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Distribution and evolution of the serine/aspartate racemase family in invertebrates

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Abstract

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.

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Abbreviations

AspR:

Aspartate racemase

DAR1:

Aplysia californica d-amino acid racemase 1

EST:

Expressed sequence tag

Got1l1:

Glutamic-oxaloacetic transaminase 1-like 1

OAS:

O-acetylserine sulfhydrylase

PLP:

Pyridoxal 5′-phosphate

RPKM:

Reads per kilobase per million reads

RPKMm:

Reads per kilobase per million mapped reads

SerR:

Serine racemase

SRA:

Sequence read archive

RTPCR:

Reverse transcription polymerase chain reaction

References

  • Abe H, Yoshikawa N, Sarower MG, Okada S (2005) Physiological function and metabolism of free d-alanine in aquatic animals. Biol Pharm Bull 28(9):1571–1577

    Article  CAS  PubMed  Google Scholar 

  • Abe K, Takahashi S, Muroki Y, Kera Y, Yamada RH (2006) Cloning and expression of the pyridoxal 5′-phosphate-dependent aspartate racemase gene from the bivalve mollusk Scapharca broughtonii and characterization of the recombinant enzyme. J Biochem 139(2):235–244. doi:10.1093/jb/mvj028

    Article  CAS  PubMed  Google Scholar 

  • Campbell LI, Rota-Stabelli O, Edgecombe GD, Marchioro T, Longhorn SJ, Telford MJ, Philippe H, Rebecchi L, Peterson KJ, Pisani D (2011) MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda. Proc Natl Acad Sci 108(38):15920–15924

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Corrigan JJ, Srinivasan N (1966) The occurrence of certain d-amino acids in insects*. Biochemistry 5(4):1185–1190

    Article  CAS  PubMed  Google Scholar 

  • D’Aniello A (2007) d-Aspartic acid: an endogenous amino acid with an important neuroendocrine role. Brain Res Rev 53(2):215–234. doi:10.1016/j.brainresrev.2006.08.005

    Article  PubMed  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Foltyn VN, Bendikov I, De Miranda J, Panizzutti R, Dumin E, Shleper M, Li P, Toney MD, Kartvelishvily E, Wolosker H (2005) Serine racemase modulates intracellular d-serine levels through an alpha, beta-elimination activity. J Biol Chem 280(3):1754–1763. doi:10.1074/jbc.M405726200

    Article  CAS  PubMed  Google Scholar 

  • Fujitani Y, Nakajima N, Ishihara K, Oikawa T, Ito K, Sugimoto M (2006) Molecular and biochemical characterization of a serine racemase from Arabidopsis thaliana. Phytochemistry 67(7):668–674. doi:10.1016/j.phytochem.2006.01.003

    Article  CAS  PubMed  Google Scholar 

  • Fujitani Y, Horiuchi T, Ito K, Sugimoto M (2007) Serine racemases from barley, Hordeum vulgare L., and other plant species represent a distinct eukaryotic group: gene cloning and recombinant protein characterization. Phytochemistry 68(11):1530–1536. doi:10.1016/j.phytochem.2007.03.040

    Article  CAS  PubMed  Google Scholar 

  • Gogami Y, Kobayashi A, Ikeuchi T, Oikawa T (2010) Site-directed mutagenesis of rice serine racemase: evidence that Glu219 and Asp225 mediate the effects of Mg2+ on the activity. Chem Biodivers 7(6):1579–1590. doi:10.1002/cbdv.200900257

    Article  CAS  PubMed  Google Scholar 

  • Goto M, Yamauchi T, Kamiya N, Miyahara I, Yoshimura T, Mihara H, Kurihara T, Hirotsu K, Esaki N (2009) Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe. J Biol Chem 284(38):25944–25952. doi:10.1074/jbc.M109.010470

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Hamase K, Morikawa A, Zaitsu K (2002) d-Amino acids in mammals and their diagnostic value. J Chromatogr B 781(1):73–91

    Article  CAS  Google Scholar 

  • Hashimoto A, Nishikawa T, Oka T, Takahashi K, Hayashi T (1992) Determination of free amino acid enantiomers in rat brain and serum by high-performance liquid chromatography after derivatization with N-tert.-butyloxycarbonyl-l-cysteine and o-phthaldialdehyde. J Chromatogr B Biomed Sci Appl 582(1):41–48

    Article  CAS  Google Scholar 

  • Hoffman HE, Jiraskova J, Ingr M, Zvelebil M, Konvalinka J (2009) Recombinant human serine racemase: enzymologic characterization and comparison with its mouse ortholog. Protein Expr Purif 63(1):62–67. doi:10.1016/j.pep.2008.09.003

    Article  CAS  PubMed  Google Scholar 

  • Hoover DM, Lubkowski J (2002) DNAWorks: an automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res 30(10):e43–e43

