Presumably, resilience of ecosystems is supported by the activity of microorganisms. Great advances in experimental techniques in biochemistry and molecular
biology have progressed our understanding of the physiological properties of microorganisms. However, it has not yet been explained in detail how the development of
resilience is achieved by these small organisms. A key to the natural principle should
reside in the function of microbial cells and their invisible interactions.
25.2 Structures Supporting Rigid Communities
25.2.1 Primary Structure: Self-Restoration
25.2.1.1 Self-repair
Early studies on bacterial genetics revealed the existence of sophisticated mechanisms of self-repair (Baharoglu and Mazel 2014). The enzyme DNA polymerase not
only catalyzes replication but also exerts proofreading activities; the enzyme forms a
molecular complex that can find its own mistakes, eliminate the wrong nucleotide
base, and reintroduce the correct one. Bacteria have developed other mechanisms to
screen for mismatches in base pairing, eliminate incorrect ones in the newly synthesized strand, and eventually redirect polymerase and ligase activities to fill in the gap
using the proper base. In eukaryotes, much more complex mechanisms maintain the
high reliability of copyediting.
Bacterial cells can also mend damaged DNA structures caused by exposure to
injurious environmental factors. For example, the widespread enzyme DNA
photolyase acts on pyrimidine dimer structures formed by UV illumination and
resolves them to restore the original form by utilizing light energy. Maintenance is
also carried out for proteins. Molecular chaperones prevent their misfolding, aggregation, and unusual accumulation. Bacterial cells can also repair damage to the cell
wall by inducing enzymes involved in peptide glycan synthesis.
Another way of survival under a threat to DNA stability is known with regard to
unique genetic features of the radio-tolerant bacterium Deinococcus. This extremophile group retains multiple copies of chromosomal DNA, which allows for growth
even under high doses of irradiation (Ishino and Narumi 2015). This survival
strategy of Deinococcus, which is based on the retention of spare genetic information, may support the hypothesis that rapid growth of many bacteria, which is
accompanied by the formation of large DNA copy numbers, serves as a self-defense
mechanism.
25.2.1.2 Adaptive Response
Bacteria have developed defensive functions against various environmental stresses,
including exposure to harmful substances, physicochemical conditions, and
25 Invisible Interactions between Microorganisms
529
biology have progressed our understanding of the physiological properties of microorganisms. However, it has not yet been explained in detail how the development of
resilience is achieved by these small organisms. A key to the natural principle should
reside in the function of microbial cells and their invisible interactions.
25.2 Structures Supporting Rigid Communities
25.2.1 Primary Structure: Self-Restoration
25.2.1.1 Self-repair
Early studies on bacterial genetics revealed the existence of sophisticated mechanisms of self-repair (Baharoglu and Mazel 2014). The enzyme DNA polymerase not
only catalyzes replication but also exerts proofreading activities; the enzyme forms a
molecular complex that can find its own mistakes, eliminate the wrong nucleotide
base, and reintroduce the correct one. Bacteria have developed other mechanisms to
screen for mismatches in base pairing, eliminate incorrect ones in the newly synthesized strand, and eventually redirect polymerase and ligase activities to fill in the gap
using the proper base. In eukaryotes, much more complex mechanisms maintain the
high reliability of copyediting.
Bacterial cells can also mend damaged DNA structures caused by exposure to
injurious environmental factors. For example, the widespread enzyme DNA
photolyase acts on pyrimidine dimer structures formed by UV illumination and
resolves them to restore the original form by utilizing light energy. Maintenance is
also carried out for proteins. Molecular chaperones prevent their misfolding, aggregation, and unusual accumulation. Bacterial cells can also repair damage to the cell
wall by inducing enzymes involved in peptide glycan synthesis.
Another way of survival under a threat to DNA stability is known with regard to
unique genetic features of the radio-tolerant bacterium Deinococcus. This extremophile group retains multiple copies of chromosomal DNA, which allows for growth
even under high doses of irradiation (Ishino and Narumi 2015). This survival
strategy of Deinococcus, which is based on the retention of spare genetic information, may support the hypothesis that rapid growth of many bacteria, which is
accompanied by the formation of large DNA copy numbers, serves as a self-defense
mechanism.
25.2.1.2 Adaptive Response
Bacteria have developed defensive functions against various environmental stresses,
including exposure to harmful substances, physicochemical conditions, and
25 Invisible Interactions between Microorganisms
529