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PLoS Genet. 2014 Jul 31;10(7):e1004463. doi: 10.1371/journal.pgen.1004463. eCollection 2014 Jul.

The coding and noncoding architecture of the Caulobacter crescentus genome.

Author information

1
Department of Developmental Biology, Stanford University, Stanford, California, United States of America.
2
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.
3
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, United States of America.

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.

PMID:
25078267
PMCID:
PMC4117421
DOI:
10.1371/journal.pgen.1004463
[Indexed for MEDLINE]
Free PMC Article

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