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Metabolic Shift (metabolic + shift)
Selected AbstractsCharacterization of a Leishmania stage-specific mitochondrial membrane protein that enhances the activity of cytochrome c oxidase and its role in virulenceMOLECULAR MICROBIOLOGY, Issue 2 2010Ranadhir Dey Summary Leishmaniasis is caused by the dimorphic protozoan parasite Leishmania. Differentiation of the insect form, promastigotes, to the vertebrate form, amastigotes, and survival inside the vertebrate host accompanies a drastic metabolic shift. We describe a gene first identified in amastigotes that is essential for survival inside the host. Gene expression analysis identified a 27 kDa protein-encoding gene (Ldp27) that was more abundantly expressed in amastigotes and metacyclic promastigotes than in procyclic promastigotes. Immunofluorescence and biochemical analysis revealed that Ldp27 is a mitochondrial membrane protein. Co-immunoprecipitation using antibodies to the cytochrome c oxidase (COX) complex, present in the inner mitochondrial membrane, placed the p27 protein in the COX complex. Ldp27 gene-deleted parasites (Ldp27,/,) showed significantly less COX activity and ATP synthesis than wild type in intracellular amastigotes. Moreover, the Ldp27,/, parasites were less virulent both in human macrophages and in BALB/c mice. These results demonstrate that Ldp27 is an important component of an active COX complex enhancing oxidative phosphorylation specifically in infectious metacyclics and amastigotes and promoting parasite survival in the host. Thus, Ldp27 can be explored as a potential drug target and parasites devoid of the p27 gene could be considered as a live attenuated vaccine candidate against visceral leishmaniasis. [source] Proteomic comparison of four Eimeria tenella life-cycle stages: Unsporulated oocyst, sporulated oocyst, sporozoite and second-generation merozoitePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 19 2009Kalpana Lal Abstract We report the proteomes of four life-cycle stages of the Apicomplexan parasite Eimeria tenella. A total of 1868 proteins were identified, with 630, 699, 845 and 1532 found in early oocysts (unsporulated), late oocysts (sporulated), sporozoites and second-generation merozoites, respectively. A multidimensional protein identification technology shotgun approach identified 812 sporozoites, 1528 merozoites and all of the oocyst proteins, whereas 2-D gel proteomics identified 230 sporozoites and 98 merozoite proteins. Comparing the invasive stages, we find moving junction components RON2 in both, whereas AMA-1 and RON4 are found only in merozoites and AMA-2 and RON5 are only found in sporozoites, suggesting stage-specific moving junction proteins. During early oocyst to sporozoite development, refractile body and most "glideosome" proteins are found throughout, whereas microneme and most rhoptry proteins are only found after sporulation. Quantitative analysis indicates glycolysis and gluconeogenesis are the most abundant metabolic groups detected in all stages. The mannitol cycle "off shoot" of glycolysis was not detected in merozoites but was well represented in the other stages. However, in merozoites we find more protein associated with oxidative phosphorylation, suggesting a metabolic shift mobilising greater energy production. We find a greater abundance of protein linked to transcription, protein synthesis and cell cycle in merozoites than in sporozoites, which may be residual protein from the preceding massive replication during schizogony. [source] Prediction of metabolic function from limited data: Lumped hybrid cybernetic modeling (L-HCM)BIOTECHNOLOGY & BIOENGINEERING, Issue 2 2010Hyun-Seob Song Abstract Motivated by the need for a quick quantitative assessment of metabolic function without extensive data, we present an adaptation of the cybernetic framework, denoted as the lumped hybrid cybernetic model (L-HCM), which combines the attributes of the classical lumped cybernetic model (LCM) and the recently developed HCM. The basic tenet of L-HCM and HCM is the same, that is, they both view the uptake flux as being split among diverse pathways in an optimal way as a result of cellular regulation such that some chosen metabolic objective is realized. The L-HCM, however, portrays this flux distribution to occur in a hierarchical way, that is, first among lumped pathways, and next among individual elementary modes (EM) in each lumped pathway. Both splits are described by the cybernetic control laws using operational and structural return-on-investments, respectively. That is, the distribution of uptake flux at the first split is dynamically regulated according to environmental conditions, while the subsequent split is based purely on the stoichiometry of EMs. The resulting model is conveniently represented in terms of lumped pathways which are fully identified with respect to yield coefficients of all products unlike classical LCMs based on instinctive lumping. These characteristics enable the model to account for the complete set of EMs for arbitrarily large metabolic networks despite containing only a small number of parameters which can be identified using minimal data. However, the inherent conflict of questing for quantification of larger networks with smaller number of parameters cannot be resolved without