The essential genome of a bacterium

Mol Syst Biol. 2011 Aug 30:7:528. doi: 10.1038/msb.2011.58.

Abstract

Caulobacter crescentus is a model organism for the integrated circuitry that runs a bacterial cell cycle. Full discovery of its essential genome, including non-coding, regulatory and coding elements, is a prerequisite for understanding the complete regulatory network of a bacterial cell. Using hyper-saturated transposon mutagenesis coupled with high-throughput sequencing, we determined the essential Caulobacter genome at 8 bp resolution, including 1012 essential genome features: 480 ORFs, 402 regulatory sequences and 130 non-coding elements, including 90 intergenic segments of unknown function. The essential transcriptional circuitry for growth on rich media includes 10 transcription factors, 2 RNA polymerase sigma factors and 1 anti-sigma factor. We identified all essential promoter elements for the cell cycle-regulated genes. The essential elements are preferentially positioned near the origin and terminus of the chromosome. The high-resolution strategy used here is applicable to high-throughput, full genome essentiality studies and large-scale genetic perturbation experiments in a broad class of bacterial species.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Caulobacter crescentus* / genetics
  • Caulobacter crescentus* / metabolism
  • Cell Cycle / genetics
  • Chromosome Mapping / methods*
  • DNA Transposable Elements
  • DNA, Intergenic
  • DNA-Directed RNA Polymerases / genetics*
  • DNA-Directed RNA Polymerases / metabolism
  • Gene Expression Regulation, Bacterial*
  • Genome, Bacterial*
  • High-Throughput Nucleotide Sequencing
  • Mutagenesis, Insertional
  • Open Reading Frames
  • Polymerase Chain Reaction
  • Promoter Regions, Genetic
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Transcription, Genetic

Substances

  • Bacterial Proteins
  • DNA Transposable Elements
  • DNA, Intergenic
  • Transcription Factors
  • DNA-Directed RNA Polymerases