The ribosome is the cellular machine that translates DNA into proteins. Its two subunits, 30S and 50S (which together make up the 70S ribosome), scan over the messenger RNA and spit out polypeptides using amino acids delivered by transfer RNA (tRNA).
The first glimpse of the much anticipated structure came in 2001 when Harry Noller's group at the University of California, Santa Cruz, published the complete bacterial ribosome structure at the modest resolution of 5.5 Å. Several subsequent efforts were published, and then in September 2006, two groups provided high resolution views of the whole ribosome. These two Hot Papers reported the 70S bacterial ribosome structure bound with messenger and transfer RNAs.
"There was no high resolution structure of the whole ribosome with tRNA and mRNA until this work came along," says Venki Ramakrishnan of...
While the two structures showed that the tRNA was distorted and bent when bound, one structure at 2.8 Å, from Ramakrishnan's group, confirmed the structure of the peptidyl-transferase center shown in previous work.
Noller's structure suggests that these nucleotides are perhaps involved in the process of building the polypeptide chain. "For many people that didn't make that much sense," says Marina Rodnina, from Witten/Herdecke University. Her group and others have conducted mutation experiments, discovering each nucleotide's role in the translation process, and showing that translation occurs well, even without the very nucleotides that Noller's group sees slipping into the transferase center.
Perhaps more importantly, Noller's structure undermines a proton shuttle mechanism that enables peptides to bond in the peptadyl-transferase center; by this mechanism a hydroxyl group carries a proton from the tRNA to the bond of the extending peptide chain, enabling amino acids to attach to each other. Thomas Steitz's lab at Yale University performed a cross-crystal average of the two data sets and found that the two structures actually conformed.
Andrei Korostelev, first author of the Noller paper, says that their group is checking out Steitz's calculations, but at first blush he accuses Steitz's analysis of being inherently biased toward Ramakrishnan's higher resolution structure.
The biochemical side
"Since we now know where the tRNAs bind and we also know that they are somewhat distorted from the structure you see of a free tRNA, that's led to lots of experiments which seek to trace the movement of the tRNA as it goes through the ribosome in great detail," says University of Pennsylvania's Barry Cooperman. His lab uses fluorescence resonance energy transfer (FRET) between single molecules to measure the strength of interactions among various parts of the ribosome. Last year they reported that the ribosome has some 10-12 intermediate states through which it moves during translation.
Many groups are trying to manipulate the ribosome's "ground state" - its conformation of lowest energy - into one of the several conformations that it might normally move through quickly. Scott Blanchard at Cornell University showed that the ribosome is a dynamic, moving machine that requires no energy or other factors to change conformation several times through the process of translation.
Jamie Cate, at the University of California, Berkeley, and collaborators have also shown how movement between conformations is essential to the ribosome's function. They published last year on how an antibiotic inhibits translation by sending one helix of the subunit swinging away from where the two subunits meet.
Meanwhile, Noller's group continues to probe the ribosome structure. Using their 2006 model as a starting point, they are exploring how a promoter region upstream of the start codon, called the Shine-Dalgarno sequence, influences the position of the 30S subunit at the beginning of translation.
But the most exciting work on the ribosome has yet to happen, says Cate. "It takes a while for structures like this to really sink in."