Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Combining microarray and genomic data to predict DNA binding motifs.

Linyong Mao1, Chris Mackenzie2, Jung H Roh2

  • 1Pacific Northwest National Laboratory, Computational Biology and Bioinformatics Group, PO Box 999, MS: K7-90, Richland, WA 99352, USA.

Microbiology (Reading, England)
|October 7, 2005
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Gene Contribution of Streptococcus dysgalactiae Subspecies equisimilis, an Emerging Pathogen, to Experimental Primate Necrotizing Myositis.

The American journal of pathology·2026
Same author

Enantioselective Rh/Cu-Catalyzed Addition of Terminal Alkynes to Allenes for the Synthesis of Chiral 1,4-Enynes.

Organic letters·2026
Same author

Segmental Isotope Labeling of the Prion Protein: Identification of a Key Residue for Copper-Mediated Interdomain Structure.

ACS chemical biology·2025
Same author

Analysis of <i>Streptococcus dysgalactiae</i> subspecies <i>equisimilis</i> gene transcripts during experimental primate necrotizing myositis.

mBio·2025
Same author

Segmental Isotope Labelling of the Prion Protein: Identification of a Key Residue for Copper-Mediated Interdomain Structure.

bioRxiv : the preprint server for biology·2025
Same author

Genes of the Fatty Acid Oxidation Pathway are Upregulated in Female as Compared to Male Cardiomyocytes.

Circulation·2025
Same journal

Investigating the mobility and host range of mobile genetic elements harbouring antimicrobial resistance genes in enterococci.

Microbiology (Reading, England)·2026
Same journal

Commonly prescribed medicines antagonise anti-MRSA antibiotics and select for resistance.

Microbiology (Reading, England)·2026
Same journal

Microbial Primer: The T6SS, a deadly bacterial harpoon.

Microbiology (Reading, England)·2026
Same journal

Disruption of efflux activity reduces biofilm formation through multiple pathways.

Microbiology (Reading, England)·2026
Same journal

Copper-driven mutualism of <i>Candida albicans</i> and <i>Staphylococcus aureus</i> interkingdom biofilms.

Microbiology (Reading, England)·2026
Same journal

<i>Entamoeba histolytica</i> spliceosome structural components.

Microbiology (Reading, England)·2026
See all related articles

This study integrates gene expression and genome sequence analysis to identify DNA binding sites for key regulators PrrA, PpsR, and FnrL in Rhodobacter sphaeroides. The findings reveal PrrA potentially regulates more genes than previously thought, offering insights into microbial gene control.

Area of Science:

  • Microbiology
  • Genomics
  • Systems Biology

Background:

  • Understanding gene expression control is crucial for biological systems.
  • Regulatory elements in genomes dictate gene regulation.
  • Photosynthetic bacteria like Rhodobacter sphaeroides have complex regulatory networks.

Purpose of the Study:

  • To predict DNA sequences binding specific regulators (PrrA, PpsR, FnrL) in Rhodobacter sphaeroides.
  • To identify co-regulated genes and their associated transcription factor recognition motifs.
  • To determine the regulatory interplay and relative importance of these three regulators.

Main Methods:

  • Combined microarray data analysis with genome sequence analysis.
  • Utilized hierarchical clustering to group genes with similar expression patterns.

Related Experiment Videos

  • Searched upstream DNA sequences for transcription factor binding motifs.

    • Main Results:

    • Successfully predicted and extended consensus sequences for FnrL and PpsR binding.
    • Identified potential DNA binding sequences for the global regulator PrrA.
    • Whole-genome analysis indicated PrrA regulates a larger number of genes compared to PpsR and FnrL.
    • Detected photosynthesis-related regulatory patterns in R. sphaeroides.

    Conclusions:

    • Integration of multiple data types is a powerful approach for inferring transcriptional regulatory patterns.
    • The study provides a refined understanding of the regulatory roles of PrrA, PpsR, and FnrL in Rhodobacter sphaeroides.
    • The findings highlight the significant role of PrrA in regulating gene expression within this bacterium.