Metabolite channeling by a dynamic metabolon

Science ◽  
2016 ◽  
Vol 354 (6314) ◽  
pp. 843.3-843 ◽  
Author(s):  
Pamela J. Hines
Keyword(s):  
Metabolite Channeling

Metabolite Channeling: Creatine Kinase Microcompartments

2013 ◽  
pp. 80-85 ◽  
Author(s):  
U. Schlattner ◽  
M. Tokarska-Schlattner ◽  
T. Wallimann
Keyword(s):  
Creatine Kinase ◽  
Metabolite Channeling

scholarly journals Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Nitish Sathyanarayanan ◽  
Giuseppe Cannone ◽  
Lokesh Gakhar ◽  
Nainesh Katagihallimath ◽  
Ramanathan Sowdhamini ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Ring Opening ◽  
Environmental Pollutants ◽  
Degradation Pathway ◽  
Substrate Channeling ◽  
Enzyme Form ◽  
X Ray Scattering ◽  
Hydrophobic Tunnel ◽  
Metabolite Channeling

Abstract Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.

scholarly journals Rapid Diffusion of Green Fluorescent Protein in the Mitochondrial Matrix

1998 ◽  
Vol 140 (4) ◽  
pp. 821-829 ◽  
Author(s):  
Arthur Partikian ◽  
Bence Ölveczky ◽  
R. Swaminathan ◽  
Yuxin Li ◽  
A.S. Verkman
Keyword(s):  
Green Fluorescent Protein ◽  
Aqueous Phase ◽  
Correlation Time ◽  
Fluorescent Protein ◽  
Rotational Correlation Time ◽  
Mitochondrial Matrix ◽  
Phase Diffusion ◽  
The Matrix ◽  
Green Fluorescent ◽  
Metabolite Channeling

Abstract. It is thought that the high protein density in the mitochondrial matrix results in severely restricted solute diffusion and metabolite channeling from one enzyme to another without free aqueous-phase diffusion. To test this hypothesis, we measured the diffusion of green fluorescent protein (GFP) expressed in the mitochondrial matrix of fibroblast, liver, skeletal muscle, and epithelial cell lines. Spot photobleaching of GFP with a 100× objective (0.8-μm spot diam) gave half-times for fluorescence recovery of 15–19 ms with >90% of the GFP mobile. As predicted for aqueous-phase diffusion in a confined compartment, fluorescence recovery was slowed or abolished by increased laser spot size or bleach time, and by paraformaldehyde fixation. Quantitative analysis of bleach data using a mathematical model of matrix diffusion gave GFP diffusion coefficients of 2–3 × 10−7 cm2/s, only three to fourfold less than that for GFP diffusion in water. In contrast, little recovery was found for bleaching of GFP in fusion with subunits of the fatty acid β-oxidation multienzyme complex that are normally present in the matrix. Measurement of the rotation of unconjugated GFP by time-resolved anisotropy gave a rotational correlation time of 23.3 ± 1 ns, similar to that of 20 ns for GFP rotation in water. A rapid rotational correlation time of 325 ps was also found for a small fluorescent probe (BCECF, ∼0.5 kD) in the matrix of isolated liver mitochondria. The rapid and unrestricted diffusion of solutes in the mitochondrial matrix suggests that metabolite channeling may not be required to overcome diffusive barriers. We propose that the clustering of matrix enzymes in membrane-associated complexes might serve to establish a relatively uncrowded aqueous space in which solutes can freely diffuse.

scholarly journals Probing Light-Dependent Regulation of the Calvin Cycle Using a Multi-Omics Approach

2021 ◽  
Vol 12 ◽  
Author(s):  
Nathaphon Yu King Hing ◽  
Uma K. Aryal ◽  
John A. Morgan
Keyword(s):  
Light Intensity ◽  
Atmospheric Carbon Dioxide ◽  
Metabolic Flux ◽  
Calvin Cycle ◽  
Model Organism ◽  
Flux Analysis ◽  
Photosynthetic Organisms ◽  
Light Intensities ◽  
External Conditions ◽  
Metabolite Channeling

Photoautotrophic microorganisms are increasingly explored for the conversion of atmospheric carbon dioxide into biomass and valuable products. The Calvin-Benson-Bassham (CBB) cycle is the primary metabolic pathway for net CO2 fixation within oxygenic photosynthetic organisms. The cyanobacteria, Synechocystis sp. PCC 6803, is a model organism for the study of photosynthesis and a platform for many metabolic engineering efforts. The CBB cycle is regulated by complex mechanisms including enzymatic abundance, intracellular metabolite concentrations, energetic cofactors and post-translational enzymatic modifications that depend on the external conditions such as the intensity and quality of light. However, the extent to which each of these mechanisms play a role under different light intensities remains unclear. In this work, we conducted non-targeted proteomics in tandem with isotopically non-stationary metabolic flux analysis (INST-MFA) at four different light intensities to determine the extent to which fluxes within the CBB cycle are controlled by enzymatic abundance. The correlation between specific enzyme abundances and their corresponding reaction fluxes is examined, revealing several enzymes with uncorrelated enzyme abundance and their corresponding flux, suggesting flux regulation by mechanisms other than enzyme abundance. Additionally, the kinetics of 13C labeling of CBB cycle intermediates and estimated inactive pool sizes varied significantly as a function of light intensity suggesting the presence of metabolite channeling, an additional method of flux regulation. These results highlight the importance of the diverse methods of regulation of CBB enzyme activity as a function of light intensity, and highlights the importance of considering these effects in future kinetic models.

