Bacterial transcription during growth arrest

Abstract

Bacteria in most natural environments spend substantial periods of time limited for essential nutrients and not actively dividing. While transcriptional activity under these conditions is substantially reduced compared to that occurring during active growth, observations from diverse organisms and experimental approaches have shown that new transcription still occurs and is important for survival. Much of our understanding of transcription regulation has come from measuring transcripts in exponentially growing cells, or from in vitro experiments focused on transcription from highly active promoters by the housekeeping RNA polymerase holoenzyme. The fact that transcription during growth arrest occurs at low levels and is highly heterogeneous has posed challenges for its study. However, new methods of measuring low levels of gene expression activity, even in single cells, offer exciting opportunities for directly investigating transcriptional activity and its regulation during growth arrest. Furthermore, much of the rich structural and biochemical data from decades of work on the bacterial transcriptional machinery is also relevant to growth arrest. In this review, the physiological changes likely affecting transcription during growth arrest are first considered. Next, possible adaptations to help facilitate ongoing transcription during growth arrest are discussed. Finally, new insights from several recently published datasets investigating mRNA transcripts in single bacterial cells at various growth phases will be explored.

Identification of Genes Required for Long-Term Survival of Legionella pneumophila in Water

“…The effects of the dotO CRISPRi knockdown were monitored phenotypically, since gene expression analysis in starved bacteria is made difficult by the large-scale drop in transcription and changes in gene expression dynamics that occur under these conditions relative to broth-grown bacteria ( 31 ). After growth in broth to postexponential phase, there was a 30-fold drop in steady-state levels of dotO transcript in the presence of dotO crRNA ( Fig.…”

Identification of genes required for long term survival of L. pneumophila in water

“…The effects of the dotO CRISPRi knockdown were followed phenotypically, as gene expression analysis in starved bacteria is made difficult by the largescale drop in transcription and changes in gene expression dynamics that occur in these conditions relative to broth-grown bacteria (29). After growth in broth to postexponential phase, there was a 30-fold drop in steady state levels of dotO transcript in the presence of dotO crRNA (Fig.…”

High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates forMycobacterium tuberculosisRNA polymerase

“…Alternatively, constitutively active promoters are affected by cell growth-rate-dependent changes in the free RNAP concentration, independent of changes in Km and/or Vmax (20)(21)(22). Classic examples of environmental adaptation in bacteria affecting transcription initiation processes include the up-regulation of betagalactosidase in response to the presence of lactose and the absence of glucose (23), and the genome-wide response to starvation known as the stringent response (24,25).…”