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Interplay between microbial d-amino acids and host d-amino acid oxidase modifies murine mucosal defence and gut microbiota

Nature Microbiology volume 1, Article number: 16125 (2016) Cite this article

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Abstract

L-Amino acids are the building blocks for proteins synthesized in ribosomes in all kingdoms of life, but d-amino acids (d-aa) have important non-ribosome-based functions1. Mammals synthesize d-Ser and d-Asp, primarily in the central nervous system, where d-Ser is critical for neurotransmission2. Bacteria synthesize a largely distinct set of d-aa, which become integral components of the cell wall and are also released as free d-aa3,4. However, the impact of free microbial d-aa on host physiology at the host–microbial interface has not been explored. Here, we show that the mouse intestine is rich in free d-aa that are derived from the microbiota. Furthermore, the microbiota induces production of d-amino acid oxidase (DAO) by intestinal epithelial cells, including goblet cells, which secrete the enzyme into the lumen. Oxidative deamination of intestinal d-aa by DAO, which yields the antimicrobial product H2O2, protects the mucosal surface in the small intestine from the cholera pathogen. DAO also modifies the composition of the microbiota and is associated with microbial induction of intestinal sIgA. Collectively, these results identify d-aa and DAO as previously unrecognized mediators of microbe–host interplay and homeostasis on the epithelial surface of the small intestine.

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Figure 1: Free d-aa in the intestinal tract are produced by the gut microbiota.
Figure 2: Intestinal epithelial cells produce DAO in response to the microbiota.
Figure 3: DAO has antimicrobial activity in vitro and in vivo.
Figure 4: Genetic inactivation of DAO alters microbiota composition and secretory IgA levels.

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References

  1. Fujii, N. & Saito, T. Homochirality and life. Chem. Record 4, 267–278 (2004).

    Article  CAS  Google Scholar 

  2. Wolosker, H., Dumin, E., Balan, L. & Foltyn, V. N. D-amino acids in the brain: D-serine in neurotransmission and neurodegeneration. FEBS J. 275, 3514–3526 (2008).

    Article  CAS  Google Scholar 

  3. Lam, H. et al. D-amino acids govern stationary phase cell wall remodeling in bacteria. Science 325, 1552–1555 (2009).

    Article  CAS  Google Scholar 

  4. Cava, F., de Pedro, M. A., Lam, H., Davis, B. M. & Waldor, M. K. Distinct pathways for modification of the bacterial cell wall by non-canonical d-amino acids. EMBO J. 30, 3442–3453 (2011).

    Article  CAS  Google Scholar 

  5. Takeuchi, O. & Akira, S. Pattern recognition receptors and inflammation. Cell 140, 805–820 (2010).

    Article  CAS  Google Scholar 

  6. Janeway, C. A. Jr & Medzhitov, R. Innate immune recognition. Annu. Rev. Immunol. 20, 197–216 (2002).

    Article  CAS  Google Scholar 

  7. Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220–230 (2012).

    Article  CAS  Google Scholar 

  8. Miyoshi, Y. et al. Chiral amino acid analysis of Japanese traditional Kurozu and the developmental changes during earthenware jar fermentation processes. J. Chromatogr. B 966, 187–192 (2014).

    Article  CAS  Google Scholar 

  9. Ohide, H., Miyoshi, Y., Maruyama, R., Hamase, K. & Konno, R. D-amino acid metabolism in mammals: biosynthesis, degradation and analytical aspects of the metabolic study. J. Chromatogr. B 879, 3162–3168 (2011).

    Article  CAS  Google Scholar 

  10. Pollegioni, L., Piubelli, L., Sacchi, S., Pilone, M. S. & Molla, G. Physiological functions of d-amino acid oxidases: from yeast to humans. Cell. Mol. Life Sci. 64, 1373–1394 (2007).

    Article  CAS  Google Scholar 

  11. Sasabe, J. et al. D-amino acid oxidase controls motoneuron degeneration through d-serine. Proc. Natl Acad. Sci. USA 109, 627–632 (2012).

