Project description:Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time. We provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling, RNA-seq, global 5’-RACE, and liquid chromatography coupled with tandem mass spectrometry (LC-MS) data to the 4-megabase C. crescentus genome. We mapped transcript units at single base-pair resolution using RNA-seq together with global 5’ RACE. Additionally, using ribosome profiling and LC-MS, we mapped translation start sites and coding regions with near complete coverage. We found most start codons lacked corresponding Shine-Dalgarno sites although ribosomes were observed to pause at internal Shine-Dalgarno sites within the ORF. These data suggest a more prevalent use of the Shine-Dalgarno sequence for ribosome pausing rather than translation initiation in C. crescentus. Overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach providing a valuable genomic resource to elucidate the complete C. crescentus genetic circuitry that controls asymmetric cell division. Ribosome profiling and RNA-seq data were collected in Caulobacter crescentus NA1000 cells grown in M2G and PYE media to map transcript and ORF features in the genome.
Project description:Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time. We provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling, RNA-seq, global 5’-RACE, and liquid chromatography coupled with tandem mass spectrometry (LC-MS) data to the 4-megabase C. crescentus genome. We mapped transcript units at single base-pair resolution using RNA-seq together with global 5’ RACE. Additionally, using ribosome profiling and LC-MS, we mapped translation start sites and coding regions with near complete coverage. We found most start codons lacked corresponding Shine-Dalgarno sites although ribosomes were observed to pause at internal Shine-Dalgarno sites within the ORF. These data suggest a more prevalent use of the Shine-Dalgarno sequence for ribosome pausing rather than translation initiation in C. crescentus. Overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach providing a valuable genomic resource to elucidate the complete C. crescentus genetic circuitry that controls asymmetric cell division.
Project description:The Caulobacter cell cycle includes sequential differentiation of the cell poles and an asymmetric cell division yielding distinct daughter cells. RNA-seq and ribosome profiling were used to measure global messenger RNA (mRNA) abundance and translation levels throughout the Caulobacter cell cycle revealing translational control in 51% of cell cycle-regulated genes. Ribosome profiling levels were temporally regulated for ten proteins encoding asymmetrically localized multi-protein assemblies that specify cell fate upon cell division, with five ORFs being regulated with a >2 fold contribution from the translation efficiency. Individual ORFs within 198 operons undergo different cell cycle patterns of translation efficiency, allowing decoupling of the expression of these co-transcribed units. This work reveals that, in addition to transcriptional control, there is prevalent translational control of cell cycle-regulated genes, providing a framework for a multi-level program of cell cycle control that generates daughter cells of different fates.