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Related Concept Videos

Operon Model01:23

Operon Model

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The operon model represents a fundamental mechanism of gene regulation in prokaryotes, enabling coordinated expression of genes involved in related metabolic or functional pathways. Operons consist of structural genes, a promoter, and an operator, with transcription regulated by repressors, activators, and small effector molecules.Structure and Function of OperonsAn operon is a cluster of structural genes transcribed together under the control of a single promoter. The promoter region...
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Operons02:09

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Prokaryotes can control gene expression through operons—DNA sequences consisting of regulatory elements and clustered, functionally related protein-coding genes. Operons use a single promoter sequence to initiate transcription of a gene cluster (i.e., a group of structural genes) into a single mRNA molecule. The terminator sequence ends transcription. An operator sequence, located between the promoter and structural genes, prohibits the operon’s transcriptional activity if bound by...
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Two-Compartment Open Model: Overview01:05

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Multicompartmental models are crucial tools in pharmacokinetics, providing a framework to understand how drugs move within the body. The two-compartment model is a crucial subtype, segmenting the body into central and peripheral compartments. The central compartment represents areas with high blood flow, such as plasma and highly perfused organs like the kidneys and liver, while the peripheral compartment signifies tissues with lower blood flow, like adipose tissue and muscle tissue.
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Combinatorial Gene Control02:33

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Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
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Repressible Operon: trp Operon01:21

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The trp operon in Escherichia coli exemplifies a repressible operon. It regulates the synthesis of tryptophan through repressor-mediated transcriptional control and attenuation. This dual regulatory mechanism ensures tryptophan biosynthesis occurs only when needed, conserving cellular resources.Structure of the trp OperonThe trp operon consists of five structural genes (trpE, trpD, trpC, trpB, and trpA) that encode enzymes for tryptophan biosynthesis. These genes are transcribed as a single...
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DOOR 2.0: presenting operons and their functions through dynamic and integrated views.

Xizeng Mao1, Qin Ma, Chuan Zhou

  • 1Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA, BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA, School of Mathematics, Shandong University, Jinan, Shandong 250100, China, College of Computer Science and Technology, Jilin University, Changchun, Jilin 130012, China and College of Computer Science, Central China Normal University, Wuhan, Hubei 430079, China.

Nucleic Acids Research
|November 12, 2013
PubMed
Summary

The updated DOOR 2.0 database now offers genome-scale operon information for over 2000 prokaryotes. This resource provides dynamic functional insights and regulatory details for transcription units.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Systems Biology

Background:

  • Operons are fundamental genetic units in prokaryotes, crucial for gene regulation.
  • Previous versions of the DOOR database provided valuable operon information but required expansion.
  • Advances in sequencing and computational methods enable more comprehensive operon analysis.

Purpose of the Study:

  • To introduce DOOR 2.0, a significantly enhanced and expanded operon database.
  • To integrate diverse functional and regulatory data for prokaryotic operons.
  • To provide advanced tools for operon prediction and data visualization.

Main Methods:

  • Curated and computationally predicted operons from 2072 complete prokaryotic genomes.
  • Integration of RNA-sequencing data for transcription unit identification and gene expression estimation.
  • Development of a web service for de novo operon prediction.
  • Implementation of a genome browser and a search engine for data exploration.

Main Results:

  • DOOR 2.0 encompasses operons for 2072 prokaryotes, a threefold increase from the previous version.
  • Includes over 250,000 transcription units with experimental or RNA-seq-based predictions.
  • Provides integrated operon-centric data: regulatory sites, gene expression, and cross-genome conservation.
  • Offers a high-performance prediction service and an intuitive visualization tool.

Conclusions:

  • DOOR 2.0 represents a major advancement in prokaryotic operon annotation and analysis.
  • The database facilitates dynamic functional and regulatory studies of operons.
  • It serves as a comprehensive resource for researchers investigating prokaryotic gene organization and regulation.