    Article  CAS  Google Scholar 

  12. Akira, S., Uematsu, S. & Takeuchi, O. Pathogen recognition and innate immunity. Cell 124, 783–801 (2006).

    Article  CAS  Google Scholar 

  13. Konno, R. & Yasumura, Y. Mouse mutant deficient in d-amino acid oxidase activity. Genetics 103, 277–285 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Espey, M. G. Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota. Free Rad. Biol. Med. 55, 130–140 (2013).

    Article  CAS  Google Scholar 

  15. Nathan, C. & Cunningham-Bussel, A. Beyond oxidative stress: an immunologist's guide to reactive oxygen species. Nature Rev. Immunol. 13, 349–361 (2013).

    Article  CAS  Google Scholar 

  16. Espaillat, A. et al. Structural basis for the broad specificity of a new family of amino-acid racemases. Acta Crystallogr. D 70, 79–90 (2014).

    Article  CAS  Google Scholar 

  17. Wang, H. et al. Catalases promote resistance of oxidative stress in Vibrio cholerae. PLoS ONE 7, e53383 (2012).

    Article  CAS  Google Scholar 

  18. Tuinema, B. R., Reid-Yu, S. A. & Coombes, B. K. Salmonella evades d-amino acid oxidase to promote infection in neutrophils. mBio 5, e01886-14 (2014).

    Article  Google Scholar 

  19. Nakamura, H., Fang, J. & Maeda, H. Protective role of d-amino acid oxidase against Staphylococcus aureus infection. Infect. Immun. 80, 1546–1553 (2012).

    Article  CAS  Google Scholar 

  20. Serata, M., Iino, T., Yasuda, E. & Sako, T. Roles of thioredoxin and thioredoxin reductase in the resistance to oxidative stress in Lactobacillus casei. Microbiology 158, 953–962 (2012).

    Article  CAS  Google Scholar 

  21. Pridmore, R. D. et al. The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc. Natl Acad. Sci. USA 101, 2512–2517 (2004).

    Article  CAS  Google Scholar 

  22. Van der Kaaij, H., Desiere, F., Mollet, B. & Germond, J. E. L-alanine auxotrophy of Lactobacillus johnsonii as demonstrated by physiological, genomic, and gene complementation approaches. Appl. Environ. Microbiol. 70, 1869–1873 (2004).

    Article  CAS  Google Scholar 

  23. Langille, M. G. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnol. 31, 814–821 (2013).

    Article  CAS  Google Scholar 

  24. Abubucker, S. et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput. Biol. 8, e1002358 (2012).

    Article  CAS  Google Scholar 

  25. Fagarasan, S. Evolution, development, mechanism and function of IgA in the gut. Curr. Opin. Immunol. 20, 170–177 (2008).

    Article  CAS  Google Scholar 

  26. Palm, N. W. et al. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 158, 1000–1010 (2014).

    Article  CAS  Google Scholar 

  27. Vaishnava, S. et al. The antibacterial lectin RegIIIγ promotes the spatial segregation of microbiota and host in the intestine. Science 334, 255–258 (2011).

    Article  CAS  Google Scholar 

  28. Zelante, T. et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 39, 372–385 (2013).

    Article  CAS  Google Scholar 

  29. Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).

    Article  Google Scholar 

  30. Roche, J. K. Isolation of a purified epithelial cell population from human colon. Methods Mol. Med. 50, 15–20 (2001).

    CAS  PubMed  Google Scholar 

  31. Hamase, K. et al. Simultaneous determination of hydrophilic amino acid enantiomers in mammalian tissues and physiological fluids applying a fully automated micro-two-dimensional high-performance liquid chromatographic concept. J. Chromatogr. A 1217, 1056–1062 (2010).

    Article  CAS  Google Scholar 

  32. Heidelberg, J. F. et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406, 477–483 (2000).

    Article  CAS  Google Scholar 

  33. Donnenberg, M. S. & Kaper, J. B. Construction of an eae deletion mutant of enteropathogenic Escherichia coli by using a positive-selection suicide vector. Infect. Immun. 59, 4310–4317 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. Wollert, T. et al. Extending the host range of Listeria monocytogenes by rational protein design. Cell 129, 891–902 (2007).

