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Volume 165, Issue 10

Comparative biochemical and structural analysis of the flavin-binding dodecins from and reveals striking differences with regard to multimerization Free

Abstract

Dodecins are small flavin-binding proteins that are widespread amongst haloarchaeal and bacterial species. Haloarchaeal dodecins predominantly bind riboflavin, while bacterial dodecins have been reported to bind riboflavin-5′-phosphate, also called flavin mononucleotide (FMN), and the FMN derivative, flavin adenine dinucleotide (FAD). Dodecins form dodecameric complexes and represent buffer systems for cytoplasmic flavins. In this study, dodecins of the bacteria (SdDod) and (ScDod) were investigated. Both dodecins showed an unprecedented low affinity for riboflavin, FMN and FAD when compared to other bacterial dodecins. Significant binding of FMN and FAD occurred at relatively low temperatures and under acidic conditions. X-ray diffraction analyses of SdDod and ScDod revealed that the structures of both dodecins are highly similar, which explains their similar binding properties for FMN and FAD. In contrast, SdDod and ScDod showed very different properties with regard to the stability of their dodecameric complexes. Site-directed mutagenesis experiments revealed that a specific salt bridge (D10–K62) is responsible for this difference in stability.

  • Received:
  • Accepted:
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Keyword(s): dodecin , riboflavin , roseoflavin and Streptomyces davaonensis
© 2019 The Authors
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2019-10-01
2024-04-24
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References

