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these are the genomic regions flanking the prophage insertion site and, thus, this
process is called 'specialized transduction' (
Berg, et al., 1983
). Still, any region of
the genome could potentially be packaged in the activated prophage.
Conjugation
Conjugation involves direct transfer of DNA from donor to recipient microbial
cell (
Sorensen et al., 2005
).
E. coli
and other Gram-negative bacteria have con-
jugation machinery that involves formation of a sex pilus, which is in contrast to
the conjugation in Gram-positive bacteria that involves direct cell-cell contact
adhesins (
Grohmann et al., 2003
). The pili and transfer function is encoded by
conjugative plasmids that can be used as a vehicle by other (transmissible) plas-
mids or chromosomal regions (
Zatyka and Thomas, 1998
). Integration of the
conjugative plasmid into the bacterial chromosome (e.g. integration of F plas-
mid episome into the chromosome via homologous recombination) can lead to
the conjugative transfer of the flanking chromosomal regions (
Holloway, 1993
;
Ambrozic et al., 1998
), which could be, for example, chromosomal islands.
Virulence-associated genes can also reside in transposable elements that fre-
quently change location between chromosome and plasmid and, in this way, can
move horizontally. These elements can be insertion sequences (IS elements), i.e.
small mobile fragments with short terminal inverted repeat sequences. These
entities can also be transposons, with or without flanking insertion sequences
termed composite and non-composite transposons respectively. Many transpo-
sons include antibiotic-resistance genes, e.g. Tn
5
carrying kanamycin, bleo-
mycin, and streptomycin resistance genes (
Reznikoff, 2008
). Also, integrons
represent multiple classes of genetic elements triggering the spread and acquisi-
tion of gene cassettes by conjugation (
Mazel, 2006
). They specify an integrase,
attachment sites, and transcriptional elements that ensure proper expression of
exogenous antibiotic-resistance determinants in recipient genomes. Examples
are MDR efflux pumps, carbapenemases, etc. (
Giedraitiene et al., 2011
).
Transformation
Transformation is the direct uptake of naked DNA, often followed by recom-
bination in the genomic DNA of recipient strain. This HGT process incorpo-
rates large discrete DNA segments as chromosomal islands (
Chen et al., 2005
).
While the phenomenon was known and used for decades in experiments with
laboratory strains of
E. coli
, natural transformation of wild-type
E. coli
strains
has been described relatively recently (
Baur et al., 1996
). Potentially any type
of DNA region could be transferred in this way. Another mechanism that is
somewhat similar to the transformation, which does not involve a specialized
genetic vehicle but where the DNA is not floating 'naked', is outer membrane
vesicle-mediated transfer in
E. coli
(
Yaron et al., 2000
). However, unlike the
transduction and conjugation, transformation mechanisms are not well under-
stood in
E. coli
.
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