Molecular Biology Select

The suffix ''–some'' is derived from the Greek word ''soma,'' which means body. Molecular biologists use the ''–some'' suffix when naming macromolecular assemblies, such as the ribosome, spliceosome, and exosome, and more recently the metabolosome and periodosome. This issue's Molecular Biology Select discusses reports that highlight the functional and structural intricacies of these systems. Ribosomes are RNA-protein complexes that are central to the process of translation during which information encoded by messenger RNA (mRNA) is converted into the protein sequence. Recent structural and functional studies have highlighted the importance of ribosomal motion during translation. In a new study, Wen et al. (2008) apply optical tweezers to study translation of single mRNA hairpins by a single ribosome, one codon at a time. First, the authors stalled a single ribosome at the 5 0 end of an mRNA hairpin construct attached to two beads. One bead was held on a micropipette tip and the second was held by an optical trap, which measures the force exerted on the mRNA. During subsequent experiments both beads were held by optical traps to improve the stability of measurements. For each measurement, translation was resumed by addition of an appropriate aminoacyl-tRNA mixture. With their setup, the investigators were able to follow translation by a single ribosome in real time by monitoring how the distance between the beads changes as the ribosome opens the hairpin and moves along the mRNA. The authors discovered that translation occurs in a discrete step-pause-step pattern, with transitions between patterns representing translation of an individual codon. Remarkably, different ribosomes produced significantly different translation trajectories, with variations in translation rate and the number, location, and length of pauses. In addition to the brief intrinsic pauses in ribosome activity (2.2 s on average), there were longer pauses (up to 1–2 min) that the authors propose might be important for translational regulation. Thus, translation seems to be a discrete process, composed of a series of translocation-pause-translocation events. Intrinsic pause length, that is the time the ribosome spends before translocating to the next codon, determines the rate of translation and might be controlled by several successive rate-limiting steps. Each translocation step is of fixed duration and is composed of three substeps, which might indicate that the ribosome moves over a single codon one base at a time. Splicing is a pre-mRNA processing step that removes sections of noncoding sequences and is catalyzed by the spliceosome, a …