Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

Proteins make up much of the biological machinery inside cells and perform the essential tasks needed to keep each cell alive. Cells contain thousands of different proteins and the instructions needed to build each protein are encoded in genes. However, these instructions cannot be used directly to manufacture the proteins. Instead, a messenger molecule called mRNA is needed to carry the information stored within genes to the parts of the cell where proteins are made. In bacteria, one mRNA molecule can include information from several genes. This group of genes is called an operon and produces a set of proteins that perform a shared task. Although these proteins work together, some of them are needed in greater numbers than others. Because they are all made using information from the same mRNA, some instructions on the mRNA must be read more times than others. It is unclear how bacterial cells control how many proteins are produced from each part of one mRNA but it is thought to relate to the three-dimensional shape of the molecule itself. Burkhardt, Rouskin, Zhang et al. have now examined the production of proteins from mRNAs in the commonly studied bacterium, Escherichia coli. The results showed that each set of instructions on the mRNA formed a three-dimensional structure that corresponds to the amount of protein produced from that portion of the mRNA. When this three-dimensional structure is more stable or rigid, the corresponding instructions tended to produce fewer proteins than if the structure was relatively simple and unstable. Further investigation showed that these three-dimensional mRNA structures could form spontaneously outside of cells, suggesting that molecules other than the mRNA itself have a relatively small role in controlling the number of proteins produced. This also suggests that the entire structure of each mRNA is important and is likely to be essential for cell survival. The next step is to understand why bacteria organise their genes in this way and how the different mRNA structures control how proteins are produced. Moreover, because many bacteria are used like biological factories to produce a variety of commercially useful molecules, these new insights have the potential to enhance a number of manufacturing processes.