Applied Microbiology and Biotechnology

, Volume 102, Issue 8, pp 3793–3803 | Cite as

Biotin-mediated growth and gene expression in Staphylococcus aureus is highly responsive to environmental biotin

  • Jiulia Satiaputra
  • Bart A. Eijkelkamp
  • Christopher A. McDevitt
  • Keith E. Shearwin
  • Grant W. Booker
  • Steven W. Polyak
Applied microbial and cell physiology


Biotin (Vitamin B7) is a critical enzyme co-factor in metabolic pathways important for bacterial survival. Biotin is obtained either from the environment or by de novo synthesis, with some bacteria capable of both. In certain species, the bifunctional protein BirA plays a key role in biotin homeostasis as it regulates expression of biotin biosynthetic enzymes in response to biotin demand and supply. Here, we compare the effect of biotin on the growth of two bacteria that possess a bifunctional BirA, namely Escherichia coli and Staphylococcus aureus. Unlike E. coli that could fulfill its biotin requirements through de novo synthesis, S. aureus showed improved growth rates in media supplemented with 10 nM biotin. S. aureus also accumulated more radiolabeled biotin from the media highlighting its ability to efficiently scavenge exogenous material. These data are consistent with S. aureus colonizing low biotin microhabitats. We also demonstrate that the S. aureus BirA protein is a transcriptional repressor of BioY, a subunit of the biotin transporter, and an operon containing yhfT and yhfS, the products of which have a putative role in fatty acid homeostasis. Increased expression of bioY is proposed to help cue S. aureus for efficient scavenging in low biotin environments.


Biotin Gene expression/regulation Staphylococcus aureus BirA Biotin protein ligase 



We thank the National BioResource Project (NIG, Japan) for the provision of bacterial strains.

Author contributions

J.S performed the experiments and data analysis and prepared the manuscript. B.A.E performed the data analysis. S.W.P. prepared the manuscript and data analysis. All authors contributed to the manuscript preparation and review.


This study was funded by the National Health and Medical Research Council of Australia Project Grant 1068885 awarded to SWP and GWB and Project Grants 1080784 and 1122582 awarded to CAM, and the Australian Research Council Discovery Project DP160101450 awarded to KES and DP150101856 and DP170102102 awarded to CAM. JS is a recipient of The University of Adelaide faculty divisional scholarship.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical approval

This article does not contain any studies with human participants performed by any of the authors.

Supplementary material

253_2018_8866_MOESM1_ESM.pdf (1 mb)
ESM 1 (PDF 1046 kb)


