TY  - JOUR
A1  - Osmanoglu, Özge
A1  - Khaled AlSeiari, Mariam
A1  - AlKhoori, Hasa Abduljaleel
A1  - Shams, Shabana
A1  - Bencurova, Elena
A1  - Dandekar, Thomas
A1  - Naseem, Muhammad
T1  - Topological Analysis of the Carbon-Concentrating CETCH Cycle and a Photorespiratory Bypass Reveals Boosted CO\(_2\)-Sequestration by Plants
JF  - Frontiers in Bioengineering and Biotechnology
N2  - Synthetically designed alternative photorespiratory pathways increase the biomass of tobacco and rice plants. Likewise, some in planta–tested synthetic carbon-concentrating cycles (CCCs) hold promise to increase plant biomass while diminishing atmospheric carbon dioxide burden. Taking these individual contributions into account, we hypothesize that the integration of bypasses and CCCs will further increase plant productivity. To test this in silico, we reconstructed a metabolic model by integrating photorespiration and photosynthesis with the synthetically designed alternative pathway 3 (AP3) enzymes and transporters. We calculated fluxes of the native plant system and those of AP3 combined with the inhibition of the glycolate/glycerate transporter by using the YANAsquare package. The activity values corresponding to each enzyme in photosynthesis, photorespiration, and for synthetically designed alternative pathways were estimated. Next, we modeled the effect of the crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (CETCH), which is a set of natural and synthetically designed enzymes that fix CO₂ manifold more than the native Calvin–Benson–Bassham (CBB) cycle. We compared estimated fluxes across various pathways in the native model and under an introduced CETCH cycle. Moreover, we combined CETCH and AP3-w/plgg1RNAi, and calculated the fluxes. We anticipate higher carbon dioxide–harvesting potential in plants with an AP3 bypass and CETCH–AP3 combination. We discuss the in vivo implementation of these strategies for the improvement of C3 plants and in natural high carbon harvesters.
KW  - CO2-sequestration
KW  - photorespiration
KW  - elementary modes
KW  - synthetic pathways
KW  - carboxylation
KW  - metabolic modeling
KW  - CETCH cycle
Y1  - 2021
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-249260
SN  - 2296-4185
VL  - 9
ER  - 
TY  - JOUR
A1  - Naseem, Muhammad
A1  - Othman, Eman M.
A1  - Fathy, Moustafa
A1  - Iqbal, Jibran
A1  - Howari, Fares M.
A1  - AlRemeithi, Fatima A.
A1  - Kodandaraman, Geema
A1  - Stopper, Helga
A1  - Bencurova, Elena
A1  - Vlachakis, Dimitrios
A1  - Dandekar, Thomas
T1  - Integrated structural and functional analysis of the protective effects of kinetin against oxidative stress in mammalian cellular systems
JF  - Scientific Reports
N2  - Metabolism and signaling of cytokinins was first established in plants, followed by cytokinin discoveries in all kingdoms of life. However, understanding of their role in mammalian cells is still scarce. Kinetin is a cytokinin that mitigates the effects of oxidative stress in mammalian cells. The effective concentrations of exogenously applied kinetin in invoking various cellular responses are not well standardized. Likewise, the metabolism of kinetin and its cellular targets within the mammalian cells are still not well studied. Applying vitality tests as well as comet assays under normal and hyper-oxidative states, our analysis suggests that kinetin concentrations of 500 nM and above cause cytotoxicity as well as genotoxicity in various cell types. However, concentrations below 100 nM do not cause any toxicity, rather in this range kinetin counteracts oxidative burst and cytotoxicity. We focus here on these effects. To get insights into the cellular targets of kinetin mediating these pro-survival functions and protective effects we applied structural and computational approaches on two previously testified targets for these effects. Our analysis deciphers vital residues in adenine phosphoribosyltransferase (APRT) and adenosine receptor (A2A-R) that facilitate the binding of kinetin to these two important human cellular proteins. We finally discuss how the therapeutic potential of kinetin against oxidative stress helps in various pathophysiological conditions.
KW  - cytokinins
KW  - 6-benzylaminopurine
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-231317
VL  - 10
ER  -