3.4 | Analysis of spacer sequences and homology to
foreign DNA
Spacers are the products of exogenous genetic elements, which records
the encounters of host with invading DNA. There was a total of 536 type
I-E, 168 I-E*, and 128 IV-A spacers present in 111 CRISPR/Cas systems.
The homology search revealed that
more than one-third of the spacers (39.30%, 327/832) were homologous to
plasmids or phages. Specially, 173 type I-E spacers (32.28%, 173/536),
59 type I-E* spacers (35.12%, 59/168), and 95 type
IV-A spacers (74.22%, 95/128) were
homologous to plasmids or phages (Figure 5A). There were cases where one
spacer sequence targeted both the plasmid and the phage. Besides, we
observed that type I-E and IV-A systems displayed a target bias towards
plasmids, whereas type I-E* systems exhibited preference for phage
targets (Figure 5A).
Through BLASTp analyses against the NCBI database, the function of
proteins targeted by spacers was further investigated. If the
hypothetical proteins, unknown and non-coding regions were not
considered, conjugation transfer proteins were the most commonly
targeted, such as TrbI, TrbD, and TrbH (Figure 5B). Notably, spacers
from K. variicola targeted MGEs from multiple species, includingK. pnenumoniae , Escherichia coli, Salmonella enterica, and
other species (Figure 6 and Table S6-S8). Moreover, 103
strains have at least one spacer targeted MGEs from K.
pneumoniae .