scholarly journals Communication and Cross-Regulation Between Multiple Concatenated Enzymatic Reaction Networks

2021 ◽  
Author(s):  
Mo Sun ◽  
Jie Deng ◽  
Andreas Walther
Keyword(s):  
Self Assembly ◽  
Enzymatic Reaction ◽  
Promoter Sequence ◽  
Rnase H ◽  
Regulatory Mechanisms ◽  
Reaction Networks ◽  
Rna Transcription ◽  
Driven Systems ◽  
Transcription Regulator ◽  
Systems Chemistry

Nature connects multiple fuel-driven chemical/enzymatic reaction networks (CRNs/ERNs) via cross-regulation to hierarchically control biofunctions for a tailored adaption in complex sensory landscapes. In contrast, emerging artificial fuel-driven systems most-ly focus on a single CRN and their implementation to direct self-assembly or material responses. In this work, we introduce a facile example of communication and cross-regulation among multiple DNA-based ERNs regulated by a concatenated RNA transcription regulator. For this purpose, we run two fuel-driven DNA-based ERNs by concurrent NAD+-fueled ligation and restriction via endo-nucleases (REases) in parallel. ERN one allows for the dynamic steady-state formation of the promoter sequence for T7 RNA poly-merase, which activates RNA transcription. The produced RNA regulator can repress or promote the second ERN via RNA-mediated strand displacement. Furthermore, adding RNase H to degrade the produced RNA can restart the reaction or tune the lag time of two ERNs, giving rise to a repression-recovery and promotion-stop processes. We believe that concatenation of multiple CRNs provides a basis for the design of more elaborate autonomous regulatory mechanisms in systems chemistry and synthetic biology.

scholarly journals A 1232 bp upstream sequence of glutamine synthetase 1b from Eichhornia crassipes is a root-preferential promoter sequence

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yanshan Zhong ◽  
Xiaodan Lu ◽  
Zhiwei Deng ◽  
Ziqing Lu ◽  
Minghui Fu
Keyword(s):  
Glutamine Synthetase ◽  
Eichhornia Crassipes ◽  
Invasive Plant ◽  
Promoter Sequence ◽  
Regulatory Mechanisms ◽  
Pcr Analysis ◽  
Regulation Mechanism ◽  
Upstream Sequence ◽  
Specific Expression ◽  
N Metabolism

Abstract Background Glutamine synthetase (GS) acts as a key enzyme in plant nitrogen (N) metabolism. It is important to understand the regulation of GS expression in plant. Promoters can initiate the transcription of its downstream gene. Eichhornia crassipes is a most prominent aquatic invasive plant, which has negative effects on environment and economic development. It also can be used in the bioremediation of pollutants present in water and the production of feeding and energy fuel. So identification and characterization of GS promoter in E. crassipes can help to elucidate its regulation mechanism of GS expression and further to control its N metabolism. Results A 1232 bp genomic fragment upstream of EcGS1b sequence from E. crassipes (EcGS1b-P) has been cloned, analyzed and functionally characterized. TSSP-TCM software and PlantCARE analysis showed a TATA-box core element, a CAAT-box, root specific expression element, light regulation elements including chs-CMA1a, Box I, and Sp1 and other cis-acting elements in the sequence. Three 5′-deletion fragments of EcGS1b upstream sequence with 400 bp, 600 bp and 900 bp length and the 1232 bp fragment were used to drive the expression of β-glucuronidase (GUS) in tobacco. The quantitative test revealed that GUS activity decreased with the decreasing of the promoter length, which indicated that there were no negative regulated elements in the EcGS1-P. The GUS expressions of EcGS1b-P in roots were significantly higher than those in leaves and stems, indicating EcGS1b-P to be a root-preferential promoter. Real-time Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) analysis of EcGS1b gene also showed higher expression in the roots of E.crassipes than in stems and leaves. Conclusions EcGS1b-P is a root-preferential promoter sequence. It can specifically drive the transcription of its downstream gene in root. This study will help to elucidate the regulatory mechanisms of EcGS1b tissue-specific expression and further study its other regulatory mechanisms in order to utilize E.crassipes in remediation of eutrophic water and control its overgrowth from the point of nutrient metabolism.

