Organization of Methanobacterium thermoautotrophicum bacteriophage psi M1 DNA

Summary M1 is a virulent bacteriophage of Methanobacterium thermoautotrophicum strain Marburg. Restriction enzyme analysis of the linear, 30.4 kb phage DNA led to a circular map of the 27.1 kb M1 genome. M1 is thus circularly permuted and exhibits terminal redundancy of approximately 3 kb. Packaging of M1 DNA from a concatemeric precursor initiates at the pac site which was identified at coordinate 4.6 kb on the circular genome map. It proceeds clockwise for at least five packaging rounds. Headful packaging was also shown for M2, a phage variant with a 0.7 kb deletion at coordinate 23.25 on the map.     

A use of Ramachandran potentials in protein solution structure determinations

A strategy is developed to use database-derived - constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived - constraints are enforced for all aminoacids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the - values for each residue are examined. In the second and final run, the database-derived - constraints are enforced only for those residues which in the first run have ended in one and the same favored - region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints.     

The carotenoids of Flavobacterium strain R1560

The main carotenoid of Flavobacterium strain R1560 has been identified as (3R,3R)-zeaxanthin. Also present were small amounts of 15-cis-phytoene, phytofluene, -carotene (7,8,7,8-tetrahydro-, -carotene plus 7,8,11,12-tetrahydro-, -carotene), neurosporene, lycopene, -zeacarotene, -carotene, -carotene, -cryptoxanthin, rubixanthin, 3-hydroxy--zeacarotene and several apo-carotenals. Zeaxanthin production was inhibited by nicotine (10 mM), and lycopene and rubixanthin accumulated. The biosynthesis of zeaxanthin is discussed in terms of pathways and also of half-molecule reaction sequences. The presence of zeaxanthin may be a characteristic of a group of Flavobacterium species, and may thus be useful in the taxonomic classification of these organisms.     

Effects of water stress on the gas exchange,the activities of some enzymes of carbon and nitrogen metabolism,and on the pool sizes of some organic acids in maize leaves

Water-stressed maize (Zea mays L.) leaves showed a large decrease in leaf conductance during photosynthesis. Net CO₂ uptake and evaporation declined fast at mild stress (=–0.6 to –1.0 MPa) and slower at more severe stress (=–1.0 to -1.2 MPa), whereas the CO₂ concentration in the intercellular spaces (C_i) did not drop to the CO₂ compensation point. The activities of the enzymes of photosynthetic carbon metabolism tested in this study dropped by approx. 30% at =-1.2 MPa. Glutamine synthetase activity was unaffected by water stress, whereas the activity of nitrate reductase was almost completely inhibited. The decline of enzyme activities in relation to was correlated with a concomitant decrease in the content of total soluble protein of the stressed leaves. The total leaf pools of malate, pyruvate and oxaloacetate decreased almost linearly in relation to , thus obviously contradicting the almost constant C_i. In comparison to the controls (=0.6 MPa) the content of citrate and isocitrate increaed markedly at =-0.9 MPa and decreased again at =-1.2 MPa.Abbreviations PCR photosynthetic carbon reduction cycle - PCO photosynthetic carbon oxidation cycle - PEP phosphoenolypyruvate - RuBP ribulose-1,5-bisphosphate     

Chloroplast volume: cell water potential relationships and acclimation of photosynthesis to leaf water deficits

