scholarly journals In-Depth Computational Analysis of Natural and Artificial Carbon Fixation Pathways

2021 ◽  
Vol 2021 ◽  
pp. 1-23
Author(s):  
Hannes Löwe ◽  
Andreas Kremling
Keyword(s):  
Kinetic Data ◽  
Carbon Fixation ◽  
Specific Activity ◽  
Cost Minimization ◽  
Tricarboxylic Acid Cycle ◽  
Design Criterion ◽  
Industrial Biotechnology ◽  
Data Set ◽  
Specific Activities

In the recent years, engineering new-to-nature CO2- and C1-fixing metabolic pathways made a leap forward. New, artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham (CBB) cycle. The question remains how to best predict their in vivo performance and what actually makes one pathway “better” than another. In this context, we explore aerobic carbon fixation pathways by a computational approach and compare them based on their specific activity and yield on methanol, formate, and CO2/H2 considering the kinetics and thermodynamics of the reactions. Besides pathways found in nature or implemented in the laboratory, this included two completely new cycles with favorable features: the reductive citramalyl-CoA cycle and the 2-hydroxyglutarate-reverse tricarboxylic acid cycle. A comprehensive kinetic data set was collected for all enzymes of all pathways, and missing kinetic data were sampled with the Parameter Balancing algorithm. Kinetic and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway-specific activities. The specific activities of the reductive glycine pathway, the CETCH cycle, and the new reductive citramalyl-CoA cycle were predicted to match the best natural cycles with superior product-substrate yield. However, the CBB cycle performed better in terms of activity compared to the alternative pathways than previously thought. We make an argument that stoichiometric yield is likely not the most important design criterion of the CBB cycle. Still, alternative carbon fixation pathways were paretooptimal for specific activity and product-substrate yield in simulations with C1 substrates and CO2/H2 and therefore hold great potential for future applications in Industrial Biotechnology and Synthetic Biology.

scholarly journals In-depth computational analysis of natural and artificial carbon fixation pathways

2021 ◽  
Author(s):  
Hannes Löwe ◽  
Andreas Kremling
Keyword(s):  
Kinetic Data ◽  
Carbon Fixation ◽  
Specific Activity ◽  
Tricarboxylic Acid Cycle ◽  
Calvin Cycle ◽  
Industrial Biotechnology ◽  
Data Set ◽  
Specific Activities ◽  
Better Than

AbstractIn the recent years, engineering new-to-nature CO2 and C1 fixing metabolic pathways made a leap forward. These new, artificial pathways promise higher yields and activity than natural ones like the Calvin-Benson-Bassham cycle. The question remains how to best predict their in vivo performance and what actually makes one pathway “better” than another.In this context, we explore aerobic carbon fixation pathways by a computational approach and compare them based on their ATP-efficiency and specific activity considering the kinetics and thermodynamics of the reactions. Beside natural pathways, this included the artificial Reductive Glycine Pathway, the CETCH cycle and two completely new cycles with superior stoichiometry: The Reductive Citramalyl-CoA cycle and the 2-Hydroxyglutarate-Reverse Tricarboxylic Acid cycle. A comprehensive kinetic data set was collected for all enzymes of all pathways and missing kinetic data was sampled with the Parameter Balancing algorithm. Kinetic and thermodynamic data were fed to the Enzyme Cost Minimization algorithm to check for respective inconsistencies and calculate pathway specific activities.We found that the Reductive Glycine Pathway, the CETCH cycle and the new Reductive Citramalyl-CoA cycle were predicted to have higher ATP-efficiencies and specific activities than the natural cycles. The Calvin Cycle performed better than previously thought, however. It can be concluded that the weaker overall characteristics in the design of the Calvin Cycle might be compensated by other benefits like robustness, low nutrient demand and a good compatibility with the host’s physiological requirements. Nevertheless, the artificial carbon fixation cycles hold great potential for future applications in Industrial Biotechnology and Synthetic Biology.

