Evolution of pathogenic Escherichia coli - Escherichia coli: Pathotypes and Principles of Pathogenesis - page 47

( Dobrindt et al., 2004 ). Originally, actually, chromosomal islands were described
as pathogenicity-associated islands (PAI), coined to define large unstable
regions (10-200 kb) harboring virulence determinants on uropathogenic
E. coli chromosomes and differing in GC content from the rest of the chromo-
some ( Hacker et al., 1990 ). Examples of PAI-coded virulence factors are LEE
island genes in EPEC and EHEC ( McDaniel et al., 1995 ); Tia adhesin in ETEC
( Fleckenstein et al., 2000 ); Protein involved in colonization (Pic) in EAEC
( Henderson et al., 1999 ); SigA in EIEC/ Shigella ( Al-Hasani et al., 2000 ); Hemo-
lysin in UPEC ( O'Hanley et al., 1991 ). Besides pathogenicity-related functions,
chromosomal islands encode genes representing a wide spectrum of traits such
as mercury resistance and siderophore synthesis ( Larbig et al., 2002 ), symbiosis
( Sullivan et al., 2002 ), sucrose and aromatic compound metabolism ( Gaillard
et al., 2006 ), etc. The genomic islands are predicted using either sequence-based
methods or comparative genomic analyses ( Gal-Mor and Finlay, 2006 ). While
sequence-based approaches rely on abnormal sequence composition (e.g. bias
in GC content, dinucleotide frequency, codon usage) or on features associ-
ated with mobile genetic elements (e.g. presence of direct repeats, insertion
sequence elements, tRNA, integrases, transposases, etc.), comparative analyses
of multiple genomes are based on detection of genomic regions with anomalous
phylogenetic patterns.
Mechanisms of HGT
There are three frequent genetic mechanisms that make the transfer of DNA
happen: transduction, conjugation, and transformation. These diverse forms
of transfer make HGT a very important process in expanding the potential of
genetic adaptation in a bacterial species ( Ochman et al., 2000 ).
Transduction
Transduction is defined as the movement of genetic material with the help of bac-
teriophages, the viruses that can inject DNA into the organisms. Lytic (virulent)
phages that usually immediately multiply and lyze the infected bacterium, some-
times carry DNA from previously infected organisms, accidently packed into the
capsule. Thus, if such DNA is injected instead of the viral genome, it can get
incorporated in the infected microbial genome. However, while lytic phage trans-
duction is commonly observed and utilized in lab experiments (e.g. P phage), it is
unclear to what extent this process occurs in nature, because in these cases there
are no traces of the viral DNA being tagged to the transduced DNA. Theoretically,
any region of the bacterial genome could be transferred in this way, including
plasmids and chromosomal islands and, thus, such a mechanism is termed 'gen-
eralized transduction' ( Berg et al., 1983 ). It is a different story with the temperate
phages that integrate into the bacterial chromosome as a prophage (see above).
Its excision from the chromosome during the lytic cycle could be accompanied
by accidental packaging (and then transfer) of non-phage DNA, but commonly