Studies were undertaken to determine if there is an association between nonstomatally-mediated acclimation of photosynthesis to low water potential (w) and the maintenance of chloroplast volume during water stress. Spinach plants either kept well watered throughout their growth (non-acclimated), or subjected to water stress such that leaf w dropped to -1.5 megapascals (MPa) and then were rewatered (acclimated) were subjected to drought episodes. During these stress periods, photosynthesis was maintained to a greater extent in acclimated plants as compared to non-acclimated plants at w below -1 MPa.Estimates of internal leaf [CO₂] suggested that photosynthetic acclimation to low w was not primarily due to altered stomatal response. As w dropped from initial values, a decline in steady state levels of ribulose 1,5-bisphosphate (RuBP) occurred in both non-acclimated and acclimated plants. RuBP decline was less severe in acclimated plants.Low w effects on chloroplast volume in non-acclimated and acclimated plants were estimated by measuring the volume of intact chloroplasts isolated from plants in solutions which were made isotonic to declining leaf osmotic potential during the drought episodes. Chloroplast volume was maintained to a greater extent at low w in acclimated, as compared with non-acclimated plants. Although substantial osmotic adjustment occurred in both non-acclimated and acclimated plants, the extent of osmotic adjustment was the same. These data were interpreted as supporting the hypothesis that cellular-level acclimation to low w is associated with chloroplast volume maintenance, and this physiological acclimation is correlated with enhanced photosynthetic capacity of the leaf at low w.Abbreviations [CO₂]_i internal leaf CO₂ concentration - s osmotic potential - RWC relative water content - RuBP ribulose 1,5-bisphosphate - w water potential     

Assessment of membrane potential changes using the carbocyanine dye,diS-C3-(5): synchronous excitation spectroscopy studies

The fluorescence of the voltage sensitive dye, diS-C₃-(5), has been analyzed by means of synchronous excitation spectroscopy. Using this rather rare fluorescence technique we have been able to distinguish between the slightly shifted spectra of diS-C₃-(5) fluorescence from cells and from the supernatant. It has been found that diS-C₃-(5) fluorescence in the supernatant can be selectively monitored at _exc = 630 nm and _em= 650 nm, while the cell associated fluorescence can be observed at _exc= 690 nm and _em = 710 nm. A modified theory for the diSC₃-(5) fluorescence response to the membrane potential is presented, according to which a linear relationship exists between the logarithmic increment of the dye fluorescence intensity in the supernatant, In I/I°, and the underlying change in the plasma membrane potential, _p=_p-°_p. The theory has been tested on human myeloid leukemia cells (line ML-1) in which membrane potential changes were induced by valinomycin clamping in various K⁺ gradients. It has been demonstrated that the membrane potential change, _p,can be measured on an absolute scale. Offprint requests to: J. Plasek     

The mitochondrial membrane potential (deltapsi(m)) in apoptosis; an update

Mitochondrial dysfunction has been shown to participate in the induction of apoptosis and has even been suggested to be central to the apoptotic pathway. Indeed, opening of the mitochondrial permeability transition pore has been demonstrated to induce depolarization of the transmembrane potential (_m), release of apoptogenic factors and loss of oxidative phosphorylation. In some apoptotic systems, loss of _m may be an early event in the apoptotic process. However, there are emerging data suggesting that, depending on the model of apoptosis, the loss of _m may not be an early requirement for apoptosis, but on the contrary may be a consequence of the apoptotic-signaling pathway. Furthermore, to add to these conflicting data, loss of _m has been demonstrated to not be required for cytochrome c release, whereas release of apoptosis inducing factor AIF is dependent upon disruption of _m early in the apoptotic pathway. Together, the existing literature suggests that depending on the cell system under investigation and the apoptotic stimuli used, dissipation of _m may or may not be an early event in the apoptotic pathway. Discrepancies in this area of apoptosis research may be attributed to the fluorochromes used to detect _m. Differential degrees of sensitivity of these fluorochromes exist, and there are also important factors that contribute to their ability to accurately discriminate changes in _m.     

Secondary structural effects on protein NMR chemical shifts

For an amino acid in protein, its chemical shift, (, )_s, is expressed as a function of its backbone torsion angles ( and ) and secondary state (s): (, )_{s=, )_coil+(, )_s}, where (, )_coil represents its chemical shift at coil state (s=coil); (, )_s (s=sheet or helix) is herein defined as secondary structural effect correction factor, which are quantitatively determined from Residue-specific Secondary Structure Shielding Surface (RSS) for ¹³CO, ¹³C, ¹³C,¹H, ¹⁵N, and ¹HN nuclei. The secondary structural effect correction factors defined in this study differ from those in earlier investigations by separating out the backbone conformational effects. As a consequence, their magnitudes are significantly smaller than those earlier reported. The present (, )_sheet and (, )_helix were found varying little with backbone conformation and the 20 amino acids, specifically for ¹³CO, ¹³C, and ¹H nuclei. This study also carries out some useful investigations on other chemical shift prediction approaches – the traditional shielding surfaces, SHIFTS, SHIFTX, PROSHIFT, and identifies some unexpected shortcomings with these methods. It provides some useful insights into understanding protein chemical shifts and suggests a new route to improving chemical shifts prediction. The RSS surfaces were incorporated into the program PRSI [Wang and Jardetzky, J. Biomol. NMR, 28: 327–340 (2004)], which is available for academic users at http://www.pronmr.com or by sending email to the author (yunjunwang@yahoo.com).     