    Article  CAS  Google Scholar 

  35. Fujisawa, T., Benno, Y., Yaeshima, T. & Mitsuoka, T. Taxonomic study of the Lactobacillus acidophilus group, with recognition of Lactobacillus gallinarum sp. nov. and Lactobacillus johnsonii sp. nov. and synonymy of Lactobacillus acidophilus group A3 (Johnson et al. 1980) with the type strain of Lactobacillus amylovorus (Nakamura 1981). Int. J. System. Bacteriol. 42, 487–491 (1992).

    Article  CAS  Google Scholar 

  36. Perna, N. T. et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529–533 (2001).

    Article  CAS  Google Scholar 

  37. Makino, K. et al. Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae. Lancet 361, 743–749 (2003).

    Article  CAS  Google Scholar 

  38. Schlievert, P. M. & Blomster, D. A. Production of staphylococcal pyrogenic exotoxin type C: influence of physical and chemical factors. J. Infect. Dis. 147, 236–242 (1983).

    Article  CAS  Google Scholar 

  39. Holloway, B. W., Krishnapillai, V. & Morgan, A. F. Chromosomal genetics of Pseudomonas. Microbiol. Rev. 43, 73–102 (1979).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Nygren, E., Li, B. L., Holmgren, J. & Attridge, S. R. Establishment of an adult mouse model for direct evaluation of the efficacy of vaccines against Vibrio cholerae. Infect. Immun. 77, 3475–3484 (2009).

    Article  CAS  Google Scholar 

  41. Angelichio, M. J., Spector, J., Waldor, M. K. & Camilli, A. Vibrio cholerae intestinal population dynamics in the suckling mouse model of infection. Infect. Immun. 67, 3733–3739 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Herlemann, D. P. et al. Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea. ISME J. 5, 1571–1579 (2011).

    Article  CAS  Google Scholar 

  43. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335–336 (2010).

    Article  CAS  Google Scholar 

  44. McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610–618 (2012).

    Article  CAS  Google Scholar 

  45. Bokulich, N. A. et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nature Methods 10, 57–59 (2013).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors thank M. Nakane (Shiseido) for technical support with 2D-HPLC, L. Comstock for help with anaerobic cultures, R. Konno for providing DAOG181R mice, Waldor laboratory colleagues and M. Silverman for their comments on the manuscript, Q. Wang for help creating the ΔoxyR strain, L. Bry for germ-free mice, G. Abu-Ali/Huttenhower Group for assistance with LEfSe and 16S metagenomic analysis and S. Aiso for support. This work was supported by the Howard Hughes Medical Institute (M.K.W.), NIH grant no. R37 AI-042347 (M.K.W.) and the Moritani Scholarship Foundation (J.S.).

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Authors and Affiliations

  1. Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Jumpei Sasabe, Ting Zhang, Brigid M. Davis & Matthew K. Waldor

  2. Howard Hughes Medical Institute, Boston, 02115, Massachusetts, USA

    Jumpei Sasabe, Ting Zhang, Brigid M. Davis & Matthew K. Waldor

  3. Keio University School of Medicine, Shinjuku-ku, 160-8582, Tokyo, Japan

    Jumpei Sasabe

  4. Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan

    Yurika Miyoshi & Kenji Hamase

  5. Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Seth Rakoff-Nahoum

  6. Shiseido Co., Ltd, Minato-ku, 105-0021, Tokyo, Japan

    Masashi Mita

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Contributions

J.S. and M.K.W. conceived and designed the study. J.S. carried out histological experiments, biochemical analyses, microbiological studies, sequence analyses, animal experiments with T.Z., and figure preparation. Y.M. and K.H. performed HPLC quantifications of chiral amino acids with technical support by M.M. S.R.-N. and B.M.D. provided scientific advice. M.K.W. supervised the experiments and directed the analysis. J.S., S.R.-N., B.M.D. and M.K.W. wrote the manuscript.

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Correspondence to Matthew K. Waldor.

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The authors declare no competing financial interests.

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Supplementary Methods, Supplementary Figures 1–13, Supplementary References (PDF 4482 kb)

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Sasabe, J., Miyoshi, Y., Rakoff-Nahoum, S. et al. Interplay between microbial d-amino acids and host d-amino acid oxidase modifies murine mucosal defence and gut microbiota. Nat Microbiol 1, 16125 (2016). https://doi.org/10.1038/nmicrobiol.2016.125

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