CRISPR-Cas systems target endogenous genes to impact bacterial physiology and alter mammalian immune responses

Abstract

CRISPR-Cas systems are an immune defense mechanism that is widespread in archaea and bacteria against invasive phages or foreign genetic elements. In the last decade, CRISPR-Cas systems have been a leading gene-editing tool for agriculture (plant engineering), biotechnology, and human health (e.g., diagnosis and treatment of cancers and genetic diseases), benefitted from unprecedented discoveries of basic bacterial research. However, the functional complexity of CRISPR systems is far beyond the original scope of immune defense. CRISPR-Cas systems are implicated in influencing the expression of physiology and virulence genes and subsequently altering the formation of bacterial biofilm, drug resistance, invasive potency as well as bacterial own physiological characteristics. Moreover, increasing evidence supports that bacterial CRISPR-Cas systems might intriguingly influence mammalian immune responses through targeting endogenous genes, especially those relating to virulence; however, unfortunately, their underlying mechanisms are largely unclear. Nevertheless, the interaction between bacterial CRISPR-Cas systems and eukaryotic cells is complex with numerous mysteries that necessitate further investigation efforts. Here, we summarize the non-canonical functions of CRISPR-Cas that potentially impact bacterial physiology, pathogenicity, antimicrobial resistance, and thereby altering the courses of mammalian immune responses.

Keywords: Biofilms; Endogenous gene targeting; Host immune response; Inflammasome; Inflammatory response; Phagocytosis.

Fig. 1

Overview of the CRISPR-Cas systems. CRISPR-Cas systems including leader, spacer and repeats are alternately arranged to form R-S structure and cas locus. The function of CRISPR-Cas systems include three stages: spacer acquisition, crRNA processing and assembly, and target degradation. The first step occurs after the foreign DNA sequence invades bacteria, and the bacterial genome intercepts a sequence from the invaded DNA fragment and integrates it into its CRISPR sequence to become a new spacer. Then, CRISPR clusters are transcribed into pre-crRNA under the initiation of the leader and further processed into mature small crRNAs. The mature crRNAs and Cas proteins assemble to form a CRISPR ribonucleoprotein (crRNP) complex. Once the same foreign DNA invades, the Cas protein complex binds, cleaves and degrades it by the base-pair principle

Fig. 2

Effect of CRISPR-Cas systems on physiological traits of bacteria. CRISPR-Cas systems affecting multiple bacterial characteristics, such as virulence, bacterial biofilm, QS and antibiotics resistance. CRISPR-Cas systems are associated with the expression of multiple virulence factors, such as vicR, gtfC, smu0630, comDE (Streptococcus sanguinis), esp, hyl, gelE, asa1, ace(E. faecalis). cas3 and cas1 genes directly or indirectly participate in and affect the formation of bacterial biofilm. There is mutual regulation between CRISPR-Cas systems and QS systems, and many genes are involved in this process, such as LasR, SmaI, SmaR cdpR, SsoPox and SmaR. CRISPR-Cas systems regulate the transfer of drug-resistant plasmids

Fig. 3

Type II and type I CRISPR-Cas systems adjust the expression of endogenous transcripts. TracrRNA and scaRNA (small, CRISPR-Cas-associated RNA) form a dual-RNA complex through sequence recognition to the CRISPR repeats. This dsRNA structure enables the free terminal of the tracrRNA to interact through a non-identity matching mRNA encoding the BLP, the stability of BLP mRNA is impeded and thereby leading to the degradation of mRNA. Type I CRISPR-Cas system of PA14 targets the mRNA of the QS regulator LasR. The crRNA1-12 structure is associated with Cascade (Csy1-4 complex) and interacts with lasR mRNA through a sequence complementing a part of crRNA1-12, and resulting in lowered lasR mRNA stability

Fig. 4

CRISPR-Cas impacts host defense by regulating several signals involving innate immunity and inflammatory responses. CRISPR-Cas may participate in the recognition of pattern recognition receptors (PRRs) (e.g., TLR2, TLR4 or other unknown PRRs) and the activation of their downstream signaling pathways. The downstream effects include altered levels of mitochondrion ROS, inflammasome, autophagy, depletion of CRISPR-Cas in P. aeruginosa strain PA14 leads to exaggerated inflammation and organ damage through rapid nuclear translocation of the transcription factor NF-κB after PRRs recognition