Local and global regulation of transcription initiation in bacteria

Abstract

Gene expression in bacteria relies on promoter recognition by the DNA-dependent RNA polymerase and subsequent transcription initiation. Bacterial cells are able to tune their transcriptional programmes to changing environments, through numerous mechanisms that regulate the activity of RNA polymerase, or change the set of promoters to which the RNA polymerase can bind. In this Review, we outline our current understanding of the different factors that direct the regulation of transcription initiation in bacteria, whether by interacting with promoters, with RNA polymerase or with both, and we discuss the diverse molecular mechanisms that are used by these factors to regulate gene expression.

Global Inhibition with Specific Activation: How p53 and MYC Redistribute the Transcriptome in the DNA Double-Strand Break Response

“…Similar arrangements of global inhibition with specific activation of gene expression, albeit by distinct mechanisms, can be found in other organisms as well, suggesting convergent evolution of a broadly useful principle in biological regulation. For example, alternative sigma factors in bacteria activate particular sets of genes during stress conditions; these compete with the housekeeping sigma factor, which is involved in general transcription (Browning and Busby, 2016). In bacteria transferred from nutrient-depleted to nutrient-rich medium, enzymes that metabolize the carbon source present in the medium are selectively transcribed, while most promoters are not active; normal promoter activity is restored upon transition to normal growth (Madar et al, 2013).…”

Mitochondrial-epigenetic crosstalk in environmental toxicology

“…The D-loop is a target of selection in bacteria, in which local sequence variation at promoters provides TF binding variability [82], so that a subset of cells will have optimal transcriptional activity at promoters under any given conditions [82]. Transcriptional initiation, elongation, and termination in mitochondria are reviewed in [78, 79] and transcriptional control in bacteria is reviewed in [82]. …”

“…TFAM is one of the most abundant proteins associated with nucleoids and its levels have been estimated to be sufficient to coat the mitochondrial genome [80]. In bacteria, formation of the nucleoid with nucleoid associated proteins (NAPs) is thought to change the level of compaction to repress transcription [82]. TFAM’s similarities to NAPs suggest a common origin.…”

“…TFAM’s similarities to NAPs suggest a common origin. Like TFAM, NAPs are abundant; some have sequence specificity that enables promoter-specific effects and some can bind numerous target sites using relaxed sequence specificity [82]. Levels of some NAPs change in response to growth phase and conditions, and composition of a nucleoid can change over time [82], suggesting a role for mitochondrial nucleoid formation and TFAM in mtDNA accessibility and environmental responsiveness.…”

6S RNA, a Global Regulator of Transcription

“…Bacterial RNA polymerase is a multisubunit enzyme, consisting of a core (E: ααββ’) that is transcriptionally competent but requires the addition of a specificity factor (sigma: σ) to form the holoenzyme (Eσ) needed to recognize promoters and initiate transcription (12, 13). All bacteria contain a housekeeping σ, usually referred to as σ 70 or σ A , which is highly abundant and required at all stages of growth.…”