The coding and noncoding architecture of the Caulobacter crescentus genome

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 c...

Full description

Saved in:
Bibliographic Details
Published in:PLoS genetics 2014-07, Vol.10 (7), p.e1004463-e1004463
Main Authors: Schrader, Jared M, Zhou, Bo, Li, Gene-Wei, Lasker, Keren, Childers, W Seth, Williams, Brandon, Long, Tao, Crosson, Sean, McAdams, Harley H, Weissman, Jonathan S, Shapiro, Lucy
Format: Article
Language:English
Subjects:
Architecture
Bacterial proteins
Bacteriology
Biology and Life Sciences
Caulobacter
Caulobacter crescentus - genetics
Cell division
Cell Division - genetics
Datasets
E coli
Gene expression
Genetic aspects
Genetic translation
Genome
Genomes
High-Throughput Nucleotide Sequencing
Liquid chromatography
Mass spectrometry
Molecular Sequence Annotation
Open Reading Frames
Physiological aspects
Protein Biosynthesis
Proteomics
Research and Analysis Methods
Ribosomes - genetics
RNA
Scientific imaging
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1004463