  1. Adikaram PR, Beckett D (2013) Protein:protein interactions in control of a transcriptional switch. J Mol Biol 425(22):4584–4594. CrossRefPubMedPubMedCentralGoogle Scholar
  2. Azhar A, Booker GW, Polyak SW (2015) Mechanisms of biotin transport. Biochem Anal Biochem 4:210. Google Scholar
  3. Bailey LM, Ivanov RA, Wallace JC, Polyak SW (2008) Artifactual detection of biotin on histones by streptavidin. Anal Biochem 373(1):71–77. CrossRefPubMedGoogle Scholar
  4. Barker DF, Campbell AM (1981) Genetic and biochemical characterization of the birA gene and its product: evidence for a direct role of biotin holoenzyme synthetase in repression of the biotin operon in Escherichia coli. J Mol Biol 146(4):469–492CrossRefPubMedGoogle Scholar
  5. Beckett D (2007) Biotin sensing: universal influence of biotin status on transcription. Annu Rev Genet 41:443–464. CrossRefPubMedGoogle Scholar
  6. Chakravartty V, Cronan JE (2012) Altered regulation of Escherichia coli biotin biosynthesis in BirA superrepressor mutant strains. J Bacteriol 194(5):1113–1126. CrossRefPubMedPubMedCentralGoogle Scholar
  7. Chakravartty V, Cronan JE (2013) The wing of a winged helix-turn-helix transcription factor organizes the active site of BirA, a bifunctional repressor/ligase. J Biol Chem 288(50):36029–36039. CrossRefPubMedPubMedCentralGoogle Scholar
  8. Cronan JE (2014a) A new pathway of exogenous fatty acid incorporation proceeds by a classical phosphoryl transfer reaction. Mol Microbiol 92(2):217–221. CrossRefPubMedGoogle Scholar
  9. Cronan JE (2014b) Biotin and lipoic acid: synthesis, attachment and regulation. EcoSal Plus.
  10. Cronan JE Jr (1988) Expression of the biotin biosynthetic operon of Escherichia coli is regulated by the rate of protein biotination. J Biol Chem 263(21):10332–10336PubMedGoogle Scholar
  11. Cronan JE Jr, Gelmann EP (1975) Physical properties of membrane lipids: biological relevance and regulation. Bacteriol Rev 39(3):232–256PubMedPubMedCentralGoogle Scholar
  12. Dong Y, Du H, Gao C, Ma T, Feng L (2012) Characterization of two long-chain fatty acid CoA ligases in the Gram-positive bacterium Geobacillus thermodenitrificans NG80-2. Microbiol Res 167(10):602–607. CrossRefPubMedGoogle Scholar
  13. Feng Y, Napier BA, Manandhar M, Henke SK, Weiss DS, Cronan JE (2014) A Francisella virulence factor catalyses an essential reaction of biotin synthesis. Mol Microbiol 91(2):300–314. CrossRefPubMedGoogle Scholar
  14. Finkenwirth F, Kirsch F, Eitinger T (2013) Solitary BioY proteins mediate biotin transport into recombinant Escherichia coli. J Bacteriol 195(18):4105–4111. CrossRefPubMedPubMedCentralGoogle Scholar
  15. Finkenwirth F, Sippach M, Landmesser H, Kirsch F, Ogienko A, Grunzel M, Kiesler C, Steinhoff HJ, Schneider E, Eitinger T (2015) ATP-dependent conformational changes trigger substrate capture and release by an ECF-type biotin transporter. J Biol Chem 290(27):16929–16942. CrossRefPubMedPubMedCentralGoogle Scholar
  16. Finkenwirth F, Kirsch F, Eitinger T (2017) Complex stability during the transport cycle of a subclass I ECF transporter. Biochemistry 56(34):4578–4583. CrossRefPubMedGoogle Scholar
  17. Gretler AC, Mucciolo P, Evans JB, Niven CF (1955) Vitamin nutrition of staphylococci with special reference to their biotin requirements. J Bacteriol 70(1):44–49PubMedPubMedCentralGoogle Scholar
  18. Hebbeln P, Rodionov DA, Alfandega A, Eitinger T (2007) Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. Proc Natl Acad Sci U S A 104(8):2909–2914. CrossRefPubMedPubMedCentralGoogle Scholar
  19. Henke SK, Cronan JE (2014) Successful conversion of the Bacillus subtilis BirA Group II biotin protein ligase into a Group I ligase. PLoS One 9(5):e96757. CrossRefPubMedPubMedCentralGoogle Scholar
  20. Henke SK, Cronan JE (2016) The Staphylococcus aureus group II biotin protein ligase BirA is an effective regulator of biotin operon transcription and requires the DNA binding domain for full enzymatic activity. Mol Microbiol 102(3):417–429. CrossRefPubMedPubMedCentralGoogle Scholar
  21. Ifuku O, Koga N, Haze S, Kishimoto J, Arai T, Wachi Y (1995) Molecular analysis of growth inhibition caused by overexpression of the biotin operon in Escherichia coli. Biosci Biotechnol Biochem 59(2):184–189CrossRefPubMedGoogle Scholar
  22. Li SJ, Cronan JE Jr (1993) Growth rate regulation of Escherichia coli acetyl coenzyme A carboxylase, which catalyzes the first committed step of lipid biosynthesis. J Bacteriol 175(2):332–340CrossRefPubMedPubMedCentralGoogle Scholar
  23. Otsuka A, Abelson J (1978) The regulatory region of the biotin operon in Escherichia coli. Nature 276(5689):689–694CrossRefPubMedGoogle Scholar
  24. Perry CA, West AA, Gayle A, Lucas LK, Yan J, Jiang X, Malysheva O, Caudill MA (2014) Pregnancy and lactation alter biomarkers of biotin metabolism in women consuming a controlled diet. J Nutr 144(12):1977–1984. CrossRefPubMedPubMedCentralGoogle Scholar