Effects of shoot and root application of thiamin on salt-stressed sunflower plants

Plants of sunflower (Helianthus annuus L. cv Giza2) were salt-stressed with a combination of NaCl and CaCl₂ inconcentrations having different osmotic potentials (s from 0 to –1.0MPa) and were treated with 5 and 10mg L^–1 of thiamin either sprayed on the shoot orapplied to the root. The membranes of leaf discs from salt-stressed plantsappeared to be less stable (more injured) under heat(51°C) and drought (40% polyethylene glycol6000) stresses than control plants. Salinity slowed the rate of growth (lengthand dry mass production), lowered leaf relative water content (RWC) and leafandroot water potential (w), decreased the contents of chlorophyll (Chl),soluble sugars (SS) and the K⁺/Na⁺ ratio butenhanced total free amino acids (TAA), Na⁺,Ca²⁺and Cl^– accumulation in the shoot and root system. Root orshoot application of thiamin reduced membrane injury by either heat ordehydration stress, lowered leaf w, improved uptake of K⁺,and increased leaf RWC, Chl, SS, TAA contents and dry mass production. Theeffects of salinity (s), thiamin (Thi.) and their interaction(s×Thi) on the parameters tested were significant.Salinity was dominant (as indicated by ² values) in affectingthe contents of Ca²⁺, Cl^–, TAA and membranestability to heat and leaf w. The role of thiamin was dominant forNa⁺, K⁺ and SS contents and the contribution ofinteraction was dominant for growth parameters, Chl. and root w.     

The use of 1JCαHα coupling constants as a probe for protein backbone conformation

Summary Simple pseudo-3D modifications to the constant-time HSQC and HCACO experiments are described that allow accurate (±0.5 Hz) measurement of one bond J_CH coupling constants in proteins that are uniformly enriched with ¹³C. An empirical ,-surface is calculated which describes the deviation of ¹J_CH from its random coil value, using 203 ¹J_CH values measured for residues in the proteins calmodulin, staphylococcal nuclease, and basic pancreatic trypsin inhibitor, for which and are know with good precision from previous X-ray crystallographic studies. Residues in -helical conformation exhibit positive deviations of 4–5 Hz, whereas deviations in -sheet are small and, on average, slightly negative. Data indicate that ¹J_CH depends primarily on , and that ¹J_CH may be useful as a qualitative probe for secondary structure. Comparison of ¹J_CH coupling constants measured in free calmodulin and in its complex with a 26-aminoacid peptide fragment of myosin light-chain kinase confirm that the calmodulin secondary structure is retained upon complexation but that disruption of the middle part of the central helix is even more extensive than in free calmodulin. Supplementary material available from the authors: One table listing 352 ¹J_CH and ¹J-values, together with ,-values for 203 residues of known conformation. Two figures showing (a) a Ramachandran plot of the ,-values of 203 residues used in deriving ¹J(,), and (b) the r.m.s.d. ¹J(,) distribution.     

Preparations of Ψ-peptide bond and peptide-aldehyde inhibitors of atrial granule serine proteinase, a candidate processing enzyme of pro-atrial natriuretic factor

