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A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis

Nature Chemical Biology volume 8, pages 926–932 (2012)Cite this article

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Abstract

Functional assignment of uncharacterized proteins is a challenge in the era of large-scale genome sequencing. Here, we combine in extracto NMR, proteomics and transcriptomics with a newly developed (knock-out) metabolomics platform to determine a potential physiological role for a ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO)-like protein from Rhodospirillum rubrum. Our studies unraveled an unexpected link in bacterial central carbon metabolism between S-adenosylmethionine–dependent polyamine metabolism and isoprenoid biosynthesis and also provide an alternative approach to assign enzyme function at the organismic level.

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Figure 1: Phylogeny and function of RLPs.
Figure 2: Characterization of the initial steps in MTA metabolism of R. rubrum by in extracto NMR.
Figure 3: Methanethiol release and DXP formation are linked in R. rubrum.
Figure 4: The proposed MTA-isoprenoid shunt in R. rubrum.
Figure 5: Analysis of MTA-derived metabolites in R. rubrum wild type and mutants without feeding of external MTA.
Figure 6: Proteome and transcriptome analysis of R. rubrum cells that were grown aerobically with sulfate or MTA as the sole sulfur source.

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Acknowledgements

This research was supported by a fellowship to T.J.E. from the Deutsche Forschungsgemeinschaft (ER 646/1-1) and research grants from the US National Institutes of Health (R01GM065155, R01GM095742, P01GM071790 and U54GM093342). We would like to thank J.E. Cronan for critical comments and C. Deane and T. Miyairi for excellent technical assistance. We also acknowledge S.C. Almo and B.S. Hillerich (New York Structural Genomics Research Consortium) for providing expression plasmids and purified cupin for in vitro assays.

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Author notes

  1. Tobias J Erb

    Present address: Present address: Institute for Microbiology, ETH Zurich, Switzerland.,

  2. Tobias J Erb and Bradley S Evans: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA

    Tobias J Erb, Bradley S Evans, Kyuil Cho, Benjamin P Warlick, B McKay Wood, Heidi J Imker, Jonathan V Sweedler & John A Gerlt

  2. Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA

    Tobias J Erb, Benjamin P Warlick & John A Gerlt

  3. Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA

    Bradley S Evans, Kyuil Cho, Jonathan V Sweedler & John A Gerlt

  4. Department of Microbiology, The Ohio State University, Columbus, Ohio, USA

    Jaya Sriram & F Robert Tabita

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Contributions

T.J.E., B.S.E. and J.A.G. conceived and designed the experiments. T.J.E. performed the experiments, with the exception of metabolome analyses, which were acquired by B.S.E., K.C. and B.M.W. and biochemical characterization of the cupin protein in vitro, which was performed by B.S.E and B.P.W. B.S.E., K.C., B.M.W. and J.V.S. developed the mass spectrometric platform and evaluated MS data. J.S. and F.R.T. created and provided the rlp mutant strain and the cupin mutant strain of R. rubrum. B.P.W. and H.J.I. provided chemicals and recombinant enzymes for the synthesis of chemicals. T.J.E. and J.A.G. wrote the paper.

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Correspondence to John A Gerlt.

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Erb, T., Evans, B., Cho, K. et al. A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis. Nat Chem Biol 8, 926–932 (2012). https://doi.org/10.1038/nchembio.1087

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