Molecular Basis of Bacterial Infections Evelien Floor
Bacterial survival strategies
Extreme conditions during infection are present in the gut, stomach, blood and skin. Phagosomes are
harmful to bacteria too. Phagosomes are therefore also part of the extreme conditions. Bacteria can
deal with unusual extreme conditions via attack or hide/power save mode. They can attack by the
production of virulence factors. There are several hide/power save modes:
Stringent response (nutrient limitation)
SOS response (DNA damage)
Endospores
Dormancy, persisters
Bacteria are able to react to stress or to prepare for stress. When they sense stress and then react it
costs time. Reacting to stress happens with the stringent response, SOS response and endospore
formation. However, it is also possible to prepare for stress with phenotypic heterogeneity. A small
part of the population survives. This is the case with persisters.
When reacting to stress the transcriptional program is
changed by the use of alternative sigma factors in
RNA polymerase. Sigma factors are some kind of
transcription factors that recognize -10 to -35
sequences. They have an affinity for groups of
genes. There are multiple different sigma factors,
but often one main factor and several for stress.
In different conditions different Sigma factors are
active. E. coli consists of 7 sigma factors while B.
subtilis consists of 18 sigma factors.
Stringent response
The bacterial growth curve in a closed system
consists of a Lag phase, exponential phase,
stationary phase and a death phase. The
stationary phase is actually a type of stress
response because the bacteria can’t continue
growing. During this phase there is starvation for
specific nutrients:
Nitrogen (amino acid) stringent response
Carbon (glucose, pyruvate) RpoS (sigma factor)
Phosphate RpoS (sigma factor)
Iron Iron transporters
In case of amino acid starvation, the tRNA will remain uncharged, there is
no amino acid coupled to the RNA. Uncharged tRNA stalls the ribosome
and bound RelA becomes active. This generates the alarmone (p)ppGpp
which is GTP with two extra phosphate groups. This initiates the stringent
response in which biosynthesis of own amino acids will take place.
Eventually protein synthesis can continue.
Starvation during infection
Salmonella enterica subspecies Typhimurium (Salmonella Typhimurium)
survives inside its SCV (modified phagosome). It translocates virulence
factors via SPI-2 T3SS who are required to survive. The only conditions to
induces SPI-2 are MG2+ and phosphate limitation.
1
, Molecular Basis of Bacterial Infections Evelien Floor
SOS response
The SOS response is a global response to DNA
damage. DNA synthesis is inhibited to allow
repair. RecA recognizes ssDNA breaks and
binds to it. Then autoproteolysis of LexA takes
place and transcription of SOS genes (~50). The
SOS genes try to repair the DNA.
DNA repair
Nucleotide excision repair will take place if the
damaged nucleotides are in one DNA strand.
Endonuclease (UvrABC) removes the damaged
nucleotides and DNA polymerase I fills the
single stranded gaps. Ligase joins the
fragments.
Recombinational repair will take place if the
damaged nucleotides are in both DNA strands.
RecA cuts the template DNA from its sister molecule. Then the template is placed and ligated in the
gap. Another repair mechanism fixes the complementary strand.
SifA gives the bacterium time to restore its DNA by setting a cell division block for approximately 40
minutes. However, recombinational repair and nucleotide excision repair can take more than 40
minutes in case of too much damage. In that case or when no template is available, translesion DNA
synthesis will take place.
Translesion DNA synthesis is done by DNA polymerase IV and V which are error prone. The DNA
breaks are fixed but with a high mutation rate. However, rather survival of some cells than no
survival at all.
DNA damage during infection
DNA damage can happen inside the phagosome because of reactive oxygen species (ROS). ROS cause
protein oxidation which results in non-functional DNA replication proteins. Also, the treatment of
fluoroquinolones induces dsDNA breaks. Fluoroquinolones inhibit topoisomerase and gyrase. This
can induce a higher mutation rate in the bacteria.
Endospores
Endospores are stress-resistant cells to heat, UV
radiation, antibiotics, chemicals and desiccation.
The typical Gram-positive or Gram-negative
membrane is altered, it therefore can deal with
stress a lot better. The cells will become dormant
with a thick coat.
