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Inhibition and Substrate Specificity Properties of FKBP22 from a Psychrotrophic Bacterium, Shewanella sp. SIB1

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Abstract

SIB1 FKBP22 is a peptidyl prolyl cis–trans isomerase (PPIase) member from a psychrotrophic bacterium, Shewanella sp. SIB1, consisting of N- and C-domains responsible for dimerization and catalytic PPIase activity, respectively. This protein was assumed to be involved in cold adaptation of SIB1 cells through its dual activity of PPIase activity and chaperone like-function. Nevertheless, the catalytic inhibition by FK506 and its substrate specificity remain unknown. Besides, ability of SIB1 FKBP22 to inhibit phosphatase activity of calcinuerin is also interesting to be studied since it may reflect wider cellular functions of SIB1 FKBP22. In this study, we found that wild type (WT) SIB1 FKBP22 bound to FK506 with IC50 of 77.55 nM. This value is comparable to that of monomeric mutants (NNC-FKBP22, C-domain+ and V37R/L41R mutants), yet significantly higher than that of active site mutant (R142A). In addition, WT SIB1 FKBP22 and monomeric variants were found to prefer hydrophobic residues preceding proline. Meanwhile, R142A mutant has wider preferences on bulkier hydrophobic residues due to increasing hydrophobicity and binding pocket space. Surprisingly, in the absence of FK506, SIB1 FKBP22 and its variants inhibited, with the exception of N-domain, calcineurin phosphatase activity, albeit low. The inhibition of SIB1 FKBP22 by FK506 is dramatically increased in the presence of FK506. Altogether, we proposed that local structure at substrate binding pocket of C-domain plays crucial role for the binding of FK506 and peptide substrate preferences. In addition, C-domain is essential for inhibition, while dimerization state is important for optimum inhibition through efficient binding to calcineurin.

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References

  1. Reimer U, Fischer G (2002) Local structural changes caused by peptidyl-prolyl cis/trans isomerization in the native state of proteins. Biophys Chem 96:203–212

    Article  CAS  PubMed  Google Scholar 

  2. Nagradova N (2010) Peptidyl-prolyl cis/trans isomerase activity in the functioning of native folded proteins. Webwed Cent Mol Biol 1:1–23

    Google Scholar 

  3. Jacob RP, Schmid FX (2008) Energetic coupling between native-state prolyl isomerization and conformational protein folding. J Mol Biol 377:1560–1575

    Article  CAS  Google Scholar 

  4. Wedmeyer WJ, Welker E, Scheraga HA (2002) Proline cis-trans isomerization and protein folding. Biochemistry 41:14637–14644

    Article  CAS  Google Scholar 

  5. Fanghanel J, Fischer G (2004) Insight into catalytic mechanism of peptidyl prolyl cis/trans isomerase. Front Biosci 9:3453–3478

    Article  PubMed  Google Scholar 

  6. Suzuki Y, Haruki M, Takano K, Morikawa M, Kanaya S (2004) Possible involvement of an FKBP family member protein from a psychrotrophic bacterium Shewanella sp. SIB1 in cold-adaptation. Eur J Biochem 271:1372–1381

    Article  CAS  PubMed  Google Scholar 

  7. Budiman C, Koga Y, Takano K, Kanaya S (2011) FK506-Binding protein 22 from a psychrophilic bacterium, a cold shock-inducible peptidyl prolyl isomerase with the ability to assist in protein folding. Int J Mol Sci 12(8):5261–5284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Suzuki Y, Win OY, Koga Y, Takano K, Kanaya S (2005) Binding analysis of a psychrotrophic FKBP22 to a folding intermediate of protein using surface plasmon resonance. FEBS Lett 579:5781–5784

    Article  CAS  PubMed  Google Scholar 

  9. Budiman C, Tadokoro T, Angkawidjaja C, Koga Y, Kanaya S (2012) Role of polar and nonpolar residues at the active site for PPIase activity of FKBP22 from Shewanella sp. SIB1. FEBS J 279(6):976–986

    Article  CAS  PubMed  Google Scholar 

  10. Suzuki Y, Takano K, Kanaya S (2005) Stabilities and activities of the N- and C-domains of FKBP22 from a psychrotrophic bacterium overproduced in E. coli. FEBS J 272:632–642

    Article  CAS  PubMed  Google Scholar 

  11. Budiman C, Bando K, Angkawidjaja C, Koga Y, Takano K, Kanaya S (2009) Engineering of monomeric FK506-binding protein 22 with peptidyl prolyl cis-trans isomerase. FEBS J 276:4091–4101

    Article  CAS  PubMed  Google Scholar 

  12. Kang CB, Hong Y, Dhe-Paganon S, Yoon HS (2008) FKBP family proteins: immunophilins with versatile biological functions. Neurosignals 16(4):318–325

    Article  CAS  PubMed  Google Scholar 

  13. Tong M, Jiang Y (2015) FK506-binding proteins and their diverse functions. Curr Mol Pharmacol 9(1):48–65

    Article  CAS  PubMed  Google Scholar 

  14. Budiman C, Angkawidjaja C, Motoike H, Koga Y, Takano K, Kanaya S (2011) Crystal structure of N-domain of FKBP22 from Shewanella sp. SIB1: dimer dissociation by disruption of Val-Leu knot. Protein Sci 20:1755–1764

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685

    Article  CAS  PubMed  Google Scholar 

  16. Goodwin TW, Morton RA (1946) The spectrophotometric determination of tyrosine and tryptophan in proteins. Biochem J 40:628–632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Scopes RK (1974) Measurement of protein by spectrophotometry at 205 nm. Anal Biochem 59:277–282

