Stabilization and activation of alpha-chymotrypsin in water-organic solvent systems by complex formation with oligoamines

Formation of enzyme-oligoamine complexes was suggested as an approach to obtain biocatalysts with enhanced resistance towards inactivation in water-organic media. Complex formation results in broadening (by 20-40% v/v ethanol) of the range of cosolvent concentrations where the enzyme retains its catalytic activity (stabilization effect). At moderate cosolvent concentrations (20-40% v/v) complex formation activates the enzyme (by 3-6 times). The magnitude of activation and stabilization effects increases with the number of possible electrostatic contacts between the protein surface and the molecules of oligoamines (OA). Circular dichroism spectra in the far-UV region show that complex formation stabilizes protein conformation and prevents aggregation in water-organic solvent mixtures. Two populations of the complexes with different thermodynamic stabilities were found in alpha-chymotrypsin (CT)-OA systems depending on the CT/OA ratio. The average dissociation constants and stoichiometries of both low- and high-affinity populations of the complexes were estimated. It appears that it is the low-affinity sites on the CT surface that are responsible for the activation effect.     

Non-uniform distribution of mitochondria in pancreatic acinar cells

The distribution of mitochondria in pancreatic acinar cells was investigated using confocal fluorescence microscopy and transmission electron microscopy (EM). Acinar cells were studied either after enzymatic isolation or in small segments of undisassociated pancreatic tissue. Loading of isolated acinar cells with Mito Tracker Green or Red, a fluorescence mitochondrial probe, showed that mitochondria are predominantly situated in the perigranular, subplasmalemmal and perinuclear regions. Subsequent applications of EM fixatives induced a leak of the fluorescent indicator to the cytosol but did not change the distribution of mitochondria. EM was then performed on isolated acinar cells and on acinar cells of pancreatic tissue segments. The intracellular distribution of mitochondria was quantified by calculating the percentage of the cross-sectional area that was occupied by mitochondria. In isolated acinar cells the highest density of mitochondria was seen in the perigranular region, where mitochondria occupied 25.69±1.58% of the area, then the subplasmalemmal region with 12.61±0.77% and the perinuclear region with 9.07±0.97% (n=26). Similar results were obtained from acinar cells of pancreatic tissue segments: the perigranular 22.9±1.95%, subplasmalemmal 12.45±0.78% and perinuclear regions 9.07±0.97% (n=26). The outer mitochondrial membranes were frequently positioned close to membranes of the ER, which followed the outer contour of mitochondria. Mitochondria were never found in direct contact with the nuclear envelope: there were usually layers of ER between the mitochondrial and nuclear membranes. Subplasmalemmal mitochondria were found in a very close proximity to the plasma membrane with no ER layers between the mitochondrial and the corresponding plasma membranes. We conclude that in pancreatic acinar cells mitochondria are preferentially distributed to perigranular, subplasmalemmal and perinuclear regions and this distribution is not affected by isolation or fixation procedures.P.R. Johnson and N.J. Dolman contributed equally to the study. This work was supported by a Medical Research Council programme grant. P.R.J. is a Medical Research Council PhD student and N.J.D. is a Wellcome Trust PhD student.     

Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle

Ribose-5-phosphate isomerase A (RpiA; EC 5.3.1.6) interconverts ribose-5-phosphate and ribulose-5-phosphate. This enzyme plays essential roles in carbohydrate anabolism and catabolism; it is ubiquitous and highly conserved. The structure of RpiA from Escherichia coli was solved by multiwavelength anomalous diffraction (MAD) phasing, and refined to 1.5 A resolution (R factor 22.4%, R(free) 23.7%). RpiA exhibits an alpha/beta/(alpha/beta)/beta/alpha fold, some portions of which are similar to proteins of the alcohol dehydrogenase family. The two subunits of the dimer in the asymmetric unit have different conformations, representing the opening/closing of a cleft. Active site residues were identified in the cleft using sequence conservation, as well as the structure of a complex with the inhibitor arabinose-5-phosphate at 1.25 A resolution. A mechanism for acid-base catalysis is proposed.     

NO-generating neurons in the medullary cardiovascular centers of rodents and carnivores

The aim of the study was to characterize the species-related differences in the distribution of nitric oxide synthase (NOS)-containing neurons in rodents and carnivores medullary cardiovascular centers that take part in regulation of the sympathetic or parasympathetic drives. The order of the mean number of NOS-containing neurons in the dorsomedial and ventrolateral medulla (per section) in different animals was as follows: dog>cat>rat. Although the density of the positive cells in the both regions was changed in the following sequence: rat=cat>dog. Within the dorsal motor nucleus of vagus significant exceeding of the mean number and density of positive cells (preganglionic vagal neurons) in dog were found. Differences in the distribution of NO-generating neurons in the medullary cardiovascular centers and the heterogeneity in the basal level of NO release may contribute to the distinctive alterations of the hemodynamic reactions in the studied species after administration of NOS inhibitors.     