scholarly journals Controlling the Kinetics of an Enzymatic Reaction through Enzyme or Substrate Confinement into Lipid Mesophases with Tunable Structural Parameters

2020 ◽  
Vol 21 (14) ◽  
pp. 5116
Author(s):  
Marco Mendozza ◽  
Arianna Balestri ◽  
Costanza Montis ◽  
Debora Berti
Keyword(s):  
Reaction Kinetics ◽  
Self Assembly ◽  
Liquid Crystalline ◽  
Structural Parameters ◽  
Enzymatic Reaction ◽  
X Ray Scattering ◽  
Nitrophenyl Phosphate ◽  
Vis Spectroscopy ◽  
Kinetics Of ◽  
Enzyme Alkaline Phosphatase

Lipid liquid crystalline mesophases, resulting from the self-assembly of polymorphic lipids in water, have been widely explored as biocompatible drug delivery systems. In this respect, non-lamellar structures are particularly attractive: they are characterized by complex 3D architectures, with the coexistence of hydrophobic and hydrophilic regions that can conveniently host drugs of different polarities. The fine tunability of the structural parameters is nontrivial, but of paramount relevance, in order to control the diffusive properties of encapsulated active principles and, ultimately, their pharmacokinetics and release. In this work, we investigate the reaction kinetics of p-nitrophenyl phosphate conversion into p-nitrophenol, catalysed by the enzyme Alkaline Phosphatase, upon alternative confinement of the substrate and of the enzyme into liquid crystalline mesophases of phytantriol/H2O containing variable amounts of an additive, sucrose stearate, able to swell the mesophase. A structural investigation through Small-Angle X-ray Scattering, revealed the possibility to finely control the structure/size of the mesophases with the amount of the included additive. A UV–vis spectroscopy study highlighted that the enzymatic reaction kinetics could be controlled by tuning the structural parameters of the mesophase, opening new perspectives for the exploitation of non-lamellar mesophases for confinement and controlled release of therapeutics.

scholarly journals Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States

2019 ◽  
Author(s):  
Jie Deng ◽  
Andreas Walther
Keyword(s):  
Molecular Recognition ◽  
Enzymatic Reaction ◽  
Reaction Network ◽  
Steady States ◽  
Hierarchical Level ◽  
Dna Nanostructures ◽  
Structural Dynamic ◽  
Systems Chemistry ◽  
Sticky End ◽  
Autonomous Evolution

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.

Complexity of molecular crowding in cell-free enzymatic reaction networks

2014 ◽  
Vol 9 (6) ◽  
pp. 406-407 ◽  
Author(s):  
Evan Spruijt ◽  
Ekaterina Sokolova ◽  
Wilhelm T. S. Huck
Keyword(s):  
Enzymatic Reaction ◽  
Reaction Networks ◽  
Molecular Crowding

scholarly journals Grip on complexity in chemical reaction networks

2017 ◽  
Vol 13 ◽  
pp. 1486-1497 ◽  
Author(s):  
Albert S Y Wong ◽  
Wilhelm T S Huck
Keyword(s):  
Complex Networks ◽  
Chemical Reaction ◽  
Biological Networks ◽  
Chemical Reaction Networks ◽  
Living Systems ◽  
Reaction Networks ◽  
Natural Systems ◽  
Systems Chemistry ◽  
Single Chemical ◽  
And Control

A new discipline of “systems chemistry” is emerging, which aims to capture the complexity observed in natural systems within a synthetic chemical framework. Living systems rely on complex networks of chemical reactions to control the concentration of molecules in space and time. Despite the enormous complexity in biological networks, it is possible to identify network motifs that lead to functional outputs such as bistability or oscillations. To truly understand how living systems function, we need a complete understanding of how chemical reaction networks (CRNs) create function. We propose the development of a bottom-up approach to design and construct CRNs where we can follow the influence of single chemical entities on the properties of the network as a whole. Ultimately, this approach should allow us to not only understand such complex networks but also to guide and control their behavior.

scholarly journals Advances in the role of m6A RNA modification in cancer metabolic reprogramming

