When translating from one language to another, a translator must often weigh synonyms: Will the meaning change if the word "convert" is used instead of "transform," or "influence" rather than "effect?" Translation takes place in the living cell as well, when the coded instructions copied from the genes are converted into proteins. The synonyms in this sort of translation, however, are to be found in the original content: Every amino acid – one of the "words" that are strung together to make a protein "sentence" – can be translated from one of several alternate DNA sequences that code for it.
The code for a single amino acid is a three-letter DNA sequence called a codon. There are 64 triplet combinations of the four letters in the gene code, but only 20 amino acids, so that a number of different codons encode for the same amino acid. Until now, scientists have largely assumed that mutations that exchange one of these synonymous codons for another – so-called silent mutations – would not have any effect on the organism, as the resulting protein is the same.
Dr. Yitzhak Pilpel of the Molecular Genetics Department and research student Orna Man, who also works under the guidance of Prof. Joel Sussman of the Structural Biology Department, thought that, like literary synonyms, the differences between these codons might be real, though subtle. In recent years, scientists have come to understand that differences in the gene code are only part of what separates one organism from the next. Much research into these differences has focused on the first stage of genetic activity, when a complex interplay of regulators controls which coded instructions for protein production will be copied, as well as when, where, and in what amounts. But Pilpel and Man thought that other factors might also come into play, and decided to investigate the codon sequences.
In research that recently appeared in Nature Genetics, the scientists showed that the choice of codon used to produce an amino acid does, indeed, influence the traits of the organism as a whole. Different codons, it seems, do their work more or less quickly, and with greater or lower efficiency.
What causes these differences? Pilpel and Man found that the reasons can be traced to a molecule called transfer RNA (tRNA). TRNAs are the work crew of protein construction: For each codon there is a corresponding tRNA molecule that "reads" the code during translation and lugs the proper amino acid over to the growing protein chain. But some tRNA molecules are more commonly available than others; it seems that the more common the tRNA for a particular codon, the faster and more efficient the translation process.
The researchers tested this idea in nine species of yeast, in which they identified 2,800 shared genes. Using their data on codons, they then calculated how efficiently these genes are translated into proteins in each species. Their findings showed that differences in codon sequence can add up to large variations in translation efficiency, and that these variations are tied to dissimilar traits in the different species. Thus, for instance, aerobic yeast cells – those that need oxygen to produce energy – were very efficient at translating the genes needed for utilizing oxygen, whereas anaerobic yeasts – those that don't use oxygen – preferred greater efficiency in other genes needed for their lifestyle. Pilpel: "Each lifestyle requires the expression of some genes to be elevated over others. These genes are probably more likely, through the forces of natural selection, to include the codons that are translated more efficiently."
Further research may show that exchanges of one synonymous codon for another may have widespread effects on function in living beings. In particular, silent mutations may play an as yet unexplored role in certain genetic diseases.
Dr. Yitzhak Pilpel's research is supported by the Leo and Julia Forchheimer Center for Molecular Genetics; the Minna James Heineman Stiftung; the Ben May Charitable Trust; the Dr. Ernst Nathan Fund for Biomedical Research; the Charles and M.R. Shapiro Foundation Endowed Biomedical Research fund; and Mr. Walter Strauss, Switzerland. Dr. Pilpel is the incumbent of the Aser Rothstein Career Development Chair of Genetic Diseases.
Charting the Bureaucracy
We depend on bureaucracy to keep our society functioning smoothly: Committees spring up to regulate the work of ministries, which in turn regulate departments and organizations, and so on. It turns out that the genome has also evolved a multi-level hierarchy for managing its activities. In the genome, this regulatory network has developed into a finely tuned, highly responsive mechanism for keeping the right genes turned on at the right time.
Gene regulation begins with the transcription factors – proteins that initiate the copying of the gene code for protein production onto the RNA. In later stages of regulation, the messenger RNA (mRNA) that ferries these instructions out of the nucleus to the cells' protein factories can be stopped, either en route or after protein production is under way. One agent of this "gene silencing" is microRNA – a short segment of non-coding RNA that identifies the target mRNA and blocks it or activates its destruction.
To get an idea of the regulatory network's "organizational chart," Dr. Yitzhak Pilpel, Prof. Moshe Oren of the Molecular Cell Biology Department, their joint research student Reut Shalgi, and Daniel Lieber performed sophisticated computational analysis on data for interactions between thousands of genes and hundreds of micro-RNAs and transcription factors. The scientists investigated the network as a whole and also looked for smaller structures embedded within the larger network. These "motifs" – combinations of network elements that repeatedly appear together – contained some important clues as to how the organization functions.
One type of motif involved two microRNAs working in concert to silence a gene or set of genes. This, says Pilpel, may enable the cell to base its decisions on the input from two different sources.
In another type of motif, transcription factors paired up with microRNAs. The transcription factor-microRNA correlations they identified showed up again when they looked at levels of these molecules in specific tissues and organs, and they believe such motifs may have special significance in regulating embryonic development. "The tight coordination of gene activation with gene silencing might involve a sort of delay mechanism that shuts off protein production at a preset time after it's begun," says Shalgi.
This research has revealed a system in which proteins and microRNAs closely communicate and work together to keep the process of gene expression in tune. It may have special significance for studies in developmental biology, as well as for the investigation of diseases in which complexes of genes play a role.