x Abu Dhabi, UAETuesday 25 July 2017

Nature's knotty problem

With more than a metre of DNA curled up in every cell of our bodies, the double-helix string will inevitably end up in a tangled mess. To enable the cells to 'read' the genetic sequences, nature has created its own solution.

Scientists are combining biochemistry and knot theory, a branch of mathematics, to understand how cells read the tangle of DNA in their central nuclei.
Scientists are combining biochemistry and knot theory, a branch of mathematics, to understand how cells read the tangle of DNA in their central nuclei.

Knots have been a source of annoyance since at least 333 BCE, when Alexander the Great was confronted by the fabled Gordian Knot during his campaign in Asia Minor. Now they are becoming a focus of fascination among scientists trying to unravel the secrets of life. New research suggests nature discovered the benefits of knowing how to handle knots long before mariners and mountaineers. That's because some of the most basic elements of life are stringy - and thus perfect knot-forming material.

One of the most remarkable scientific facts is that virtually every cell in our bodies contains over a metre of the genetic molecule DNA. Crammed into the central nucleus, its stringlike double helix structure would seem a dead cert for ending up in an unholy tangle, and in 1976 scientists discovered the all too predictable result: knots. Predictable, perhaps - but also perplexing, as the very processes of life depend on cells being able to "read" the genetic sequences strung along DNA. A single mistake can result in potentially fatal diseases, including cancer. But if the instructions are wrapped up in knots, how can a cell read them reliably?

In the search for answers, researchers had to breach academic boundaries and combine biochemistry with knot theory, the branch of mathematics with the tools for making sense of the chaos inside cells. They were rewarded by uncovering one of the most impressive examples of the power of evolution. Over millions of years, cells have developed a set of special enzymes which do for DNA what Alexander the Great did for the knot at Gordium - but with a lot more subtlety. Known as topoisomerases, they are able to home in on the tangles of DNA in cells, break the molecule at precisely the right places, remove any knots or twists, and then put the whole thing back together again.

By allowing DNA to be read properly, these molecular-sized Alexanders are vital to health and well-being. The flip-side of the discovery has proved no less important, by opening up new ways of combating disease. Drugs companies have exploited the critical function of topoisomerases to develop antibiotics such as Ciprofloxacin, which interferes with the ability of bacteria to sort out their own DNA, thus killing them and stopping infection from spreading.

Some new anti-cancer treatments are based on the same idea, and interfere with the notoriously uncontrolled proliferation of cancer cells. Last year GlaxoSmithKline won approval for the use of a topoisomerase inhibitor called Hycamtin for use in treating ovarian and lung cancer. The US National Cancer Institute has another, batracylin, undergoing clinical trials for treating patients with tumours that have spread around their bodies.

Meanwhile, researchers are still uncovering new ways in which nature has equipped cells to deal with the nuisance of knots. While DNA uses topoisomerases to rid itself of unwanted knots, the wonder is that the molecule is not riddled with the things. After all, the risk of stringy objects ending up knotted grows rapidly with length - as we all know from everyday experience (though it took mathematicians until 1988 to actually prove it).

So why is the long, thin DNA molecule relatively free of them? Last July, a team led by Professor Andrzej Stasiak of the Centre for Integrative Genomics at the University of Lausanne, Switzerland, came up with some answers after using computers to simulate how DNA is stored in cells. Molecular biologists have long known that DNA is "supercoiled" into special twisted shapes, which helps cram more of the molecule into cells. In another example of nature's ingenuity, the supercoiling is performed by DNA gyrase, an enzyme that first forms a loop out of the DNA, cuts into it and passes one part over another, introducing twists which force the DNA into braid-like patterns. According to the simulations by Prof Stasiak and his colleagues, these braids are at much lower risk of forming knots - suggesting that supercoiling is about more than just cramming a lot of DNA into a very small space.

While knots are anathema for DNA, new research suggests they are positively welcomed by some of those other molecules vital for life, proteins. Constructed by cells according to the genetic instructions of DNA, proteins emerge from dedicated "factories" as strings of amino acids, which then curl up into complex shapes that dictate what the protein will do. And some proteins end up with a knot buried deep inside.

The discovery of these knots, announced in 2000 by Dr William Taylor of the National Institute for Medical Research in London, surprised many. What purpose do they serve, and how are they created? Unlike everyday knots, they can't be the result of blind chance: shape is crucial to the function of proteins, so the knots must be formed with as much care as DNA takes in ridding itself of the things.

Some light has now been cast on the process by Dr Anna Mallam and her colleagues at the University of Cambridge, in experiments with a protein made by a bacterium which ends up with a simple overhand knot trapped inside. The results, published last week in the Proceedings of the National Academy of Sciences, suggest the knot is made as the bacterium forms the chain of amino acids, which form a loop and thread through themselves before the whole protein curls up into its final shape.

This still leaves the question of why some proteins bother to perform such intricate manoeuvres. Like DNA, most proteins seem keen to avoid knots, but some clearly derive benefit from them; one suggestion is that it makes them stronger. The short answer is no one knows - and finding out looks set to keep scientists tied up for some while yet. Robert Matthews is Visiting Reader in Science at Aston University,

Birmingham, England