What color is the sky before a storm? 🌩 Brits may write “grEy” while Americans write “grAy” but both recognize it as meaning a color between white & black. Similarly, the 3-letter genetic “words” that “spell” the amino acid building blocks of proteins can be written with different spellings. All organisms can understand these words (the GENETIC CODE is universal), BUT different organisms prefer different spellings (CODON BIAS). If you want to get an organism to express a protein for you, you might want to “be polite” and use their spelling! CODON OPTIMIZATION 👇

PROTEINS are like charm bracelets made up of AMINO ACIDS, where the chain links are a generic peptide backbone and the charms sticking off are the unique side chains (for more check out #20DaysOfAminoAcids). The order of the charms largely determines how the protein folds & functions. 

This order is written in DNA form in the protein’s gene. Through the process of TRANSCRIPTION, this DNA version gets copied into a messenger RNA (mRNA) version (really similar except DNA has one less oxygen on its sugar part and, instead of the nucleotide letter T, RNA has U). more here: http://bit.ly/2yCisGq

Different amino acids are specified by 3-letter “words” called CODONS. There are 4 nucleotide letters – A, C, G, & T/U – so 64 possible codons. BUT there are only 20 (common) amino acids. 3 of the codons don’t spell an amino acid – instead they spell STOP & signal the end of the protein. But that still leaves 61. So some amino acids have multiple codons (DEGENERACY (redundancy)). BUT any 1 codon will only ever spell 1 amino acid (NOT ambiguous)

The charm bracelet is put together amino acid by amino acid through the process of TRANSLATION. Molecular machinery called RIBSOSOMES help link them together, but they rely on servants called transfer RNAs (tRNAs) to bring them the right amino acid charm to add. 

tRNA is a type of “functional RNA” meaning that, unlike the messenger RNA (mRNA) intermediary that’s just an RNA copy of the DNA gene, tRNA never gets made into protein – but it does help make other proteins by TRANSFERing free-floating amino acids to a growing protein chain! 

One part of tRNA binds a specific amino acid and the other end contains a 3-nucleotide ANTICODON that is complementary to the matching 3-letter CODON on the mRNA. Different tRNAs have different ANTICODONS & carry different amino acids. 

Because of degeneracy, multiple servants may bring the same amino acids (e.g. “gray” and “grey” both bring the same colored charm), but the ribosome’s a bit of a snob – it will only add that amino acid if it’s brought by the right servant. And the servant it wants is determined by the CODON in the mRNA. Organisms make each type of tRNA servant, but how many of each they have depends on how popular the corresponding codon spelling is – they stock up on the ones they have to use the most. 

If you’re selling a color-themed word magnet set in America, you’d probably include more “grAy” than “grEy” because that’s what your customers will demand more of. And vice versa in England. If an American needs a “grEy” magnet, this might slow down their sentence-making because they’ll have to do a bunch of digging through magnets to find one. So if you want to sell a magnet set, consider your audience’s preferences – replace those “grAy” magnets with “grEy” or vice vera. 

Similarly, we can order genes codon-optimized for the cell type we want to express them in (e.g. bacteria, yeast, insect cells). Companies like GenScript use algorithms to determine what the optimal codons are based in large part on what codons are most “popular” in those cells. Then they synthesize the genes to match. 

Each tRNA only ever brings 1 type of amino acid, BUT some tRNA can read multiple codons because there’s some “wiggle room” in the 3rd position – in this so called “wobble position” non-canonical base-pairing is sometimes allowed so you don’t need 61 different tRNAs (you need at least 32, some cells use more). This is why a lot of the degenerate codons have the same 2 first letters. This also provides a source of genetic protection – if the 3rd base gets mutated the protein made may still be ok!

Even when a tRNA can read 2 codons, 1 form is “preferred” – the tRNA can read either, but it works better for one of them. So even if the cells have lots of the tRNA that can read that codon, you’ll get better results if you use the one it prefers. Codon optimization can improve recombinant protein expression, but it can also be expensive, so you probably don’t want to try it unless you’re having problems with the native version. BUT making point mutations (changing single codons) is much easier than replacing lots of them, and we do this ourselves a lot. When I do this site-directed mutagenesis, I consult a codon usage bias table like this https://www.biologicscorp.com/tools/CodonUsage#.XFcv_89KhsM

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