Unknown,Transcriptomics,Genomics,Proteomics

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Global spatial organization of M-NM-3 proteobacterial nucleoids is determined by specific long-range interactions (E. coli)

ABSTRACT: GCC was used to determine the structure of E. coli grown in LB or treated with SHX. The bacterial genome is highly condensed into a nucleoid structure. Here we present global analyses of the genome spatial organization for two M-NM-3-proteobacteria: Escherichia coli and Pseudomonas aeruginosa by Genome Conformation Capture. Long distance interactions occurred within the E. coli and P. aeruginosa nucleoids with frequencies that were affected by growth condition and gene dosage. Spatial clustering of genes that are either up or down-regulated depended on the environmental signals, indicating a non-random functional organization of the nucleoid. The largest changes in gene expression upon amino acid starvation occurred in genes that participate in long-range interactions. These genes remained highly spatially clustered when transcript levels decreased. Environment specific interactions were related to DNA motifs but did not correlate with binding sites for nucleoid associated proteins. Overall we identify spatial organization as a significant factor in bacterial gene regulation and suggest that the prokaryotic operon is not simply a linear entity. 4 samples grown in LB; 4 samples treated with SHX. For Genome Conformation Capture (GCC) analyses, E. coli strains were recovered from -80M-BM-0C on LB agar (2%) plates for 24 hours. LB medium (3ml) starter cultures were inoculated and grown (37M-BM-0C, 220rpm, 16h). The Optical Density (OD600) of cultures was measured and used to inoculate LB test cultures to an OD600 of ~0.02. The test cultures were grown (37M-BM-0C, 220rpm) until the OD600 reached ~0.25 and then harvested. For the serine hydroximate (SHX) treated samples the cultures were treated with SHX (500 M-BM-5g/ml, 30 min) before harvesting. E. coli chromatin was prepared according to Rodley et al. (2009)with the following modifications. A total of 5*109 cells were cross-linked with formaldehyde (1% final v/v, 20min, RT) and then quenched with glycine (125mM final, 10min). Cells were collected by centrifugation (4000rpm, 15min, 4M-BM-0C), washed twice (1% PBS, 1% TritonX-100, 5ml/50ml culture) and pelleted (4000rpm, 15min, 4M-BM-0C). Cell pellets were suspended in 800M-NM-

ORGANISM(S): Escherichia coli

SUBMITTER: Justin O'Sullivan

PROVIDER: E-GEOD-40603 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription.

Cagliero Cedric C Grand Ralph S RS Jones M Beatrix MB Jin Ding J DJ O'Sullivan Justin M JM

Nucleic acids research 20130430 12

To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced ...[more]

PMID: 23632166

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Dataset Information

Global spatial organization of M-NM-3 proteobacterial nucleoids is determined by specific long-range interactions (E. coli)

Publications

Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription.

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