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Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus

Nature Chemical Biology volume 9, pages 277–283 (2013)Cite this article

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Abstract

LysW has been identified as a carrier protein in the lysine biosynthetic pathway that is active through the conversion of α-aminoadipate (AAA) to lysine. In this study, we found that the hyperthermophilic archaeon, Sulfolobus acidocaldarius, not only biosynthesizes lysine through LysW-mediated protection of AAA but also uses LysW to protect the amino group of glutamate in arginine biosynthesis. In this archaeon, after LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions. The crystal structure of ArgX, the enzyme responsible for modification and protection of the amino moiety of glutamate with LysW, was determined in complex with LysW. Structural comparison and enzymatic characterization using Sulfolobus LysX, Sulfolobus ArgX and Thermus LysX identify the amino acid motif responsible for substrate discrimination between AAA and glutamate. Phylogenetic analysis reveals that gene duplication events at different stages of evolution led to ArgX and LysX.

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Figure 1: Relationship between arginine biosynthesis and lysine biosynthesis.
Figure 2: In vivo functions of homologs of lysine biosynthetic genes in S. acidocaldarius.
Figure 3: Analysis of Saci_0751 activity.
Figure 4: Overall structure of StArgX–StLysW complex.
Figure 5: Conformational change of StArgX upon binding StLysW and glutamate and recognition of substrates.
Figure 6: 50% bootstrap consensus tree of 90 lysX (argX)–like gene products based on maximum likelihood analysis.

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Acknowledgements

This work was supported in part by a grant-in-aid for scientific research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan (grant nos. 21380057 and 24228001 to M.N.), Nagase Science and Technology Foundation to M.N., and from the Asahi Glass Foundation to M.N.

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Author notes

  1. Takuya Ouchi & Akira Horie

    Present address: Present address: Nihon Unisys, Ltd., Tokyo, Japan (T.O.) and Central Laboratories for Frontier Technology, Kirin Co. Ltd., Yokohama, Japan (A.H.).,

Authors and Affiliations

  1. Biotechnology Research Center, The University of Tokyo, Tokyo, Japan

    Takuya Ouchi, Takeo Tomita, Akira Horie, Ayako Yoshida, Kento Takahashi, Saori Kosono, Tomohisa Kuzuyama & Makoto Nishiyama

  2. Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan

    Hiromi Nishida

  3. Max Planck Institute for Terrestrial Microbiology, Marburg, Germany

    Kerstin Lassak & Sonja-Verena Albers

  4. Division of Biochemical Analysis, Central Laboratory of Medical Sciences, Juntendo University School of Medicine, Tokyo, Japan

    Hikari Taka, Reiko Mineki & Tsutomu Fujimura

  5. Atopy (Allergy) Research Center, Juntendo University School of Medicine, Tokyo, Japan

    Chiharu Nishiyama

  6. Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan

    Ryoji Masui & Seiki Kuramitsu

  7. RIKEN SPring-8 Center, Hyogo, Japan

    Ryoji Masui, Seiki Kuramitsu & Makoto Nishiyama

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Contributions

Research planning and supervision were by T.T., T.K. and M.N.; biochemical experiments were by T.O., K.T., A.H., A.Y. and S. Kosono; phylogenetic analysis was by H.N.; gene knockout and replacement of S. acidocaldarius was by K.L. and S.-V.A.; LC-MS/MS and MALDI-TOF MS was by H.T., R. Mineki, T.F. and C.N.; StArgX was purified by T.O., A.H., A.Y., R. Masui and S. Kuramitsu; Crystallographic analysis was by T.O., A.H. and T.T.; and the manuscript was written by T.O., T.T., H.N., S.-V.A. and M.N.

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Correspondence to Makoto Nishiyama.

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Ouchi, T., Tomita, T., Horie, A. et al. Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus. Nat Chem Biol 9, 277–283 (2013). https://doi.org/10.1038/nchembio.1200

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