Stoicheiometry of dicyclohexylcarbodiimide-ATPase interaction in mitochondria

1. The oligomeric dicyclohexylcarbodiimide (DCCD)-binding protein of mitochondrial ATPase was studied using (a) the relationship between [¹⁴C]DCCD binding and inhibition of ATPase activities and (b) the analysis of the kinetics of inhibition. 2. The [¹⁴C]DCCD binding to bovine heart mitochondria is linearly proportional to the inhibition of ATP hydrolysis up to a 50% decrease of the original activity resulting in 0.6 mol DCCD bound covalently to the specific inhibitory site (Hous?t?k, J., Svoboda, P., Kopecký, J., Kuz?ela, S?. and Drahota, Z. (1981) Biochim. Biophys. Acta 634, 331–339) per mol of the fully inhibited enzyme. 3. Kinetics of the inhibition of both the ATPase activity (heart and liver mitochondria) and ADP-stimulated respiration (liver) reveal that 1 mol DCCD per mol ATPase eliminates both the synthetic and the hydrolytic activities. It is inferred that the activity-binding correlation underestimates the number of DCCD-reactive sites. 4. The second-order rate constant of the DCCD-ATPase interaction (k) is inversely related to the concentration of membranes, indicating that DCCD reaches the inhibitory site by concentrating in the hydrophobic (phospholipid) environment. 5. At a given concentration of liver mitochondria, comparable k values are obtained both for the inhibition of ATP hydrolysis (k=5.35·10²M^?1·min^?1) and ADP-stimulated respiration (k=5.67·10²M^?1·min^?1). 6. It is concluded that both the synthetic and the hydrolytic functions of ATPase are inhibited via a common single DCCD-reactive site. This site is represented by one of the several polypeptide chains forming the oligomer of the DCCD-binding protein. The inhibitor-ATPase interaction does not exhibit cooperativity, indicating that the preferential reactivity towards DCCD is an inherent property of the inhibitory site.     

Occurrence of bifidobacteria in faeces of calves fed milk or a combined diet

The development of faecal bacteria composition in calves fed milk or a combined diet was investigated from 4 to 21 days of age. On day 7, bifidobacteria in faeces of milk-fed calves already increased from about 7.6 to 9.2 log CFU/g and did not change until the end of the study, whereas in calves fed the combined diet bifidobacteria only moderately increased to 7.9 log CFU/g and decreased slowly until day 21. The counts of bifidobacteria in calves on a combined diet were significantly (p < 0.01) lower compared to those in milk-fed calves. Bifidobacterial counts determined by cultivation or by fluorescence in situ hybridisation (FISH) did not differ significantly. Our results showed that the occurrence of bifidobacteria in calf faeces is highly dependent on the diet composition. Faecal bacteria flora of calves fed exclusively by milk is rich in bifidobacteria, but in calves on a combined diet coliforms dominated.     

Universal primers for detection of common bacterial pathogens causing prosthetic joint infection

The diagnosis of low grade prosthetic joint infection is difficult and time consuming. Nested-PCR for universal bacterial DNA segments detection of "orthopaedic" bacteria was tested in a laboratory setting. This method is based on amplification of the 16S bacterial ribosomal RNA coding sequences. 11 species of the most frequent bacterial pathogens (Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pyogenes, Streptococcus agalactiae, Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae, Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa, Serratia marcescens) involved in prosthetic joint infections were studied. All could be detected rapidly and sensitively by this method.     

Biological activities of organic compounds adsorbed onto ambient air particles: comparison between the cities of Teplice and Prague during the summer and winter seasons 2000-2001

