A Novel Feedback Loop That Controls Bimodal Expression of Genetic Competence

Abstract

Gene expression can be highly heterogeneous in isogenic cell populations. An extreme type of heterogeneity is the so-called bistable or bimodal expression, whereby a cell can differentiate into two alternative expression states. Stochastic fluctuations of protein levels, also referred to as noise, provide the necessary source of heterogeneity that must be amplified by specific genetic circuits in order to obtain a bimodal response. A classical model of bimodal differentiation is the activation of genetic competence in Bacillus subtilis. The competence transcription factor ComK activates transcription of its own gene, and an intricate regulatory network controls the switch to competence and ensures its reversibility. However, it is noise in ComK expression that determines which cells activate the ComK autostimulatory loop and become competent for genetic transformation. Despite its important role in bimodal gene expression, noise remains difficult to investigate due to its inherent stochastic nature. We adapted an artificial autostimulatory loop that bypasses all known ComK regulators to screen for possible factors that affect noise. This led to the identification of a novel protein Kre (YkyB) that controls the bimodal regulation of ComK. Interestingly, Kre appears to modulate the induction of ComK by affecting the stability of comK mRNA. The protein influences the expression of many genes, however, Kre is only found in bacteria that contain a ComK homologue and, importantly, kre expression itself is downregulated by ComK. The evolutionary significance of this new feedback loop for the reduction of transcriptional noise in comK expression is discussed. Our findings show the importance of mRNA stability in bimodal regulation, a factor that requires more attention when studying and modelling this non-deterministic developmental mechanism.

Viscous drag on the flagellum activates Bacillus subtilis entry into the K‐state

“…We next addressed which step in the comK signaling pathway is affected by the absence of flagella. Central to K‐state decision‐making is a positive feedback in which ComK directly activates its own promoter (van Sinderen and Venema, ; Maamar and Dubnau, ; Smits et al ., ; Gamba et al ., ). The decision to enter the K‐state is governed by the basal level expression from P comK , defined as expression in a ΔcomK mutant, in which the feedback is interrupted (Leisner et al ., ; Mirouze et al ., ).…”

The heterocyst regulatory protein HetP and its homologs modulate heterocyst commitment in Anabaena sp. strain PCC 7120

“…Prokaryotes with morphologically and physiologically distinct cell types have also been examined as model developmental systems and several have been investigated in mechanistic detail. Bacterial sporulation, competence for DNA uptake, flagellar motility, and the switch to a dormant persister state are all developmental decisions that hinge on the accumulation of an autoregulatory activator, either a transcription factor or σ factor, relative to some minimum stoichiometric threshold (14)(15)(16)(17)(18)(19)(20). Importantly, however, these prokaryotic model systems all exhibit nonterminal…”

Competence inhibition by the XrpA peptide encoded within the comX gene of Streptococcus mutans

“…As research has continued with these systems, the apparently straightforward paradigms once described for control of quorum sensing and intercellular communication have been assimilated into increasingly complex and diverse models for cellular reprogramming. Examples of such complexity can be found with negative feedback associated with the late competence gene dprA of Streptococcus pneumoniae (Weng et al ., ), identification of the novel protein Kre that controls the bimodal regulation of ComK in Bacillus subtilis (Gamba et al ., ), and the recent discovery of a short, leaderless, intercellular peptide signal in Group A Streptococcus (Do et al ., ) that regulates protease expression. Similar advances in understanding of regulatory systems have been realized using S. mutans as a model organism (Lemos et al ., ).…”