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Transfer RNA Synthesis02:36

Transfer RNA Synthesis

One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Getting an A with the 3Cs: Chromosome Conformation Capture for Undergraduates
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CBDB: the codon bias database.

Adam Hilterbrand1, Joseph Saelens, Catherine Putonti

  • 1Department of Biology, Loyola University Chicago, 1032 W Sheridan Road, Chicago, IL 60660, USA.

BMC Bioinformatics
|April 28, 2012
PubMed
Summary
This summary is machine-generated.

The Codon Bias Database (CBDB) offers codon usage bias data for over 300 bacterial genomes, aiding research into evolutionary mechanisms. Most bacterial genera share similar codon composition, highlighting evolutionary relationships beyond species level.

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Area of Science:

  • Genomics and Evolutionary Biology
  • Microbial Genetics
  • Bioinformatics

Background:

  • Codon usage bias, a non-random selection of codons, is observed in many genomes.
  • Mechanisms driving codon bias, including translational selection, mutational bias, and drift, are actively researched.
  • Correlations between host and pathogen codon usage suggest evolutionary interplay.

Purpose of the Study:

  • To introduce the Codon Bias Database (CBDB), a novel web resource for bacterial codon bias.
  • To facilitate comparative analyses of codon usage across bacterial strains and species.
  • To support research on phage adaptation and host-pathogen co-evolution.

Main Methods:

  • Compilation of codon bias data for the highly expressed gene set from over 300 bacterial genomes.
  • Inclusion of annotations, sequences, and codon bias measurements for each bacterial strain.
  • Selection of bacterial genera with sequenced and annotated bacteriophages for phage adaptation studies.

Main Results:

  • The Codon Bias Database (CBDB) provides a centralized repository of codon usage bias measures.
  • Data includes look-up tables and bias measures for diverse bacterial genera, species, and strains.
  • Analysis reveals that most members within a bacterial genus share similar codon composition.

Conclusions:

  • Comparative analysis of codon usage provides insights into evolutionary shaping and underlying mechanisms.
  • The CBDB serves as a valuable resource for studying bacterial evolution and host-pathogen dynamics.
  • Intra-genus codon composition similarity suggests strong evolutionary constraints at the genus level.