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Related Concept Videos

ortho–para-Directing Activators: –CH3, –OH, –⁠NH2, –OCH301:11

ortho–para-Directing Activators: –CH3, –OH, –⁠NH2, –OCH3

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All ortho–para directors, excluding halogens, are activating groups. These groups donate electrons to the ring, making the ring carbons electron-rich. Consequently, the reactivity of the aromatic ring towards electrophilic substitution increases. For instance, the nitration of anisole is about 10,000 times faster than the nitration of benzene. The electron-donating effect of the methoxy group in anisole activates the ortho and para positions on the ring and stabilizes the corresponding...
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The Diels–Alder reaction brings together a diene and a dienophile to form a six-membered ring. Both components have unique characteristics that influence the rate of the reaction.
Characteristics of the diene
Conformation
The simplest example of a diene is 1,3-butadiene, an acyclic conjugated π system. At room temperature, the molecule exists as a mixture of s-cis and s-trans conformers by virtue of rotation around the carbon–carbon single bond. Although the s-trans isomer is...
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The Diels–Alder reaction is an example of a thermal pericyclic reaction between a conjugated diene and an alkene or alkyne, commonly referred to as a dienophile. The reaction involves a concerted movement of six π electrons, four from the diene and two from the dienophile, forming an unsaturated six-membered ring. As a result, these reactions are classified as [4+2] cycloadditions.
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DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation.

Shuzhen Li1, Wenli Shen2, Shengyang Lian3

  • 1CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.

Journal of Hazardous Materials
|June 24, 2022
PubMed
Summary
This summary is machine-generated.

A new database, DARHD, catalogs aromatic ring-hydroxylating dioxygenase (ARHD) alpha subunits, revealing microbial diversity crucial for pollutant biodegradation. Most existing primers show limited coverage, highlighting the need for improved tools to study these essential environmental enzymes.

Keywords:
Aromatic ring-hydroxylating dioxygenaseDatabaseDiversityPrimerα subunit

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Area of Science:

  • Environmental microbiology
  • Biochemistry
  • Molecular biology

Background:

  • Biodegradation of aromatic compounds is vital for environmental pollutant control.
  • Aromatic ring-hydroxylating dioxygenases (ARHDs) catalyze the initial, rate-limiting step in aerobic aromatic biodegradation.
  • The ARHD alpha subunit is a key biomarker for functional microbial studies, but its diversity and primer coverage are poorly understood.

Purpose of the Study:

  • To establish a comprehensive sequence database for the ARHD alpha subunit.
  • To assess the diversity of ARHD alpha subunits and their corresponding primer coverage.
  • To provide guidance for future primer design and application in environmental studies.

Main Methods:

  • Collected amino acid sequences of the ARHD alpha subunit.
  • Selected 103 seed sequences and performed homolog searches and keyword confirmation against GenBank to build the DARHD database.
  • Retrieved 6367 sequences and assessed 136 pairs of published primers for coverage.

Main Results:

  • The DARHD database contains 6367 sequences from 407 bacterial genera capable of degrading 38 aromatic substrates.
  • Intricate relationships were observed between ARHD gene names, aromatic substrates, and microbial taxa.
  • Most previously published primers exhibited low coverage for the ARHD alpha subunit.

Conclusions:

  • The study provides new insights into the diversity of the ARHD alpha subunit.
  • The developed DARHD database is a valuable resource for studying microbial biodegradation of aromatic compounds.
  • Findings highlight the limitations of current primers and guide the development of more effective tools for environmental monitoring.