  25. Polyak SW, Abell AD, Wilce MCJ, Zhang L, Booker GW (2012) Structure, function and selective inhibition of bacterial acetyl-CoA carboxylase. Appl Microbiol Biotechnol 93(3):983–992. CrossRefPubMedGoogle Scholar
  26. Porter JR, Pelczar MJ (1941) The nutrition of Staphylococcus aureus the influence of biotin, BioS IIB and vitamin H on the growth of several strains. J Bacteriol 41(2):173–192PubMedPubMedCentralGoogle Scholar
  27. Ringlstetter SL (2010) Identification of the biotin transporter in Escherichia coli, biotinylation of histones in Saccharomyces cerevisiae and analysis of biotin sensing in Saccharomyces cerevisiae. Doctoral thesis, Universität Regensburg, Germany.
  28. Rodionov DA, Mironov AA, Gelfand MS (2002) Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res 12(10):1507–1516. CrossRefPubMedPubMedCentralGoogle Scholar
  29. Said HM (2009) Cell and molecular aspects of human intestinal biotin absorption. J Nutr 139(1):158–162. CrossRefPubMedPubMedCentralGoogle Scholar
  30. Saier MH Jr (2000) Families of transmembrane transporters selective for amino acids and their derivatives. Microbiology 146(Pt 8):1775–1795. CrossRefPubMedGoogle Scholar
  31. Salaemae W, Azhar A, Booker GW, Polyak SW (2011) Biotin biosynthesis in Mycobacterium tuberculosis: physiology, biochemistry and molecular intervention. Protein Cell 2(9):691–695. CrossRefPubMedPubMedCentralGoogle Scholar
  32. Salaemae W, Booker GW, Polyak SW (2016) The role of biotin in bacterial physiology and virulence: a novel antibiotic target for Mycobacterium tuberculosis. Microbiol Spectrum 4(2):VMBF-0008-2015.
  33. Satiaputra J, Shearwin KE, Booker GW, Polyak SW (2016) Mechanisms of biotin-regulated gene expression in microbes. Synth Syst Biotechnol 1(1):17–24. CrossRefPubMedPubMedCentralGoogle Scholar
  34. Soares da Costa TP, Yap MY, Perugini MA, Wallace JC, Abell AD, Wilce MCJ, Polyak SW, Booker GW (2014) Dual roles of F123 in protein homodimerization and inhibitor binding to biotin protein ligase from Staphylococcus aureus. Mol Microbiol 91(1):110–120. CrossRefPubMedGoogle Scholar
  35. Sternicki LM, Wegener KL, Bruning JB, Booker GW, Polyak SW (2017) Mechanisms governing precise protein biotinylation. Trends Biochem Sci 42(5):383–394. CrossRefPubMedGoogle Scholar
  36. St-Pierre F, Cui L, Priest DG, Endy D, Dodd IB, Shearwin KE (2013) One-step cloning and chromosomal integration of DNA. ACS Synth Biol 2(9):537–541. CrossRefPubMedGoogle Scholar
  37. Streaker ED, Beckett D (1998) A map of the biotin repressor-biotin operator interface: binding of a winged helix-turn-helix protein dimer to a forty base-pair site. J Mol Biol 278(4):787–800. CrossRefPubMedGoogle Scholar
  38. Weaver LH, Kwon K, Beckett D, Matthews BW (2001) Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator. Proc Natl Acad Sci U S A 98(11):6045–6050. CrossRefPubMedPubMedCentralGoogle Scholar
  39. Woong Park S, Klotzsche M, Wilson DJ, Boshoff HI, Eoh H, Manjunatha U, Blumenthal A, Rhee K, Barry CE 3rd, Aldrich CC, Ehrt S, Schnappinger D (2011) Evaluating the sensitivity of Mycobacterium tuberculosis to biotin deprivation using regulated gene expression. PLoS Pathog 7(9):e1002264. CrossRefPubMedPubMedCentralGoogle Scholar
  40. Xu Y, Beckett D (1996) Evidence for interdomain interaction in the Escherichia coli repressor of biotin biosynthesis from studies of an N-terminal domain deletion mutant. Biochemistry 35(6):1783–1792. CrossRefPubMedGoogle Scholar
  41. Yang B, Feng L, Wang F, Wang L (2015) Enterohemorrhagic Escherichia coli senses low biotin status in the large intestine for colonization and infection. Nat Commun 6:6592. CrossRefPubMedPubMedCentralGoogle Scholar
  42. Ye H, Cai M, Zhang H, Li Z, Wen R, Feng Y (2016) Functional definition of BirA suggests a biotin utilization pathway in the zoonotic pathogen Streptococcus suis. Sci Rep 6:26479. CrossRefPubMedPubMedCentralGoogle Scholar
  43. Zhang P (2013) Structure and mechanism of energy-coupling factor transporters. Trends Microbiol 21(12):652–659. CrossRefPubMedGoogle Scholar
  44. Zhang YM, Rock CO (2008) Membrane lipid homeostasis in bacteria. Nat Rev Microbiol 6(3):222–233. CrossRefPubMedGoogle Scholar
  45. Zhang H, Wang Q, Fisher DJ, Cai M, Chakravartty V, Ye H, Li P, Solbiati JO, Feng Y (2016) Deciphering a unique biotin scavenging pathway with redundant genes in the probiotic bacterium Lactococcus lactis. Sci Rep 6:25680. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Jiulia Satiaputra
    • 1
  • Bart A. Eijkelkamp
    • 2
  • Christopher A. McDevitt
    • 2
  • Keith E. Shearwin
    • 1
  • Grant W. Booker
    • 1
  • Steven W. Polyak
    • 1
  1. 1.School of Biological SciencesUniversity of AdelaideAdelaideAustralia
  2. 2.Research Centre for Infectious Diseases, School of Biological SciencesUniversity of AdelaideAdelaideAustralia

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