Type I-F CRISPR-Cas Distribution and Array Dynamics in Legionella pneumophila

Abstract

In bacteria and archaea, several distinct types of CRISPR-Cas systems provide adaptive immunity through broadly similar mechanisms: short nucleic acid sequences derived from foreign DNA, known as spacers, engage in complementary base pairing with invasive genetic elements setting the stage for nucleases to degrade the target DNA. A hallmark of type I CRISPR-Cas systems is their ability to acquire spacers in response to both new and previously encountered invaders (naïve and primed acquisition, respectively). Our phylogenetic analyses of 43 L. pneumophila type I-F CRISPR-Cas systems and their resident genomes suggest that many of these systems have been horizontally acquired. These systems are frequently encoded on plasmids and can co-occur with nearly identical chromosomal loci. We show that two such co-occurring systems are highly protective and undergo efficient primed acquisition in the lab. Furthermore, we observe that targeting by one system’s array can prime spacer acquisition in the other. Lastly, we provide experimental and genomic evidence for a model in which primed acquisition can efficiently replenish a depleted type I CRISPR array following a mass spacer deletion event.

Pruning and Tending Immune Memories: Spacer Dynamics in the CRISPR Array

“…In addition, new spacers should be free of mismatches that accumulate for older spacers as their targets develop escape mutations ( Deveau et al, 2008 ; Semenova et al, 2011 ; Cady et al, 2012 ; Rao et al, 2016 ). From that we could expect that leader-adjacent spacers would be prioritized for defense, and these spacers do indeed produce more robust interference ( McGinn and Marraffini, 2016 ; Rao et al, 2016 ; Deecker and Ensminger, 2020 ). The mechanism underlying this difference is not entirely clear.…”

“…Second, it became clear that spacer-repeat units could be duplicated or deleted from the array. These changes were often observed in the middle of the array, while the distal end (termed “trailer” or “anchor” end) was typically conserved ( Pourcel et al, 2005 ; Lillestol et al, 2006 ; Horvath et al, 2008 ; Lopez-Sanchez et al, 2012 ; Weinberger et al, 2012 ; Lam and Ye, 2019 ; Deecker and Ensminger, 2020 ). Evidence of losses or duplications was first inferred by comparing arrays from related strains; arrays that differed only by the absence of one or more contiguous spacers were thought to be the result of deletions ( Figure 1A ; Pourcel et al, 2005 ; Lillestol et al, 2006 ; Held et al, 2010 ; Gudbergsdottir et al, 2011 ; Lopez-Sanchez et al, 2012 ; Achigar et al, 2017 ).…”

“…Since primed adaptation tolerates these changes, a spacer that might otherwise be obsolete can contribute to CRISPR immunity by updating the CRISPR array. Experimentally, spacers in the middle of an array ( L. pneumophila ) were shown to give relatively inefficient interference but still effectively support priming ( Deecker and Ensminger, 2020 ). Thus turnover of older spacers may not always appear steady or strictly chronological.…”

Legionella pneumophila CRISPR-Cas suggests recurrent encounters with Gokushovirinae

“…Many L. pneumophila isolates maintain active and adaptive CRISPR-Cas systems (21,23,24), providing another avenue by which to explore the species' relationship with phage.…”

Immune Lag Is a Major Cost of Prokaryotic Adaptive Immunity During Viral Outbreaks

“…Yet, in natural systems, host populations are rarely completely immune to their viral pathogens. CRISPR spacers can be lost [36, 37, 22, 38, 39, 15], and viral escape mutants with point mutations in protospacer regions frequently emerge [40, 41], both leading CRISPR-Cas to be a somewhat transient form of immunity [31]. In natural communities, entirely new species of virus, to which the host lacks preexisting immunity, may migrate into the system via dispersal [42].…”