    Article  CAS  PubMed  Google Scholar 

  18. Harrison RK, Stein RL (1990) Mechanistic studies of peptidyl prolyl cis-trans isomerase: evidence for catalysis by distortion. Biochemistry 29:1684–1689

    Article  CAS  PubMed  Google Scholar 

  19. Monaghan P, Bell AA (2005) Plasmodium falciparum FK506-binding protein (FKBP) with peptidyl-prolyl cis-trans isomerase and chaperone activities. Mol Biochem Parasitol 139:185–195

    Article  CAS  PubMed  Google Scholar 

  20. Rahfeld JU, Rucknagel KP, Stoller G, Horne SM, Schierhorn A, Young KD, Fischer G (1996) Isolation and amino acid sequence of a new 22-kDa FKBP-like peptidyl-prolyl cis/trans-isomerase of Escherichia coli similarity to Mip-like proteins of pathogenic bacteria. J Biol Chem 271:22130–22138

    Article  CAS  PubMed  Google Scholar 

  21. Wallemacq PE, Reding R (1993) FK506 (Tacrolimus), a novel immunosuppressant in organ transplantation: clinical, biomedical, and analytical aspects. Clin Chem 39:2219–2228

    CAS  PubMed  Google Scholar 

  22. Van Duyne GD, Standaert RF, Karplus PA, Schreiber SL, Clardy J (1993) Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J Mol Biol 229:105–124

    Article  PubMed  Google Scholar 

  23. Rosen MK, Yang D, Martin PK, Schreiber SL (1993) Activation of an inactive immunophilin by mutagenesis. J Am Chem Soc 115:821–822

    Article  CAS  Google Scholar 

  24. Galat A, Lane WS, Standaert RF, Schreiber SL (1992) Biochemistry 31:2427–2434

    Article  CAS  PubMed  Google Scholar 

  25. Ludwig B, Rahfeld JU, Schmidt B, Mann K, Wintermeyer E, Fischer G, Hacker J (1994) FEMS Microbiol Lett 118:23–30

    Article  CAS  PubMed  Google Scholar 

  26. Siekierka JJ, Hung SH, Poe M, Lin CS, Sigal NH (1989) A cytosolic binding protein for the immunosuppressant FK506 has peptidyl-prolyl isomerase activity but is distinct from cyclophilin. Nature 341:755–757

    Article  CAS  PubMed  Google Scholar 

  27. Siekierka JJ, Wiederrecht G, Greulich H, Boulton D, Hung SH, Cryan J, Hodges PJ, Sigal NH (1990) The cytosolic-binding protein for the immunosuppressant FK-506 is both a ubiquitous and highly conserved peptidyl-prolyl cis-trans isomerase. J Biol Chem 265:21011–21015

    CAS  PubMed  Google Scholar 

  28. DeCenzo MT, Park ST, Jarrett BP, Aldape RA, Futer O, Murcko MA, Livingston DJ (1996) FK506-binding protein mutational analysis: defining the active-site residue contributions to catalysis and the stability of ligand complexes. Protein Eng 9:173–180

    Article  CAS  PubMed  Google Scholar 

  29. Futer O, DeCenzo MT, Aldape RA, Livingston DJ (1995) FK506 binding protein mutational analysis. Defining the surface residue contributions to stability of the calcineurin co-complex. J Biol Chem 270:18935–18940

    Article  CAS  PubMed  Google Scholar 

  30. Rahfeld JU, Rucknagel KP, Schelbert B, Ludwig B, Hacker J, Mann K, Fischer G (1994) Confirmation of the existence of a third family among peptidyl-prolyl cis/trans isomerases. Amino acid sequence and recombinant production of parvulin. FEBS Lett 352:180–184

    Article  CAS  PubMed  Google Scholar 

  31. Shirane M, Nakayama KI (2003) Inherent calcineurin inhibitor FKBP38 targets Bcl-2 to mitochondria and inhibits apoptosis. Nat Cell Biol 5(1):28–37

    Article  CAS  PubMed  Google Scholar 

  32. Li TK, Baksh S, Cristillo AD, Bierer BE (2002) Calcium- and FK506-independent interaction between the immunophilin FKBP51 and calcineurin. J Cell Biochem 84(3):460–471

    Article  CAS  PubMed  Google Scholar 

  33. Hu K, Galius V, Pervushin K (2006) Structural plasticity of peptidyl-prolyl isomerase sFkpA is a key to its chaperone function as revealed by solution NMR. Biochemistry 45:11983–11991

    Article  CAS  PubMed  Google Scholar 

  34. Rusnak F, Mertz P (2000) Calcineurin: Form and function. Physiol Rev 80(4):1483–1521

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

Authors thank Dr S. Kanaya (Department of Material and Life Science, Osaka University, Japan) for providing the expression system for SIB1 FKBP22 used in this study.

Funding

This work was partly supported by Research Grants of Universiti Malaysia Sabah (SBK0089-ST-2014) and collaborative research with Bogor Agricultural University, Indonesia.

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Authors and Affiliations

  1. Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia

    Cahyo Budiman, Herman Umbau Lindang, Bo Eng Cheong & Kenneth F. Rodrigues

  2. Faculty of Animal Science, Bogor Agricultural University, Bogor, 16680, Indonesia

    Cahyo Budiman

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  1. Cahyo Budiman
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  2. Herman Umbau Lindang
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  3. Bo Eng Cheong
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  4. Kenneth F. Rodrigues
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Correspondence to Cahyo Budiman.

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Budiman, C., Lindang, H.U., Cheong, B.E. et al. Inhibition and Substrate Specificity Properties of FKBP22 from a Psychrotrophic Bacterium, Shewanella sp. SIB1. Protein J 37, 270–279 (2018). https://doi.org/10.1007/s10930-018-9772-z

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