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Revealing the hidden functional diversity of an enzyme family

Nature Chemical Biology volume 10, pages 42–49 (2014)Cite this article

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Abstract

Millions of protein database entries are not assigned reliable functions, preventing the full understanding of chemical diversity in living organisms. Here, we describe an integrated strategy for the discovery of various enzymatic activities catalyzed within protein families of unknown or little known function. This approach relies on the definition of a generic reaction conserved within the family, high-throughput enzymatic screening on representatives, structural and modeling investigations and analysis of genomic and metabolic context. As a proof of principle, we investigated the DUF849 Pfam family and unearthed 14 potential new enzymatic activities, leading to the designation of these proteins as β-keto acid cleavage enzymes. We propose an in vivo role for four enzymatic activities and suggest key residues for guiding further functional annotation. Our results show that the functional diversity within a family may be largely underestimated. The extension of this strategy to other families will improve our knowledge of the enzymatic landscape.

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Figure 1: The BKACE active site pocket and reaction.
Figure 2: Substrates used in enzymatic assays.
Figure 3: Enzymatic screening of the BKACE family.
Figure 4: Dividing the BKACE family into groups of similar active sites.
Figure 5: Proposed in vivo roles of the newly discovered BKACEs.

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Acknowledgements

We are grateful to M. Besnard-Gonnet, D. Baud and A. Fossey for excellent technical assistance and to S. Tricot and L. Stuani for MS analyses. We also thank P.L. Saaidi, G. Cohen and M. Stam for helpful discussions and D. Roche, P. Bowe and A. Tolonen for useful comments on the manuscript. This work was supported by grants from Commissariat à l'énergie atomique et aux énergies alternatives (CEA), the CNRS and the University of Evry. A.A.T. Smith has been supported by the MICROME project, European Union Framework Program 7 Collaborative Project (222886-2).

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Author notes

  1. Adam Alexander Thil Smith

    Present address: Present address: Sleep/Wake Research Centre, Massey University, Wellington, New Zealand.,

  2. Karine Bastard and Adam Alexander Thil Smith: These authors contributed equally to this work.

Authors and Affiliations

  1. Direction des Sciences du Vivant, Commissariat à l'energie atomique et aux énergies alternatives (CEA), Institut de Génomique, Evry, France

    Karine Bastard, Adam Alexander Thil Smith, Carine Vergne-Vaxelaire, Alain Perret, Anne Zaparucha, Raquel De Melo-Minardi, Aline Mariage, Magali Boutard, Adrien Debard, Christophe Lechaplais, Christine Pelle, Virginie Pellouin, Nadia Perchat, Jean-Louis Petit, Annett Kreimeyer, Claudine Medigue, Jean Weissenbach, François Artiguenave, Véronique De Berardinis, David Vallenet & Marcel Salanoubat

  2. CNRS-UMR8030, Evry, France

    Karine Bastard, Adam Alexander Thil Smith, Carine Vergne-Vaxelaire, Alain Perret, Anne Zaparucha, Raquel De Melo-Minardi, Aline Mariage, Magali Boutard, Adrien Debard, Christophe Lechaplais, Christine Pelle, Virginie Pellouin, Nadia Perchat, Jean-Louis Petit, Annett Kreimeyer, Claudine Medigue, Jean Weissenbach, François Artiguenave, Véronique De Berardinis, David Vallenet & Marcel Salanoubat

  3. Université d'Evry Val d'Essonne, Evry, France

    Karine Bastard, Adam Alexander Thil Smith, Carine Vergne-Vaxelaire, Alain Perret, Anne Zaparucha, Raquel De Melo-Minardi, Aline Mariage, Magali Boutard, Adrien Debard, Christophe Lechaplais, Christine Pelle, Virginie Pellouin, Nadia Perchat, Jean-Louis Petit, Annett Kreimeyer, Claudine Medigue, Jean Weissenbach, François Artiguenave, Véronique De Berardinis, David Vallenet & Marcel Salanoubat

  4. Department of Computer Science, Federal University of Minas Gerais, Belo Horizonte, Brazil

    Raquel De Melo-Minardi

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Contributions

D.V. and M.S. designed and supervised this study. K.B. and A.A.T.S. conducted all of the bioinformatics analyses. F.A. and R.D.M.-M. initiated structural bioinformatics. C.V.-V. and A.Z. contributed to the chemical sections. K.B., A.A.T.S., D.V. and M.S. wrote the manuscript. C.M. and J.W. contributed to the design of this study. A.K. gave support to metabolic analysis. A.P. and V.D.B. supervised experiments, and J.-L.P., V.P., A.D., A.M., N.P., M.B., C.L. and C.P. performed the experiments.

Corresponding author

Correspondence to Marcel Salanoubat.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Data Set descriptions, Supplementary Results, Supplementary Notes 1–4, Supplementary Tables 1–6 and Supplementary Figures 1–7. (PDF 3235 kb)

Supplementary Data Set 1

Multiple sequence alignment of the 725 sequences of the DUF849 family. (TXT 278 kb)

Supplementary Data Set 2

The different clusters of the 725 sequences depending on active site composition, genomic context, phylogeny and sequence similarity. (XLSX 65 kb)

Supplementary Data Set 3

Primer sequences of the 322 candidates proteins. (XLSX 49 kb)

Supplementary Data Set 4

Pre-process data of the enzymatic screening. (XLSX 78 kb)

Supplementary Data Set 5

The “active site” hierarchical tree of the 725 sequences of the DUF849 family in nexus format. (TXT 10 kb)

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Bastard, K., Smith, A., Vergne-Vaxelaire, C. et al. Revealing the hidden functional diversity of an enzyme family. Nat Chem Biol 10, 42–49 (2014). https://doi.org/10.1038/nchembio.1387

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