Anatomy of the stimulative sequences flanking the ARS consensus sequence of chromosome VI in Saccharomyces cerevisiae

We have analyzed the relationship between autonomously replicating sequence (ARS) structure and function for three ARS (ARS605, ARS607 and ARS609) from chromosome VI of Saccharomyces cerevisiae by systematic XhoI-linker mutation in the ARS consensus sequence (ACS) and flanking sequences. All mutations that encroached upon the ACS destroyed ARS activity. DNA sequences stimulative for ARS function were identified on either side of the ACS of ARS605 and only on the 3'-side of the ACS of ARS607. In ARS609, however, no such stimulative sequences were observed. Base substitutions complementary to the wild-type sequence of those stimulative regions, in ARS605 and ARS607, that did not change the AG of unwinding nor affected ARS activity suggests that these regions have, at least, a function as DNA-unwinding elements (DUE). ARS605, ARS607 and ARS609 DNA are of low AG value and showed hypersensitivity to single-strand-specific nuclease when inserted in negatively supercoiled plasmid. Linker mutations inhibitory for ARS activity (5L11 and 7L14) also caused significant changes in local nucleotide (nt) sensitivity within the ACS and its adjoining regions. Complementary base substitutions, however, did not affect these changes in local nt sensitivity. These results imply that the stimulative regions flanking the ACS are necessary to produce an optimum conformation around the ACS which may be important for full ARS activity.     

1.56 Å structure of mature truncated human fibroblast collagenase

The X-ray crystal structure of a 19 kDa active fragment of human fibroblast collagenase has been determined by the multiple isomorphous replacement method and refined at 1.56 Å resolution to an R-factor of 17.4%. The current structure includes a bound hydroxamate inhibitor, 88 waters and three metal atoms (two zincs and a calcium). The overall topology of the enzyme, comprised of a five stranded β-sheet and three α-helices, is similar to the thermolysin-like metalloproteinases. There are some important differences between the collagenase and thermolysin families of enzymes. The active site zinc ligands are all histidines (His-218, His-222, and His-228). The presence of a second zinc ion in a structural role is a unique feature of the matrix metalloproteinases. The binding properties of the active site cleft are more dependent on the main chain conformation of the enzyme (and substrate) compared with thermolysin. A mechanism of action for peptide cleavage similar to that of thermolysin is proposed for fibroblast collagenase. © 1994 Wiley-Liss, Inc.     

Cold adaption of enzymes: Structural comparison between salmon and bovine trypsins

The crystal structure of an anionic form of salmon trypsin has been determined at 1.82 Å resolution. We report the first structure of a trypsin from a phoikilothermic organism in a detailed comparison to mammalian trypsins in order to look for structural rationalizations for the cold-adaption features of salmon trypsin. This form of salmon trypsin (T II) comprises 222 residues, and is homologous to bovine trypsin (BT) in about 65% of the primary structure. The tertiary structures are similar, with an overall displacement in main chain atomic positions between salmon trypsin and various crystal structures of bovine trypsin of about 0.8 Å. Intramolecular hydrogen bonds and hydrophobic interactions are compared and discussed in order to estimate possible differences in molecular flexibility which might explain the higher catalytic efficiency and lower thermostability of salmon trypsin compared to bovine trypsin. No overall differences in intramolecular interactions are detected between the two structures, but there are differences in certain regions of the structures which may explain some of the observed differences in physical properties. The distribution of charged residues is different in the two trypsins, and the impact this might have on substrate affinity has been discussed. © 1994 Wiley-Liss, Inc.     

