Related Experiment Video
Updated: Jul 10, 2026
10:56
Metabolic Labeling and Profiling of Transfer RNAs Using Macroarrays
Published on: January 16, 2018
Proteomic identification of tmRNA substrates
Sue-Jean Hong1, Faith H Lessner, Elisabeth M Mahen
1Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
Summary
The tmRNA-SmpB system tags proteins for degradation. In Caulobacter crescentus, its absence delays DNA replication initiation by affecting DNA repair and replication proteins.
Area of Science:
- Molecular Biology
- Cell Biology
- Microbiology
Background:
- The tmRNA-SmpB system is crucial for releasing stalled ribosomes and targeting nascent polypeptides for degradation.
- Disruptions in tmRNA activity can lead to growth and developmental defects in various organisms.
- In Caulobacter crescentus, loss of tmRNA function results in a delayed initiation of DNA replication, impacting the cell cycle.
Purpose of the Study:
- To elucidate the molecular mechanisms underlying the delayed DNA replication initiation in Caulobacter crescentus cells lacking tmRNA activity.
- To identify proteins tagged by tmRNA under normal growth conditions in C. crescentus.
- To investigate the role of tmRNA-mediated protein tagging in regulating DNA replication, recombination, and repair pathways.
Main Methods:
- Proteomic analysis to identify tmRNA-tagged proteins in Caulobacter crescentus.
- Bioinformatic analysis to identify overrepresented functional categories among tagged proteins.
- Sequence analysis to determine conserved motifs at tmRNA tagging sites.
Main Results:
- Identified 73 C. crescentus proteins tagged by tmRNA under normal growth conditions.
- Found an overrepresentation of proteins involved in DNA replication, recombination, and repair among tmRNA substrates.
- Discovered a conserved nucleotide motif upstream of the tagging site essential for wild-type tmRNA tagging.
Conclusions:
- Misregulation of DNA replication, recombination, and repair factors due to impaired tmRNA activity likely causes the observed delay in DNA replication initiation.
- The identified conserved nucleotide motif is critical for the specificity of tmRNA-mediated protein tagging.
- This study provides insights into the role of the tmRNA-SmpB system in maintaining cell cycle integrity through the regulation of DNA metabolism proteins.
Related Concept Videos
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
02:36Transfer 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...
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...
01:19Translocation of Proteins into the Mitochondria
Mitochondrial precursors are translocated to the internal subcompartments via independent mechanisms involving distinct protein machineries called translocases.
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
Sorting of outer membrane proteins:
Mitochondrial outer membrane proteins are of two types: the transmembrane, beta-barrel porins, and the membrane-anchored, alpha-helical proteins. Beta-barrel porin precursors are translocated by the TOM complex and inserted into the outer mitochondrial membrane by the SAM complex. In contrast,...
01:20Cotranslational Protein Translocation
Translocation of proteins across membranes is an ancient process that occurs even in bacteria and archaebacteria. In fact, the components of the translocation machinery are still conserved between prokaryotes and eukaryotes.
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
Sec61 channel partners for cotranslational translocation
During cotranslational translocation, the Sec61 channel partners with the signal recognition particle (SRP), the signal recognition particle receptor (SR), and the ribosomes to transport the nascent polypeptide chain...
02:26tRNA Activation
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...