  1. Fischer M, Bacher A. Biosynthesis of flavocoenzymes. Nat Prod Rep 2005; 22:324–350 [View Article]
     [Google Scholar]
  2. Joosten V, van Berkel WJH. Flavoenzymes. Curr Opin Chem Biol 2007; 11:195–202 [View Article]
     [Google Scholar]
  3. Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ et al. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli . Nat Chem Biol 2009; 5:593–599 [View Article]
     [Google Scholar]
  4. García-Angulo VA. Overlapping riboflavin supply pathways in bacteria. Crit Rev Microbiol 2017; 43:196–209 [View Article]
     [Google Scholar]
  5. Jaehme M, Slotboom DJ. Diversity of membrane transport proteins for vitamins in bacteria and archaea. Biochim Biophys Acta 2015; 1850:565–576 [View Article]
     [Google Scholar]
  6. Serrano A, Ferreira P, Martínez-Júlvez M, Medina M. The prokaryotic FAD synthetase family: a potential drug target. Curr Pharm Des 2013; 19:2637–2648 [View Article]
     [Google Scholar]
  7. Monaco HL. Crystal structure of chicken riboflavin-binding protein. Embo J 1997; 16:1475–1483 [View Article]
     [Google Scholar]
  8. White HB, Merrill AH. Riboflavin-Binding proteins. Annu Rev Nutr 1988; 8:279–299 [View Article]
     [Google Scholar]
  9. Grininger M, Staudt H, Johansson P, Wachtveitl J, Oesterhelt D. Dodecin is the key player in flavin homeostasis of archaea. J Biol Chem 2009; 284:13068–13076 [View Article]
     [Google Scholar]
  10. Bourdeaux F, Hammer CA, Vogt S, Schweighöfer F, Nöll G et al. Flavin Storage and Sequestration by Mycobacterium tuberculosis Dodecin. ACS Infect Dis 2018; 4:1082–1092 [View Article]
     [Google Scholar]
  11. Liu F, Xiong J, Kumar S, Yang C, Ge S et al. Structural and biophysical characterization of Mycobacterium tuberculosis dodecin Rv1498A. J Struct Biol 2011; 175:31–38 [View Article]
     [Google Scholar]
  12. Vinzenz X, Grosse W, Linne U, Meissner B, Essen L-O. Chemical engineering of Mycobacterium tuberculosis dodecin hybrids. Chem Commun 2011; 47:11071–11073 [View Article]
     [Google Scholar]
  13. Bieger B, Essen LO, Oesterhelt D. Crystal structure of halophilic dodecin: a novel, dodecameric flavin binding protein from Halobacterium salinarum . Structure 2003; 11:375–385
     [Google Scholar]
  14. Grininger M, Seiler F, Zeth K, Oesterhelt D. Dodecin sequesters FAD in closed conformation from the aqueous solution. J Mol Biol 2006; 364:561–566 [View Article]
     [Google Scholar]
  15. Staudt H, Oesterhelt D, Grininger M, Wachtveitl J. Ultrafast excited-state deactivation of flavins bound to dodecin. J Biol Chem 2012; 287:17637–17644 [View Article]
     [Google Scholar]
  16. Meissner B, Schleicher E, Weber S, Essen LO. The dodecin from Thermus thermophilus, a bifunctional cofactor storage protein. J Biol Chem 2007; 282:33142–33154 [View Article]
     [Google Scholar]
  17. Arockiasamy A, Aggarwal A, Savva CG, Holzenburg A, Sacchettini JC. Crystal structure of calcium dodecin (Rv0379), from Mycobacterium tuberculosis with a unique calcium-binding site. Protein Sci 2011; 20:827–833 [View Article]
     [Google Scholar]
  18. Landwehr W, Kämpfer P, Glaeser SP, Rückert C, Kalinowski J et al. Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov. Int J Syst Evol Microbiol 2018; 68:382-393393 [View Article]
     [Google Scholar]
  19. Pedrolli DB, Jankowitsch F, Schwarz J, Langer S, Nakanishi S et al. Riboflavin analogs as antiinfectives: occurrence, mode of action, metabolism and resistance. Curr Pharm Des 2012
     [Google Scholar]
  20. Langer S, Hashimoto M, Hobl B, Mathes T, Mack M. Flavoproteins are potential targets for the antibiotic roseoflavin in Escherichia coli . J Bacteriol 2013; 195:4037–4045 [View Article]
     [Google Scholar]
  21. Langer S, Nakanishi S, Mathes T, Knaus T, Binter A et al. The flavoenzyme azobenzene reductase AzoR from Escherichia coli binds roseoflavin mononucleotide (RoFMN) with high affinity and is less active in its RoFMN form. Biochemistry 2013; 52:4288–4295 [View Article]
     [Google Scholar]
  22. Pedrolli DB, Jankowitsch F, Schwarz J, Langer S, Nakanishi S et al. Natural riboflavin analogs. Methods Mol Biol 2014; 1146:41–63 [View Article]
     [Google Scholar]
  23. Mathes T, Vogl C, Stolz J, Hegemann P. In vivo generation of flavoproteins with modified cofactors. J Mol Biol 2009; 385:1511–1518 [View Article]
     [Google Scholar]
  24. Ludwig P, Sévin DC, Busche T, Kalinowski J, Bourdeaux F et al. Characterization of the small flavin-binding dodecin in the roseoflavin producer Streptomyces davawensis . Microbiology 2018; 164:908–919 [View Article]
     [Google Scholar]
  25. Magill NG, Cowan AE, Koppel DE, Setlow P. The internal pH of the forespore compartment of Bacillus megaterium decreases by about 1 pH unit during sporulation. J Bacteriol 1994; 176:2252–2258 [View Article]
     [Google Scholar]
  26. Wilks JC, Slonczewski JL. pH of the cytoplasm and periplasm of Escherichia coli: rapid measurement by green fluorescent protein fluorimetry. J Bacteriol 2007; 189:5601–5607 [View Article]
     [Google Scholar]
  27. Quirós L, Salas J. Intracellular water volume and internal pH of Streptomyces antibioticus spores. FEMS Microbiol Lett 1996; 141:245–249 [View Article]
     [Google Scholar]
  28. Chae W-B, Kim Y-B, Choi S-W, Lee H-B, Kim E-K. Enhancing the sporulation of Streptomyces kasugaensis by culture optimization. Korean J Chem Eng 2009; 26:438–443 [View Article]
     [Google Scholar]
  29. Bertani G. Lysogeny at mid-twentieth century: P1, P2, and other experimental systems. J Bacteriol 2004; 186:595–600 [View Article]
     [Google Scholar]
  30. Pedrolli DB, Matern A, Wang J, Ester M, Siedler K et al. A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis . Nucleic Acids Res 2012; 40:8662–8673 [View Article]
     [Google Scholar]
  31. Jankowitsch F, Schwarz J, Rückert C, Gust B, Szczepanowski R et al. Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. J Bacteriol 2012; 194:6818–6827 [View Article]
     [Google Scholar]
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Comparative biochemical and structural analysis of the flavin-binding dodecins from Streptomyces davaonensis and Streptomyces coelicolor reveals striking differences with regard to multimerization
Microbiology 165, 1095 (2019); https://doi.org/10.1099/mic.0.000835
/content/journal/micro/10.1099/mic.0.000835
/content/journal/micro/10.1099/mic.0.000835
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