Distribution and evolution of the serine/aspartate racemase family in invertebrates.
Free D-amino acids have been found in various invertebrate phyla, while amino acid racemase genes have been identified in few species. The purpose of this study is to elucidate the distribution, function, and evolution of amino acid racemases in invertebrate animals. We searched the GenBank databases, and found 11 homologous serine racemase genes from eight species in eight different invertebrate phyla. The cloned genes were identified based on their maximum activity as Acropora millepora (Cnidaria) serine racemase (SerR) and aspartate racemase (AspR), Caenorhabditis elegans (Nematoda) SerR, Capitella teleta (Annelida) SerR, Crassostrea gigas (Mollusca) SerR and AspR, Dugesia japonica (Platyhelminthes) SerR, Milnesium tardigradum (Tardigrada) SerR, Penaeus monodon (Arthropoda) SerR and AspR and Strongylocentrotus purpuratus (Echinodermata) AspR. We found that Acropora, Aplysia, Capitella, Crassostrea and Penaeus had two amino acid racemase paralogous genes and these paralogous genes have evolved independently by gene duplication at their recent ancestral species. The transcriptome analyses using available SRA data and enzyme kinetic data suggested that these paralogous genes are expressed in different tissues and have different functions in vivo. Phylogenetic analyses clearly indicated that animal SerR and AspR are not separated by their particular racemase functions and form a serine/aspartate racemase family cluster. Our results revealed that SerR and AspR are more widely distributed among invertebrates than previously known. Moreover, we propose that the triple serine loop motif at amino acid positions 150-152 may be responsible for the large aspartate racemase activity and the AspR evolution from SerR.
Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi, 780-8520, Japan. k-uda@kochi-u.ac.jp.|Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY, 40546-0312, USA. k-uda@kochi-u.ac.jp.
Kouji
K
Uda
Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi, 780-8520, Japan.
Keita
K
Abe
Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi, 780-8520, Japan.
Yoko
Y
Dehara
Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi, 780-8520, Japan.
Kiriko
K
Mizobata
Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi, 780-8520, Japan.
Natsumi
N
Sogawa
Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi, 780-8520, Japan.
Yuki
Y
Akagi
Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi, 780-8520, Japan.
Mai
M
Saigan
Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY, 40546-0312, USA.
Atanas D
AD
Radkov
Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY, 40546-0312, USA.
Luke A
LA
Moe
D000591:Amino Acid Isomerases / Q000235:genetics* / Q000378:metabolism; D000595:Amino Acid Sequence; D000818:Animals; D001224:Aspartic Acid / Q000378:metabolism*; D001483:Base Sequence; D003001:Cloning, Molecular; D004926:Escherichia coli / Q000235:genetics; D007448:Invertebrates / Q000201:enzymology* / Q000235:genetics; D010802:Phylogeny; D011732:Pyridoxal Phosphate / Q000378:metabolism; D019998:Racemases and Epimerases / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012694:Serine / Q000378:metabolism*; D000099300:Serine Racemase
D000591:Amino Acid Isomerases; D001224:Aspartic Acid; D011732:Pyridoxal Phosphate; D019998:Racemases and Epimerases; D012694:Serine; D000099300:Serine Racemase; C019749:aspartate racemase
Aspartate racemase; D-Amino acid; D-Asp; D-Ser; Serine racemase