9.4.2.3 Insertion-Excision
Phase variation by insertion-excision involves a mobile
genetic element, such as an insertion sequence (IS), and is
reversible when excision of the element is perfect.
Many examples involving IS have been described,
such as surface properties in Shigella flexneri (Mills et al.
1992) and biofilm formation in Staphylococcus aureus
(Kiem et al. 2004).
In Legionella pneumophila, the causative pathogen of
legionellosis, an avirulent variant form devoid of LPS and
flagella, can be isolated at high frequency. During the transition from wild type to variant, a 30-kb region is excised from
the chromosome and replicates in the variant like a high-copy
number plasmid (Luneberg et al. 2001). During reversion, this
region is inserted back into the chromosome at the initial
location. Variants, although less competitive for infection of
the host, could be adapted to the aquatic environment where
L. pneumophila usually lives (Luneberg et al. 2001).
9.4.2.4 Duplication
Pseudomonas tolaasii, the causal agent of brown blotch
disease of mushroom Agaricus bisporus, can generate
in vitro nonpathogenic, non-mucoid variants with enhanced
mobility. The pheN regulatory gene, whose deduced product
displays homology to both sensor and regulator domains
of the conserved family of two-component systems, is
duplicated during the phenotypic conversion (Han et al.
1997). A duplication of 661 bp within the sensor domain
of pheN leads to the formation of two truncated ORFs.
Reversion of the variant form to the wild type occurs via
the precise deletion of the 661-bp duplicated region. Wild
type and variants are adapted to different environmental
niches; the wild type would penetrate and proliferate in
fungal tissues, inducing their degradation, whereas the
variant type would be more adapted to telluric life.
In Streptococcus pneumoniae, a human pathogen responsible for otitis, pneumonia, and meningitis, the appearance
of small colonies lacking capsule is due to a duplication
(11–239 bp) in the first gene of the biosynthetic pathway
of capsules (Waite et al. 2001). Reversion to capsulated
cells can occur via a precise excision of the duplication.
The ability to regulate the synthesis of capsule is advantageous when invading eukaryotic cells; indeed, adherence
and invasion would be 200-fold less efficient for a capsulated strain than for a noncapsulated strain, but after cellular
invasion, the capsule prevents S. pneumoniae from being
eliminated by phagocytosis.
9.4.2.5 Deletion
Phenotypic conversion by deletion is an irreversible
phenomenon concerning regions of varying sizes (from
a few bp to several hundred kb). In Yersinia pestis, the
causal agent of bubonic plague, avirulent nonpigmented
mutants are frequently observed, and these phenotypes are
due to the deletion of a 102-kb region flanked by a repeated
element (Fetherston et al. 1992). In the plant growthpromoting bacteria Azospirillum lipoferum, the emergence
of variants affected in the assimilation of carbohydrates and
mobility is correlated with the loss of a 750-kb plasmid
(Vial et al. 2006).
9.4.2.6 Slipped-Strand Mispairing
Phase variation may be due to frequent and reversible
changes in the length of short DNA repeats, generally composed of stretches of polypurines and/or polypyrimidines.
Loss or gain of repeat units implies a mechanism of slippedmispairing strain (SSM), a RecA-dependent process occurring during chromosomal replication, DNA repair, and
recombination processes requiring DNA synthesis. When
this event occurs in the coding region of a gene, changes
in the number of repeat units result in frameshift mutations,
thereby switching the expression of the encoded protein
“ON” or “OFF.” Gain or loss of repeat units can also affect
transcription initiation by altering the relative positioning of
the RNA polymerase-binding sites at the promoter or the
termination site.
Opacity proteins of Neisseria gonorrhoeae and Neisseria
meningitidis allowing bacterial adhesion and invasion of
host tissues undergo antigenic variation through gene conversion and phase variation by SSM. Expression of other
surface components (capsule, outer membrane proteins) can
also be regulated by SSM (van der Woude and Baumler
2004; Wisniewski-Dye ´ and Vial 2008).
Synthesis of pili in Haemophilus influenzae is regulated
at the transcriptional level by SSM of two divergently
oriented genes, hifA and hifB, involved in the biosynthesis
of pili. Their overlapping promoter region contains repetitive TA units; variation in the number of TA units changes
the spacing between the À35 and À10 sequences and results
in the control of transcription initiation (van Ham et al.
1993).
9.4.2.7 Multiple Events Affecting a Single Gene
Ralstonia solanacearum, the causal agent of bacterial
wilting of over 200 plants, can undergo a phenotypic
conversion in vitro and in planta: the variants are avirulent
or less virulent. Different types of mutations in the phcA
gene, encoding a regulator, have been characterized:
deletions (in the reading frame or in the promoter region),
duplications, IS insertions, or base substitutions (Brumbley
et al. 1993). Revertants recovering a functional phcA gene
can be isolated in the presence of the plant for variants
having a duplication of 64 bp or IS inserted into phcA
(Poussier et al. 2003). The variant form, with increased
9 Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions. . .
