Trends in Microbiology
Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli
Introduction
Biological systems need to monitor the environment and respond to changes. Gene expression is largely controlled at the level of transcription by transcription factors (TFs). In addition to a DNA-binding domain, TFs have structural domains for covalent or allosteric modifications such as the binding of specific metabolites or chemical signaling molecules 1, 2, 3, 4, 5. Specific signals determine the conformation of the TF that interacts with particular DNA-binding sites or with the rest of the transcriptional machinery 6, 7. Thus, metabolites that affect TFs constitute common signals for endogenous and exogenous changes and are the links between the genetic and metabolic networks. A specific example of this is a global study in yeast that revealed the differential patterns of expression caused by endogenous and exogenous environmental changes [8].
Here, we propose a classification of TFs based on the type of signals and direct-binding metabolites that TFs detect, specifically, whether such signals are exogenous, endogenous or a combination of both. Although it is primarily focused on Escherichia coli, we believe that this classification might also work for other bacteria. Approximately 70% of the known regulatory interactions in E. coli involve TFs using signal metabolites to modulate their activities 9, 10.
As far as we know, this is the first attempt towards a large-scale classification of sensing systems and transcriptional responses at the cellular level in bacteria. The mathematical description of such biologically more realistic regulatory networks represents a novel challenge. Our proposed classification also provides the foundations for understanding the dynamics and topology of the regulatory network as it senses changes in the environment.
Section snippets
Classification of transcription factors
TFs are ‘two-head molecules’ (as Francis Jacob called them): one head is the DNA-binding site and the other the allosteric site to which a metabolite binds non-covalently [11]. It is convenient to think in more abstract terms of meta-allosteric or generalized allosteric sites that include both the classic non-covalent binding and covalent chemical modifications (e.g. phosphorylation) because their roles are similar for physiological and topological descriptions of the network. These
Influences of the sensing classes on the regulatory network
To understand the role of the different sensing classes from a topological perspective, it is necessary to determine how gene distribution is regulated by the different classes of TFs. Approximately 50% of the genes in E. coli are regulated by more than one TF [21]. Figure 2a shows the overlap of regulated operons as governed by internal, external and hybrid classes of TFs. The hierarchy of sensing classes by number of regulated genes is internal>external>hybrid (see Supplementary Figure 2). A
Co-regulation between subclasses of TFs
The external-sensing TFs of the two-component systems (E-TC) have a slightly higher tendency to co-regulate with internal-sensing TFs for DNA-binding (I-DB) (Figure 2b). This interesting observation suggests that, to regulate gene expression, the cell integrates the status of signals that are not transportable with the topology of the DNA. Similarly, external-sensing TFs using transported metabolites (E-TM) work together with TFs that sense metabolites generated internally (I-SM). Indeed, it is
Internal-sensing regulators control external and hybrid systems
A limited number of TFs in each class have a known role in transcriptional regulation (40% of the external-sensing class, 41% of internal and 73% of hybrid). Auto-regulation is dominant in each class of sensing system, whereas regulation of TFs by a TF member of the same class is equally frequent only within the internal class (Figure 2d). By analyzing regulation between TFs of different systems, the dominant influence of internal-system TFs on the transcription of TFs of other systems is
Internal-sensing connections are mostly exerted by global regulators
The dense co-regulation of the internal class of TFs might be a consequence of the regulatory contribution of five of the seven global TFs defined in E. coli [21] being internal-sensing TFs. CRP (cAMP receptor protein), which senses levels of cAMP, and FNR (fumarate- and nitrate-reductase regulatory protein), which senses the redox state of the cell by binding to [4Fe–4S]2+ or [2Fe–2S]2+, belong to the I-SM sub-class. FIS (factor for inversion stimulation), IHF (integration host factor) and Hns
Functional analysis of gene products regulated by external- and internal-sensing TFs
Our proposed classification of TFs raises several questions: what do the different classes (namely external, internal and hybrid) comprise in terms of cell function? How do these classes compare in terms of their activities at the cellular level?
To understand the distribution of functional categories in these classes, the database of clusters of orthologous groups (COG) was used [22] to describe the functions of gene products in the cell. Figure 3 shows the distribution of COG categories for
Concluding remarks
Regulatory networks have not been analyzed in conjunction with their meta-allosteric interactions that connect them with metabolism. The analysis of the E. coli network based on external, internal and hybrid TF sensing is a first step in this direction. We conclude that the global transcriptional response is mainly directed by the internal class of sensing based on the following observations: (i) TFs responding to the internal class of signals control most of the regulons; (ii) TFs of external
Acknowledgements
We thank G. Moreno-Hagelsieb and E. Pérez-Rueda for their critical review of the manuscript, and V. Jímenez, S. Gama-Castro, M. Peralta-Gil, A. Santos, E. Díaz and F. Sánchez for their technical support. This work was partially supported by NIH grant RO1 GM 071962 and PAPIIT-UNAM IN214905.We also acknowledge three anonymous referees and the Editor for their helpful suggestions.
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