The only software-controlled molecular assembler we know about is the ribosome – the biological machine that reads the sequence of bases on a strand of messenger RNA, and, converting this genetic code into a sequence of amino acids, synthesises the protein molecule that corresponds to the gene whose information was transferred by the RNA. An article in this week’s Nature (abstract, subscription required for full paper, see also this editor’s summary) describes a remarkable experimental study of the way the RNA molecule is pulled through the ribosome as each step of its code is read and executed. This experimental tour-de-force of single molecule biophysics, whose first author is Jin-Der Wen, comes from the groups of Ignacio Tinoco and Carlos Bustamante at Berkeley.
The experiment starts by tethering a strand of RNA between two micron-size polystyrene beads. One bead is held firm on a micropipette, while the other bead is held in an optical trap – the point at which a highly focused laser beam has its maximum intensity. The central part of the RNA molecule is twisted into a single hairpin, and the ribosome binds to the RNA just to one side of this hairpin. As the ribosome reads the RNA molecule, it pulls the hairpin apart, and the resulting lengthening of the RNA strand is directly measured from the change in position of the anchoring bead in its optical trap. What’s seen is a series of steps – the ribosome moves about 2.7 nm in about a tenth of a second, then pauses for a couple of seconds before making another step.
This distance corresponds exactly to the size of the triplet of bases that represent a single character of the genetic code – the codon. What we are seeing, then, is the ribosome pausing on a codon to read it, before pulling the tape through to read the next character. What we don’t see in this experiment, though we know it’s happening, is the addition of a single amino acid to the growing protein chain during this read step. This takes place by means of the binding to RNA codon, within the ribosome, of a shorter strand of RNA – the transfer RNA – to which the amino acid is attached. What the experiment does make clear that the operation of this machine is by no means mechanical and regular. The times taken for the ribosome to move from the reading position for one codon to the next – the translocation times – are fairly tightly distributed around an average value of around 0.08 seconds, but the dwell times on each codon vary from a fraction of a second up to a few seconds. Occasionally the ribosome stops entirely for a few minutes.
This experiment is far from the final word on the way ribosomes operate. I can imagine, for example, that people are going to be making strenuous efforts to attach a probe directly to the ribosome, rather than, as was done here, inferring its motion from the location of the end of the RNA strand. But it’s fascinating to have such a direct probe of one of the most central operations of biology. And for those attempting the very ambitious task of creating a synthetic analogue of a ribosome, these insights will be invaluable.