319
Phase variation by insertion-excision involves a mobile
genetic element, such as an insertion sequence (IS), and is
reversible when excision of the element is perfect.
Many examples involving IS have been described,
such as surface properties in Shigella flexneri (Mills et al.
1992) and biofilm formation in Staphylococcus aureus
(Kiem et al. 2004).
In Legionella pneumophila, the causative pathogen of
legionellosis, an avirulent variant form devoid of LPS and
flagella, can be isolated at high frequency. During the transition from wild type to variant, a 30-kb region is excised from
the chromosome and replicates in the variant like a high-copy
number plasmid (Luneberg et al. 2001). During reversion, this
region is inserted back into the chromosome at the initial
location. Variants, although less competitive for infection of
the host, could be adapted to the aquatic environment where
L. pneumophila usually lives (Luneberg et al. 2001).
9.4.2.4 Duplication
Pseudomonas tolaasii, the causal agent of brown blotch
disease of mushroom Agaricus bisporus, can generate
in vitro nonpathogenic, non-mucoid variants with enhanced
mobility. The pheN regulatory gene, whose deduced product
displays homology to both sensor and regulator domains
of the conserved family of two-component systems, is
duplicated during the phenotypic conversion (Han et al.
1997). A duplication of 661 bp within the sensor domain
of pheN leads to the formation of two truncated ORFs.
Reversion of the variant form to the wild type occurs via
the precise deletion of the 661-bp duplicated region. Wild
type and variants are adapted to different environmental
niches; the wild type would penetrate and proliferate in
fungal tissues, inducing their degradation, whereas the
variant type would be more adapted to telluric life.
In Streptococcus pneumoniae, a human pathogen responsible for otitis, pneumonia, and meningitis, the appearance
of small colonies lacking capsule is due to a duplication
(11–239 bp) in the first gene of the biosynthetic pathway
of capsules (Waite et al. 2001). Reversion to capsulated
cells can occur via a precise excision of the duplication.
The ability to regulate the synthesis of capsule is advantageous when invading eukaryotic cells; indeed, adherence
and invasion would be 200-fold less efficient for a capsulated strain than for a noncapsulated strain, but after cellular
invasion, the capsule prevents S. pneumoniae from being
eliminated by phagocytosis.
9.4.2.5 Deletion
Phenotypic conversion by deletion is an irreversible
phenomenon concerning regions of varying sizes (from
a few bp to several hundred kb). In Yersinia pestis, the
causal agent of bubonic plague, avirulent nonpigmented
mutants are frequently observed, and these phenotypes are
due to the deletion of a 102-kb region flanked by a repeated
element (Fetherston et al. 1992). In the plant growthpromoting bacteria Azospirillum lipoferum, the emergence
of variants affected in the assimilation of carbohydrates and
mobility is correlated with the loss of a 750-kb plasmid
(Vial et al. 2006).
9.4.2.6 Slipped-Strand Mispairing
Phase variation may be due to frequent and reversible
changes in the length of short DNA repeats, generally composed of stretches of polypurines and/or polypyrimidines.
Loss or gain of repeat units implies a mechanism of slippedmispairing strain (SSM), a RecA-dependent process occurring during chromosomal replication, DNA repair, and
recombination processes requiring DNA synthesis. When
this event occurs in the coding region of a gene, changes
in the number of repeat units result in frameshift mutations,
thereby switching the expression of the encoded protein
“ON” or “OFF.” Gain or loss of repeat units can also affect
transcription initiation by altering the relative positioning of
the RNA polymerase-binding sites at the promoter or the
termination site.
Opacity proteins of Neisseria gonorrhoeae and Neisseria
meningitidis allowing bacterial adhesion and invasion of
host tissues undergo antigenic variation through gene conversion and phase variation by SSM. Expression of other
surface components (capsule, outer membrane proteins) can
also be regulated by SSM (van der Woude and Baumler
2004; Wisniewski-Dye ´ and Vial 2008).
Synthesis of pili in Haemophilus influenzae is regulated
at the transcriptional level by SSM of two divergently
oriented genes, hifA and hifB, involved in the biosynthesis
of pili. Their overlapping promoter region contains repetitive TA units; variation in the number of TA units changes
the spacing between the À35 and À10 sequences and results
in the control of transcription initiation (van Ham et al.
1993).
9.4.2.7 Multiple Events Affecting a Single Gene
Ralstonia solanacearum, the causal agent of bacterial
wilting of over 200 plants, can undergo a phenotypic
conversion in vitro and in planta: the variants are avirulent
or less virulent. Different types of mutations in the phcA
gene, encoding a regulator, have been characterized:
deletions (in the reading frame or in the promoter region),
duplications, IS insertions, or base substitutions (Brumbley
et al. 1993). Revertants recovering a functional phcA gene
can be isolated in the presence of the plant for variants
having a duplication of 64 bp or IS inserted into phcA
(Poussier et al. 2003). The variant form, with increased
9 Adaptations of Prokaryotes to Their Biotopes and to Physicochemical Conditions. . .
319