Related Experiment Video
Updated: Jun 7, 2026
12:57
Genome-wide Quantification of Translation in Budding Yeast by Ribosome Profiling
Published on: December 21, 2017
Control of translation efficiency in yeast by codon-anticodon interactions
Daniel P Letzring1, Kimberly M Dean, Elizabeth J Grayhack
1Department of Biochemistry and Biophysics, University of Rochester Medical School, Rochester, New York 14642, USA.
RNA (New York, N.Y.)
|October 26, 2010
Summary
The arginine codon CGA significantly reduces gene expression in yeast by hindering translation. This inhibition is mainly caused by wobble decoding and can be worsened by adjacent CGA codons.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Synonymous codon choice impacts gene translation efficiency.
- Mechanisms and magnitude of codon-mediated effects, especially in eukaryotes, remain poorly understood.
Purpose of the Study:
- To systematically analyze codon effects on gene expression in Saccharomyces cerevisiae.
- To elucidate the mechanisms behind codon-mediated translational regulation.
Main Methods:
- Performed the first systematic analysis of individual codon effects on expression in yeast.
- Investigated the role of wobble decoding using a specific tRNA mutation.
- Analyzed the impact of codon pairs and associated RNA fragment generation.
Main Results:
- The arginine codon CGA strongly inhibits gene expression in a dosage-dependent manner.
- CGA-mediated inhibition is primarily due to wobble decoding, suppressed by a specific tRNA.
- CGA codon pairs are more inhibitory than single CGA codons, linked to RNA fragment production.
Conclusions:
- Decoding by the ribosome and neighboring site interactions mediate codon-specific translation efficiency.
- The arginine codon CGA is a key regulator of translation efficiency in yeast.
- Understanding codon usage is crucial for optimizing gene expression.
Related Concept Videos
02:07Improving Translational Accuracy
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
01:29Translational Regulation
Translational regulation in prokaryotes ensures efficient protein synthesis by controlling ribosome access to mRNA. This regulation is mediated by secondary RNA structures, including translational riboswitches, RNA thermometers, and small RNAs (sRNAs), which respond to intracellular and environmental signals to modulate gene expression.Translational RiboswitchesRiboswitches in the leader region of mRNAs can regulate translation by altering the accessibility of the Shine-Dalgarno (SD) sequence,...
02:28Leaky Scanning
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R stands for...
01:29Coordination of Gene Expression Processes in Bacteria
The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
02:24Regulation of Expression Occurs at Multiple Steps
Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
02:33Initiation of Translation
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.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...