The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii

The S-adenosyl-L-methionine (SAM)-dependent methyltransferases represent a diverse and biologically important class of enzymes. These enzymes utilize the ubiquitous methyl donor SAM as a cofactor to methylate proteins, small molecules, lipids, and nucleic acids. Here we present the crystal structure of PH1915 from Pyrococcus horikoshii OT3, a predicted SAM-dependent methyltransferase. This protein belongs to the Cluster of Orthologous Group 1092, and the presented crystal structure is the first representative structure of this protein family. Based on sequence and 3D structure analysis, we have made valuable functional insights that will facilitate further studies for characterizing this group of proteins. Specifically, we propose that PH1915 and its orthologs are rRNA- or tRNA-specific methyltransferases.     

Habitat structure and the dispersal of male and female bottlenose dolphins (Tursiops truncatus)

Bottlenose dolphins (Tursiops truncatus) are widely distributed and a high degree of morphometric and genetic differentiation has been found among both allopatric and parapatric populations. We analysed 145 samples along a contiguous distributional range from the Black Sea to the eastern North Atlantic for mitochondrial and nuclear genetic diversity, and found population structure with boundaries that coincided with transitions between habitat regions. These regions can be characterized by ocean floor topography, and oceanographic features such as surface salinity, productivity and temperature. At the extremes of this range there was evidence for the directional emigration of females. Bi-parentally inherited markers did not show this directional bias in migration, suggesting a different dispersal strategy for males and females at range margins. However, comparative assessment based on mitochondrial DNA and nuclear markers indicated that neither sex showed a strong bias for greater dispersal on average. These data imply a mechanism for the evolutionary structuring of populations based on local habitat dependence for both males and females.     

Adaptive male effects on female ageing in seed beetles

Selection can favour the evolution of a high reproductive rate early in life even when this results in a subsequent increase in the rate of mortality, because selection is relatively weak late in life. However, the optimal reproductive schedule of a female may be suboptimal to any one of her mates, and males may thus be selected to modulate female reproductive rate. Owing to such sexual conflict, coevolution between males and females may contribute to the evolution of senescence. By using replicated beetle populations selected for reproduction at an early or late age, we show that males evolve to affect senescence in females in a manner consistent with the genetic interests of males. 'Late' males evolved to decelerate senescence and increase the lifespan of control females, relative to 'early' males. Our findings demonstrate that adaptive evolution in one sex may involve its effects on senescence in the other, showing that the evolution of optimal life histories in one sex may be either facilitated or constrained by genes expressed in the other.     

Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework

The resolution of higher level phylogeny of the coleoid cephalopods (octopuses, squids, and cuttlefishes) has been hindered by homoplasy among morphological characters in conjunction with a very poor fossil record. Initial molecular studies, based primarily on small fragments of single mitochondrial genes, have produced little resolution of the deep relationships amongst coleoid cephalopod families. The present study investigated this issue using 3415 base pairs (bp) from three nuclear genes (octopine dehydrogenase, pax-6, and rhodopsin) and three mitochondrial genes (12S rDNA, 16S rDNA, and cytochrome oxidase I) from a total of 35 species (including representatives of each of the higher level taxa). Bayesian analyses were conducted on mitochondrial and nuclear genes separately and also all six genes together. Separate analyses were conducted with the data partitioned by gene, codon/rDNA, gene+codon/rDNA or not partitioned at all. In the majority of analyses partitioning the data by gene+codon was the appropriate model with partitioning by codon the second most selected model. In some instances the topology varied according to the model used. Relatively high posterior probabilities and high levels of congruence were present between the topologies resulting from the analysis of all Octopodiform (octopuses and vampire "squid") taxa for all six genes, and independently for the datasets of mitochondrial and nuclear genes. In contrast, the highest levels of resolution within the Decapodiformes (squids and cuttlefishes) resulted from analysis of nuclear genes alone. Different higher level Decapodiform topologies were obtained through the analysis of only the 1st+2nd codon positions of nuclear genes and of all three codon positions. It is notable that there is strong evidence of saturation among the 3rd codon positions within the Decapodiformes and this may contribute spurious signal. The results suggest that the Decapodiformes may have radiated earlier and/or had faster rates of evolution than the Octopodiformes. The following taxonomic conclusions are drawn from our analyses: (1) the order Octopoda and suborders Cirrata, Incirrata, and Oegopsida are monophyletic groups; (2) the family Spirulidae (Ram's horn squids) are the sister taxon to the family Sepiidae (cuttlefishes); (3) the family Octopodidae, as currently defined, is paraphyletic; (4) the superfamily Argonautoidea are basal within the suborder Incirrata; and (5) the benthic octopus genera Benthoctopus and Enteroctopus are sister taxa.