Mechanisms of non-Shine-Dalgarno translation initiation
The mechanism of translation initiation in bacteria was first examined in E. coli, where the presence of a Shine-Dalgarno site preceding the start codon leads to the initiation of translation in the proper reading frame.  Now with thousands of sequenced bacterial genomes it was discovered that less than 1/2 of all bacterial protein coding genes are preceded by a Shine-Dalgarno site.  Additionally, individual bacterial species including many cyanobacteria and bacteroidetes, lack Shine-Dalgarno sites in nearly 90% of their genes!  We are therefore investigating the mechanisms of non-Shine-Dalgarno initiation by utilizing Caulobacter crescentusCaulobacter contains Shine-Dalgarno sites in only 23.5% of its genes, has a doubling time of less than 2 hours, has well established genetic tools, and has a well annotated transcriptome.  We are currently utilizing ribosome profiling, translation reporters, and in vitro reconstituted translation initiation assays to dissect the factors required for non-Shine-Dalgarno initiation in Caulobacter.

RNA-mediated mechanisms of cell cycle-regulation
The Caulobacter cell cycle is controlled by a genetic and biochemical circuit that functions in space and time to control the the transcription of ~20% of the entire genome.  We recently found that approximately half of these mRNAs contained translational control to regulate the timing of expression.  We are interested in the regulatory logic of RNA-mediated control and how it is integrated with the cell cycle-regulatory circuit.