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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.
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Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
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PRODORIC2: the bacterial gene regulation database in 2018.

Denitsa Eckweiler1, Christian-Alexander Dudek2, Juliane Hartlich1

  • 1Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany.

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The PRODORIC2 database now offers an expanded collection of bacterial DNA binding sites and regulatory information. This resource aids researchers in understanding gene expression and bacterial adaptation through improved usability and new data.

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Bacteria adapt to environmental changes through differential gene expression regulated by DNA binding transcription factors.
  • The PRODORIC2 database serves as a comprehensive repository for prokaryotic transcription factor binding sites.
  • It is an improved and user-friendly redesign of the original PRODORIC database.

Purpose of the Study:

  • To present the updated PRODORIC2 database, highlighting its new features and expanded content.
  • To provide researchers with an enhanced resource for studying bacterial gene regulation.
  • To facilitate genome-wide pattern searches using transcription factor binding site data.

Main Methods:

  • Redesign of the PRODORIC database to improve user-friendliness and technical performance.
  • Inclusion of over 1000 new transcription factor binding sites and 110 new position weight matrices.
  • Integration of binding sites derived from high-throughput experiments and data for new bacterial species.

Main Results:

  • PRODORIC2 offers a significantly larger and more accessible collection of prokaryotic transcription factor binding sites.
  • The database includes new data for 6 bacterial species, including the Rhodobacteraceae family.
  • Comprehensive data for Clostridium difficile transcription factors and sigma factors are now available.

Conclusions:

  • PRODORIC2 is a valuable, publicly accessible resource for studying bacterial transcription factor binding sites.
  • The database's improvements enhance its utility for research in bacterial adaptation and gene regulation.
  • The inclusion of diverse datasets supports broader genomic analyses and comparative studies.