNAAlay and the synthetic tRNAAlay occupy the same position as the natural tRNAAlay after electrophoresis on a 20% polyacrylamide gel. They have the same chemical composition (containing 9 modified nucleotides of 7 different species) and structure as the natural tRNAAlay and are biologically active, i.e. accepting and transferring alanine into proteins in a cell-free protein synthesizing system, the accepting activity of the synthetic product is 52-66% of that of the natural tRNAAlay and 91-106% of that of the reconstituted product of the two natural half molecules. The incorporation activity of alanine into proteins of the synthetic 3H-alanine tRNAAlay is 63%, corresponding to 91% of that of the natural tRNAAlay and 115% of that of the reconstituted product of the two natural half molecules. To the best of our knowledge, this is the first time that a natural RNA with biological activity is synthesized.

Synthesis of the 3'-half molecule of yeast alanine tRNA

This paper deals with the synthesis of the 3'-half molecule of yeast alanine transfer RNA (tRNAAlay) by ligation with T4 RNA ligase of three component oligonucleotide fragments corresponding to nucleotides 36-45(I), 46-57(II) and 58-76(III) in succession extending from the 3'-end to the 5'-end. First, in a ratio of acceptor to donor at 1.5 to 1, we adopted a method of three successive reactions, namely, the 5'-phosphorylation of the nonadecamer (III), ligation with the dodecamer (II) and the 5'-phosphorylation of the ligation product formed; with one isolation step and obtained the 5'-phosphorylated 31mer(46-76) (IV) in an overall yield of 70%. Then the 31mer(IV) as a donor was ligated with 3 times of decamer (I) to form the 41mer(36-76) (V), the 3'-half molecule of tRNAAlay. The yield was 67%. After 5'-phosphorylation, (V) was ligated with the natural 5'-half molecule to form the semi-synthetic tRNAAlay, which was biologically active, i.e. accepting and transferring (3H)-alanine into proteins.

The oxidation of yeast Complex III. Evidence for a very rapid electron equilibration between cytochrome c1 and the iron-sulfur center

The reoxidation of reduced cytochrome c1 by potassium ferricyanide follows pseudo-first order kinetics with k = 4 x 10(4) M-1 s-1. However, the reoxidation of this cytochrome in two-electron reduced Complex III does not follow any simple rate law although the overall rate of reaction is essentially unchanged. The observed kinetics can be well fitted with a model in which ferricyanide reacts exclusively with cytochrome c1 together with very rapid electron transfer from the reduced iron-sulfur center to cytochrome c1. Neither removal of coenzyme Q from the complex nor prior incubation with antimycin A had any effect on the observed kinetics of reoxidation.