In order to react effectively to changes in the surroundings, bacteria must be able to quickly turn specific genes on or off. Although the overall mechanisms behind gene regulation have long been known, the fine details have eluded scientists for decades. Researchers at Uppsala University in Sweden can now provide a picture of how proteins regulate genetic expression at the atomic level. Genes can be regarded as blueprints for all of the molecular machines—normally proteins—that perform the tasks an organism needs for survival. Under different living conditions, different types of proteins are needed to break down the available types of nutrients, for example. Because the surroundings can change rapidly, it is also important for bacteria and other organisms to be able to quickly reconfigure their biochemical operations in order to adapt to the new environment. This is done through regulation of the activity of proteins that already exist in the cell, but also by the binding of special proteins—transcription factors—to specific sites on the DNA, turning certain genes on or off, which in turn regulates the cell's production of various proteins. The latter might seem impossible, as an arbitrary transcription factor normally exists in just a handful of copies inside a bacterial cell, and one of them has to find a specific binding site on the DNA spiral, which contains some five million base pairs, in order to turn a gene on or off, says Dr. Erik Marklund, one of the lead authors of the new study. Roughly 40 years ago, it was observed that these transcription factors find their binding sites on DNA much more quickly than free diffusion in three dimensions would allow.
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