Hijacking the Hijackers: Escherichia coli Pathogenicity Islands Redirect Helper Phage Packaging for Their Own Benefit

摘要

class="head no_bottom_margin" id="sec1title">IntroductionThe acquisition of mobile genetic elements (MGEs) that carry virulence factors is a major event that can transform an avirulent or weakly virulent strain into a multi-resistant hypervirulent strain. In spite of the importance of their consequences, the mechanisms underlying the genetic transfer of pathogenicity islands among bacteria remain unidentified in most cases. In recent years, we have described and characterized a new class of chromosomally integrated mobile pathogenicity islands: the phage-inducible chromosomal islands (PICIs) (). The PICIs are widespread among Gram-positive cocci and Gram-negative bacteria (, ), and they are clinically relevant because they carry and disseminate genes for bacterial superantigens, virulence, and antibiotic resistance (). Following induction by a helper phage, PICIs excise from the bacterial chromosome, replicate, and are packaged into phage-like particles composed of phage virion proteins, leading to very high frequencies of intra- as well as inter-generic transfer (, , ).Although the biology of the Gram-positive PICIs has been extensively studied (), it remains a mystery how the PICI elements present in the Gram-negative bacteria hijack the phage machinery for their preferential packaging and transfer in nature and how these elements interfere with helper phage reproduction. To address these questions, we have analyzed one of these elements, EcCICFT073, present in the uropathogenic Escherichia coli CFT073 strain. This PICI raised our curiosity because of its role in virulence and because this element can be mobilized by the archetypical E. coli λ and 80 phages (). More importantly, our previous results had demonstrated that EcCICFT073 can interfere with phage reproduction using a novel mechanism of phage interference. Although most Gram-positive PICIs interfere with phage reproduction by promoting the formation of small PICI capsids that are much too small for the larger phage genomes (, , , , , ), that was not the case for the EcCICFT073 element, which is packaged into phage-sized capsid (href="#bib11" rid="bib11" class=" bibr popnode">Fillol-Salom et al., 2018).How do cos phages, such as λ and 80, package their DNA? The terminase of phage λ is among the best biochemically characterized proteins that catalyze this process and provides an ideal model for DNA packaging. The enzyme is a hetero-oligomer composed of gpNu1 (also called small terminase [TerS]) and gpA (large terminase [TerL]) subunits. Genome packaging begins with terminase assembly at cos, the packaging initiation site in the DNA concatemer. The λ cos sequence has three regions required to interact with the packaging machinery: cosQ; cosN; and cosB. Termination of phage packaging requires cosQ, and TerL completes this process by cutting the DNA at cosN. Initiation of DNA packaging requires both cosN and cosB sites; cosB consists of three binding sites or R elements (R3, R2, and R1) that are required for λ TerS binding to initiate the phage packaging process (href="#bib26" rid="bib26" class=" bibr popnode">Rao and Feiss, 2008; href="#mmc1" rid="mmc1" class=" supplementary-material">Figure S1).In a previous study, we found that EcCICFT073 requires the phage-encoded TerS for packaging. We also demonstrated that EcCICFT073 carries two cos sites, cos1 and cos2, with cos1 being required for the λ- and 80-mediated transfer of the element (href="#bib11" rid="bib11" class=" bibr popnode">Fillol-Salom et al., 2018). Surprisingly, although both EcCICFT073 cos sites have cosQ and cosN sequences that resemble those present in the E. coli λ and 80 phages, we were unable to identify the phage cosB element in the EcCICFT073 region (href="#mmc1" rid="mmc1" class=" supplementary-material">Figure S1A; href="#bib11" rid="bib11" class=" bibr popnode">Fillol-Salom et al., 2018). This observation posed the question, if EcCICFT073 requires the phage machinery for packaging, why does it carry a different cosB sequence in its genome, which would be poorly recognized by the phage TerS protein? Does EcCICFT073 encode uncharacterized proteins involved in PICI packaging? And how does EcCICFT073 interfere with phage reproduction? We have unraveled here the mechanism of molecular piracy used by the E. coli PICIs to be highly and preferentially packaged and transferred in nature.