Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Systematic discovery of analogous enzymes in thiamin biosynthesis

Nature Biotechnology volume 21, pages 790–795 (2003)Cite this article

Abstract

In all genome-sequencing projects completed to date, a considerable number of 'gaps' have been found in the biochemical pathways of the respective species. In many instances, missing enzymes are displaced by analogs, functionally equivalent proteins that have evolved independently and lack sequence and structural similarity. Here we fill such gaps by analyzing anticorrelating occurrences of genes across species. Our approach, applied to the thiamin biosynthesis pathway comprising approximately 15 catalytic steps, predicts seven instances in which known enzymes have been displaced by analogous proteins. So far we have verified four predictions by genetic complementation, including three proteins for which there was no previous experimental evidence of a role in the thiamin biosynthesis pathway. For one hypothetical protein, biochemical characterization confirmed the predicted thiamin phosphate synthase (ThiE) activity. The results demonstrate the ability of our computational approach to predict specific functions without taking into account sequence similarity.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: The THI-PP biosynthesis pathway3,4,5,36.
Figure 2: Distribution across species of genes associated with THI-PP biosynthesis.
Figure 3: Genetic complementation of putative analogous enzymes.
Figure 4: Thiamin phosphate synthase (TPS) activity of the thermophilic T. maritima TM0790 gene product.

Similar content being viewed by others

References

  1. Burdick, D. in Kirk-Othmer Encyclopedia of Chemical Technology, vol. 25 (ed. Howe-Grant, M.) 152–171 (Wiley, New York, 1998).

    Google Scholar 

  2. Fenster, R. Feed Additives: A Global Market Study (PJB Publications, Richmond, Surrey, UK, 2001).

    Google Scholar 

  3. Begley, T.P. et al. Thiamin biosynthesis in prokaryotes. Arch. Microbiol. 171, 293–300 (1999).

    Article  CAS  Google Scholar 

  4. Hohmann, S. & Meacock, P.A. Thiamin metabolism and thiamin diphosphate-dependent enzymes in the yeast Saccharomyces cerevisiae: genetic regulation. Biochim. Biophys. Acta 1385, 201–219 (1998).

    Article  CAS  Google Scholar 

  5. White, R.L. & Spenser, I.D. in Escherichia coli and Salmonella. Cellular and Molecular Biology, edn. 2, vol. 1 (ed. Neidhardt, F.C.) 680–686 (ASM Press, Washington, DC, 1996).

    Google Scholar 

  6. Xi, J., Ge, Y., Kinsland, C., McLafferty, F.W. & Begley, T.P. Biosynthesis of the thiazole moiety of thiamin in Escherichia coli: identification of an acyldisulfide-linked protein-protein conjugate that is functionally analogous to the ubiquitin/E1 complex. Proc. Natl. Acad. Sci. USA 98, 8513–8518 (2001).

    Article  CAS  Google Scholar 

  7. Allen, S., Zilles, J.L. & Downs, D.M. Metabolic flux in both the purine mononucleotide and histidine biosynthetic pathways can influence synthesis of the hydroxymethyl pyrimidine moiety of thiamine in Salmonella enterica. J. Bacteriol. 184, 6130–6137 (2002).

    Article  CAS  Google Scholar 

  8. Fitch, W.M. Distinguishing homologous from analogous proteins. Syst. Zool. 19, 99–113 (1970).

    Article  CAS  Google Scholar 

  9. Koonin, E.V., Mushegian, A.R. & Bork, P. Non-orthologous gene displacement. Trends Genet. 12, 334–336 (1996).

    Article  CAS  Google Scholar 

  10. Enright, A.J., Iliopoulos, I., Kyrpides, N.C. & Ouzounis, C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86–90 (1999).

    Article  CAS  Google Scholar 

  11. Marcotte, E.M. et al. Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751–753 (1999).

    Article  CAS  Google Scholar 

  12. Dandekar, T., Snel, B., Huynen, M. & Bork, P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324–328 (1998).

    Article  CAS  Google Scholar 

  13. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D. & Maltsev, N. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96, 2896–2901 (1999).

    Article  CAS  Google Scholar 

  14. Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D. & Yeates, T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96, 4285–4288 (1999).

    Article  CAS  Google Scholar 

  15. Galperin, M.Y. & Koonin, E.V. Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18, 609–613 (2000).

    Article  CAS  Google Scholar 

  16. Daugherty, M., Vonstein, V., Overbeek, R. & Osterman, A. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J. Bacteriol. 183, 292–300 (2001).

    Article  CAS  Google Scholar 

  17. Dynes, J.L. & Firtel, R.A. Molecular complementation of a genetic marker in Dictyostelium using a genomic DNA library. Proc. Natl. Acad. Sci. USA 86, 7966–7970 (1989).

    Article  CAS  Google Scholar 

  18. Myllykallio, H. et al. An alternative flavin-dependent mechanism for thymidylate synthesis. Science 297, 105–107 (2002).

    Article  CAS  Google Scholar 

  19. Vander Horn, P.B., Backstrom, A.D., Stewart, V. & Begley, T.P. Structural genes for thiamine biosynthetic enzymes (thiCEFGH) in Escherichia coli K-12. J. Bacteriol. 175, 982–992 (1993).

    Article  CAS  Google Scholar 

  20. Webb, E. & Downs, D. Characterization of thiL, encoding thiamin-monophosphate kinase, in Salmonella typhimurium. J. Biol. Chem. 272, 15702–15707 (1997).

    Article  CAS  Google Scholar 

  21. Nosaka, K., Kaneko, Y., Nishimura, H. & Iwashima, A. Isolation and characterization of a thiamin pyrophosphokinase gene, THI80, from Saccharomyces cerevisiae. J. Biol. Chem. 268, 17440–17447 (1993).

