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An enzymatic pathway in the human gut microbiome that converts A to universal O type blood

Nature Microbiology volume 4, pages 1475–1485 (2019)Cite this article

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Abstract

Access to efficient enzymes that can convert A and B type red blood cells to ‘universal’ donor O would greatly increase the supply of blood for transfusions. Here we report the functional metagenomic screening of the human gut microbiome for enzymes that can remove the cognate A and B type sugar antigens. Among the genes encoded in our library of 19,500 expressed fosmids bearing gut bacterial DNA, we identify an enzyme pair from the obligate anaerobe Flavonifractor plautii that work in concert to efficiently convert the A antigen to the H antigen of O type blood, via a galactosamine intermediate. The X-ray structure of the N-acetylgalactosamine deacetylase reveals the active site and mechanism of the founding member of an esterase family. The galactosaminidase expands activities within the CAZy family GH36. Their ability to completely convert A to O of the same rhesus type at very low enzyme concentrations in whole blood will simplify their incorporation into blood transfusion practice, broadening blood supply.

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Fig. 1: Basic A, B and H antigens on RBCs.
Fig. 2: Overview of ORFs on the sequenced fosmids.
Fig. 3: Combinatorial activity of FpCBM32 and FpGH36 on A antigen substrate.
Fig. 4: Deacetylation pathway for A antigen cleavage.
Fig. 5: Crystal structure of FpGalNAc deacetylase.
Fig. 6: Validation of enzymatic blood type conversion.

Data availability

The datasets generated and/or analysed during this study are available from the corresponding author on reasonable request. Structure datasets generated during the current study are available in the PDB repository under accession numbers 6N1A and 6N1B. The protein CspGH36 identified during the current study is deposited in GenBank under the accession code MK500922.

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Acknowledgements

We thank H. Brumer for the use of his Dionex high-performance liquid chromatography system, H.-M. Chen for the synthesis of Gal-α-MU and GalNAc-α-MU and T. Lowary for a set of α-GalNAc-containing oligosaccharide substrates. We acknowledge the participation of the Protein-Glycan Interaction Resource of the CFG (supporting grant R24 GM098791) and the National Center for Functional Glycomics at Beth Israel Deaconess Medical Center, Harvard Medical School (supporting grant P41 GM103694). We thank L. Worrall and N. Cavaney for collecting the X-ray diffraction data and the Canadian Light source for access. The infrastructure at the Centre for Blood Research is supported by the Canada Foundation for Innovation and the British Columbia Knowledge Development Fund. J.N.K. is a recipient of a Michael Smith Foundation for Health Research Scholar award. P.R. was supported by a Leopoldina-Postdoc-Fellowship from the Deutsche Akademie der Naturforscher Leopoldina. Financial support from the Canadian Institutes for Health Research (CIHR grant MOP-136940) is gratefully acknowledged by J.N.K. and S.G.W. H.M. is supported by a Canadian Blood Services-MITACS fellowship and an NSERC CREATE Nanomat scholarship.

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Author notes

  1. These authors contributed equally: Lyann Sim, Haisle Moon.

Authors and Affiliations

  1. Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada

    Peter Rahfeld, Lyann Sim & Stephen G. Withers

  2. Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada

    Peter Rahfeld, Lyann Sim & Stephen G. Withers

  3. Department of Pathology and Laboratory Medicine, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada

    Haisle Moon, Iren Constantinescu & Jayachandran N. Kizhakkedathu

  4. Centre for Blood Research, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada

    Haisle Moon, Iren Constantinescu & Jayachandran N. Kizhakkedathu

  5. Department of Microbiology and Immunology, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada

    Connor Morgan-Lang & Steven J. Hallam

  6. Graduate Program in Bioinformatics, Genome Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada

    Connor Morgan-Lang

  7. Department of Biochemistry, Life Sciences Centre, University of British Columbia, Vancouver, British Columbia, Canada

    Stephen G. Withers

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Contributions

P.R. performed the majority of the screening and characterization work as well as preparing figures and tables and providing a first draft of the manuscript; L.S. performed all work related to three-dimensional structural analysis; H.M. performed the majority of the testing with RBCs, in conjunction with I.C., and contributed to the writing; C.M.-L. performed much of the bioinformatics analysis; S.J.H. provided expertise in metagenomic analysis and supervision of the bioinformatics; J.N.K. supervised all work related to testing with RBCs and edited the manuscript; S.G.W. conceived the project, supervised the enzymology and coordinated the writing of the manuscript.

Corresponding author

Correspondence to Stephen G. Withers.

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The University of British Columbia has filed a patent related to this work on which P.R., J.N.K. and S.G.W. are named as authors.

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Supplementary information

Supplementary Information

Supplementary Discussion, Supplementary References, Supplementary Figs. 1–22 and Supplementary Tables 1–18.

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Supplementary Datasets 1 and 2

FpGalNAcDeAc_D2ext glycan array data and circular dichroism spectrometer data.

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Rahfeld, P., Sim, L., Moon, H. et al. An enzymatic pathway in the human gut microbiome that converts A to universal O type blood. Nat Microbiol 4, 1475–1485 (2019). https://doi.org/10.1038/s41564-019-0469-7

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