    Article  PubMed Central  PubMed  Google Scholar 

  • Horio M, Ishima T, Fujita Y, Inoue R, Mori H, Hashimoto K (2013) Decreased levels of free d-aspartic acid in the forebrain of serine racemase (Srr) knock-out mice. Neurochem Int 62(6):843–847. doi:10.1016/j.neuint.2013.02.015

    Article  CAS  PubMed  Google Scholar 

  • Ito T, Murase H, Maekawa M, Goto M, Hayashi S, Saito H, Maki M, Hemmi H, Yoshimura T (2012) Metal ion dependency of serine racemase from Dictyostelium discoideum. Amino Acids 43(4):1567–1576. doi:10.1007/s00726-012-1232-z

    Article  CAS  PubMed  Google Scholar 

  • Ito T, Maekawa M, Hayashi S, Goto M, Hemmi H, Yoshimura T (2013) Catalytic mechanism of serine racemase from Dictyostelium discoideum. Amino Acids 44(3):1073–1084. doi:10.1007/s00726-012-1442-4

    Article  CAS  PubMed  Google Scholar 

  • Jiraskova-Vanickova J, Ettrich R, Vorlova B, E Hoffman H, Lepsik M, Jansa P, Konvalinka J (2011) Inhibition of human serine racemase, an emerging target for medicinal chemistry. Current Drug Targets 12(7):1037–1055

  • Katane M, Homma H (2011) d-Aspartate–an important bioactive substance in mammals: a review from an analytical and biological point of view. J Chromatogr B Anal Technol Biomed Life Sci 879(29):3108–3121. doi:10.1016/j.jchromb.2011.03.062

    Article  CAS  Google Scholar 

  • Kim PM, Duan X, Huang AS, Liu CY, Ming GL, Song H, Snyder SH (2010) Aspartate racemase, generating neuronal d-aspartate, regulates adult neurogenesis. Proc Natl Acad Sci USA 107(7):3175–3179. doi:10.1073/pnas.0914706107

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Maezawa T, Tanaka H, Nakagawa H, Ono M, Aoki M, Matsumoto M, Ishida T, Horiike K, Kobayashi K (2014) Planarian d-amino acid oxidase is involved in ovarian development during sexual induction. Mech Dev 132:69–78. doi:10.1016/j.mod.2013.12.003

    Article  CAS  PubMed  Google Scholar 

  • Matsuda S, Katane M, Maeda K, Kaneko Y, Saitoh Y, Miyamoto T, Sekine M, Homma H (2015) Biosynthesis of d-aspartate in mammals: the rat and human homologs of mouse aspartate racemase are not responsible for the biosynthesis of d-aspartate. Amino Acids. doi:10.1007/s00726-015-1926-0

    PubMed  Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628

    Article  CAS  PubMed  Google Scholar 

  • Nylander JA, Wilgenbusch JC, Warren DL, Swofford DL (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24(4):581–583

    Article  CAS  PubMed  Google Scholar 

  • Ohnishi M, Saito M, Wakabayashi S, Ishizuka M, Nishimura K, Nagata Y, Kasai S (2008) Purification and characterization of serine racemase from a hyperthermophilic archaeon, Pyrobaculum islandicum. J Bacteriol 190(4):1359–1365. doi:10.1128/JB.01184-07

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Okuma E, Fujita E, Amano H, Noda H, Abe H (1995) Distribution of free d-amino acids in the tissues of Crustaceans. Fish Sci 61(1):157–160

    CAS  Google Scholar 

  • Okuma E, Watanabe K, Abe H (1998) Distribution of free d-amino acids in Bivalve Mollusks and the effects of physiological conditions on the levels of d-and l-alanine in the tissues of the hard clam Meretrix lusoria. Fish Sci 64(4):606–611

    Article  CAS  Google Scholar 

  • Preston R (1987) Occurrence of d-amino acids in higher organisms: a survey of the distribution of d-amino acids in marine invertebrates. Comp Biochem Physiol Part B Comp Biochem 87(1):55–62

    Article  Google Scholar 

  • Radkov AD, Moe LA (2014) Bacterial synthesis of d-amino acids. Appl Microbiol Biotechnol 98(12):5363–5374. doi:10.1007/s00253-014-5726-3

    Article  CAS  PubMed  Google Scholar 

  • Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572–1574

    Article  CAS  PubMed  Google Scholar 

  • Rosenberg H, Ennor A (1961) The occurrence of free d-serine in the earthworm. Biochem J 79(2):424

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Saitoh Y, Katane M, Kawata T, Maeda K, Sekine M, Furuchi T, Kobuna H, Sakamoto T, Inoue T, Arai H, Nakagawa Y, Homma H (2012) Spatiotemporal localization of d-amino acid oxidase and d-aspartate oxidases during development in Caenorhabditis elegans. Mol Cell Biol 32(10):1967–1983. doi:10.1128/MCB.06513-11

