Journal of Molecular Evolution

, Volume 46, Issue 4, pp 401–408

A unique fungal lysine biosynthesis enzyme shares a common ancestor with tricarboxylic acid cycle and leucine biosynthetic enzymes found in diverse organisms

  • Steven D. Irvin
  • Jnanendra K. Bhattacharjee


Fungi have evolved a unique α-amino-adipate pathway for lysine biosynthesis. The fungal-specific enzyme homoaconitate hydratase from this pathway is moderately similar to the aconitase-family proteins from a diverse array of taxonomic groups, which have varying modes of obtaining lysine. We have used the similarity of homoaconitate hydratase to isopropylmalate isomerase (serving in leucine biosynthesis), aconitase (from the tricarboxylic acid cycle), and ironresponsive element binding proteins (cytosolic aconitase) from fungi and other eukaryotes, eubacteria, and archaea to evaluate possible evolutionary scenarios for the origin of this pathway. Refined sequence alignments show that aconitase active site residues are highly conserved in each of the enzymes, and intervening sequence sites are quite dissimilar. This pattern suggests strong purifying selection has acted to preserve the aconitase active site residues for a common catalytic mechanism; numerous other substitutions occur due to adaptive evolution or simply lack of functional constraint. We hypothesize that the similarities are the remnants of an ancestral gene duplication, which may not have occurred within the fungal lineage. Maximum likelihood, neighbor joining, and maximum parsimony phylogenetic comparisons show that the a-aminoadipate pathway enzyme is an outgroup to all aconitase family proteins for which sequence is currently available.

Key words

Homoaconitate hydratase Homoaconitase Lysine biosynthesis a-Aminoadipate pathway Molecular evolution Amino acid metabolism Gene duplication Adaptive evolution Evolutionary origin 


