Partially edited RNAs are intermediates of RNA editing in plant mitochondria

RNA editing in flowering plant mitochondria addresses several hundred specific C nucleotides in individual sequence contexts in mRNAs and tRNAs. Many of the in vivo steady state RNAs are edited at some sites but not at others. It is still unclear whether such incompletely edited RNAs can either be completed or are aborted. To learn more about the dynamics of the substrate recognition process, we investigated in vitro RNA editing at a locus in the atp4 mRNA where three editing sites are clustered within four nucleotides. A single cis-element of about 20 nucleotides serves in the recognition of at least two sites. Competition with this sequence element suppresses in vitro editing. Surprisingly, unedited and edited competitors are equally effective. Experiments with partially pre-edited substrates indicate that indeed the editing status of a substrate RNA does not affect the binding affinity of the specificity factor(s). RNA molecules in which all editing sites are substituted by either A or G still compete, confirming that editing site recognition can occur independently of the actual editing site. These results show that incompletely edited mRNAs can be substrates for further rounds of RNA editing, resolving a long debated question.     

Action of transglucosidase from Aspergillus niger on maltoheptaose and [U-C]maltose

Oligosaccharides synthesized from a mixture of maltoheptaose and [U-¹³C]maltose with transglucosidase [EC 2.4.1.24] from Aspergillus niger were investigated. When the reaction mixture was incubated at 15 °C for 1 h, several types of oligosaccharides with DP (degree of polymerization) 2 to DP8 containing α-d-Glcp-(1→6)-maltoheptaose were detected by liquid chromatography-mass spectrometry (LC-MS) and methylation analysis. Most of these compounds consisted of α-(1→4) linkages in the main chain and α-(1→6) linkages at the non-reducing ends. However, when the reaction mixture was incubated for 96 h, most of these products were converted into oligosaccharides with DP2 to DP5 consisting of only α-(1→6) linkages. These results suggested that A. niger transglucosidase rapidly transferred glucosyl residues to maltooligosaccharides, and gradually hydrolyzed both α-(1→4) linkages and α-(1→6) linkages at the non-reducing end, and transformed these into smaller molecules of mainly α-(1→6) linkages.     

Structure of the high-molecular weight exopolysaccharide isolated from Lactobacillus pentosus LPS26

The strain Lactobacillus pentosus LPS26 produces a capsular polymer composed of a high- (2.0 × 10⁶ Da) (EPS A) and a low-molecular mass (2.4 × 10⁴ Da) (EPS B) polysaccharide when grown on semi-defined medium containing glucose as the carbon source. The structure of EPS A and its deacetylated form has been determined by monosaccharide and methylation analysis as well as by 1D/2D NMR studies (¹H and ¹³C). We conclude that EPS A is a charged heteropolymer, with a composition of d-glucose, d-glucuronic acid and l-rhamnose in a molar ratio 1:2:2. The repeating unit is a pentasaccharide with two O-acetyl groups at O-4 of the 3-substituted α-d-glucuronic acid and at O-2 of the 3-substituted β-l-rhamnose, respectively.→4)-α-d-Glcp-(1→3)-α-d-GlcpA4Ac-(1→3)-α-l-Rhap-(1→4)-α-d-GlcpA-(1→3)-β-l-Rhap2Ac-(1→This unbranched structure is not common in EPSs produced by Lactobacilli. Moreover, the presence of acetyl groups in the structure is an unusual feature which has only been reported in L. sake 0-1 [Robijn et al. Carbohydr. Res., 1995, 276, 117-136].     