Endospore formation is specific for low guanine
and cytosine Gram positive bacterial species:
Bacillus species (anthracis, subtilis, cereus)
o Rod-shaped
o Soil bacterium
o Aerobe (facultative anaerobe)
Clostridium species (dificile, tetani, botulinum)
o Irregular rod-shaped
o Soil bacterium
o Anaerobe
2
Bacterial survival strategies
Extreme conditions during infection are present in the gut, stomach, blood and skin. Phagosomes are
harmful to bacteria too. Phagosomes are therefore also part of the extreme conditions. Bacteria can
deal with unusual extreme conditions via attack or hide/power save mode. They can attack by the
production of virulence factors. There are several hide/power save modes:
Stringent response (nutrient limitation)
SOS response (DNA damage)
Endospores
Dormancy, persisters
Bacteria are able to react to stress or to prepare for stress. When they sense stress and then react it
costs time. Reacting to stress happens with the stringent response, SOS response and endospore
formation. However, it is also possible to prepare for stress with phenotypic heterogeneity. A small
part of the population survives. This is the case with persisters.
When reacting to stress the transcriptional program is
changed by the use of alternative sigma factors in
RNA polymerase. Sigma factors are some kind of
transcription factors that recognize -10 to -35
sequences. They have an affinity for groups of
genes. There are multiple different sigma factors,
but often one main factor and several for stress.
In different conditions different Sigma factors are
active. E. coli consists of 7 sigma factors while B.
subtilis consists of 18 sigma factors.
Stringent response
The bacterial growth curve in a closed system
consists of a Lag phase, exponential phase,
stationary phase and a death phase. The
stationary phase is actually a type of stress
response because the bacteria can’t continue
growing. During this phase there is starvation for
specific nutrients:
Nitrogen (amino acid) stringent response
Carbon (glucose, pyruvate) RpoS (sigma factor)
Phosphate RpoS (sigma factor)
Iron Iron transporters
In case of amino acid starvation, the tRNA will remain uncharged, there is
no amino acid coupled to the RNA. Uncharged tRNA stalls the ribosome
and bound RelA becomes active. This generates the alarmone (p)ppGpp
which is GTP with two extra phosphate groups. This initiates the stringent
response in which biosynthesis of own amino acids will take place.
Eventually protein synthesis can continue.
Starvation during infection
Salmonella enterica subspecies Typhimurium (Salmonella Typhimurium)
survives inside its SCV (modified phagosome). It translocates virulence
factors via SPI-2 T3SS who are required to survive. The only conditions to
induces SPI-2 are MG2+ and phosphate limitation.
1
, Molecular Basis of Bacterial Infections Evelien Floor
SOS response
The SOS response is a global response to DNA
damage. DNA synthesis is inhibited to allow
repair. RecA recognizes ssDNA breaks and
binds to it. Then autoproteolysis of LexA takes
place and transcription of SOS genes (~50). The
SOS genes try to repair the DNA.
DNA repair
Nucleotide excision repair will take place if the
damaged nucleotides are in one DNA strand.
Endonuclease (UvrABC) removes the damaged
nucleotides and DNA polymerase I fills the
single stranded gaps. Ligase joins the
fragments.
Recombinational repair will take place if the
damaged nucleotides are in both DNA strands.
RecA cuts the template DNA from its sister molecule. Then the template is placed and ligated in the
gap. Another repair mechanism fixes the complementary strand.
SifA gives the bacterium time to restore its DNA by setting a cell division block for approximately 40
minutes. However, recombinational repair and nucleotide excision repair can take more than 40
minutes in case of too much damage. In that case or when no template is available, translesion DNA
synthesis will take place.
Translesion DNA synthesis is done by DNA polymerase IV and V which are error prone. The DNA
breaks are fixed but with a high mutation rate. However, rather survival of some cells than no
survival at all.
DNA damage during infection
DNA damage can happen inside the phagosome because of reactive oxygen species (ROS). ROS cause
protein oxidation which results in non-functional DNA replication proteins. Also, the treatment of
fluoroquinolones induces dsDNA breaks. Fluoroquinolones inhibit topoisomerase and gyrase. This
can induce a higher mutation rate in the bacteria.
Endospores
Endospores are stress-resistant cells to heat, UV
radiation, antibiotics, chemicals and desiccation.
The typical Gram-positive or Gram-negative
membrane is altered, it therefore can deal with
stress a lot better. The cells will become dormant
with a thick coat.
Endospore formation is specific for low guanine
and cytosine Gram positive bacterial species:
Bacillus species (anthracis, subtilis, cereus)
o Rod-shaped
o Soil bacterium
o Aerobe (facultative anaerobe)
Clostridium species (dificile, tetani, botulinum)
o Irregular rod-shaped
o Soil bacterium
o Anaerobe
2
