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Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria.

Kouji Uda1, Rie Nishimura2, Yuexuan Li2

  • 1Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780-8520, Japan. k-uda@kochi-u.ac.jp.

Journal of Molecular Evolution
|January 17, 2025
PubMed
Summary

Bacterial serine racemase (SerR) homologs, unlike widespread animal forms, show diverse enzymatic activities including arginine racemase. This suggests independent evolution of substrate specificity from a common ancestor, driven by key amino acid residues.

Keywords:
d-amino acidArginine racemaseAspartate racemaseSerine racemase

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Area of Science:

  • Biochemistry and Molecular Biology
  • Evolutionary Biology
  • Enzymology

Background:

  • Amino acid racemases interconvert L- and D-amino acids, crucial for cellular homeostasis.
  • Serine racemase (SerR) is primarily found in animals, with bacterial homologs recently identified but poorly understood.
  • The evolutionary distribution and functional roles of bacterial SerR homologs remain largely unexplored.

Purpose of the Study:

  • To investigate the evolutionary origins and functional diversity of bacterial serine racemase (SerR) homologs.
  • To characterize the enzymatic activities of cloned SerR homologs from diverse bacterial species.
  • To elucidate the molecular basis for substrate specificity and catalytic activity in SerR homologs.

Main Methods:

  • Cloned and expressed 20 SerR homologous genes from 13 bacterial species across five phyla.
  • Characterized enzymatic activities, including serine dehydratase and racemase activities for various amino acids.
  • Performed phylogenetic analysis, amino acid sequence alignment, and site-directed mutagenesis.

Main Results:

  • Six bacterial SerR homologs exhibited serine dehydratase activity.
  • The remaining SerR homologs displayed racemase activity towards serine, aspartate, asparagine, or arginine.
  • Several bacterial SerR homologs showed significant arginine racemase activity, with specific kinetic parameters (Km, kcat) determined.
  • Phylogenetic analysis indicated a common ancestral gene for bacterial and eukaryotic SerR homologs.
  • Residues near the substrate-binding site (positions 146-148) were identified as critical for substrate specificity and/or catalytic activity.

Conclusions:

  • Bacterial and eukaryotic SerR homologs share a common evolutionary origin.
  • Substrate specificity in SerR homologs has evolved independently multiple times.
  • Specific amino acid residues play a key role in determining the functional diversification of SerR homologs.