I can see CRISPR now, even when phage are gone: a view on alternative CRISPR-Cas functions from the prokaryotic envelope

Abstract

Purpose of review: CRISPR-Cas systems are prokaryotic immune systems against invading nucleic acids that adapt as new environmental threats arise. There are emerging examples of CRISPR-Cas functions in bacterial physiology beyond their role in adaptive immunity. This highlights the poorly understood, but potentially common, moonlighting functions of these abundant systems. We propose that these noncanonical CRISPR-Cas activities have evolved to respond to stresses at the cell envelope.

Recent findings: Here, we discuss recent literature describing the impact of the extracellular environment on the regulation of CRISPR-Cas systems, and the influence of CRISPR-Cas activity on bacterial physiology. These described noncanonical CRISPR-Cas functions allow the bacterial cell to respond to the extracellular environment, primarily through changes in envelope physiology.

Summary: This review discusses the expanding noncanonical functions of CRISPR-Cas systems, including their roles in virulence, focusing mainly on their relationship to the cell envelope. We first examine the effects of the extracellular environment on regulation of CRISPR-Cas components, and then discuss the impact of CRISPR-Cas systems on bacterial physiology, concentrating on their roles in influencing interactions with the environment including host organisms.

Figure 1. Activation of CRISPR-Cas systems in response to environmental changes

CRISPR-Cas systems can be activated in response to the broader environmental stressors of nutrient starvation, stationary phase growth, and iron limitation. Likewise, CRISPR-Cas systems can be activated directly in response to envelope stressors, such as phage infection and high temperature. These examples highlight the influence of the extracellular environment on the regulation of CRISPR-Cas systems.

Figure 2. CRISPR-Cas mediated physiological changes

CRISPR-Cas systems influence bacterial physiology, altering population behavior and host-microbe interactions through events that are centered at the envelope. In Francisellanovicida, Cas9, tracrRNA and scaRNA form a complex that represses a bacterial lipoprotein mRNA (BLP). Repression of the BLP increases membrane integrity, conferring resistance to membrane targeting antibiotics and enabling evasion of the host immune system, increasing virulence. Cas9 from Neisseria meningitidis and Cas2 from Legionella pneumophila type II systems increase host-cell attachment and intracellular survival. In Xenorhabdus nematophila, Cas6 and a CRISPRRNA (crRNA) of the type I-E system are required for host colonization. In Myxococcusxanthus, the type III CRISPR-Cas system regulates exopolysacchride production (EPS) to enable chemotaxis, while negatively effecting fruiting body formation. Conversely, Cas5, Cas7, and Cas8 of its type III CRISPR-Cas system are necessary for fruiting body formation and sporulation. Finally, in Pseudomonas aeruginosa, all interference components of the Type I CRISPR system are required for biofilm formation and swarming motility. These examples provide a framework for understanding the alternative functions of CRISPR-Cas systems from interactions at the prokaryotic envelope.