## 2 A Generalized Regulatory Framework of N-AHL-Based Quorum Sensing  
In general terms, N-AHL-based QS signaling is often referred to as mere autoinduction, requiring only a synthase and a sensor/regulator protein. However, in the absence of regulation of QS, autoinduction would increase signal levels without limit. A down-regulation loop (Figure 1), which turns on at higher signal concentrations is the simplest way to limit and stabilize the signal levels. There are a variety of mechanisms that can play this role in QS systems. For example, the master regulator TraM can form a non-functional heterodimer with the TraR regulator in _Agrobacteriumumefaciens_[18, 19]. The DNA-binding negative regulator RsaL acts as a homo-dimer by binding on the bi-directional _rsaL-luxl_ promoter [20]. RsaM is another small regulatory protein believed to be acting in a similar way to RsaL in many _Burkholderia_ species [21]. The crucial role of these negative regulators is highlighted by the fact that their deletion leads to signal overproduction and a less virulent bacterial phenotype. Bacterial genomes also encode enzymes that degrade AHLs in response to the stress signal ppGpp, which can also efficiently down-regulate QS signaling [22, 23]. Down-regulation can also be achieved by RNA-based mechanisms. For example, some QS systems act by activating in their ground state an RNA-binding protein that inhibits transcription of synthases, and then gradually removing the inhibition when signal concentrations are increased [24, 25]. Meanwhile, another class of QS regulation system is believed to use sRNA species that considerably decrease the mRNA of the LuxR genes at low population density [26, 27, 28]. For the sake of completeness we mention that downregulation can also be achieved by simple resource limitation where a reduction in number of QS cells would decrease of the QS signal concentration itself. Regulatory circuits in which an element can both activate and inhibit another element are termed incoherent feed forward loops (IFFLs) [29, 30]. In contrast to simple feed forward arrangements, IFFLs can exhibit a number of complex behavior patterns (for a review see [31]). While simple feed forward  
Figure 1: Regulatory outline of N-AHL-based QS signaling. Pointed arrows indicate activation, and the hammerhead arrow indicates inhibition. circuits have no inherent limits on their output, IFFL networks have bounded output, which ensures robustness against fluctuations in the input signal levels. The net result is the stabilization of the output signals mentioned above. Another noteworthy property of IFFL networks is adaptation: under appropriate circumstances the circuits will react to the change rather than to the level of the signal [32, 33]. Theoretically, this property may also allow bacteria to react to changes rather than the level of the population density. There are interesting variations also in the regulatory mechanism of the autoinduction loop itself. Although this mechanism is often thought to follow the _luxR/luxI_ scenario in which the dimeric LuxR protein forms a regulatory complex with N-AHL, there are a growing number of cases where this happens in a different way. For example, a few members of the LuxR family are able to fold, dimerize, bind DNA, and regulate transcription in the absence of AHLs. Moreover, these proteins are antagonized by their cognate AHLs in the sense that some of the receptors/DNA complexes are disrupted by AHLs _in vitro_[34]. In the canonical AHL QS circuits the signal synthase is a LuxI type enzyme that synthesizes the signal molecule from S-adenosyl-methionine and an intra-cellularly synthesized acyl moiety delivered by an acyl carrier protein (ACP). However, more and more systems have been discovered where the acyl moiety is provided by acyl coenzyme A. Some of these systems use exogenous acyl (e.g., _p_-coumarate) moieties for signal synthesis, which provides a route to respond to environmental stimuli [35, 36, 37, 38].