Ribosomes are the major focus of our research, both their expression and function. The synthesis of rRNA is a complex and highly regulated process that provides the cell with just the right amount of ribosomes over a broad range of growth conditions. One important aspect of rRNA expression we are studying is transcription antitermination. Antitermination is a process in which RNA polymerase is modified such that two of its basic properties, elongation rate and terminator sensitivity, are dramatically altered. After modification, RNA polymerase reads through specific terminators and has increased transcription elongation rates. We identified the RNA sequences in rRNA operons needed to signal these antitermination modifications of RNA polymerase and have recently identified the cellular factors involved, a major breakthrough for us. We are currently studying the interactions of these factors with each other, with the antiterminator RNA, and with polymerase. Our goal is to provide a detailed description of RNA polymerase modifications and protein/nucleic acid interactions that are required for fast and efficient rRNA transcription, and relate these changes to cell physiology.

We have also developed E. coli rrn deletion strains whose only rrn operon is encoded on a plasmid. These strains allow the manipulation of a single, homogenous population of ribosomes so that the effect of specific mutations can be analyzed. The ability to work with homogenous ribosomes in the living cell provides a unique opportunity to set up an assay for every known ribosome function, isolate mutations that perturb that function, and work out precisely where various molecular interactions take place on or within the ribosome. For example, the discovery that the ribosome can play an active, rather than passive, role in monitoring peptide synthesis in vivo has substantial ramifications for controlling gene expression at a rather sophisticated level. We are using one such peptide-monitoring regulatory system with our deletion strains and plasmid-encoded rrn mutants to explore how specific effectors and poison peptides are sensed by and then interact with the ribosome to alter the expression of the operon being translated. Our goal in these studies is to provide an in vivo mutational analysis of ribosome structure and function.

See information about the Biennial Meeting on Post-Initiation Activities of RNA Polmerases.