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Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment.

Suenaga H - Front Microbiol (2015)

Bottom Line: Enzymes are the basis of metabolism in all living organisms and, therefore, enzyme adaptation plays a crucial role in the adaptation of microorganisms.Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes.This perspective article presents a summary of targeted metagenomic approaches useful for this purpose.

View Article: PubMed Central - PubMed

Affiliation: Bioproduction Research Institute - National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba, Japan.

ABSTRACT
Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and, therefore, enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose.

No MeSH data available.


The relationship between activity and thermostability of purified metagenomic extradiol dioxygenase (EDO) enzymes. The size of each circle is proportional to the number of EDO enzymes in the group. The arrow indicates the proposed genetic evolutionary pathway. The thermostable ancestral groups, group 1 and 3, may have adaptively evolved toward the more active group 2 via group 5 and 6 by sacrificing unessential thermostability. EDO enzymes that acquired higher activities (group 2) were more frequently discovered in the retrieved enzyme collection.
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Figure 1: The relationship between activity and thermostability of purified metagenomic extradiol dioxygenase (EDO) enzymes. The size of each circle is proportional to the number of EDO enzymes in the group. The arrow indicates the proposed genetic evolutionary pathway. The thermostable ancestral groups, group 1 and 3, may have adaptively evolved toward the more active group 2 via group 5 and 6 by sacrificing unessential thermostability. EDO enzymes that acquired higher activities (group 2) were more frequently discovered in the retrieved enzyme collection.

Mentions: Extradiol dioxygenases (EDOs) are enzymes that play an important role in the catabolism of aromatic compounds (Sipilä et al., 2008; Brennerova et al., 2009), cleaving the aromatic ring of catechol compounds, which are common intermediates in the aerobic microbial degradation of natural and xenobiotic aromatic compounds (Furukawa et al., 2004). Based on the activity of EDO enzymes, 96,000 fosmid clones were screened, and subsequent sequencing of positive fosmids led to the identification of 43 novel EDO genes (Suenaga et al., 2007, 2009). Using combinations of single nucleotide polymorphisms (SNPs), a possible evolutionary lineage of the EDO genes was constructed (Figure 1) and suggested that these genes evolved from a common ancestor (group 1 and 3), then diverged through the accumulation of various nucleotide mutations. Furthermore, investigation of the kinetic properties and thermal stability of the purified EDO enzymes showed an apparent trade-off between activity and stability (Figure 1). Bloom et al. (2006) reported that cytochrome P450 BM3 mutants with higher stabilities were more likely to acquire new or improved functions through random mutagenesis. They concluded that protein stability promotes adaptive protein evolution. Similarly, in EDO enzymes, the most thermostable ancestral groups (group 1 and 3) may have evolved toward more active groups (group 2 through group 5 and 6) by sacrificing thermostability. Note that EDO enzymes that had acquired higher activities (group 2 and 5) were more frequently discovered in the retrieved EDO clones, likely reflecting the allele frequencies in the environment.


Targeted metagenomics unveils the molecular basis for adaptive evolution of enzymes to their environment.

Suenaga H - Front Microbiol (2015)

The relationship between activity and thermostability of purified metagenomic extradiol dioxygenase (EDO) enzymes. The size of each circle is proportional to the number of EDO enzymes in the group. The arrow indicates the proposed genetic evolutionary pathway. The thermostable ancestral groups, group 1 and 3, may have adaptively evolved toward the more active group 2 via group 5 and 6 by sacrificing unessential thermostability. EDO enzymes that acquired higher activities (group 2) were more frequently discovered in the retrieved enzyme collection.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585196&req=5

Figure 1: The relationship between activity and thermostability of purified metagenomic extradiol dioxygenase (EDO) enzymes. The size of each circle is proportional to the number of EDO enzymes in the group. The arrow indicates the proposed genetic evolutionary pathway. The thermostable ancestral groups, group 1 and 3, may have adaptively evolved toward the more active group 2 via group 5 and 6 by sacrificing unessential thermostability. EDO enzymes that acquired higher activities (group 2) were more frequently discovered in the retrieved enzyme collection.
Mentions: Extradiol dioxygenases (EDOs) are enzymes that play an important role in the catabolism of aromatic compounds (Sipilä et al., 2008; Brennerova et al., 2009), cleaving the aromatic ring of catechol compounds, which are common intermediates in the aerobic microbial degradation of natural and xenobiotic aromatic compounds (Furukawa et al., 2004). Based on the activity of EDO enzymes, 96,000 fosmid clones were screened, and subsequent sequencing of positive fosmids led to the identification of 43 novel EDO genes (Suenaga et al., 2007, 2009). Using combinations of single nucleotide polymorphisms (SNPs), a possible evolutionary lineage of the EDO genes was constructed (Figure 1) and suggested that these genes evolved from a common ancestor (group 1 and 3), then diverged through the accumulation of various nucleotide mutations. Furthermore, investigation of the kinetic properties and thermal stability of the purified EDO enzymes showed an apparent trade-off between activity and stability (Figure 1). Bloom et al. (2006) reported that cytochrome P450 BM3 mutants with higher stabilities were more likely to acquire new or improved functions through random mutagenesis. They concluded that protein stability promotes adaptive protein evolution. Similarly, in EDO enzymes, the most thermostable ancestral groups (group 1 and 3) may have evolved toward more active groups (group 2 through group 5 and 6) by sacrificing thermostability. Note that EDO enzymes that had acquired higher activities (group 2 and 5) were more frequently discovered in the retrieved EDO clones, likely reflecting the allele frequencies in the environment.

Bottom Line: Enzymes are the basis of metabolism in all living organisms and, therefore, enzyme adaptation plays a crucial role in the adaptation of microorganisms.Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes.This perspective article presents a summary of targeted metagenomic approaches useful for this purpose.

View Article: PubMed Central - PubMed

Affiliation: Bioproduction Research Institute - National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba, Japan.

ABSTRACT
Microorganisms have a wonderful ability to adapt rapidly to new or altered environmental conditions. Enzymes are the basis of metabolism in all living organisms and, therefore, enzyme adaptation plays a crucial role in the adaptation of microorganisms. Comparisons of homology and parallel beneficial mutations in an enzyme family provide valuable hints of how an enzyme adapted to an ecological system; consequently, a series of enzyme collections is required to investigate enzyme evolution. Targeted metagenomics is a promising tool for the construction of enzyme pools and for studying the adaptive evolution of enzymes. This perspective article presents a summary of targeted metagenomic approaches useful for this purpose.

No MeSH data available.