Pseudo-peptide bond inhibitors (-bond inhibitors) and peptide-aldehyde inhibitors of atrial granule serine proteinase, the candidate processing enzyme of pro-atrial natrieuretic factor, are prepared in high yield and purity by novel synthetic routes. The -bond compounds retain essential residues for enzyme binding, but place the enzyme inhibition site in the midst of the peptide sequence. Thus, Bz-APR--LR and Bz-APR--SLRR can be considered readthrough inhibitors of atrial granule serine proteinase. The most potent -peptide, Bz-APR--SLRR (IC₅₀=250 M), is about fivefold less potent than the best peptide-aldehyde inhibitor (EACA-APR-CHO), and both the -bond and peptide-aldehyde compounds are competitive, reversible inhibitors of the enzyme. The -bond peptides containing two C-terminal Arg residues are three-to tenfold more potent than the analogous compounds containing only one C-terminal Arg residue, confirming the importance of both Arg residues in the enzyme processing recognition site. As expected, because of their moderate potencies, the -peptides are not useful affinity ligands for purification of atrial granule serine proteinase, but both peptide aldehydes are effective affinity ligands [Damodaran and Harris (1995),J. Protein Chem., this issue].Abbreviations AGSP atrial granule serine proteinase - ANF atrial natriuretic factor - Bz benzoyl - DIEA diisopropylethylamine - DIPCDI diisopropylcarbodiimide - DMF dimethylformamide - DMSO dimethylsulfoxide - EACA 6(e)-aminocaproic acid - EtOAc ethyl acetate - HEPES N-2-hydroxyethylpiperazine-N-propanesulfonic acid - HOBt N-hydroxybenzotriazole - HPLC high-performance liquid chrornatography - NMR nuclear magnetic resonance - PEG polyethylene glycol-3350 - PyBOP benzotriazole-1-yl-oxy-trispyrrolidino-phosphonium-hexafluorophospate - TEA triethylamine - TFA trifluoroacetic acid - THF tetrahydrofuran - TLC thin-layer chromatography - UV ultraviolet - pseudo-peptide bond -CH₂-NH-. Single-letter abbreviations are used to denote amino acids     

Temperature and moisture effects on C and N mineralization from surface applied clover residue

A better understanding of the effect of temperature (T) and moisture on soil microbial activity should improve our ability to predict N mineralization from soil organic matter and crop residues. The objective of this study was to evaluate the effects of water potential () and T on C and N mineralization from unamended Cecil loamy sand soil (clayey, kaolinitic, thermic Typic Kanhapludult) and from crimson clover (Trifolium incarnatum L.) residues applied on the soil surface. Cecil soil was packed into acrylic plastic cylinders, adjusted to -5.0, -1.5, -0.03, or -0.003 MPa, treated with clover residues on the surface or left unamended, and incubated at 10, 20, 28, or 35°C for 21 d. Headspace gas samples for CO2 and N2O determinations were taken periodically and NH3 evolved was trapped. Inorganic N in soil and residue extracts was analyzed after 21 d. When increased from -5.0 to -0.003 MPa, total CO2 evolved from unamended soil increased linearly with ln(-), whereas total CO2 evolved from clover residue increased exponentially with . In both cases the effect of was enhanced as T increased. Two-dimensional (T, ) equations were developed to describe these effects. Apparent net mineralized N from the clover residue increased with until it reached a maximum between -0.5 and -0.03 Mpa.     

Estimation of Membrane Potential Δψ in Reconstituted Plasma Membrane Vesicles Using a Numerical Model of Oxonol VI Distribution

A model of membrane potential-dependent distribution of oxonol VI to estimate the electrical potential difference across Schizosaccharomyces pombe plasma membrane vesicles (PMV) has been developed. was generated by the H⁺-ATPase reconstituted in the PMV. The model treatment was necessary since the usual calibration of the dye fluorescence changes by diffusion potentials (K⁺ + valinomycin) failed. The model allows for fitting of fluorescence changes at different vesicle and dye concentrations, yielding in ATP-energized PMV of 80 mV. The described model treatment to estimate may be applicable for other reconstituted membrane systems.     

