(GH 10) share a similar catalytic pocket as well as identical catalytic residues (a pair
of Glu). How these enzymes are able to ionize the catalytic residues in this wide
range of pH and mediate the biocatalysis is fascinating.
The pH profile of enzymes such as glycosyl hydrolases is determined by the
catalytic residues pKa values [209, 218, 219] which in turn are dependent on the
microenvironment surrounding the catalytic residue. Thus, the nature of amino acids
in the active site region plays a significant role in shaping the pH-activity profile of
the enzymes. In general, amino acids with positive charges and hydrogen bonds
lower pKa values, while carboxyl groups can increase or decrease the pKa values
based on the electrostatic interaction between residues [220]. Thus, certain amino
acids in the active site vicinity determine the pKa values by altering the active site
electrostatic and dynamic aspects [221] through direct or indirect interaction with the
catalytic residues. This kind of key residues, at least partially, determines the
pH-dependent activities of enzymes [222], and mutational studies on such residues
often shift the mutated enzyme pH-activity profile [223–225].
3.6 Adaptation to Low Nutrient Bioavailability
Nutrient bioavailability is a less studied challenge in high pH habitats. pH affects the
availability of certain nutrients by determining its state (e.g., solubility), reaction
with other substances, stability, etc. For instance, water in soda lakes is saturated
with CO 2 that forms HCO 3
À /CO 3
2À which interacts with and precipitates divalent
metal ions, making it less bioavailable. Thus, it is necessary for alkaliphiles to
develop mechanisms that circumvent the problems related to the poor bioavailability
of such nutrients. This can be achieved by deploying efficient retrieving systems for
deficient nutrients or decreasing dependency on poorly available nutrients. In line
with this, purification and characterization of some alkaline active extracellular
enzymes revealed that the enzymes evolved some adaptive features including high
affinity to metal cofactors [226] or became less dependent on it [227]. In fact, these
properties are among the reasons why enzymes of alkaliphiles are desirable in
detergent applications, resistant to the detergent chelator’s effect.
Alkaliphiles are known to have efficient system of capturing and translocating
scarce metal ions to the cytoplasm. One of the relatively well-studied scarce metals is
iron. Iron is important in ATP production, and it is a crucial cofactor for enzymes
involved in a variety of metabolic processes, and hence, it is essential for almost all
organisms. Although it is one of the most abundant elements in nature, it is not
readily available. Therefore, organisms employ different strategies to secure enough
iron from their surroundings. As the solubility of iron decreases with increasing pH,
it is vital for alkaliphiles to evolve a means to acquire iron. At alkaline conditions,
iron exists in ferric state (Fe
+3 ) which reacts and forms the poorly soluble Fe(OH) 3 .
Thus, in alkaline environments, the bioavailability of iron is far below the requirement for living cells. At pH 10, the concentration of bioavailable iron is estimated to
be approximately 10
À23 M [228], which is much lower than the 10
À18 M level at
Challenges and Adaptations of Life in Alkaline Habitats
117
of Glu). How these enzymes are able to ionize the catalytic residues in this wide
range of pH and mediate the biocatalysis is fascinating.
The pH profile of enzymes such as glycosyl hydrolases is determined by the
catalytic residues pKa values [209, 218, 219] which in turn are dependent on the
microenvironment surrounding the catalytic residue. Thus, the nature of amino acids
in the active site region plays a significant role in shaping the pH-activity profile of
the enzymes. In general, amino acids with positive charges and hydrogen bonds
lower pKa values, while carboxyl groups can increase or decrease the pKa values
based on the electrostatic interaction between residues [220]. Thus, certain amino
acids in the active site vicinity determine the pKa values by altering the active site
electrostatic and dynamic aspects [221] through direct or indirect interaction with the
catalytic residues. This kind of key residues, at least partially, determines the
pH-dependent activities of enzymes [222], and mutational studies on such residues
often shift the mutated enzyme pH-activity profile [223–225].
3.6 Adaptation to Low Nutrient Bioavailability
Nutrient bioavailability is a less studied challenge in high pH habitats. pH affects the
availability of certain nutrients by determining its state (e.g., solubility), reaction
with other substances, stability, etc. For instance, water in soda lakes is saturated
with CO 2 that forms HCO 3
À /CO 3
2À which interacts with and precipitates divalent
metal ions, making it less bioavailable. Thus, it is necessary for alkaliphiles to
develop mechanisms that circumvent the problems related to the poor bioavailability
of such nutrients. This can be achieved by deploying efficient retrieving systems for
deficient nutrients or decreasing dependency on poorly available nutrients. In line
with this, purification and characterization of some alkaline active extracellular
enzymes revealed that the enzymes evolved some adaptive features including high
affinity to metal cofactors [226] or became less dependent on it [227]. In fact, these
properties are among the reasons why enzymes of alkaliphiles are desirable in
detergent applications, resistant to the detergent chelator’s effect.
Alkaliphiles are known to have efficient system of capturing and translocating
scarce metal ions to the cytoplasm. One of the relatively well-studied scarce metals is
iron. Iron is important in ATP production, and it is a crucial cofactor for enzymes
involved in a variety of metabolic processes, and hence, it is essential for almost all
organisms. Although it is one of the most abundant elements in nature, it is not
readily available. Therefore, organisms employ different strategies to secure enough
iron from their surroundings. As the solubility of iron decreases with increasing pH,
it is vital for alkaliphiles to evolve a means to acquire iron. At alkaline conditions,
iron exists in ferric state (Fe
+3 ) which reacts and forms the poorly soluble Fe(OH) 3 .
Thus, in alkaline environments, the bioavailability of iron is far below the requirement for living cells. At pH 10, the concentration of bioavailable iron is estimated to
be approximately 10
À23 M [228], which is much lower than the 10
À18 M level at
Challenges and Adaptations of Life in Alkaline Habitats
117