Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology

Abstract

Gene expression occurs in two essential steps: transcription and translation. In bacteria, the two processes are tightly coupled in time and space, and highly regulated. Tight regulation of gene expression is crucial. It limits wasteful consumption of resources and energy, prevents accumulation of potentially growth inhibiting reaction intermediates, and sustains the fitness and potential virulence of the organism in a fluctuating, competitive and frequently stressful environment. Since the onset of studies on regulation of enzyme synthesis, numerous distinct regulatory mechanisms modulating transcription and/or translation have been discovered. Mostly, various regulatory mechanisms operating at different levels in the flow of genetic information are used in combination to control and modulate the expression of a single gene or operon. Here, we provide an extensive overview of the very diverse and versatile bacterial gene regulatory mechanisms with major emphasis on their combined occurrence, intricate intertwinement and versatility. Furthermore, we discuss the potential of well-characterized basal expression and regulatory elements in synthetic biology applications, where they may ensure orthogonal, predictable and tunable expression of (heterologous) target genes and pathways, aiming at a minimal burden for the host.

A universal method for gene expression engineering

“…Gene expression is modulated by the interaction of a complex transcription machinery with DNA 1 . In eubacteria, RNA polymerase initiates transcription after forming a complex with a sigma(σ)- factor, which recognises specific DNA sequence motifs.…”

TBDB – A database of structurally annotated T-box riboswitch:tRNA pairs

“…Minimum free energy (MFE) calculations were performed using ViennaRNA on refined terminator and antiterminator structures. (20,683) in our collection originate from the phyla Firmicutes. T-boxes shown are displayed in decreasing order of abundance in the TBDB collection, with Ile being the most commonly represented and Glu the least.…”

“…For example, a recent study used a glyQS T-box to engineer a ribozyme that can specifically charge tRNA gly for use in cell-free protein synthesis [19]. Tboxes also have the potential to be used as a generalizable 'registry-of-parts', capable of independently sensing amino acid levels in the environment with a single RNA element [20]. Furthermore, due to their prevalence and importance in gram-positive bacteria, T-boxes are also being studied as targets for antibiotic therapeutics [21,22].…”

Reconstruction of Fur pan-regulon uncovers the complexity and diversity of transcriptional regulation inE. coli

“…Transcription factors (TFs) control gene expression by direct or indirect activation or repression of target genes. The binding state of TFs depends on the environmental conditions, such as presence or absence of effectors, and other physical stimuli 1 . Many global TFs are highly conserved, which play defining physiological roles in a wide range of bacteria, enabling them to adapt to changing environments 2 .…”