Genetic differentiation in carbon isotope discrimination and gas exchange in Pseudotsuga menziesii

Patterns of genetic variation in gas-exchange physiology were analyzed in a 15-year-old Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) plantation that contains 25 populations grown from seed collected from across the natural distribution of the species. Seed was collected from 33°30 to 53°12 north latitude and from 170 m to 2930 m above sea level, and from the coastal and interior (Rocky Mountain) varieties of the species. Carbon isotope discrimination () ranged from 19.70() to 22.43() and was closely related to geographic location of the seed source. The coastal variety (20.50 (SE=0.21)) was not significantly different from the interior variety (20.91 (0.15)). Instead, most variation was found within the interior variety; populations from the southern Rockies had the highest discrimination (21.53 (0.20)) (lowest water-use efficiency). Carbon isotope discrimination (), stomatal conductance to water vapor (g), the ratio of intercellular to ambient CO₂ concentration (c_i/c_a), and intrinsic water-use efficiency (A/g) were all correlated with altitude of origin (r=0.76, 0.73, 0.74, and –0.63 respectively); all were statistically significant at the 0.01 level. The same variables were correlated with both height and diameter at age 15 (all at P0.0005). Observed patterns in the common garden did not conform to our expectation of higher WUE, measured by both A/g and , in trees from the drier habitats of the interior, nor did they agree with published in situ observations of decreasing g and with altitude. The genetic effect opposes the altitudinal one, leading to some degree of homeostasis in physiological characteri tics in situ.     

Resource-mediated effects of stream pollution on food absorption of Asellus aquaticus (L.) populations

The role of interactions between chemical perturbations and biological constraints on detritivores occurring in polluted streams were investigated by analysing food absorption variation with stress. Absorption rate and efficiency of four Asellus aquaticus (L.) populations from differently polluted habitats were quantified with respect to the microbial guilds colonizing detritus. A twin tracer method was used. Detritus was microbially colonized in standard conditions and on each stream bottom to control for potential resource-independent variations among individuals. The relationship between length and weight was also determined on a random sample of individuals of each population. Differences of 14.6% in potential absorption efficiency and 11.3% in potential absorption rate were observed between populations from the least and the most polluted habitat. Actual (realized) variations were much stronger: from a minimum of a 60.1% reduction in absorption efficiency to a maximum of 93.8% for the rate. The realized food absorption and the individual weight per length showed the same pattern of variation among populations. This suggested that the availability of energy to isopods in nature was related to stream pollution and resource quality. Bottomup interactions appear to be the most relevant pathway through which chemical water pollution affects the Asellus populations studied. The potential resource-independent variations among individuals are also likely to be explained by temporal cascading of resource-mediated effects.     

Elevated CO2 and plant nitrogen-use: is reduced tissue nitrogen concentration size-dependent?

Plants often respond to elevated atmospheric CO₂ levels with reduced tissue nitrogen concentrations relative to ambient CO₂-grown plants when comparisons are made at a common time. Another common response to enriched CO₂ atmospheres is an acceleration in plant growth rates. Because plant nitrogen concentrations are often highest in seedlings and subsequently decrease during growth, comparisons between ambient and elevated CO₂-grown plants made at a common time may not demonstrate CO₂-induced reductions in plant nitrogen concentration per se. Rather, this comparison may be highlighting differences in nitrogen concentration between bigger, more developed plants and smaller, less developed plants. In this study, we directly examined whether elevated CO₂ environments reduce plant nitrogen concentrations independent of changes in plant growth rates. We grew two annual plant species. Abutilon theophrasti (C₃ photosynthetic pathway) and Amaranthus retroflexus (C₄ photosynthetic pathway), from seed in glass-sided growth chambers with atmospheric CO₂ levels of 350 mol·mol^–1 or 700 mol·mol^–1 and with high or low fertilizer applications. Individual plants were harvested every 2 days starting 3 days after germination to determine plant biomass and nitrogen concentration. We found: 1. High CO₂-grown plants had reduced nitrogen concentrations and increased biomass relative to ambient CO₂-grown plants when compared at a common time; 2. Tissue nitrogen concentrations did not vary as a function of CO₂ level when plants were compared at a common size; and 3. The rate of biomass accumulation per rate of increase in plant nitrogen was unaffected by CO₂ availability, but was altered by nutrient availability. These results indicate that a CO₂-induced reduction in plant nitrogen concentration may not be due to physiological changes in plant nitrogen use efficiency, but is probably a size-dependent phenomenon resulting from accelerated plant growth.     

