Producing More Biomolecules That Mitigate the pH Drift With rising intracellular pH, the level of some biomolecules such as ATP synthase, Na
+
/H
+ antiporter,
squalene, SCWPs, etc. increases [21, 102, 106, 128, 130, 148]. As aforementioned,
these biomolecules play a significant role in the pH homeostasis of alkaliphiles, and
hence, the upregulations of these biomolecules contribute to mitigate further increase
in cytoplasmic pH. For instance, an increased level of ATP synthase expression
results in pumping more H
+ to the cytoplasm which eases the cytoplasmic pH rise,
while accumulation of squalene effectively limits H
+ leakage and OH
À ingress. In
some organisms, cytoplasmic alkalinization is accompanied by metabolic acid
production [102] which alleviates the cytoplasmic pH rise and protects the cell
from the subsequent demise. In fact, many alkaliphiles are known producing organic
acids and even reduce the culture pH significantly [56, 105].
Compensating Loss Due to Denaturation With the rise in cytoplasmic pH, the
activity and integrity of intracellular biomolecules deteriorate. To compensate this
loss, cells increase the production level of pH labile biomolecules. For example, as
translation slows down and mRNAs are not stable at elevated pH, cells increase the
level of mRNA to maintain the necessary level of protein synthesis [183, 184].
3.4.2 Activating Protein Damage Repair and Degradation Systems
The cells also use another strategy to maintain the necessary level of functional
biomolecules, repairing the damage incurred by cytoplasmic alkalinization. Thus, it
is expected that the cells activate their systems involved in repairing damages and/or
recycling inactivated biomolecules. Among the damage repair systems, an increase
in the level of chaperone and protein damage repair enzyme has been reported in
relation to alkalinization [148, 185]. Many intracellular macromolecules that are
vital for life are labile at high pH. The stability and activity of DNA, RNA, proteins,
lipids, etc. can be severely affected by prolongated exposure to high pH. In general,
it has been known that when cells are exposed to stress, the repair systems are often
activated to mend problems suffered by the stress. Here, it may be relevant to
mention the formation of isoaspartate and the associated repair system. Isoaspartate
is an isomer of aspartic acid formed through the nucleophile attack of the γ-carbon in
asparagine or aspartic acid residue side chains which forms a succinimide intermediate as illustrated in Fig. 11. The formation of isoaspartate affects the function
and stability of many proteins [186–188]. In addition, the reaction can lead to
deamidation of asparagine and formation of D-amino acids [189, 190]. If this
damage remains uncorrected, the protein cannot properly perform its task. Thus, it
is necessary that such protein damages must be repaired to maintain optimal cellular
activities or the damaged protein should be degraded and removed. Cells produce
L-isoaspartyl protein carboxyl methyltransferase (PCM), an enzyme which identifies
and repairs such protein damages [191]. PCM encoding gene is widely distributed
among unicellular and multicellular organisms [192], and in bacteria, it is linked to
long-term stress survival [193]. High pH is known to aggravate isoaspartate
Challenges and Adaptations of Life in Alkaline Habitats
113
+
/H
+ antiporter,
squalene, SCWPs, etc. increases [21, 102, 106, 128, 130, 148]. As aforementioned,
these biomolecules play a significant role in the pH homeostasis of alkaliphiles, and
hence, the upregulations of these biomolecules contribute to mitigate further increase
in cytoplasmic pH. For instance, an increased level of ATP synthase expression
results in pumping more H
+ to the cytoplasm which eases the cytoplasmic pH rise,
while accumulation of squalene effectively limits H
+ leakage and OH
À ingress. In
some organisms, cytoplasmic alkalinization is accompanied by metabolic acid
production [102] which alleviates the cytoplasmic pH rise and protects the cell
from the subsequent demise. In fact, many alkaliphiles are known producing organic
acids and even reduce the culture pH significantly [56, 105].
Compensating Loss Due to Denaturation With the rise in cytoplasmic pH, the
activity and integrity of intracellular biomolecules deteriorate. To compensate this
loss, cells increase the production level of pH labile biomolecules. For example, as
translation slows down and mRNAs are not stable at elevated pH, cells increase the
level of mRNA to maintain the necessary level of protein synthesis [183, 184].
3.4.2 Activating Protein Damage Repair and Degradation Systems
The cells also use another strategy to maintain the necessary level of functional
biomolecules, repairing the damage incurred by cytoplasmic alkalinization. Thus, it
is expected that the cells activate their systems involved in repairing damages and/or
recycling inactivated biomolecules. Among the damage repair systems, an increase
in the level of chaperone and protein damage repair enzyme has been reported in
relation to alkalinization [148, 185]. Many intracellular macromolecules that are
vital for life are labile at high pH. The stability and activity of DNA, RNA, proteins,
lipids, etc. can be severely affected by prolongated exposure to high pH. In general,
it has been known that when cells are exposed to stress, the repair systems are often
activated to mend problems suffered by the stress. Here, it may be relevant to
mention the formation of isoaspartate and the associated repair system. Isoaspartate
is an isomer of aspartic acid formed through the nucleophile attack of the γ-carbon in
asparagine or aspartic acid residue side chains which forms a succinimide intermediate as illustrated in Fig. 11. The formation of isoaspartate affects the function
and stability of many proteins [186–188]. In addition, the reaction can lead to
deamidation of asparagine and formation of D-amino acids [189, 190]. If this
damage remains uncorrected, the protein cannot properly perform its task. Thus, it
is necessary that such protein damages must be repaired to maintain optimal cellular
activities or the damaged protein should be degraded and removed. Cells produce
L-isoaspartyl protein carboxyl methyltransferase (PCM), an enzyme which identifies
and repairs such protein damages [191]. PCM encoding gene is widely distributed
among unicellular and multicellular organisms [192], and in bacteria, it is linked to
long-term stress survival [193]. High pH is known to aggravate isoaspartate
Challenges and Adaptations of Life in Alkaline Habitats
113