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Related Concept Videos

Aromatic Compounds: Overview01:25

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In general, the term ‘aromatic’ indicates a pleasant smell or fragrance from fresh flowers, freshly prepared coffee, etc. In the early history of organic chemistry, many benzene derivatives were isolated from the pleasant odor oils of the plants. For example, vanillin was isolated from the oil of vanilla, methyl salicylate from the oil of wintergreen, and cinnamaldehyde from the oil of cinnamon. They all had a pleasant odor; hence the name aromatic was given.
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Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
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Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
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Heterocyclic aromatic compounds are cyclic compounds that are aromatic and have one or more heteroatoms—atoms other than carbon, in the ring. Depending upon the number of atoms present in the ring, they can be either five or six-membered. Examples of five-membered heterocyclic aromatic compounds include pyrrole, furan, thiophene, and imidazole. Pyrrole consists of one nitrogen atom having one lone pair of electrons. Furan and thiophene have one oxygen and one sulfur heteroatom,...
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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
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ARBRE: Computational resource to predict pathways towards industrially important aromatic compounds.

Anastasia Sveshnikova1, Homa MohammadiPeyhani1, Vassily Hatzimanikatis1

  • 1Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland.

Metabolic Engineering
|April 5, 2022
PubMed
Summary

A new computational tool, ARBRE, aids synthetic biology by predicting novel biosynthetic pathways for aromatic compounds. This resource expands known biochemical networks, enabling discovery of valuable industrial chemicals.

Keywords:
Aromatic compoundsBiosynthesisEnzyme predictionMetabolic networkPathway predictionReaction predictionSynthetic biology

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Area of Science:

  • Biochemistry
  • Computational Biology
  • Synthetic Biology

Background:

  • Synthetic biology and metabolic engineering require computational tools for predicting biosynthetic pathways of industrially relevant compounds, often derived from aromatic amino acids.
  • Existing pathway search tools have limitations in reaction scope, compound coverage, and evaluation metrics.

Purpose of the Study:

  • To introduce ARBRE (Aromatic compounds RetroBiosynthesis Repository and Explorer), a novel computational resource for predicting and exploring biosynthetic pathways.
  • To provide a comprehensive biochemical reaction network and toolbox focused on aromatic amino acid biosynthesis.

Main Methods:

  • Developed ARBRE with a biochemical reaction network including over 33,000 known and 390,000 predicted novel reactions.
  • Integrated over 74,000 compounds, incorporating over 1,000 previously unnetworked molecules from PubChem by assigning enzymatic reactions.
  • Utilized generalized enzymatic reaction rules for novel reaction prediction.

Main Results:

  • ARBRE encompasses a large-scale reaction network (33,000+ known, 390,000+ novel reactions) and compound database (74,000+).
  • Successfully integrated over 1,000 molecules from PubChem into the biochemical network.
  • Demonstrated ARBRE's utility in pathway search, enzyme annotation, ranking, visualization, and network expansion.

Conclusions:

  • ARBRE offers a significant computational resource for predicting and ranking biosynthetic pathways towards industrially important aromatic compounds.
  • The freely available toolbox and web version promote open science and community-driven discovery in metabolic engineering.
  • ARBRE facilitates the exploration of novel compound derivations, particularly from lignin degradation products.