Use of 14CO2 in estimating rates of hepatic gluconeogenesis

1992 ◽  
Vol 263 (1) ◽  
pp. E36-E41 ◽  
Author(s):  
E. Esenmo ◽  
V. Chandramouli ◽  
W. C. Schumann ◽  
K. Kumaran ◽  
J. Wahren ◽  
...  
Keyword(s):  
Blood Glucose ◽  
Specific Activity ◽  
Tricarboxylic Acid Cycle ◽  
Tricarboxylic Acid ◽  
Hepatic Gluconeogenesis ◽  
Acid Cycle ◽  
Specific Activities ◽  
Glucose Formation

Estimating the rate of hepatic gluconeogenesis in vivo from the incorporation of 14C from 14CO2 into glucose requires determination of the rates in liver of equilibration of oxaloacetate with fumarate, conversion of oxaloacetate to phosphoenolpyruvate (PEP), and conversion of PEP to pyruvate, all relative to the rate of tricarboxylic acid cycle flux. With the use of a model of mitochondrial metabolism and gluconeogenesis, expressions are derived relating specific activity of carboxyl of PEP from 14CO2 to those rates and specific activity of mitochondrial CO2. If those rates and specific activity of mitochondrial CO2 are known, specific activity of PEP, calculated using the expressions, should, on a mole basis, be one-half the specific activity of the glucose formed. At steady state, in the 60-h fasted individual, where glucose formation is solely by gluconeogenesis, twice estimated specific activity of PEP should then approximate that of blood glucose. Estimates of relative rates in 60-h fasted humans, previously made from distribution of 14C in glutamate from phenylacetylglutamine excreted when [3-14C]lactate and phenylacetate were given, were applied to the expressions. Specific activity of mitochondrial CO2 was equated to that of CO2 expired by 60-h fasted subjects given NaH14CO3 and alpha-[1-14C]ketoisocaproate. Predicted specific activities approximated actual specific activities of blood glucose when NaH14CO3 was administered. alpha-[1-14C]ketoisocaproate administrations gave underestimates. This is attributable to differences between specific activities of hepatic mitochondrial CO2 and expired CO2, which is evidenced by higher incorporations of 14C in glucose than in expired CO2 from alpha-[1-14C]ketoisocaproate than from NaH14CO3.(ABSTRACT TRUNCATED AT 250 WORDS

scholarly journals Regulation of lipogenic capacity in lactating rats

1982 ◽  
Vol 208 (3) ◽  
pp. 611-618 ◽  
Author(s):  
M R Grigor ◽  
A Geursen ◽  
M J Sneyd ◽  
S M Warren
Keyword(s):  
Mammary Gland ◽  
Fatty Acid ◽  
Malic Enzyme ◽  
Fatty Acid Synthase ◽  
Specific Activity ◽  
Mammary Glands ◽  
Lipogenic Enzymes ◽  
Pregnancy And Lactation ◽  
Specific Activities

1. The rate of mammary-gland lipogenesis measured in vivo from 3H2O was suppressed after decreasing the milk demand by decreasing the number of pups from ten to two or three, as well as by giving diets containing lipid [Grigor & Warren (1980) Biochem. J. 188, 61-65]. 2. The specific activities of the lipogenic enzymes fatty acid synthase, glucose 6-phosphate dehydrogenase and ‘malic’ enzyme increased between 6- and 10-fold in the mammary gland and between 2- and 3-fold in the livers during the first 10 days of lactation. The increases in specific activity coupled with the doubling of liver mass which occurred during pregnancy and lactation resulted in considerable differences in total liver activities when compared with virgin animals. 3. Although consumption of a diet containing 20% peanut oil suppressed the activities of the three lipogenic enzymes in the livers, only the ‘malic’ enzyme was affected in the mammary glands. 4. In contrast, decreased milk demand did not affect the specific activities of any of the liver enzymes, whereas it resulted in suppression of all three lipogenic enzymes of the mammary glands. There was no effect on either the cytoplasmic malate dehydrogenase or the lactate dehydrogenase of the mammary gland. 5. In all the experiments performed, the activity of the fatty acid synthase correlated with the amount of material precipitated by the rabbit antibody raised against rat fatty acid synthase.

