It is obvious that the data on high pH adaptations of alkaliphiles is still trickling
in. However, it seems that far little is done in some areas. One of such cases is protein
synthesis, which is one of the most crucial life processes vital for survival and
growth. Several factors can influence this fascinating process, and pH is one of them.
The optimum pH (pH 8.2–8.5) for cell-free protein translation systems of alkaliphilic
origin have been reported to be only 0.5 pH units higher than that of neutralophiles
[202]. However, the cytoplasmic pH of actively growing alkaliphiles can be much
higher (>pH 10) such as when cells are grown close to pH 13, and hence, one
expects lower rate of protein synthesis. On the other hand, alkaliphiles in general are
known to grow faster than non-alkaliphiles [177], which suggest that alkaliphiles
may have a very efficient protein synthesis at elevated pH. However, there is no
available information how extreme alkaliphiles evolved their protein synthesis
apparatus. Similarly, the adaptation of extreme alkaliphiles that shield their DNA
and RNA from the effect of high pH is unknown. Since the pKa of guanine (G) and
thymine (T) is in the range of pH 9–10 [203], above pH 10, these residues get
deprotonated and remain as negatively charged conjugate bases. This can break the
hydrogen bonding between the two strands of the DNA helix and result in denaturation of DNA. This makes the DNA strand prone for damage and disrupts the
replication and transcription processes. It has been reported that alkali stressed
E. coli cells induce recA-independent DNA damage repair system [204], which
suggests the possible involvement of the repair system in high pH adaptation of
alkaliphiles. But the repair system is not enough by itself. There should be mechanism(s) that protect these vital macromolecules from high pH hostility.
3.5 Production of Extracellular Biomolecules Which Are
Operationally Stable in Alkaline Milieu
Cells release products to their immediate environment to harvest nutrients, defense/
competitional purposes, for communication, etc. At least theoretically, these products are evolved to work optimally in the host environment. Thus, products secreted
by alkaliphiles are expected to be operationally stable in their high pH habitats.
Among such products, enzymes have attracted a great deal of attention. Studies on
alkaline active enzymes are done to understand the molecular mechanisms behind
their structural and functional adaptation to high pH environment. Comparative
sequence analysis and mutational studies revealed that alkaline-active enzymes
exhibit reduced alkali susceptible residues and tend to increase alkali tolerant
residues, especially in their exposed surfaces. The ionization state of residues such
as Asp, Glu, His, Lys, and Arg side chains is determined by the pH of the
environment. Thus, the distribution and frequency of these ionizable residues partly
determine the pH adaptation of proteins. In line with this, Lys, Arg, Asn, His, Glu,
and Asp residue content has been studied in relation to high pH adaptation [205–
209]. These studies revealed the tendency of alkaline-active enzymes to have more
Arg, His, and Gln in their structures. Since Arg has a higher pKa than Lys,
Challenges and Adaptations of Life in Alkaline Habitats
115
in. However, it seems that far little is done in some areas. One of such cases is protein
synthesis, which is one of the most crucial life processes vital for survival and
growth. Several factors can influence this fascinating process, and pH is one of them.
The optimum pH (pH 8.2–8.5) for cell-free protein translation systems of alkaliphilic
origin have been reported to be only 0.5 pH units higher than that of neutralophiles
[202]. However, the cytoplasmic pH of actively growing alkaliphiles can be much
higher (>pH 10) such as when cells are grown close to pH 13, and hence, one
expects lower rate of protein synthesis. On the other hand, alkaliphiles in general are
known to grow faster than non-alkaliphiles [177], which suggest that alkaliphiles
may have a very efficient protein synthesis at elevated pH. However, there is no
available information how extreme alkaliphiles evolved their protein synthesis
apparatus. Similarly, the adaptation of extreme alkaliphiles that shield their DNA
and RNA from the effect of high pH is unknown. Since the pKa of guanine (G) and
thymine (T) is in the range of pH 9–10 [203], above pH 10, these residues get
deprotonated and remain as negatively charged conjugate bases. This can break the
hydrogen bonding between the two strands of the DNA helix and result in denaturation of DNA. This makes the DNA strand prone for damage and disrupts the
replication and transcription processes. It has been reported that alkali stressed
E. coli cells induce recA-independent DNA damage repair system [204], which
suggests the possible involvement of the repair system in high pH adaptation of
alkaliphiles. But the repair system is not enough by itself. There should be mechanism(s) that protect these vital macromolecules from high pH hostility.
3.5 Production of Extracellular Biomolecules Which Are
Operationally Stable in Alkaline Milieu
Cells release products to their immediate environment to harvest nutrients, defense/
competitional purposes, for communication, etc. At least theoretically, these products are evolved to work optimally in the host environment. Thus, products secreted
by alkaliphiles are expected to be operationally stable in their high pH habitats.
Among such products, enzymes have attracted a great deal of attention. Studies on
alkaline active enzymes are done to understand the molecular mechanisms behind
their structural and functional adaptation to high pH environment. Comparative
sequence analysis and mutational studies revealed that alkaline-active enzymes
exhibit reduced alkali susceptible residues and tend to increase alkali tolerant
residues, especially in their exposed surfaces. The ionization state of residues such
as Asp, Glu, His, Lys, and Arg side chains is determined by the pH of the
environment. Thus, the distribution and frequency of these ionizable residues partly
determine the pH adaptation of proteins. In line with this, Lys, Arg, Asn, His, Glu,
and Asp residue content has been studied in relation to high pH adaptation [205–
209]. These studies revealed the tendency of alkaline-active enzymes to have more
Arg, His, and Gln in their structures. Since Arg has a higher pKa than Lys,
Challenges and Adaptations of Life in Alkaline Habitats
115