Use of synthetic lethal mutants to clone and characterize a novel CTP synthetase gene in Saccharomyces cerevisiae

In the pyrimidine biosynthetic pathway, CTP synthetase catalyses the conversion of uridine 5-triphosphate (UTP) to cytidine 5-triphosphate (CTP). In the yeast Saccharomyces cerevisiae, the URA7 gene encoding this enzyme was previously shown to be nonessential for cell viability. The present paper describes the selection of synthetic lethal mutants in the CTP biosynthetic pathway that led us to clone a second gene, named URA8, which also encodes a CTP synthetase. Comparison of the predicted amino acid sequences of the products of URA7 and URA8 shows 78% identity. Deletion of the URA8 gene is viable in a haploid strain but simultaneous presence of null alleles both URA7 and URA8 is lethal. Based on the codon bias values for the two genes and the intracellular concentrations of CTP in strains deleted for one of the two genes, relative to the wild-type level, URA7 appears to be the major gene for CTP biosynthesis. Nevertheless, URA8 alone also allows yeast growth, at least under standard laboratory conditions.     

Two distinct P element subfamilies in the genome of Drosophila bifasciata

The genome of Drosophila bifasciata harbours two distinct subfamilies of P-homologous sequences, designated M-type and O-type elements based on similarities to P element sequences from other species. Both subfamilies have some general features in common: they are of similar length (M-type: 2935 bp, O-type: 2986 bp), are flanked by direct repeats of 8 by (the presumptive target sequence), contain terminal inverted repeats, and have a coding region consisting of four exons. The splice sites are at homologous positions and the exons have the coding capacity for proteins of 753 amino acids (M-type) and 757 amino acids (O-type). It seems likely that both types of element represent functional transposons. The nucleotide divergence of the two P element subfamilies is high (31%). The main structural difference is observed in the terminal inverted repeats. Whereas the termini of M-type elements consist of 31 by inverted repeats, the inverted repeats of the O-type elements are interrupted by non-complementary stretches of DNA, 12 by at the 5 end and 14 by at the 3 end. This peculiarity is shared by all members of the O-type subfamily. Comparison with other P element sequences indicates incongruities between the phylogenies of the species and the P transposons. M-type and O-type elements apparently have no common origin in the D. bifasciata lineage. The M-type sequence seems to be most closely related to the P element from Scaptomyza pallida and thus could be considered as a more recent invader of the D. bifasciata gene pool. The origin of the O-type elements cannot be unequivocally deduced from the present data. The sequence comparison also provides new insights into conserved domains with possible implications for the function of P transposons.     

Genetic interaction between the Ras-CAMP pathway and the Dis2s1/Glc7 protein phosphatase in Saccharomyces cerevisiae

The Saccharomyces cerevisiae DIS2S1/GLC7 gene encodes a type 1 protein phosphatase indispensable for cell proliferation. We found that introduction of a multicopy DIS2S1 plasmid impaired growth of cells with reduced activity of the cAMP-dependent protein kinase. In order to understand further the interaction between the two enzymes, a temperature-sensitive mutation in the DIS2S1 gene was isolated. The mutant accumulated less glycogen than wild type at the permissive temperature, indicating that activity of the Dis2s1 protein phosphatase is attenuated by the mutation. Furthermore, the dis2s1 ^ts mutation was shown to be suppressed by a multicopy plasmid harboring PDE2, a gene for cAMP phosphodiesterase. These results indicate that the Ras-cAMP pathway interacts genetically with the DIS2S1/GLC7 gene.     

Analysis of DNA polymerase activity in Petunia protoplasts treated with clastogenic agents

Clastogenic agents, i.e. agents that can induce chromosome or DNA breakage, have been shown to enhance the rale of direct gene transfer to protoplasts. The effect was analysed at the enzymatic level using protoplast homogenates as well as intact protoplasts. For that purpose existing procedures were modified to enable measurement of DNA polymerase in vivo. In the system used, external DNA was able to enter the cells without the addition of membrane-permeabilizing compounds. When comparing total DNA polymerase activity of protoplasts irradiated with X-rays or UV-light with that of untreated cells we did not observe significant differences. Incubation of protoplasts with high doses of bleomycin affected total DNA polymerase activity negatively. but dideoxythymidine triphosphate-sensitive activity was not influenced. We conclude that the DNA strand-breaks induced by low doses of X-rays. UV-light or bleomycin do not increase the total or the repair-DNA polymerase activity and. therefore. that the increase in the transformation rates after DNA strand-breaking is not preceded by enhanced DNA polymerase activity.     

Bi-directional transfer of nitrogen between alfalfa and bromegrass: Short and long term evidence

Transfer of N from legumes to associated non-legumes has been demonstrated under a wide range of conditions. Because legumes are able to derive their N requirements from N₂ fixation, legumes can serve, through the transfer of N, as a source of N for accompanying non-legumes. Studies, therefore, are often limited to the transfer of N from the legume to the non-legume. However, legumes preferentially rely on available soil N as their source of N. To determine whether N can be transferred from a non-legume to a legume, two greenhouse experiments were conducted. In the short-term N-transfer experiment, a portion of the foliage of meadow bromegrass (Bromus riparius Rhem.) or alfalfa (Medicago sativa L.) was immersed in a highly labelled ¹⁵N-solution and following a 64 h incubation, the roots and leaves of the associated alfalfa and bromegrass were analyzed for ¹⁵N. In the long-term N transfer experiment, alfalfa and bromegrass were grown in an ¹⁵N-labelled nutrient solution and transplanted in pots with unlabelled bromegrass and alfalfa plants. Plants were harvested at 50 and 79 d after transplanting and analyzed for ¹⁵N content. Whether alfalfa or bromegrass were the donor plants in the short-term experiment, roots and leaves of all neighbouring alfalfa and bromegrass plants were enriched with ¹⁵N. Similarly, when alfalfa or bromegrass was labelled in the long-term experiment, the roots and shoots of neighbouring alfalfa and bromegrass plants became enriched with ¹⁵N. These two studies conclusively show that within a short period of time, N is transferred from both the N₂-fixing legume to the associated non-legume and also from the non-legume to the N₂-fixing legume. The occurrence of a bi-directional N transfer between N₂-fixing and non-N₂-fixing plants should be taken into consideration when the intensity of N cycling and the directional flow of N in pastures and natural ecosystems are investigated.     

