Abstract
In eukaryotes, the location of a gene on the chromosome is known to affect its expression, but such position effects are poorly understood in bacteria. Here, using Escherichia coli K-12, we demonstrate that expression of a reporter gene cassette, comprised of the model E. coli lac promoter driving expression of gfp, varies by ∼300-fold depending on its precise position on the chromosome. At some positions, expression was more than 3-fold higher than at the natural lac promoter locus, whereas at several other locations, the reporter cassette was completely silenced: effectively overriding local lac promoter control. These effects were not due to differences in gene copy number, caused by partially replicated genomes. Rather, the differences in gene expression occur predominantly at the level of transcription and are mediated by several different features that are involved in chromosome organization. Taken together, our findings identify a tier of gene regulation above local promoter control and highlight the importance of chromosome position effects on gene expression profiles in bacteria.
Highlights
The nucleoid is a highly compact and organized structure occupying the majority of the intracellular cytoplasmic space in most bacteria [1,2]
The cassette consisted of the E. coli lac promoter controlling production of Emerald GFP: expression of gfp was triggered by addition of isopropyl -D1-thiogalactopyranoside (IPTG)
GFP fluorescence measurements were taken during logarithmic growth in minimal media, supplemented with IPTG, and we observed that chromosomal position modulates gene expression from the reporter cassette over a ∼300-fold range (Figure 2)
Summary
The nucleoid is a highly compact and organized structure occupying the majority of the intracellular cytoplasmic space in most bacteria [1,2]. Comprised of chromosomal DNA, protein and RNA, the nucleoid in Escherichia coli and Salmonella is arranged into topologically isolated loops, each ∼10 kb in length, which are further organized into four spatially isolated, structured macrodomains and two non-structured regions [3,4,5]. Organization of the nucleoid is mediated by DNA supercoiling, macromolecular crowding and by a number of nucleoid associated proteins (NAPs), the precise impact of each on the overall structure is not fully understood. Proteinaceous transcriptionally silent regions of the chromosome have been identified as potential organizational hubs that may insulate the topologically isolated loops and macrodomains [10]. Termed transcriptionally silent Extended Protein Occupancy Domains (tsEPODs), these domains overlap with regions bound by NAPs, but neither the precise protein organization nor whether tsEPODs contain predominantly poor promoters, or active promoters silenced by the associated proteins, is known
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