CRISPR-Cas systems: role in cellular processes beyond adaptive immunity

Abstract

Clustered regularly interspaced short palindromic repeats and associated Cas proteins (CRISPR-Cas) are the only known adaptive immune system in prokaryotes. CRISPR-Cas system provides sequence-specific immunity against invasion by foreign genetic elements. It carries out its functions by incorporating a small part of the invading DNA sequence, termed as spacer into the CRISPR array. Although the CRISPR-Cas systems are mainly responsible for adaptive immune functions, their alternative role in the gene regulation, bacterial pathophysiology, virulence, and evolution has started to unravel. In several species, these systems are revealed to regulate the processes beyond adaptive immunity by employing various components of CRISPR-Cas machinery, independently or in combination. The molecular mechanisms entailing the regulatory processes are not clear in most of the instances. In this review, we have discussed some well-known and some recently established noncanonical functions of CRISPR-Cas system and its fast-extending applications in other biological processes.

Keywords: CRISPR-Cas; CRISPR-Cas alternative roles; CRISPR-Cas application; CRISPR-Cas in gene regulation; Genome remodeling.

Fig. 1

CRISPR-Cas system mechanism of action (the pictorial presentation over here depicts the mechanism of action of type I-E CRISPR-Cas system characterized from E. coli). CRISPR-Cas system protects the organism from incoming phage or plasmid infection by incorporating a small stretch of DNA into the CRISPR array with the help of Cas1 and Cas2 protein dimmers. This process is known as adaptation or acquisition. Cas1 and Cas2 are the universal protein as are found in most CRISPR types. During the next infection from the same phage or plasmid, the CRISPR array is transcribed to produce the pre-crRNA in the expression step, which is then cleaved by Cas6 protein to produce a repeat-spacer unit called crRNA. The palindromic repeat sequences lead to the formation of hairpin-loop structure which in association with spacer sequence functions as a guide for the Cas proteins. After recognizing and binding the protospacer sequence, it loads the cascade complex. In the final interference step, Cas3 protein, a part of cascade complex, comprising the nuclease activity cleaves the non-target strands in 3’ to 5’ direction leaving 200–300 bp nick. The degradation of the nicked DNA is further completed by cascade-independent activity of ssDNA nuclease activity of Cas3

Fig. 2

CRISPR-Cas in response to stress; in response to different environmental stress, the CRISPR-Cas system is activated by different mechanisms. These stress factors include cell membrane damage by phage infection; envelop stress, heat shock/high temperatures, oxidative stress, and other cellular signaling molecules or DNA damaging factors. The exact downstream mechanism after the activation of the CRISPR-Cas system by which the cell tackles the environmental stress is not identified yet

Fig. 3

CRISPR-Cas mediated physiological processes; CRISPR-Cas is activated due to extracellular signals such as phage infection, DNA invasion, and environmental stress. Upon activation, the CRISPR array and Cas proteins either function in combination or alone to carry out the various biological processes. CRISPR array usually mediates the pathophysiological changes or gene regulation processes by directly targeting the DNA or mRNA by a self-targeting spacer. Cas proteins modulate the cell physiology, virulence, and bacterial behavior either by activating the downstream pathways or by direct interaction with the other proteins or molecules. These processes are multifaceted, and the mechanism entailing various pathways awaits experimental elucidation