DNA-dependent in vitro synthesis of ribosomal proteins,protein elongation factors,and RNA polymerase subunit α: Inhibition by ppGpp

We have previously shown that the synthesis of ribosomal proteins (r proteins) in E. coli cells is under stringent control (Dennis and Nomura, 1974). Since guanosine tetraphosphate (ppGpp) had been implicated in stringent control, we examied the effects of ppGpp on the in vitro synthesis of r proteins directed by DNA from transducing phage λfus3 and λrif^d18. λfus3 carries genes for protein elongation factors EF-Tu and EF-G, and RNA polymerase subunit α, in addition to genes for approximately 27 r proteins. λrif^d18 carries genes for EF-Tu, RNA polymerase subunits β and β^I, and a set of rRNAs, in addition to genes for approximately five r proteins. We have shown that low concentrations of ppGpp (0.2–0.3 mM) specifically inhibit DNA-dependent r protein synthesis in this system, and that this inhibition takes place directly, rather than as a consequence of the inhibition of rRNA synthesis by ppGpp. In addition, we have also shown that ppGpp inhibits the synthesis of EF-G, EF-Tu, and RNA polymerase subunit α, as well as rRNAs.     

Lipase-catalyzed synthesis of poly(ε-caprolactone) and characterization of its solid-state properties

Abstract

Ring-opening polymerization of ε-caprolactone has been successfully conducted using an immobilized form of Candida antarctica lipase B as catalyst. The effects of enzyme concentration, reaction medium, reaction temperature and time on monomer conversion and product molecular weight were investigated. Through optimization of reaction conditions, poly(ε-caprolactone) (PCL) was obtained with 99% monomer conversion and a number-average molecular weight (M_n) of 18870 g/mol. The reaction system was then scaled up, and PCL was synthesized in 78% isolated yield, with M_n and polydispersity index of 41540 g/mol and 1.69, respectively. The solid-state properties of this sample were systematically evaluated using thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD) and polarized optical microscopy (POM). The product PCL showed excellent thermal stability, with degradation of the main chain in the temperature range of 280–450°C. Remarkably, this high molecular weight PCL was a typical crystalline polymer with a high degree of crystallinity observed by DSC, WAXD and POM.     

Post exercise carbohydrate–protein supplementation: phosphorylation of muscle proteins involved in glycogen synthesis and protein translation

The enzymes Akt, mTOR, p70(S6K), rpS6, GSK3, and glycogen synthase interact in the control of protein and/or glycogen synthesis in skeletal muscle, and each has been found to respond to exercise and nutrient supplementation. In the present study, we tested the hypothesis that nutrient supplementation post exercise, in the form of a carbohydrate-protein (CHO-PRO) supplement, would alter the phosphorylation state of these enzymes in a manner that should increase muscle protein and glycogen synthesis above that produced by exercise alone. After a 45 min cycling session followed by sprints and again 15 min later, the subjects (n = 8) ingested 400 ml of a CHO-PRO drink (7.8% dextrose and 1.8% protein-electrolyte) or a placebo drink, as assigned using a randomized, counter-balanced design with repeated measures. Biopsies of the vastus lateralis were taken before exercise and at 45 min of recovery. At 45 min after supplementation, CHO-PRO treatment yielded greater phosphorylation of Akt (65%), mTOR (86%), rpS6 (85-fold), and GSK3alpha/beta (57%) than pre-exercise levels (p < 0.05). Although p70(S6k) showed an exercise response after 45 min, there were no differences between treatments. Glycogen synthase (GS) phosphorylation was significantly reduced 45 min after exercise for both treatments, but the reduction in phosphorylation was greatest during the CHO-PRO treatment (3-fold decrease; p < 0.05), indicating greater activation of GS following supplementation. No difference between treatments was detected prior to exercise for any of the enzymes. These results suggest that a post exercise CHO-PRO supplement alters the phosporylation levels of the enzymes tested in a manner that should accelerate muscle glycogen synthesis and protein initiation during recovery from cycling exercise.     

Co-expression of α′ and β subunits of β-conglycinin in rice seeds and its effect on the accumulation behavior of the expressed proteins

A transgenic rice that produces both the α′ and β subunits of β-conglycinin has been developed through the crossing of two types of transgenic rice. Although the accumulation level of the α′ subunit in the α′β-transgenic rice was slightly lower than that in the transgenic rice producing only the α′ subunit, the accumulation level of the β subunit in the α′β-transgenic rice was about 60% higher than that in the transgenic rice producing only the β subunit. Results from sequential extraction and gel-filtration experiments indicated that part of the β subunit formed heterotrimers with the α′ subunit in a similar manner as in soybean seeds and that the heterotrimers interacted with glutelin via cysteine residues. These results imply that the accumulation level of the β subunit in the α′β-transgenic rice increases by an indirect interaction with glutelin. Immunoelectron microscopy revealed that the α′ and β subunits are localized in a low electron-dense region of protein body-II (PB-II) and that α′ homotrimers in the α′β-transgenic rice seeds seem to accumulate outside of this low electron-dense region.     

