title: The coding and noncoding architecture of the Caulobacter crescentus genome.
abstract: 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 coding DNA sequence (CDS). 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.
authors: Department of Developmental Biology, Stanford University, Stanford, California, United States of America.
authors: Jared M
authors: JM
authors: Schrader
authors: Department of Developmental Biology, Stanford University, Stanford, California, United States of America.
authors: Bo
authors: B
authors: Zhou
authors: Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America.
authors: Gene-Wei
authors: GW
authors: Li
authors: Department of Developmental Biology, Stanford University, Stanford, California, United States of America.
authors: Keren
authors: K
authors: Lasker
authors: Department of Developmental Biology, Stanford University, Stanford, California, United States of America.
authors: W Seth
authors: WS
authors: Childers
authors: Department of Developmental Biology, Stanford University, Stanford, California, United States of America.
authors: Brandon
authors: B
authors: Williams
authors: Department of Developmental Biology, Stanford University, Stanford, California, United States of America.
authors: Tao
authors: T
authors: Long
authors: Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America.
authors: Sean
authors: S
authors: Crosson
authors: Department of Developmental Biology, Stanford University, Stanford, California, United States of America.
authors: Harley H
authors: HH
authors: McAdams
authors: Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America.
authors: Jonathan S
authors: JS
authors: Weissman
authors: Department of Developmental Biology, Stanford University, Stanford, California, United States of America.
authors: Lucy
authors: L
authors: Shapiro
mesh_terms: D016935:Caulobacter crescentus / Q000235:genetics*; D002455:Cell Division / Q000235:genetics; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D014176:Protein Biosynthesis; D012270:Ribosomes / Q000235:genetics