A Trade-off between the Fitness Cost of Functional Integrases and Long-term Stability of Integrons

Abstract

Horizontal gene transfer (HGT) plays a major role in bacterial microevolution as evident from the rapid emergence and spread of antimicrobial drug resistance. Few studies have however addressed the population dynamics of newly imported genetic elements after HGT. Here, we show that newly acquired class-1 integrons from Salmonella enterica serovar Typhimurium and Acinetobacter baumannii, free of associated transposable elements, strongly reduce host fitness in Acinetobacter baylyi. Insertional inactivation of the integron intI1 restored fitness, demonstrating that the observed fitness costs were due to the presence of an active integrase. The biological cost of harboring class-1 integrons was rapidly reduced during serial transfers due to intI1 frameshift mutations leading to inactivated integrases. We use a mathematical model to explore the conditions where integrons with functional integrases are maintained and conclude that environmental fluctuations and episodic selection is necessary for the maintenance of functional integrases. Taken together, the presented data suggest a trade-off between the ability to capture gene cassettes and long-term stability of integrons and provide an explanation for the frequent observation of inactive integron-integrases in bacterial populations.

The evolutionary dynamics of integrons in changing environments

“…Our results indicate that reshuffling of cassettes within an integron can confer a selective advantage to a functional integrase that comes about through changes in gene expression that are often strong enough to outweigh substantial fitness costs of the integrase. Our model, albeit focusing on a single population, reproduces several empirical observations seen across bacterial strains and species, including a relatively high prevalence of mutationally inactivated integrases in both clinical isolates and experimentally evolved strains (Gillings et al, 2005;Nemergut et al, 2008;Starikova et al, 2012) and cassette arrays that are highly variable in terms of cassette composition and order (reviewed in Gillings, 2014). Taken together, our results support the view that integron integrases are selectively maintained because they enable their hosts to efficiently use cassette arrays as a 'reservoir of standing genetic variability' (Cambray et al, 2010).…”

“…To gain more knowledge on the basic processes controlling the frequencies of antibiotic resistance in bacterial populations, it is essential that we better understand the population dynamics and evolution of bacteria with acquired MGEs encoding antibiotic resistance in both the presence and absence of antibiotic selective pressures (Johnsen et al, 2009). With the exception of work focusing on plasmids (Bouma and Lenski, 1988;Dahlberg and Chao, 2003;San Millan et al, 2014;Gullberg et al, 2014), surprisingly few studies have addressed the impact of MGE acquisitions on bacterial population dynamics (but see Starikova et al, 2012;Starikova et al, 2013). One class of MGEs with a prominent role in the emergence and spread of antibiotic resistance determinants where studies on the population dynamics following acquisition are particularly limited are the mobile resistance integrons, and especially the class 1 integrons.…”

“…Yet, the selective forces responsible for the evolution and maintenance of integrons are poorly understood. The recent documentation of substantial fitness costs imposed by newly acquired integrase genes (Starikova et al, 2012) highlights the need to identify evolutionary benefits of integrases and integrons that can overcome such fitness costs. Experimental evidence indicates that through reshuffling of cassettes within the integron, the bacteria gain access to genes that were previously not expressed because they were too distant from the promoter (Collis and Hall, 1995;reviewed in Cambray et al, 2010), but this idea has never been formally scrutinized.…”

Growth phase-specific evolutionary benefits of natural transformation in Acinetobacter baylyi

“…The Com+ DNA group displayed a bi-modal distribution and was only significantly lower than the Com − group treatment at the 50th percentile, but not at the 75th percentile (P = 0.008 and P = 0.09, respectively; Figure 1c). To verify that the differences observed between Com+ and Com − populations relative to the respective ancestors reflected higher fitness, competitions between fitness representative (Starikova et al, 2012) evolved populations were performed. As expected, evolved Com+ populations outcompeted evolved Com − populations during the first 24 h of the competitions and this advantage was offset favoring the Com − populations between 24 and 90 h (Figure 3).…”

“…Selection rate constants (r) were estimated for the entire 90-h passage as described in (Travisano and Lenski, 1996) with the modification of using 'per passage' as denominator instead of 'per day'. Standard Darwinian relative fitness (w) measurements (Lenski et al, 1991) were estimated during the first 24 h of competitions as described in Starikova et al (2012), except for the incubation at 37°C and shaking at 120 rounds per minute. To quantify the potential differences in stationary and death phase between competing clones and/or populations we measured the difference in survival (su).…”