Related Experiment Video

Updated: Aug 29, 2026

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
04:04

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

Published on: January 20, 2023

The tmRNA website: reductive evolution of tmRNA in plastids and other endosymbionts

Pulcherie Gueneau de Novoa1, Kelly P Williams

  • 1Centro de Biofisica y Bioquimica, Instituto Venezolano de Investigaciones Cientificas, Altos de Pipe, MI, Venezuela.

Nucleic Acids Research
|December 19, 2003
PubMed

Insights

tmRNA, which combines tRNA and mRNA functions, helps stalled ribosomes. New sequences reveal plastid tmRNAs often lack pseudoknots, unlike bacterial versions, possibly due to relaxed evolutionary pressure in endosymbiotic lifestyles.

Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • tmRNA (transfer messenger RNA) possesses both tRNA and mRNA characteristics, crucial for resolving ribosome stalling.
  • The tmRNA website serves as a central repository for tmRNA research, including sequences, alignments, and structural data.
  • Previous research has cataloged bacterial tmRNA sequences and structures, highlighting the role of pseudoknots.

Purpose of the Study:

  • To expand the tmRNA sequence database with new entries, particularly from plastids and bacterial endosymbionts.
  • To analyze the structural variations, specifically pseudoknot presence and location, in newly identified tmRNA sequences.
  • To investigate the evolutionary implications of structural differences in tmRNA between free-living bacteria and endosymbionts.

Main Methods:

  • Curating and sequencing tmRNA from various sources, including plastids and bacterial endosymbionts.
  • Utilizing BLAST server for sequence comparison and analysis.
  • Comparative analysis of secondary structures, focusing on pseudoknot distribution and the tRNA-like domain.

Main Results:

  • Addition of numerous new tmRNA sequences, including the shortest known sequence, from plastids across all three primary lineages.
  • Demonstration of a collective loss of pseudoknots in plastid tmRNAs compared to typical bacterial tmRNAs.
  • Identification of a truncated pseudoknot-string region in the tmRNA of the endosymbiont Tremblaya princeps.

Conclusions:

  • Plastid tmRNAs exhibit significant structural divergence from bacterial tmRNAs, characterized by pseudoknot reduction.
  • The loss of pseudoknots in plastid tmRNAs may be linked to the relaxed selective pressures associated with endosymbiotic lifestyles.
  • Structural variations in tmRNA suggest adaptation to different cellular environments and evolutionary trajectories.

More Related Videos

Discrimintion and Mapping of the Primary and Processed Transcripts in Maize Mitochondrion Using a Circular RT-PCR-based Strategy07:26

Discrimintion and Mapping of the Primary and Processed Transcripts in Maize Mitochondrion Using a Circular RT-PCR-based Strategy

Published on: July 29, 2019

In vitro tRNA Methylation Assay with the Entamoeba histolytica DNA and tRNA Methyltransferase Dnmt2 (Ehmeth) Enzyme12:36

In vitro tRNA Methylation Assay with the Entamoeba histolytica DNA and tRNA Methyltransferase Dnmt2 (Ehmeth) Enzyme

Published on: October 19, 2010

Related Concept Videos

Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
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...
Bacterial Transcription01:53

Bacterial Transcription

RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Evolution of New Traits in Microbes01:24

Evolution of New Traits in Microbes

Microorganisms evolve rapidly due to their large population sizes and short generation times, often exhibiting measurable changes within days under laboratory conditions. Natural selection acts on standing genetic variation, enabling the retention and amplification of beneficial traits that confer fitness advantages in changing environments.Adaptive Pigment Regulation in RhodobacterIn Rhodobacter, a genus of purple non-sulfur bacteria, light-harvesting pigments such as bacteriochlorophyll and...
Protein Transport to the Inner Chloroplast Membrane01:18

Protein Transport to the Inner Chloroplast Membrane

Proteins targeted to the inner chloroplast membrane, or plastid proteins, are transported by two general pathways: the stop-transfer and the re-insertion or post-import pathways. Most plastid proteins carry N-terminal transit sequences and internal import sequences targeting it to the specific chloroplast subcompartment. Proteins targeted by the stop-transfer pathway have internal hydrophobic sequences that inhibit their translocation into the stroma. As a result, these precursors are arrested...
Export of Mitochondrial and Chloroplast Genes02:19

Export of Mitochondrial and Chloroplast Genes

A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred irrespective...