able, suitable, is a term now used in many languages in
evolutionary biology to indicate the ability of an organism
to reproduce and transmit its genes. By their small size
relative to their volume and metabolism associated with
their envelopes, prokaryotic cells are in constant interaction with their environment. They are constantly forced
to adapt to changing conditions of environmental
parameters. These conditions can vary over very short
distances and very short time scales. Prokaryotic
cells must be able to respond to changes in micro-spatial
and temporal gradients in a timely manner. To follow
the evolution of various environmental parameters, such
as osmotic pressure, ionic strength, pH, temperature,
concentrations of nutrients, or toxic substances, is a necessity for survival. Among microorganisms, prokaryotes
are those who are most capable of wide adaptability
and resistance to changing conditions of the environment.
Prokaryotes are practically the only organisms able to
resist or even thrive over the extreme conditions of life
that exist on our planet (cf. Chap. 10). For this purpose,
prokaryotic cells have developed adaptive systems
that induce morphological changes (such as variations in
size, changes in envelopes features, productions of protective features such as capsules or spores*, etc.) or changes
in the metabolism and physiology of the cell. These
systems are based either on signal transduction proteins
that are able to perceive changes in environmental
parameters and to transmit information to modify
other proteins by different molecular mechanisms,
resulting in metabolic or behavioral adjustments, or on
the regulation of transcription at the genetic level and
modifications in the protein expression pattern. In a
complex microbial community, other responses may
occur linked to the “quorum sensing” (cf. Sect. 9.3) or the
phenomena of competition and antibiosis (cf. Sect. 9.4).
This chapter presents the main systems for molecular
adaptation to environmental conditions (cf. Sects. 9.2, 9.3,
9.4, and 9.5) and the behavioral responses of prokaryotes in
various habitats, including biofilms (cf. Sects. 9.6, 9.7, and
9.8). The answers to the most extreme conditions encountered in archaea but also in some bacteria are presented in
Chap. 10.
9.2
Main Regulation Systems
One of the major modes of adaptation is the ability to
respond to changing conditions of the physicochemical
parameters of the biotope; this ability is called regulation,
and it is done at different levels, that of transcription*, of
translation*, and at the posttranslational level.
9.2.1 Regulation of Transcription
In eukaryotes, the availability of large regions for expression
of the genome depends on the structure of chromatin, which
can be altered due to the attachment of specific proteins, the
histones, which is controlled by DNA methylation, by noncoding RNAs (ncRNA), or by proteins binding to DNA.
These adaptation strategies are also used by bacteria and
archaea: the histones have been described in Archaea
(Reeve et al. 2004); ncRNA exists in bacteria (Box 9.1) as
well as proteins that bind to DNA.
Box 9.1: Small RNAs for Important Functions
Wafa Achouak
Bacteria use different mechanisms to respond to environmental stresses. Small noncoding RNA regulators
(ncRNAs) are integrated into regulatory networks and
are involved in regulating the stress response, iron
homeostasis, virulence, quorum sensing, sporulation,
and many other functions. The ncRNAs are found in
eukaryotes, bacteria, and archaea.
History and Prediction Tools
The ncRNAs have long escaped biochemical and
genetic studies because they do not code for proteins,
and they are not subject to nonsense mutations. Since
they are often encoded in intergenic regions, they also
escape transcriptomic analyses using microarrays
containing only those genes that code for proteins. The
first ncRNAs were discovered four decades ago, and for
a long time, only a dozen were known in Escherichia
coli. Approximately 80 have currently been identified
(Wassarman et al. 2001), and approximately 20 have
been described in other bacteria (Bacillus subtilis, Vibrio cholerae, Pseudomonas aeruginosa, Staphylococcus
aureus, and Listeria monocytogenes). They have a size
ranging from 50 to 500 bases, are located in intergenic
regions, but can also be encoded by the antisense strand
of genes encoding proteins.
