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6.2 The Story of CRISPR
Clustered regularly interspaced short palindromic repeats serve as the immune system of many archaea and bacteria. It is an example of adaptive immune system and
involves short length of nucleotides (RNA or DNA elements) obtained from either
from bacteriophages or other foreign mobile genetic elements that invade the bacterial or archaeal hosts (Zhang et al. 2014b; Adli 2018). In 1987, Yoshizumi and his
colleagues while carrying out a study on “iap” gene observed repeat sequences in
the gene. This was attributed to the accidental cloning of CRISPR along with iap
gene (Ishino et al. 1987). These repeats contained many interspersed sequences
whose function was then unknown. Later in 1993, the diversity of these sequences
was observed and this property was used to design a method named spoligotyping
(analysis of polymorphism and repeated units). In 2001, these interspersed
sequences were named as CRISPR (Mojica and Montoliu 2016; Horvath and
Barrangou 2010). It has been found that these repeats are followed by a set of
homologous genes termed as CRISPR associated (Cas) genes. Motifs of helicases
and nucleases were found in these Cas proteins advocating their involvement in the
skeleton of CRISPR loci. The CRISPR locus constitutes of three main parts viz.,
Cas genes, leader sequences and spacer arrays (Horvath and Barrangou 2010;
Marraffini and Sontheimer 2010). CRISPR-Cas network is a potential robust
immune system that occurs in bacteria and archaea that provides immunity to the
bacteria against the invaders. The network comprises not just of bacteriophages but
also mobile genetic elements (Hale et al. 2009).
CRISPR-Cas networks are categorized into two classes on the basis of associated
effector modules. Class 1 CRISPR-Cas system forms multiple complexes due to
multi-protein effector molecules, whereas in class 2 category CRISPR-Cas utilizes
single protein effector molecule. CRISPR-Cas is further subdivided into types
(I-VI) and subtypes based on signature genes and their characteristic arrangements.
Class 1 CRISPR-Cas system represents majority (~ 90%) of the CRISPR-Cas loci
and comprises of type I, III and IV. Cas3 is the signature gene present in the loci of
all type I CRISPR-Cas systems. Cas10 and Csf1 are signature genes for type III and
IV, respectively. The second class of CRISPR-Cas network includes type II, type V
and type VI with the signature gene Cas9, Cas12 (Cpf1), and Cas13 respectively
(McDonald et al. 2019). The types of CRISPR-Cas systems are further categorized
into the following subtypes: type I subtypes (I-A, I-B, I-C, I-U, I-D, I-E, I-F), type
II subtypes (II-A, II-B, II-C), type III subtypes (III-A, III-B, III-C, III-D), type V
subtypes (V-A, V-B, V-C, V-D, V-E, V-U), and three type VI subtypes (VI-A, VI-B,
VI-C) (Makarova et al. 2015; Koonin et al. 2017). Cas1 and Cas2 proteins are found
in almost all CRISPR-Cas systems which play a significant role in spacer acquisition in CRISPR mechanism (Nuñez et al. 2014). The divergent class and large number of Cas proteins make the classification of CRISPR-Cas network challenging
(Makarova and Koonin 2015; Makarova et al. 2015; Koonin et al. 2017). The characteristics of the subsets of CRISPR-Cas are mentioned in Table 6.1.
In 2005, a research suggested that the spacers are derived from extra chromosomal DNA or foreign invaders like bacteriophage. The spacer array was the indication that CRISPR was part of adaptive immune system of bacteria (Pourcel et al.
6 Role of Gene Editing Tool CRISPR-Cas in the Management of Antimicrobial…
6.2 The Story of CRISPR
Clustered regularly interspaced short palindromic repeats serve as the immune system of many archaea and bacteria. It is an example of adaptive immune system and
involves short length of nucleotides (RNA or DNA elements) obtained from either
from bacteriophages or other foreign mobile genetic elements that invade the bacterial or archaeal hosts (Zhang et al. 2014b; Adli 2018). In 1987, Yoshizumi and his
colleagues while carrying out a study on “iap” gene observed repeat sequences in
the gene. This was attributed to the accidental cloning of CRISPR along with iap
gene (Ishino et al. 1987). These repeats contained many interspersed sequences
whose function was then unknown. Later in 1993, the diversity of these sequences
was observed and this property was used to design a method named spoligotyping
(analysis of polymorphism and repeated units). In 2001, these interspersed
sequences were named as CRISPR (Mojica and Montoliu 2016; Horvath and
Barrangou 2010). It has been found that these repeats are followed by a set of
homologous genes termed as CRISPR associated (Cas) genes. Motifs of helicases
and nucleases were found in these Cas proteins advocating their involvement in the
skeleton of CRISPR loci. The CRISPR locus constitutes of three main parts viz.,
Cas genes, leader sequences and spacer arrays (Horvath and Barrangou 2010;
Marraffini and Sontheimer 2010). CRISPR-Cas network is a potential robust
immune system that occurs in bacteria and archaea that provides immunity to the
bacteria against the invaders. The network comprises not just of bacteriophages but
also mobile genetic elements (Hale et al. 2009).
CRISPR-Cas networks are categorized into two classes on the basis of associated
effector modules. Class 1 CRISPR-Cas system forms multiple complexes due to
multi-protein effector molecules, whereas in class 2 category CRISPR-Cas utilizes
single protein effector molecule. CRISPR-Cas is further subdivided into types
(I-VI) and subtypes based on signature genes and their characteristic arrangements.
Class 1 CRISPR-Cas system represents majority (~ 90%) of the CRISPR-Cas loci
and comprises of type I, III and IV. Cas3 is the signature gene present in the loci of
all type I CRISPR-Cas systems. Cas10 and Csf1 are signature genes for type III and
IV, respectively. The second class of CRISPR-Cas network includes type II, type V
and type VI with the signature gene Cas9, Cas12 (Cpf1), and Cas13 respectively
(McDonald et al. 2019). The types of CRISPR-Cas systems are further categorized
into the following subtypes: type I subtypes (I-A, I-B, I-C, I-U, I-D, I-E, I-F), type
II subtypes (II-A, II-B, II-C), type III subtypes (III-A, III-B, III-C, III-D), type V
subtypes (V-A, V-B, V-C, V-D, V-E, V-U), and three type VI subtypes (VI-A, VI-B,
VI-C) (Makarova et al. 2015; Koonin et al. 2017). Cas1 and Cas2 proteins are found
in almost all CRISPR-Cas systems which play a significant role in spacer acquisition in CRISPR mechanism (Nuñez et al. 2014). The divergent class and large number of Cas proteins make the classification of CRISPR-Cas network challenging
(Makarova and Koonin 2015; Makarova et al. 2015; Koonin et al. 2017). The characteristics of the subsets of CRISPR-Cas are mentioned in Table 6.1.
In 2005, a research suggested that the spacers are derived from extra chromosomal DNA or foreign invaders like bacteriophage. The spacer array was the indication that CRISPR was part of adaptive immune system of bacteria (Pourcel et al.
6 Role of Gene Editing Tool CRISPR-Cas in the Management of Antimicrobial…