Genetic engineering bits and pieces: Codon bias

Random thing I learned today: One of the many details one has to pay attention to when genetically modifying an organism revolves around a thing called codon bias. What led me to this bit of information is part of a writing assignment for the course "Laboratory Fundamentals of Biological Engineering", taught at MIT. Here's part of the documentation for this course. The question was this:
"Would you expect the phage to tolerate p8 modifications that encode all Leucines with the CTA codon instead of the CTG codon? Would you expect the phage to tolerate these same modifications to p3?"

When the authors ask whether the phage would "tolerate" this or that modification, I assume they mean to ask whether the phage would still be active and reasonably effective after the modification. Leucine is an amino acid. p8 signifies the protein VIII of bacteriophage (a virus that infects bacteria) M13. Proteins, of course, are chains of amino acids. A codon is a triplet of nucleotides that codes for an amino acid. Some amino acids have more than one codon associated with them, which is possible because triplets of A, C, G, T can encode 4^3 = 64 amino acids, but cells only use 20.
It turns out that not all codons are created equal - within an organism, there is usually a bias towards some codons over others - some codons occur more frequently than others. This is associated with the relative abundance of the corresponding tRNAs (transfer RNAs). tRNAs are molecules that "carry" an amino acid on one side and a triplet of ribonucleotides on the other. They are used in building the actual amino acid chains of proteins. Here's an illustration from the Wikipedia entry on tRNA:



The more tRNAs of a certain type there are, the more proteins incorporating the amino acid associated with this codon can be built in a fixed timeframe. Compare this to a factory setting: If you have ten workers that are assigned to mount a tire on a car, then you can mount at most ten tires simultaneously. If you have twenty workers assigned to this task, then you can mount at most twenty tires at a time and so on.
It turns out that E. coli, the host that M13 is supposed to infect in the course's experiments, has a codon bias towards CTG for Leucerine. As can be seen in Table 2, here, the frequency of the codon CTG for Leucerine is 0.49, while the frequency for CTA is only 0.04. In Table 3 of the same document, it becomes apparent that the tRNA concentration associated with CTA is "minor", compared to that associated with CTG. This means that there will be few CTA-tRNAs floating around an E. coli cell.
Now, a virus such as M13 "hijacks" the cellular machinery of its host to replicate and assemble itself. It has to make do with what it finds in its host cell. And if it finds very few of the resources it needs to replicate itself, then its chances of survival are diminished.
M13's p8 is its coat protein - the protein that builds its outer shell. A wild-type virus needs 2700  copies of those. p3 is the phage tail, of which there are only five per virus.
So one answer to the question is: The phage may still be active and effective if you change the CTA codons in p3 to CTG codons, because the low number of CTG-tRNAs floating around may still be enough to make the five required copies per phage, but it will probably take a hit if you change the CTA codons to CTG in the gene that codes for p8.
To summarize: while there are many other factors that play into this whole protein synthesis performance thing, codon bias is definitely something to keep in mind when reengineering organisms.

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