Partially purified Carica papaya lipase: a versatile biocatalyst for the hydrolytic resolution of (R,S)-2-arylpropionic thioesters in water-saturated organic solvents

With the hydrolytic resolution of (R,S)-naproxen 2,2,2-trifluoroethyl thioesters in water-saturated isooctane as a model system, improvements of the specific lipase activity and thermal stability were found when a crude Carica papaya lipase (CPL) was partially purified and employed as the biocatalyst. The partially purified Carica papaya lipase (PCPL) was furthermore explored as an effective enantioselective biocatalyst for the hydrolytic resolution of (R,S)-profen thioesters in water-saturated organic solvents. The kinetic analysis in water-saturated isooctane indicated that both acyl donor and acyl acceptor have profound influences on the lipase activity, E-value, and enantioselectivity. Inversion of the enantioselectivity from (S)- to (R)-thioester was found for (R,S)-fenoprofen and (R,S)-ketoprofen thioesters that contained a bulky substituent at the meta-position of 2-phenyl moiety of the acyl part. Kinetic constants for the acylation step were furthermore estimated for elucidating the kinetic data and postulating an active site model. The thermodynamic analysis indicated that the enantiomer discrimination was driven by the difference of activation enthalpy (DeltaDeltaH) and that of activation entropy (DeltaDeltaS), yet the latter was dominated for most of the reacting systems. The postulated active site model was supported from the variation of DeltaDeltaH and DeltaDeltaS with the acyl moiety, in which a good linear enthalpy-entropy compensation relationship was also illustrated. A comparison of the performances between Candida rugosa lipase (CRL) and PCPL indicated that PCPL was superior to CRL in terms of the better thermal stability, similar or better lipase activity for the fast-reacting substrate, time-course-stability, and lower enzyme cost.     

Agronomic effectiveness of partially acidulated phosphate rock as influenced by soil phosphorus-fixing capacity

A greenhouse study compared the effect of soil P-fixing capacity on the relative argonomic effectiveness (RAE) of partially acidulated phosphate rock (PAPR) and water-soluble P. Such information is lacking in the literature. Six soils varying widely in P-fixing capacity (5.6%–56.1%) were used. A phosphate rock (Huila PR) from Colombia was acidulated with H₂SO₄ at 50% of the level necessary to achieve full conversion to single superphosphate (SSP). Rates of P applied from PAPR or SSP were 0,05, 100, and 300 mg P kg⁻¹. The P fertilizers were mixed with the soils, and maize was grown for 6 weeks before harvest. The results show that the effectiveness of PAPR in increasing dry-matter yield and P uptake over yield and uptake obtained with SSP linearly increased as the soil P-fixing capacity increased. PAPR and SSP were equally effective in increasing dry-matter yield or P uptake at P-fixing capacities of 28% or 36%, respectively. PAPR was found to be more effective than SSP in soils (treated with Fe-gel) with P-fixing capacity higher than these values. The internal efficiency, which is defined as the ratio between dry-matter yield and P uptake, was the same for both PAPR and SSP in all the soils.     

Control of potato pale cyst-nematode, Globodera pallida, with a granular nematicide and partially resistant potatoes

The effects of oxamyl applied to the seedbed and growing partially resistant potatoes in controlling potato pale cyst-nematode, Globodera pallida, were assessed in eleven field experiments on sandy, peaty and silty loam soils in England from 1986 to 1988. Standardised procedures allowed valid comparisons to be made between data from the three experiments in 1987 and from the seven experiments in 1988. In soil moderately or heavily infested with G. pallida, oxamyl frequently increased tuber yields of susceptible cv. Désirée and of partially resistant potatoes and lessened crude nematode increase (Pf/Pi) significantly at some sites but not at others. Although 2.8 kg oxamyl ha“¹ often increased tuber yields significantly, it was significantly less effective than 5.6 kg in controlling G. pallida at one site and at another site G. pallida increased more than in untreated plots. Potatoes partially resistant to G. pallida were more effective that oxamyl in controlling nematode increase at some sites but not at others. Combined use of oxamyl and partially resistant potatoes was generally more effective in controlling G. pallida than either measure alone. As measured by a ‘control coefficient’ (weight of tubers over 40mm diameter (t ha“¹) 4-crude nematode increase (Pf/Pi)), the most effective integrated control of G. pallida was obtained by growing cvs Glenna, Morag or Santé in soil treated with 5.6 kg oxamyl ha^-1.     

