An Essential Nonredundant Role for Mycobacterial DnaK in Native Protein Folding

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All living organisms use protein chaperones to prevent proteins from becoming insoluble either spontaneously or during cellular stress that can damage proteins. The HSP70 chaperone DnaK has been well characterized in E. coli and is important for that bacterium to resist protein denaturation from heat, but is dispensable for cell growth in the absence of stress due to redundancy with other chaperone systems. However, the function of chaperones in bacterial pathogens, which are exposed to protein stress within the host, has received less attention. Here we examine the function of DnaK in mycobacteria, a genus that includes multiple human pathogens, and find that DnaK is required for cell growth. This essential function is due to a lack of redundancy with other chaperone systems for the folding of proteins, even in the absence of stress. These findings expand the paradigm of DnaK function and identify DnaK as a promising target for antibiotic development for mycobacteria.

Vyšlo v časopise: An Essential Nonredundant Role for Mycobacterial DnaK in Native Protein Folding. PLoS Genet 10(7): e32767. doi:10.1371/journal.pgen.1004516
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004516

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Zdroje

1. DeuerlingE, PatzeltH, VorderwulbeckeS, RauchT, KramerG, et al. (2003) Trigger Factor and DnaK possess overlapping substrate pools and binding specificities. Mol Microbiol 47: 1317–1328.

2. KernerMJ, NaylorDJ, IshihamaY, MaierT, ChangHC, et al. (2005) Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 122: 209–220.

3. MogkA, DeuerlingE, VorderwulbeckeS, VierlingE, BukauB (2003) Small heat shock proteins, ClpB and the DnaK system form a functional triade in reversing protein aggregation. Mol Microbiol 50: 585–595.

4. TomoyasuT, MogkA, LangenH, GoloubinoffP, BukauB (2001) Genetic dissection of the roles of chaperones and proteases in protein folding and degradation in the Escherichia coli cytosol. Mol Microbiol 40: 397–413.

5. SaibilH (2013) Chaperone machines for protein folding, unfolding and disaggregation. Nat Rev Mol Cell Biol 14: 630–642.

6. BukauB, WalkerGC (1989) Cellular defects caused by deletion of the Escherichia coli dnaK gene indicate roles for heat shock protein in normal metabolism. J Bacteriol 171: 2337–2346.

7. CalloniG, ChenT, SchermannSM, ChangHC, GenevauxP, et al. (2012) DnaK functions as a central hub in the E. coli chaperone network. Cell Rep 1: 251–264.

8. ItikawaH, FujitaH, WadaM (1986) High temperature induction of a stringent response in the dnaK(Ts) and dnaJ(Ts) mutants of Escherichia coli. J Biochem 99: 1719–1724.

9. PaekKH, WalkerGC (1987) Escherichia coli dnaK null mutants are inviable at high temperature. J Bacteriol 169: 283–290.

10. StrausD, WalterW, GrossCA (1990) DnaK, DnaJ, and GrpE heat shock proteins negatively regulate heat shock gene expression by controlling the synthesis and stability of sigma 32. Genes Dev 4: 2202–2209.

11. OhE, BeckerAH, SandikciA, HuberD, ChabaR, et al. (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147: 1295–1308.

12. BruelN, Castanie-CornetMP, CirinesiAM, KoningsteinG, GeorgopoulosC, et al. (2012) Hsp33 controls elongation factor-Tu stability and allows Escherichia coli growth in the absence of the major DnaK and trigger factor chaperones. J Biol Chem 287: 44435–44446.

13. DeuerlingE, Schulze-SpeckingA, TomoyasuT, MogkA, BukauB (1999) Trigger factor and DnaK cooperate in folding of newly synthesized proteins. Nature 400: 693–696.

14. TeterSA, HouryWA, AngD, TradlerT, RockabrandD, et al. (1999) Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains. Cell 97: 755–765.

