Thermodynamics of RNA-RNA binding

BACKGROUND: Reliable prediction of RNA-RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA-mRNA binding and antisense interactions. The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to 'open' the binding site and (2) the energy gained from hybridization. METHODS: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired. RESULTS: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable with a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target. AVAILABILITY: RNAup will be distributed as part of the Vienna RNA Package, www.tbi.univie.ac.at/~ivo/RNA/     

Nonrandom structure in the urea-unfolded Escherichia coli outer membrane protein X (OmpX)

On the basis of sequence-specific resonance assignments for the complete polypeptide backbone and most of the amino acid side chains by heteronuclear nuclear magnetic resonance (NMR) spectroscopy, the urea-unfolded form of the outer membrane protein X (OmpX) from Escherichia coli has been structurally characterized. (1)H-(1)H nuclear Overhauser effects (NOEs), dispersion of the chemical shifts, amide proton chemical shift temperature coefficients, amide proton exchange rates, and (15)N[(1)H]-NOEs show that OmpX in 8 M urea at pH 6.5 is globally unfolded, but adopts local nonrandom conformations in the polypeptide segments of residues 73-82 and 137-145. For these two regions, numerous medium-range and longer-range NOEs were observed, which were used as the input for structure calculations of these polypeptide segments with the program DYANA. The segment 73-82 forms a quite regular helical structure, with only loosely constrained amino acid side chains. In the segment 137-145, the tryptophan residue 140 forms the core of a small hydrophobic cluster. Both nonrandom structures are present with an abundance of about 25% of the protein molecules. The sequence-specific NMR assignment and the physicochemical characterization of urea-denatured OmpX presented in this paper are currently used as a platform for investigations of the folding mechanism of this integral membrane protein.     

Enhancement of glucose transport in rat thymocytes by different radical sources

This study demonstrates that oxidative stress induced in rat thymocytes by the hydrophilic 2,2'-azobis(2-amidinopropane)dihydrochloride (AAPH), the lipophilic cumene hydroperoxide (CumOOH) and the freely diffusible H₂O₂ is associated with an activation of facilitative glucose transport rate, mediated by GLUT1, the major transporter in this cell type. We compared the effects of the three tested radical sources on the kinetic transport parameters, showing that the transport rate enhancement in the treated cells can be ascribed to an increase in the V_max value, apart from the site of generation of the oxidative stress. The enhancement of glucose transport by the three oxidants in thymocytes was significantly attenuated both by protein tyrosine kinase inhibitors as genistein and tyrphostin A23 and by U73122, a phospholipase C inhibitor. Genistein and U73122 reversed also the cited increase of V_max values. It is concluded that the stimulation of glucose transport in response to different oxidants is mediated, at least in part, through reactive oxygen species (ROS)-induced stimulation of protein tyrosine kinase and phospholipase C pathways.     

Two birds with one stone: genes that encode products targeted to two or more compartments

Eukaryotic cells are divided into multiple membrane-bound compartments, all of which contain proteins. A large subset of these proteins perform functions that are required in more than one compartment. Although in most cases proteins carrying out the same function in different compartments are encoded by different genes, this is not always true. Numerous examples have now been found where a single gene encodes proteins (or RNAs) found in two (or more) cell organelles or membrane systems. Some particularly clear examples come from protein synthesis itself: plant cells contain three protein-synthesizing compartments, the cytosol, the mitochondrial matrix and the plastid stroma. All three compartments thus require tRNAs and aminoacyl-tRNA synthetases. Some mitochondrial tRNAs and their aminoacyl-tRNA synthetases are identical to their cytosolic counterparts and they are encoded by the same genes. Similarly, some mitochondrial and plastid aminoacyl-tRNA synthetases are encoded by the same nuclear genes. The various ways in which differentially targeted products can be generated from single genes is discussed.     

Study of the Effect of Phosphorus on Mineral Nutrition of Faba Bean « Vicia fabae L.»

Our study focuses on the study of the phosphorus efficiency on the mineral nutrition of a leguminous plant; to study this efficiency, we tested the effect of increasing doses of phosphorus on the mineral nutrition of faba bean and on the concentration of Nt (total nitrogen), Pi (available phosphorus), KE (exchangeable potassium), C (organic carbon), and the organic matter (OM) rate in the rhizospheric soil after harvest, as well as the concentration of N, P, K, Na, and Ca in the roots, stems, leaves, and seeds of faba bean. The faba bean crop was subjected to four phosphorus doses (P0?=?0 kg/ha; P1?=?70 kg/ha; P2?=?140 kg/ha; P3?=?210 kg/ha). The main results obtained showed that the concentration of the mineral elements in the different faba bean parts reacted differently to the phosphorus treatments. Regarding the dosage of nutrients in the different parts of the faba bean, the results obtained highlight that Pi deficiency in the soil does not only affect phosphate nutrition but can also affect the absorption of other mineral elements, a synergy is recorded between the K concentration in the roots and in the stems with the organic carbon in the soil, and an antagonism between K and Na in the different parts of the plant. All the results obtained in this work show that a phosphate fertilization for doses between 70 kg/ha and 140 kg/ha of P2O5 improves the microbial life of soil microorganisms.

