Abstract
In free-living bacteria, the ability to regulate gene expression is at the core of adapting and interacting with the environment. For these systems to have a logic, a signal must trigger a genetic change that helps the cell to deal with what implies its presence in the environment; briefly, the response is expected to include a feedback to the signal. Thus, it makes sense to think of genetic sensory mechanisms of gene regulation. Escherichia coli K-12 is the bacterium model for which the largest number of regulatory systems and its sensing capabilities have been studied in detail at the molecular level. In this special issue focused on biomolecular sensing systems, we offer an overview of the transcriptional regulatory corpus of knowledge for E. coli that has been gathered in our database, RegulonDB, from the perspective of sensing regulatory systems. Thus, we start with the beginning of the information flux, which is the signal’s chemical or physical elements detected by the cell as changes in the environment; these signals are internally transduced to transcription factors and alter their conformation. Signals transduced to effectors bind allosterically to transcription factors, and this defines the dominant sensing mechanism in E. coli. We offer an updated list of the repertoire of known allosteric effectors, as well as a list of the currently known different mechanisms of this sensing capability. Our previous definition of elementary genetic sensory-response units, GENSOR units for short, that integrate signals, transport, gene regulation, and the biochemical response of the regulated gene products of a given transcriptional factor fit perfectly with the purpose of this overview. We summarize the functional heterogeneity of their response, based on our updated collection of GENSORs, and we use them to identify the expected feedback as part of their response. Finally, we address the question of multiple sensing in the regulatory network of E. coli. This overview introduces the architecture of sensing and regulation of native components in E.coli K-12, which might be a source of inspiration to bioengineering applications.
Highlights
The ability to adapt to changes in the environment is a fundamental property of life, which in bacterial systems has been studied for decades at the molecular level, thanks to advances in genetics and the relative simplicity of these organisms.During more than two and a half decades our laboratory has been gathering knowledge on the regulation of transcription initiation and the organization and expression of the regulated genes in Escherichia coli K-12
This knowledge can be accessed in two databases, RegulonDB, and EcoCyc (Santos-Zavaleta et al, 2019; Keseler et al, 2021). This corpus shows the complex architecture of multiple sensing and regulatory systems currently known in E. coli and is the basis for the review presented here from the perspective of sensing systems
The most common way to share progress has been in terms of the number of the main players of gene regulation, such as transcription factors (TFs), the operator DNA sequences to which TFs bind, called TF binding sites (TFBS), and TF regulatory sites (TFRSs) when there is evidence of their regulatory role in addition to binding, promoters, and other regulatory elements, including transcription start sites (TSSs) and transcription units (Figure 1)
Summary
The ability to adapt to changes in the environment is a fundamental property of life, which in bacterial systems has been studied for decades at the molecular level, thanks to advances in genetics and the relative simplicity of these organisms. They were used to predict metabolites allosterically regulating a TF, after the observation that 83% of TFs for which a binding molecule was known had it in their GENSOR unit (Ledezma-Tejeida et al, 2017). As discussed below under “Genomic processing of multiple signals in E. coli,” this is still a simplification of the complex architecture of sensing and genetic regulation exerted by TFs in orchestrating changes in gene expression They have been useful as a first multilevel integration, as discussed elsewhere (Ledezma-Tejeida et al, 2019). Only when acyl-CoAs are present, the ethanol biosynthetic pathway is transcriptionally derepressed and biodiesel synthesis is carried out, avoiding high concentrations of ethanol in the cell, improving the stability of the strain (Zhang et al, 2012)
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