An amino acid can be recruited by several unique codons, like a door that can be opened by a variety of different keys. Interestingly, even though the amino acid endpoint of synonymous codons is the same, the amount of protein eventually expressed is different. Up until now, the mechanism behind this difference in protein expression has been unclear.
Now, using the idea that some codons are “fast” and some are “slow,” researchers have shown that a ribosome can seemingly get “stuck” at a slow codon roadblock during elongation, causing ribosomal traffic jams or preventing new ribosomes from attaching to the mRNA in the first place. This prevents the gene from being quickly transcribed and reduces the amount of protein produced.
Tobias Von der Haar, Dominique Chu, and their team of systems biologists at the University of Kent in the UK used a computer model to determine which codons were fast and which were slow. A fast codon is usually elongated quickly—the codon has a lot of appropriate tRNAs nearby and the ribosome scoots away as soon as the amino acid is attached. A slow codon has few appropriate tRNAs nearby; the ribosome has to dismiss all the wrong tRNAs first, wasting time.
“People had worked out the biochemistry of the decoding process really well, so we put that information into computer models and basically predicted how fast or slow any particular codon is,” said von der Haar. The study authors then created three constructs of the HIS3 yeast gene: one with a set of slow codons, one with the wild type versions of the codons, and one with a set of fast codons. (All codons encoded the same amino acids.) They inserted the constructs into yeast and measured how much protein was expressed. As expected, they found that yeast with the fast codons produced the most protein, followed by the wild type sequence, and, in last place, the slow codon construct.
After looking at several different possible causes for the increased protein synthesis, the researchers found that the speed of decoding had a strong correlation with protein expression levels.
Then, using a computer program modeling eukaryotic translation, the team came up with a model of codon usage-dependent gene expression. They found that once an mRNA binds to a ribosome, elongation must happen quickly if the start site is to be free for the next ribosome to attach and protein expression to continue. When slow codons hinder elongation, initiation of translation is also slowed, and less protein is expressed. Even farther from the start codon, the ribosomes can back up, slowing initiation and reducing protein expression.
Von der Haar is now looking for other examples of genes that use fast versus slow codons to alter expression levels in order to see how widespread this control mechanism is. Aside from providing researchers with a better understanding of translational control, the biotechnology industry could also use this new finding to optimize recombinant protein expression in synthetic biology and bioprocessing. “So far, people have just copied highly expressed messages from nature, but now we’ve added a more knowledge-based approach to how you can define a fast and a good sequence,” said von der Haar. “In bioprocessing, getting as much protein as possible is always the goal.”
Chu D, Kazana E, Bellanger N, Singh T, Tuite MF, von der Haar T. Translation elongation can control translation initiation on eukaryotic mRNAs. EMBO J. 2014 Jan 1;33(1):21-34. doi: 10.1002/embj.201385651