# Unbridled Integons: A Matter of Host Factors
## 2 The Unique Integon Genetic System  
Integons are bacterial recombination systems acting as platforms capable of capturing, stockpiling, reordering, and expressing DNA sequences embedded in promoterless cassettes. The type of integrins that were the first discovered are the MI [1]. These integrins are \"mobile\" since they are always associated with transposons and carried on conjugative plasmids. They contain mostly antibiotic resistance cassettes and remain the best studied integrins [2]. This is justified when considering the ever-increasing antibiotics pressure around the world [3] and the over-representation of integron-containing bacteria in the clinical context, where they cause 22% to 59% of infections [4]. Multi-resistance to antibiotics in bacterial pathogens is already one of the biggest threats to public health, and the integer is one leading cause of such phenotypes [5]. The reason for this is that integrons allow cells to concentrate resistance genes to many different antibiotics while limiting the cost associated with the presence of a resistance gene in the absence of the ad hoc antibiotic [6]. Apart from antibiotic resistance genes, integron cassettes can encode many other functions, especially within the other type of integrins carried by chromosomes and so-called sedentary chromosomal integrons. SCI are found in approximately 10% of all currently sequenced genomes [7], particularly in almost all _Vibrio_ species [8]. The functions found in SCI probably allow the bacterium to respond to stresses that are relevant to its lifestyle playing a role in bacterial evolution [9]. Both MI and SCI share the same general organization: a stable platform and a variable array of cassettes (Figure 1). The stable platform of the integron contains (i) the integrase gene (_intl_) under the control of its promoter \(\mathrm{P_{int}}\), (ii) the _attl_ integration site, and (iii) the cassette \(\mathrm{P_{C}}\) promoter driving the expression of the genes encoded in the cassette array located downstream. The variable part consists of an array of cassettes, each of which are generally composed of a promoterless gene associated with a recombination site called _attC_. Only the first few cassettes (those closest to the \(\mathrm{P_{C}}\) promoter) can be expressed, while the rest represent a low-cost memory of valuable functions for the cell [10]. Upon expression of the integrase, the cassettes can be excised (_attC_\(\times\)_attC_ recombination events, Figure 1) and then re-integrated at the _attl_ integration site (_attC_\(\times\)_attl_ recombination events), thus becoming expressed. The combination of excision and integration of cassettes, i.e., their shuffling, allow bacteria to screen for the set of functions that might optimize their survival in a given environment. The integer integrase has a very singular place among the broad family of the tyrosine recombinases. Indeed, while it recognizes the _attl_ site under its double-stranded (ds) form through its primary sequence (Figure 2A), this is not the case for the _attC_ sites (Figure 2B). _atttC_ sites show a very limited conservation in sequence but all share an imperfect palindromic organization that allows for the formation of a single-stranded (ss) secondary structure that is recognized and recombined by Intl (Figure 2B). Although both the bottom and the top strand of an _attC_ site can form a secondary structure, the recombination of the bottom strand (bs) is about \(10^{3}\) more efficient, and the structural features of the site play a central role in this strand selectivity [11; 12; 13]. The imperfections in the palindromic organization of the _atttC_ sites drive specific structural features upon folding (Unpaired Central Spacer (UCS), the Extra Helical Bases (EHB), and the Variable Terminal Structure (VTS)) which direct the strand specificity toward bs binding and recombination [12].