     

Cellular metamorphosis. II. The larval labial gland duct and its prospective adult fates in the tobacco hornworm.

The larval labial gland of the sphingid moth, Manduca sexta, produces a viscous secretion, presumably a lubricant, facilitating the burrowing which precedes pupation. During metamorphosis, the gland transforms into a salivary organ, producing an invertase-rich digestive secretion. The single-cell type found in the duct of the larval gland transforms into the four structurally and functionally distinct cell types found in the four sequentially arranged secretory and conductive regions of the adult salivary gland. Surgical experiments were performed to study the prospective fates of different parts of the larval gland. The glands were bisected and one or both fragments were left in situ to undergo metamorphosis. In addition, fragments of the larval gland were implanted in pupal hosts and went through metamorphosis free of their prior attachments. The four linearly arrayed adult regions originate from correspondingly positioned areas in the larval duct.     

Blocking intrahepatic deletion of activated CD8+ T cells by an altered peptide ligand

BACKGROUND: Activated CD8(+) T cells are retained by the healthy liver where the majority undergo apoptosis. The intrahepatic apoptosis of activated CD8(+) T cells is enhanced by the presence of SIINFEKL peptide. It is of great interest to identify strategies for maintaining intrahepatic T cell number and function in the presence of SIINFEKL peptides. AIM: Our aim was to test if low affinity peptides can block SIINFEKL peptide induced T cell deletion. METHODS: We used an in vivo model of intrahepatic CD8(+) T cell deletion with peptides of different affinities. RESULTS AND DISCUSSION: We show that the intrahepatic deletion of CD8(+) T cells by SIINFEKL peptide results in loss of in vivo cytotoxic T lymphocyte function. In contrast we show that a low affinity peptide (G4) does not result in intrahepatic deletion of CD8(+) T cells. High concentrations G4 peptide can however block intrahepatic deletion of activated CD8(+) T cells, and prevent loss of in vivo cytotoxicity due to SIINFEKL peptide. This is the first demonstration of blocking of SIINFEKL peptide induced CD8(+) T cell deletion in the liver, with enhancement of in vivo cytotoxicity.     

Asymmetric interaction between rod cyclic GMP phosphodiesterase gamma subunits and alphabeta subunits

Rod phosphodiesterase (PDE6) is the central effector enzyme in vertebrate visual transduction. Holo-PDE6 consists of two similar catalytic subunits (Palphabeta) and two identical inhibitory subunits (Pgamma). Palphabeta is the only heterodimer in the PDE superfamily, yet its significance for the function of PDE6 is poorly understood. An unequal interaction of Pgamma with Pbeta as compared with Palpha in the PDE6 complex has not been reported. We investigated the interaction interface between full-length Pgamma and Palphabeta, by differentiating Pgamma interaction with each individual Palphabeta subunit through radiolabel transfer from various positions throughout the entire Pgamma molecule. The efficiency of radiolabel transfer indicates that the close vicinity of serine 40 on Pgamma makes a major contribution to the interaction with Palphabeta. In addition, a striking asymmetry of interaction between the Pgamma polycationic region and the Palphabeta subunits was observed when the stoichiometry of Pgamma versus the Palphabeta dimer was below 2. Preferential photolabeling on Pbeta from Pgamma position 40 and on Palpha from position 30 increased while lowering the Pgamma/Palphabeta ratio, but diminished when the Pgamma/Palphabeta ratio was over 2. Our finding leads to the conclusion that two classes of Pgamma binding sites exist on Palphabeta, each composed of GAF domains in both Palpha and Pbeta, differing from the conventional models suggesting that each Pgamma binds only one of the Palphabeta catalytic subunits. This new model leads to insight into how the unique Palphabeta heterodimer contributes to the sophisticated regulation in visual transduction through interaction with Pgamma.     

Integrated analysis for identifying Portulaca oleracea and its sub-species based on chloroplastic and nuclear DNA barcoding

The taxonomy of Portulaca oleracea has been considered as being complex since the aggregate is composed of many subspecies or a group of micro-species based on seed-coat characters, seed size, and chromosome number. In order to enlarge the background of the extent of genetic variability between and within Tunisian P. oleracea accessions, a combined morphological and molecular approach was adapted, in the present survey. The morphological analyses of the spontaneous Tunis population display high intra population variability characterized by two distinct morphotypes corresponding to the botanical forms (wild and cultivated plant). Furthermore, the molecular approach based on sequences data related to chloroplastic and ribosomal DNA, was used to understand this variability. The obtained results highlighted the greater molecular variability of this plant and allowed to segregate between morphotypes and genotypes of Portulaca. Mostly, this work shows the important contribution of DNA barcoding approach in resolving low-level-taxonomy problems to distinguish between natural populations and varieties.