Microcosm_ E. Coli and the New Science of Life - Carl Zimmer [14]
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