The capital of the Czech Republic, Prague, appears today to be one of the most polluted residential areas in the country, whereas air pollution in the Northern Bohemia region (the former "Black Triangle Region") has substantially decreased during the last decade, especially with respect to the gaseous pollutant SO(2). This study evaluated the biological activities of complex mixtures of organic compounds adsorbed onto ambient air particles (PM10) collected during the summer and winter seasons of 2000-2001 at three monitoring sites--Teplice (TP), Prague-Smíchov (PRG-SM) (city centre) and Prague-Libus (PRG-LB) (suburban area). The following short-term in vitro assays with strikingly different endpoints were used: a bacterial mutagenicity test using the Salmonella typhimurium tester strain TA98 and YG1041, an acellular assay (CT DNA) combined with 32P-postlabelling to evaluate DNA adduct-forming potency and the chick embryotoxicity screening test (CHEST). The results of the mutagenicity test with the YG1041 strain, the acellular genotoxicity (DNA adducts) and the embryotoxicity tests responded to the amount of eight carcinogenic polycyclic aromatic hydrocarbons (PAHs) analysed in the EOM (dichloromethane extractable organic matter) samples tested. Nevertheless, the biological effects of the EOM did not differ between locations. The highest biological activity of the ambient air in terms of organic compounds associated with particles (per unit volume of air) was seen in the Prague city centre during both summer and winter seasons. At this location, B[a]P concentration ranged from 0.1 to 8.9 ng/m(3) (mean 0.3 and 3.6 ng/m(3) for summer and winter seasons, respectively), 13 PAHs ranged from 11 to 343 ng/m(3) (mean 52 and 160 ng/m(3) for summer and winter seasons, respectively). Generally, using in vitro tests, higher ambient air activity was found in the winter season as compared with the summer season at all three monitoring sites (TA98 +S9, approximately 4-fold; YG1041 -S9, approximately 5-fold; YG1041 +S9, approximately 8-fold; CT DNA +S9, approximately 10-fold; CHEST, approximately 10-fold; B[a]P, carcinogenic PAHs and total PAHs analysed, more than 10-fold). The different proportions of individual PAHs found in the summer and winter samples suggested traffic as a major emission source in the summer and, additionally, residential heating in the winter season at all three monitoring sites. The DNA adduct patterns resulting from the in vitro acellular assay also demonstrated similar major emission sources at all three locations. The study shows that particle-bound carcinogenic-PAH concentrations may be taken as an index for the biologically active (mutagenic, genotoxic, embryotoxic) components in air particulate samples. Therefore, high-quality monitoring data of carcinogenic PAHs may be useful for epidemiological studies of the impact of air pollution on the health of the population and for helping decision makers to improve our environment.     

Auxin transport - shaping the plant

Plant growth is marked by its adaptability to continuous changes in environment. A regulated, differential distribution of auxin underlies many adaptation processes including organogenesis, meristem patterning and tropisms. In executing its multiple roles, auxin displays some characteristics of both a hormone and a morphogen. Studies on auxin transport, as well as tracing the intracellular movement of its molecular components, have suggested a possible scenario to explain how growth plasticity is conferred at the cellular and molecular level. The plant perceives stimuli and changes the subcellular position of auxin-transport components accordingly. These changes modulate auxin fluxes, and the newly established auxin distribution triggers the corresponding developmental response.     

Identifying stabilizing key residues in proteins using interresidue interaction energy matrix

We are proposing an interresidue interaction energy map (IEM)--a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. We will show that the IEM can serve as a means for identifying key residues responsible for the stability of a protein. Our method can be compared with the interresidue contact map but has the advantage of weighting the contacts by the stabilization energy content which they bring to the protein structure. For the theoretical adjustment of the proposed method, we chose the Trp-cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical force-field methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trp-cage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein. We have further tested our method on the Trp2Cage miniprotein--a P12W mutant of the Trp-cage and on two proteins from the rubredoxin family that differ in their thermostability. Our method correctly identified the thermodynamically more stable variants in both cases and therefore can also be used as a tool for the relative measurement of protein stability. Finally, we will point out the important role played by dispersion energy, which contributes significantly to the total stabilization energy and whose role in aromatic pairs is clearly dominant. Surprisingly, the dispersion energy plays an even more important role in the interaction of prolines with aromatic systems.     

Recombinant human serine racemase: enzymologic characterization and comparison with its mouse ortholog

D-serine plays a key role in glutamatergic neurotransmission in mammalian brain as a co-agonist of N-methyl-D-aspartate receptors. The enzyme responsible for D-serine biosynthesis, serine racemase (SR), is therefore a promising target for treatment of neuropathologies related to glutamate receptor excitotoxicity, such as stroke or Alzheimer's disease. Much of the experimental work to date has been performed on mouse serine racemase, which shares a high level of sequence identity with its human ortholog. In this work, we report the synthesis of a human SR gene variant optimized for heterologous expression in Escherichia coli and describe the expression and purification of active recombinant human SR. This strategy may be of general interest to researchers wishing to express mammalian proteins in a bacterial system. Furthermore, we conduct a thorough analysis of the kinetics and inhibitor-sensitivity of the recombinant enzyme, and we provide the first direct comparison of human and mouse SR based on our kinetic data. The orthologs behave similarly overall and exhibit identical inhibition profiles, validating the use of mouse models in SR research.     

Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violaceae)

The phylogenies of allopolyploids take the shape of networks and cannot be adequately represented as bifurcating trees. Especially for high polyploids (i.e., organisms with more than six sets of nuclear chromosomes), the signatures of gene homoeolog loss, deep coalescence, and polyploidy may become confounded, with the result that gene trees may be congruent with more than one species network. Herein, we obtained the most parsimonious species network by objective comparison of competing scenarios involving polyploidization and homoeolog loss in a high-polyploid lineage of violets (Viola, Violaceae) mostly or entirely restricted to North America, Central America, or Hawaii. We amplified homoeologs of the low-copy nuclear gene, glucose-6-phosphate isomerase (GPI), by single-molecule polymerase chain reaction (PCR) and the chloroplast trnL-F region by conventional PCR for 51 species and subspecies. Topological incongruence among GPI homoeolog subclades, owing to deep coalescence and two instances of putative loss (or lack of detection) of homoeologs, were reconciled by applying the maximum tree topology for each subclade. The most parsimonious species network and the fossil-based calibration of the homoeolog tree favored monophyly of the high polyploids, which has resulted from allodecaploidization 9-14 Ma, involving sympatric ancestors from the extant Viola sections Chamaemelanium (diploid), Plagiostigma (paleotetraploid), and Viola (paleotetraploid). Although two of the high-polyploid lineages (Boreali-Americanae, Pedatae) remained decaploid, recurrent polyploidization with tetraploids of section Plagiostigma within the last 5 Ma has resulted in two 14-ploid lineages (Mexicanae, Nosphinium) and one 18-ploid lineage (Langsdorffianae). This implies a more complex phylogenetic and biogeographic origin of the Hawaiian violets (Nosphinium) than that previously inferred from rDNA data and illustrates the necessity of considering polyploidy in phylogenetic and biogeographic reconstruction.     

Cooperative mechanism of RNA packaging motor

P4 is a hexameric ATPase that serves as the RNA packaging motor in double-stranded RNA bacteriophages from the Cystoviridae family. P4 shares sequence and structural similarities with hexameric helicases. A structure-based mechanism for mechano-chemical coupling has recently been proposed for P4 from bacteriophage phi12. However, coordination of ATP hydrolysis among the subunits and coupling with RNA translocation remains elusive. Here we present detailed kinetic study of nucleotide binding, hydrolysis, and product release by phi12 P4 in the presence of different RNA and DNA substrates. Whereas binding affinities for ATP and ADP are not affected by RNA binding, the hydrolysis step is accelerated and the apparent cooperativity is increased. No nucleotide binding cooperativity is observed. We propose a stochastic-sequential cooperativity model to describe the coordination of ATP hydrolysis within the hexamer. In this model the apparent cooperativity is a result of hydrolysis stimulation by ATP and RNA binding to neighboring subunits rather than cooperative nucleotide binding. The translocation step appears coupled to hydrolysis, which is coordinated among three neighboring subunits. Simultaneous interaction of neighboring subunits with RNA makes the otherwise random hydrolysis sequential and processive.     

Local, efflux-dependent auxin gradients as a common module for plant organ formation

Plants, compared to animals, exhibit an amazing adaptability and plasticity in their development. This is largely dependent on the ability of plants to form new organs, such as lateral roots, leaves, and flowers during postembryonic development. Organ primordia develop from founder cell populations into organs by coordinated cell division and differentiation. Here, we show that organ formation in Arabidopsis involves dynamic gradients of the signaling molecule auxin with maxima at the primordia tips. These gradients are mediated by cellular efflux requiring asymmetrically localized PIN proteins, which represent a functionally redundant network for auxin distribution in both aerial and underground organs. PIN1 polar localization undergoes a dynamic rearrangement, which correlates with establishment of auxin gradients and primordium development. Our results suggest that PIN-dependent, local auxin gradients represent a common module for formation of all plant organs, regardless of their mature morphology or developmental origin.