Lethality of a tritiated amino acid in early mouse embryos

Development ◽  
1985 ◽  
Vol 88 (1) ◽  
pp. 209-217
Author(s):  
Janet L. Wiebold ◽  
Gary B. Anderson
Keyword(s):  
Specific Activity ◽  
Subsequent Development ◽  
Blastocyst Stage ◽  
Mouse Embryos ◽  
Radiation Induced ◽  
Specific Activities ◽  
Tritiated Amino Acids ◽  
Early Mouse

2- to 4-cell and morula- to blastocyst-stage mouse embryos were cultured for 1 h in tritiated leucine at two specific activities and their subsequent development followed in vitro and in vivo (after transfer to recipients), respectively. 2- to 4-cell embryos that incorporated an average of 42 d.p.m. per embryo were impaired in their ability to develop to the morula and blastocyst stage. Recipients receiving morulae and blastocysts that had incorporated an average of 384 d.p.m. per embryo failed to produce young. Reduction of the specific activity improved the viability of embryos both in vitro and in vivo but development was still less than that of unlabelled embryos. Protein degradation curves were different for both 2- to 4-cell and morulato blastocyst-stage embryos labelled at the two different specific activities. Most studies using tritiated amino acids have employed higher specific activities than those used here and they may have to be reevaluated due to the possibility of radiation-induced artifacts.

scholarly journals Activity and Concentration of Antithrombin III in Plasma and Serum

1977 ◽  
Author(s):  
L. Róka ◽  
H. Bleyl
Keyword(s):  
Antithrombin Iii ◽  
Specific Activity ◽  
Simultaneous Occurrence ◽  
Single Individual ◽  
Chromogenic Substrate ◽  
Plasma Samples ◽  
Specific Activities ◽  
Antithrombin Iii Activity ◽  
Heparin Affinity

The concentration and activity of antithrombin III contained in plasma and serum of a single individual were compared with each other. The concentration of antithrombin III was determined by means of the rockett technique according to Laurell, antithrombin activity was measured by thrombin neutralization, residual thrombin activity was quantified using the chromogenic substrate Chromozym TH. The patients’ plasmas examined could be divided into different groups according to their antithrombin III specific activity. Most of the samples contained about 34 U/mg, the specific activities of two other groups were about 20 u/mg and 15 U/mg respectively. Only 3 samples contained more than 45 U/mg. In plasma samples with low specific antithrombin III activity the simultaneous occurrence of free antithrombin and an antithrombin-thrombin complex formed in vivo has been demonstrated by means of the two-dimensional Immunoelectrophoresis with heparin added to the agarose-gel medium. (Sas et al., 1975). The antithrombin-thrombin complex could be separated from free antithrombin by adsorption to a heparin-agarose column and fractionated elution, using the different heparin affinity of complex-bound and free antithrombin.

scholarly journals Platelet Alterations Caused by Antiplatelet Antibodies in the Circulation

1977 ◽  
Author(s):  
T. Nagasawa ◽  
B.K. Kim ◽  
M.G. Baldini
Keyword(s):  
Platelet Count ◽  
Specific Activity ◽  
Rabbit Model ◽  
Antiplatelet Antibodies ◽  
Large Numbers ◽  
Severe Reduction ◽  
Series Of Experiments ◽  
Specific Activities

