Entamoeba histolytica: kinetic and molecular evidence of a previously unidentified pyruvate kinase

We report the kinetic characterization of a previously unidentified pyruvate kinase (PK) activity in extracts from Entamoeba histolytica trophozoites. This activity was about 74% of the activity of pyruvate phosphate dikinase. EhPK differed from most PKs in that its pH optimum was 5.5-6.5 and was inhibited by high PEP concentrations (1-5mM); these are concentrations at which PK is usually assayed. The optimal temperature was above 40 degrees C with negligible activity below 20 degrees C. EhPK exhibited hyperbolic kinetics with respect to both PEP (K(m) = 0.018 mM) and ADP (K(m) = 1.05 mM). However, it exhibited a sigmoidal behavior with respect to PEP at sub-saturating ADP concentrations. EhPK did not require monovalent cations for activity. Fructose-1,6 bisphosphate was a potent non-essential activator; it increased the affinity for ADP without modification of the V(max) or the affinity for PEP. Phosphate, citrate, malate, and alpha-ketoglutarate significantly inhibited EhPK activity. A putative EhPK gene fragment found in EhDNA was analyzed. The data indicate that E. histolytica trophozoites contain an active PK, which might contribute to the generation of glycolytic ATP for parasite survival.     

KymoAnalyzer: a software tool for the quantitative analysis of intracellular transport in neurons

In axons, proper localization of proteins, vesicles, organelles, and other cargoes is accomplished by the highly regulated coordination of kinesins and dyneins, molecular motors that bind to cargoes and translocate them along microtubule (MT) tracks. Impairment of axonal transport is implicated in the pathogenesis of multiple neurodegenerative disorders including Alzheimer's and Huntington's diseases. To understand how MT‐based cargo motility is regulated and to delineate its role in neurodegeneration, it is critical to analyze the detailed dynamics of moving cargoes inside axons. Here, we present KymoAnalyzer, a software tool that facilitates the robust analysis of axonal transport from time‐lapse live‐imaging sequences. KymoAnalyzer is an open‐source software that automatically classifies particle trajectories and systematically calculates velocities, run lengths, pauses, and a wealth of other parameters that are characteristic of motor‐based transport. We anticipate that laboratories will easily use this package to unveil previously uncovered intracellular transport details of individually‐moving cargoes inside neurons.      

Experimental validation of metabolic pathway modeling

In the search for new drug targets in the human parasite Entamoeba histolytica, metabolic control analysis was applied to determine, experimentally, flux control distribution of amebal glycolysis. The first (hexokinase, hexose-6-phosphate isomerase, pyrophosphate-dependent phosphofructokinase (PP(i)-PFK), aldolase and triose-phosphate isomerase) and final (3-phosphoglycerate mutase, enolase and pyruvate phosphate dikinase) glycolytic segments were reconstituted in vitro with recombinant enzymes under near-physiological conditions of pH, temperature and enzyme proportion. Flux control was determined by titrating flux with each enzyme component. In parallel, both glycolytic segments were also modeled by using the rate equations and kinetic parameters previously determined. Because the flux control distribution predicted by modeling and that determined by reconstitution were not similar, kinetic interactions among all the reconstituted components were experimentally revised to unravel the causes of the discrepancy. For the final segment, it was found that 3-phosphoglycerate was a weakly competitive inhibitor of enolase, whereas PP(i) was a moderate inhibitor of 3-phosphoglycerate mutase and enolase. For the first segment, PP(i) was both a strong inhibitor of aldolase and a nonessential mixed-type activator of amebal hexokinase; in addition, lower V(max) values for hexose-6-phosphate isomerase, PP(i)-PFK and aldolase were induced by PP(i) or ATP inhibition. It should be noted that PP(i) and other metabolites were absent from the 3-phosphoglycerate mutase and enolase or aldolase and hexokinase kinetics experiments, but present in reconstitution experiments. Only by incorporating these modifications in the rate equations, modeling predicted values of flux control distribution, flux rate and metabolite concentrations similar to those experimentally determined. The experimentally validated segment models allowed 'in silico experimentation' to be carried out, which is not easy to achieve in in vivo or in vitro systems. The results predicted a nonsignificant effect on flux rate and flux control distribution by adding parallel routes (pyruvate kinase for the final segment and ATP-dependent PFK for the first segment), because of the much lower activity of these enzymes in the ameba. Furthermore, modeling predicted full flux-control by 3-phosphoglycerate mutase and hexokinase, in the presence of low physiological substrate and product concentrations. It is concluded that the combination of in vitro pathway reconstitution with modeling and enzyme kinetics experimentation permits a more comprehensive understanding of the pathway behavior and control properties.     

The bifunctional aldehyde–alcohol dehydrogenase controls ethanol and acetate production in Entamoeba histolytica under aerobic conditions

By applying metabolic control analysis and inhibitor titration we determined the degree of control (flux control coefficient) of pyruvate:ferredoxin oxidoreductase (PFOR) and bifunctional aldehyde–alcohol dehydrogenase (ADHE) over the fluxes of fermentative glycolysis of Entamoeba histolytica subjected to aerobic conditions. The flux-control coefficients towards ethanol and acetate formation determined for PFOR titrated with diphenyleneiodonium were 0.07 and 0.09, whereas for ADHE titrated with disulfiram were 0.33 and ?0.19, respectively. ADHE inhibition induced significant accumulation of glycolytic intermediates and lower ATP content. These results indicate that ADHE exerts significant flux-control on the carbon end-product formation of amoebas subjected to aerobic conditions.     