15. UllersRS, LuirinkJ, HarmsN, SchwagerF, GeorgopoulosC, et al. (2004) SecB is a bona fide generalized chaperone in Escherichia coli. Proc Natl Acad Sci U S A 101: 7583–7588.

16. VorderwulbeckeS, KramerG, MerzF, KurzTA, RauchT, et al. (2005) Low temperature of GroEL/ES overproduction permits growth of Escherichia coli cells lacking trigger factor DnaK. FEBS Lett 579: 181–187.

17. BandyopadhyayB, Das GuptaT, RoyD, Das GuptaSK (2012) DnaK dependence of the mycobacterial stress-responsive regulator HspR is mediated through its hydrophobic C-terminal tail. J Bacteriol 194: 4688–4697.

18. RamanS, SongT, PuyangX, BardarovS, JacobsWRJr, et al. (2001) The alternative sigma factor SigH regulates major components of oxidative and heat stress responses in Mycobacterium tuberculosis. J Bacteriol 183: 6119–6125.

19. StewartGR, SnewinVA, WalzlG, HussellT, TormayP, et al. (2001) Overexpression of heat-shock proteins reduces survival of Mycobacterium tuberculosis in the chronic phase of infection. Nat Med 7: 732–737.

20. MalenH, BervenFS, FladmarkKE, WikerHG (2007) Comprehensive analysis of exported proteins from Mycobacterium tuberculosis H37Rv. Proteomics 7: 1702–1718.

21. Berredo-PinhoM, KalumeDE, CorreaPR, GomesLH, PereiraMP, et al. (2011) Proteomic profile of culture filtrate from the Brazilian vaccine strain Mycobacterium bovis BCG Moreau compared to M. bovis BCG Pasteur. BMC Microbiol 11: 80.

22. HickeyTB, ThorsonLM, SpeertDP, DaffeM, StokesRW (2009) Mycobacterium tuberculosis Cpn60.2 and DnaK are located on the bacterial surface, where Cpn60.2 facilitates efficient bacterial association with macrophages. Infect Immun 77: 3389–3401.

23. FlotoRA, MacAryPA, BonameJM, MienTS, KampmannB, et al. (2006) Dendritic cell stimulation by mycobacterial Hsp70 is mediated through CCR5. Science 314: 454–458.

24. SpieringR, van der ZeeR, WagenaarJ, van EdenW, BroereF (2013) Mycobacterial and mouse HSP70 have immuno-modulatory effects on dendritic cells. Cell Stress Chaperones 18: 439–446.

25. RodinaA, PatelPD, KangY, PatelY, BaakliniI, et al. (2013) Identification of an allosteric pocket on human hsp70 reveals a mode of inhibition of this therapeutically important protein. Chem Biol 20: 1469–1480.

26. PatelPD, YanP, SeidlerPM, PatelHJ, SunW, et al. (2013) Paralog-selective Hsp90 inhibitors define tumor-specific regulation of HER2. Nat Chem Biol 9: 677–684.

27. SaitoH, UchidaH (1977) Initiation of the DNA replication of bacteriophage lambda in Escherichia coli K12. J Mol Biol 113: 1–25.

28. SaitoH, UchidaH (1978) Organization and expression of the dnaJ and dnaK genes of Escherichia coli K12. Mol Gen Genet 164: 1–8.

29. ItikawaH, RyuJ (1979) Isolation and characterization of a temperature-sensitive dnaK mutant of Escherichia coli B. J Bacteriol. 138: 339–344.

30. RodriguesL, RamosJ, CoutoI, AmaralL, ViveirosM (2011) Ethidium bromide transport across Mycobacterium smegmatis cell-wall: correlation with antibiotic resistance. BMC Microbiol 11: 35.

31. RodriguesL, WagnerD, ViveirosM, SampaioD, CoutoI, et al. (2008) Thioridazine and chlorpromazine inhibition of ethidium bromide efflux in Mycobacterium avium and Mycobacterium smegmatis. J Antimicrob Chemother 61: 1076–1082.

