The Myth Of The Tangled Spaghetti

E. coli's brainy tongue does not fit well into the traditional picture of bacteria as primitive, simple creatures. Well into the twentieth century, bacteria remained saddled with a reputation as relics of life's earliest stages. They were supposedly nothing more than bags of enzymes with some loose DNA tossed in like a bowl of tangled spaghetti. "Higher" organisms, on the other hand—including animals, plants, fungi—were seen as having marvelously organized cells. They all keep their DNA neatly wound up around spool-shaped proteins and bundled together into chromosomes. The chromosomes are tucked into a nucleus. The cells have other compartments, in which they carry out other jobs, such as generating energy or putting the finishing touches on proteins. The cells themselves have structure, thanks to a skeletal network of fibers crisscrossing their girth.

The contrast between these two kinds of cells—sloppy and neat—seemed so stark in the mid-1900s that scientists used it to divide all of life into two great groups. All species that carried a nucleus were eukaryotes, meaning "true kernels" in Greek. All other species—including E. coli—were now prokaryotes. Before the kernel there were prokaryotes, primitive and disorganized. Only later did eukaryotes evolve, bringing order to the world.

There's a kernel of truth to this story. The last common ancestor of all living things almost certainly didn't have a nucleus. It probably looked vaguely like today's prokaryotes. Eukaryotes split off from prokaryotes more than 3 billion years ago, and only later did they acquire a full-fledged nucleus and other distinctive features. But it is all too easy to see more differences between prokaryotes and eukaryotes than actually exist. The organization of eukaryotes jumps out at the eye. It is easy to see the chromosomes in a human cell, the intricately folded Golgi apparatus, the sausage-shaped mitochondria. The geography is obvious. But prokaryotes, it turns out, have a geography as well. They keep their molecules carefully organized, but scientists have only recently begun to discover the keys to that order.

Many of those keys were first discovered in E. coli. E. coli must grapple with several organizational nightmares in order to survive, but none so big as keeping its DNA in order. Its chromosome is a thousand times longer than the microbe itself. If it were packed carelessly into the microbe's interior, its double helix structure would coil in on itself like twisted string, creating an awful snarl. It would be impossible for the microbe's gene-reading enzymes to make head or tail of such a molecule.

There's another reason why E. coli must take special care of its DNA: the molecule is exquisitely vulnerable to attack. As the microbe turns food into energy, its waste includes charged atoms, which can crash into DNA, creating nicks in the strands. Water molecules are attracted to nicks, where they rip the bonds between the two DNA strands, pulling the chromosome apart like a zipper.

Only in the past few years have scientists begun to see how E. coli organizes its DNA. Their experiments suggest that it folds its chromosome into hundreds of loops, held in place by tweezerlike proteins. Each loop twists in on itself, but the tweezers prevent the coiling from spreading to the rest of the chromosome. When E. coli needs to read a particular gene, a cluster of proteins moves to the loop where the gene resides. It pulls the two strands of DNA apart, allowing other proteins to slide along one of the strands and produce an RNA copy of the gene. Still other proteins keep the strands apart so that they won't snarl and tangle during the copying. Once the RNA molecule has been built, the proteins close the strands of the DNA again. E. coli's tweezers also make the damage from unzipping DNA easier to manage. When a nick appears in the DNA, only a single loop will come undone because the tweezers keep the damage from spreading farther. E. coli can then use repair enzymes to stitch up the wounded loop.

E. coli faces a far bigger challenge to its order when it reproduces. To reproduce, it must create a copy of its DNA, pull those chromosomes to either end of its interior, and slice itself in half. Yet E. coli can do all of that with almost perfect accuracy in as little as twenty minutes.

The first step in building a new E. coli—copying more than a million base pairs of DNA—begins when two dozen different kinds of enzymes swoop down on a single spot along E. coli's chromosome. Some of them pull the two strands of DNA apart while others grip the strands to prevent them from twisting away or collapsing back on each other. Two squadrons of enzymes begin marching down each strand, grabbing loose molecules to build it a partner. The squadrons can add a thousand new bases to a DNA strand every second. They manage this speed despite running into heavy traffic along the way. Sometimes they encounter the sticky tweezers that keep DNA in order; scientists suspect that the tweezers must open to let the replication squadrons pass through, then close again. The squadrons also end up stuck behind other proteins that are slowly copying genes into RNA and must wait patiently until they finish up and fall away before racing off again. Despite these obstacles, the DNA-building squadrons are not just fast but awesomely accurate. In every 10 billion bases they add, they may leave just a single error behind.

As these enzymes race around E. coli's DNA, two new chromosomes form and move to either end of the microbe. Although scientists have learned a great deal about how E. coli copies its DNA, they still debate how exactly the chromosomes move. Perhaps they are pulled, perhaps they are pushed. However they move, they remain tethered like two links in a chain. A special enzyme handles the final step of snipping them apart and sealing each back together. Once liberated, the chromosomes finish moving apart, and E. coli can begin to divide itself in two.

The microbe must slice itself precisely, in both space and time. If it starts dividing before its chromosomes have moved away, it will cut them into pieces. If it splits itself too far toward either end, one of its offspring will have a pair of chromosomes and the other will have none. These disasters almost never take place. E. coli nearly always divides itself almost precisely at its midpoint, and almost always after its two chromosomes are safely tucked away at either end.

A few types of proteins work together to create this precise dance. When E. coli is ready to divide, a protein called FtsZ begins to form a ring along the interior wall of the microbe at midcell. It attracts other proteins, which then begin to close the ring. Some proteins act like winches, helping to drag the chromosomes away from the closing ring. Others add extra membrane molecules to seal the ends of the two new microbes.

FtsZ proteins form their ring without consulting a map of the microbe, without measuring it with a ruler. Instead, it appears that FtsZ is forced by other proteins to form the ring at midcell. Another protein, called MinD, forms into spirals that grow along the inside wall of the microbe. The MinD spiral can scrape off any FtsZ it encounters attached to the wall. But the MinD spiral itself is fleeting. Another protein attaches to the back end of the spiral and pulls the MinD proteins off the wall one at a time.

A pattern emerges: the MinD spiral grows from one end toward the middle but falls apart before it gets there. The dislodged

MinD proteins float around the cell and begin to form a new spiral at the other end. But as the MinD spiral grows toward the middle again, its back end gets destroyed once more. The MinD spiral bounces back and forth, taking about a minute to move from one end of the microbe to the other.

The bouncing MinD spiral scrapes away FtsZ from most of the cell. Only in the middle can FtsZ have any hope of forming the ring. And even there FtsZ is blocked most of the time by the chromosome and its attendant proteins. Only after the chromosome has been duplicated and the two copies are moving away from the middle is there enough room for FtsZ to take hold and start cutting the microbe in two.

E. coli may not have the obvious anatomy of a eukaryote cell, but it has a structure nevertheless. It is a geography of rhythms, a map of flux.

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