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Xiu Han ◽  
Lin Wang ◽  
Qingzhen Han
Keyword(s):  
Cancer Cells ◽  
Epigenetic Modification ◽  
Metabolic Reprogramming ◽  
Regulatory Mechanisms ◽  
Rna Modification ◽  
Biological Functions ◽  
Rna Transcription ◽  
Cellular Processes ◽  
Metabolic Genes

Abstract N6-methyladenosine (m6A) modification is the most common internal modification of eukaryotic mRNA and is widely involved in many cellular processes, such as RNA transcription, splicing, nuclear transport, degradation, and translation. m6A has been shown to plays important roles in the initiation and progression of various cancers. The altered metabolic programming of cancer cells promotes their cell-autonomous proliferation and survival, leading to an indispensable hallmark of cancers. Accumulating evidence has demonstrated that this epigenetic modification exerts extensive effects on the cancer metabolic network by either directly regulating the expression of metabolic genes or modulating metabolism-associated signaling pathways. In this review, we summarized the regulatory mechanisms and biological functions of m6A and its role in cancer metabolic reprogramming.

Modular Design of Small Enzymatic Reaction Networks Based on Reversible and Cleavable Inhibitors

2019 ◽  
Vol 131 (41) ◽  
pp. 14681-14685
Author(s):  
Aleksandr A. Pogodaev ◽  
Cristina Lía Fernández Regueiro ◽  
Miglė Jakštaitė ◽  
Marijn J. Hollander ◽  
Wilhelm T. S. Huck
Keyword(s):  
Modular Design ◽  
Enzymatic Reaction ◽  
Reaction Networks

scholarly journals Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States

2019 ◽  
Author(s):  
Jie Deng ◽  
Andreas Walther
Keyword(s):  
Molecular Recognition ◽  
Enzymatic Reaction ◽  
Reaction Network ◽  
Steady States ◽  
Hierarchical Level ◽  
Dna Nanostructures ◽  
Structural Dynamic ◽  
Systems Chemistry ◽  
Sticky End ◽  
Autonomous Evolution

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization system. The systems are based on a monomeric species pool that is fueled by ATP and orchestrated by an enzymatic reaction network (ERN) of ATP-powered ligation and concurrent cleavage. Such systems display autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomer of dimers to ultimately randomized polymer structure before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition with respect to the structure-forming step (ATP-powered ligation) by encoding different sticky-end overhangs into the ligation area. However, all formed structures are equally degraded, and the orthogonal molecular recognition of the different starting species are harmonized during the constantly occurring restriction process, leading in consequence to a reconfiguration of the driven dynamic nanostructures on a higher hierarchical level. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.

scholarly journals Automated exploration of DNA-based structure self-assembly networks

2021 ◽  
Vol 8 (10) ◽  
Author(s):  
L. Cazenille ◽  
A. Baccouche ◽  
N. Aubert-Kato
Keyword(s):  
Dna Sequences ◽  
Self Assembly ◽  
Search Space ◽  
Dna Origami ◽  
Reaction Pathways ◽  
Reaction Networks ◽  
Dna Structures ◽  
Search Spaces ◽  
Dna Strands ◽  
Domain Level

Finding DNA sequences capable of folding into specific nanostructures is a hard problem, as it involves very large search spaces and complex nonlinear dynamics. Typical methods to solve it aim to reduce the search space by minimizing unwanted interactions through restrictions on the design (e.g. staples in DNA origami or voxel-based designs in DNA Bricks). Here, we present a novel methodology that aims to reduce this search space by identifying the relevant properties of a given assembly system to the emergence of various families of structures (e.g. simple structures, polymers, branched structures). For a given set of DNA strands, our approach automatically finds chemical reaction networks (CRNs) that generate sets of structures exhibiting ranges of specific user-specified properties, such as length and type of structures or their frequency of occurrence. For each set, we enumerate the possible DNA structures that can be generated through domain-level interactions, identify the most prevalent structures, find the best-performing sequence sets to the emergence of target structures, and assess CRNs' robustness to the removal of reaction pathways. Our results suggest a connection between the characteristics of DNA strands and the distribution of generated structure families.

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