It is known that antiplatelet antibodies cause loss of platelet cytoplasmic and granular contents in vitro. It is, however, unknown whether similar platelet changes occur in vivo, in the circulation, leading to destruction and phagocytosis of platelets in the R.E. system. To study this possibility a rabbit model was devised. Severe and stable thrombocytopenia was first produced in rabbits by one intravenous injection of Adriamycin. Large numbers of allogenic platelets labeled in vitro with 51Cr and 14C-serotonin were then infused to raise the circulating platelet count to 180-250 × 103/mm3. A dilute heteroimmune antiplatelet serum prepared in the guinea pig was infused intravenously and platelet samples were collected four times during the subsequent 30 minutes to 24 hours. Platelet hexokinase and β-glucuronidase, 14C-serotonin and 51Cr were measured. Within the first 60 min the specific activity of 51Cr in platelets decreased by 21%, 14C-serotonin declined by 30%, hexokinase by 5% and β-glucuronidase by 29%. During the subsequent 24 hours only 51Cr and hexokinase registered a mild decrease but 51C-serotonin and β-glucuronidase remained essentially unchanged. In a second series of experiments the effect of platelet alloantibodies was studied in rabbits previously immunized with allogenic platelets. The decline in the specific activities of the enzymes and 14C-serotonin was similar to that observed in animals treated with heteroimmune sera but loss of 51Cr was more severe. These results demonstrate that the platelets remaining in the circulation after the disappearance of the immediate effect of hetero- or alloantibodies were qualitatively altered with a severe reduction of their granular and cytoplasmic contents.

Proteinsynthese in grünen Blättern

1964 ◽  
Vol 19 (3) ◽  
pp. 235-248 ◽  
Author(s):  
Benno Parthier
Keyword(s):  
Amino Acids ◽  
Specific Activity ◽  
Subcellular Fractions ◽  
Mechanical Destruction ◽  
Cell Organization ◽  
Specific Activities ◽  
Short Time ◽  
Natural Cell

In the green leaves of Nicotiana rustica, protein synthesis of various subcellular fractions has been investigated in vivo after 14CO2-photosynthesis and also in vitro by incorporation of radioactive amino acids. Following photosynthesis, homogenization of the tissues, and differential centrifugation of the homogenates, the results show that all structural particles of the cell are able to use photosynthetically formed amino acids for the incorporation into their proteins. The proteins with the highest specific activities are found in the mitochondria-rich fractions, and with the lowest in the soluble cytoplasma supernatant. High specific activities are also observed in the ribosomal-rich fraction in short-time experiments, and also in the chloroplasts after exposure of the leaves to light. After an osmotic-mechanical destruction of the isolated 14C-labelled chloroplasts, the specific activities of lamellar proteins exceed the colourless soluble proteins of the chloroplasts. A green fraction, sedimented at 1,000 g, and perhaps mainly consisting of broken and leached chloroplasts, shows the highest specific activity of all chloroplast fractions. Obviously, due to the destruction of the natural cell organization, in vitro experiments give not only drastically decreased specific activities but also another distribution of the incorporated amino acids between the subcellular fractions, compared with experiments in vivo.

Does muscle creatine phosphokinase have access to the total pool of phosphocreatine plus creatine?

1998 ◽  
Vol 274 (3) ◽  
pp. R868-R872 ◽  
Author(s):  
Peter W. Hochachka ◽  
Mark K. P. Mossey
Keyword(s):  
Creatine Phosphokinase ◽  
Specific Activity ◽  
Current Theory ◽  
Acid Extraction ◽  
Fiber Types ◽  
Metabolic States ◽  
Total Pool ◽  
Specific Activities ◽  
Fast Twitch

Two fundamental assumptions underlie currently accepted dogma on creatine phosphokinase (CPK) function in phosphagen-containing cells: 1) CPK always operates near equilibrium and 2) CPK has access to, and reacts with, the entire pool of phosphocreatine (PCr) and creatine (Cr). We tested the latter assumption in fish fast-twitch or white muscle (WM) by introducing [14C]Cr into the WM pool in vivo. To avoid complications arising from working with muscles formed from a mixture of fast and slow fibers, it was advantageous to work with fish WM because it is uniformly fast twitch and is anatomically separated from other fiber types. According to current theory, at steady state after [14C]Cr administration, the specific activities of PCr and Cr should be the same under essentially all conditions. In contrast, we found that, in various metabolic states between rest and recovery from exercise, the specific activity of PCr greatly exceeds that of Cr. The data imply that a significant fraction of Cr is not free to rapidly exchange with exogenously added [14C]Cr. Releasing of this unlabeled or “cold” Cr on acid extraction accounts for lowered specific activities. This unexpected and provocative result is not consistent with traditional models of phosphagen function.