32. ViveirosM, MartinsA, PaixaoL, RodriguesL, MartinsM, et al. (2008) Demonstration of intrinsic efflux activity of Escherichia coli K-12 AG100 by an automated ethidium bromide method. Int J Antimicrob Agents 31: 458–462.

33. SchroderH, LangerT, HartlFU, BukauB (1993) DnaK, DnaJ and GrpE form a cellular chaperone machinery capable of repairing heat-induced protein damage. EMBO J 12: 4137–4144.

34. SzaboA, LangerT, SchroderH, FlanaganJ, BukauB, et al. (1994) The ATP hydrolysis-dependent reaction cycle of the Escherichia coli Hsp70 system DnaK, DnaJ, and GrpE. Proc Natl Acad Sci U S A 91: 10345–10349.

35. HesterkampT, BukauB (1998) Role of the DnaK and HscA homologs of Hsp70 chaperones in protein folding in E.coli. EMBO J 17: 4818–4828.

36. EvansMS, SanderIM, ClarkPL (2008) Cotranslational folding promotes beta-helix formation and avoids aggregation in vivo. J Mol Biol 383: 683–692.

37. ShimizuY, InoueA, TomariY, SuzukiT, YokogawaT, et al. (2001) Cell-free translation reconstituted with purified components. Nat Biotechnol 19: 751–755.

38. UgrinovKG, ClarkPL (2010) Cotranslational folding increases GFP folding yield. Biophys J 98: 1312–1320.

39. KelleherAR, KimballSR, DennisMD, SchilderRJ, JeffersonLS (2013) The mTORC1 signaling repressors REDD1/2 are rapidly induced and activation of p70S6K1 by leucine is defective in skeletal muscle of an immobilized rat hindlimb. Am J Physiol Endocrinol Metab 304: E229–236.

40. LemosJA, LuzardoY, BurneRA (2007) Physiologic effects of forced down-regulation of dnaK and groEL expression in Streptococcus mutans. J Bacteriol 189: 1582–1588.

41. da SilvaAC, SimaoRC, SusinMF, BaldiniRL, AvedissianM, et al. (2003) Downregulation of the heat shock response is independent of DnaK and sigma32 levels in Caulobacter crescentus. Mol Microbiol 49: 541–553.

42. TillyK, SpenceJ, GeorgopoulosC (1989) Modulation of stability of the Escherichia coli heat shock regulatory factor sigma. J Bacteriol 171: 1585–1589.

43. KumarM, SourjikV (2012) Physical map and dynamics of the chaperone network in Escherichia coli. Mol Microbiol 84: 736–747.

44. WinklerJ, SeybertA, KonigL, PruggnallerS, HaselmannU, et al. (2010) Quantitative and spatio-temporal features of protein aggregation in Escherichia coli and consequences on protein quality control and cellular ageing. EMBO J 29: 910–923.

45. ThompsonAD, BernardSM, SkiniotisG, GestwickiJE (2012) Visualization and functional analysis of the oligomeric states of Escherichia coli heat shock protein 70 (Hsp70/DnaK). Cell Stress Chaperones 17: 313–327.

46. SugimotoS, SaruwatariK, HigashiC, SonomotoK (2008) The proper ratio of GrpE to DnaK is important for protein quality control by the DnaK-DnaJ-GrpE chaperone system and for cell division. Microbiology 154: 1876–1885.

47. SchweizerE, HofmannJ (2004) Microbial type I fatty acid synthases (FAS): major players in a network of cellular FAS systems. Microbiol Mol Biol Rev 68: 501–517 table of contents.

48. ZimhonyO, VilchezeC, JacobsWRJr (2004) Characterization of Mycobacterium smegmatis expressing the Mycobacterium tuberculosis fatty acid synthase I (fas1) gene. J Bacteriol 186: 4051–4055.

