Prokaryotic gene expression in vitro: transcription-translation coupled systems

Totally asymmetric exclusion process with extended objects: a model for protein synthesis

The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied totally asymmetric exclusion process, in which particles typically cover a single lattice site, to include cases with extended objects. Exact solutions can be determined for a uniform closed system. We analyze the uniform open system through two approaches. First, a continuum limit produces a modified diffusion equation for particle density profiles. Second, an extremal principle based on domain wall theory accurately predicts the phase diagram and currents in each phase. Finally, we briefly consider approximate approaches to a nonuniform open system with quenched disorder in the particle hopping rates and compare these approaches with Monte Carlo simulations.

Differential pattern of misreading induced by streptomycin in vitro

A simplified, plasmid-directed coupled system was used to study the effect of streptomycin on the accuracy of natural messenger translation in vitro. The interaction of six different codons with their cognate tRNAs and 18 non-cognate tRNAs was analysed in the presence and absence of the antibiotic. Streptomycin appeared to modify, to a varying extent, the frequency of errors in codon-anticodon recognition. From this observation, some rules for mistranslation were inferred.

Accuracy of natural messenger translation: analysis of codon-anticodon recognition in a simplified cell-free system

A simplified plasmid-directed coupled system [Robakis, N., Cenatiempo, Y., Meza-Basso, L., Brot, N., & Weissbach, H. (1983) Methods Enzymol. 101, 690-706] was used to study the accuracy of natural messenger translation in vitro. In this system, protein synthesis is limited to the formation of the N-terminal di- or tripeptide of the gene product. Such a control is obtained by restricting the supply of aminoacyl-tRNAs in the assay medium to those corresponding specifically to the first two or three triplets in the mRNA coding sequence. We analyzed comparatively the interaction of 6 different codons with their cognate tRNAs and 18 noncognate tRNAs able to recognize triplets differing from the legitimate sequences by one base only. Special attention was paid to the single base errors occurring at the first and second codon positions during ribosomal selection of aminoacyl-tRNA molecules. The noncognate tRNAs were assayed either in the absence of the legitimate tRNAs or under competition conditions. They were chosen so that all the possibilities for misreading any particular base as each of the other three bases could be studied. First, it was mainly observed that translation mistakes can be equally detected in the first and second codon positions; there is no compelling evidence for a most or least accurate site. Second, pyrimidines seem to be read more accurately than purines. In particular, U cannot be read as either C or G, and C can hardly be mistaken for any other base.(ABSTRACT TRUNCATED AT 250 WORDS)