Metabolic Engineering of Acinetobacter baylyi ADP1 for Improved Growth on Gluconate and Glucose

A high growth rate in bacterial cultures is usually achieved by optimizing growth conditions, but metabolism of the bacterium limits the maximal growth rate attainable on the carbon source used. This limitation can be circumvented by engineering the metabolism of the bacterium. Acinetobacter baylyi has become a model organism for studies of bacterial metabolism and metabolic engineering due to its wide substrate spectrum and easy-to-engineer genome. It produces naturally storage lipids, such as wax esters, and has a unique gluconate catabolism as it lacks a gene for pyruvate kinase. We engineered the central metabolism of A. baylyi ADP1 more favorable for gluconate catabolism by expressing the pyruvate kinase gene (pykF) of Escherichia coli. This modification increased growth rate when cultivated on gluconate or glucose as a sole carbon source in a batch cultivation. The engineered cells reached stationary phase on these carbon sources approximately twice as fast as control cells carrying an empty plasmid and produced similar amount of biomass. Furthermore, when grown on either gluconate or glucose, pykF expression did not lead to significant accumulation of overflow metabolites and consumption of the substrate remained unaltered. Increased growth rate on glucose was not accompanied with decreased wax ester production, and the pykF-expressing cells accumulated significantly more of these storage lipids with respect to cultivation time.     

Top-down or Bottom-up Effects by Fish: Issues of Concern in Biomanipulation of Lakes

A large-scale biomanipulation trial was carried out on Lake Vesijärvi in Finland during 1989–1993. Following the mass removal of coarse fish the biomass of cyanobacteria collapsed from 1.4 g/m^?3 to below 0.4 g/m^?3, while total phosphorus concentration declined from 45 μ g/L to 30 μ g/L. No relevant changes in zooplankton communities were observed. The results suggest that the success of food web manipulation as a tool for lake restoration is not necessarily dependent on the grazing rate of zooplankton. The effects of reduced fish-mediated internal loading and recycling of nutrients are in many cases stronger than those of reduced planktivory. Alternative stable states of water quality may also exist in lakes not covered by macrophytes, owing to the changes in the behavior of fish stocks. Year-to-year variation in the littoral zone may cause large oscillations in lake ecosystems—for example, through the recruitment of fish. In addition, the nutrients translocated by fish from the littoral zone may affect the nutrient dynamics of the pelagial plankton community. In terms of phytoplankton species composition and the ratio of phosphorus to chlorophyll a, the water quality in Lake Vesijärvi has improved in a stepwise fashion within the last 10 years. This is probably due to the fact that the five-year mass removal of fish in Enonselkä fulfilled the requirement of sustained management of fish stocks in order to maintain nonequilibrial conditions between alternate stable states. The prediction of the water quality development is obscured, however, by spatial and temporal within-lake variation, which sets high requirements for sampling programs.     

EVOLUTION OF DIFFERENT GALL TYPES IN WILLOW-FEEDING SAWFLIES (HYMENOPTERA: TENTHREDINIDAE)

The sawflies that feed on the plant family Salicaceae can be divided into eight informal groups based on larval feeding habit or gall type: (1) species with free-living larvae; (2) leaf folders; (3) leaf blade gallers; (4) apical leaf gallers; (5) basal leaf gallers; (6) midrib and petiole gallers; (7) stem gallers; and (8) bud gallers. It has been proposed that the galling habit evolved from free-living larvae via leaf folders, and that the different gall types evolved gradually in the sequence mentioned above. Thus, the galling site would have “wandered” from the leaf margin toward the stem as a result of gradual changes in oviposition site preference. Allozyme data from eight informative loci were used to reconstruct the phylogeny of 18 representative sawfly species. The results suggest that indeed leaf folders seem to be a basal group; leaf blade gallers evolved independently of the other true gallers; apical and basal leaf gallers are not the ancestors of petiole and bud gallers, but they may share a common galling ancestor; bud gallers evolved from midrib/petiole gallers; and stem gallers are polyphyletic. The cause for the observed wandering of the galling site could be intraspecific competition due to a possible “nutrient shading effect” of galls situated closer to the host plant's main vascular system.     

Simulation tools for biochemical networks: evaluation of performance and usability

MOTIVATION: Simulation of dynamic biochemical systems is receiving considerable attention due to increasing availability of experimental data of complex cellular functions. Numerous simulation tools have been developed for numerical simulation of the behavior of a system described in mathematical form. However, there exist only a few evaluation studies of these tools. Knowledge of the properties and capabilities of the simulation tools would help bioscientists in building models based on experimental data. RESULTS: We examine selected simulation tools that are intended for the simulation of biochemical systems. We choose four of them for more detailed study and perform time series simulations using a specific pathway describing the concentration of the active form of protein kinase C. We conclude that the simulation results are convergent between the chosen simulation tools. However, the tools differ in their usability, support for data transfer to other programs and support for automatic parameter estimation. From the experimentalists' point of view, all these are properties that need to be emphasized in the future.     

