Broad-scale redistribution of mRNA abundance and transcriptional machinery in response to growth rate in Salmonella enterica serovar Typhimurium

Abstract

We have investigated the connection between the four-dimensional architecture of the bacterial nucleoid and the organism's global gene expression programme. By localizing the transcription machinery and the transcriptional outputs across the genome of the model bacterium Salmonella enterica serovar Typhimurium at different stages of the growth cycle, a surprising disconnection between gene dosage and transcriptional output was revealed. During exponential growth, gene output occurred chiefly in the Ori (origin), Ter (terminus) and NSL (non-structured left) domains, whereas the Left macrodomain remained transcriptionally quiescent at all stages of growth. The apparently high transcriptional output in Ter was correlated with an enhanced stability of the RNA expressed there during exponential growth, suggesting that longer mRNA half-lives compensate for low gene dosage. During exponential growth, RNA polymerase (RNAP) was detected everywhere, whereas in stationary phase cells, RNAP was concentrated in the Ter macrodomain. The alternative sigma factors RpoE, RpoH and RpoN were not required to drive transcription in these growth conditions, consistent with their observed binding to regions away from RNAP and regions of active transcription. Specifically, these alternative sigma factors were found in the Ter macrodomain during exponential growth, whereas they were localized at the Ori macrodomain in stationary phase.

Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization—A Timing Chain for the Bacterial Growth Cycle?

“…Briefly, during the E. coli growth cycle, the transcriptional activation of the chromosomal OriC and Ter poles occurs consecutively [ 12 ]. A similar, yet more nuanced pattern was observed in Salmonella enterica [ 118 ]. On nutritional shift-up, under conditions of high negative superhelicity, the transcription of the relatively G/C-rich chromosomal OriC pole is activated, whereas that of the Ter pole is repressed [ 12 ].…”

“…Conversely, on the transition to the stationary phase associated with the global relaxation of the DNA, the relatively A/T-rich Ter pole is activated, whereas the OriC pole is repressed. Since it is assumed, as mentioned above, that the chromosome configuration and genomic transcription are interdependent [ 6 , 15 , 16 , 119 , 120 ], the successive activation of OriC and Ter poles likely reflects the coordinately changing configuration and genetic activity of the chromosome, which is associated with the global redistribution of RNAP in the nucleoid [ 118 , 121 ]. In this regard, the non-random distribution of the binding sites of the NAPs and especially of the DNA gyrase and major RNAP sigma factors along the OriC-Ter axis that were observed in the E. coli genome [ 6 , 14 ], are suggestive.…”

The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978

“…Specifically, A. baumannii was cultured in L-broth and sampled throughout growth at OD 600 0.25, 0.75, 1.8, 2.5, 2.8, in liquid M9 minimal medium with different sole carbon sources (xylose, fumarate), and grown on an L-agar plate for 16 h at 37°C, and in liquid L-broth at OD 600 0.3 at 25°C. These conditions encompass high nutrient (L-broth) and low nutrient (M9) conditions; amino acids (L-broth) and carbohydrates (M9) as primary carbon sources; solid (L-agar) and liquid media; host (37°C) and external (25°C); and a full range of growth states, including stages of rapid growth in which bulk transcription rates are very high, to stationary phase in both rich and energy poor media, when transcriptional output is low and favors long-lived transcripts ( 29 ). We also isolated RNA from several ‘shock’ conditions, including disinfectant shock, osmotic shock (addition of sodium chloride), limitation of iron availability (addition of 2,2′-dipyridyl), translational stress (addition of kanamycin), oxidative stress (addition of hydrogen peroxide), temperature shift from ambient to body temperature (25–37°C), and the addition of ethanol (which increases virulence in A. baumannii infection of Dictyostelium discoideum and Caenorhabditis elegans ( 30 )).…”

Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes in Salmonella enterica serovar Typhimurium: impacts on physiology and virulence

“…The genes ihfA and ihfB are located in the Right replichore of the Salmonella chromosome, 350 kbp apart () [55, 56]. The ihfB gene is in the Right macrodomain and ihfA is in the Ter macrodomain, one of the major superstructural territories of the chromosome [57]. Each ihf gene is part of a complex operon that includes genes involved in various aspects of bacterial metabolism: ihfA has its own promoter but is also transcribed with the pheST operon, encoding the phenylalanine tRNA synthetase () [15, 58], while ihfB has its own promoter and is co-transcribed with rpsA , the gene encoding the S1 ribosomal protein () [15, 59, 60].…”

“…1a) [55,56]. The ihfB gene is in the Right macrodomain and ihfA is in the Ter macrodomain, one of the major superstructural territories of the chromosome [57]. Each ihf gene is part of a complex operon that includes genes involved in various aspects of bacterial metabolism: ihfA has its own promoter but is also transcribed with the pheST operon, encoding the phenylalanine tRNA synthetase (Fig.…”