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Related Concept Videos

Transfer RNA Synthesis02:36

Transfer RNA Synthesis

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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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Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...
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Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
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Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses
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Isolation of Translating Ribosomes Containing Peptidyl-tRNAs for Functional and Structural Analyses

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The tmRNA website.

Corey M Hudson1, Kelly P Williams2

  • 1Sandia National Laboratories, Department of Systems Biology, Livermore, CA 94551, USA.

Nucleic Acids Research
|November 8, 2014
PubMed
Summary
This summary is machine-generated.

Transfer-messenger RNA (tmRNA) and SmpB protein help bacterial ribosomes when they reach the end of mRNA without a stop codon. The tmRNA Website now offers expanded tmRNA and SmpB sequence data and new search software.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Transfer-messenger RNA (tmRNA) and its protein partner SmpB are essential for rescuing stalled bacterial ribosomes.
  • These components are conserved across most bacterial genomes and found in some organelles.
  • Ribosome stalling occurs when translation terminates prematurely due to the absence of a stop codon on mRNA.

Purpose of the Study:

  • To announce the relocation and enhancement of the tmRNA Website.
  • To provide an updated and expanded repository of tmRNA and SmpB sequences and associated data.
  • To introduce new bioinformatics tools for identifying these genetic elements.

Main Methods:

  • The tmRNA Website was migrated to a new domain: http://bioinformatics.sandia.gov/tmrna/.
  • A significant update increased the number of unique tmRNA sequences from 492 to 1716.
  • A new database for SmpB protein sequences was integrated, linked to corresponding tmRNA entries.

Main Results:

  • The updated website now hosts a substantially larger collection of tmRNA sequences.
  • A comprehensive database of SmpB sequences is available, facilitating comparative analysis.
  • New software tools are provided for the discovery and analysis of tmRNA and SmpB sequences.

Conclusions:

  • The enhanced tmRNA Website provides a valuable, expanded resource for researchers studying bacterial translation and ribosome rescue.
  • The integrated databases and new software improve accessibility and utility for genomic and molecular biology studies.
  • This resource supports ongoing research into the fundamental mechanisms of protein synthesis in bacteria.