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Related Concept Videos

Transcriptional Regulation: Riboswitches01:23

Transcriptional Regulation: Riboswitches

Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Yeasts are single-celled organisms, but unlike bacteria, they are eukaryotes (cells with a nucleus). Cell signaling in yeast is similar to signaling in other eukaryotic cells. A ligand, such as a protein or a small molecule released from a yeast cell, attaches to a receptor on the cell surface. The binding stimulates second-messenger kinases to activate or inactivate transcription factors that further regulate gene expression. Many of the yeast intracellular signaling cascades have similar...
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Strain improvement is a foundational strategy in industrial microbiology aimed at maximizing microbial productivity, particularly because natural isolates typically yield commercially valuable products in very low concentrations. Although optimizing the culture medium and environmental conditions can improve yields, these adjustments are inherently limited by the organism’s genetic potential. As a result, the focus shifts toward genetic modifications to enhance biosynthetic capacity. The...
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The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
Transcription of prokaryotic...
Transcription Attenuation in Prokaryotes02:42

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Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...

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Related Experiment Video

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Reverse engineering the yeast RNR1 transcriptional control system.

Grace Mao1, James P Brody

  • 1Department of Biomedical Engineering, Henry Samueli School of Engineering, University of California Irvine, Irvine, California, United States of America.

Plos One
|November 25, 2010
PubMed
Summary

This study introduces a new method to understand gene transcription regulation. By measuring protein-DNA binding in yeast, researchers deciphered the combinatorial logic controlling the RNR1 gene

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Area of Science:

  • Molecular Biology
  • Genetics
  • Systems Biology

Background:

  • Transcription is regulated by complex protein interactions with genomic DNA.
  • Predictive models for combinatorial transcriptional control are a key goal in modern biology.
  • The yeast RNR1 gene exhibits periodic cell cycle transcription.

Purpose of the Study:

  • To demonstrate a novel method for deciphering transcriptional regulation logic.
  • To investigate the combinatorial binding of nuclear proteins to specific DNA sequences in the RNR1 promoter.
  • To correlate protein-DNA binding dynamics with RNR1 gene expression during the cell cycle.

Main Methods:

  • Utilized synchronized Saccharomyces cerevisiae cultures.
  • Extracted nuclear proteins and quantified binding to seven specific 16-base pair DNA sequences using surface plasmon resonance (SPR).
  • Correlated SPR-measured protein binding data with existing RNR1 mRNA expression data.

Main Results:

  • SPR signals exhibited significant cell cycle-dependent variations.
  • Protein binding patterns were linked to RNR1 transcription.
  • Identified specific binding site requirements for transcription initiation.

Conclusions:

  • The developed method is feasible for deciphering combinatorial transcriptional logic.
  • The study provides insights into the regulatory mechanisms of the RNR1 gene.
  • Highlights the dynamic nature of protein-DNA interactions in cell cycle control.