Application of Petri Net Theory for Modelling and Validation of Menthol Biosynthesis

2020 ◽  
Vol 5 (4) ◽  
pp. 312-318
Author(s):  
Swati Dubey ◽  
Sheela Joshi ◽  
Goshali Dwivedi ◽  
Rajendra Prasad
Keyword(s):  
Petri Net ◽  
Metabolic Networks ◽  
Biological Data ◽  
Isopentenyl Diphosphate ◽  
Initial State ◽  
Network Modelling ◽  
Geranyl Diphosphate ◽  
Dimethylallyl Diphosphate ◽  
Essential Step ◽  
Analysis Technique

An essential step in network modelling is to validate the network model. Petri net theory provides algorithms and methods, which can be applied directly to metabolic network modelling and analysis in order to validate the model. This paper describes the thriving application of Petri net theory for model validation of biosynthesis of menthol using the well-established Petri net analysis technique of place and transition invariants. Because of the complexity of metabolic networks and their regulation, formal modelling is a useful method to improve the understanding of these systems. A petri net representation, its validation and simulation of biosynthesis of menthol from geranyl diphosphate (GPP) has been performed with the objective of understating new insights of the structure of this pathway affecting the synthesis of menthol. The model has been validated for its P-invariant and T-invariant. T-invariant analysis suggest absence of any loop in the net which restore the initial state suggesting all reactions to be only forward. The net is covered by positive P-invariants and bounded. The net is utilized to simulate the time (pt) with concentrations of GPP, (−)- limonene, (+)-pulegone, (−)-menthone and (−)-menthol. Dimethylallyl diphosphate and isopentenyl diphosphate were the main precursors for this biosynthesis. Biological data needed for simulation where obtained from extensive survey of literature. The results were shown graphically and the nature of graphs represent the variation of concentrations with time.

scholarly journals Biosynthesis of pinene in purple non-sulfur photosynthetic bacteria

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Xiaomin Wu ◽  
Guang Ma ◽  
Chuanyang Liu ◽  
Xin-yuan Qiu ◽  
Lu Min ◽  
...  
Keyword(s):  
Fusion Protein ◽  
Heterologous Expression ◽  
Rhodobacter Sphaeroides ◽  
Photosynthetic Bacteria ◽  
Fine Chemicals ◽  
Isopentenyl Diphosphate ◽  
Isopentenyl Diphosphate Isomerase ◽  
Geranyl Diphosphate ◽  
Ribosome Binding ◽  
Geranyl Diphosphate Synthase

Abstract Background Pinene is a monoterpene, that is used in the manufacture of fragrances, insecticide, fine chemicals, and renewable fuels. Production of pinene by metabolic-engineered microorganisms is a sustainable method. Purple non-sulfur photosynthetic bacteria belong to photosynthetic chassis that are widely used to synthesize natural chemicals. To date, researches on the synthesis of pinene by purple non-sulfur photosynthetic bacteria has not been reported, leaving the potential of purple non-sulfur photosynthetic bacteria synthesizing pinene unexplored. Results Rhodobacter sphaeroides strain was applied as a model and engineered to express the fusion protein of heterologous geranyl diphosphate synthase (GPPS) and pinene synthase (PS), hence achieving pinene production. The reaction condition of pinene production was optimized and 97.51 μg/L of pinene was yielded. Then, genes of 1-deoxy-d-xylulose 5-phosphate synthase, 1-deoxy-d-xylulose 5-phosphate reductoisomerase and isopentenyl diphosphate isomerase were overexpressed, and the ribosome binding site of GPPS-PS mRNA was optimized, improving pinene titer to 539.84 μg/L. Conclusions In this paper, through heterologous expression of GPPS-PS, pinene was successfully produced in R. sphaeroides, and pinene production was greatly improved by optimizing the expression of key enzymes. This is the first report on pinene produce by purple non-sulfur photosynthetic bacteria, which expands the availability of photosynthetic chassis for pinene production.

scholarly journals Finding Cut-Offs in Leaderless Rendez-Vous Protocols is Easy

2021 ◽  
pp. 42-61
Author(s):  
A. R. Balasubramanian ◽  
Javier Esparza ◽  
Mikhail Raskin
Keyword(s):  
Lower Bounds ◽  
Petri Net ◽  
Special Class ◽  
Upper Bounds ◽  
Initial State ◽  
Reachability Problem ◽  
Final State ◽  
Final Configuration ◽  
Finite State ◽  
State Agents

AbstractIn rendez-vous protocols an arbitrarily large number of indistinguishable finite-state agents interact in pairs. The cut-off problem asks if there exists a number B such that all initial configurations of the protocol with at least B agents in a given initial state can reach a final configuration with all agents in a given final state. In a recent paper [17], Horn and Sangnier prove that the cut-off problem is equivalent to the Petri net reachability problem for protocols with a leader, and in "Image missing" for leaderless protocols. Further, for the special class of symmetric protocols they reduce these bounds to "Image missing" and "Image missing" , respectively. The problem of lowering these upper bounds or finding matching lower bounds is left open. We show that the cut-off problem is "Image missing" -complete for leaderless protocols, "Image missing" -complete for symmetric protocols with a leader, and in "Image missing" for leaderless symmetric protocols, thereby solving all the problems left open in [17].

scholarly journals Genetic evidence of branching in the isoprenoid pathway for the production of isopentenyl diphosphate and dimethylallyl diphosphate inEscherichia coli