Leaf osmotic potentials of 104 plant species in relation to habitats and plant functional types in Hunshandak Sandland,Inner Mongolia,China

Leaf osmotic potentials ( _s) of 104 plant species from different habitats, i.e., fixed sand dunes, lowland and wetlands in Hunshandak Sandland, Inner Mongolia, China, were investigated. The values of _s were strongly species-specific, and varied from –6.54 MPa ( Caragana microphylla), to –0.44 MPa ( Digitaria ischaemum); 75% of plants investigated had _s from –1.01 to –3.0 MPa. Shrubs were found to have the lowest _s, with an average value of –3.19 MPa, while grasses showed the highest _s. The order of plant _s is shrubs<trees<grasses. The result may relate to anatomical features of shrubs. C₄ photosynthetic pathway plants showed lower _s values. The _s values of 104 species were negatively correlated with their rooting depths ( r ²=0.42; P <0.001). High hydraulic pressure resulting from the deep roots may well explain this trend. The value of _s increased as the environment became wetter, ranging from –0.79 MPa in wetlands to –2.09 MPa in fixed sand dunes. Although soil salt content was higher in wetlands, we did not find any effect on _s.An erratum to this article can be found at     

Measurements of electrical potential differences across yeast plasma membranes with microelectrodes are consistent with values from steady-state distribution of tetraphenylphosphonium inPichia humboldtii

Summary Electrical potential differences across the plasma membrane () of the yeastPichia humboldtii were measured with microelectrodes (filled with 0.1m KCl) inserted into cells immobilized in microfunnels. The registered signals were reproducible and stable for several minutes. On attainment of stable reading for the specific membrane resistanceR _sp was determined by applying square-current pulses to the preparation. Both andR _sp were pH dependent and displayed equal but opposite deflection, reaching its maximal value of –88±9 mV (n=13) andR _sp its minimal value of 10 k·cm² (maximal conductance) at pH 6.5. Uncouplers and the polyene antibiotic nystatin depolarized the cells, decreasing to –21±15 mV (n=10) with concomitant decrease ofR _sp. Comparison of values from microelectrode measurements with those calculated from the steady-state distribution of tetraphenylphosphonium ions agreed within 10 mV under all physiological conditions tested, except at pH values above 7.0. During microelectrode insertion transient voltage signals (a few msec long) were detected by means of an oscilloscope. These voltage signals were superimposed on the stable recordings described above. These short voltage signals disappeared in uncoupled cells. The closely related values obtained by two independent methods (direct measurements with microelectrodes and calculation from steady-state distribution of a lipophilic cation) provide evidence that these values reffect the true membrane potential of intact cells.     

Chloroplast acclimation to low osmotic potential

Photosynthetic potential of isolated chloroplasts was investigated during in situ water deficits. An eight day stress cycle imposed on spinach plants reduced leaf _w by 0.57MPa, and leaf by 0.50MPa, resulting in partial turgor maintenance during the stress cycle. Pressure/volume curves confirmed the occurrence of osmotic adjustment. Leaf depression was associated with an altered response of chloroplasts to low in vitro. Optimum reaction medium for photosynthesis shifted from –1.04 to –1.57MPa, and low was not as inhibitory to photosynthesis of plastids pre-exposed to stress in situ. These data indicate that chloroplasts acclimate to low external in response to leaf water deficits. This response was still evident four days after a stress cycle ended, but was nearly reversed eight days after stress. Repeated stress cycles in situ did not increase the degree of chloroplast acclimation to low in vitro. Fast dehydration of leaves did not induce this apparent chloroplast acclimation.Abbreviations osmotic potential - _w water potential - PEG polyethylene glycol 8000 - MPa megapascals     