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  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–110PubMedGoogle Scholar
  2. Bakhiet N, Forney FW, Stahly DP, Daniels L (1984) Lysine biosynthesis in Methanobacterium thermoautotrophicum is by the diaminopimelic acid pathway. Curr Microbiol 10:195–198CrossRefGoogle Scholar
  3. Bhattacharjee JK (1992) Evolution of the a-aminoadipate pathway for the synthesis of lysine in fungi. In: Mortlock RP (ed) The Evolution of metabolic function. CRC Press, LondonGoogle Scholar
  4. Bruns RD, Vilgalys R, Barns SM, Gonzalez D, Hibbett DS, Lane DJ, Simon L, Stickel S, Szaro TM, Weisburg WG, Sogin ML (1992) Evolutionary relationships within the fungi: analyses of nuclear small subunit rRNA sequences. Mol Phylo Evol 1:231–241CrossRefGoogle Scholar
  5. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb J-F, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NSM, Weidman JF, Fuhrmann JL, Presley EA, Nguyen D, Utterback TR, Kelley JM, Peterson JD, Sadow PW, Hanna MC, Cotton MD, Hurst MA, Roberts KM, Kaine BP, Borodovsky M, Klenk H-P, Fraser CM, Smith HO, Woese CR, Venter JC (1996) Complete genome sequence of the methanogenic archaeon, Metha- nococcus jannaschii. Science 273 (5278):1058–1073PubMedCrossRefGoogle Scholar
  6. Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. In Dayhoff MO (ed) Atlas of protein sequence and structure, vol 5, suppl 3. Natl Biomed Res Found., Silver Spring, MD, pp 345–352Google Scholar
  7. Felsenstein J (1993) PHYLIP (phylogeny inference package) version 3.572. Distributed by the author. Department of Genetics, University of Washington, Seattle, WAGoogle Scholar
  8. Hentze MW, Argos P (1991) Homology between IRE-BP, a regulatory RNA-binding protein, aconitase, and isopropylmalate isomerase. Nucleic Acids Res 19:1739–1740PubMedCrossRefGoogle Scholar
  9. Jensen RA (1976) Enzyme recruitment in evolution of new function. Ann Rev Microbiol 30:409–25CrossRefGoogle Scholar
  10. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282PubMedGoogle Scholar
  11. Kaptain S, Downey WE, Tang CK, Philpott C, Haile DJ, Orloff DG, Harford JB, Rouault TA, Klausner RD (1991) A regulated RNA binding protein also possesses aconitase activity. Proc Natl Acad Sci 88:10109–10113PubMedCrossRefGoogle Scholar
  12. Lauble H, Kennedy MC, Beinert H, Stout CD (1992) Crystal structures of aconitase with isocitrate and nitroisocitrate bound. Biochemistry 31:2735–2748PubMedCrossRefGoogle Scholar
  13. Margulis L (1996) Archeal-eubacterial mergers in the origin of Eukarya. Proc Natl Acad Sci USA 93:1071–1076PubMedCrossRefGoogle Scholar
  14. Page RDM (1996) TREEVIEW: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357–358PubMedGoogle Scholar
  15. Robertson DE, Noll D, Roberts MF (1992) Free amino acid dynamics in marine methanogens. beta-Amino acids as compatible solutes. J Biol Chem 267:14893–14901PubMedGoogle Scholar
  16. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  17. Schäfer S, Paalme T, Vilu R, Fuchs G (1989) 13C-NMR study of acetate assimilation in Thermoproteus neutrophilus. Eur J Biochem 186:695–700PubMedCrossRefGoogle Scholar
  18. Strassman M (1964) Lysine biosynthesis in yeast. Abstr 6th Intern Congr Biochem 5:373–374Google Scholar
  19. Strassman M (1964) Lysine Biosynthesis in yeast. Abstr 6th Intern Congr Biochem 5:373–374Google Scholar
  20. Strassman M, Ceci LN (1966) Enzymatic formation of cishomoaconitic acid, an intermediate in lysine biosynthesis in yeast. J Biol Chem 241:5401–5407PubMedGoogle Scholar
  21. Strassman M, Weinhouse S (1953) Biosynthetic pathways. III. The biosynthesis of lysine by Torulopsis utilis. J Am Chem Soc 75: 1680–1684CrossRefGoogle Scholar
  22. Strimmer K, von Haeseler A (1996) Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964–969Google Scholar
  23. Swofford DL (1993) PAUP, Version 3.1. Illinois Natural History Survey, Champaign, ILGoogle Scholar
  24. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  25. Umbarger HE (1978) Amino acid biosynthesis and its regulation. Annu Rev Biochem 47:533–606CrossRefGoogle Scholar
  26. Van der Auwera G, De Baere R, Van de Peer Y, De Rijk P, Van der Broeck I, De Wächter R (1995) The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of the Hyphochytrium catenoides. Mol Biol Evol 12:671–678PubMedGoogle Scholar
  27. Vogel HJ (1960) Two modes of lysine synthesis among lower fungi: evolutionary significance. Biochim Biophys Acta 41:172–174CrossRefGoogle Scholar
  28. Vogel HJ (1965) Lysine biosynthesis and evolution. In: V Bryson (ed) Evolving genes and proteins. Academic Press, New York, pp 25–40Google Scholar
  29. Wang L, Okamoto S, Bhattacharjee JK (1989) Cloning and physical characterization of linked genes (LYS4, LYS15) of Saccharomyces cerevisiae. Curr Genet 16:7–12PubMedCrossRefGoogle Scholar
  30. Weidner G, Steffan B, Brakhage AA (1997) The Aspergillus nidulans lysF gene encodes homoaconitase, an enzyme involved in the fungus-specific lysine biosynthesis pathway. Mol Gen Genet 255:237- 247PubMedCrossRefGoogle Scholar
  31. Zheng L, Kennedy MC, Beinert H, Zalkin H (1992) Mutational analysis of active site residues in pig heart aconitase. J Biol Chem 267: 7895–7903PubMedGoogle Scholar

Copyright information

© Springer-Verlag New York Inc 1998

Authors and Affiliations

  • Steven D. Irvin
    • 1
  • Jnanendra K. Bhattacharjee
    • 1
  1. 1.Department of Microbiology32 Pearson Hall, Miami UniversityOxfordUSA
  2. 2.Section of Genetics and DevelopmentCornell UniversityIthacaUSA

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