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Shibata K, Tarui A, Todoroki N, Kawamoto S, Takahashi S, Kera Y, R-h Yamada (2001) Occurrence of N-methyl-l-aspartate in bivalves and its distribution compared with that of N-methyl-d-aspartate and D, l-aspartate. Comp Biochem Physiol B Biochem Mol Biol 130(4):493–500

    Article  CAS  PubMed  Google Scholar 

  • Shibata K, Watanabe T, Yoshikawa H, Abe K, Takahashi S, Kera Y, Yamada RH (2003) Purification and characterization of aspartate racemase from the bivalve mollusk Scapharca broughtonii. Comp Biochem Physiol B Biochem Mol Biol 134(2):307–314

    Article  PubMed  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tanaka-Hayashi A, Hayashi S, Inoue R, Ito T, Konno K, Yoshida T, Watanabe M, Yoshimura T, Mori H (2015) Is d-aspartate produced by glutamic-oxaloacetic transaminase-1 like 1 (Got1l1): a putative aspartate racemase? Amino Acids 47(1):79–86. doi:10.1007/s00726-014-1847-3

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Uda K, Suzuki T (2007) A novel arginine kinase with substrate specificity towards d-arginine. Protein J 26(5):281–291

    Article  CAS  PubMed  Google Scholar 

  • Uo T, Ueda M, Nishiyama T, Yoshimura T, Esaki N (2001) Purification and characterization of alanine racemase from hepatopancreas of black-tiger prawn, Penaeus monodon. J Mol Catal B Enzym 12(1):137–144

    Article  CAS  Google Scholar 

  • Wang L, Ota N, Romanova EV, Sweedler JV (2011) A novel pyridoxal 5′-phosphate-dependent amino acid racemase in the Aplysia californica central nervous system. J Biol Chem 286(15):13765–13774. doi:10.1074/jbc.M110.178228

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wolosker H, Sheth KN, Takahashi M, Mothet J-P, Brady RO, Ferris CD, Snyder SH (1999) Purification of serine racemase: biosynthesis of the neuromodulator d-serine. Proc Natl Acad Sci 96(2):721–725

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Wolosker H, D’Aniello A, Snyder S (2000) d-aspartate disposition in neuronal and endocrine tissues: ontogeny, biosynthesis and release. Neuroscience 100(1):183–189

    Article  CAS  PubMed  Google Scholar 

  • Yamauchi T, Goto M, Wu HY, Uo T, Yoshimura T, Mihara H, Kurihara T, Miyahara I, Hirotsu K, Esaki N (2009) Serine racemase with catalytically active lysinoalanyl residue. J Biochem 145(4):421–424. doi:10.1093/jb/mvp010

    Article  CAS  PubMed  Google Scholar 

  • Yoshikawa N, Dhomae N, Takio K, Abe H (2002) Purification, properties, and partial amino acid sequences of alanine racemase from the muscle of the black tiger prawn Penaeus monodon. Comp Biochem Physiol B: Biochem Mol Biol 133(3):445–453

    Article  Google Scholar 

  • Yoshikawa N, Okada S, Abe H (2009) Molecular characterization of alanine racemase in the kuruma prawn Marsupenaeus japonicus. J Biochem 145(2):249–258. doi:10.1093/jb/mvn162

    Article  CAS  PubMed  Google Scholar 

  • Yoshikawa N, Ashida W, Hamase K, Abe H (2011) HPLC determination of the distribution of d-amino acids and effects of ecdysis on alanine racemase activity in kuruma prawn Marsupenaeus japonicus. J Chromatogr B Anal Technol Biomed Life Sci 879(29):3283–3288. doi:10.1016/j.jchromb.2011.04.026

    Article  CAS  Google Scholar 

  • Yuasa HJ, Takubo M, Takahashi A, Hasegawa T, Noma H, Suzuki T (2007) Evolution of vertebrate indoleamine 2, 3-dioxygenases. J Mol Evol 65(6):705–714

    Article  CAS  PubMed  Google Scholar 

  • Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H (2012) The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490(7418):49–54

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by a Grant-in-Aid for Scientific Research in Japan to KU (24770068 and 15K07152).

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Authors and Affiliations

  1. Laboratory of Biochemistry, Faculty of Science, Kochi University, Kochi, 780-8520, Japan

    Kouji Uda, Keita Abe, Yoko Dehara, Kiriko Mizobata, Natsumi Sogawa, Yuki Akagi & Mai Saigan

  2. Department of Plant and Soil Sciences, 311 Plant Science Building, University of Kentucky, Lexington, KY, 40546-0312, USA

    Kouji Uda, Atanas D. Radkov & Luke A. Moe

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  1. Kouji Uda
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  2. Keita Abe
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  3. Yoko Dehara
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Correspondence to Kouji Uda.

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Uda, K., Abe, K., Dehara, Y. et al. Distribution and evolution of the serine/aspartate racemase family in invertebrates. Amino Acids 48, 387–402 (2016). https://doi.org/10.1007/s00726-015-2092-0

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