Tools for Predicting ncRNA
• Bioinformatics: The algorithms developed for the
prediction of ncRNA target noncoding regions and
W. Achouak
UMR 7265 CNRS-CEA-Aix Marseille University,
Institute of Environmental Biology and Biotechnology
IBEB/DSV/CEA, CEA Cadarache,
13108 Saint-Paul-lez-Durance, France
(continued)
294
P. Normand et al.
evolutionary biology to indicate the ability of an organism
to reproduce and transmit its genes. By their small size
relative to their volume and metabolism associated with
their envelopes, prokaryotic cells are in constant interaction with their environment. They are constantly forced
to adapt to changing conditions of environmental
parameters. These conditions can vary over very short
distances and very short time scales. Prokaryotic
cells must be able to respond to changes in micro-spatial
and temporal gradients in a timely manner. To follow
the evolution of various environmental parameters, such
as osmotic pressure, ionic strength, pH, temperature,
concentrations of nutrients, or toxic substances, is a necessity for survival. Among microorganisms, prokaryotes
are those who are most capable of wide adaptability
and resistance to changing conditions of the environment.
Prokaryotes are practically the only organisms able to
resist or even thrive over the extreme conditions of life
that exist on our planet (cf. Chap. 10). For this purpose,
prokaryotic cells have developed adaptive systems
that induce morphological changes (such as variations in
size, changes in envelopes features, productions of protective features such as capsules or spores*, etc.) or changes
in the metabolism and physiology of the cell. These
systems are based either on signal transduction proteins
that are able to perceive changes in environmental
parameters and to transmit information to modify
other proteins by different molecular mechanisms,
resulting in metabolic or behavioral adjustments, or on
the regulation of transcription at the genetic level and
modifications in the protein expression pattern. In a
complex microbial community, other responses may
occur linked to the “quorum sensing” (cf. Sect. 9.3) or the
phenomena of competition and antibiosis (cf. Sect. 9.4).
This chapter presents the main systems for molecular
adaptation to environmental conditions (cf. Sects. 9.2, 9.3,
9.4, and 9.5) and the behavioral responses of prokaryotes in
various habitats, including biofilms (cf. Sects. 9.6, 9.7, and
9.8). The answers to the most extreme conditions encountered in archaea but also in some bacteria are presented in
Chap. 10.
9.2
Main Regulation Systems
One of the major modes of adaptation is the ability to
respond to changing conditions of the physicochemical
parameters of the biotope; this ability is called regulation,
and it is done at different levels, that of transcription*, of
translation*, and at the posttranslational level.
9.2.1 Regulation of Transcription
In eukaryotes, the availability of large regions for expression
of the genome depends on the structure of chromatin, which
can be altered due to the attachment of specific proteins, the
histones, which is controlled by DNA methylation, by noncoding RNAs (ncRNA), or by proteins binding to DNA.
These adaptation strategies are also used by bacteria and
archaea: the histones have been described in Archaea
(Reeve et al. 2004); ncRNA exists in bacteria (Box 9.1) as
well as proteins that bind to DNA.
Box 9.1: Small RNAs for Important Functions
Wafa Achouak
Bacteria use different mechanisms to respond to environmental stresses. Small noncoding RNA regulators
(ncRNAs) are integrated into regulatory networks and
are involved in regulating the stress response, iron
homeostasis, virulence, quorum sensing, sporulation,
and many other functions. The ncRNAs are found in
eukaryotes, bacteria, and archaea.
History and Prediction Tools
The ncRNAs have long escaped biochemical and
genetic studies because they do not code for proteins,
and they are not subject to nonsense mutations. Since
they are often encoded in intergenic regions, they also
escape transcriptomic analyses using microarrays
containing only those genes that code for proteins. The
first ncRNAs were discovered four decades ago, and for
a long time, only a dozen were known in Escherichia
coli. Approximately 80 have currently been identified
(Wassarman et al. 2001), and approximately 20 have
been described in other bacteria (Bacillus subtilis, Vibrio cholerae, Pseudomonas aeruginosa, Staphylococcus
aureus, and Listeria monocytogenes). They have a size
ranging from 50 to 500 bases, are located in intergenic
regions, but can also be encoded by the antisense strand
of genes encoding proteins.
Tools for Predicting ncRNA
• Bioinformatics: The algorithms developed for the
prediction of ncRNA target noncoding regions and
W. Achouak
UMR 7265 CNRS-CEA-Aix Marseille University,
Institute of Environmental Biology and Biotechnology
IBEB/DSV/CEA, CEA Cadarache,
13108 Saint-Paul-lez-Durance, France
(continued)
294
P. Normand et al.