Influence of organization of native protein structure on its folding: Modeling of the folding of α-helical proteins

An important question that is addressed here is whether the modeling of protein folding can catch the difference between the folding of proteins with similar structures but with different folding mechanisms. In this work, the modeling of folding of four α-helical proteins from the homeodomain family, which are similar in size, was done using the Monte Carlo and dynamic programming methods. A frequently observed order of folding of α-helices for each protein was determined using the Monte Carlo method. A correlation between the experimental folding rate and the number of Monte Carlo steps was also demonstrated. Amino acid residues that are important for the folding were determined using the dynamic programming method. The defined regions correlate with the order of folding of secondary-structure elements in the proteins both in experiments and in modeling.     

The PucC protein of Rhodobacter capsulatus mitigates an inhibitory effect of light-harvesting 2 α and β proteins on light-harvesting complex 1

Rhodobacter capsulatus contains lhaA and pucC genes that have been implicated in light-harvesting complex 1 and 2 (LH1 and LH2) assembly. The proteins encoded by these genes, and homologues in other photosynthetic organisms, have been classified as the bacteriochlorophyll delivery (BCD) family of the major facilitator superfamily. A new BCD family phylogenetic tree reveals that several PucC, LhaA and Orf428-related sequences each form separate clusters, while plant and cyanobacterial homologues cluster more distantly. The PucC protein is encoded in the pucBACDE superoperon which also codes for LH2 α (PucA) and β (PucB) proteins. PucC was previously shown to be necessary for formation of LH2. This article gives evidence indicating that PucC has a shepherding activity that keeps the homologous α and β proteins of LH1 and LH2 apart, allowing LH1 to assemble properly. This shepherding function was indicated by a 62% reduction in LH1 levels in ΔLHII strains carrying plasmids encoding pucBA along with a C-terminally truncated pucC gene. More severe reductions in LH1 were seen when the truncated pucC gene was co-expressed in the presence of C-terminal PucC::PhoA fusion proteins. It appears that interaction between truncated PucC::PhoA fusion proteins and the truncated PucC protein disrupts LH1 assembly, pointing towards a PucC dimeric or multimeric functional unit.     

The absorption of orally supplied β-alanine and its effect on muscle carnosine synthesis in human vastus lateralis

Summary. β-Alanine in blood-plasma when administered as A) histidine dipeptides (equivalent to 40 mg · kg⁻¹ bwt of β-alanine) in chicken broth, or B) 10, C) 20 and D) 40 mg · kg⁻¹ bwt β-alanine (CarnoSyn™, NAI, USA), peaked at 428 ± SE 66, 47 ± 13, 374 ± 68 and 833 ± 43 μM. Concentrations regained baseline at 2 h. Carnosine was not detected in plasma with A) although traces of this and anserine were found in urine. Loss of β-alanine in urine with B) to D) was <5%. Plasma taurine was increased by β-alanine ingestion but this did not result in any increased loss via urine. Pharmacodynamics were further investigated with 3 × B) per day given for 15 d. Dietary supplementation with I) 3.2 and II) 6.4 g · d⁻¹ β-alanine (as multiple doses of 400 or 800 mg) or III) L-carnosine (isomolar to II) for 4 w resulted in significant increases in muscle carnosine estimated at 42.1, 64.2 and 65.8%.     

The influence of protein coding sequences on protein folding rates of all-β proteins

It is currently believed that the protein folding rate is related to the protein structures and its amino acid sequence. However, few studies have been done on the problem that whether the protein folding rate is influenced by its corresponding mRNA sequence. In this paper, we analyzed the possible relationship between the protein folding rates and the corresponding mRNA sequences. The content of guanine and cytosine (GC content) of palindromes in protein coding sequence was introduced as a new parameter and added in the Gromiha's model of predicting protein folding rates to inspect its effect in protein folding process. The multiple linear regression analysis and jack-knife test show that the new parameter is significant. The linear correlation coefficient between the experimental and the predicted values of the protein folding rates increased significantly from 0.96 to 0.99, and the population variance decreased from 0.50 to 0.24 compared with Gromiha's results. The results show that the GC content of palindromes in the corresponding protein coding sequence really influences the protein folding rate. Further analysis indicates that this kind of effect mostly comes from the synonymous codon usage and from the information of palindrome structure itself, but not from the translation information from codons to amino acids.     