Optimization of transient gene expression in pollen of Norway spruce (Picea abies) by particle acceleration

In order to optimize transient gene expression in Norway spruce pollen after DNA delivery with particle bombardment, effects of different conditions during homhardmenl were analysed using β-glucuroniduse (GUS) driven by the rice Act I promoter and Inciferase (LUS) driven by the tomato !at 52 promoter as reporter genes. Transient gene expression was significantly increased hy using two bombardments. Also the distance from the stopping plate to the sample was critical to gam maximum gene expression. There was no significant difference between gold and tungsten particles, and the number of positively stained pollen increased with increasing DNA concentration, from 5 to 40 pg DNA added in the DNA/tungsten solution The DNA delivery to Norway spruce pollen was most efficient at a chamber pressure above 70 kPa.     

Transfer of nitrogen from damaged roots of white clover (Trifolium repens L.) to closely associated roots of intact perennial ryegrass (Lolium perenne L)

An experiment is described in which the magnitude of N transferred from damaged white clover roots to perennial ryegrass was determined, using ¹⁵N labelling of the grass plant. There was no effect on the growth and N-fixation of the clover plants after removing part of the root system. The ¹⁵N data suggested that N had been acquired by all grass plants, even in plants grown alone with no further N supplied after labelling. However, after quantifying the mobile and stored N pools of the grass plants it was evident that significant transfer of N from clover to grass only took place from damaged clover roots. Dilution of the atom% ¹⁵N in the roots of the grass plants grown alone, and in association with undamaged clover roots, was explained by remobilisation of N within the plant.     

Direct assessment of symbiotically fixed nitrogen in the rhizosphere of alfalfa

Rhizodeposition has been proposed as one mechanism for the accumulation of significant amounts of N in soil during legume growth. The objective of this experiment was to directly quantify losses of symbiotically fixed N from living alfalfa (Medicago sativa L.) roots to the rhizosphere. We used ¹⁵N-labeled N₂ gas to tag recently fixed N in three alfalfa lines [cv. Saranac, Ineffective Saranac (an ineffectively nodulated line), and an unnamed line in early stages of selection for apparent N excretion] growing in 1-m long polyvinylchloride drainage lysimeters in loamy sand soil in a greenhouse. Plants were in the late vegetative to flowering growth stage during the 2-day labelling period. We determined the fate of this fixed N in various plant organs and soil after a short equilibration period (2 to 4 days) and after one regrowth period (35 to 37 days). Extrapolated N₂ fixation rates (46 to 77g plant^–1 h^–1) were similar to rates others have measured in the field. Although there was significant accretion of total N in rhizosphere compared to bulk soil, less than 1% was derived from newly fixed N and there were no differences between the excreting line and Saranac. Loss of N in percolate water was small. These results provide the first direct evidence that little net loss of symbiotically-fixed N occurs from living alfalfa roots into surrounding soil. In addition, these results confirm our earlier findings, which depended on indirect ¹⁵N labelling techniques. Net N accumulation in soil during alfalfa growth is likely due to other processes, such as decomposition of roots, nodules, and above ground litter, rather than to N excretion from living roots and nodules.     

Gene transfer to inflorescence and flower meristems using ballistic micro-targeting

Direct gene transfer to floral meristems could contribute to cell-fate mapping, to the study of flower-specific genes and promoters, and to the production of transgenic gametes via the transformation of sporogenic tissues. Despite the wide potential of its applications, direct gene transfer to floral meristems has not been achieved so far because of the lack of suitable technology. We show in this paper that ballistic micro-targeting is the technique of choice for this purpose, and in this way, we were able to transfer genes efficiently into excised wheat immature spikes. Particle size was adjusted for optimal penetration into the L1 and L2 cell layers of the spikes with limited cell damage. Spikes at different developmental stages were shot either with a plasmid containing two genes involved in anthocyanin biosynthesis or with a plasmid bearing the uidA (-glucuronidase) gene. The transient expression of these marker genes was observed in the different developmental stages tested and in cells of both the L1 and the L2 layers. The transient expression of the uidA gene was significantly increased when the sucrose concentration in the culture medium was increased from 0.06 to 0.52 M. At the highest concentration, 100% of the targeted spikes expressed the uidA gene, with an average of 69 blue cells per spike. Twelve days after microtargeting, multicellular sectors showing transgene expression and containing up to 17 cells were found in 85% of the shot immature inflorescences. This indicated that targeted cells survived particle bombardment. Sectors were found in primordia of both vegetative and reproductive organs.     

Reflections on biosystems motivating supramolecular engineering

Some goals of bioelectronics—interfacing biology and electronics — are the understanding of supramolecular bioprocesses and the construction of supramolecular devices. The principles for the design and fabrication of machineries with functional components of molecular size are inspired by reflecting on biosystems, and it seems important to consider such principles. We first discuss attempts to construct supramolecular machines, and then we consider the bacterial reaction centre as an example where supramolecular engineering helps to elucidate a bioprocess. We then discuss possible mechanisms leading to the emergence of life-like systems in the light of the basic principles used to design supramolecular devices. Finally, we reflect on prospects in molecular engineering inspired by studying the emergence of life-like systems.