Potential-sensitive response mechanism of diS-C3-(5) in biological membranes

Summary The potential-sensitive response mechanism of 3,3-dipropylthiodicarbocyanine iodide (diS-C₃-(5)) was examined based on our previous model of diS-C₃-(5) interaction with brush border membrane vesicles (BBMV) in the absence of a membrane potential. The model contained binding (6 msec), reorientation (30 msec), dimerization (<10 nsec), and translocation (1 sec) reaction steps (Cabrini & Verkman, 1986.J. Membrane Biol. 90:163–175). Transmembrane potentials () were induced in BBMV by K⁺ gradients and valinomycin. Steady-state diS-C₃-(5) fluorescence (excitation 622 nm, emission 670 nm) increased linearly with . The reorientation and translocation reaction steps were resolved by the stopped-flow technique as a biexponential decrease in fluorescence following mixture of diS-C₃-(5) with BBMV at varying . The fractional amplitude of the faster exponential increased from 0.36 to 0.73 with increasing (–17 to 87 mV); the time constant for the faster exponential (30–35 msec) was independent of . There were single exponential kinetics (0.5–1.5 sec) for diS-C₃-(5) fluorescence response to a rapid (<2 msec) change in in the absence of a diS-C₃-(5) concentration gradient. These results, and similar findings in placental brush border vesicles, red cell vesicles, and phosphatidylcholine vesicles, support a translocation mechanism for diS-C₃-(5) response, where induced membrane potentials drive diS-C₃-(5) redistribution between sites at the inner and outer membrane leaflets, with secondary effects on diS-C₃-(5) dimerization and solution/membrane partitioning. Fluorescence lifetime and dynamic depolarization measurements showed no significant change in diS-C₃-(5) rotational characteristics or in the polarity of the diS-C₃-(5) environment with changes in . Based on the experimental results, a mathematical model is developed to explain the quantitative changes in diS-C₃-(5) fluorescence which accompany changes in at arbitrary dye/lipid ratios.     

Protocol-dependence of equivalent circuit parameters of toad urinary bladder

Summary Determinations of current-voltage relationships are widely employed in the characterization of epithelial sodium transport. In order to determine the protocol dependence of transport parameters in the toad urinary bladder, studies were carried out in the presence and absence of amiloride, an inhibitor of active sodium transport. With symmetric positive and negative perturbations of the transepithelial electrical potential difference (0±100 mV) for 30 sec, the amiloride-sensitive current-voltage (i ^a -) relationship was near linear over the range –75+100 mV, indicating constancy of the conductance ^a and the apparent electromotive force E _Na, lumped parameters of the standard electrical equivalent circuit model of the active transport system. With a reverse protocol (±1000 mV) or 15 min perturbations thei ^a - relationships were highly nonlinear. Nonlinearity reflected voltage dependence of parameters: perturbations that increased active transport decreased E _Na and increased ^a, as evaluated from 10 sec perturbations of ; slowing of active transport produced the converse changes. These effects are usefully analyzed in both quasi-steady states and true steady states by means of a detailed equivalent circuit incorporating the significant ionic currents across each plasma membrane. Precise understanding of the significance of ^a and E _Na will require characterization of the partial ionic conductances on perturbation of .     

An elongated segment of DNA observed between two human α globin genes

Summary Detailed restriction enzyme analysis of the DNA from a Chinese female showed that one of her chromosomes had a >17.5 kb deletion of DNA, including the , 2, and 1 globin genes, which is present in many Southeast Asians with an -thalassemia-1 chromosome. Her normal chromosome had the expected cluster of -like globin genes (5----2-1-3), but the segment of DNA between the two globin genes was elongated by some 0.5–0.7 kb. Analyses of various restriction sites suggested that this normal variant of the human globin gene complex is due to a crossover between a normal chromosome with () and a chromosome with an -thalassemia-2 (–^3.7) and an -21-hybrid gene.     

The activity of nitrate reductase and the pool sizes of some amino acids and some sugars in water-stressed maize leaves

The activity of nitrate reductase and the pool sizes of some amino acids and some sugars were measured in relation to the leaf water potential () of maize leaves. The activity of nitrate reductase was severely inhibited in water-stressed maize leaves. This was not due to substrate shortage or the presence of an inhibitor at reduced leaf water potential. While the typical proteinogenic amino acids valine, tyrosine, leucine and isoleucine were almost undetectable in the leaves of the control plants, their concentrations markedly increased with declining , thus indicating protein degradation. The concentrations of serine, glycine and glutamate increased upon water stress, their total amount in severely stressed leaves ranging 5- to 6-fold higher than the total amount of valine, tyrosine, leucine and isoleucine at this stage of water deficit. The pool sizes of glucose, fructose and sucrose decreased in relation to decreasing . The total amount of organic solutes remained almost constant at least up to a of approx.—1.0 MPa and then dropped to about 50% when reached –1.25 MPa.Abbreviations PCR photosynthetic carbon reduction cycle - PCO photosynthetic carbon oxidation cycle - PAR photosynthetically active radiation