S-linked protein homocysteinylation: identifying targets based on structural, physicochemical and protein–protein interactions of homocysteinylated proteins

An elevated level of homocysteine, a thiol-containing amino acid is associated with a wide spectrum of disease conditions. A majority (>80 %) of the circulating homocysteine exist in protein-bound form. Homocysteine can bind to free cysteine residues in the protein or could cleave accessible cysteine disulfide bonds via thiol disulfide exchange reaction. Binding of homocysteine to proteins could potentially alter the structure and/or function of the protein. To date only 21 proteins have been experimentally shown to bind homocysteine. In this study we attempted to identify other proteins that could potentially bind to homocysteine based on the criteria that such proteins will have significant 3D structural homology with the proteins that have been experimentally validated and have solvent accessible cysteine residues either with high dihedral strain energy (for cysteine–cysteine disulfide bonds) or low pKa (for free cysteine residues). This analysis led us to the identification of 78 such proteins of which 68 proteins had 154 solvent accessible disulfide cysteine pairs with high dihedral strain energy and 10 proteins had free cysteine residues with low pKa that could potentially bind to homocysteine. Further, protein–protein interaction network was built to identify the interacting partners of these putative homocysteine binding proteins. We found that the 21 experimentally validated proteins had 174 interacting partners while the 78 proteins identified in our analysis had 445 first interacting partners. These proteins are mainly involved in biological activities such as complement and coagulation pathway, focal adhesion, ECM-receptor, ErbB signalling and cancer pathways, etc. paralleling the disease-specific attributes associated with hyperhomocysteinemia.     

Individual and combined effect of (±)-α-hydrastine and (±)-β-hydrastine on spore germination of some fungi

(+/-)-alpha-Hydrastine and (+/-)-beta-hydrastine were isolated from Corydalis longipes; both exhibited considerable efficacy against spore germination of some saprophytic and phytopathogenic fungi. While (+/-)-alpha-hydrastine was effective against most of the fungi, Helminthosporium echinoclova was least affected even at the highest dose (150 ppm). (+/-)-beta-Hydrastine was equally effective against several fungi. Mixture of both compounds was more effective than each one individually. Helminthosporium species were again the most resistant toward the mixture. The effect of both alkaloids independently on germination and development of E. pisi conidia on excised pea leaves was also shown. After pre-inoculation with (+/-)-alpha-hydrastine, the effect was more pronounced than the addition post-inoculation; maximum inhibition occurred at 200 ppm. (+/-)-beta-Hydrastine also reduced germination of conidia but was less effective than (+/-)-alpha-hydrastine. The number of primary and secondary branches of conidia and number of appressoria were not affected significantly by either compound.     

A diastereoselective synthesis of 7α-nitromethyl steroid derivative and its use for an efficient synthesis of eplerenone

A novel and efficient method of stereoselectively introducing α-nitromethyl group to C-7 position of 11α-hydroxyl canrenone 4 was described. In addition, this method was successfully applied in a total synthesis of Eplerenone 8. The route was characteristic of simple operation, moderate reaction conditions with 5 steps and 55% total yield, at the same time, without any expensive or toxic reagent in use.     

Recent reports on the effect of low doses of ionizing radiation and its dose–effect relationship

Recently, the risk associated with low doses of ionizing radiation has gained new interest. Here, we analyze and discuss the major differences between two reports recently published on this issue; the report of the French Academy of Sciences and of the French Academy of Medicine published in March 2005, and the BEIR VII—Phase 2 Report of the American National Academy of Sciences published as a preliminary version in July 2005. The conclusion of the French Report is that the linear no-threshold relationship (LNT) may greatly overestimate the carcinogenic effect of low doses (<100 mSv) and even more that of very low doses (<10 mSv), such as those delivered during X-ray examinations. Conversely, the conclusion of the BEIR VII report is that LNT should be used for assessing the detrimental effects of these low and very low doses. The causes of these diverging conclusions should be carefully examined. They seem to be mostly associated with the interpretation of recent biological data. The point of view of the French Report is that these recent data are incompatible with the postulate on which LNT is implicitly based, namely the constancy of the carcinogenic effect per unit dose, irrespective of dose and dose rate.     

Evolution of contest competition and its effect on host–parasitoid dynamics

In experimental populations of the cowpea bean weevil Callosobruchus maculatus (Coleoptera: Bruchidae) and a parasitic wasp Heterospilus prosopidis (Hymenoptera: Braconidae), large changes in the abundances and the fluctuations of both species occurred after approximately 20 generations. In this paper, we examine the hypothesis that this observed change in the dynamics may have been caused by an evolutionary shift in the mode of competition among the bean weevils. A Nicholson-Bailey type model is developed using parameters measured from the experiments. The host larvae can differ in the type of competitive behaviour that they exhibit, which can be either of a contest type or of a scramble type. If a bean contains one or more larvae of the contest type, only one of these will survive and any scramble-type larvae in the bean will be killed. If no contest-type larvae are present within a bean, multiple individuals of the scramble type can emerge from a single bea n. The model assumes many genotypes, differing in the fraction of offspring of the two types. If a high per capita resource availability is maintained, then the scramble type is selected for, but if resources are limited, then the contest type is selected for. The host population at the start of the experiment, taken from a stock culture, was composed mostly of the scramble type. The model is successful in explaining the initial quick increase in the host's abundance, followed by the evolutionary increase in the fraction of the contest type among hosts, resulting in the more stable population dynamics of the host–parasitoid system, as observed in the experiments. However, it predicts a parasitoid abundance much higher than that observed. We discuss alternative hypotheses to explain the observed evolutionary shift in the population dynamics. We also examine the effect of the difference in size of the beans in the stock culture and those used in the experiments.     

