scholarly journals Branch point control at malonyl-CoA node: A computational framework to uncover the design principles of an ideal genetic-metabolic switch

2019 ◽  
Author(s):  
Peng Xu
Keyword(s):  
Fatty Acids ◽  
Binding Affinity ◽  
Transcriptional Repressor ◽  
Design Principles ◽  
Optimal Controller ◽  
Metabolic Switch ◽  
Computational Framework ◽  
Target Molecule ◽  
Malonyl Coa ◽  
Metabolic Sink

AbstractLiving organism is an intelligent system encoded by hierarchically-organized information to perform precisely-controlled biological functions. Biophysical models are important tools to uncover the design rules underlying complex genetic-metabolic circuit interactions. Based on a previously engineered synthetic malonyl-CoA switch (Xu et al, PNAS 2014), we have formulated nine differential equations to unravel the design principles underlying an ideal metabolic switch to improve fatty acids production in E. coli. By interrogating the physiologically accessible parameter space, we have determined the optimal controller architecture to configure both the metabolic source pathway and metabolic sink pathway. We determined that low protein degradation rate, medium strength of metabolic inhibitory constant, high metabolic source pathway induction rate, strong binding affinity of the transcriptional activator toward the metabolic source pathway, weak binding affinity of the transcriptional repressor toward the metabolic sink pathway, and a strong cooperative interaction of transcriptional repressor toward metabolic sink pathway benefit the accumulation of the target molecule (fatty acids). The target molecule (fatty acid) production is increased from 50% to 10-folds upon application of the autonomous metabolic switch. With strong metabolic inhibitory constant, the system displays multiple steady states. Stable oscillation of metabolic intermediate is the driving force to allow the system deviate from its equilibrium state and permits bidirectional ON-OFF gene expression control, which autonomously compensates enzyme level for both the metabolic source and metabolic sink pathways. The computational framework may facilitate us to design and engineer predictable genetic-metabolic switches, quest for the optimal controller architecture of the metabolic source/sink pathways, as well as leverage autonomous oscillation as a powerful tool to engineer cell function.

Distinct Modulation of Wild-Type and Selective Gene Mutated Vitamin D Receptor by Essential Poly Unsaturated Fatty Acids

2021 ◽  
Vol 21 ◽  
Author(s):  
Hari Balaji ◽  
Selvaraj Ayyamperuma ◽  
Niladri Saha ◽  
Shyam Sundar Pottabathula ◽  
Jubie Selvaraj ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Vitamin D ◽  
Ligand Binding ◽  
Vitamin D Deficiency ◽  
Binding Affinity ◽  
Unsaturated Fatty Acids ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Binding Energies ◽  
Wild Type

: Vitamin-D deficiency is a global concern. Gene mutations in the vitamin D receptor’s (VDR) ligand binding domain (LBD) variously alter the ligand binding affinity, heterodimerization with retinoid X receptor (RXR) and inhibit coactivator interactions. These LBD mutations may result in partial or total hormone unresponsiveness. A plethora of evidence report that selective long chain polyunsaturated fatty acids (PUFAs) including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and arachidonic acid (AA) bind to the ligand-binding domain of VDR and lead to transcriptional activation. We therefore hypothesize that selective PUFAs would modulate the dynamics and kinetics of VDRs, irrespective bioactive of vitamin-D binding. The spatial arrangements of the selected PUFAs in VDR active site were examined by in-silico docking studies. The docking results revealed that PUFAs have fatty acid structure-specific binding affinity towards VDR. The calculated EPA, DHA & AA binding energies (Cdocker energy) were lesser compared to vitamin-D in wild type of VDR (PDB id: 2ZLC). Of note, the DHA has higher binding interactions to the mutated VDR (PDB id: 3VT7) when compared to the standard Vitamin-D. Molecular dynamic simulation was utilized to confirm the stability of potential compound binding of DHA with mutated VDR complex. These findings suggest the unique roles of PUFAs in VDR activation and may offer alternate strategy to circumvent vitamin-D deficiency.

Improved energy homeostasis of the heart in the metabolic state of exercise

2000 ◽  
Vol 279 (4) ◽  
pp. H1490-H1501 ◽  
Author(s):  
Gary W. Goodwin ◽  
Heinrich Taegtmeyer ◽  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Fatty Acid Oxidation ◽  
Energy Homeostasis ◽  
Acid Oxidation ◽  
High Fat ◽  
Nonesterified Fatty Acids ◽  
Malonyl Coa ◽  
Metabolic Conditions ◽  
High Lactate

We postulate that metabolic conditions that develop systemically during exercise (high blood lactate and high nonesterified fatty acids) are favorable for energy homeostasis of the heart during contractile stimulation. We used working rat hearts perfused at physiological workload and levels of the major energy substrates and compared the metabolic and contractile responses to an acute low-to-high work transition under resting versus exercising systemic metabolic conditions (low vs. high lactate and nonesterified fatty acids in the perfusate). Glycogen preservation, resulting from better maintenance of high-energy phosphates, was a consequence of improved energy homeostasis with high fat and lactate. We explained the result by tighter coupling between workload and total β-oxidation. Total fatty acid oxidation with high fat and lactate reflected increased availability of exogenous and endogenous fats for respiration, as evidenced by increased long-chain fatty acyl-CoA esters (LCFA-CoAs) and by an increased contribution of triglycerides to total β-oxidation. Triglyceride turnover (synthesis and degradation) also appeared to increase. Elevated LCFA-CoAs caused high total β-oxidation despite increased malonyl-CoA. The resulting bottleneck at mitochondrial uptake of LCFA-CoAs stimulated triglyceride synthesis. Our results suggest the following. First, both malonyl-CoA and LCFA-CoAs determine total fatty acid oxidation in heart. Second, concomitant stimulation of peripheral glycolysis and lipolysis should improve cardiac energy homeostasis during exercise. We speculate that high lactate contributes to the salutary effect by bypassing the glycolytic block imposed by fatty acids, acting as an anaplerotic substrate necessary for high tricarbocylic acid cycle flux from fatty acid-derived acetyl-CoA.