Warm-up phenomenon and cardiac autonomic control in patients with coronary artery disease

Decreased heart rate variability (HRV) and heart rate turbulence (HRT) are independent predictors of mortality after acute myocardial infarction (AMI). There are no previous studies on the relationship between warm-up phenomenon and cardiac autonomic control in stable coronary artery disease (CAD). We investigated the responses in HRV to repeated exercise induced ischemia and differences in global HRV and HRT in patients with and without adaptation to ischemia (warm-up phenomenon). Fifty male patients with CAD underwent two successive exercise tests with ambulatory electrocardiogram (ECG) recordings. HRV was evaluated using time and frequency domain measures and HRT was determined among patients with ventricular premature complexes (VPCs). The patients were divided in two groups on the basis of either positive (warm-up+) or negative (warm-up-) ischemia adaptation. Total power, ULF and VLF power and pNN50 calculated from the entire ECG recording were higher in the group demonstrating warm-up phenomenon (P<0.05 for all). In the assessment of the four short-term stationary phases (pre-and post-test 1 and 2) total power, VLF power and pNN50 were significantly higher in the warm-up positive group already at the baseline (P<0.05 for all). Furthermore, in the entire recordings total power, ULF and VLF power and SDNN correlated positively with the decrease in ischemic burden in the recovery phase (P相似文献   

Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors

Proline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the flavin-dependent oxidation of proline to Delta(1)-pyrroline-5-carboxylate. Here we present a structure-based study of the PRODH active site of the multifunctional Escherichia coli proline utilization A (PutA) protein using X-ray crystallography, enzyme kinetic measurements, and site-directed mutagenesis. Structures of the PutA PRODH domain complexed with competitive inhibitors acetate (K(i) = 30 mM), L-lactate (K(i) = 1 mM), and L-tetrahydro-2-furoic acid (L-THFA, K(i) = 0.2 mM) have been determined to high-resolution limits of 2.1-2.0 A. The discovery of acetate as a competitive inhibitor suggests that the carboxyl is the minimum functional group recognized by the active site, and the structures show how the enzyme exploits hydrogen-bonding and nonpolar interactions to optimize affinity for the substrate. The PRODH/L-THFA complex is the first structure of PRODH with a five-membered ring proline analogue bound in the active site and thus provides new insights into substrate recognition and the catalytic mechanism. The ring of L-THFA is nearly parallel to the middle ring of the FAD isoalloxazine, with the inhibitor C5 atom 3.3 A from the FAD N5. This geometry suggests direct hydride transfer as a plausible mechanism. Mutation of conserved active site residue Leu432 to Pro caused a 5-fold decrease in k(cat) and a severe loss in thermostability. These changes are consistent with the location of Leu432 in the hydrophobic core near residues that directly contact FAD. Our results suggest that the molecular basis for increased plasma proline levels in schizophrenic subjects carrying the missense mutation L441P is due to decreased stability of human PRODH2.     

Mitochondrial DNA polymorphisms as risk factors for Parkinson’s disease and Parkinson’s disease dementia

The activity of complex I of the mitochondrial respiratory chain has been found to be decreased in patients with Parkinsons disease (PD), but no mutations have been identified in genes encoding complex I subunits. Recent studies have suggested that polymorphisms in mitochondrial DNA (mtDNA)-encoded complex I genes (MTND) modify susceptibility to PD. We hypothesize that the risk of PD is conveyed by the total number of nonsynonymous substitutions in the MTND genes in various mtDNA lineages rather than by single mutations. To test this possibility, we determined the number of nonsynonymous substitutions of the seven MTND genes from 183 Finns. The differences in the total number of nonsynonymous substitutions and the nonsynonymous to synonymous substitution rate ratio (K_a/K_s) of MTND genes between the European mtDNA haplogroup clusters (HV, JT, KU, IWX) were analysed by using a statistical approach. Patients with PD (n=238) underwent clinical examination together with mtDNA haplogroup analysis and the clinical features between patient groups defined by the number of nonsynonymous substitutions were compared. Our analysis revealed that the haplogroup clusters HV and KU had a lower average number of amino acid replacements and a lower K_a/K_s ratio in the MTND genes than clusters JT and IWX. Supercluster JTIWX with the highest number of amino acid replacements was more frequent among PD patients and even more frequent among patients with PD who developed dementia. Our results suggest that a relative excess of nonsynonymous mutations in MTND genes in supercluster JTWIX is associated with an increased risk of PD and the disease progression to dementia.     

Observational evidence that maladaptive gene flow reduces patch occupancy in a wild insect metapopulation

Theory predicts that dispersal throughout metapopulations has a variety of consequences for the abundance and distribution of species. Immigration is predicted to increase abundance and habitat patch occupancy, but gene flow can have both positive and negative demographic consequences. Here, we address the eco‐evolutionary effects of dispersal in a wild metapopulation of the stick insect Timema cristinae, which exhibits variable degrees of local adaptation throughout a heterogeneous habitat patch network of two host‐plant species. To disentangle the ecological and evolutionary contributions of dispersal to habitat patch occupancy and abundance, we contrasted the effects of connectivity to populations inhabiting conspecific host plants and those inhabiting the alternate host plant. Both types of connectivity should increase patch occupancy and abundance through increased immigration and sharing of beneficial alleles through gene flow. However, connectivity to populations inhabiting the alternate host‐plant species may uniquely cause maladaptive gene flow that counters the positive demographic effects of immigration. Supporting these predictions, we find the relationship between patch occupancy and alternate‐host connectivity to be significantly smaller in slope than the relationship between patch occupancy and conspecific‐host connectivity. Our findings illustrate the ecological and evolutionary roles of dispersal in driving the distribution and abundance of species.