NilD CRISPR RNA contributes to Xenorhabdus nematophila colonization of symbiotic host nematodes

Abstract

Summary The bacterium Xenorhabdus nematophila is a mutualist of entomopathogenic Steinernema carpocapsae nematodes and facilitates infection of insect hosts. X. nematophila colonizes the intestine of S. carpocapsae which carries it between insects. In the X. nematophila colonization-defective mutant nilD6::Tn5, the transposon is inserted in a region lacking obvious coding potential. We demonstrate that the transposon disrupts expression of a single CRISPR RNA, NilD RNA. A variant NilD RNA also is expressed by X. nematophila strains from S. anatoliense and S. websteri nematodes. Only nilD from the S. carpocapsae strain of X. nematophila rescued the colonization defect of the nilD6::Tn5 mutant, and this mutant was defective in colonizing all three nematode host species. NilD expression depends on the presence of the associated Cas6e but not Cas3, components of the Type I-E CRISPR-associated machinery. While cas6e deletion in the complemented strain abolished nematode colonization, its disruption in the wild-type parent did not. Likewise, nilD deletion in the parental strain did not impact colonization of the nematode, revealing that the requirement for NilD is evident only in certain genetic backgrounds. Our data demonstrate that NilD RNA is conditionally necessary for mutualistic host colonization and suggest that it functions to regulate endogenous gene expression.

Characterization and evolution of Salmonella CRISPR-Cas systems

“…For example, these systems have been shown to be involved in biofilm formation (Zegans et al, 2009), host infection in humans and amoeba (Gunderson & Cianciotto, 2013;Sampson et al, 2013), symbiotic colonization in nematodes (Veesenmeyer et al, 2014) and DNA damage (Babu et al, 2011). If an alternative function exists in Salmonella and is potentially driven, at least in part, by complementarity between a crRNA and its genetic target, our finding that 15 % of spacers target bacterial genomes and that nearly one-fifth of these protospacers are within Salmonella genomes supports this hypothesis.…”

Stress as a Normal Cue in the Symbiotic Environment

“…Bacteriophage-mucin binding interactions have been shown to structure colonization of mucosal layers in the mammalian gut [58, 59], and the accumulation of bacteriophage in sputum or EPS may enhance the protective function of this barrier towards antimicrobials or other chemical stresses [61]. In addition, a functional CRISPR foreign DNA defense system is required for Xenorhabdus nematophila to colonize the gut of its nematode host [62] (Figure 2), suggesting that bacteriophage may be a stressful attribute of the nematode gut microbiota. It is likely that these and other microbe-associated stresses, combined with tissue and immune-derived stress, constrain the growth and partitioning of nutrients among microbes in the host environment.…”

Nuclease Activity of Legionella pneumophila Cas2 Promotes Intracellular Infection of Amoebal Host Cells

“…Because the cas2 mutants exhibit their defect in the absence of added phage, plasmid, or nucleic acid and because L. pneumophila mutants lacking cas9, cas1, cas4, or the CRISPR array are not impaired (15), the infection event mediated by L. pneumophila Cas2 must be distinct from the functions that have been traditionally ascribed to Cas proteins and CRISPR-Cas systems. There are now a variety of studies demonstrating that there are roles for other Cas proteins that are unrelated to phage/plasmid immunity (21,(25)(26)(27)(28)(29); e.g., Cas9 of Francisella novicida promotes virulence in a murine model of disease (30), and Campylobacter jejuni Cas9 enhances invasion of epithelial cells (31).…”