The effect of norflurazon on protein composition and chlorophyll organization in pigment–protein complex of Photosystem II

The pyridazinone-type herbicide norflurazon SAN 9789 inhibiting the biosynthesis of long-chain carotenoids results in significant decrease in PS II core complexes and content of light-harvesting complex (LHC) polypeptides in the 29.5–21 kDa region. The Chl a forms at 668, 676, and 690 nm that belong to LHC and antenna part of PS I disappear completely after treatment. The intensity of the Chl b form at 648 nm is sharply decreased in treated seedlings grown under 30 or 100 lx light intensity. The bands of carotenoid absorption at 421, 448 (Chl a), 452, 480, 492, 496 (β-carotene), and 508 nm also disappear. The band shift from 740 to 720 nm and decrease in its intensity relative to the 687 nm emission peak in the low-temperature fluorescence spectrum (77 K) suggests a disturbance of energy transfer from LHC to the Chla form at 710–712 nm.     

Compartmentation of uridine 5′-triphosphate occurs during synthesis of cytoplasmic and mitochondrial ribosomal RNAs of cultured tomato cells but not during synthesis of cytoplasmic ribosomal and transfer RNAs

Compartmentation of uridine 5-triphosphate (UTP) was studied during the nucleolar synthesis of cytoplasmic ribosomal RNA (cyt-rRNA) and the synthesis of cytoplasmic transfer RNA (cyt-tRNA) in the nuclear matrix as well as the synthesis of mitochondrial ribosomal RNA (mt-rRNA) in tomato (Lycopersicon esculentum Mill. cv. Lukullus) cell-suspension culture using the approach of Wiegers et al. (Eur. J. Biochem. 64, 535–540, 1976). Before measurements were made, it was ensured that: (i) there was steady-state labeling of all RNAs studied as well as UTP; (ii) there was stability of cyt-tRNA and cyt-rRNA; (iii) there was no label randomization through degradation of [³H]uridine; (iv) there were significant differences in the specific radioactivity of UTP, the final immediate precursor of RNA, after supplying the cells with two different exogenous [³H]uridine concentrations.By comparing the steady-state specific radioactivity of UTP with that of cyt-tRNA and cyt-18S rRNA during constant [³H]uridine supply, we found that the three molecules had equal specific radioactivities which, however, differed significantly from that of the mt-rRNA. With a 20-fold higher uridine concentration, i.e. a 20-fold lower specific radioactivity of exogenous [³H]uridine, the specific radioactivity of cyt-rRNA, cyt-tRNA and UTP decreased proportionally whereas that of mt-RNA increased. These results argue against different UTP pools during synthesis of cyt-rRNA and cyt-tRNA, but indicate compartmentation of UTP during rRNA synthesis in the nucleus and the mitochondria of tomato cells.Abbreviations CMP cytidine 5-monophosphate - cyt-rRNA cytoplasmic ribosomal RNA - cyt-tRNA cytoplasmic transfer RNA - mt-rRNA mitochondrial rRNA - NC nitrocellulose - PAGE polyacrylamide gel electrophoresis - TLC thin-layer chromatography - Tris 2-amino-2-(hydroxymethyl)-1,3-propanediol - UDP uridine 5-diphosphate - UMP uridine 5-monophosphate - UTP uridine 5-triphosphate     

Further observations on the effect of ethionine on the synthesis of β-galactosidase inEscherichia coli: Formation of an immunologically cross-reacting protein

It was found that ethionine partially inhibits the transport of the inducer (TMG) of β-galactosidase into the cells ofEscherichia coli ML-30. The synthesis of β-galactosidase-specific messenger RNA is not inhibited. Ethionine appears to be incorporated into proteins synthesized by the strains used. The incorporation of ethionine into the molecule of β-galactosidase results in the synthesis of an enzymically inactive, immunologically cross-reacting protein.     

Design and synthesis of protein kinase Cα activators based on 'out of pocket' interactions

Novel types of PKCα activators based on isobenzofuranone bearing a myo-inositol moiety were designed and synthesized. The derivatives with bulky substituents on the myo-inositol moiety significantly activated PKCα, but their binding sites were not the same as that of phorbol ester.