    CAS  PubMed  Google Scholar 

  22. Praekelt, U.M., Byrne, K.L. & Meacock, P.A. Regulation of THI4 (MOL1), a thiamine-biosynthetic gene of Saccharomyces cerevisiae. Yeast 10, 481–490 (1994).

    Article  CAS  Google Scholar 

  23. Pang, A.S., Nathoo, S. & Wong, S.L. Cloning and characterization of a pair of novel genes that regulate production of extracellular enzymes in Bacillus subtilis. J. Bacteriol. 173, 46–54 (1991).

    Article  CAS  Google Scholar 

  24. Miranda-Rios, J. et al. Expression of thiamin biosynthetic genes (thiCOGE) and production of symbiotic terminal oxidase cbb3 in Rhizobium etli. J. Bacteriol. 179, 6887–6893 (1997).

    Article  CAS  Google Scholar 

  25. Rodionov, D.A., Vitreschak, A.G., Mironov, A.A. & Gelfand, M.S. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J. Biol. Chem. 277, 48949–48959 (2002).

    Article  CAS  Google Scholar 

  26. Petersen, L.A. & Downs, D.M. Identification and characterization of an operon in Salmonella typhimurium involved in thiamine biosynthesis. J. Bacteriol. 179, 4894–4900 (1997).

    Article  CAS  Google Scholar 

  27. Chiu, H.J., Reddick, J.J., Begley, T.P. & Ealick, S.E. Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 A resolution. Biochemistry 38, 6460–6470 (1999).

    Article  CAS  Google Scholar 

  28. Baker, L.J., Dorocke, J.A., Harris, R.A. & Timm, D.E. The crystal structure of yeast thiamin pyrophosphokinase. Structure (Camb) 9, 539–546 (2001).

    Article  CAS  Google Scholar 

  29. Machado, C.R. et al. Dual role for the yeast THI4 gene in thiamine biosynthesis and DNA damage tolerance. J. Mol. Biol. 273, 114–121 (1997).

    Article  CAS  Google Scholar 

  30. Kim, Y.S. et al. A Brassica cDNA clone encoding a bifunctional hydroxymethylpyrimidine kinase/thiamin-phosphate pyrophosphorylase involved in thiamin biosynthesis. Plant Mol. Biol. 37, 955–966 (1998).

    Article  CAS  Google Scholar 

  31. Gourley, D.G. et al. The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction. Nat. Struct. Biol. 6, 521–525 (1999).

    Article  CAS  Google Scholar 

  32. Snel, B., Lehmann, G., Bork, P. & Huynen, M.A. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res. 28, 3442–3444 (2000).

    Article  CAS  Google Scholar 

  33. von Mering, C. et al. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31, 258–261 (2003).

    Article  CAS  Google Scholar 

  34. Vandeyar, M.A. & Zahler, S.A. Chromosomal insertions of Tn917 in Bacillus subtilis. J. Bacteriol. 167, 530–534 (1986).

    Article  CAS  Google Scholar 

  35. Tatusov, R.L., Koonin, E.V. & Lipman, D.J. A genomic perspective on protein families. Science 278, 631–637 (1997).

    Article  CAS  Google Scholar 

  36. Schwartz, C.J., Djaman, O., Imlay, J.A. & Kiley, P.J. The cysteine desulfurase, IscS, has a major role in in vivo Fe-S cluster formation in Escherichia coli. Proc. Natl. Acad. Sci. USA 97, 9009–9014 (2000).

    Article  CAS  Google Scholar 

  37. Huynen, M.A. & Bork, P. Measuring genome evolution. Proc. Natl. Acad. Sci. USA 95, 5849–5856 (1998).

    Article  CAS  Google Scholar 

  38. Karp, P.D. Pathway databases: a case study in computational symbolic theories. Science 293, 2040–2044 (2001).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported in part by grants from the Consejo Nacional de Ciencia y Tecnología (Mexico), Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México (Mexico), Netherlands Organization for Scientific Research, the Deutsche Forschungsgemeinschaft (Germany) and Bundesministerium für Forschung und Bildung (Germany). E.M. thanks the Alexander von Humboldt Stiftung. We thank R. Hernandez and P. Gaytan for technical assistance. We are indebted to T.P. Begley for providing HMP and a plasmid with the thiD gene from E. coli and to D.M. Downs, M. Soberón, J. Miranda and R. Russell for critical reading of the manuscript.

Author information

Author notes

  1. Berend Snel

    Present address: Nijmegen Centre for Molecular Life Sciences, p/a CMBI, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands

  2. Enrique Morett and Jan O Korbel: These authors contributed equally to this work.

Authors and Affiliations

  1. Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, 62210, Morelos, Mexico

    Enrique Morett, Emmanuvel Rajan, Gloria Saab-Rincon, Leticia Olvera & Maricela Olvera

  2. European Molecular Biology Laboratory, Meyerhofstraβe 1, Heidelberg, 69117, Germany

    Jan O Korbel, Steffen Schmidt, Berend Snel & Peer Bork

  3. Max-Delbrück-Center for Molecular Medicine, Berlin-Buch, 13092, Germany

    Jan O Korbel, Steffen Schmidt & Peer Bork

  4. Department of Parasitology, University of Heidelberg, INF 324, Heidelberg, 69120, Germany

    Steffen Schmidt

Authors
  1. Enrique Morett
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jan O Korbel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Emmanuvel Rajan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gloria Saab-Rincon
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Leticia Olvera
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Maricela Olvera
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Steffen Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Berend Snel
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Peer Bork
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Enrique Morett or Peer Bork.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Morett, E., Korbel, J., Rajan, E. et al. Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat Biotechnol 21, 790–795 (2003). https://doi.org/10.1038/nbt834

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt834

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing