Impact of plasmid architecture on stability and yEGFP3 reporter gene expression in a set of isomeric multicopy vectors in yeast

Multicopy episomal plasmids in yeast, used whenever elevated levels of foreign or homologous gene expression are necessary, are known to be less stable compared to the endogenous 2-μm plasmid they are based on, at least without selective pressure. Considering that rich medium favors growth rate and, simultaneously, is less expensive than selective medium, enhancing stability in non-selective medium is extremely desirable. In this study, we changed the architecture of a multicopy model expression plasmid, creating six isoforms (same size, same DNA content but different positions and orientations of the expression block) and studied mitotic stability, copy number, as well as reporter yEGFP3 expression between isoforms. With one isoform being significantly more stable than the others and another one exhibiting elevated plasmid copy numbers in rich medium, we show that consideration of the arrangement of the plasmid elements might be crucial for productivity employing Saccharomyces cerevisiae as a host. We strongly believe that the ideal architecture has to be assessed for each case and assembly strategy has to begin by evaluating the stability of the vector backbone before insertion of the desired gene. For the plasmid set studied, yEGFP3 reporter production depends more on mitotic stability than on elevated plasmid copy numbers in a small number of cells retaining the plasmid under non-selective conditions.

     

Neutral and Phospholipids of the Myxococcus xanthus Lipodome during Fruiting Body Formation and Germination

Myxobacteria are well-known for their complex life cycle, including the formation of spore-filled fruiting bodies. The model organism Myxococcus xanthus exhibits a highly complex composition of neutral and phospholipids, including triacylglycerols (TAGs), diacylglycerols (DAGs), phosphatidylethanolamines (PEs), phosphatidylglycerols (PGs), cardiolipins (CLs), and sphingolipids, including ceramides (Cers) and ceramide phosphoinositols (Cer-PIs). In addition, ether lipids have been shown to be involved in development and signaling. In this work, we describe the lipid profile of M. xanthus during its entire life cycle, including spore germination. PEs, representing one of the major components of the bacterial membrane, decreased by about 85% during development from vegetative rods to round myxospores, while TAGs first accumulated up to 2-fold before they declined 48 h after the induction of sporulation. Presumably, membrane lipids are incorporated into TAG-containing lipid bodies, serving as an intermediary energy source for myxospore formation. The ceramides Cer(d-19:0/iso-17:0) and Cer(d-19:0/16:0) accumulated 6-fold and 3-fold, respectively, after 24 h of development, identifying them to be novel putative biomarkers for M. xanthus sporulation. The most abundant ether lipid, 1-iso-15:0-alkyl-2,3-di-iso-15:0-acyl glycerol (TG1), exhibited a lipid profile different from that of all TAGs during sporulation, reinforcing its signaling character. The absence of all these lipid profile changes in mutants during development supports the importance of lipids in myxobacterial development. During germination of myxospores, only the de novo biosynthesis of new cell membrane fatty acids was observed. The unexpected accumulation of TAGs also during germination might indicate a function of TAGs as intermediary storage lipids during this part of the life cycle as well.     

Unusual Spectral Properties of Bacteriophytochrome Agp2 Result from a Deprotonation of the Chromophore in the Red-absorbing Form Pr

Phytochromes are widely distributed photoreceptors with a bilin chromophore that undergo a typical reversible photoconversion between the two spectrally different forms, Pr and Pfr. The phytochrome Agp2 from Agrobacterium tumefaciens belongs to the group of bathy phytochromes that have a Pfr ground state as a result of the Pr to Pfr dark conversion. Agp2 has untypical spectral properties in the Pr form reminiscent of a deprotonated chromophore as confirmed by resonance Raman spectroscopy. UV/visible absorption spectroscopy showed that the pK_a is >11 in the Pfr form and ∼7.6 in the Pr form. Unlike other phytochromes, photoconversion thus results in a pK_a shift of more than 3 units. The Pr/Pfr ratio after saturating irradiation with monochromatic light is strongly pH-dependent. This is partially due to a back-reaction of the deprotonated Pr chromophore at pH 9 after photoexcitation as found by flash photolysis. The chromophore protonation and dark conversion were affected by domain swapping and site-directed mutagenesis. A replacement of the PAS or GAF domain by the respective domain of the prototypical phytochrome Agp1 resulted in a protonated Pr chromophore; the GAF domain replacement afforded an inversion of the dark conversion. A reversion was also obtained with the triple mutant N12S/Q190L/H248Q, whereas each single point mutant is characterized by decelerated Pr to Pfr dark conversion.     

Effects of selenium deficiency on fatty acid metabolism in rats fed fish oil-enriched diets.

The hepatic fatty acid metabolism was investigated in rats stressed by selenium deficiency and enhanced fish oil intake. Changes in the composition of lipids, peroxides, and fatty acids were studied in the liver of rats fed either a Sedeficient (8 microg Se/kg) or a Se-adequate (300 microg Se/kg) diet, both rich in n-3 fatty acid-containing fish oil (100 g/kg diet) and vitamin E (146 mg alpha-tocopherol/kg diet). The two diets were identical except for their Se content. Se deficiency led to a decrease in hair coat density and quality as well as to changes in liver lipids, individual lipid fractions and phospholipid fatty acid composition of the liver. The low Se status did reduce total and reduced glutathione in the liver but did not affect the hepatic malondialdehyde level. In liver phospholipids (PL), Se deficiency significantly reduced levels of palmitic acid [16:0], fatty acids of the n-3 series such as DHA [22:6 n-3], and other long-chain polyunsaturates C-20-C-22, but increased n-6 fatty acids such as linoleic acid (LA) [18:2 n-6]. Thus, the conversion of LA to arachidonic acid was reduced and the ratio of n-6/n-3 fatty acids was increased. As in liver PL, an increase in the n-6/n-3 ratio was also observed in the mucosal total fatty acids of the small intestine. These results suggest that in rats with adequate vitamin E and enhanced fish oil intake, Se deficiency affects the lipid concentration and fatty acid composition in the liver. The changes may be related to the decreased levels of selenoenzymes with antioxidative functions. Possible effects of Se on absorption, storage and desaturation of fatty acids were also discussed.     

The role of plant species in biomass production and response to elevated CO2 and N

In an experiment that factorially manipulated plant diversity, CO₂, and N, we quantified the effects of the presence of species on assemblage biomass over 10 time points distributed over 5 years. Thirteen of the 16 species planted had statistically significant effects on aboveground and/or belowground biomass. Species differed dramatically in their effects on biomass without any relationship between aboveground and below‐ground effects. Temporal complementarity among species in their effects seasonally, successionally, and in response to a dry summer maintained the diversity–biomass relationships over time and may be the cause behind higher diversity plots having less variation in biomass over time. The response of plant biomass to elevated N, but not CO₂, was at times entirely dependent on the presence of a single species.     

Cytotoxic capacity of hepatitis C virus (HCV)--specific lymphocytes after in vitro immunization with HCV-derived lipopeptides.

BACKGROUND: Hepatitis C virus (HCV)-derived lipopeptides can induce epitope-specific immune responses in lymphocytes from HCV-naive individuals. We analyzed whether such T cells generated by in vitro immunization with HCV core-derived lipopeptides exert HCV-specific cytolytic activity. METHODS: Using a sensitive flow cytometric cytotoxicity assay we characterized HCV-specific cytotoxicity in T cells generated in vitro with HCV core-derived 25-mer lipopeptides. In addition, we studied expressions of Fas ligand and perforin and interferon-gamma (IFN-gamma) secretion in HLA-A2-HCV(core_35-44) tetramer-positive T cells generated with lipopeptide amino acid 20-44 (LP20-44). RESULTS: CD8+ T cells induced in vitro with HCV core-derived lipopeptides only infrequently exerted HCV-specific cytotoxicity, irrespective of whether antigen-coated T2 cells or autologous B lymphoblasts were used as targets. Detailed analysis of HLA-A2-HCV(core_35-44) tetramer-positive T cells generated with LP20-44 revealed that in vitro immunization resulted in T cells that secreted IFN-gamma after antigen-specific restimulation and that upregulated expression of Fas ligand but not of perforin. CONCLUSIONS: Our data confirm at the functional level that HCV lipopeptides induce antigen-specific T lymphocytes that produce IFN-gamma but exert significant cytotoxicity in only a minority of experiments, probably because expression of cytolytic effector molecules is not enhanced in their granules.     

Dynamics of plant and arthropod diversity during old field succession

The successional dynamics of arthropod diversity in 18 abandoned agricultural fields (age 15-54 yr) at Cedar Creek. MN. USA were determined using sweep net sampling (44833 individuals of 618 species). Total arthropod species richness and equitability (J), but not abundance, increased significantly with field successional age. Herbivore and parasite species richness, but not detritivore and predator species richness, also increased significantly with field age. All of these arthropod variables were significantly positively correlated with plant species richness in the fields. When plant species richness was included as a covariate in regressions, there were no longer any significant effects of field age. These results supported the hypothesis that increases in arthropod diversity with field age are influenced by increases in plant diversity. The additional significant positive dependence of herbivore species richness on predator species richness suggests that predator-prey interactions may also influence the successional dynamics of arthropod diversity. Nine of the ten most common arthropod species decreased in abundance with field age, two of them significantly. The abundances of these two generalist forb-feeding species, Melanoplus femurrubrum (Orthoptera: Acrididae) and Scaphytopius acutus (Homoptera: Cicadellidae). each depended significantly on amount of forbs. The average body size of arthropod species (total and herbivores) decreased significantly with field age. An efficiency vs specialization hypothesis predicts such a decrease. Because plants in later secondary succession are generally less palatable, a diversity of smaller, potentially more specialized herbivores may have an advantage over larger and more efficient herbivores in later succession.     

Chemical synthesis of human protein S thrombin-sensitive module and first epidermal growth factor module

Human plasma protein S is a nonenzymatic cofactor for activated protein C (APC) in the inactivation of coagulation factors Va and VIIIa, and helps to provide an essential negative feedback on blood coagulation. Previous indirect evidence suggested that the thrombin-sensitive region (TSR:residues 47–75, 1 disulfide) and the first epidermal growth factorlike region (EGF1: residues 76–116, 3 disulfides) of protein S may be functionally important for expression of its APC cofactor activity. To study the functional importance of these modules directly, access to the isolated TSR and EGF1 modules would be preferred. Recombinant expression of protein S intact TSR and correctly folded EGF1 has not been possible. Here we describe the synthesis of both TSR and EGF1 modules by stepwise solid phase peptide synthesis using the in situ neutralization/2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate activation procedure for tert-butoxycarbonyl chemistry. For the TSR, correct intramodular disulfide bonding was confirmed. To overcome folding difficulties with the EGF1, a two-step oxidation procedure was used in which the cysteines involved in the middle, crossing, disulfide bond (Cys⁸⁵-Cys¹⁰²) remained protected with acetamidomethyl (Acm) groups after hydrogen fluoride treatment of the peptide resin. Selective formation of the first two disulfide bonds (Cys⁸⁰-Cys⁹³ and Cys¹⁰⁴-Cys¹¹³) was followed by release of the Acm groups and subsequent formation of the third disulfide bond (Cys⁸⁵-Cys¹⁰²). CD studies revealed 54% of β-sheet/turn in the EGF1 that is characteristic for EGF modules. Deuterium exchange studies suggested a very tightly packed core in EGF1 that is not accessible to the bulk solvent, likely a result from the compact structure caused by its three disulfide bonds. The 30% β-sheet structure observed in the TSR involved amide protons that could be readily exchanged by deuterons, likely reflecting a more flexible structure of the TSR loop in contrast to the rigid structure of EGF1. The establishment of synthetic access to the TSR and EGF1 of protein S provides a versatile tool to study interactions of these modules with the blood coagulation components of the anticoagulant plasma protein C pathway. © 1998 John Wiley & Sons, Inc. Biopoly 46: 53–63, 1998