Efficient Perovskite Solar Cells Fabricated by Co Partially Substituted Hybrid Perovskite

In the past years, hybrid perovskite materials have attracted great attention due to their superior optoelectronic properties. In this study, the authors report the utilization of cobalt (Co²⁺) to partially substitute lead (Pb²⁺) for developing novel hybrid perovskite materials, CH₃NH₃Pb_1‐xCo_xI₃ (where x is nominal ratio, x = 0, 0.1, 0.2 and 0.4). It is found that the novel perovskite thin films possess a cubic crystal structure with superior thin film morphology and larger grain size, which is significantly different from pristine thin film, which possesses the tetragonal crystal structure, with smaller grain size. Moreover, it is found that the 3d orbital of Co²⁺ ensures higher electron mobilities and electrical conductivities of the CH₃NH₃Pb_1‐xCo_xI₃ thin films than those of pristine CH₃NH₃Pb₄ thin film. As a result, a power conversion efficiency of 21.43% is observed from perovskite solar cells fabricated by the CH₃NH₃Pb_0.9Co_0.1I₃ thin film. Thus, the utilization of Co, partially substituting for Pb to tune physical properties of hybrid perovskite materials provides a facile way to boost device performance of perovskite solar cells.     

Molecular dynamics simulations of the native and partially folded states of ubiquitin: influence of methanol cosolvent, pH, and temperature on the protein structure and dynamics

A series of explicit-solvent molecular dynamics simulations of the protein ubiquitin are reported, which investigate the effect of environmental factors (presence of methanol cosolvent in the aqueous solution, neutral or low pH value, room or elevated temperature) on the structure, stability, and dynamics of the protein. The simulations are initiated either from the native structure of the protein or from a model of a partially folded state (A-state) that is known to exist at low pH in methanol-water mixtures. The main results of the simulations are: (1) The ubiquitin native structure is remarkably stable at neutral pH in water; (2) the addition of the methanol cosolvent enhances the stability of the secondary structure but weakens tertiary interactions within the protein; (3) this influence of methanol on the protein structure is enhanced at low pH, while the effect of lowering the pH in pure water is limited; and (4) the A-state of ubiquitin can be described as a set of relatively rigid secondary structure elements (a native-like beta-sheet and native-like alpha-helix plus two nonnative alpha-helices) connected by flexible linkers.     

Partially Unfolded Forms of the Prion Protein Populated under Misfolding-promoting Conditions: CHARACTERIZATION BY HYDROGEN EXCHANGE MASS SPECTROMETRY AND NMR*

The susceptibility of the cellular prion protein (PrP^C) to convert to an alternative misfolded conformation (PrP^Sc), which is the key event in the pathogenesis of prion diseases, is indicative of a conformationally flexible native (N) state. In the present study, hydrogen-deuterium exchange (HDX) in conjunction with mass spectrometry and nuclear magnetic resonance spectroscopy were used for the structural and energetic characterization of the N state of the full-length mouse prion protein, moPrP(23–231), under conditions that favor misfolding. The kinetics of HDX of 34 backbone amide hydrogens in the N state were determined at pH 4. In contrast to the results of previous HDX studies on the human and Syrian hamster prion proteins at a higher pH, various segments of moPrP were found to undergo different extents of subglobal unfolding events at pH 4, a pH at which the protein is known to be primed to misfold to a β-rich conformation. No residual structure around the disulfide bond was observed for the unfolded state at pH 4. The N state of the prion protein was observed to be at equilibrium with at least two partially unfolded forms (PUFs). These PUFs, which are accessed by stochastic fluctuations of the N state, have altered surface area exposure relative to the N state. One of these PUFs resembles a conformation previously implicated to be an initial intermediate in the conversion of monomeric protein into misfolded oligomer at pH 4.