scholarly journals Monitoring of changes in hepatic fatty acid and glycerolipid metabolism during the starved-to-fed transition in vivo. Studies on awake, unrestrained rats

1993 ◽  
Vol 289 (1) ◽  
pp. 49-55 ◽  
Author(s):  
A M B Moir ◽  
V A Zammit
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Liver Mitochondria ◽  
In Vivo Studies ◽  
Maximal Effect ◽  
Jugular Veins ◽  
Selective Labelling ◽  
Malonyl Coa ◽  
Cpt I

1. The technique of selective labelling of hepatic fatty acids in vivo [Moir and Zammit (1992) Biochem. J. 283, 145-149] has been used to monitor non-invasively the metabolism of fatty acids in the livers of awake unrestrained rats during the starved-to-refed transition. Values for the incorporation of labelled fatty acid into liver and plasma glycerolipids and into exhaled carbon dioxide after injection of labelled lipoprotein and Triton WR 1339 into rats with chronically cannulated jugular veins were obtained for successive 1 h periods from the start of refeeding of 24 h-starved rats. 2. Starvation for 24 h resulted in marked and reciprocal changes in the incorporation of label into glycerolipids and exhaled 14CO2, such that a 4-fold higher value was obtained for the oxidation/esterification ratio in livers of starved rats compared with fed animals. 3. Refeeding of starved rats did not return this ratio to the value observed for fed animals for at least 7 h; during the first 3 h of refeeding the ratio was at least as high as that for starved rats. Between 4 h and 6 h of refeeding the ratio was still approx. 70% of that in starved animals, and 2.5-fold higher than in fed rats. 4. These data support the hypothesis that the capacity of the liver to oxidize fatty acids is maintained at a high level during the initial stages of refeeding [Grantham and Zammit (1986) Biochem. J. 239, 485-488] and that control of the flux of hepatic fatty acids into the oxidative pathway is largely lost from the reaction catalysed by mitochondrial overt carnitine palmitoyltransferase (CPT I) during this phase of recovery from the starved state. 5. Refeeding also resulted in a rapid (< 1 h) increase in hepatic malonyl-CoA concentrations to values intermediate between those in livers of fed and starved animals. The sensitivity of CPT I to malonyl-CoA inhibition in isolated liver mitochondria was only partially reversed even after 5 h of refeeding. 6. Refeeding resulted in an acute 35% inhibition of the fraction of synthesized triacylglycerol that was secreted into the plasma; the maximal effect occurred 2-3 h after the start of refeeding. The inhibition of the fractional secretion rate was fully reversed after 5 h of refeeding. 7. The amount of 14C label that was incorporated into phospholipids as a fraction of total glycerolipid synthesis was doubled within 2 h of the start of refeeding.(ABSTRACT TRUNCATED AT 400 WORDS)

Effect of Thiolactomycin on de novo Fatty Acid Biosynthesis in Plants

1990 ◽  
Vol 45 (5) ◽  
pp. 518-520 ◽  
Author(s):  
Manfred Focke ◽  
Andrea Feld ◽  
Hartmut K. Lichtenthaler
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
Fatty Acid Biosynthesis ◽  
De Novo ◽  
Fatty Acid Synthetase ◽  
Acetate Incorporation ◽  
Acid Biosynthesis ◽  
Acetyl Coa ◽  
Malonyl Coa ◽  
Total Fatty Acids

Thiolactomycin was shown to be a potent inhibitor of de novo fatty acid biosynthesis in intact isolated chloroplasts (measured as [14C]acetate incorporation into total fatty acids). In our attempt to further localize the inhibition site we confirmed the inhibition with a fatty acid synthetase preparation, measuring the incorporation of [14C]malonyl-CoA into total fatty acids. From the two proposed enzymic targets of the fatty acid synthetase by thiolactomycin we could exclude the acetyl-CoA: ACP transacetylase. It appears that the inhibition by thiolactomycin occurs on the level of the condensing enzymes, i.e. the 3-oxoacyl-ACP synthases. We also demonstrated that the two starting enzymes of de novo fatty acid biosynthesis, the acetyl-CoA synthetase and the acetyl-CoA carboxylase, are not affected by thiolactomycin.

scholarly journals Fatty Acids with in Vitro Binding Affinity for Human Opioid Receptors from the Fungus Emericella nidulans

2013 ◽  
Vol 61 (44) ◽  
pp. 10476-10480 ◽  
Author(s):  
Amer H. Tarawneh ◽  
Francisco León ◽  
Mohamed M. Radwan ◽  
Xiaoning Wang ◽  
Olivia R. Dale ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Binding Affinity ◽  
Opioid Receptors ◽  
Emericella Nidulans ◽  
In Vitro Binding ◽  
Vitro Binding

Synthesis of branched-chain and odd-numbered fatty acids from malonyl-CoA

1960 ◽  
Vol 3 (1) ◽  
pp. 101-106 ◽  
Author(s):  
Margorie G. Horning ◽  
Donald B. Martin ◽  
Arthur Karmen ◽  
P.Roy Vagelos
Keyword(s):  
Fatty Acids ◽  
Malonyl Coa ◽  
Branched Chain
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