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is characterized by a particular set of activities or sequences that lead up to the
interference of the foreign viral particle. In the adaptation phase, the infection is
recognized and potential spacer sequences are identified and are inserted within the
genome. In the expression phase, the CRISPR locus is transcribed into a precursor
RNA (pre-crRNA). The adjacent cas genes are transcribed to form the Cas proteins,
which then cleave the pre-crRNA to a mature crRNA. In the final interference stage, the
mature crRNA acts in concert with a few of the expressed Cas proteins. It recog-
nizes the target nucleic acid region and destabilizes it. Thus, in its entirety, this
process grants immunity to prokaryotes.
CRISPR adaptation is the first stage or phase of the entire process and is impor-tant as it provides memory of a prior infection and thus helps in the expression and
interference phases that come in later. Adaptation involves spacer acquisition, which
is not completely understood yet. It is apparent that two of the conserved Cas pro-
teins, Cas1 and Cas2, play an important role in identifying and acquiring spacers
into the CRISPR array for subsequent steps of expression and interference against
the phage-virus attacking the prokaryotic genome. This entire process can be whit-
tled down to two levels, selection of the protospacer and subsequent generation of
the spacer, and that is succeeded by integration of the spacer into the CRISPR array
Fig. 6.1 The steps involved in the adaptive immunity in bacteria and archaea that is achieved with
the help of the CRISPR-Cas system. It involves three phases or stages: adaptation, expression, and
interference
A. Bandyopadhyay et al.