49. RussmannF, StempMJ, MonkemeyerL, EtchellsSA, BracherA, et al. (2012) Folding of large multidomain proteins by partial encapsulation in the chaperonin TRiC/CCT. Proc Natl Acad Sci U S A 109: 21208–21215.

50. NetzerWJ, HartlFU (1997) Recombination of protein domains facilitated by co-translational folding in eukaryotes. Nature 388: 343–349.

51. JonasK, LiuJ, ChienP, LaubMT (2013) Proteotoxic stress induces a cell-cycle arrest by stimulating Lon to degrade the replication initiator DnaA. Cell 154: 623–636.

52. KangPJ, CraigEA (1990) Identification and characterization of a new Escherichia coli gene that is a dosage-dependent suppressor of a dnaK deletion mutation. J Bacteriol 172: 2055–2064.

53. OjhaA, AnandM, BhattA, KremerL, JacobsWRJr, et al. (2005) GroEL1: a dedicated chaperone involved in mycolic acid biosynthesis during biofilm formation in mycobacteria. Cell 123: 861–873.

54. GreendykeR, RajagopalanM, ParishT, MadirajuMV (2002) Conditional expression of Mycobacterium smegmatis dnaA, an essential DNA replication gene. Microbiology 148: 3887–3900.

55. StewartGR, WernischL, StablerR, ManganJA, HindsJ, et al. (2002) Dissection of the heat-shock response in Mycobacterium tuberculosis using mutants and microarrays. Microbiology 148: 3129–3138.

56. RosenzweigR, MoradiS, Zarrine-AfsarA, GloverJR, KayLE (2013) Unraveling the mechanism of protein disaggregation through a ClpB-DnaK interaction. Science 339: 1080–1083.

57. OllingerJ, O'MalleyT, KesickiEA, OdingoJ, ParishT (2012) Validation of the essential ClpP protease in Mycobacterium tuberculosis as a novel drug target. J Bacteriol 194: 663–668.

58. RajuRM, UnnikrishnanM, RubinDH, KrishnamoorthyV, KandrorO, et al. (2012) Mycobacterium tuberculosis ClpP1 and ClpP2 function together in protein degradation and are required for viability in vitro and during infection. PLoS Pathog 8: e1002511.

59. AkopianT, KandrorO, RajuRM, UnnikrishnanM, RubinEJ, et al. (2012) The active ClpP protease from M. tuberculosis is a complex composed of a heptameric ClpP1 and a ClpP2 ring. EMBO J 31: 1529–1541.

60. SnapperSB, MeltonRE, MustafaS, KieserT, JacobsWRJr (1990) Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol Microbiol 4: 1911–1919.

61. BarkanD, StallingsCL, GlickmanMS (2011) An improved counterselectable marker system for mycobacterial recombination using galK and 2-deoxy-galactose. Gene 470: 31–36.

62. ViveirosM, RodriguesL, MartinsM, CoutoI, SpenglerG, et al. (2010) Evaluation of efflux activity of bacteria by a semi-automated fluorometric system. Methods Mol Biol 642: 159–172.

63. Sebastiaan WinklerG, LacomisL, PhilipJ, Erdjument-BromageH, SvejstrupJQ, et al. (2002) Isolation and mass spectrometry of transcription factor complexes. Methods 26: 260–269.

64. Erdjument-BromageH, LuiM, LacomisL, GrewalA, AnnanRS, et al. (1998) Examination of micro-tip reversed-phase liquid chromatographic extraction of peptide pools for mass spectrometric analysis. J Chromatogr A 826: 167–181.

65. BeverlyLJ, LockwoodWW, ShahPP, Erdjument-BromageH, VarmusH (2012) Ubiquitination, localization, and stability of an anti-apoptotic BCL2-like protein, BCL2L10/BCLb, are regulated by Ubiquilin1. Proc Natl Acad Sci U S A 109: E119–126.