FEBS Letters ◽  
2000 ◽  
Vol 473 (3) ◽  
pp. 328-332 ◽  
Author(s):  
Manuel Rodrı́guez-Concepción ◽  
Narciso Campos ◽  
Luisa Marı́a Lois ◽  
Carlos Maldonado ◽  
Jean-François Hoeffler ◽  
...  
Keyword(s):  
Genetic Evidence ◽  
Isopentenyl Diphosphate ◽  
Inescherichia Coli ◽  
Isoprenoid Pathway ◽  
Dimethylallyl Diphosphate

scholarly journals QM/MM studies of the type II isopentenyl diphosphate–dimethylallyl diphosphate isomerase demonstrate a novel role for the flavin coenzyme

RSC Advances ◽  
2017 ◽  
Vol 7 (36) ◽  
pp. 22286-22293
Author(s):  
Qianqian Hou ◽  
Kang Wang ◽  
Feng Xu ◽  
Wenshen Zhang ◽  
Kejian Ji ◽  
...  
Keyword(s):  
Isopentenyl Diphosphate ◽  
Type Ii ◽  
Isopentenyl Pyrophosphate ◽  
Dimethylallyl Diphosphate ◽  
Dimethylallyl Pyrophosphate

The type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2) catalyzes the reversible isomerization of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP).

PROTOCOL SPECIFICATION DESIGN USING AN OBJECT-BASED PETRI NET FORMALISM

1999 ◽  
Vol 09 (01) ◽  
pp. 97-125
Author(s):  
VLADIMIR P. SLIVA ◽  
TADAO MURATA ◽  
SOL M. SHATZ
Keyword(s):  
Petri Net ◽  
Communication Protocols ◽  
Destination Node ◽  
Analysis Method ◽  
Initial State ◽  
Protocol Specification ◽  
Module Analysis ◽  
Software Models ◽  
Object Based

This paper presents a method for modeling of communication protocols using G-Nets — an object-based Petri net formalism. Our approach focuses on specification of one entity in one node at one time, with the analysis that allows consideration of other layers and nodes in addition to module analysis. We extend G-Nets by the notion of timers, which aids the construction of protocol software models. Our method prevents some types of potential deadlocks and livelocks from being introduced into the produced net models. We present certain net synthesis rules to prevent some potential design errors by including error cases in the model. Thus, our node (site) interplay modeling includes cases in which a message may arrive corrupted or can be lost entirely before it would get to its destination node. Also, since our models have deadlock-preserving skeletons, the verification of global deadlock non-existence can be performed on the less complex skeleton rather than on the full G-Net model. Our analysis method discovers some deadlocks plus other unacceptable markings, which do not allow restoration of the initial state. Finding potential livelocks or overspecification is also a part of the analysis.

scholarly journals Isoprenoid biosynthesis in higher plants and in Escherichia coli: on the branching in the methylerythritol phosphate pathway and the independent biosynthesis of isopentenyl diphosphate and dimethylallyl diphosphate

2002 ◽  
Vol 366 (2) ◽  
pp. 573-583 ◽  
Author(s):  
Jean-François HOEFFLER ◽  
Andréa HEMMERLIN ◽  
Catherine GROSDEMANGE-BILLIARD ◽  
Thomas J. BACH ◽  
Michel ROHMER
Keyword(s):  
Escherichia Coli ◽  
Higher Plants ◽  
Mevalonic Acid ◽  
Cell Suspension Cultures ◽  
Mep Pathway ◽  
Isopentenyl Diphosphate ◽  
Higher Plant ◽  
Methylerythritol Phosphate Pathway ◽  
Dimethylallyl Diphosphate ◽  
Deuterium Retention

In the bacterium Escherichia coli, the mevalonic-acid (MVA)-independent 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway is characterized by two branches leading separately to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). The signature of this branching is the retention of deuterium in DMAPP and the deuterium loss in IPP after incorporation of 1-[4-2H]deoxy-d-xylulose ([4-2H]DX). Feeding tobacco BY-2 cell-suspension cultures with [4-2H]DX resulted in deuterium retention in the isoprene units derived from DMAPP, as well as from IPP in the plastidial isoprenoids, phytoene and plastoquinone, synthesized via the MEP pathway. This labelling pattern represents direct evidence for the presence of the DMAPP branch of the MEP pathway in a higher plant, and shows that IPP can be synthesized from DMAPP in plant plastids, most probably via a plastidial IPP isomerase.

The deoxyxylulose phosphate pathway of isoprenoid biosynthesis. Discovery and function of the ispDEFGH genes and their cognate enzymes

2003 ◽  
Vol 75 (2-3) ◽  
pp. 393-405 ◽  
Author(s):  
F. Rohdich ◽  
Stefan Hecht ◽  
Adelbert Bacher ◽  
Wolfgang Eisenreich
Keyword(s):  
Biosynthetic Pathway ◽  
Mevalonate Pathway ◽  
Isoprenoid Biosynthesis ◽  
Catalytic Action ◽  
Isopentenyl Diphosphate ◽  
Dimethylallyl Diphosphate ◽  
And Function

Isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) serve as the universal precursors for the biosynthesis of terpenes. Besides the well-known mevalonate pathway, a second biosynthetic pathway conducive to IPP and DMAPP via 1-deoxy-d-xylulose-5-phosphate and 2C-methyl-d-erythritol-4-phosphate has been discovered recently in plants and certain eubacteria. 2C-Methyl-d-erythritol-4-phosphate, the first committed intermediate of the deoxyxylulose phosphate pathway, is converted into 2C-methyl-d-erythritol 2,4-cyclodiphosphate by the catalytic action of three enzymes specified by the ispDEF genes. The cyclic diphosphate is reductively opened by the IspG protein affording 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate. This compound can be converted into IPP as well as DMAPP by the catalytic action of IspH protein. The enzymes of this pathway are potential targets for novel antibacterial, antimalarial, and herbicide agents.

Sign in / Sign up

Export Citation Format

Share Document