a mechanism for parameter tuning of an empirical nature. In this work, this is accomplished by manipulating the relative importance of EMs by tuning the cybernetic control of mode-averaged enzyme activity with an empirical parameter. In a case study involving aerobic batch growth of Saccharomyces cerevisiae, L-HCM is compared with LCM. The former provides a much more satisfactory prediction than the latter when parameters are identified from a few primary metabolites. On the other hand, the classical model is more accurate than L-HCM when sufficient datasets are involved in parameter identification. In applying the two models to a chemostat scenario, L-HCM shows a reasonable prediction on metabolic shift from respiration to fermentation due to the Crabtree effect, which LCM predicts unsatisfactorily. While L-HCM appears amenable to expeditious estimates of metabolic function with minimal data, the more detailed dynamic models [such as HCM or those of Young et al. (Young et al., Biotechnol Bioeng, 2008; 100: 542,559)] are best suited for accurate treatment of metabolism when the potential of modern omic technology is fully realized. However, in view of the monumental effort surrounding the development of detailed models from extensive omic measurements, the preliminary insight into the behavior of a genotype and metabolic engineering directives that can come from L-HCM is indeed valuable. Biotechnol. Bioeng. 2010;106: 271,284. © 2010 Wiley Periodicals, Inc. [source] Proteome analysis of antibody-producing CHO cell lines with different metabolic profilesBIOTECHNOLOGY & BIOENGINEERING, Issue 2 2007Deborah E. Pascoe Abstract Two-dimensional gel electrophoresis and tandem mass spectrometry were used to identify proteins associated with a metabolic shift during fed-batch cultures of two recombinant antibody-producing CHO cell lines. The first cell line underwent a marked change in lactate metabolism during culture, initially producing lactate and then consuming it, while the second cell line produced lactate for a similar duration but did not later consume it. The first cell line displayed a declining specific antibody productivity during culture, correlating to the 2-D gel results and the intracellular antibody concentration determined by HPLC. Several statistical analysis methods were compared during this work, including a fixed fold-change criterion and t -tests using standard deviations determined in several ways from the raw data and mathematically transformed data. Application of a variance-stabilizing transformation enabled the use of a global empirical standard deviation in the t -tests. Most of the protein spots changing in each cell line did not change significantly in the other cell line. A substantial fraction of the changing proteins were glycolytic enzymes; others included proteins related to antibody production, protein processing, and cell structure. Enolase, pyruvate kinase, BiP/GRP78, and protein disulfide isomerase were found in spots that changed over time in both cell lines, and some protein changes differed from previous reports. These data provide a foundation for future investigation of metabolism in industrially relevant mammalian cell culture processes, and suggest that along with differences between cell types, the proteins expressed in cultures with low lactate concentrations may depend on how those conditions were generated. Biotechnol. Bioeng. 2007;98: 391,410. © 2007 Wiley Periodicals, Inc. [source] A single nutrient feed supports both chemically defined NS0 and CHO fed-batch processes: Improved productivity and lactate metabolismBIOTECHNOLOGY PROGRESS, Issue 5 2009Ningning Ma Abstract A chemically defined nutrient feed (CDF) coupled with basal medium preloading was developed to replace a hydrolysate-containing feed (HCF) for a fed-batch NS0 process. The CDF not only enabled a completely chemically defined process but also increased recombinant monoclonal antibody titer by 115%. Subsequent tests of CDF in a CHO process indicated that it could also replace the hydrolysate-containing nutrient feed in this expression system as well as providing an 80% increase in product titer. In both CDF NS0 and CHO processes, the peak lactate concentrations were lower and, more interestingly, lactate metabolism shifted markedly from net production to net consumption when cells transitioned from exponential to stationary growth phase. Subsequent investigations of the lactate metabolic shift in the CHO CDF process were carried out to identify the cause(s) of the metabolic shift. These investigations revealed several metabolic features of the CHO cell line that we studied. First, glucose consumption and lactate consumption are strictly complementary to each other. The combined cell specific glucose and lactate consumption rate was a constant across exponential and stationary growth phases. Second, Lactate dehydrogenase (LDH) activity fluctuated during the fed-batch process. LDH activity was at the lowest when lactate concentration started to decrease. Third, a steep cross plasma membrane glucose gradient exists. Intracellular glucose concentration was more than two orders of magnitude lower than that in the medium. Fourth, a large quantity of citrate was diverted out of mitochondria to the medium, suggesting a partially truncated tricarboxylic acid (TCA) cycle in CHO cells. Finally, other intermediates in or linked to the glycolytic pathway and the TCA cycle, which include alanine, citrate, isocitrate, and succinate, demonstrated a metabolic shift similar to that of lactate. Interestingly, all these metabolites are either in or linked to the pathway downstream of pyruvate, but upstream of fumarate in glucose metabolism. Although the specific mechanisms for the metabolic shift of lactate and other metabolites remain to be elucidated, the increased understanding of the metabolism of CHO cultures could lead to future improvements in medium and process development. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Cybernetic Modeling and Regulation of Metabolic Pathways in Multiple Steady States of Hybridoma CellsBIOTECHNOLOGY PROGRESS, Issue 5 2000Maria Jesus Guardia Hybridoma cells utilize a pair of complementary and partially substitutable substrates, glucose and glutamine, for growth. It has been shown that cellular metabolism shifts under different culture conditions. When those cultures at different metabolic states are switched to a continuous mode, they reach different steady states under the same operating conditions. A cybernetic model was constructed to describe the complementary and partial substitutable nature of substrate utilization. The model successfully predicted the metabolic shift and multiple steady-state behavior. The results are consistent with the experimental observation that the history of the culture affects the resulting steady state. [source] Thermodynamic Analysis of Energy Transfer in Acidogenic CulturesENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 5 2008J.-R. Bastidas-Oyanedel Abstract A global thermodynamic analysis, normally used for pure cultures, has been performed for steady-state data sets from acidogenic mixed cultures. This analysis is a combination of two different thermodynamic approaches, based on tabulated standard Gibbs energy of formation, global stoichiometry and medium compositions. It takes into account the energy transfer efficiency, ,, together with the Gibbs free energy dissipation, ,Go, analysis of the different data. The objective is to describe these systems thermodynamically without any heat measurement. The results show that , is influenced by environmental conditions, where increasing hydraulic retention time increases its value all cases. The pH effect on , is related to metabolic shifts and osmoregulation. Within the environmental conditions analyzed, , ranges from 0.23 for a hydraulic retention time of 20,h and pH,4, to 0.42 for a hydraulic retention time of 8,h and a pH ranging from 7,8.5. The estimated values of ,Go are comparable to standard Gibbs energy of dissipation reported in the literature. For the data sets analyzed, ,Go ranges from ,1210,kJ/molx, corresponding to a stirring velocity of 300,rpm, pH,6 and a hydraulic retention time of 6,h, to ,20744,kJ/molx for pH,4 and a hydraulic retention time of 20,h. For average conclusions, the combined approach based on standard Gibbs energy of formation and global stoichiometry, used in this thermodynamic analysis, allows for the estimation of Gibbs energy dissipation values from the extracellular medium compositions in acidogenic mixed cultures. Such estimated values are comparable to the standard Gibbs energy dissipation values reported in the literature. It is demonstrated that , is affected by the environmental conditions, i.e., stirring velocity, hydraulic retention time and pH. However, a relationship that relates this parameter to environmental conditions was not found and will be the focus of further research. [source] Thermal acclimation of photosynthesis: a comparison of boreal and temperate tree species along a latitudinal transectPLANT CELL & ENVIRONMENT, Issue 6 2010DYLAN N. DILLAWAY ABSTRACT Common gardens were established along a ,900 km latitudinal transect to examine factors limiting geographical distributions of boreal and temperate tree species in eastern North America. Boreal representatives were trembling aspen (Populus tremuloides Michx.) and paper birch (Betula papyrifera Marsh.), while temperate species were eastern cottonwood (Populus deltoides Bartr ex. Marsh var. deltoides) and sweetgum (Liquidambar styraciflua L.). The species were compared with respect to adjustments of leaf photosynthetic metabolism along the transect, with emphasis on temperature sensitivities of the maximum rate of ribulose bisphosphate (RuBP) carboxylation (EV) and regeneration (EJ). During leaf development, the average air temperature (Tgrowth) differed between the coolest and warmest gardens by 12 °C. Evidence of photosynthetic thermal acclimation (metabolic shifts compensating for differences in Tgrowth) was generally lacking in all species. Namely, neither EV nor EJ was positively related to Tgrowth. Correspondingly, the optimum temperature (Topt) of ambient photosynthesis (Asat) did not vary significantly with Tgrowth. Modest variation in Topt was explained by the combination of EV plus the slope and curvature of the parabolic temperature response of mesophyll conductance (gm). All in all, species differed little in photosynthetic responses to climate. Furthermore, the adaptive importance of photosynthetic thermal acclimation was overshadowed by gm's influence on Asat's temperature response. [source] | ||||||||||