Source: Stephanie Mitchell/Harvard Staff Photographer

A recent paper published by Arvind Subramaniam (pictured above) and co-authors in Proceedings of National Academy of Sciences have attempted to provide a solution to a decades old problem in genetics.

Though the genetic code, the rules by which DNA gets transcribed to RNA and then translated to proteins, is quite well understood, but what has remained puzzling is the degeneracy of the genetic codeunderlying protein synthesis. Now before understanding more about what they did, let me give you a brief primer on the problem itself.

What is it all about ?

Decoding of DNA is accomplished by the ribosome, which links amino acids in an order specified by mRNA (messenger RNA), usingtransfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time.  So mathematically we can calculate that, with four different nucleotides (in RNA), a three nucleotide code  could code for a maximum of 43 or 64 amino acids. However, in the process of translation (RNA to proteins) only 20 kinds of standard amino acids are produced. So, many of these groups of nucleotides, called codons  produce same amino acids i.e, code synonymously.  For example, the amino acid can be produced in six different ways. A cool figure below shows all the 64 codons and the different amino acids they code for.


This apparent degeneracy has been a core problem in genetics, i.e, whether those seemingly synonymous codons truly produced the same amino acids, or whether they represented a second, hidden genetic code. Now Harvard researchers have published a possible solution to this problem, and they hope the solution would lead to developing new methods to fight resistant bacteria.

How did they solve it?

To try and decipher this synonymous coding problem, they decide to use a simple bacterium Escherichia coli. First they considered the synonymous codons for seven amino acids: Leucine, Arginine, Serine, Proline, Isoleucine, Glutamine, and Phenylalanine. This set of seven amino acids is representative of the degeneracy of the genetic code,as it includes six-, four-, three-, and twofold degenerate codon families. Then they constructed a library of 29 yellow fluorescent protein (YFP) gene variants, in such a way that each version of the gene could code for a specific amino acid. Then all these genes were inserted into E.coli. To test whether the codons function similarly or not, they applied environmental perturbations on E.coli. This perturbation was in the form of amino acid availability. They monitored growth and YFP synthesis in these strains during amino acid-rich growth as well as during limitation for each of the seven amino acids.

What they found, was quite startling that under different environmental conditions (amino acid availability) the codons produced proteins at a different rate.  If the bacteria are in an environment where they can grow and thrive (amino acid rich), each synonymous codon produces the same amount of protein, but if they are starved of an amino acid, some codons produce a hundredfold more proteins than others.

The reason for such differences in protein production lie in the nature oftRNA, the Transport RNA which ferries the amino acids to the cellular machinery that manufactures proteins. The authors managed to rule out the usual rules associated with tRNA abundance and codon usage. Rather,it was the competition among tRNA isoacceptors foraminoacylation which was the underlying reason for the robustness of protein synthesis. In plain-speak, what this means that different tRNA molecules have different levels of amino acid carrying efficiency. So, if some tRNA molecules are not able to deliver the amino acid to where it needs to be, the cell would not be able to manufacture the proteins it needs. In an environment where amino acids are in short supply, that ability to hold onto them becomes very important.While the system helps cells to make certain proteins efficiently under stressful conditions, it also acts as a biological fail-safe  allowing the near-complete shutdown in the production of other proteins as a way to preserve limited resources.

What now?

Given the universality of the genetic code, it would very interesting to explore what role (if any) differences in the seemingly synonymous portions of the genetic code may have in other organisms. Also, in diseases like cancer, the cancerous cells deplete amino acids faster than normal cells, so given that environmental perturbations lead to different protein production efficiencies, would it be possible to devise any interventions or treatments to combat them!!

More on this:

  1.  Degeneracy and complexity in biological systems, Edelman GM, Gally JA, Proceedings of National Academy of Sciences, 2001
  2. Cooperation between translating ribosomes and RNA polymerase in transcription elongationProshkin S, Rahmouni AR, Mironov A, Nudler E, Science, 2010
  3. The GCN2-ATF4 pathway is critical for tumour cell survival and proliferation in response to nutrient deprivation, Ye J, et al., EMBO J, 2010
  4. High levels of tRNA abundance and alteration of tRNA charging by bortezomib in multiple myeloma, Zhou Y, Goodenbour JM, Godley LA, Wickrema A, Pan T, Biochem Biophys Res Commun, 2009

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