1036.2 What Is CRISPR?
Bacteria and archaea are the largest group of life forms on Earth. They are grouped
under prokaryotes, generally indicating single-celled organisms that do not possess
highly complicated cells or genome structures. This lack of complexity makes them
prime targets of viruses and phages. But, since every organism is primed with a
sense of survival, it does not come as a surprise that prokaryotes possess some sort
of defense mechanism to protect them against such attacks. But, viruses pose a very
real threat to bacteria and archaea in the way that they can easily bypass most defen-
sive measures that are undertaken by the latter. Therefore, for survival, bacteria and
archaea developed a complex adaptive immune system that allows them to counter
this threat. Since for every bacterial cell there are a lot virus-based predators, an
adaptive immune system is helpful, and it is the CRISPR system that acts like an
adaptive immune system for prokaryotes [ 23 ].
Clustered regularly interspaced short palindromic repeats (CRISPR for short) area set of DNA sequence repeats, present inside the genome of prokaryotes, which
can function individually to help confer adaptive immunity to bacteria. The com-
bined CRISPR-Cas system is able to target both DNA and RNA viruses depending
on the type that attacks the bacteria [ 24 ]. The CRISPR locus was observed for the
first time in the genome of Escherichia coli accidentally [ 25 ], and at that time was
not understood in great detail. Later experiments by different groups confirmed the
presence of direct repeats in a number of prokaryotes. The recognition elements that
are used to neutralize viral elements are termed “spacers” and are incorporated
between direct repeats. After infection by a new virus, new spacers can be identified
and incorporated in the genome of the host bacteria or archaea, serving as potential
recognition elements in the future [ 26 ]. Also, for the immune system to work
perfectly, it needs a set of CRISPR-associated or cas genes that are located next to
the CRISPR locus [ 23 , 27 ].
The CRISPR-Cas system comprises Cas proteins that enact different activities,such as those of helicases or nucleases [ 28 ]. The CRISPR-Cas system is classified
on the basis of the signature protein it expresses. The system contains two classes
that are subdivided into six types, with three in each class. Each type has further
subtypes. Two proteins, Cas1 and Cas2, are ubiquitous to most of the CRISPR sys-
tems, the function attached to them being the adaptation of new spacers in the
CRISPR array [ 27 ]. Another conserved region across all CRISPR systems is a short
sequence that is located upstream (according to the direction of the transcription) to
the CRISPR array known as the leader sequence [ 29 ]. Class 1 is divided into types
I, III, and V as in all three types multiple Cas proteins are required to cleave the
target DNA. The class 2 system is divided into types II, IV, and VI because only a
single large protein is employed by these to cleave the target DNA [ 30 ]. These six
types are further subdivided into 19 subtypes according to the signature protein
expressed [ 31 ]. It is important to understand how the immunity against an infection
proceeds in a prokaryote to better understand the CRISPR system. The entire pro-
cess has three stages: adaptation, expression, and interference (Fig. 6.1). Each stage
6 CRISPR: From Prokaryotic Immune Systems to Plant Genome Editing Tools