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Updated: Aug 25, 2025
13:14
Genetic Barcoding with Fluorescent Proteins for Multiplexed Applications
Published on: April 14, 2015
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Multiplexing mechanical and translational cues on genes.
Martijn Zuiddam1, Bahareh Shakiba1, Helmut Schiessel2
1Institute Lorentz for Theoretical Physics, Leiden University, Leiden, the Netherlands.
Biophysical Journal
|October 14, 2022
Summary
The genetic code can store multiple layers of information beyond protein sequence. This study demonstrates simultaneous adjustment of translation efficiency and nucleosome positioning without altering the encoded protein.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The genetic code's degeneracy allows for storing additional information beyond amino acid sequences.
- Previous research suggests roles for DNA sequences in nucleosome positioning and translational efficiency.
- These layers of information can influence gene expression and protein folding.
Purpose of the Study:
- To demonstrate the feasibility of encoding multiple information layers within a single gene sequence.
- To quantify the simultaneous modulation of translation efficiency and nucleosome positioning.
- To explore methods for preserving or adjusting these layers during gene transfer between organisms.
Main Methods:
- Representing genes as weighted graphs encompassing all synonymous sequences.
- Utilizing shortest path algorithms on these graphs to identify optimal synonymous codons.
- Analyzing the impact of sequence modifications on both translational efficiency and predicted nucleosome positioning.
Main Results:
- Successfully identified synonymous gene variants that allow for independent or simultaneous tuning of translation efficiency and nucleosome positioning.
- Demonstrated that significant adjustments can be made without altering the final amino acid sequence.
- Showcased the ability to restore translational efficiency in a heterologous host (yeast) while maintaining the nucleosome landscape.
Conclusions:
- The DNA sequence offers a versatile platform for encoding multiple biological signals.
- Synonymous codon optimization can be employed to simultaneously control gene expression dynamics and chromatin structure.
- This approach has implications for synthetic biology and understanding gene regulation across species.
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