Kinetic modeling can describe in vivo glycolysis in Entamoeba histolytica

Glycolysis in the human parasite Entamoeba histolytica is characterized by the absence of cooperative modulation and the prevalence of pyrophosphate-dependent (over ATP-dependent) enzymes. To determine the flux-control distribution of glycolysis and understand its underlying control mechanisms, a kinetic model of the pathway was constructed by using the software gepasi. The model was based on the kinetic parameters determined in the purified recombinant enzymes, and the enzyme activities, and steady-state fluxes and metabolite concentrations determined in amoebal trophozoites. The model predicted, with a high degree of accuracy, the flux and metabolite concentrations found in trophozoites, but only when the pyrophosphate concentration was held constant; at variable pyrophosphate, the model was not able to completely account for the ATP production/consumption balance, indicating the importance of the pyrophosphate homeostasis for amoebal glycolysis. Control analysis by the model revealed that hexokinase exerted the highest flux control (73%), as a result of its low cellular activity and strong AMP inhibition. 3-Phosphoglycerate mutase also exhibited significant flux control (65%) whereas the other pathway enzymes showed little or no control. The control of the ATP concentration was also mainly exerted by ATP consuming processes and 3-phosphoglycerate mutase and hexokinase (in the producing block). The model also indicated that, in order to diminish the amoebal glycolytic flux by 50%, it was required to decrease hexokinase or 3-phosphoglycerate mutase by 24% and 55%, respectively, or by 18% for both enzymes. By contrast, to attain the same reduction in flux by inhibiting the pyrophosphate-dependent enzymes pyrophosphate-phosphofructokinase and pyruvate phosphate dikinase, they should be decreased > 70%. On the basis of metabolic control analysis, steps whose inhibition would have stronger negative effects on the energy metabolism of this parasite were identified, thus becoming alternative targets for drug design.     

Global patterns of stream detritivore distribution: implications for biodiversity loss in changing climates

Aim We tested the hypothesis that shredder detritivores, a key trophic guild in stream ecosystems, are more diverse at higher latitudes, which has important ecological implications in the face of potential biodiversity losses that are expected as a result of climate change. We also explored the dependence of local shredder diversity on the regional species pool across latitudes, and examined the influence of environmental factors on shredder diversity. Location World‐wide (156 sites from 17 regions located in all inhabited continents at latitudes ranging from 67° N to 41° S). Methods We used linear regression to examine the latitudinal variation in shredder diversity at different spatial scales: alpha (α), gamma (γ) and beta (β) diversity. We also explored the effect of γ‐diversity on α‐diversity across latitudes with regression analysis, and the possible influence of local environmental factors on shredder diversity with simple correlations. Results Alpha diversity increased with latitude, while γ‐ and β‐diversity showed no clear latitudinal pattern. Temperate sites showed a linear relationship between γ‐ and α‐diversity; in contrast, tropical sites showed evidence of local species saturation, which may explain why the latitudinal gradient in α‐diversity is not accompanied by a gradient in γ‐diversity. Alpha diversity was related to several local habitat characteristics, but γ‐ and β‐diversity were not related to any of the environmental factors measured. Main conclusions Our results indicate that global patterns of shredder diversity are complex and depend on spatial scale. However, we can draw several conclusions that have important ecological implications. Alpha diversity is limited at tropical sites by local factors, implying a higher risk of loss of key species or the whole shredder guild (the latter implying the loss of trophic diversity). Even if regional species pools are not particularly species poor in the tropics, colonization from adjacent sites may be limited. Moreover, many shredder species belong to cool‐adapted taxa that may be close to their thermal maxima in the tropics, which makes them more vulnerable to climate warming. Our results suggest that tropical streams require specific scientific attention and conservation efforts to prevent loss of shredder biodiversity and serious alteration of ecosystem processes.     

Large-scale manipulation of mayfly recruitment affects population size

Recruitment establishes the initial size of populations and may influence subsequent population dynamics. Although strong inference can be made from empirical relationships between recruitment and population sizes, a definitive test of recruitment limitation requires manipulating recruitment at relevant spatial and temporal scales. We manipulated oviposition of the mayfly Baetis bicaudatus in multiple streams and measured the abundance of late-stage larvae at the end of the cohort. Based on fundamental knowledge of mayfly behavior, we increased, eliminated, or left unmodified preferred mayfly oviposition sites in 45-m reaches of streams (N = 4) of one high-altitude drainage basin in western Colorado, USA. We compared egg densities before (2001) and after the manipulation (2002) using paired t tests and compared larval densities before and after the manipulation among treatments using repeated measures analysis of variance. This manipulation altered not only egg densities, but also larval abundances 1 year later. Compared to the previous year, we experimentally increased egg densities at the addition sites by approximately fourfold, reduced egg densities to zero in the subtraction sites, and maintained egg densities in the control sites. After the manipulation, larval densities increased significantly by a factor of approximately 2.0 in the addition sites and decreased by a factor of approximately 2.5 in the subtraction sites. This outcome demonstrates that dramatic changes in recruitment can limit larval population size at the scale of a stream reach, potentially masking previously observed post-recruitment processes explaining the patterns of variation in abundance of a stream insect. Furthermore, our results emphasize the importance of preferred oviposition habitats to population sizes of organisms.