Cerebral metabolism of doubly labeled glucose in humans in vivo

1965 ◽  
Vol 20 (1) ◽  
pp. 117-130 ◽  
Author(s):  
William Sacks
Keyword(s):  
Specific Activity ◽  
Cerebral Metabolism ◽  
Venous Blood ◽  
Tritiated Water ◽  
Krebs Cycle ◽  
Succinic Semialdehyde ◽  
Active Pool ◽  
Specific Activities ◽  
Experimental Values

With glucose-3-C14 as injected substrate, the production of C14O2 almost kept pace with the net uptake of C14 by brain. Brain C14O2 specific activities practically coincided with venous blood glucose specific activities. This rapid production of C14O2 with little or no dilution of C14 led to the derivation of theoretical curves for glucose-2-, glucose-1-, or glucose-6-C14 experiments. The dissimilarity between theoretical and experimental values suggested that there is a significant dilution of C14 in traversing the Krebs cycle. Equations derived from hypothetical metabolic pathways which included a pool of substrate, x, were employed to match theoretical with average experimental values. In experiments with doubly labeled glucose-C14-T, brain TOH (tritiated water) specific activities were used to derive brain C14O2 specific activity values which closely approximated actual results. A scheme for human cerebral metabolism of glucose in vivo, which includes a small, metabolically active pool of glutamate, ggr-aminobutyrate, and succinic semialdehyde, is proposed. brain glucose oxidation; in vivo brain metabolism; isotopic glucose metabolism; glucose-C14-T cerebral metabolism Submitted on February 3, 1964

Structural and Metabolic Interrelationships Among Glycerophosphatides of Rat Liver In Vivo

1971 ◽  
Vol 49 (12) ◽  
pp. 1347-1356 ◽  
Author(s):  
B. J. Holub ◽  
A. Kuksis
Keyword(s):  
Rat Liver ◽  
De Novo ◽  
Specific Activity ◽  
Acyl Transfer ◽  
De Novo Synthesis ◽  
Individual Molecular Species ◽  
Relative Specific Activity ◽  
Proportional Contribution ◽  
Specific Activities

The specific activities of individual molecular species of rat liver diacylglycerylphosphorocholine (PC), diacylglycerylphosphoroethanolamine (PE), and diacylglycerophosphorylinositol (MPI) were determined and compared following intravenous injection of glycerol-14C. PC, PE, and MPI contained 41, 51, and 83%, respectively, tetraenoic species, and 40,17, and 9% combined mono-, di-, and trienoic species. The rest of the phosphatide mass of PC, PE, and MPI was contributed by 18, 32, and 8% penta- and hexaenoic species, respectively. The proportions of chemical classes of the glycerophosphatides differed by 1.1- to 18-fold while the fatty acid associations within the unsaturation classes common to these phosphatides varied 2.2- to 17-fold. After 5 min exposure to radioactive glycerol, the mono-, di-, and trienoic species of the PC, PE, and MPI possessed 13–18, 15–50, and 6–42 times, respectively, the specific activity of the tetraenes of the corresponding phosphatide classes. While the pentaenoic and hexaenoic species of PC and MPI had specific activities three to five times those of the respective tetraenes, the higher polyenes of PE were considerably more radioactive and approached the specific activity of the dienoic species of this phosphatide. With progressing time up to 60 min, the tetraenoic species of PC, PE, and MPI showed increases in relative specific activity of 50, 64, and 109%, respectively, in the three phosphatides. These results are consistent with an effective de novo synthesis of the oligoenoic species and a transacylation of the tetraenoic species of all liver glycerophosphatides tested. The proportional contribution of de novo synthesis in comparison to acyl transfer is apparently greater to the formation of PC and PE than to that of MPI.

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