Comparison of production efficiency among field crops related to nitrogen nutrition and application

It has been generally considered that the low productivity of Leguminosae is caused by accumulation in the reproductive organs of a large amount of protein and lipid, since the biochemical costs of synthesizing these compounds is higher than that for carbohydrate. However, we report here on results which show that: the growth efficiencies (dry matter accumulated/ (dry matter accumulated + respiration)) of reproductive organs of Gramineae and Leguminosae were similar; the growth efficiency of rice in the vegetative stage was greater than that of soybean and field bean, regardless of nitrogen application rate; and when ¹⁴CO₂, ¹⁴C-sucrose or ¹⁴C-asparagine were introduced to the leaf at the maturation stage, respiratory loss of the introduced ¹⁴C was greater in soybean and field bean, especially in the light, than in rice. Thus, it is assumed that the low productivity in Leguminosae is caused by a larger respiratory loss under both dark and light condition in the shoot, and not in the reproductive organs.     

Effects of short-term salinity on leaf gas exchange of the fig (Ficus carica L.)

The influence of short-term salinity (day 1–day 2: 50 mol m^–3 NaCl, day 3–day 7: 100 mol m^–3 NaCl in the nutrient solution) on leaf gas exchange characteristics were studied in two fig clones (Ficus carica L.), whose root mass had been varied in relation to the leaf area. The stomatal conductance was diminished by NaCl in the first week of treatment. NaCl slightly reduced the calculated intercellular partial pressure of CO₂. The net photosynthetic rate of plants with many roots was stimulated by NaCl on some days of the first week of treatment, whereas the net assimilation rate of the plants with few roots remained unaltered or decreased by NaCl. Only the assimilation of the salt-treated plants of one clone for some days during the first week of treatment seemed to be influenced by stomatal conductance. Nonstomatal factors were primarily responsible for the changes in CO₂ uptake in response to salt and/or root treatment. The water use efficiency increased during several days of the first week of NaCl treatment. Decreased stomatal conductance, increased water use efficiency and stimualtion of the net CO₂ assimilation rate appear to enhance salt tolerance during the first few days of salinity. ei]H Lambers     

Defining phosphorus efficiency in plants

The many different definitions for "nutrient efficiency" make the use of the term ambiguous. We evaluated nutrient efficiency using data from a study of response to phosphorus (P) supply in white clover (Trifolium repens L.) and lucerne (Medicago sativa L.). Application of various criteria identified in the literature as measures of nutrient efficiency did not clarify differences between purportedly P efficient and inefficient germplasm. Germplasm differed in maximum shoot and total dry mass and in solution P concentration ([P]_s) required to achieve 80% maximum yield, but not in P concentration of tissue ([P]_t), internal P utilization, or P uptake per unit of fine root dry mass. Differences in yield may have resulted from factors other than efficient use of P. To reduce the confounding effects that other factors have on nutrient efficiency, it is essential that equivalent yields of germplasm be demonstrated where nutrients are not limiting. Mechanisms that enable enhanced nutrient efficiency can be identified less ambiguously using this approach.Joint contribution of the Minn. Agric. Exp. Stn. and the USDA-ARS     

Nutrient fluxes in the shifting cultivation system of south-west Côte d'Ivoire

At two sites, one with a 4-year-old (4-Y) secondary vegetation and the other with a 20-year-old (20-Y) vegetation, the influence of burning slashed vegetation on crop performance was studied during three seasons. In the first season after clearing, also the influence on weed growth was studied. At both sites, burning significantly decreased the number of weed seedlings. The lowest number of seedlings was found on the burnt plots of the 20-Y site. Burning increased yield and nutrient uptake significantly in the first and second season after clearing. In the third season after burning, only at the 4-Y site a significantly higher yield and nutrient uptake were found. At the 20-Y site the effect had disappeared. Calculations of efficiency of utilization of absorbed N, P and K indicated that P was the least available nutrient, also after burning. At both sites three consecutive crops absorbed approximately 40% of P applied in ash, while the cumulative recovery of K was at least 36% at the 4-Y site and at least 59% at the 20-Y site. On non-burnt plots, yields were not lower in the third season than in the first season after clearing, thus indicating that the inherent soil fertility did not decrease. Hence, yield decline on the burnt plots could be ascribed to ash depletion. It was concluded that in the local shifting cultivation system, the combination of ash depletion and infestation of weeds are the main reasons for abandoning the fields.