Reengineering of the human pyruvate dehydrogenase complex: from disintegration to highly active agglomerates

2017 ◽  
Vol 474 (5) ◽  
pp. 865-875 ◽  
Author(s):  
Jin Guo ◽  
Samira Hezaveh ◽  
Jana Tatur ◽  
An-Ping Zeng ◽  
Uwe Jandt
Keyword(s):  
Pyruvate Dehydrogenase ◽  
Pyruvate Dehydrogenase Complex ◽  
Catalytic Reactions ◽  
Catalytic Core ◽  
Highly Active ◽  
Multiple Copies ◽  
Fundamental Research ◽  
Metabolite Channeling ◽  
Enzyme Cascades ◽  
Dehydrogenase Complex

The pyruvate dehydrogenase complex (PDC) plays a central role in cellular metabolism and regulation. As a metabolite-channeling multi-enzyme complex it acts as a complete nanomachine due to its unique geometry and by coupling a cascade of catalytic reactions using ‘swinging arms'. Mammalian and specifically human PDC (hPDC) is assembled from multiple copies of E1 and E3 bound to a large E2/E3BP 60-meric core. A less restrictive and smaller catalytic core, which is still active, is highly desired for both fundamental research on channeling mechanisms and also to create a basis for further modification and engineering of new enzyme cascades. Here, we present the first experimental results of the successful disintegration of the E2/E3BP core while retaining its activity. This was achieved by C-terminal α-helixes double truncations (eight residues from E2 and seven residues from E3BP). Disintegration of the hPDC core via double truncations led to the formation of highly active (approximately 70% of wildtype) apparently unordered clusters or agglomerates and inactive non-agglomerated species (hexamer/trimer). After additional deletion of N-terminal ‘swinging arms’, the aforementioned C-terminal truncations also caused the formation of agglomerates of minimized E2/E3BP complexes. It is likely that these ‘swinging arm’ regions are not solely responsible for the formation of the large agglomerates.

scholarly journals Composition of phenolics and volatiles in strawberry cultivars and influence of preharvest hexanal treatment on their profiles

2015 ◽  
Vol 95 (1) ◽  
pp. 115-126 ◽  
Author(s):  
Azizah Misran ◽  
Priya Padmanabhan ◽  
J. Alan Sullivan ◽  
Shahrokh Khanizadeh ◽  
Gopinadhan Paliyath
Keyword(s):  
Phenolic Compounds ◽  
Solid Phase ◽  
Volatile Components ◽  
Strawberry Fruit ◽  
Southern Ontario ◽  
Qualitative And Quantitative ◽  
Volatile Profiles ◽  
Metabolite Channeling ◽  
Strawberry Cultivars

Misran, A., Padmanabhan, P., Sullivan, J. A., Khanizadeh, S. and Paliyath, G. 2015. Composition of phenolics and volatiles in strawberry cultivars and influence of preharvest hexanal treatment on their profiles. Can. J. Plant Sci. 95: 115–126. Biochemical changes of quality-determining components were evaluated in strawberry fruit subjected to preharvest spray treatments using a hexanal-containing formulation that is known to enhance shelf life and quality of fruits. Phenolic compounds and volatiles of fruits of four strawberry cultivars (Mira, Jewel, Kent, and St. Pierre) grown in southern Ontario were characterized by HPLC-MS and solid phase micro extraction (SPME) analysis. Qualitative and quantitative profiles of phenolic compounds varied among the cultivars. In all the cultivars, anthocyanins constituted the most prominent class of phenolic compounds. Volatile profiles of strawberry homogenate differed among the cultivars. Changes in phenolics and volatiles composition were determined in fruits of Mira and Jewel after spraying with a hexanal-containing formulation at weekly intervals. In Jewel, preharvest hexanal spraying altered the profiles of polyphenolic components, while minimal changes were noticed in Mira. Interestingly, very few differences were identified in ester profiles of treated and untreated Mira. In general, hexanal spray application resulted in a decrease in the abundance of several volatile components including esters, ketones, and lactones in treated Jewel compared with the control. The results suggest that cultivar-specific quality changes may result from a preharvest application of hexanal formulations, which may also imply different patterns of metabolite channeling and delay of fruit ripening processes.

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